Protein Three -Dimensional Structure: Theoretical and Computational Aspects of Structure Prediction Based on the Amino Acid Sequence

Given that the repertoire of secondary structure classifications is limited, we asked if there is a limited set, even if large, of structural features that describe the protein three-dimensional structure adequately. Towards this end, we created libraries of peptide fragments of sizes 7 to 13 respectively and clustered them based on structural similarity. Analysis of these clustered fragments show that these adequately describe the protein structure space. In order to use this paradigm for ab initio structure prediction, we examined sequence-structure relationships in these clusters. It turns out that while structural characterization is nearly complete, the mapping from sequence to structure is not unique and no significant correlations exist between the sequences in a given structural cluster. Examination of numerous protein structures using sequence-structure correlations show that there are regions in proteins which show a degree of correlation. These are perhaps the folding motifs in proteins and this warrants further examination.

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

2015

Author dc:creator

• Pappas, Georgios Joannis, Jr

Contributors dc:contributor

• Subramaniam, Shankar

• Biophysics, General

Language dc:language

eng

Identifier

(MiAaPQ)AAI9944960

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/85492