Molecular dynamics of apo-adenylate kinase: A distance replica exchange method for the free energy of conformational fluctuations
Article Abstract:
Molecular dynamics (MD) is used to study a large domain motion in adenylate kinase from Escherichia coli (AKE). The distance replica exchange method (DREM) has provided a sufficient enhancement in sampling that, over the simulation length, convergence with respect to motions that reflect the large-scale movement of AKE is achieved.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Molecular dynamics of apo-adenylate kinase: A principal component analysis
Article Abstract:
Adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes large-scale motions of its Lid and AMP-binding domains when its open form closes over its substrates, AMP and [Mg.sup.2+]-ATP.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Hamiltonian and distance replica exchange method studies of met-enkephalin
Article Abstract:
The conformational space of Met-enkephalin, an opioid pentapeptide with sequence of Tyr-Gly-Gly-Phe-Met explored by using explicit solvent molecular dynamics simulations is presented.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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