On interaction patterns in proteins

Özbaykal, Gizem (2015) On interaction patterns in proteins. [Thesis]

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Proteins act like molecular machines that perform various functions in cellular activities. The physical laws determine the rules of atomic arrangements, however the organization of amino acids in proteins inherit evolutionary information. Understanding the three-dimensional structures of proteins are crucial for the exploration of the strong relationship between structure and functionality. This provides motivation to inspect how the network structure a ects communication in global scale. In this thesis, we study the interaction patterns in proteins to explore what kind of local mechanisms and global properties they inherit. Using the spatial information of amino acids, simpli ed models of complex molecular systems are built. We generate synthetic structures that resemble proteins in terms of network properties such as degree distribution and clustering characteristics. The di erences between synthetic structures and proteins are traced to distinguish proteins from non-protein structures. Such a di erentiation points out patterns that are peculiar to proteins and reveal the randomness within the proteins. We introduce the Mutation-Minimization (MuMi) method which mimics single point alanine mutation scan to investigate how proteins respond to naturally occurring random perturbations. Our approach enables us to unravel motifs that are common in protein structures and point out amino acids that have signi cant functional roles in biological activities.
Item Type: Thesis
Uncontrolled Keywords: Complex systems. -- Random graphs. -- Clustering. -- Atomic clusters. -- Single-point mutations. -- Karmaşık sistemler. -- Rastgele ağlar. -- Kümelenme. -- Atomik kümeler. -- Tek nokta mutasyonlar.
Subjects: T Technology > TA Engineering (General). Civil engineering (General) > TA401-492 Materials of engineering and construction. Mechanics of materials
Divisions: Faculty of Engineering and Natural Sciences > Academic programs > Materials Science & Eng.
Faculty of Engineering and Natural Sciences
Depositing User: IC-Cataloging
Date Deposited: 16 Oct 2017 11:24
Last Modified: 26 Apr 2022 10:11
URI: https://research.sabanciuniv.edu/id/eprint/34045

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