PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Drug Discovery: Solving the Structure of an Anti-hypertension Drug Target
July 2015
Retrospective: 7,000 Structures Closer to Understanding Biology
July 2015
Design and Evolution: Bespoke Design of Repeat Proteins
June 2015
Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity
June 2015
Design and Evolution: Tunable Antibody Binders
June 2015
Design and Evolution: Unveiling Translocator Proteins
June 2015
Evolution of Photoconversion
June 2015
Families in Gene Neighborhoods
June 2015
Protein Folding and Misfolding: A TRiC-ster that Follows the Rules
March 2015
Protein Folding and Misfolding: Beneficial Aggregation
March 2015
Peptidyl-carrier Proteins
October 2014
Predicting Protein Crystal Candidates
October 2014
Protein and Peptide Synthesis: Coming Full Circle
October 2014
Protein and Peptide Synthesis: Sensing Energy Balance
October 2014
Mining Protein Dynamics
May 2014
Novel Proteins and Networks: Assigning Function
May 2014
Novel Proteins and Networks: Polysaccharide Metabolism in the Human Gut
May 2014
Design and Discovery: Evolutionary Dynamics
January 2014
Design and Discovery: Identifying New Enzymes and Metabolic Pathways
January 2014
Design and Discovery: Virtual Drug Screening
January 2014
Caught in the Act
December 2013
Microbiome: Insights into Secondary Bile Acid Synthesis
September 2013
Microbiome: Structures from Lactic Acid Bacteria
September 2013
The Immune System: A Brotherhood of Immunoglobulins
June 2013
The Immune System: Super Cytokines
June 2013
Design and Discovery: A Cocktail for Proteins Without ID
February 2013
Design and Discovery: Enzyme Reprogramming
February 2013
Design and Discovery: Extreme Red Shift
February 2013
Design and Discovery: Flexible Backbone Protein Redesign
February 2013
Designer Proteins
February 2013
Membrane Proteome: Sphingolipid Synthesis Selectivity
December 2012
Symmetry from Asymmetry
October 2012
Serum albumin diversity
August 2012
Pocket changes
July 2012
Predictive protein origami
July 2012
Targeting Enzyme Function with Structural Genomics
July 2012
Finding function for enolases
June 2012
Substrate specificity sleuths
April 2012
Disordered Proteins
February 2012
Metal mates
February 2012
Making invisible proteins visible
October 2011
Alpha/Beta Barrels
October 2010
Deducing function from small structural clues
February 2010
Extremely salty
February 2010
Membrane proteins spotted in their native habitat
January 2010
How does Dali work?
December 2009
Secretagogin
December 2009
Designing activity
September 2008

Research Themes Protein design

Extremely salty

PSI-SGKB [doi:10.1038/fa_psisgkb.2010.01]
Featured Article - February 2010
Short description: Salt-loving archaea use small negative amino acids to survive hostile conditions.

Halophilic adaptation does not affect the overall protein fold. Overlay of wild-type ProtL (blue) and the designed obligate halophilic mutant Kx6E (purple). The structure of Kx6E was obtained in the presence of salt. The mutated side chains have been highlighted.

Some organisms thrive in very salty conditions such as the Great Salt Lake in Utah or the Dead Sea at the mouth of the river Jordan. Salt-loving (halophilic) archaea have evolved to cope with this environment and their proteins have adapted to what would normally be destabilizing conditions.

Halophilic proteins have a characteristic, biased, amino-acid composition, favoring glutamic acids and shunning lysines on their surface. This results in an increased negative surface charge, but how does this help the proteins maintain their structure in salty conditions? Oscar Millet and team report in PLoS Biology that the small size of these amino acids is the key to survival.

The team carried out extensive site-directed mutagenesis on three proteins: a halophile, the homologous domain from a mesophile (an organism that thrives in the absence of salt) and an unrelated mesophile protein. Specifically, they looked at the 1A domain of NAD+-dependent DNA ligase N from the halophilic archaeon Haloferax volcanii; the homologous domain from the mesophilic bacterium Escherichia coli and the IgG-binding domain of protein L (ProtL) from another mesophile, Streptococcus magnus.

Millet and colleagues mutated the surface residues aspartic acid, glutamic acid, lysine, arginine, serine and glutamine, and grouped the mutations into three types —charge-preserving, size-preserving, and mutations that change both shape and size — in order to study their structural and thermodynamic effects.

In particular, they made multiple mutations in the mesophilic ProtL domain and determined the high-resolution NMR structures of two highly mutated forms. Kx6E is made by mutating six lysine residues to glutamic acid, and is only stable in halophilic conditions. Its structure was solved in 500 mM sodium chloride (PDB 2KAC). Kx5Q by contrast has five lysines replaced with glutamines (PDB 2JZP) and was solved in low salt conditions. Despite the different buffer conditions, the structures are very similar to the wild type (PDB 1HZ6), and no new inter-side-chain interactions are seen, so the halophilicity of Kx6E must originate elsewhere.

Millet's team used the structural data to calculate the solvent-accessible area of the proteins, and found that the increase in halophilicity correlated well with a decrease in side-chain solvent-accessible area. Thus the abundance of glutamic acids at the surface of halophilic proteins can be explained in terms of their size, rather than their charge. Their smaller size decreases the solvent-accessible area, meaning that fewer water molecules are needed to solvate the protein. This appears to be the key to haloadaptation.

But that leaves the puzzle of why small charged residues are preferred and not small neutral residues. This is probably because these charged residues reduce protein aggregation and lower the isoelectric point for solubility.

Maria Hodges

References

  1. X. Tadeo et al. Structural basis for the aminoacid composition of proteins from halophilic archea.
    PLoS Biol. 7, e1000257 (2009). doi:10.1371/journal.pbio.1000257

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health