Modeling the free energy landscape of biomolecules via dihedral angle principal component analysis of molecular dynamics simulations

Modellierung der freien Energiefläche von Biomolekülen durch Torsionswinkel-Principal-Component-Analysis von Molekulardynamiksimulationen

  • This work presents a contribution to the literature on methods in search of lowdimensional models that yield insight into the equilibrium and kinetic behavior of peptides and small proteins. A deep understanding of various methods for projecting the sampled configurations of molecular dynamics simulations to obtain a low-dimensional free energy landscape is acquired. Furthermore low-dimensional dynamic models for the conformational dynamics of biomolecules in reduced dimensionality are presented. As exemplary systems, mainly short alanine chains are studied. Due to their size they allow for performing long simulations. They are simple, yet nontrivial systems, as due to their flexibility they are rapidly interconverting conformers. Understanding these polypeptide chains in great detail is of considerable interest for getting insight in the process of protein folding. For example, K. Dill et al. conclude in their review [28] about the protein folding problem that "the once intractable Levinthal puzzle now seems to have a very simple answer: a protein can fold quickly and solve its large global optimization puzzle simply through piecewise solutions of smaller component puzzles".
  • Das Ziel der vorliegenden Arbeit ist es, einen Beitrag zur Entwicklung von Methoden zur Modellierung von freien Energieflächen von Biomolekülen zu leisten. Ausgehend von Molekulardynamik-Simulationen geht es insbesondere darum, niedrig-dimensionale Modelle für die Beschreibung von Konformationen und der Kinetik von Peptiden und kleinen Proteinen zu erhalten.

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Author:Alexandros AltisGND
Referee:Gerhard StockORCiDGND, Karin Hauser
Document Type:Doctoral Thesis
Date of Publication (online):2009/04/24
Year of first Publication:2008
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Granting Institution:Johann Wolfgang Goethe-Universität
Date of final exam:2009/04/20
Release Date:2009/04/24
Tag:Torsionswinkel; dPCA
dihedral angles; free energy landscape
GND Keyword:Molekulardynamik; Computersimulation; Hauptkomponentenanalyse; Freie Energie
Page Number:129
Institutes:Biochemie, Chemie und Pharmazie / Biochemie und Chemie
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 54 Chemie / 540 Chemie und zugeordnete Wissenschaften
Licence (German):License LogoDeutsches Urheberrecht