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Identifier

000456149

Title

Studying the effect of protein structure characteristics on the evolutionary rate of proteins

Alternative Title

Μελέτη της επίδραση χαρακτηριστικών δομής των πρωτεϊνών στον ρυθμό εξέλιξής τους

Author

Κυπριανίδη, Θεοδώρα Α.

Thesis advisor

Παυλίδης, Παύλος

Reviewer

Παυλίδης, Ιωάννης
Ηλιόπουλος, Ιωάννης

Abstract

The aim of this study is to investigate if the evolutionary rate of proteins is affected, firstly by structural characteristics of proteins and then by protein localization. Information about the evolutionary rate of proteins can provide valuable insights into the functional and structural importance of specific protein regions; furthermore it yields information about the evolutionary history, relationships and functional divergence and finally it can be useful in evolutionary biology, bio-informatics and drug discovery fields. Regarding structural characteristics of proteins, secondary structure characteristics were studied, particularly Alpha helices and Beta sheets in a data set that was extracted from the Protein Data Bank. The intention was to investigate how the quantity of protein secondary structural elements affects its evolutionary rate. We found that proteins containing more amino acids assigned as Beta sheets rather than Alpha helices, tend to evolve faster. We classified our proteins in KEGG pathways, in order to conduct pathway analysis, and compared the evolutionary rates of proteins containing bigger percentage of Alpha helices and Beta sheets within each pathway. From the Uniprot database we extracted the possible locations for each protein and examined their impact on evolutionary rate. Furthermore, we performed a Gene Ontology analysis on both Alpha helix and Beta sheet proteins to identify their corresponding biological processes, molecular functions, and cellular components. This analysis aimed to investigate whether these two types of proteins participate in different gene ontology terms, which could potentially explain the observed differences in their evolutionary rates. We found that B proteins are found more in the extracellular region while A proteins inside the cell; this could possibly explain their difference in the evolutionary rates. For the second part of the study concerning protein localization we used a data set from the G.Gkouridis lab (IMBB-FORTH), there are three protein locations, i.e., heavy membranes, light membranes and solution to investigate (i) if the protein localization affects the evolutionary rate of proteins, and (ii) if secondary structure elements in different locations affect the evolutionary rate.

Language

English

Subject

A-helices

B-sheets

Evolutionary rate of proteins

Membrane proteins

Soluble proteins

Α-έλικες

Β-πτυχές

Διαλύτες πρωτεΐνες

Μεμβρανικές πρωτεΐνες