David D. Thomas, Fellow

Computational Simulation of Muscle Protein Dynamics

Recent experiments using electron paramagnetic resonance (EPR) spectroscopy indicate a rotation of the myosin light chain domain during muscle contraction. EPR techniques measure the orientation of a spin label attached to the protein at any location. The researchers predicted optimal sites for labeling the myosin molecule by calculating an order parameter and simulating the EPR spectra based on the orientation of a spin label during molecular dynamics simulations. Simulations can also provide the orientation of the spin label with respect to the actin protein axis, while experiments are limited to describing relative changes in the molecule’s orientation. These computational techniques improve experimental efficiency and further the understanding of structural changes in molecules during muscle contraction. As part of their study in muscle biomolecular dynamics, the research group set out to understand the molecular dynamics of force generation and movement in muscle. The group deduced the orientation and mobility of contractile proteins by examining and deconvoluting the EPR spectra and anisotropy decays of spin labels and optical probes attached to the particular components. Additionally, they tested models of molecular motion by simulating the EPR spectra and anisotropy decays predicted by the models.

Research Group and Collaborators

Mike Autry, Graduate Student Researcher
Vincent Barnett, Faculty Collaborator
Roberta Bennett, Faculty Collaborator
Adam Butenski-Bartlett, Supercomputing Institute Undergraduate Intern
Claire N. Chisolm, Supercomputing Institute Undergraduate Intern
David Dreytser, Undergraduate Student Researcher
Michael J. Enz, Undergraduate Student Researcher
Diane Eschliman, Graduate Student Researcher
Yao Fan, Graduate Student Researcher
Jack Grinband, Graduate Student Researcher
Edmund Howard, Graduate Student Researcher
Jawed Karim, Undergraduate Student Researcher
Tara Kirby, Graduate Student Researcher
Vicci Korman, Research Associate
Leslie L. Laconte, Graduate Student Researcher
Dawn Lowe, Graduate Student Researcher
John J. Matta, Research Associate
John Muriuki, Undergraduate Student Researcher
Yuri Nesmelov, Research Associate
Irina Nesmelova, Research Associate
Ewa Prochniewicz-Nakayama, Research Associate
Osha Roopnarine, Faculty Collaborator
Wendy Smith, Graduate Student Researcher
John Stamm, Graduate Student Researcher
Jack T. Surek, Graduate Student Researcher
Hui Tang, Graduate Student Researcher
Mohac Tekmen, Graduate Student Researcher
Zeb Thomas, Staff
Vincent Voelz, Research Associate
David Wacker, Undergraduate Student Researcher
Gabe Westmaas, Research Associate
Sichun Yang, Graduate Student Researcher
Jamillah Zamoon, Graduate Student Researcher
Jianfang Zong, Graduate Student Researcher