PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
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All E-Collection Articles.

There are currently 399 articles in the collection. Here they are listed chronologically, most recent first.

2015

Retrospective: Producing Proteins the PSI:Biology Way

Technical Highlight - July 2015
PSI:Biology developed new expression vectors and other tools and tricks to obtain samples of its challenging protein targets.

Community-Nominated Targets

Featured System - July 2015
The Community-Nominated Targets program has allowed PSI to collaborate with researchers on hundreds of systems of high biological significance.

Retrospective: 7,000 Structures Closer to Understanding Biology

Featured Article - July 2015
As PSI:Biology comes to a close this month, we take a look back at all the biological advances made by the PSI Network.

Drug Discovery: Solving the Structure of an Anti-hypertension Drug Target

Featured Article - July 2015
Serial femtosecond crystallography is used to solve the structure of angiotensin II type 1 receptor.

Families in Gene Neighborhoods

Technical Highlight - June 2015
A bioinformatics strategy takes advantage of the proximal organization of genes encoding proteins involved in metabolic pathways to predict protein function.

Design and Evolution: Tunable Antibody Binders

Technical Highlight - June 2015
Reengineering the binding interface of Protein G yields a variant with stronger Fab binding and pH-tunable affinity.

Design and Evolution: Bespoke Design of Repeat Proteins

Technical Highlight - June 2015
A combination of sequence and structure information is used to design new repeat proteins.

Evolution of Photoconversion

Featured System - June 2015
PSI researchers have discovered that protein flexibility is a key element in the evolutionary pathway for developing photoconvertable GFP-like proteins.

Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity

Featured Article - June 2015
Reconstructed ancient ancestors of Src and Abl shed light on Gleevec's specificity.

Design and Evolution: Unveiling Translocator Proteins

Featured Article - June 2015
Structural and functional analyses provide new insights on the physiological roles of TSPOs.

A Solution for Near-Atomic Resolution Cryo-EM

Technical Highlight - May 2015
Two methods for macromolecular structure determination via near-atomic resolution cryo-EM help fill a resolution gap.

Cryo-EM Beyond 3-Å Resolution

Technical Highlight - May 2015
The 2.8-Å resolution cryo-EM reconstruction of a thermophilic 20S proteasome identifies rotamers and water molecules.

Signaling with DivL

Featured System - May 2015
DivL shares many structural features with other bacterial signaling proteins, but has been modified by evolution to reverse the typical directionality of signaling.

Signaling: A Platform for Opposing Functions

Featured Article - May 2015
A modeled structure reveals the regulatory complexities of a TORC1-interacting complex.

Signaling: Securing Lipid-Protein Partnership

Featured Article - May 2015
Crystal structures provide a glimpse into how phosphoinositides stabilize nuclear hormones.

Automating NMR Structures

Technical Highlight - April 2015
An automated NMR protocol is used to solve the structure of a 25-kDa protein.

Expanding the Reach of SAD

Technical Highlight - April 2015
Two recent methods increase the range of SAD phasing to more challenging protein structures.

Ryanodine Receptor

Featured System - April 2015
PSI researchers take a close look at a gated calcium channel that controls muscle contraction.

Channels and Transporters: Reorienting a Peptide in the Pocket

Featured Article - April 2015
In POT transporters, peptide length determines whether the orientation of the ligand is lateral or vertical.

Channels and Transporters: BEST in Show

Featured Article - April 2015
Crystal structures of bestrophin ion channels unravel the molecular basis of retinopathies.

Protein Folding and Misfolding: It's the Journey, Not the Destination

Technical Highlight - March 2015
Computational analysis suggests ∼10% of pathogenic mutations interfere with membrane integration.

Protein Folding and Misfolding: Refolding in Membrane Mimetic

Technical Highlight - March 2015
Using a membrane mimetic system, researchers produce properly folded integral membrane proteins that are suitable for subsequent X-ray crystallography analysis.

Dynamic DnaK

Featured System - March 2015
PSI researchers have used an engineered version of DnaK to reveal the open state of an Hsp70 protein chaperone.

Protein Folding and Misfolding: Beneficial Aggregation

Featured Article - March 2015
The ERAD-associated lectin Yos9 forms aggregates in the presence of misfolded substrates.

Protein Folding and Misfolding: A TRiC-ster that Follows the Rules

Featured Article - March 2015
Experimental and computational techniques establish substrate recognition rules for the chaperonin TRiC.

Molecular Portraits of the Cell

Technical Highlight - February 2015
The cellPACK software generates three-dimensional mesoscale models for a detailed look at biological systems like the cell.

Nuclear Pore Complex: Higher Resolution of Macromolecules

Technical Highlight - February 2015
Integrating mass spectrometry data for crosslinked oligomers reveals details of the yeast nuclear pore complex.

Piecing Together the Nuclear Pore Complex

Featured System - February 2015
PSI researchers have solved another piece in the puzzle for revealing an atomic-level model of the nuclear pore complex.

Nuclear Pore Complex: A Flexible Transporter

Featured Article - February 2015
Structural flexibility in HEAT motifs enables proteins to pass through the nuclear pore complex.

Nuclear Pore Complex: Integrative Approach to Probe Nup133

Featured Article - February 2015
The integration of three structural methods offers insight into membrane association of the NPC.

Greasing the Path for SFX

Technical Highlight - January 2015
Grease is an ideal microcrystal carrier medium for serial femtosecond crystallography.

Updating ModBase

Technical Highlight - January 2015
An expanded ModBase comparative protein structure database and toolkit enables insights into protein function, including determinants of HIV-1 protease specificity.

CCR5 and HIV Infection

Featured System - January 2015
A new PSI structure shows how the anti-HIV drug maraviroc locks the coreceptor CCR5 in an inactive state.

HIV/AIDS: Pre-fusion Env Exposed

Featured Article - January 2015
A crystal structure of the pre-fusion HIV-1 Env captures gp41 and provides insights into immune recognition.

HIV/AIDS: Slide to Enter

Featured Article - January 2015
A sliding hinge in gp41 promotes HIV membrane fusion and viral infection.
Top of page
2014

Time-Resolved Crystallography with HATRX

Technical Highlight - December 2014
Time-resolved crystallography on standard synchrotron beamlines is possible with a method based on Hadamard encoding.

Transmembrane Spans

Technical Highlight - December 2014
Analyses of nine topology prediction programs identify those with the greatest prediction accuracy for specific transmembrane transport protein families, and lead the authors to propose several distinguishable evolutionary pathways for these proteins.

Iron-Sulfur Cluster Biosynthesis

Featured System - December 2014
PSI researchers are exploring the complex biological machinery that builds iron-sulfur clusters.

Mitochondrion: Setting a New TRAP1

Featured Article - December 2014
An asymmetric Hsp90 structure supports a new mechanism for coupling ATP hydrolysis with substrate turnover.

Mitochondrion: Flipping for UCP2

Featured Article - December 2014
NMR studies reveal how UCP2 facilitates translocation of protons across the mitochondrial membrane via fatty acids.

Microbiome: Fiber Degraders Revealed

Technical Highlight - November 2014
A combination of phylogenetic, genomic and structural analyses identifies two new glycoside hydrolase families.

Microbiome: Expanding the Gut Gene Catalog

Technical Highlight - November 2014
An international effort has identified nearly ten million genes belonging to microbes hosted by diverse human guts.

Deciphering Microbial DUFs

Featured System - November 2014
PSI researchers are characterizing domains of unknown function in microbes, and discovering new protein folds in the process.

Microbiome: When Form Doesn't Equal Function

Featured Article - November 2014
The characterization of three proteins from the human microbiome extends our understanding of PLP-dependent enzymes.

Microbiome: Artificial Sweeteners Induce Unhealthy Metabolism

Featured Article - November 2014
Artificial sweeteners alter metabolism through shifts in the distribution of gut microbiota species.

Electron Diffraction Made Practical

Technical Highlight - October 2014
Continuous-rotation MicroED solves protein structures by electron diffraction of microcrystals.

Predicting Protein Crystal Candidates

Technical Highlight - October 2014
An improved algorithm predicts whether a protein will be amenable to crystallization for structural studies.

Peptidyl-carrier Proteins

Featured System - October 2014
PSI researchers have determined the structure of a new class of peptidyl-carrier proteins, helping to understand how cells make exotic peptides without using ribosomes.

Protein and Peptide Synthesis: Coming Full Circle

Featured Article - October 2014
A search for a plant peptidase ends with the discovery of one of the fastest peptide ligases.

Protein and Peptide Synthesis: Sensing Energy Balance

Featured Article - October 2014
Complementary structural, genetic, biochemical and biophysical approaches identify a new translation regulator that responds to changing ATP/ADP ratios.

Repairing a Rift

Technical Highlight - September 2014
Computational and crystallographic analyses identify new hybrid folds that fill gaps in existing structural space.

Complex Search

Technical Highlight - September 2014
A search engine identifies assemblies with structural similarities, providing biologically relevant insights not accessible by comparison of individual proteins.

P2Y Receptors and Blood Clotting

Featured System - September 2014
PSI researchers have revealed a novel rearrangement in a purine-binding GPCR, opening new avenues for the design of blood clotting drugs.

Drug Targets: S1R's Ligands and Partners

Featured Article - September 2014
Stabilization of oligomers by small-molecule ligands suggests a mechanism for regulating a membrane protein chaperone.

Drug Targets: Bile Acids in Motion

Featured Article - September 2014
Crystal structures of sodium-dependent bile acid transporters provide insight into transport mechanism.

Correlative Microscopy on Ice

Technical Highlight - August 2014
New methods for correlated cryo-electron tomography and super-resolution fluorescence imaging are now described.

Structures Without Damage

Technical Highlight - August 2014
Radiation damage-free protein structures can be solved using an X-ray free-electron laser and large single crystals.

Power in Numbers

Featured System - August 2014
PSI researchers have determined the structure of a transcriptional regulator involved in quorum sensing in an important pathogenic bacterium.

Quorum Sensing: A Groovy New Component

Featured Article - August 2014
A first-in-family structure of a Pseudomonas-specific protein provides clues to its role in quorum sensing.

Quorum Sensing: E. coli Gets Involved

Featured Article - August 2014
The crystal structure of E. coli SdiA provides insights into substrate selectivity and oxidation-dependent regulation.

iTRAQing the Ubiquitinome

Technical Highlight - July 2014
An inflammatory signal triggers broad changes to protein ubiquitination and chromatin regulation in immune cells.

Error Prevention

Technical Highlight - July 2014
Protein crystallographers must be careful to prevent avoidable errors in the PDB.

DNAJA1 and Pancreatic Cancer

Featured System - July 2014
PSI researchers have determined the structure of a DnaJ cochaperone and studied its role in pancreatic cancer.

Cell Adhesion and Metastasis: Unraveling Talin

Featured Article - July 2014
In the absence of a 3D crystal structure of talin, a structural model based on EM reconstruction and known structures of individual domains provides insight into its mechanism of action.

Cell Adhesion and Metastasis: DnaJ, Meet JNK

Featured Article - July 2014
A chaperone–cochaperone interaction suppresses the JNK pathway and provides a novel target for pancreatic cancer drug discovery.

Immunity: Conformational Capture

Technical Highlight - June 2014
Protocols for phage display enable the generation of highly customizable synthetic antibodies against specific molecular complexes or conformational states.

Immunity: Clustering Immunoglobulins

Technical Highlight - June 2014
An algorithm identifies functional clusters of cell surface-anchored and secreted immunoglobulin superfamily proteins through the comparison of conserved regions and taking into account known protein–protein interaction data.

Bacterial CDI Toxins

Featured System - June 2014
PSI researchers have solved the structures of several potent bacterial toxins, along with their antidotes.

Immunity: One Antibody to Rule Them All

Featured Article - June 2014
Structural studies of antibody F045–092 explain its ability to neutralize all H3-subtype influenza strains.

Immunity: Tissue Contribution

Featured Article - June 2014
Tissue-expressed PD-L1 is important in controlling colon inflammation.

Mining Protein Dynamics

Technical Highlight - May 2014
A method for prediction of protein dynamics from primary sequence can map functional regions and help predict the effects of mutations.

A Refined Refinement Strategy

Technical Highlight - May 2014
Combinatorial use of refinement algorithms leads to improved structure determination.

New NTF2-like Domains

Featured System - May 2014
PSI researchers are exploring the range of structures adopted by a versatile protein fold.

Novel Proteins and Networks: Assigning Function

Featured Article - May 2014
Structural modeling and docking of substrates identifies a biochemical pathway that is validated experimentally.

Novel Proteins and Networks: Polysaccharide Metabolism in the Human Gut

Featured Article - May 2014
Comparative genomics identifies new components and regulatory networks for the utilization of complex carbohydrates by Bacteroides thetaiotaomicron.

Combining Methods to Solve Protein Assemblies

Technical Highlight - April 2014
A hybrid approach that integrates four mass spectrometry methods with structural modeling takes on tough protein complexes.

Membrane Proteome: Microcrystals Yield Big Data

Technical Highlight - April 2014
An X-ray free-electron laser helps determine the first room-temperature structure of a G protein-coupled receptor.

Glucagon Receptor

Featured System - April 2014
PSI researchers have solved the structures of a GPCR that binds to peptide hormones, revealing new modes of GPCR recognition.

Membrane Proteome: Pumping Out Heavy Metal

Featured Article - April 2014
Crystal structures of a heavy-metal efflux pump reveal intermediate transport states.

Membrane Proteome: A Cap on Transport

Featured Article - April 2014
Structural and biophysical analyses of a membrane carrier ectodomain reveal a Ca2+-dependent switch that regulates ATP flux across the mitochondrial inner membrane.

Virology: Making Sensitive Magic

Technical Highlight - March 2014
Dynamic nuclear polarization is used to enhance the sensitivity of an MAS NMR experiment, allowing detection of inhibitor binding to the M2 proton channel.

Virology: Visualizing Cyanophage Assembly

Technical Highlight - March 2014
The first application of ZPC cryoET provides insight into cyanophage assembly process.

Viroporins

Featured System - March 2014
PSI researchers have determined the structures of several viral pore-forming proteins, revealing common functional features.

Virology: Zeroing in on HBV Egress

Featured Article - March 2014
Crystal structures of human γ2-adaptin in complex with a peptide from HBV preS1 suggest a path to antivirals.

Virology: A Bat Influenza Hemagglutinin

Featured Article - March 2014
The crystal structure of HA antigen from H17N10 bat influenza virus shows how its receptor binding site has diverged from human flu strains.

Optimizing Damage

Technical Highlight - February 2014
Radiation damage is inherent to the X-ray diffraction experiment. A new metric predicts crystal lifetime, allowing for more efficient and effective data collection strategies.

Coaxing Rare Codons

Technical Highlight - February 2014
A new series of protein expression vectors with 'built in' tRNA genes that recognize rare codons promises to accelerate and enhance the determination of novel protein structures.

Cas4 Nuclease and Bacterial Immunity

Featured System - February 2014
A distinctive toroidal structure, a metal ion and an iron-sulfur cluster allow Cas4 to unwind and process phage DNA in the process of CRISPR-associated immunity.

Microbial Pathogenesis: Targeting Drug Resistance in Mycobacterium tuberculosis

Featured Article - February 2014
Whole-cell screening for antituberculosis compounds combined with identification of resistance-linked mutations provide novel scaffolds for drug development.

Microbial Pathogenesis: A GNAT from Pseudomonas

Featured Article - February 2014
A multidisciplinary approach offers a detailed view of a bacterial acetyltransferase.

Getting Better at Low Resolution

Technical Highlight - January 2014
Combining the sampling methodology and energy function of Rosetta and the X-ray refinement methodology of Phenix improves refinement of low-resolution X-ray crystallographic data.

Design and Discovery: Virtual Drug Screening

Technical Highlight - January 2014
Optimized crystal structure-based models yield diverse hits in a virtual screen targeting G protein-coupled receptor allosteric and orthosteric ligand-binding sites.

Discovering Deaminases

Featured System - January 2014
The Enzyme Function Initiative uses a structure-guided approach to predict functions of enzymes based on their amino acid sequence. This approach has revealed a variety of novel deaminases.

Design and Discovery: Identifying New Enzymes and Metabolic Pathways

Featured Article - January 2014
Homology modeling and metabolite docking predict in vitro enzymatic activities and physiological functions.

Design and Discovery: Evolutionary Dynamics

Featured Article - January 2014
Differential dynamics in the dihydrofolate reductase family reveal how the enzyme has evolved to function in various cellular environments.
Top of page
2013

Epigenetics: Tracing Histone Demethylase Inhibitors

Technical Highlight - December 2013
The fluorescent analog of a histone demethylase inhibitor enables quantitative binding assays.

Caught in the Act

Technical Highlight - December 2013
Inventive selection strategies yield antibodies that capture distinctive states of target proteins.

Methylation of Arginine

Featured System - December 2013
Protein methylation is widely used for regulation of proteins inside cells. A recent PSI structure reveals the interaction between an arginine methyltransferase and the machinery that regulates its action.

Epigenetics: Getting MAD

Featured Article - December 2013
The identification of the first N-6-methyladenine deaminase from the NCBI database of prokaryotic genomes highlights the value of the database to the experimental annotation of novel enzymes.

Epigenetics: HAT1 Makes Its Mark

Featured Article - December 2013
The crystal structure of human histone acetyltransferase 1 in complex with acetyl coenzyme A and a histone H4 peptide reveals the basis for substrate specificity and catalysis.

Building a Structural Library

Technical Highlight - November 2013
The Borges algorithm uses tertiary structural information from small structural fragments in the PDB to obtain phases for X-ray diffraction data.

Cancer Networks: Predicting Catalytic Residues from 3D Protein Structures

Technical Highlight - November 2013
Identifying the structural features that can predict catalytic amino acids will enhance the functional assignment of unknown proteins in structural databases.

G Proteins and Cancer

Featured System - November 2013
G-proteins play an essential role in cell signaling, a role that is corrupted in many types of cancer cells.

Cancer Networks: IFI16-mediated p53 Activation

Featured Article - November 2013
Structural and functional analyses of the p53-binding HIN domains of IFI16 reveal their mechanism of action.

Cancer Networks: Solving a Tumor Suppressor Protein

Featured Article - November 2013
Structural characterization of CDK2AP1 reveals a disordered N-terminal region and a four-helix C-terminal domain.

Drug Discovery: Finding Druggable Targets

Technical Highlight - October 2013
A guide to selecting strategic targets for pharmacological intervention and drug design in microbiomes is presented for Streptococcus mutans.

Drug Discovery: Identifying Dynamic Networks by CONTACT

Technical Highlight - October 2013
A new automated algorithm uses X-ray data to identify dynamic contact networks involved in enzyme catalysis.

Serum Albumins and Allergies

Featured System - October 2013
A new structure of bovine serum albumin reveals three calcium-binding sites and sheds light on the unusual allergenicity of the molecule.

Drug Discovery: Modeling NET Interactions

Featured Article - October 2013
A structural model of the norepinephrine transporter is used in a virtual ligand screen to identify new drug interactions.

Drug Discovery: Antidepressant Potential of 6-NQ SERT Inhibitors

Featured Article - October 2013
Molecular docking models are combined with in vitro and in vivo assays to evaluate the therapeutic potential of 6-nitroquipazine analogs as antidepressants.

Microbiome: Solid-State NMR, Crystallized

Technical Highlight - September 2013
The structure of a bacterial membrane protein was determined using solid-state NMR methods on protein microcrystals.

Microbiome: The Dynamics of Infection

Technical Highlight - September 2013
A combination of systems approaches reveals how Salmonella displaces commensal gut bacteria to establish infections.

Bacteria and Bile Salts

Featured System - September 2013
PSI researchers have solved the first structure of a bacterial enzyme involved in the removal of bile acid hydroxyl groups in the human gut.

Microbiome: Structures from Lactic Acid Bacteria

Featured Article - September 2013
Structures of GH1-family 6-P-β-glucosidases in complex with ligands reveal determinants for substrate recognition.

Microbiome: Insights into Secondary Bile Acid Synthesis

Featured Article - September 2013
Structural characterization of a gut microbe dehydrogenase illuminates cofactor specificity and mechanism of proton relay.

Membrane Proteome: Unveiling the Human α-helical Membrane Proteome

Technical Highlight - August 2013
All PSI Membrane Protein Structure Centers and one large-scale production center have joined forces to create a strategy to maximize our understanding of the human transmembrane proteome.

Membrane Proteome: Making DNA Nanotubes for NMR Structure Determination

Technical Highlight - August 2013
A protocol for designing DNA nanotube liquid crystals to be used as a weak-alignment medium for high-resolution NMR is presented.

CAAX Endoproteases

Featured System - August 2013
Structures of two Ste24p-family proteases locate the active site inside a hollow, membrane-spanning chamber.

Membrane Proteome: A Funnel-like Viroporin

Featured Article - August 2013
The NMR structure of HCV p7 channel reveals a funnel-like architecture, providing insight into cation conductance and drug-mediated inhibition.

Membrane Proteome: GPCR Substrate Recognition and Functional Selectivity

Featured Article - August 2013
Crystal structures of 5-HT receptors bound to antimigraine drugs offer insights into ligand specificity and signaling bias.

Protein-Nucleic Acid Interaction: Inhibition Through Allostery

Technical Highlight - July 2013
NMR studies highlight the importance of investigating transitional species to fully understand protein function.

Setting New Standards in SAS

Technical Highlight - July 2013
New approaches for data analysis boost confidence in SAS models.

Stabilizing DNA Single Strands

Featured System - July 2013
PSI researchers have determined the structure of a new single-stranded DNA-binding domain, revealing a surprising connection between the kingdoms of life.

Protein-Nucleic Acid Interaction: A Modified SAM to Modify tRNA

Featured Article - July 2013
Basic metabolism may seem quite old-school, but the structure of a biosynthetic enzyme offers several surprises.

Protein-Nucleic Acid Interaction: Versatile Glutamate

Featured Article - July 2013
A cyanobacterial transcription factor recognizes three consecutive cytosines in promoter DNA using a single glutamate residue.

The Immune System: Super Cytokines

Technical Highlight - June 2013
Crystal structures of cytokine receptor complexes pinpoint target regions to create 'superkines' with altered cell specificity.

The Immune System: A Brotherhood of Immunoglobulins

Technical Highlight - June 2013
The Brotherhood algorithm groups proteins into functional families using indirect sequence similarity.

Tuning Immune Response with Costimulation

Featured System - June 2013
PSI researchers are studying molecules that stimulate and inhibit our immune response, ensuring that it is activated only when necessary.

The Immune System: A Strong Competitor

Featured Article - June 2013
HLA-DO is an MHCII mimic that prevents the association of HLA-DM to MHCII.

The Immune System: Strand Swapping for T-Cell Inhibition

Featured Article - June 2013
An immunoglobulin protein with a role in antigen-independent T-cell signaling dimerizes via a strand-swapped interface.

Infectious Diseases: Determining the Essential Structome

Technical Highlight - May 2013
Twenty-five potential drug targets emerge from the Burkholderia structome through an integrated pipeline.

Infectious Diseases: Targeting Meningitis

Technical Highlight - May 2013
Screens with substrates and inhibitors, followed by molecular modeling, reveal details of an enzyme's ligand binding specificity.

NDM-1 and Antibiotics

Featured System - May 2013
With structural biology and computational analysis, PSI Biology researchers have revealed the catalytic pathway of an antibiotic-destroying enzyme.

Infectious Diseases: A Pathogen Ubiquitin Ligase

Featured Article - May 2013
A novel bacterial effector protein functions as a ubiquitin E3 ligase.

Infectious Diseases: A Shared Syringe

Featured Article - May 2013
Tail sheath proteins of one viral family share a common fold and conformational changes despite low sequence identity.

Protein Interaction Networks: Reading Between the Lines

Technical Highlight - April 2013
An additional separation is added to LC-MS to obtain more information about quaternary structure of complexes.

Protein Interaction Networks: Adding Structure to Protein Networks

Technical Highlight - April 2013
Interactome3D is a tool and resource for annotating protein networks with three-dimensional structure information.

PDZ Domains

Featured System - April 2013
PDZ domains are specialists in protein recognition, but PSI Biology researchers are revealing their abilities to bind to membranes as well.

Protein Interaction Networks: Morph to Assemble

Featured Article - April 2013
The scaffold protein IscU alternates between structured and disordered conformations during iron-sulfur cluster assembly and delivery.

Protein Interaction Networks: When the Sum Is Greater than the Parts

Featured Article - April 2013
Integration of low-resolution approaches yields functional and evolutionary insights into the NPC.

Cell-Cell Interaction: Nanoparticles in Cell Camouflage

Technical Highlight - March 2013
Membranes of white blood cells are harnessed to improve drug-delivery vehicles.

Cell-Cell Interaction: Magic Structure from Microcrystals

Technical Highlight - March 2013
Structure determination of a membrane protein using poorly diffracting microcrystals illustrates a powerful new application of solid-state NMR spectroscopy.

Alpha-Catenin Connections

Featured System - March 2013
Structures of alpha-catenin and vinculin are revealing a highly dynamic interaction in adherens junctions.

Cell-Cell Interaction: Modulating Self Recognition Affinity

Featured Article - March 2013
Subtle changes that distinguish homophilic and heterophilic interactions in a cell surface molecule are revealed.

Cell-Cell Interaction: A FERM Connection

Featured Article - March 2013
The structure of a KRIT1–HEG1 complex reveals a new binding mechanism for FERM domains.

Design and Discovery: A Cocktail for Proteins Without ID

Technical Highlight - February 2013
A screen of natural metabolite ligands provides clues to protein function.

Design and Discovery: Flexible Backbone Protein Redesign

Technical Highlight - February 2013
Protein redesign via backbone perturbations enables efficient expansion of sequence diversity while maintaining fold and thermostability.

Designer Proteins

Featured System - February 2013
PSI biology researchers have discovered several rules for protein folding and used them to design five entirely new proteins.

Design and Discovery: Enzyme Reprogramming

Featured Article - February 2013
Rational structure-based design of a de novo Due Ferri protein alters its substrate and reactivity.

Design and Discovery: Extreme Red Shift

Featured Article - February 2013
Structure-guided mutagenesis of a protein-chromophore complex enables engineering of prediction-defying red shift.

Microbial Pathogenesis: Computational Epitope Prediction

Technical Highlight - January 2013
A computational approach uses structural information to identify epitopes within antigenic proteins.

Microbial Pathogenesis: Influenza Inhibitor Screen

Technical Highlight - January 2013
A cell-free binding assay is optimized step by step and applied in high throughput to screen for small molecule inhibitors of an influenza protein.

Bacterial Hemophores

Featured System - January 2013
PSI biology researchers are exploring the proteins that pathogenic bacteria use to gather scarce heme groups, and the iron ions they carry.

Microbial Pathogenesis: Measles Virus Attachment

Featured Article - January 2013
The third structure of a host receptor bound to measles virus hemagglutinin pinpoints a hydrophobic lock hole.

Microbial Pathogenesis: NEAT Iron

Featured Article - January 2013
Structural transitions in a bacterial hemophore suggest a mechanism that couples hemoglobin binding and heme capture.
Top of page
2012

Membrane Proteome: Soft Sampling

Technical Highlight - December 2012
A novel method for processing non-uniformly sampled NMR data is orders of magnitude faster and permits very sparse sampling for challenging applications.

Membrane Proteome: Tuning Membrane Protein Expression

Technical Highlight - December 2012
A tunable E. coli strain results in less protein aggregation in vivo and more functional, membrane-inserted protein.

Archaeal Lipids

Featured System - December 2012
PSI:Biology Researchers have revealed how archaea build their unusually temperature-tolerant lipids.

Membrane Proteome: Sphingolipid Synthesis Selectivity

Featured Article - December 2012
Substrate specificity in trypanosomal sphingolipid synthases can be determined by variation in as few as three residues.

Membrane Proteome: Capturing Multiple Conformations

Featured Article - December 2012
Four novel crystallized conformers of the betaine/Na+ symporter BetP suggest a structural mechanism for molecular transport.

Membrane Proteome: Every Protein Has Its Tag

Technical Highlight - November 2012
A tag variation strategy enables increased membrane protein production.

Membrane Proteome: Specific vs. Non-specific weak interactions

Technical Highlight - November 2012
Using a series of NMR experiments, weak interactions between membrane proteins can be classified as specific or nonspecific.

Cytochrome Oxidase

Featured System - November 2012
Cytochrome oxidase is the foundation of aerobic respiration.

Membrane Proteome: Building a Carrier

Featured Article - November 2012
NMR methods and molecular fragment searching are used to generate a structural model of a mitochondrial carrier protein.

Membrane Proteome: The ABCs of Transport

Featured Article - November 2012
Structural analyses of two ABC transporters reveal how diverse transmembrane domain architectures determine substrate specificity and transport mechanisms.

Fluorescence- and Chromatography-Based Protein Thermostability Assay

Technical Highlight - October 2012
A new thermostability assay for medium- to high-throughput screening helps identify membrane protein crystallization conditions.

Insert Here

Technical Highlight - October 2012
A method to identify fusion partners for GPCRs can lead to new structures.

Bacterial Phosphotransferase System

Featured System - October 2012
Bacteria are thrifty cells.

Lethal Tendencies

Featured Article - October 2012
The crystal structure of MtfA reveals a self-inhibited member of the lethal factor family of endopeptidases.

Symmetry from Asymmetry

Featured Article - October 2012
Structural analysis of an intermediate filament protein reveals how an asymmetric dimeric coiled-coil assembles into a symmetric tetrameric structure.

Automatic NMR

Technical Highlight - September 2012
A new protocol for automated NMR protein structure determination minimizes instrument time and efficiently produces high-quality structures.

NMR structure test

Technical Highlight - September 2012
RPF, an 'R-factor'-like protein structure validation tool, shows its mettle for the validation of NMR structures.

Solute Channels

Featured System - September 2012
Cells maintain a steady traffic of small molecules across their membranes.

Regulatory insights

Featured Article - September 2012
Structures of the JH2 pseudokinase domain provide clues to its role in normal and disease-associated JAK signaling.

A signal sensing switch

Featured Article - September 2012
The structure of the sensor complex for the TMAO receptor sheds light on bacterial two-component signaling.

Native phasing

Technical Highlight - August 2012
Anomalous diffraction from multiple crystals allows phasing of data from native proteins.

To structure, faster

Technical Highlight - August 2012
Backbone structure determination of human integral membrane proteins is enabled by cell-free protein expression followed by solution NMR spectroscopy.

AlkB Homologs

Featured System - August 2012
Evolution is a great tinkerer, and when cells discover a useful plan for a protein, it is often pressed to service in other capacities.

Budding ensemble

Featured Article - August 2012
An integration of several structural approaches has generated a model for how vesicle budding may be coordinated by ESCRT complexes.

Serum albumin diversity

Featured Article - August 2012
Serum albumin is an abundant plasma protein that can cause allergic reactions. The crystal structures of bovine, horse and rabbit serum albumin now provide insight into these properties.

Pocket changes

Technical Highlight - July 2012
Pocketome, an encyclopedia of small-molecule binding sites, helps analyze druggable sites.

Predictive protein origami

Technical Highlight - July 2012
Membrane protein 3D folds are accurately predicted from evolutionary constraints derived from genomic sequencing.

Targeting Enzyme Function with Structural Genomics

Featured System - July 2012
Prediction of the function of a new enzyme based only on its sequence, or even on its structure, is still a major challenge, and will be a major prize for biomedical research when effective methods are developed.

Receptor bias

Featured Article - July 2012
Fluorine NMR characterization of the β2-adrenergic receptor uncovers conformational states that may bias GPCR signaling pathways.

Gauging needle structure

Featured Article - July 2012
Solid-state NMR and computer modeling yield a highly resolved atomic model of the type III secretion system needle.

S is for solubility

Technical Highlight - June 2012
Segmental labeling of a protein with an NMR-invisible solubility tag yields previously inaccessible structural information.

More in one

Technical Highlight - June 2012
FunTree integrates multiple kinds of data to address evolution of enzyme function in structurally defined superfamilies.

Anthrax Stealth Siderophores

Featured System - June 2012
Iron is an essential mineral, used by many enzymes for its ability to trap small molecules like oxygen and to act as a conduit of electron transfer.

The machines behind the spindle assembly checkpoint

Featured Article - June 2012
The crystal structure of the mitotic checkpoint complex is reported.

Finding function for enolases

Featured Article - June 2012
Using homology models to direct biochemical and structural studies allows researchers to characterize a broad set of dipeptide epimerase specificities in the enolase superfamily.

EM-proving protein structures

Technical Highlight - May 2012
A new version of EM-Fold combines medium-resolution data with computational techniques to achieve atomic resolution structures.

EM for the (small) masses

Technical Highlight - May 2012
A new strategy using Fabs allows visualization of small protein molecules by cryoEM.

G Protein-Coupled Receptors

Featured System - May 2012
In the past five years, the field of GPCR structure has exploded.

A Pseudomonas L-serine dehydrogenase

Featured Article - May 2012
Structural studies of an uncharacterized Pseudomonas aeruginosa enzyme reveal a dehydrogenase with a substrate preference for L-serine.

Methyl maintenance

Featured Article - May 2012
A structure of a DNA methyltransferase complex highlights how autoinhibitory and active mechanisms ensure substrate selectivity.

Smaller may be better

Technical Highlight - April 2012
Serial femtosecond crystallography coupled to an X-ray free electron laser may be the next big step for protein crystallography.

Blind faith

Technical Highlight - April 2012
A rigorous assessment of automated NMR structure determination demonstrates the reliability of the method.

Pilus Assembly Protein TadZ

Featured System - April 2012
Many bacteria are covered with long filaments, called pili or fimbriae, that help them interact and attach to their environment.

Chaperone interactions

Featured Article - April 2012
The structure of a yeast co-chaperone reveals interactions essential for Fe-S cluster biogenesis.

Substrate specificity sleuths

Featured Article - April 2012
Crystal structures of constitutive and immunoproteasomes in the presence and absence of inhibitor reveal the structural basis for substrate and inhibitor specificity.

Just blot and see

Technical Highlight - March 2012
A simple method for transferring proteins onto EM grids may speed up single-particle analyses of large protein complexes.

Refining protein structure prediction

Technical Highlight - March 2012
Molecular dynamics simulations are shown to systematically improve template-based models of protein structure.

Revealing the Nuclear Pore Complex

Featured System - March 2012
This is an exciting time for the study of the nuclear pore complex, the highway of transport between the cytoplasm and nucleus, and also a central player in nuclear organization and gene regulation.

Topping off the proteasome

Featured Article - March 2012
The structure of the entire proteasome complex provides insight into key functions while raising questions for future studies.

Twist to open

Featured Article - March 2012
A structure of an engineered potassium channel suggests a novel model for the gating mechanism.

Overexpressed problems

Technical Highlight - February 2012
An analysis of the effects of protein overexpression gives insight into the difficulties of preparing intramembrane proteins for crystallization.

Metal mates

Technical Highlight - February 2012
Experimental validation of a designed metal-mediated dimer highlights the potential of computational methods.

Disordered Proteins

Featured System - February 2012
Looking through the thousands of structures in the PDB, we get the impression that proteins must have a stable, folded structure to be functional.

Anchoring's the way

Featured Article - February 2012
New insights into the regulation of AQP0 reveal mechanisms involved in cataract development.

Buena VISTA

Featured Article - February 2012
A novel immunoglobulin ligand with functions in autoimmunity and cancer surveillance is characterized.

Gentle membrane protein extraction

Technical Highlight - January 2012
Noncovalent chelation of nickel-doped PEG polymers to His-tagged integral membrane proteins permits the solubilization of functional proteins in low-detergent or detergent-free aqueous buffer.

Devil is in the details

Technical Highlight - January 2012
Assessment of the biannual CASP experiment emphasizes the need for improved methods to model unique structural features.

Making Lipopolysaccharide

Featured System - January 2012
Many bacteria surround themselves with a protective coat, to resist attack from antibiotics, predators, and the immune system.

Analyzing an allergen

Featured Article - January 2012
Computational, structural, and biochemical analysis of peanut Ara h 1 gives insights into understanding and diagnosing nut allergies.

Pulling on loose ends

Featured Article - January 2012
Structural analyses of the first identified activase for red-type Rubiscos reveal key insights into Rubisco activation.
Top of page
2011

Not so cool

Technical Highlight - December 2011
A comparison of X-ray diffraction datasets obtained at ambient and cryogenic temperatures reveals temperature-dependent effects on structural models.

Follow the RNA leader

Technical Highlight - December 2011
An NMR method characterizes an RNA structural switch that regulates HIV-1 genome packaging.

Superbugs and Antibiotic Resistance

Featured System - December 2011
Antibiotics were used as weapons to fight bacteria long before Alexander Fleming discovered penicillin.

Reading out regioselectivity

Featured Article - December 2011
The structures of four glycosyltransferases operating within a single biosynthetic pathway point to conserved and divergent mechanisms for controlling the regioselective addition of sugar donors, with implications for glycosyltransferase engineering.

Terminal activation

Featured Article - December 2011
The recent crystal structure of the human BIG2 Sec7 domain reveals a novel ARF-interacting motif that regulates ARF activation.

Playing while you work

Technical Highlight - November 2011
Foldit players successfully solve the crystal structure of a retroviral protease that had resisted previous determination.

PDZ domains: sometimes it takes two

Technical Highlight - November 2011
A systems approach reveals an unexpectedly high frequency of PDZ domain dimerization.

The Perils of Protein Secretion

Featured System - November 2011
Salmonella bacteria are tiny terrorists that infect cells and ultimately destroy them.

A change to resistance

Featured Article - November 2011
Two structures of NDM-1 β-lactamase show how this enzyme can confer resistance to many antibiotics.

An effective and cooperative dimer

Featured Article - November 2011
NMR studies reveal the dimer interface of the effector domain (ED) of NS1A from influenza A virus and provide insight into how dimerization of the ED provides cooperative dsRNA binding and other functions of NS1A.

Making invisible proteins visible

Technical Highlight - October 2011
Protein flexibility allows conversion of an invisible excited state to a ground state with implications for rational protein design.

Fit to serve

Technical Highlight - October 2011
A new web server promises to make MultiFit even more accessible and easy to use.

Bacterial Armor

Featured System - October 2011
Bacteria are found in nearly every corner of the world, evolving unique mechanisms to survive in their different environments.

Docking and rolling

Featured Article - October 2011
GPCR Dock 2010 reveals just how far homology modeling has come and how far it still has to go.

TLR4 regulation: heads or tails?

Featured Article - October 2011
The crystal structure of the TLR4 regulator RP105–MD-1 reveals a unique head-to-head conformation and provides a glimpse into the mechanism of TLR4 regulation.

Solving a problem in phases

Technical Highlight - September 2011
A new approach promises to eliminate a major hurdle to structure determination of membrane proteins using electron crystallography.

A fragmented approach to membrane protein structures

Technical Highlight - September 2011
An innovative method combines NMR experiments and a database search to determine the structure of a challenging membrane protein.

Exploring the Secretome of Gut Bacteria

Featured System - September 2011
We often think of bacteria as our enemies, as something we need to fight with antiseptics and antibiotics.

Breaking down the defenses

Featured Article - September 2011
The structure of ISG15 bound to NS1B gives insight into the mechanism by which influenza B virus specifically targets humans.

Ribose production on demand

Featured Article - September 2011
A previously unidentified enzymatic activity provides the driving force that leads to NADPH-independent ribose production.

One from many

Technical Highlight - August 2011
Xsolve utilizes many different approaches to streamline and enhance automated structure determination.

Molecular replacement by magnetic resonance

Technical Highlight - August 2011
A new method coupled with accurate NMR structures yields highly reliable search models for molecular replacement.

Rb Tumor Suppressor and Cancer

Featured System - August 2011
One of the overarching goals of structural genomics is to characterize the structure and function of entire systems of proteins.

Moving some metal

Featured Article - August 2011
The crystal structure of a copper-transporting P1B-type ATPase provides valuable insight into how mutations contribute to Menkes' and Wilson's diseases.

Raising a glass to GLIC

Featured Article - August 2011
The pentameric ligand-gated ion channels (pLGICs) are known to be affected by alcohol in eukaryotes. Analyses of the prokaryotic GLIC suggest that it may be a good structural model for the effects of n-alcohols on pLGICs.

Structure from sequence

Technical Highlight - July 2011
A new computational tool will allow researchers to easily predict RNA structural modules from the sequence alone.

Rosetta hone

Technical Highlight - July 2011
A method using structural modeling tools to improve molecular replacement promises to allow structural determination for cases that resist solution by current methods.

RNA Chaperone NMB1681

Featured System - July 2011
The small protein NMB1681 has been proposed to act as an RNA chaperone, but unlike a chaperone at a high school dance, NMB1681 acts as a molecular matchmaker, trying to bring together the molecules it watches over, rather than keeping them apart.

Seeing HetR

Featured Article - July 2011
The structure of the transcription factor HetR now indicates how it might function during cyanobacterial differentiatation.

Looking for lipids

Featured Article - July 2011
The structure of UNC119 by itself and with a substrate shows how it binds lipids to regulate G protein trafficking.

Solutions in the solution

Technical Highlight - June 2011
A high-throughput analysis demonstrates the complementary power of SAXS with other structural techniques.

An easier solution for symmetry

Technical Highlight - June 2011
A new method from the Rosetta suite allows for the determination of symmetric oligomeric protein structures in solution using primarily RDCs and chemical shifts.

Ribofuranosyl Binding Protein

Featured System - June 2011
Molecular recognition is at the very heart of life.

Binding complement with complementarity

Featured Article - June 2011
The structure of complement C3d with complement receptor 2 answers lingering questions about the interaction of these two proteins.

Sugar transport

Featured Article - June 2011
The structure of an EIIC from Bacillus cereus shows the architecture of this important class of sugar transporters.

Beyond crystals, solutions, and powders

Technical Highlight - May 2011
A new approach improves the functionality of an alternative use for synchrotron beams.

No more labeled lipids

Technical Highlight - May 2011
Blocking the production of phospholipids allows for clearer NMR signals in cSPP systems.

A2A Adenosine Receptor

Featured System - May 2011
With proteins, small motions often have large effects.

A molecular switch for neuronal growth

Featured Article - May 2011
Proteoglycans can exert opposing effects on neuronal growth by competing to control the oligomerization of a common cell surface receptor.

Cell wall recycler

Featured Article - May 2011
The crystal structure of the bacterial cell wall recycling protein Mpl reveals similarities as well as differences compared with functionally related Mur ligases.

Capsid assembly in motion

Technical Highlight - April 2011
Using hydrogen–deuterium exchange, Gag immature, mature and cleavage-mutant particles are now examined to follow the dynamic changes that occur during capsid assembly.

One at a time

Technical Highlight - April 2011
A trio of new approaches pushes forward the utility of single-molecule imaging.

TrkH Potassium Ion Transporter

Featured System - April 2011
Cells are filled with a salty soup of metal ions.

A glimpse of NDRG2

Featured Article - April 2011
While the NDRG family has been implicated in a number of diseases and cancers, the molecular function of these factors remains unclear. The structures of NDRG2 reveal unusual features that give insight into these functions.

Added benefits

Featured Article - April 2011
Biochemical, structural and genetic analyses reveal that the E. coli Cas1 protein YgbT belongs to a novel family of nucleases and that, in addition to antiviral immunity, the CRISPR–Cas system functions in DNA repair.

Snapshot crystallography

Technical Highlight - March 2011
Two independent studies have now used femtosecond pulses from a hard-X-ray free electron laser to push forward the boundaries of structure determination.

NMR challenges current protein hydration dogma

Technical Highlight - March 2011
For decades, scientists have struggled to understand protein interactions with water. NMR spectroscopy using reverse micelles suggests that the dynamics of water on the surface of proteins are quite variable and tend to cluster, overturning the current orthodoxy.

Nitrile Reductase QueF

Featured System - March 2011
Nature uses exotic chemistry to build its diverse collection of molecules.

Tip formin

Featured Article - March 2011
Single-molecule fluorescence polarization shows how mDia1 rotates along actin filaments.

Subtly different

Featured Article - March 2011
The crystal structure of the D3 dopamine receptor reveals how to selectively target D2-like receptors.

FERM-ly bound

Technical Highlight - February 2011
X-ray crystallography of protein complex resolves a controversy regarding domain interactions.

A growing family

Technical Highlight - February 2011
Combining structural and computational methods helps to define a family of proteins.

Tryptophanyl-tRNA Synthetase

Featured System - February 2011
Biology is full of surprises, and they often tell us important things about ourselves.

Inhibiting factor

Featured Article - February 2011
Transcription initiation and elongation by RNA polymerase is inhibited by GreA. A recent crystal structure reveals the mechanism.

PASK staying active

Featured Article - February 2011
The PAS-domain regulated kinase (PASK) has been implicated in nutrition sensing and signaling to facilitate a metabolic response to changing nutritional status. The crystal structure of PASK now indicates a basis for the unusual activation properties and substrate selectivity of this kinase.

Predicting functions within a superfamily

Technical Highlight - January 2011
A detailed analysis of the HUP superfamily provides the groundwork for automated function prediction.

A new amphiphile for crystallizing membrane proteins

Technical Highlight - January 2011
An easy-to-use chemical approach for stabilizing, extracting and crystallizing integral membrane proteins.

CXCR4

Featured System - January 2011
The GPCR (G protein-coupled receptor) community is suffering from an embarrassment of riches.

Regulating nitrogen assimilation

Featured Article - January 2011
By combining their efforts, researchers at two PSI centers provide new insights into a switch that controls nitrogen metabolism in microorganisms.

Subtle shifts

Featured Article - January 2011
The crystal structure of EF-Tu bound to the 70S ribosome solves a 40-year-old puzzle.
Top of page
2010

Five ways recent mass spec developments enhance structural biology

Technical Highlight - December 2010
Recent technical developments have helped mass spectrometry take its place as an essential structural biology tool.

'Super-resolution' large complexes

Technical Highlight - December 2010
Low-resolution diffraction data hampers structural determination of macromolecular complexes. There is a way round it.

Nitrobindin

Featured System - December 2010
Proteins perform most of the nanoscale tasks inside of cells, but occasionally, they need help from more exotic molecules.

Sugar switch

Featured Article - December 2010
Recent work gives insight into how microbes in our gut flora take advantage of passing nutrients, in this case, specific digestible carbohydrates.

Guard cells pick up the SLAC

Featured Article - December 2010
Guard cells rely on anion channels to regulate stomata in response to environmental cues. A new crystal structure gives insight into how stomata close.

Scaling up mutational scanning

Technical Highlight - November 2010
Mutating a protein's sequence is a useful way of uncovering functionally important residues. A large-scale method tracking up to 600,000 variants at once will speed up this analysis.

Solving homodimeric structures with NMR

Technical Highlight - November 2010
Complexes are very difficult to solve in solution but are important biologically. Combining multiple approaches is the way forward.

Isoxanthopterin Deaminase

Featured System - November 2010
How do you discover the function of a new protein? Structural genomics researchers are faced with this problem every day, and they have developed a toolbox full of methods to help solve it.

ABA receptor diversity

Featured Article - November 2010
There are 14 members in the ABA receptor family in Arabidopsis thaliana. How these receptors differ in their response to a synthetic, seed-specific ABA agonist is now explored in two independent papers, using a combination of crystallography, NMR and biochemical approaches.

COX inhibition: Naproxen by proxy

Featured Article - November 2010
Structural basis of COX inhibition suggests that adverse effects of NSAIDs will not be easily avoided.

Function following form

Special - October 2010
The genome projects have yielded the sequences of many genes of unknown function. Insight into the mechanisms of action of the products of these genes can come from collaboration between structural biology and follow-up functional analyses..

Know thy enemy … structurally

Special - October 2010
Visualizing molecules linked to disease can give insight into how to strike back. All the more reason for aiming to solve structures of these proteins.

Alpha/Beta Barrels

Featured System - October 2010
How are these six proteins similar? They all perform very different functions: they represent five different classes of enzymes, and one is a non-enzymatic protein.

Proteinase K and Digalacturonic Acid

Featured System - September 2010
X-ray crystallography is one of the most exact experimental techniques, but ironically, it is also one that relies on sheer luck.

tRNA Isopentenyltransferase MiaA

Featured System - August 2010
Cells always seem to find the best way of doing things.

Zinc Transporter ZntB

Featured System - July 2010
Zinc is an essential component of many cellular processes.

CASD-NMR: assessing automated structure determination by NMR

Technical Highlight - June 2010
Are we close to automated structures being as good as expert-deduced NMR structures?

Gene Composer

Technical Highlight - June 2010
Use this software suite to design protein constructs and codon engineered genes for structural proteomics.

RBBP9 (Retinoblastoma Binding Protein 9)

Featured System - June 2010
Biological complexity is at its most complex when we look to signaling.

Peptidoglycan binding: Calcium-free killing

Featured Article - June 2010
NMR spectroscopy reveals the molecular basis for Ca2+-independent recognition by bactericidal Reg family lectins.

Importance of extension for integrin

Featured Article - June 2010
An extended conformation of α5ß1 integrin is important for cell spreading and adhesion complex formation.

Modeling RNA structures

Technical Highlight - May 2010
The number of three-dimensional RNA structures is rapidly increasing, but are we getting close to being able to accurately predict new native structures?

Some crystals like it hot

Technical Highlight - May 2010
Having trouble crystallizing a protein from a thermophile? Try keeping your crystal plate warm.

Mre11 Nuclease

Featured System - May 2010
All living things on the Earth store their genetic information in long strands of DNA.

Seek and destroy 8-oxoguanine

Featured Article - May 2010
A systematic search reveals the first 8-oxoguanine deaminase.

Treating sleeping sickness

Featured Article - May 2010
A potential new drug kills the bloodstream parasite that causes this disease.

Assigning protein function: GeMMA

Technical Highlight - April 2010
A new approach to automated functional subfamily classification works on huge superfamilies and is well suited to structural genomics.

Removing the NMR bottleneck

Technical Highlight - April 2010
Protein backbone information in combination with the structure-prediction method Rosetta are sufficient for accurate structures up to 25 kDa.

Phytochrome

Featured System - April 2010
Most animals, including ourselves, use sophisticated eyes to see light.

Bacterial spore kinase

Featured Article - April 2010
A genomic, phylogenetic and structural study hints that these kinases have functional roles that might be druggable.

The cancer kinome

Featured Article - April 2010
Structural genomics has an important role to play in guiding development of specific anti-cancer drugs.

NMR has its wiki way

Technical Highlight - March 2010
A wiki containing all the procedures and experimental set-ups used by the Northeast Structural Genomics Consortium is ideal for training new spectrometrists.

Spot protein-protein interactions… fast

Technical Highlight - March 2010
Nanowire transistors act as high-throughput biosensors for detecting protein interactions.

Antibiotics and Ribosome Function

Featured System - March 2010
Antibiotics are often discovered in nature, where they are lethal weapons in the fight between different organisms.

Safer Alzheimer's drugs?

Featured Article - March 2010
Inhibitors that only partially block phosphodiesterase activity look likely to reduce the nasty side effects of full inhibitors.

Formate transporter or channel?

Featured Article - March 2010
The mystery of how formate crosses the membrane is now solved.

Tips for crystallizing membrane proteins in lipidic mesophases

Technical Highlight - February 2010
Advice on this useful technique for crystallizing integral membrane proteins.

Deducing function from small structural clues

Technical Highlight - February 2010
Find structural similarities without relying on fold classification by using the MarkUs server.

Alg13 Subunit of N-Acetylglucosamine Transferase

Featured System - February 2010
Eukaryotic cells have an elaborate mechanism for adding sugar chains to their proteins.

Urea transporter

Featured Article - February 2010
The X-ray crystal structure of a bacterial homolog of the mammalian urea transporter reveals a highly specific, channel-like transport mechanism.

Extremely salty

Featured Article - February 2010
Salt-loving archaea use small negative amino acids to survive hostile conditions.

Spot the pore

Technical Highlight - January 2010
Straightforward web-based software pinpoints the central channel of any transmembrane protein.

Five good reasons to use single protein production for membrane proteins

Technical Highlight - January 2010
A refinement of the SPP method eliminates lengthy purification steps in the pursuit of membrane proteins suitable for structural studies.

Hemolysin BL

Featured System - January 2010
Bacteria are master weapon makers.

First bacterial PH domain

Featured Article - January 2010
The discovery of Pleckstrin-homology-like domains in prokaryotes suggests an ancient evolutionary origin for the PH superfamily.

Membrane proteins spotted in their native habitat

Featured Article - January 2010
A modest reshaping of the lipid bilayer allows water molecules to hydrate voltage-gating channels and focus the electrical field.
Top of page
2009

Learning from failure

Technical Highlight - December 2009
With more than 200,000 protein targets there are bound to be a few proteins that just won't yield structures. To avoid repeating a costly failure, check our databases before you start.

How does Dali work?

Technical Highlight - December 2009
Comparing three-dimensional protein structures can reveal functional clues. The Dali server is one of the most popular ways to achieve this.

Secretagogin

Featured System - December 2009
Cells typically deplete themselves of calcium, expending considerable energy to pump calcium ions out of the cell or into special compartments inside the cell.

Two-component signaling

Featured Article - December 2009
The structure of a sensor histidine kinase in complex with its effector response regulator reveals the details of the phosphoryl transfer reaction.

Tackling the phase problem

Technical Highlight - November 2009
The first report of a protein structure obtained without molecular replacement or derivatives from a protein diffracting to 2.0 Å gives hope for direct methods for solving macromolecular structures.

One system to express them all

Technical Highlight - November 2009
A fast and effective protein-expression system that works for any organism could revolutionize protein production.

Pseudouridine Synthase TruA

Featured System - November 2009
Evolution is a great tinkerer.

ABA receptor...this time for real?

Featured Article - November 2009
After years of controversy, two groups have independently identified the same receptor family for the plant stress hormone abscisic acid.

Network coverage

Featured Article - November 2009
A comprehensive atomic-resolution analysis of the centralmetabolic system of Thermotoga maritima sheds light on protein evolution.

Face off

Technical Highlight - October 2009
Many annotations of the cytosolic sulfotransferase in publicly available databases are found to be wrong.

The power of SAXS

Technical Highlight - October 2009
Can small angle X-ray scattering bridge the growing gap between structural information and genomic and proteomic advances?

Guanine Nucleotide Exchange Factor Vav1 and Rho GTPase Rac1

Featured System - October 2009
Our cells are filled with a cytoskeleton that provides an infrastructure for support, transport, and locomotion.

Get3 into the groove

Featured Article - October 2009
Unlike most membrane proteins, SNAREs enter the endoplasmic reticulum after translation. The structure of the ATPase needed for entry reveals the likely mechanism.

Unusual cell division

Featured Article - October 2009
Streptomyces' unique mechanism for cell division comes under the spotlight and reveals the importance of the protein SsgB.

Crystallizing glycoproteins

Technical Highlight - September 2009
The researchers who published the Ebola virus glycoprotein structure explain how to successfully express, purify and crystallize glycoproteins.

The future of NMR

Technical Highlight - September 2009
With the time needed to solve structures by NMR spectroscopy reduced to weeks or even days, how much better can NMR get?

Toxin-antitoxin VapBC-5

Featured System - September 2009
Living cells are full of surprises and mysteries.

Anthrax evasion tactics

Featured Article - September 2009
The crystal structure of a crucial anthrax capsule enzyme will aid the search for new therapies.

GPCR subunits: Separate but not equal

Featured Article - September 2009
A functional complementation assay reveals that maximal heterotrimeric G-protein activation is achieved by agonist binding to one subunit of a dopamine D2 receptor dimer.

Crystals from recalcitrant proteins

Technical Highlight - August 2009
Adding small quantities of protease is the most effective rescue strategy for those proteins that just won't form well-diffracting crystals.PLoS ONE 4, e5094 (2009)

GPCR modeling: any good?

Technical Highlight - August 2009
Results from a competition that invited groups to predict the structure of a GPCR show some promise, but accurate modeling of these receptors remains a challenge.Nature Rev. Drug Discov. 8, 455-463 (2009)

Salicylic Acid Binding Protein 2

Featured System - August 2009
Centuries ago, both the ancient Greeks and native Americans discovered that willow bark and other plants can dull pain.

Surviving in an acid environment

Featured Article - August 2009
The Escherichia coli O157:H7 amino acid antiporter structure reveals clues to how this bacterium survives in the harsh stomach environment.Science 324, 1565-1568 (2009)

Antibiotic target

Featured Article - August 2009
An unusual reaction in the production of thymine offers hope for anti-tuberculosis drugs.Nature 458, 919-923 (2009)

Protein modeling made easy

Technical Highlight - July 2009
Working on a protein with no known structure? Try the Phyre server for simple-to-interpret protein models.Nature Protoc. 4, 363-371 (2009)

GFP to the rescue

Technical Highlight - July 2009
Modified 'superfolder' green fluorescent protein can quickly establish whether a protein is soluble.J. Struct. Funct. Genomics 10, 47-55 (2009)

Lysostaphin

Featured System - July 2009
Antibiotics are one of the major triumphs of twentieth century science, but unfortunately, the bacteria are fighting back.

Ykul structure solves bacterial signaling puzzle

Featured Article - July 2009
The crystal structure of the phosphodiesterase YkuI reveals how it binds cyclic di-GMP and might explain its activation.J. Biol. Chem. 284, 13174-13184 (2009)

Proofreading RNA

Featured Article - July 2009
The structure of RNA polymerase II caught in the 'backtracked' state reveals how it ensures faithful transcription.Science 324, 1203-1206 (2009)

Solve your solubility problems

Technical Highlight - June 2009
Wheat germ cell-free extract might be the answer to protein production difficulties.FEBS J. 273, 4160-4169 (2006)

Tips for crystallizing membrane proteins

Technical Highlight - June 2009
A practical guide to cloning, expressing, purifying and crystallizing membrane proteins.Nat. Protoc. 4, 619-637 (2009)

Hda and DNA Replication

Featured System - June 2009
Cell division requires careful bookkeeping.

You look familiar: the Type VI secretion system

Featured Article - June 2009
New structures raise the perplexing question of which came first, the bacterial secretion system or the bacteriophage tail.Proc. Natl Acad. Sci. USA 106, 4154-4159 (2009)

Tackling influenza

Featured Article - June 2009
Structural studies reveal a new target for anti-influenza drugs that should work whatever the influenza virus strain.Nature 458, 909-913 (2009)

Faster solid-state NMR

Technical Highlight - May 2009
Improved sensitivity for solid-state nuclear magnetic resonance spectroscopy makes this technique useful for large biomolecules.Nature Meth. 6, 215-218 (2009)

Improve your cloning efficiency

Technical Highlight - May 2009
New vectors and a step-by-step protocol will make ligation-independent cloning even simpler.Methods Mol. Biol. 498, 105-115 (2009)

Bacterial Leucine Transporter, LeuT

Featured System - May 2009
Many antidepressant drugs, as well as drugs of abuse such as cocaine, block the traffic of neurotransmitters across the cell membrane of nerve axons and glial cells.

Mitotic checkpoint control

Featured Article - May 2009
The molecular basis of inhibition of the anaphase-promoting complex/cyclosome revealed.Science 323, 1477-1481 (2009)

Controlling p53

Featured Article - May 2009
Pirh2 promotes the ubiquitylation of the transcriptionally active form of p53 using an unusual two-site interaction strategy.Nat. Struc. Mol. Biol. 15, 1334-1342 (2008)

Model proteins in your lunch break

Technical Highlight - April 2009
How to build yourself a three-dimensional protein model in under 2 hours.Nature Protocols 4, 1-13 (2009)

Powerful NMR

Technical Highlight - April 2009
Achieving solution structures of proteins that produce NMR spectra with a high degree of signal overlap will be easier with a new approach to NMR data acquisition.Angewandte Chemie 48, 1479-1483 (2009)

Ribonuclease and Ribonuclease Inhibitor

Featured System - April 2009
The complex between ribonuclease and ribonuclease inhibitor is one of the tightest known intermolecular interactions, but researchers at the CESG are trying to change that.

The elusive helicase

Featured Article - April 2009
A combination of NMR, mutagenesis and biochemistry reveals the dynamic nature of the eIF4A/4G/4H helicase complex.Cell 136, 447-470 (2009)

Unique SARS

Featured Article - April 2009
The solution structure of the SARS unique domain confirms that it binds single-stranded RNA and hints at its function.J. Virol. 83, 1823-1836 (2009)

Chaperone-assisted crystallography

Technical Highlight - March 2009
Addition of single-domain antibodies to target proteins increases crystallization success and provides phasing information, making the structure easier to solve.Prot. Sci. 17, 1175-1187 (2008)

Protein nanopores

Technical Highlight - March 2009
Ultra high-speed DNA sequencing could be a step nearer as the protein channel MpsA is found to be an excellent nanopore.Proc. Natl. Acad. Sci. USA 105, 20647-20652 (2008)

Aquaglyceroporin

Featured System - March 2009
The protozoan parasites that cause malaria multiply rapidly in the blood of infected individuals.

Anthrax stealth molecule

Featured Article - March 2009
Bacillus anthracis relies on an unusual metabolite to evade human innate immunity and to be fully virulent in the host.Proc. Natl Acad. Sci. USA 105, 17133-17138 (2008)

Death clusters

Featured Article - March 2009
The structure of the Fas–FADD death domain complex reveals how it switches on apoptosis solely through oligomerization and clustering.Nature, doi: 10.1038/nature07606

Drug targets to aim for

Technical Highlight - February 2009
The TDR Targets database combines genomic data on tropical-disease pathogens with structural and biochemical information to help researchers draw up a shortlist of potential drug targets.Nature Rev. Drug Disc. 7, 900-907 (2008)

Dealing with difficult families

Technical Highlight - February 2009
A 'genome pool' strategy that targets multiple members of a protein family boosts structure determination rates, particularly when tricky proteins are avoided.Structure 16, 1659-1667 (2008)

CBS Domain Protein TA0289

Featured System - February 2009
Research in bioinformatics has shown that proteins are often modular, and that these modules are often mixed and matched to form new proteins.

Transporter mechanism in sight

Featured Article - February 2009
Structural studies of the leucine transporter reveal details of the early steps in substrate transport across the membrane.Science 322, 1655-1661 (2008)

High-energy storage system

Featured Article - February 2009
Despite the cellular importance of inorganic polyphosphate, particularly in bacteria, exactly how it is processed is not known. Two new polyphosphate kinase structures should make things clearer.Proc Natl Acad Sci USA 105, 17730-17735 (2008)

Speedy cloning and mutagenesis for structural genomics

Technical Highlight - January 2009
A ligase-independent approach to cloning rapidly produces large numbers of constructs for expression testing and crystallization trials.Proteins 71, 982-994 (2008)

An “X-ray” ruler

Technical Highlight - January 2009
X-ray scattering from gold-labelled, double-stranded DNA is a powerful technique for investigating nucleic acid structure.Science 322, 446-449 (2008)

Poly(A) RNA recognition

Featured Article - January 2009
Homodimerization of type II poly(A)-binding proteins prevents binding in the absence of RNA.Proc Natl Acad Sci. USA 105, 15317-15322 (2008)

A new class of bacterial E3 ubiquitination enzymes

Featured Article - January 2009
A structurally and mechanically distinct class of ubiquitin ligases has been discovered, and a single mutation changes this enzyme from a ligase to a potent thioesterase.Nature Struct. Mol. Biol. 15, 1293-1301 (2008)
Top of page
2008

Click for cancer-protein interactions

Technical Highlight - December 2008
The Human Cancer Pathway Protein Interaction Network (HCPIN) website makes structural information about cancer-related proteins easily accessible.Mol. Cell. Proteomics 7, 2048-2060 (2008)

Methylation boosts protein crystallization

Technical Highlight - December 2008
Reductive methylation is a simple, inexpensive and efficient method for improving the quality of protein crystals for structural studies.Nat. Meth. 5, 853-854 (2008)

Imidazolonepropionase (HutI)

Featured System - December 2008
Histidine is an essential amino acid with several interesting chemical properties.

Activating BAX

Featured Article - December 2008
The structure of the pro-apoptotic protein BAX with a bound BIM BH3 'death helix' reveals that a previously unsuspected binding site on BAX triggers activation of the BAX cell-death pathway.Nature 455, 1076-1081 (2008)

A pocket guide to GPCRs

Featured Article - December 2008
The structure of the G-protein-coupled receptor adenosine receptor A2A reveals differences between its ligand-binding site and those of other family members, and begins to explain this family's diversity.Science, doi:10.1126/science.1164772

Scavenger Decapping Enzyme DcpS

Featured System - November 2008
Messenger RNA molecules are temporary molecules.

Modeling with SAXS

Technical Highlight - October 2008
J. Mol. Biol. 382, 1089-1106 (2008)

Tuning membrane protein overexpression

Technical Highlight - October 2008
Proc. Natl Acad. Sci. USA 105, 14371-14376 (2008)

Bacteriophage Lambda cII Protein

Featured System - October 2008
Living cells are constantly making decisions: when to eat, when to move, even when to die.

New metal-binding domain

Featured Article - October 2008
J. Biol. Chem., doi:10.1074/jbc.M804746200 (2008)

Antiviral evasion

Featured Article - October 2008
Proc. Natl Acad. Sci. USA 105, 13093-13098 (2008)

Designing activity

Technical Highlight - September 2008
Science 319, 1387-1391 (2008)

Getting fixated

Technical Highlight - September 2008
Nature Methods 5, 53-55 (2008)

T-Rex

Featured System - September 2008
The repressor protein T-Rex has the difficult job of distinguishing the difference between NAD+ and NADH.

Blocking AmtB

Featured Article - September 2008
Proc Natl Acad Sci USA 104, 42-47 (2007)

SARS connections

Featured Article - September 2008
J Virol 82, 5279-5294 (2008)

Aspartate Dehydrogenase

Featured System - August 2008
Aspartate dehydrogenase is a new enzyme discovered by Northeast Structural Genomics Consortium.

RNase T

Featured System - July 2008
Living cells are filled with RNases, but not highly destructive ones like our digestive RNase.

SARS Coronavirus Nonstructural Protein 1

Featured System - June 2008
Researchers at the Joint Center for Structural Genomics have obtained the first look at nsp1 (nonstructural protein 1), a major factor in the pathogenicity of the coronavirus that causes SARS (severe acute respiratory syndrome).

Chronophin

Featured System - May 2008
The cell is a busy place with thousands of things happening at once.
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