Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

Capra, John A.; Laskowski, Roman A.; Thornton, Janet M.; Singh, Mona; Funkhouser, Thomas

doi:10.1371/journal.pcbi.1000585

Cited by 401 publications

(359 citation statements)

References 71 publications

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“…Conversely, some functional assay formats and direct ligandbinding methods (e.g., isothermal titration calorimetry, surface plasmon resonance) may detect the effect of a small molecule binding to a secondary site but be unable to distinguish it from a competitive ligand. Furthermore, many computational methods have been developed to predict ligand-binding sites from protein sequence conservation, 3D structure (12), or both (13). These tools have had some success in predicting sites from the apo structure (14), including the presence of cryptic pockets (15).…”

Section: Fragment-based Drug Designmentioning

confidence: 99%

Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

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

103

106

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Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.protein structure | protein function | X-ray crystallography | fragment-based drug design

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Section: Fragment-based Drug Designmentioning

confidence: 99%

Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

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

103

106

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“…The analysis of solvent accessibility requires detailed knowledge of 29 ligand binding sites, which is limited to proteins with known ligand-bound structures. The second 30 approach uses evolutionary conservation of amino acids (Capra et al 2009;Lichtarge and Sowa 2002). 31 For example, amino acids in catalytic sites of enzymes are more conserved on average (Bartlett et al 32 2002).…”

Section: Introduction 23mentioning

confidence: 99%

Selection Shapes the Robustness of Ligand-Binding Amino Acids

2013

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The phenotypes of biological systems are to some extent robust to genotypic changes. Such robustness exists on multiple levels of biological organization. We analyzed this robustness for two categories of amino acids in proteins. Specifically, we studied the codons of amino acids that bind or do not bind small molecular ligands. We asked to what extent codon changes caused by mutation or mistranslation may affect physicochemical amino acid properties or protein folding. We found that the codons of ligand-binding amino acids are on average more robust than those of non-binding amino acids. Because mistranslation is usually more frequent than mutation, we speculate that selection for error mitigation at the translational level stands behind this phenomenon. Our observations suggest that natural selection can affect the robustness of very small units of biological organization.

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“…Structural genomics research has also lead to methods, commercial instrumentation, labware, and reagents for high throughput cloning, expression, and crystallization of proteins [12][13][14][15][16]. New software tools for structure prediction [17,19], design of experiments, laboratory information management, novel structure based informatics [20][21][22], such as function prediction from structure, have also been developed [23][24][25].…”

Section: Introductionmentioning

confidence: 99%

Practical applications of structural genomics technologies for mutagen research

Zemła

Segelke

2011

Mutation Research/Genetic Toxicology and Environmental Mutagene

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Here we present a perspective on a range of practical uses of structural genomics for mutagen research. Structural genomics is an overloaded term and requires some definition to bound the discussion; we give a brief description of public and private structural genomics endeavors, along with some of their objectives, their activities, their capabilities, and their limitations. We discuss how structural genomics might impact mutagen research in three different scenarios: at a structural genomics center, at a lab with modest resources that also conducts structural biology research, and at a lab that conducting mutagen research absent experimental structural biology. Applications span functional annotation of single genes, to constructing gene networks and pathways, to an integrated systems biology approach. Structural genomics centers can take advantage of systems biology models to target high value targets for structure determination and in turn extend systems models to better understand systems biology diseases or phenomenon. Individual investigator run structural biology laboratories can collaborate with structural genomics centers, but can also take advantage of technical advances and tools developed by structural genomics centers and can employ a structural genomics approach to advancing biological understanding. Individual investigator run non-structural biology laboratories can also collaborate with structural genomics center, possibly influencing targeting decisions, but can also use structure based annotation tools enabled by the growing coverage of protein fold space provided by structural genomics. Better functional annotation can inform pathway and systems biology models.

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Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

Cited by 401 publications

References 71 publications

Detection of secondary binding sites in proteins using fragment screening

Detection of secondary binding sites in proteins using fragment screening

Selection Shapes the Robustness of Ligand-Binding Amino Acids

Practical applications of structural genomics technologies for mutagen research

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