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Identifier

000419310

Title

Molecular dynamics simulations of proteins

Alternative Title

Μοριακές προσομοιώσεις πρωτεϊνών

Author

Αρνιττάλη Μαρία

Thesis advisor

Χαρμανδάρης, Ευάγγελος

Reviewer

Κοκκινίδης, Μιχαήλ
Ρισσάνου, Αναστασία

Abstract

Proteins are large biomolecules, which perform a great variety of functions in the living systems. The structure of biological macromolecules, like proteins can be provided by experiments. However it is very difficult to get insight into the atomic structures and the way that their various properties change in time experimentally. Molecular Dynamics simulations have become a powerful technique in studying biological macromolecules, like proteins. In the current work, we investigate two proteins in the native state, the repressor of primer (Rop), and its loopless mutation (RM6), in aqueous solution. We report data concerning hydrogen bonding, structural properties and stereochemical quality of the systems. Our results provide information both in molecular and in atomic level. The native state is stable in Rop protein as well as in RM6 protein. In terms of Rop protein, Ala is the only amino acid among the residues of the loop that hydrogen bonding with both helices simultaneously. There are slightly different between Rop protein and RM6 protein. Comparisons between Rop protein and its mutation RM6 have been also performed. The analysis of our simulations show that native state of proteins is stable under specific conditions. Additionally, hydorgens bonds are responsible for the stability of the secondary structure in both proteins. Electrostatic interactions are very important for the stability of the native state. Moreover, we could demonstrate the structure of our model with the Ramachandran plot.

Language

English, Greek

Subject

ROP

Μοριακή δυναμική

Issue date

2018-11-23

Collection

School/Department--School of Sciences and Engineering--Department of Mathematics and Applied Mathematics--Post-graduate theses

Type of Work--Post-graduate theses

Permanent Link

https://elocus.lib.uoc.gr//dlib/c/c/7/metadata-dlib-1542966148-885863-9393.tkl