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Abstract
Algorithms for comparing protein structure are frequently used for function annotation. By searching for subtle similarities among very different proteins, these algorithms can identify remote homologs with similar biological functions. In contrast, few comparison algorithms focus on specificity annotation, where the identification of subtle differences among very similar proteins can assist in finding small structural variations that create differences in binding specificity. Few specificity annotation methods consider electrostatic fields, which play a critical role in molecular recognition. To fill this gap, this paper describes VASP-E (Volumetric Analysis of Surface Properties with Electrostatics), a novel volumetric comparison tool based on the electrostatic comparison of protein-ligand and protein-protein binding sites. VASP-E exploits the central observation that three dimensional solids can be used to fully represent and compare both electrostatic isopotentials and molecular surfaces. With this integrated representation, VASP-E is able to dissect the electrostatic environments of protein-ligand and protein-protein binding interfaces, identifying individual amino acids that have an electrostatic influence on binding specificity. VASP-E was used to examine a nonredundant subset of the serine and cysteine proteases as well as the barnase-barstar and Rap1a-raf complexes. Based on amino acids established by various experimental studies to have an electrostatic influence on binding specificity, VASP-E identified electrostatically influential amino acids with 100% precision and 83.3% recall. We also show that VASP-E can accurately classify closely related ligand binding cavities into groups with different binding preferences. These results suggest that VASP-E should prove a useful tool for the characterization of specific binding and the engineering of binding preferences in proteins.
Highlights
Software for comparing protein structures is widely used to make inferences about protein function
To examine electrostatic influences on specificity in proteins, this paper presents VASP-E, a software tool that generates solid representations of the electrostatic potential fields that surround proteins
We observed that solid representations of electrostatic fields could identify electrostatic conservations and variations that relate to similarities and differences in binding specificity between proteins and small molecules
Summary
Software for comparing protein structures is widely used to make inferences about protein function. Most approaches use atom coordinates or molecular surfaces [19,20,21,22] as digital representations of protein geometry Other characteristics, such as evolutionary significance [23,24,25], hydrophobicity [26] and electrostatic potential [5,23,27] are attached to this geometric representation as labels. Comparisons of these data often generate a score, such as the root mean squared distance (RMSD), that summarizes structural, biological, and chemical similarities among two or more structures. Proteins with very different sequences sometimes exhibit unusually similar RMSDs, revealing shared origins in antiquity [28,29,30]
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