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, Emil; Makowski, Mariusz; Ołdziej, Stanisław; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A.

doi:10.1093/protein/gzp028

Cited by 21 publications

(17 citation statements)

References 36 publications

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“…If, for the purposes of comparison, the w AA (r) values were matched at solvent-separated radii, then the Pangali et al results show stronger contact hydrophobic attractions than does the PC theory, qualitatively in agreement with the present work. Recent molecular dynamics simulations for Xe(aq) or CH 4 (aq) pairs (42)(43)(44) agree qualitatively with the present results and thus support this conclusion. Inclusion of longer-ranged attractive interactions, i.e., London dispersion interactions, can change these B 2 values and trends depending on the balance of solute-solute and solute-water interactions (11,16,18).…”

Section: Resultssupporting

confidence: 91%

Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic

Chaudhari

Holleran

Ashbaugh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The osmotic second virial coefficients, B 2 , for atomic-sized hard spheres in water are attractive (B 2 < 0) and become more attractive with increasing temperature (ΔB 2 /ΔT < 0) in the temperature range 300 K ≤ T ≤ 360 K. Thus, these hydrophobic interactions are attractive and endothermic at moderate temperatures. Hydrophobic interactions between atomic-sized hard spheres in water are more attractive than predicted by the available statistical mechanical theory. These results constitute an initial step toward detailed molecular theory of additional intermolecular interaction features, specifically, attractive interactions associated with hydrophobic solutes.protein folding | self-assembly | Pratt-Chandler theory S olvent-mediated, noncovalent interactions within biomolecular structures are decisive for their stability and functionality over an extended range of conditions (1). Hydrophobic interactions-a principal category of noncovalent interactions in water-exhibit strong and characteristic temperature dependences (2). Molecular-scale theories of hydrophobic interactions are judged by their ability to capture those temperature dependences. Defensible theories might eventually illuminate a valid explanation and might find broader utility in modeling biomolecular structure and function.The osmotic second virial coefficienthas so far been the only direct experimental check on the molecular theory of hydrophobic interactions between slightly soluble gases (A) in liquid water (3-6). Here g AA (r) is the usual radial distribution function of AA pairs at infinite dilution. Because of low solubilities for solutes of interest, the necessary experiments are challenging. The initial comparisons between the only available molecular-scale theory, the Pratt-Chandler (PC) theory (7), and direct measurements of B 2 showed poor agreement (3-5, 8).Explanations for the discrepancy have been suggested (9-11), but the underlying disagreement has persisted (12). One explanation for this discrepancy focused on the differences between the actual interactions for accessible experimental cases and the hard-sphere solute-water interactions natural for the molecular theory. In this setting, direct high-resolution determination of hydrophobic interactions for the hard-sphere models treated by the theory would be a helpful step, but that has not been accomplished so far. The case of atomic-sized hardsphere solutes has not been treated specifically, mostly because hard-sphere models are inconvenient in available molecular dynamics simulations.These problems are of basic importance because hydrophobic interactions are acknowledged as the dominant factor that drives protein folding (13,14). Hydrophobic interactions are also expected to become more favorable with increasing temperature for physiological temperatures. Hydrophobic interactions can then be described as favorable for aggregation and endothermic at moderate temperatures. This is a primary conceptual puzzle that theories of hydrophobic effects should clarify.Summaries of the substa...

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Section: Resultssupporting

confidence: 91%

Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic

Chaudhari

Holleran

Ashbaugh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…The results of the study reported in this work as well as those of our previous work 13 strongly suggest that the dimensionless potentials of mean force of pairs of nonpolar solutes depend weaker on temperature in the region of contact minimum than the potential of mean force. This is consistent with the fact that hydrophobic association as an entropy-driven phenomenon.…”

Section: Discussionsupporting

confidence: 85%

“…In these studies, diverse methodologies and water models were used for PMF determination, namely, simulations of 8 solute molecules in a periodic box with TIP3P, TIP4P, TIP5P, SPC, or SPCE water and direct calculation of solute pair-correlation function, 11–12 thermodynamic integration and the SPC water model, 9 and the particle-insertion method and the TIP4P water model. 10 Recently, 13 we carried out molecular dynamics simulations for a pair of interacting methane particles at different temperatures in NVT or NPT protocols in TIP3P water model. 14 Based on our MD results, we determined the potential of mean force and dimensionless potential of mean force curves.…”

Section: Introductionmentioning

confidence: 99%

“…One important conclusion from the work discussed above 13 is that the assumption, that the depth of the minimum of the side chain – side chain interaction component of coarse-grained potentials is independent of temperature, neglects its actual increase with increasing temperature. The neglect of this increase is equivalent to assuming that the strength of the simulated interactions between nonpolar side chains decreases with temperature at contact distance, which does not agree with the experimental finding that increasing temperature leads to hydrophobic association, or early protein-folding stages.…”

Section: Introductionmentioning

confidence: 99%

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Toward Temperature-Dependent Coarse-Grained Potentials of Side-Chain Interactions for Protein Folding Simulations. II. Molecular Dynamics Study of Pairs of Different Types of Interactions in Water at Various Temperatures

et al. 2012

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By means of molecular dynamics simulations of 15 pairs of molecules selected to model the interactions of nonpolar, nonpolar and polar, nonpolar and charged, polar, and polar and charged side chains in water, we determined the potentials of mean force (PMFs) of pairs of interacting molecules in water as functions of distance between the interacting particles or their distance and orientations at three temperatures: 283 K, 323 K and 373 K, respectively. The systems were found to fall into the following four categories as far as the temperature dependence of the potential of mean force is concerned: (i) pairs, for which association is entropy-driven (ii) pairs, for which association is energy-driven, (iii), pairs of positively-charged solute molecules, for which association is energy-driven with unfavorable entropy change, and (iv) the remaining systems for which temperature dependence is weak. For each pair of PMFs entropic and energetic contributions have been discussed.

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“…The PMF is one of the free-energy properties with which to calculate the physicochemical properties of the systems studied. The calculated PMFs can subsequently be used to compute measurable physicochemical characteristics of the systems studied, such as, for example, association constants, 23–25 and are also suitable when direct experiment is inapplicable (for example to study hydrophobic association 26,27 ) or to lower the cost of experiment. 28–30 The PMFs can also be used to determine the preferred mode of interaction of the molecules or groups under study in water.…”

Section: Introductionmentioning

confidence: 99%

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

2017

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The physics-based potentials of side-chain–side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge–dipole or dipole–dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain–side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP; an α-helical hairpin).

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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

Cited by 21 publications

References 36 publications

Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic

Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic

Toward Temperature-Dependent Coarse-Grained Potentials of Side-Chain Interactions for Protein Folding Simulations. II. Molecular Dynamics Study of Pairs of Different Types of Interactions in Water at Various Temperatures

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

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