Senior Project Advisor

Filip Jagodzinski

Document Type

Project

Publication Date

Fall 2020

Keywords

PDZ Domains, Biology, Computer Science, Bioinformatics, Proteins

Abstract

Studies of protein mutants in wet laboratory experiments are expensive and time consuming. Computational experiments that simulate the motions of protein with amino acid substitutions can complement wet lab experiments for studying the effects of mutations. In this work we present a computational pipeline that performs exhaustive single-point amino acid substitutions in silico. We perform energy minimization as part of molecular dynamics (MD) of our generated mutant proteins, and the wild type, and log the energy potentials for each step of the simulations. We motivate several metrics that rely on the energy minimization curves of the wild type and mutant, to explore quantitatively the effects of the mutations. Two case studies are discussed and analyzed to showcase the utility of our approach to identify the least and most impactful mutations.

Index Terms—Energy minimization, mutation, computational biochemistry, structural biology

Department

Computer Science

Subjects - Topical (LCSH)

Computational biology; Molecular dynamics; Mutation (Biology); Proteins--Biotechnology

Genre/Form

technical reports

Type

Text

Rights

Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.

Language

English

Format

application/pdf

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