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Research Abstracts Online
January 2008 - March 2009

University of Minnesota Twin Cities
College of Biological Sciences and 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 molecular dynamics associated with force-generating proteins during muscle contraction and membrane ion pumps and channels as they excite and relax muscle. To test and refine structural models of conformational transitions in muscle proteins, these researchers use site-directed spectroscopic probes to detect biologically relevant motions. This work is clearly dependent upon choosing appropriate labeling sites and accurately interpreting spectroscopic data. The researchers use molecular dynamics (MD) simulations of spin-labeled proteins to accurately predict the shape of electron paramagnetic resonance (EPR) spectra before they do their experiments. They can thus design more effective labeling sites for measuring distances and dynamics. Direct simulation of EPR spectra enables the researchers to interpret ambiguous data. By using MD simulations, they can model structural transitions that occur in response to events such as phosphorylation of muscle regulatory regions or in protein binding.

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, Supercomputing Institute Research Scholar
Yao Fan, Graduate Student
Alex Florea, Undergraduate Student
Piyala Guhathakurta, Research Associate
Edmund Howard, Graduate Student
Henry Jakubowski, Department of Chemistry, College of Saint Benedict/Saint John’s University, Collegeville, Minnesota
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
Alan Lueke, Graduate Student
John Matta, Research Associate
Ryan Mello, Graduate Student
Yuriy Nesmelov, Faculty Collaborator
Irina Nesmelova, Research Associate
Beverly Ostrowski, Research Associate
Germana Paterlini, Certusoft, Inc., Minneapolis, Minnesota
Ewa Prochniewicz-Nakayama, Research Associate
Zachary Rhodes, Graduate Student
Seth Robia, Research Associate
Osha Roopnarine, Faculty Collaborator
Wendy Smith, Research Associate
Daniel Spakowicz, Staff
Terry Steele, Graduate Student
Jack T. Surek, Graduate Student
Bengt Svensson, Research Associate
Mohac Tekmen, Graduate Student
Kurt Torgersen, Graduate Student
Nicolas Ward, Undergraduate Student
Deb Winters, Graduate Student
Xue Wu, Visiting Researcher
Christina Yi, Undergraduate Student
Jamillah Zamoon, Graduate Student