Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering

Computational and biophysical methods for the discovery and optimization of covalent drugs

Drugs that act by covalently attaching to their targets have been used to treat human diseases for over a hundred years. However, the deliberate design of covalent drugs was discouraged due to concerns of toxicity and off-target effects. Recent successes in covalent drug discovery have sparked fresh interest in this field. New screening and testing methods aimed at covalent inhibitors can play pivotal roles in facilitating the discovery process. This feature article focuses on computational and biophysical advances originating from our labs over the past decade and how these approaches have contributed to the design of prolyl oligopeptidase (POP) and SARS-CoV-2 3CLpro covalent inhibitors.

Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins

Rotamers, namely amino acid side chain conformations common to many different peptides, can be compiled into libraries. These rotamer libraries are used in protein modeling, where the limited conformational space occupied by amino acid side chains is exploited. Here, we construct a sequence-dependent rotamer library from simulations of all possible tripeptides, which provides rotameric states dependent on adjacent amino acids. We observe significant sensitivity of rotamer populations to sequence and find that the library is successful in locating side chain conformations present in crystal structures. The library is designed for applications with basin-hopping global optimization, where we use it to propose moves in conformational space. The addition of rotamer moves significantly increases the efficiency of protein structure prediction within this framework, and we determine parameters to optimize efficiency.

PON-SC - program for identifying steric clashes caused by amino acid substitutions

Background

Amino acid substitutions due to DNA nucleotide replacements are frequently disease-causing because of affecting functionally important sites. If the substituting amino acid does not fit into the protein, it causes structural alterations that are often harmful. Clashes of amino acids cause local or global structural changes. Testing structural compatibility of variations has been difficult due to the lack of a dedicated method that could handle vast amounts of variation data produced by next generation sequencing technologies.

Results

We developed a method, PON-SC, for detecting protein structural clashes due to amino acid substitutions. The method utilizes side chain rotamer library and tests whether any of the common rotamers can be fitted into the protein structure. The tool was tested both with variants that cause and do not cause clashes and found to have accuracy of 0.71 over five test datasets.

Conclusions

We developed a fast method for residue side chain clash detection. The method provides in addition to the prediction also visualization of the variant in three dimensional structure.

Electronic supplementary material

The online version of this article (10.1186/s12859-017-1947-7) contains supplementary material, which is available to authorized users.

Quantifying side-chain conformational variations in protein structure

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.