A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A

2011 ◽  
Vol 7 (6) ◽  
pp. 1943-1950 ◽  
Author(s):  
Toni Giorgino ◽  
Gianni De Fabritiis
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
High Throughput ◽  
Steered Molecular Dynamics ◽  
Gramicidin A ◽  
Ion Permeation ◽  
Energy Profile ◽  
Free Energy Profile

scholarly journals Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 245-259
Author(s):  
Yoshifumi Fukunishi ◽  
Saki Hongo ◽  
Masami Lintuluoto ◽  
Hiroshi Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Energy Profile ◽  
Free Energy Profile

scholarly journals Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers

2014 ◽  
Vol 126 (3) ◽  
pp. 637-647 ◽  
Author(s):  
YOUSEF NADEMI ◽  
SEPIDEH AMJAD IRANAGH ◽  
ABBAS YOUSEFPOUR ◽  
SEYEDEH ZAHRA MOUSAVI ◽  
HAMID MODARRESS
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Dynamics Simulations

scholarly journals The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics

2014 ◽  
Vol 11 (97) ◽  
pp. 20140399 ◽  
Author(s):  
L. Bongini ◽  
V. Lombardi ◽  
P. Bianco
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Average Distance ◽  
Sampling Technique ◽  
Energy Difference ◽  
Umbrella Sampling ◽  
Energy Profile ◽  
Structural Explanation ◽  
Free Energy Profile ◽  
Transition Mechanism

The overstretching transition in torsionally unconstrained DNA is studied by means of atomistic molecular dynamics simulations. The free-energy profile as a function of the length of the molecule is determined through the umbrella sampling technique providing both a thermodynamic and a structural characterization of the transition pathway. The zero-force free-energy profile is monotonic but, in accordance with recent experimental evidence, becomes two-state at high forces. A number of experimental results are satisfactorily predicted: (i) the entropic and enthalpic contributions to the free-energy difference between the basic (B) state and the extended (S) state; (ii) the longitudinal extension of the transition state and (iii) the enthalpic contribution to the transition barrier. A structural explanation of the experimental finding that overstretching is a cooperative reaction characterized by elementary units of approximately 22 base pairs is found in the average distance between adenine/thymine-rich regions along the molecule. The overstretched DNA adopts a highly dynamical and structurally disordered double-stranded conformation which is characterized by residual base pairing, formation of non-native intra-strand hydrogen bonds and effective hydrophobic screening of apolar regions.

Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp90

2013 ◽  
Vol 588 ◽  
pp. 226-230 ◽  
Author(s):  
Kazutomo Kawaguchi ◽  
Hiroaki Saito ◽  
Susumu Okazaki ◽  
Hidemi Nagao
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Terminal Domain
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