PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
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E-Collection

Research Themes
Cancer
Cell biology
DNA and RNA
Drug discovery
Epigenetics
Immunology
Infectious diseases
Membrane proteins
Microbiome
Novel Proteins
Protein design
Protein-protein interactions

Technology Topics
Target Selection
Reagents
Cloning
Protein Expression
Purification
Crystallography
NMR
Electron Microscopy
SAXS
Mass Spectrometry
Annotation/Function
Modeling
Hybrid/Integrative Methods
Dissemination Tools

E-Collection Research Themes: Protein design

Related Articles

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.

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.

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.

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: 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: Unveiling Translocator Proteins

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

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.

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.

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.

Protein Folding and Misfolding: Beneficial Aggregation

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

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.

Predicting Protein Crystal Candidates

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

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.

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.

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.

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.

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: 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.

Caught in the Act

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

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.

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.

The Immune System: A Brotherhood of Immunoglobulins

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

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.

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: 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.

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.

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.

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.

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.

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.

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.

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.

Metal mates

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

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.

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.

Deducing function from small structural clues

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

Extremely salty

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

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.

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.

Designing activity

Technical Highlight - September 2008
Science 319, 1387-1391 (2008)
Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health