Tuhin Ghosh

Rensselaer Polytechnic Institute, New York City, NY, United States

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Publications (9)41.01 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties and pressure stability of proteins, and can be potentially extended for applications to protein complexes and assemblies.
    Proteins Structure Function and Bioinformatics 12/2009; 78(7):1641-51. · 3.34 Impact Factor
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    ABSTRACT: We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer-water attractions stabilizes folded states significantly, the former dominated by the hydration contribution. That hydration contribution can be described by the surface tension model, DeltaG = gamma(T)DeltaA, where the surface tension, gamma, is lengthscale-dependent and decreases monotonically with temperature. The resulting variation of the hydration entropy with polymer lengthscale is consistent with theoretical predictions of Huang and Chandler [Huang DM, Chandler D (2000) Proc Natl Acad Sci USA 97:] that explain the blurring of entropy convergence observed in protein folding thermodynamics. Analysis of water structure shows that the polymer-water hydrophobic interface is soft and weakly dewetted, and is characterized by enhanced interfacial density fluctuations. Formation of this interface, which induces polymer folding, is strongly opposed by enthalpy and favored by entropy, similar to the vapor-liquid interface.
    Proceedings of the National Academy of Sciences 02/2007; 104(3):733-8. · 9.81 Impact Factor
  • Tuhin Ghosh, Amrit Kalra, Shekhar Garde
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    ABSTRACT: Salting-out of hydrophobic solutes in aqueous salt solutions and their relevance to salt effects on biophysical phenomena are now well appreciated. Although salt effects on hydrophobic transfer have been well studied, to our knowledge, no quantitative molecular simulation study of salt-induced strengthening of hydrophobic interactions has yet been reported. Here we present quantitative characterization of salt-induced strengthening of hydrophobic interactions at the molecular and nanoscopic length scales through molecular dynamics simulations. Specifically, we quantify the effect of NaCl on the potential of mean force between molecular hydrophobic solutes (methanes) and on conformational equilibria of a 25-mer hydrophobic polymer that efficiently samples ensembles of compact and extended states in water. In both cases, we observe relative stabilization of compact conformations that is accompanied by a clear depletion of salt density (preferential exclusion) and a slight enhancement of water density (preferential hydration) in the solute vicinity. We show that the structural details of salt exclusion can be related to the salt-induced free energy changes using preferential interaction coefficients. We also test the applicability of surface-area-based models to describe the salt-induced free energy changes. These models provide a useful empirical description that can be used to predict the effects of salt on conformational equilibria of hydrophobic solutes. However, we find that the effective increase in the surface tension of the solute-aqueous solution interface depends on the type and concentration of salt as well as the length-scale (i.e., molecular vs nanoscopic) of the conformational change. These calculations underscore the utility of simulation studies to connect quantitatively structural details at the molecular level (described by preferential hydration/exclusion) to macroscopic solvation thermodynamics. The hydrophobic polymer also provides a useful model for studies of effect of thermodynamic variables (P, T, salt/additives) on many-body hydrophobic interactions at nanometer length scales.
    The Journal of Physical Chemistry B 02/2005; 109(1):642-51. · 3.61 Impact Factor
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    ABSTRACT: The packing and orientation of water molecules in the vicinity of solutes strongly influence the solute hydration thermodynamics in aqueous solutions. Here we study the charge density dependent hydration of a broad range of spherical monovalent ionic solutes (with solute diameters from approximately 0.4 nm to 1.7 nm) through molecular dynamics simulations in the simple point charge model of water. Consistent with previous experimental and theoretical studies, we observe a distinct asymmetry in the structure and thermodynamics of hydration of ions. In particular, the free energy of hydration of negative ions is more favorable than that of positive ions of the same size. This asymmetry persists over the entire range of solute sizes and cannot be captured by a continuum description of the solvent. The favorable hydration of negative ions arises primarily from the asymmetric charge distribution in the water molecule itself, and is reflected in (i) a small positive electrostatic potential at the center of a neutral solute, and (ii) clear structural (packing and orientation) differences in the hydration shell of positive and negative ions. While the asymmetry arising from the positive potential can be quantified in a straightforward manner, that arising from the structural differences in the fully charged states is difficult to quantify. The structural differences are highest for the small ions and diminish with increasing ion size, converging to hydrophobiclike hydration structure for the largest ions studied here. We discuss semiempirical measures following Latimer, Pitzer, and Slansky [J. Chem. Phys. 7, 108 (1939)] that account for these structural differences through a shift in the ion radius. We find that these two contributions account completely for the asymmetry of hydration of positive and negative ions over the entire range of ion sizes studied here. We also present preliminary calculations of the dependence of ion hydration asymmetry on the choice of water model that demonstrate its sensitivity to the details of ion-water interactions.
    The Journal of Chemical Physics 04/2004; 120(9):4457-66. · 3.12 Impact Factor
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    ABSTRACT: We test molecular level hypotheses for the high thermal stability of alpha-helical conformations of alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid peptide with explicit treatment of water. To assess the contribution of large side chains to alpha-helix stability through backbone desolvation and salt-bridge formation, we simulate the alanine-rich peptide, Ac-YAEAAKAAEAAKAAEAAKAF-Nme, referred to as the EK peptide, that has three pairs of "i, i + 3" glutamic acid(-) and lysine(+) substitutions. Efficient configurational sampling of the EK peptide over a wide temperature range enabled by the replica exchange molecular dynamics technique allows characterization of the stability of alpha-helix with respect to heat-induced unfolding. We find that near ambient temperatures, the EK peptide predominately samples alpha-helical configurations with 80% fractional helicity at 300 K. The helix melts over a broad range of temperatures with melting temperature, T(m), equal to 350 K, that is significantly higher than the T(m) of a 21-residue polyalanine peptide, A(21). Salt-bridges between oppositely charged Glu(-) and Lys(+) side chains can, in principle, provide thermal stability to alpha-helical conformers. For the specific EK peptide sequence, we observe infrequent formation of Glu-Lys salt-bridges (with approximately 10-20% probability) and therefore we conclude that salt-bridge formation does not contribute significantly to the EK peptide's helical stability. However, lysine side chains are found to shield specific "i, i + 4" backbone hydrogen bonds from water, indicating that large side-chain substituents can play an important role in stabilizing alpha-helical configurations of short peptides in aqueous solution through mediation of water access to backbone hydrogen bonds. These observations have implications on molecular engineering of peptides and biomolecules in the design of their thermostable variants where the shielding mechanism can act in concert with other factors such as salt-bridge formation, thereby increasing thermal stability considerably.
    Biophysical Journal 12/2003; 85(5):3187-93. · 3.67 Impact Factor
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    ABSTRACT: We test molecular level hypotheses for the high thermal stability of α-helical conformations of alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid peptide with explicit treatment of water. To assess the contribution of large side chains to α-helix stability through backbone desolvation and salt-bridge formation, we simulate the alanine-rich peptide, Ac-YAEAAKAAEAAKAAEAAKAF-Nme, referred to as the EK peptide, that has three pairs of “i, i+3” glutamic acid(−) and lysine(+) substitutions. Efficient configurational sampling of the EK peptide over a wide temperature range enabled by the replica exchange molecular dynamics technique allows characterization of the stability of α-helix with respect to heat-induced unfolding. We find that near ambient temperatures, the EK peptide predominately samples α-helical configurations with 80% fractional helicity at 300K. The helix melts over a broad range of temperatures with melting temperature, Tm, equal to 350K, that is significantly higher than the Tm of a 21-residue polyalanine peptide, A21. Salt-bridges between oppositely charged Glu− and Lys+ side chains can, in principle, provide thermal stability to α-helical conformers. For the specific EK peptide sequence, we observe infrequent formation of Glu-Lys salt-bridges (with ∼10–20% probability) and therefore we conclude that salt-bridge formation does not contribute significantly to the EK peptide's helical stability. However, lysine side chains are found to shield specific “i, i+4” backbone hydrogen bonds from water, indicating that large side-chain substituents can play an important role in stabilizing α-helical configurations of short peptides in aqueous solution through mediation of water access to backbone hydrogen bonds. These observations have implications on molecular engineering of peptides and biomolecules in the design of their thermostable variants where the shielding mechanism can act in concert with other factors such as salt-bridge formation, thereby increasing thermal stability considerably.
    Biophysical Journal 01/2003; 85(5):3187-3193. · 3.67 Impact Factor
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    ABSTRACT: We use molecular dynamics (MD) simulations of solutions of hydrophobic solutes in explicit water to study the many-body character of hydrophobic interactions at the level of solute−solute−solute three-particle correlations. Comparisons of the calculated three-particle potentials of mean force (PMF) with that obtained by adding solute−solute pair PMFs are used to quantify the many-body effect. Our results shed light on both the range and magnitude of many-body (i.e., nonadditivity) effects. We find that the nonadditivity effects depend on the specific configuration of the three interacting particles and are short-ranged, restricted primarily to locations of the third solute within the first two solvation shells of the primary solute pair. The contact and solvent-separated configurations show anticooperative behavior (i.e., the actual three-particle PMF is less favorable than the pairwise additive approximation), whereas cooperativity is observed at the desolvation barrier. Increasing the solute size makes the nonadditive effects uniformly more anticooperative. Nonadditivity behavior is also short-ranged at higher pressures and in NaCl solutions. Interestingly, increasing pressure changes the nonadditivity effects toward cooperativity, whereas the opposite is true upon the addition of salt to the solution. The implications of these results on more complex self-assembly processes are discussed.
    Journal of Physical Chemistry B - J PHYS CHEM B. 12/2002; 107(2).
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    ABSTRACT: We use long molecular dynamics simulations of methane molecules in explicit water at three different temperatures at pressures of 1 and 4000 atm to calculate entropic and enthalpic contributions to the free energy of methane–methane association. In agreement with previous simulation studies, we find that the contact minimum is dominated by entropy whereas the solvent-separated minimum is stabilized by favorable enthalpy of association. Both the entropy and enthalpy at the contact minimum change negligibly with increasing pressure leading to the relative pressure insensitivity of the contact minimum configurations. In contrast, we find that the solvent-separated configurations are increasingly stabilized at higher pressures by enthalpic contributions that prevail over the slightly unfavorable entropic contributions to the free energy. The desolvation barrier is dominated by unfavorable enthalpy of maintaining a dry volume between methanes. However, the increasing height of the desolvation barrier with increasing pressures results from entropy changes at the barrier configurations. Further resolution of the enthalpy of association shows that major contributions to the enthalpy arise from changes in water–water interactions and the mechanical work (PΔV) expended in bringing the methanes to a separation of r. A connection of these thermodynamic features with the underlying changes in water structure is made by calculating methane–methane–water oxygen triplet correlation functions. © 2002 American Institute of Physics.
    The Journal of Chemical Physics 02/2002; 116(6):2480-2486. · 3.12 Impact Factor
  • T Ghosh, A E García, S Garde
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    ABSTRACT: We report results on the pressure effects on hydrophobic interactions obtained from molecular dynamics simulations of aqueous solutions of methanes in water. A wide range of pressures that is relevant to pressure denaturation of proteins is investigated. The characteristic features of water-mediated interactions between hydrophobic solutes are found to be pressure-dependent. In particular, with increasing pressure we find that (1) the solvent-separated configurations in the solute-solute potential of mean force (PMF) are stabilized with respect to the contact configurations; (2) the desolvation barrier increases monotonically with respect to both contact and solvent-separated configurations; (3) the locations of the minima and the barrier move toward shorter separations; and (4) pressure effects are considerably amplified for larger hydrophobic solutes. Together, these observations lend strong support to the picture of the pressure denaturation process proposed previously by Hummer et al. (Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1552): with increasing pressure, the transfer of water into protein interior becomes key to the pressure denaturation process, leading to the dissociation of close hydrophobic contacts and subsequent swelling of the hydrophobic protein interior through insertions of water molecules. The pressure dependence of the PMF between larger hydrophobic solutes shows that pressure effects on the interaction between hydrophobic amino acids may be considerably amplified compared to those on the methane-methane PMF.
    Journal of the American Chemical Society 12/2001; 123(44):10997-1003. · 10.68 Impact Factor