University of Minnesota
University Relations

Minnesota Supercomputing Institute

Log out of MyMSI

Research Abstracts Online
January 2009 - March 2010

Main TOC ....... College TOC 1 ...... College TOC 2 ....... Next Abstract

University of Minnesota Twin Cities
College of Biological Sciences
Medical School
Department of Biochemistry, Molecular Biology, and Biophysics

PI: David D. Thomas, Fellow

Molecular Dynamics of Muscle Proteins

The goal of this research is to understand the structural dynamics associated with force-generating proteins during muscle contraction and to elucidate the molecular mechanisms of catalysis and regulation of the Ca-ATPase (SERCA) that pumps calcium into the sarcoplasmic reticulum and thus relaxes the muscle. Structural and functional models, derived from structural information from x-ray crystallography and electron microscopy, are tested experimentally by an approach based on site-directed labeling and EPR and fluorescence spectroscopy. Specifically, structural models of conformational transitions in muscle proteins are tested and refined by results from the spectroscopic techniques with the aim to detect biologically relevant protein motions. No single method can provide needed information about changes in structure and interactions that occur under functional conditions. A multidisciplinary approach is needed that includes computational simulations that are necessary to connect models with experiment. This work is clearly dependent upon choosing appropriate labeling sites and accurately interpreting spectroscopic data. Molecular dynamics (MD) simulations of spin labeled proteins have enabled these researchers to accurately predict the shape of electron paramagnetic resonance (EPR) spectra, which means they can design more effective labeling sites for measuring distances and dynamics. Direct simulation of EPR spectra has expanded the ability to interpret ambiguous data. MD simulations have also allowed modeling of structural transitions that occur in response to events such as phosphorylation of muscle regulatory regions or in protein binding. From these MD simulations thermodynamical properties have been determined. The interpretation of spectroscopic data in these systems requires significant computational resources. This project includes ab initio quantum chemistry calculations and molecular dynamics simulations of spectroscopic probes and simulations on large protein complexes.

Group Members

Roman Agafonov, Graduate Student
Joseph Autry, Research Associate
Vincent Barnett, Faculty Collaborator
Sarah Blakely, Graduate Student
Matthew Devaney, Staff
Lennane Michel Espinoza-Fonseca, Research Associate
Alex Floresa, Undergraduate Student
Piyala Guhathakurta, Research Associate
Edmund Howard, Graduate Student
David J. E. Kast, Graduate Student
Daniel J. Kennedy, Supercomputing Institute Undergraduate Intern
Jennifer Klein, Graduate Student
Leanne Kolb, Graduate Student
Alexey Konovalov, Research Associate
Vicci Korman, Research Associate
Jennifer Levine, Graduate Student
Ji Li, Graduate Student
Dawn Lowe, Faculty Collaborator
John Matta, Research Associate
Ryan Mello, Graduate Student
Rebecca Moen, Graduate Student
Wendy Nelson, Research Associate
Yuriy Nesmelov, Faculty Collaborator
Beverly Ostrowski, Research Associate
Chin-Ju Park, Research Associater
Germana Paterlini, Certusoft, Inc., Minneapolis, Minnesota
Eric Perkins, Staff
Carl Palnaszek, Research Associate
Ewa Prochniewicz-Nakayama, Research Associate
Todd Rappe, Research Associate
Zachary Rhodes, Graduate Student
Seth Robia, Research Associate
Osha Roopnarine, Faculty Collaborator
Daniel Spakowicz, Staff
Jack T. Surek, Graduate Student
Bengt Svensson, Research Associate
Mohac Tekmen, Graduate Student
Yaroslav Tkachev, Graduate Student
Kurt Torgersen, Graduate Student
Yi Z. Wang, Supercomputing Institute Undergraduate Intern
Deb Winters, Graduate Student
Jamillah Zamoon, Graduate Student