Coarse graining biomolecular systems

Summary, in English

Proteins in the living cell can interact with a wide variety of solutes, ranging from ions, peptides, other proteins, DNA to membranes. Charged groups play a major role and solution conditions such as pH and ionic strength can modulate the interactions significantly. Describing these systems in a statistical mechanical framework involves thousands of pair-interactions and therefore a certain amount of coarse graining is often required. We here present a conceptually simple "mesoscopic" protein model where the detailed charge distribution and surface topology is well preserved. Monte Carlo simulations based on this model can be used to accurately reproduce second virial coeffients, pH titration curves and binding constants of proteins.

• Author: Mikael Lund
• Editor: Bo Kågström; Erik Elmroth; Jack Dongarra; Jerzy Waśniewski
• Publishing year: 2007
• Language: English
• Pages: 73-81
• Publication/Series: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
• Volume: 4699 LNCS
• Links: http://dx.doi.org/10.1007/978-3-540-75755-9_9
• Document type: Conference paper
• Publisher: Springer
• Topic: Theoretical Chemistry (including Computational Chemistry)
• Conference name: 8th International Workshop on Applied Parallel Computing, PARA 2006
• Conference date: 2007-06-18 - 2007-06-21
• Conference place: Umea, Sweden
• Status: Published
• ISBN/ISSN/Other: ISSN: 0302-9743; ISSN: 1611-3349; ISBN: 9783540757542