Exploring the Conformational Dynamics of Alanine Dipeptide in Solution Subjected to an External Electric Field: A Nonequilibrium Molecular Dynamics Simulation.

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context, we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and nontrivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.

[1]  H. Treutlein,et al.  Comparative study of insulin chain-B in isolated and monomeric environments under external stress. , 2008, The journal of physical chemistry. B.

[2]  Amedeo Caflisch,et al.  Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water , 1999 .

[3]  Martin Gruebele,et al.  The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin. , 2009, Faraday discussions.

[4]  N. English,et al.  Nonequilibrium molecular dynamics study of electric and low-frequency microwave fields on hen egg white lysozyme. , 2009, The Journal of chemical physics.

[5]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[6]  K. Gruber,et al.  Can electromagnetic fields influence the structure and enzymatic digest of proteins? A critical evaluation of microwave-assisted proteomics protocols , 2012, Journal of proteomics.

[7]  M. Tuckerman.  Statistical Mechanics: Theory and Molecular Simulation , 2010 .

[8]  M. Cieplak,et al.  Proteins in the electric field near the surface of mica. , 2013, The Journal of chemical physics.

[9]  A. Vogel,et al.  Femtosecond-laser-induced nanocavitation in water: implications for optical breakdown threshold and cell surgery. , 2008, Physical review letters.

[10]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[11]  H. Bohr,et al.  Microwave-enhanced folding and denaturation of globular proteins. , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[12]  Okan Esenturk,et al.  Applications of terahertz spectroscopy in biosystems. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.

[13]  P. Black,et al.  Cellular-telephone use and brain tumors. , 2001, The New England journal of medicine.

[14]  G. Ciccotti,et al.  Hydrodynamics from statistical mechanics: combined dynamical-NEMD and conditional sampling to relax an interface between two immiscible liquids. , 2011, Physical chemistry chemical physics : PCCP.

[15]  Fabrizio Mancinelli,et al.  Non‐thermal effects of electromagnetic fields at mobile phone frequency on the refolding of an intracellular protein: Myoglobin , 2004, Journal of cellular biochemistry.

[16]  R. Kubo.  Statistical-Mechanical Theory of Irreversible Processes : I. General Theory and Simple Applications to Magnetic and Conduction Problems , 1957 .

[17]  G. Ciccotti,et al.  Direct Computation of Dynamical Response by Molecular Dynamics: The Mobility of a Charged Lennard-Jones Particle , 1975 .

[18]  Frank Noé,et al.  Markov state models based on milestoning. , 2011, The Journal of chemical physics.

[19]  P. Rios,et al.  Complex network analysis of free-energy landscapes , 2007, Proceedings of the National Academy of Sciences.

[20]  E. Lindahl,et al.  Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. , 2010, Journal of chemical theory and computation.

[21]  G. Ciccotti,et al.  “Thought-experiments” by molecular dynamics , 1979 .

[22]  G. Ciccotti,et al.  Bulk viscosity of the Lennard-Jones system at the triple point by dynamical nonequilibrium molecular dynamics. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[23]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[24]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[25]  Alexander D. MacKerell,et al.  Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations , 2004, J. Comput. Chem..

[26]  F. Biscarini,et al.  Effects of electric field stress on a beta-amyloid peptide. , 2009, The journal of physical chemistry. B.

[27]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[28]  E. Stuve,et al.  Phase transitions in vapor-deposited water under the influence of high surface electric fields , 2000 .

[29]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[30]  David W. P. Thomas,et al.  Cell biology: Non-thermal heat-shock response to microwaves , 2000, Nature.

[31]  Irene Yarovsky,et al.  Electric field effects on insulin chain-B conformation. , 2005, The journal of physical chemistry. B.

[32]  L. Astrakas,et al.  Structural destabilization of chignolin under the influence of oscillating electric fields , 2012 .

[33]  L. Astrakas,et al.  Electric field effects on chignolin conformation , 2011 .

[34]  M. Karplus,et al.  Deformable stochastic boundaries in molecular dynamics , 1983 .

[35]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[36]  Angel Díaz-Ortiz,et al.  Microwaves in organic synthesis. Thermal and non-thermal microwave effects. , 2005, Chemical Society reviews.

[37]  Niall J. English,et al.  Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide , 2012, J. Comput. Chem..

[38]  Melville S. Green,et al.  Markoff Random Processes and the Statistical Mechanics of Time‐Dependent Phenomena. II. Irreversible Processes in Fluids , 1954 .

[39]  G. Ciccotti,et al.  Theoretical foundation and rheological application of non-equilibrium molecular dynamics , 1993 .

[40]  H. Bohr,et al.  Microwave enhanced kinetics observed in ORD studies of a protein. , 2000, Bioelectromagnetics.

[41]  H. Treutlein,et al.  Effect of frequency on insulin response to electric field stress. , 2007, The journal of physical chemistry. B.