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https://hdl.handle.net/2142/85463
Description
Title
Enforced Large-Scale Motions in Proteins
Author(s)
Isralewitz, Barry
Issue Date
2007
Doctoral Committee Chair(s)
Schulten, Klaus
Department of Study
Biophysics and Computational Biology
Discipline
Biophysics and Computational Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biophysics, General
Language
eng
Abstract
"Steered molecular dynamics (SMD) simulations are performed on several model biomolecular systems in order to promote large structural changes in each. External forces are applied to molecular dynamics simulations to promote ligand exit from bacteriorhodopsin, unraveling of titin and fibronectin domains, and rotation of the central stalk within an ATP synthase F1 unit. SMD methods employed include linear constant-velocity extension, multiple-trial segmented path creation, and torque application to enforce angular velocities. The synthesis-direction rotation of ATP synthase central stalk led to: (i) several changes consistent with synthesis nearly 100 A away from the area of torque application, (ii) winding of the coiled-coil stalk, and (iii) a multi-step pathway that allows a key residue (""arginine-finger"" alphaTPArg-373) to enter the ATP binding pocket, thereby inducing catalysis. Spontaneous motions of isolated ATP synthase catalytic subunits are also examined. The subunits, starting from different experimentally observed conformations, perform a combination of twisting and bending motions as they move toward a common conformation, which suggest specific mechanical roles for the subunits in central stalk rotation."
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