Bulletin of the American Physical Society
APS March Meeting 2012
Volume 57, Number 1
Monday–Friday, February 27–March 2 2012; Boston, Massachusetts
Session Z41: Focus Session: Non-Covalent Protein Interactions
11:15 AM–1:51 PM,
Friday, March 2, 2012
Sponsoring Units: DBIO GSNP
Chair: Corey O'Hern, Yale University
Abstract ID: BAPS.2012.MAR.Z41.3
Abstract: Z41.00003 : The power of simple hard-sphere models in protein structure prediction*
12:27 PM–1:03 PM
Preview Abstract Abstract
There are several force-fields that are currently used to describe the potential energy of biological macromolecules such as proteins. These typically include many parameters, derived from a combination of statistical, experimental sources. These work on average to describe a protein, but the large number of parameters moves this description further away from a true physical understanding than is desirable. Our approach is to investigate to what extent simple hard sphere models can be used to model and predict the behavior of different aspects of protein structure. We present the results of specific calculations. The distributions of the side-chain dihedral angle chi1 of Val and Thr in proteins of known structure show distinctive features: Val side chains predominantly adopt dihedral angle, chi1, of 180, whereas Thr side chains typically adopt a dihedral angle, chi1, of 60 or 300. Several hypotheses have been proposed to explain these differences, including inter-residue steric clashes and hydrogen-bonding interactions. In contrast, we show that the observed side-chain dihedral angle distributions for both Val and Thr can be explained using only local steric interactions in a dipeptide mimetic. Our results emphasize the power of a simple physics-based approaches and their importance for future advances in protein engineering and design.
*In collaboration with Alice Zhou and Corey O'Hern, Yale University.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2012.MAR.Z41.3
The American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics.
1 Physics Ellipse, College Park, MD 20740-3844
Editorial Office 1 Research Road, Ridge, NY 11961-2701 (631) 591-4000
Office of Public Affairs 529 14th St NW, Suite 1050, Washington, D.C. 20045-2001 (202) 662-8700