Grid-based nonequilibrium multiple-time scale molecular dynamics/Brownian dynamics simulations of ligand-receptor interactions in structured protein systems

2003 ◽  
Author(s):  
Yaohang Li ◽  
M. Mascagni ◽  
M.H. Peters
Keyword(s):  
Molecular Dynamics ◽  
Time Scale ◽  
Brownian Dynamics ◽  
Multiple Time ◽  
Multiple Time Scale ◽  
Receptor Interactions ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Grid Based

scholarly journals Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

2011 ◽  
Vol 134 (1) ◽  
pp. 014103 ◽  
Author(s):  
Joseph A. Morrone ◽  
Thomas E. Markland ◽  
Michele Ceriotti ◽  
B. J. Berne
Keyword(s):  
Molecular Dynamics ◽  
Time Scale ◽  
Colored Noise ◽  
Multiple Time ◽  
Multiple Time Scale

scholarly journals Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics

2012 ◽  
Vol 9 (76) ◽  
pp. 2845-2855 ◽  
Author(s):  
A. M. Stadler ◽  
C. J. Garvey ◽  
A. Bocahut ◽  
S. Sacquin-Mora ◽  
I. Digel ◽  
...  
Keyword(s):  
Body Temperature ◽  
Time Scale ◽  
Brownian Dynamics ◽  
Conformational Dynamics ◽  
Coarse Grained ◽  
Mean Square ◽  
Temperature Range ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Average Body

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus ; domestic chicken, Gallus gallus domesticus and human, Homo sapiens ) and an ectotherm (salt water crocodile, Crocodylus porosus ) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.

Reply to Comment on: Reversible multiple time scale molecular dynamics

1993 ◽  
Vol 99 (3) ◽  
pp. 2278-2279 ◽  
Author(s):  
M. Tuckerman ◽  
B. J. Berne ◽  
G. J. Martyna
Keyword(s):  
Molecular Dynamics ◽  
Time Scale ◽  
Multiple Time ◽  
Multiple Time Scale

Multiple time scale Hartree-Fock molecular dynamics

1993 ◽  
Vol 45 (1) ◽  
pp. 59-70 ◽  
Author(s):  
Bernd Hartke ◽  
Douglas A. Gibson ◽  
Emily A. Carter
Keyword(s):  
Molecular Dynamics ◽  
Time Scale ◽  
Multiple Time ◽  
Multiple Time Scale ◽  
Hartree Fock
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