Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Ripoll, Daniel R.; Scheraga, Harold A.

doi:10.1021/jp0582484

Cited by 8 publications

(21 citation statements)

References 16 publications

(95 reference statements)

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“…The replica-exchange method and its multiplexing variation are described in the literature, 50,[61][62][63] and its implementation in the previous version of UNRES is described in our recent work. 48,49 Therefore, here we provide only a brief description and the modification introduced to account for the temperature dependence of the force field.…”

Section: Sampling and Computing Thermodynamic Quantities With The Temmentioning

confidence: 99%

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Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins

et al. 2006

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We report the modification and parameterization of the united-residue (UNRES) force field for energy-based protein-structure prediction and protein-folding simulations. We tested the approach on three training proteins separately: 1E0L (β), 1GAB (α), and 1E0G (α + β). Heretofore, the UNRES force field had been designed and parameterized to locate native-like structures of proteins as global minima of their effective potential-energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES, and applied it with success to simulate protein folding pathways. How ever, the force field turned out to be largely biased towards α-helical structures in canonical simulations because the conformational entropy had been neglected in the parameterization. We applied the hierarchical optimization method developed in our earlier work to optimize the force field, in which the conformational space of a training protein is divided into levels each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy-function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential-energy function.

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Section: Sampling and Computing Thermodynamic Quantities With The Temmentioning

confidence: 99%

“…To generate the decoy sets, we use the multiplexing replica exchange molecular dynamics (MREMD) method which we recently 49 implemented in the UNRES force field. In section 2.1, we recall the UNRES model and force field that was used prior to this work.…”

Section: Introductionmentioning

confidence: 99%

Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins

et al. 2006

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“…The function U a in Eq. 67,[111][112][113] For the study of singlemethane hydration, we first use Monte Carlo sampling to generate a large collection of configurations of N = 395 water molecules. Clearly, U a = U a ͑r a ; r 1 , r 2¯rN ͒, where r a is the position vector of the inserted methane; but translational invariance of the solvent 48,110 implies that after averaging over water degrees of freedom the value of ͗Ve −␤U a ͘ N is independent of r a .…”

Section: ͑3͒mentioning

confidence: 99%

Pressure and temperature dependence of hydrophobic hydration: Volumetric, compressibility, and thermodynamic signatures

Moghaddam

Chan

2007

The Journal of Chemical Physics

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The combined effect of pressure and temperature on hydrophobic hydration of a nonpolar methanelike solute is investigated by extensive simulations in the TIP4P model of water. Using test-particle insertion techniques, free energies of hydration under a range of pressures from 1 to 3000 atm are computed at eight temperatures ranging from 278.15 to 368.15 K. Corresponding enthalpy, entropy, and heat capacity accompanying the hydration process are estimated from the temperature dependence of the free energies. Partial molar and excess volumes calculated using pressure derivatives of the simulated free energies are consistent with those determined by direct volume simulations; but direct volume determination offers more reliable estimates for compressibility. At 298.15 K, partial molar and excess isothermal compressibilities of methane are negative at 1 atm. Partial molar and excess adiabatic (isentropic) compressibilities are estimated to be also negative under the same conditions. But partial molar and excess isothermal compressibilities are positive at high pressures, with a crossover from negative to positive compressibility at approximately 100-1000 atm. This trend is consistent with experiments on aliphatic amino acids and pressure-unfolded states of proteins. For the range of pressures simulated, hydration heat capacity exhibits little pressure dependence, also in apparent agreement with experiment. When pressure is raised at constant room temperature, hydration free energy increases while its entropic component remains essentially constant. Thus, the increasing unfavorability of hydration under raised pressure is seen as largely an enthalpic effect. Ramifications of the findings of the authors for biopolymer conformational transitions are discussed.

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“…However, at present, UNRES includes statistical potentials of side-chain interaction determined from the PDB (Liwo et al, 1997), which have been implemented as independent of temperature. To replace the statistical potentials in UNRES with physics-based potentials, we are conducting a series of molecular simulation studies of models of pairs of amino acid side chains in water, taking into account the dependence of the PMF on orientation (Makowski, 2007a(Makowski, , 2007b(Makowski, , 2007c, which are a follow-up of our earlier more general studies of hydrophobic interactions (Czaplewski et al, 2000(Czaplewski et al, , 2002(Czaplewski et al, , 2003(Czaplewski et al, , 2005. The dependence of the PMF of selected pairs of amino acid side chains on their orientation in bulk water and in cylindrical hydrophobic nanopores was also studied recently by Vaitheeswaran and Thirumalai (2008).…”

Section: Introductionmentioning

confidence: 99%

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures

Sobolewski

Makowski

Ołdziej

et al. 2009

Protein Engineering, Design and Selection

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By means of molecular dynamics simulations of a pair of methane molecules in a TIP3P periodic water box with the NVT scheme at six temperatures and, additionally, the NPT scheme at three temperatures ranging from T = 283 to 373 K, we determined the potential of mean force (PMF) of pairs of interacting methane molecules in water as functions of distance between the methane molecules. The PMFs converge to a single baseline only for r> 11 A at all temperatures. The curves of the dimensionless PMF obtained at different temperatures with the NVT scheme overlap almost perfectly in the region of the contact minimum and still very well in the regions of the desolvation maximum and the solvent-separated minimum, which suggests that the temperature-dependent hydrophobic interaction potentials at constant volume in united-residue force fields can be obtained by scaling the respective dimensionless potentials by RT, R being the universal gas constant. For the dimensionless potentials of mean force obtained with the NPT scheme, the depth of the contact minimum increases, whereas the height of the desolvation maximum and the depth of the solvent-separated minimum decrease with temperature, in agreement with results reported in the literature.

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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”

Cited by 8 publications

References 16 publications

Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins

Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins

Pressure and temperature dependence of hydrophobic hydration: Volumetric, compressibility, and thermodynamic signatures

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures

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