Coil–Globule–Coil Transition of PNIPAm in Aqueous Methanol: Coupling All-Atom Simulations to Semi-Grand Canonical Coarse-Grained Reservoir

Conformational transitions of (bio)macromolecules in aqueous mixtures are intimately linked to local concentration fluctuations of different solvent components. Though computer simulations are ideally suited to investigate such phenomena, in conventional setups the excess of one cosolvent close to the solute leads to depletion elsewhere, requiring very large simulation domains to avoid system size effects. We, here, propose an approach to overcome this depletion effect, which combines the adaptive resolution scheme (AdResS) with a Metropolis particle exchange criterion. In AdResS, a small all-atom region, containing the solute, is coupled to a coarse-grained reservoir, where the particle exchange is performed. The particle exchange would be almost impossible had they been performed in an all-atom setup of a dense molecular liquid. As a first application of the method, we study the concentration driven reentrant collapse and swelling transition of poly(N-isopropylacrylamide) (PNIPAm) in aqueous methanol an...

[1]  D. W. Bolen,et al.  Predicting the energetics of osmolyte-induced protein folding/unfolding. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[3]  K. Kremer,et al.  Preferential Solvation of Triglycine in Aqueous Urea: An Open Boundary Simulation Approach. , 2012, Journal of chemical theory and computation.

[4]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

[5]  Dick Bedeaux,et al.  Kirkwood-Buff Integrals for Finite Volumes. , 2013, The journal of physical chemistry letters.

[6]  T. Birshtein,et al.  Coil-Globule Type Transitions in Polymers. 2. Theory of Coil-Globule Transition in Linear Macromolecules , 1991 .

[7]  Kurt Kremer,et al.  Kirkwood-Buff Analysis of Liquid Mixtures in an Open Boundary Simulation. , 2012, Journal of chemical theory and computation.

[8]  Howard G. Schild,et al.  Cononsolvency in mixed aqueous solutions of poly(N-isopropylacrylamide) , 1991 .

[9]  Dirk Reith,et al.  Deriving effective mesoscale potentials from atomistic simulations , 2002, J. Comput. Chem..

[10]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[11]  C. Wu,et al.  Reentrant coil-to-globule-to-coil transition of a single linear homopolymer chain in a water/methanol mixture. , 2001, Physical review letters.

[12]  M. Stevens,et al.  Study of the Polymer Length Dependence of the Single Chain Transition Temperature in Syndiotactic Poly(N-isopropylacrylamide) Oligomers in Water , 2012 .

[13]  Matej Praprotnik,et al.  Concurrent triple-scale simulation of molecular liquids. , 2008, The Journal of chemical physics.

[14]  Hans Hasse,et al.  Molecular dynamics and experimental study of conformation change of poly(N-isopropylacrylamide) hydrogels in mixtures of water and methanol. , 2012, The journal of physical chemistry. B.

[15]  Kurt Kremer,et al.  Structure Formation of Toluene around C60: Implementation of the Adaptive Resolution Scheme (AdResS) into GROMACS. , 2012, Journal of chemical theory and computation.

[16]  Pep Español,et al.  Hamiltonian adaptive resolution simulation for molecular liquids. , 2012, Physical review letters.

[17]  Helmut Grubmüller,et al.  Polar or Apolar—The Role of Polarity for Urea-Induced Protein Denaturation , 2008, PLoS Comput. Biol..

[18]  K. Kremer,et al.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.

[19]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[20]  K. Binder,et al.  An algorithm for the semi-grand-canonical simulation of asymmetric polymer mixtures , 1994 .

[21]  Chi Wu,et al.  Comparison of the Coil-to-Globule and the Globule-to-Coil Transitions of a Single Poly(N-isopropylacrylamide) Homopolymer Chain in Water , 1998 .

[22]  M. Record,et al.  Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer , 2011, Proceedings of the National Academy of Sciences.

[23]  B. Berne,et al.  Comment on "urea-mediated protein denaturation: a consensus view". , 2011, The journal of physical chemistry. B.

[24]  F. Tanaka,et al.  Temperature dependent phase behavior of PNIPAM microgels in mixed water/methanol solvents , 2013 .

[25]  Matej Praprotnik,et al.  Statistical Physics Problems in Adaptive Resolution Computer Simulations of Complex Fluids , 2011 .

[26]  Michele Parrinello,et al.  Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism. , 2011, Journal of the American Chemical Society.

[27]  B. Hess,et al.  Cation specific binding with protein surface charges , 2009, Proceedings of the National Academy of Sciences.

[28]  B. Pettitt,et al.  Protein folding, stability, and solvation structure in osmolyte solutions. , 2005, Biophysical journal.

[29]  L Delle Site,et al.  Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir. , 2011, Physical review letters.

[30]  Valerie Daggett,et al.  The molecular basis for the chemical denaturation of proteins by urea , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[31]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[32]  Matej Praprotnik,et al.  Multiscale simulation of soft matter: from scale bridging to adaptive resolution. , 2008, Annual review of physical chemistry.

[33]  Q. Cui,et al.  Preferential interactions between small solutes and the protein backbone: a computational analysis. , 2010, Biochemistry.

[34]  B. Hammouda,et al.  Co-Nonsolvency of Poly(n-isopropylacrylamide) in Deuterated Water/Ethanol Mixtures , 2013 .

[35]  J. Kirkwood,et al.  The Statistical Mechanical Theory of Solutions. I , 1951 .