ASEdb: a database of alanine mutations and their effects on the

  free energy of binding in protein interactions

Thorn, Kurt S.; Bogan, Andrew A.

doi:10.1093/bioinformatics/17.3.284

Cited by 370 publications

(338 citation statements)

References 17 publications

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“…This might be the origin of PPI hotspots that have been observed previously. [60][61][62][63] However, we now conjecture that such hot spots are comprised of multiple as opposed to one or two residues. Finally, we believe that the classical concept of protein-protein binding sites, with just a few HIs per protein with clear borders, needs to be revisited.…”

Section: Discussionmentioning

confidence: 82%

Are protein-protein interfaces special regions on a protein’s surface?

Tonddast-Navaei

Skolnick

2015

The Journal of Chemical Physics

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Protein-protein interactions (PPIs) are involved in many cellular processes. Experimentally obtained protein quaternary structures provide the location of protein-protein interfaces, the surface region of a given protein that interacts with another. These regions are termed half-interfaces (HIs). Canonical HIs cover roughly one third of a protein's surface and were found to have more hydrophobic residues than the non-interface surface region. In addition, the classical view of protein HIs was that there are a few (if not one) HIs per protein that are structurally and chemically unique. However, on average, a given protein interacts with at least a dozen others. This raises the question of whether they use the same or other HIs. By copying HIs from monomers with the same folds in solved quaternary structures, we introduce the concept of geometric HIs (HIs whose geometry has a significant match to other known interfaces) and show that on average they cover three quarters of a protein's surface. We then demonstrate that in some cases, these geometric HI could result in real physical interactions (which may or may not be biologically relevant). The composition of the new HIs is on average more charged compared to most known ones, suggesting that the current protein interface database is biased towards more hydrophobic, possibly more obligate, complexes. Finally, our results provide evidence for interface fuzziness and PPI promiscuity. Thus, the classical view of unique, well defined HIs needs to be revisited as HIs are another example of coarse-graining that is used by nature. C

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Section: Discussionmentioning

confidence: 82%

Are protein-protein interfaces special regions on a protein’s surface?

Tonddast-Navaei

Skolnick

2015

The Journal of Chemical Physics

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“…For this process, we extracted information for 262 mutations in 13 protein-protein complexes (details in the legend to Fig. 5), as available from ASEdb, the Alanine Scanning Energetics database (17), and found their location in the core or the rim region of the interfaces. If we consider hot-spot residues as those that show a ⌬⌬G value of 2 kcal͞mol or more upon mutation to alanine, there are 37 such hot spots in the core region and 11 in the rim.…”

Section: Contribution Of the Side Chain Of A Residue To ⌬⌬Gmentioning

confidence: 99%

“…A hot spot has been defined as a residue that when mutated to alanine leads to a significant drop in the binding constant (typically 10-fold or higher), as determined by the change in the free energy of binding (⌬⌬G). A wealth of data on alanine scans is now accessible through the internet (17) for systematic analyses (18). There has also been development in computational methods for the prediction of the experimentally measured free-energy change by alanine substitution (19,20).…”

mentioning

confidence: 99%

Conservation and relative importance of residues across protein-protein interfaces

Guharoy

Chakrabarti

2005

Proc. Natl. Acad. Sci. U.S.A.

245

205

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A core region surrounded by a rim characterizes biological interfaces. We ascertain the importance of the core by showing the sequence entropies of the residues comprising the core to be smaller than those in the rim. Such a distinction is not seen in the 2-fold-related, nonphysiological interfaces formed in crystal lattices of monomeric proteins, thereby providing a procedure for characterizing the oligomeric state from crystal structures of protein molecules. This method is better than those that rely on the comparison of the sequence entropies in the interface and the rest of the protein surface, especially in cases where the surface harbors additional binding sites. To a good approximation there is a correlation between the accessible surface area lost because of complexation and ⌬⌬G values obtained through alanine-scanning mutagenesis (26 -38 cal per Å 2 of the surface buried) for residues located in the core, a relationship that is not discernable for rim residues. If, however, a residue participates in hydrogen bonding across the interface, the extent of stabilization is 52 cal͞mol per 1 Å 2 of the nonpolar surface area buried by the residue. As opposed to an amino acid classification used earlier, an environment-based grouping of residues yields a better discrimination in the sequence entropy between the core and the rim.protein-protein interaction ͉ hot spots in the interface ͉ residue conservation ͉ crystal packing ͉ quaternary structure prediction

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“…The method has subsequently been used successfully to map, e.g. functional epitopes in proteins and the energetics of molecular interactions (28,29). A similar Cysscanning mutagenesis was subsequently employed to study the formation of disulfide bridges in lysozyme (30).…”

Section: Introduction Of Unnatural Amino Acids Via Ribosomal Protein mentioning

confidence: 99%

Cys-X Scanning for Expansion of Active-site Residues and Modulation of Catalytic Functions in a Glutathione Transferase

Norrgård

Hellman

Mannervik

2011

Journal of Biological Chemistry

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We propose Cys-X scanning as a semisynthetic approach to engineer the functional properties of recombinant proteins. As in the case of Ala scanning, key residues in the primary structure are identified, and one of them is replaced by Cys via site-directed mutagenesis. The thiol of the residue introduced is subsequently modified by alternative chemical reagents to yield diverse Cys-X mutants of the protein. This chemical approach is orthogonal to Ala or Cys scanning and allows the expansion of the repertoire of amino acid side chains far beyond those present in natural proteins. In its present application, we have introduced Cys-X residues in human glutathione transferase (GST) M2-2, replacing Met-212 in the substrate-binding site. To achieve selectivity of the modifications, the Cys residues in the wild-type enzyme were replaced by Ala. A suite of simple substitutions resulted in a set of homologous Met derivatives ranging from normethionine to S-heptyl-cysteine. The chemical modifications were validated by HPLC and mass spectrometry. The derivatized mutant enzymes were assayed with alternative GST substrates representing diverse chemical reactions: aromatic substitution, epoxide opening, transnitrosylation, and addition to an ortho-quinone. The Cys substitutions had different effects on the alternative substrates and differentially enhanced or suppressed catalytic activities depending on both the Cys-X substitution and the substrate assayed. As a consequence, the enzyme specificity profile could be changed among the alternative substrates. The procedure lends itself to largescale production of Cys-X modified protein variants.The ϳ20 proteogenic amino acids provide combinations in protein structures that bring forth a perplexing variety of functions. Nevertheless, it is a reasonable assumption that expansion of the repertoire of amino acid residues in a protein could result in changes of functional properties that cannot be accomplished with the natural set of building blocks. In biological systems, the limited number of amino acids that can be assembled by ribosomal protein synthesis is complemented by a wide variety of post-translational modifications catalyzed by specific enzymes (1). Such modifications are nonetheless subject to the restrictions set by specific recognition motifs in the target proteins as well as by the selectivities of the modifying enzymes. On the other hand, recombinant proteins have the distinct advantage that they can be subjected to chemical modifications ex vivo and may, under appropriate circumstances, undergo numerous chemical modifications beyond the scope of biological modifying agents. In general, Cys residues in proteins can be selectively modified with an extremely broad range of electrophilic chemical reagents, and the cysteine residues can be introduced in strategic positions by means of site-directed mutagenesis.Ala scanning is a well established method by which target residues in a peptide sequence are substituted by Ala (2). A similar Cys scanning has been employed for ana...

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ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions

Cited by 370 publications

References 17 publications

Are protein-protein interfaces special regions on a protein’s surface?

Are protein-protein interfaces special regions on a protein’s surface?

Conservation and relative importance of residues across protein-protein interfaces

Cys-X Scanning for Expansion of Active-site Residues and Modulation of Catalytic Functions in a Glutathione Transferase

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