Analysis of key parameters for molecular dynamics of pMHC molecules

Autor(en)

Ulrich Omasits, Bernhard Knapp, Martin Neumann, Othmar Steinhauser, Hannes Stockinger, Rene Kobler, Wolfgang Schreiner

Abstrakt

Molecular dynamics (MD) studies of human major histocompatibility complex (MHC) HLAB*2705 complexing two different peptides were performed. During simulation one peptide partially detached from the MHC while the other peptide switched back and forth between several different configurations. These different configurations relate to conformational substates and can be assigned to different levels of chemical activity or even the molecular mechanisms of immunological signalling. To ensure reliable immunological conclusions from MD simulations we prepare the methodological tools by carefully evaluating initial conditions, system simplification, solvation shell thickness, water model/force field combination and simulation length. We also derive a guideline for appropriate model selection. This kind of quality assessment is seen a mandatory prerequisite for coming studies linking peptide-loaded MHC dynamics to T-cell activation.

Organisation(en)

Computergestützte Physik und Physik der Weichen Materie, Institut für Computergestützte Biologische Chemie

Externe Organisation(en)

Medizinische Universität Wien, Johannes Kepler Universität Linz

Journal

Molecular Simulation

Band

34

Seiten

781-793

Anzahl der Seiten

12

ISSN

0892-7022

DOI

https://doi.org/10.1080/08927020802256298

Publikationsdatum

2008

Peer-reviewed

Ja

ÖFOS 2012

301303 Medizinische Biochemie

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/12e7af0a-fa07-472d-9d25-07efbaf03ce2