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.

United States, Conformational analysis

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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.

Analysis

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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.

Hamiltonian systems, Enkephalins, Entropy (Physics), Entropy (Thermodynamics), Chemical properties

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