Information-Based Torsion Angle Potential for Proteins and Applications

Statistical potentials offer a significant bioinformation-based alternative to physical potentials in protein structure prediction and design. As an introduction we survey the aspects and methods involved in the derivation and applicability of various statistical potentials. The statistical potential created in this work is based on a reduced protein representation described by the residue sequence and the backbone structure including the Cbeta atoms. This potential has two components constructed separately. The component characterizes the protein interactions between the neighboring residues along the sequence. As structural variables we use the principal internal degrees of freedom, which are the backbone ϕ and psi dihedral angles corresponding to each residue. We quantify the correlation between every pair of adjacent dihedrals (ϕi, psii) and (psii, ϕ i+1) in the context of local residue sequence (Ri--1, Ri, Ri+1) by extracting and processing the related information from a database of protein loops structures. We focus in detail on an important application of our local potential: the sequence design of peptidic inhibitors for HIV-1 protease. The second component of our statistical potential is designed mainly for assessing the "non-local" protein interactions and is obtained from a distance-based potential applied to our particular protein representation. In association with an adequate search technique we find an efficient way to assemble the two parts of our statistical potential, which appropriately combines both local and non-local contributions. We successfully apply the resulting method to the protein loop modeling.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics and Computational Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2014

Author dc:creator

• Rata, Ionel

Contributors dc:contributor

• Jakobsson, Eric

• Biophysics, General

Identifier

(UMI)AAI3363068

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/72401