151
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Abstract
Hydrophobic interactions guide protein folding, multidomain protein assembly, receptor-ligand binding, membrane formation, and cellular transportation. On the macroscale, hydrophobic interactions consist of the aggregation of "oil-like" objects in water by minimizing the interfacial energy. However, studies of the hydration behavior of small hydrophobic molecules have shown that the microscopic (~1 nm) hydration mechanism differs fundamentally from its macroscopic counterpart. Theoretical studies over the last two decades have pointed to an intricate dependence of molecular hydration mechanisms on the length scale. The microscopic-to-macroscopic crossover length scale is critically important to hydrophobic interactions in polymers, proteins, and other macromolecules. Accurate experimental determination of hydration mechanisms and interaction strengths directly influence our understanding of protein folding. In this Account, we discuss our recent measurements of the hydration energies of single hydrophobic homopolymers as they unfold. We describe in detail our single molecule force spectroscopy technique, the interpretation of the single polymer force curve, and how it relates to the hydration free energy of a hydrophobic polymer. Specifically, we show how temperature, side-chain sizes and solvent conditions, affect the driving force of hydrophobic collapse. The experiments reveal that the size of the nonpolar polymer side-chains changes the thermal signatures of hydration. The sizes of the polymer side-chains bridge the length scale where theories had predicted a transition between entropically driven microscopic hydration and enthalpically driven macroscopic hydrophobic hydration. Our experimental results revealed a crossover length scale of approximately 1 nm, similar to the results from recent theoretical studies. Experiments that probe solvent dependency show that the microscopic polymer hydration is correlated with macroscopic interfacial tension. Consistent with theoretical predictions, the solvent conditions affect the microscopic and macroscopic hydrophobic strengths in similar ways. Although the extended polymers and proteins span hundreds of nanometers, the experiments show that their hydration behavior is determined by the size of a single hydrophobic monomer. As the hydrophobic particle size decreases from the macroscopic to the microscopic regime, the scaling relationship changes from a dependence on interfacial area to a dependence on volume. Therefore, under these conditions, the driving force for the aggregation of hydrophobic molecules is reduced, which has significant implications for the strength of hydrophobic interactions in molecular systems, particularly in protein folding.
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Affiliation(s)
- Isaac T. S. Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S3H6, Canada
| | - Gilbert C. Walker
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S3H6, Canada
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152
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Ali A, Bidhuri P. Solvation thermodynamics of xylitol in water and in aqueous amino acids at 298.15 K. J PHYS ORG CHEM 2012. [DOI: 10.1002/poc.3061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Anwar Ali
- Department of Chemistry, Physical Chemistry Research Lab; Jamia Millia Islamia (Central University); New Delhi 110025 India
| | - Priyanka Bidhuri
- Department of Chemistry, Physical Chemistry Research Lab; Jamia Millia Islamia (Central University); New Delhi 110025 India
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153
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Godec A, Merzel F. Physical origin underlying the entropy loss upon hydrophobic hydration. J Am Chem Soc 2012; 134:17574-81. [PMID: 23003674 DOI: 10.1021/ja306464u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the molecular scale HE has an entropic origin. It is believed that hydrophobic particles induce order in the surrounding water by reducing the volume of configuration space available for hydrogen bonding. Here we show with computer simulation results that this traditional picture, based on average structural features of hydration water, configurational properties of single water molecules, and up to pairwise correlations, is not correct. Analyzing collective fluctuations in water clusters we are able to provide a fundamentally new picture of HE based on pronounced many-body correlations affecting the switching of hydrogen bonds (HBs) between molecules. These correlations emerge as a nonlocal compensation of reduced fluctuations of local electrostatic fields in the presence of an apolar solute. We propose an alternative view which may also be formulated as a maximization principle: The electrostatic noise acting on water molecules is maximized under the constraint that each water molecule on average maintains as many HBs as possible. In the presence of the solute the maximized electrostatic noise is a result of nonlocal fluctuations in the labile HB network giving rise to strong correlations among at least up to four water molecules.
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Affiliation(s)
- Aljaž Godec
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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154
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Akdogan Y, Reichenwallner J, Hinderberger D. Evidence for water-tuned structural differences in proteins: an approach emphasizing variations in local hydrophilicity. PLoS One 2012; 7:e45681. [PMID: 23049837 PMCID: PMC3458090 DOI: 10.1371/journal.pone.0045681] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/22/2012] [Indexed: 11/19/2022] Open
Abstract
We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands’ points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have recently determined the DEER-derived solution structure of HSA and here present the corresponding BSA solution structure. The characteristic asymmetric FA distribution in the crystal structure of HSA can surprisingly be observed by DEER in BSA in solution. This indicates that the BSA conformational ensemble in solution seems to be narrow and close to the crystal structure of HSA. In contrast, for HSA in solution a much more symmetric FA distribution was found. Thus, conformational adaptability and flexibility dominate in the HSA solution structure while BSA seems to lack these properties. We further show that differences in amino acid hydropathies of specific structural regions in both proteins can be used to correlate the observed difference in the global (tertiary) solution structures with the differences on the primary structure level.
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Affiliation(s)
- Yasar Akdogan
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jörg Reichenwallner
- Max Planck Institute for Polymer Research, Mainz, Germany
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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155
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Vila Verde A, Bolhuis PG, Campen RK. Statics and Dynamics of Free and Hydrogen-Bonded OH Groups at the Air/Water Interface. J Phys Chem B 2012; 116:9467-81. [DOI: 10.1021/jp304151e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Ana Vila Verde
- Van’t Hoff Institute
for Molecular Science, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Peter G. Bolhuis
- Van’t Hoff Institute
for Molecular Science, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - R. Kramer Campen
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin,
Germany
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156
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Lewis JI, Moss DJ, Knotts TA. Multiple molecule effects on the cooperativity of protein folding transitions in simulations. J Chem Phys 2012; 136:245101. [DOI: 10.1063/1.4729604] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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157
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Jamadagni SN, Godawat R, Garde S. Hydrophobicity of proteins and interfaces: insights from density fluctuations. Annu Rev Chem Biomol Eng 2012; 2:147-71. [PMID: 22432614 DOI: 10.1146/annurev-chembioeng-061010-114156] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Macroscopic characterizations of hydrophobicity (e.g., contact angle measurements) do not extend to the surfaces of proteins and nanoparticles. Molecular measures of hydrophobicity of such surfaces need to account for the behavior of hydration water. Theory and state-of-the-art simulations suggest that water density fluctuations provide such a measure; fluctuations are enhanced near hydrophobic surfaces and quenched with increasing surface hydrophilicity. Fluctuations affect conformational equilibria and dynamics of molecules at interfaces. Enhanced fluctuations are reflected in enhanced cavity formation, more favorable binding of hydrophobic solutes, increased compressibility of hydration water, and enhanced water-water correlations at hydrophobic surfaces. These density fluctuation-based measures can be used to develop practical methods to map the hydrophobicity/philicity of heterogeneous surfaces including those of proteins. They highlight that the hydrophobicity of a group is context dependent and is significantly affected by its environment (e.g., chemistry and topography) and especially by confinement. The ability to include information about hydration water in mapping hydrophobicity is expected to significantly impact our understanding of protein-protein interactions as well as improve drug design and discovery methods and bioseparation processes.
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Affiliation(s)
- Sumanth N Jamadagni
- The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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158
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Impact of chemical heterogeneity on protein self-assembly in water. Proc Natl Acad Sci U S A 2012; 109:7636-41. [PMID: 22538814 DOI: 10.1073/pnas.1120646109] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobicity is thought to underlie self-assembly in biological systems. However, the protein surface comprises hydrophobic and hydrophilic patches, and understanding the impact of such a chemical heterogeneity on protein self-assembly in water is of fundamental interest. Here, we report structural and thermodynamic investigations on the dimer formation of full-length amyloid-β proteins in water associated with Alzheimer's disease. Spontaneous dimerization process--from the individual diffusive regime at large separations, through the approach stage in which two proteins come close to each other, to the structural adjustment stage toward compact dimer formation--was captured in full atomic detail via unguided, explicit-water molecular dynamics simulations. The integral-equation theory of liquids was then applied to simulated protein structures to analyze hydration thermodynamic properties and the water-mediated interaction between proteins. We demonstrate that hydrophilic residues play a key role in initiating the dimerization process. A long-range hydration force of enthalpic origin acting on the hydrophilic residues provides the major thermodynamic force that drives two proteins to approach from a large separation to a contact distance. After two proteins make atomic contacts, the nature of the water-mediated interaction switches from a long-range enthalpic attraction to a short-range entropic one. The latter acts both on the hydrophobic and hydrophilic residues. Along with the direct protein-protein interactions that lead to the formation of intermonomer hydrogen bonds and van der Waals contacts, the water-mediated attraction of entropic origin brings about structural adjustment of constituent monomer proteins toward the formation of a compact dimer structure.
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159
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Köddermann T, Klembt S, Klasen D, Paschek D, Kragl U, Ludwig R. The Effect of Neutral Ion Aggregate Formation on the Electrical Conductivity of an Ionic Liquid and its Mixtures with Chloroform. Chemphyschem 2012; 13:1748-52. [DOI: 10.1002/cphc.201100838] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/10/2012] [Indexed: 11/09/2022]
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160
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Accordino SR, Malaspina DC, Rodriguez Fris JA, Alarcón LM, Appignanesi GA. Temperature dependence of the structure of protein hydration water and the liquid-liquid transition. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:031503. [PMID: 22587099 DOI: 10.1103/physreve.85.031503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 03/12/2012] [Indexed: 05/31/2023]
Abstract
We study the temperature dependence of the structure and orientation of the first hydration layers of the protein lysozyme and compare it with the situation for a model homogeneous hydrophobic surface, a graphene sheet. We show that in both cases these layers are significantly better structured than bulk water. The geometrical constraint of the interface makes the water molecules adjacent to the surface lose one water-water hydrogen bond and expel the fourth neighbors away from the surface, lowering local density. We show that a decrease in temperature improves the ordering of the hydration water molecules, preserving such a geometrical effect. For the case of graphene, this favors an ice Ih-like local structuring, similar to the water-air interface but in the opposite way along the c axis of the basal plane (while the vicinal water molecules of the air interface orient a hydrogen atom toward the surface, the oxygens of the water molecules close to the graphene plane orient a lone pair in such a direction). In turn, the case of the first hydration layers of the lysozyme molecule is shown to be more complicated, but still displaying signs of both kinds of behavior, together with a tendency of the proximal water molecules to hydrogen bond to the protein both as donors and as acceptors. Additionally, we make evident the existence of signatures of a liquid-liquid transition (Widom line crossing) in different structural parameters at the temperature corresponding to the dynamic transition incorrectly referred to as "the protein glass transition."
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Affiliation(s)
- S R Accordino
- Sección Fisicoquímica INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
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161
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Huang N, Schlesinger D, Nordlund D, Huang C, Tyliszczak T, Weiss TM, Acremann Y, Pettersson LGM, Nilsson A. Microscopic probing of the size dependence in hydrophobic solvation. J Chem Phys 2012; 136:074507. [DOI: 10.1063/1.3684893] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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162
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Wagoner JA, Pande VS. A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent. J Chem Phys 2012; 134:214103. [PMID: 21663340 DOI: 10.1063/1.3595262] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A common theme of studies using molecular simulation is a necessary compromise between computational efficiency and resolution of the forcefield that is used. Significant efforts have been directed at combining multiple levels of granularity within a single simulation in order to maintain the efficiency of coarse-grained models, while using finer resolution in regions where such details are expected to play an important role. A specific example of this paradigm is the development of hybrid solvent models, which explicitly sample the solvent degrees of freedom within a specified domain while utilizing a continuum description elsewhere. Unfortunately, these models are complicated by the presence of structural artifacts at or near the explicit/implicit boundary. The presence of these artifacts significantly complicates the use of such models, both undermining the accuracy obtained and necessitating the parameterization of effective potentials to counteract the artificial interactions. In this work, we introduce a novel hybrid solvent model that employs a smoothly decoupled particle interface (SDPI), a switching region that gradually transitions from fully interacting particles to a continuum solvent. The resulting SDPI model allows for the use of an implicit solvent model based on a simple theory that needs to only reproduce the behavior of bulk solvent rather than the more complex features of local interactions. In this study, the SDPI model is tested on spherical hybrid domains using a coarse-grained representation of water that includes only Lennard-Jones interactions. The results demonstrate that this model is capable of reproducing solvent configurations absent of boundary artifacts, as if they were taken from full explicit simulations.
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Affiliation(s)
- Jason A Wagoner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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163
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Pascal TA, Lin ST, Goddard W, Jung Y. Stability of Positively Charged Solutes in Water: A Transition from Hydrophobic to Hydrophilic. J Phys Chem Lett 2012; 3:294-298. [PMID: 26285842 DOI: 10.1021/jz201612y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To improve the description of solvation thermodynamics of biomolecules, we report here the dependence of solvation on the curvature and surface charge of positively charged solutes in water based on extensive molecular dynamics simulations analyzed using the two-phase thermodynamic method. At a surface charge of +0.4e, the compensating forces of favorable electrostatic stabilization and entropic destabilization cancel almost exactly, representing a molecular crossover point from hydrophobic to hydrophilic behavior, independent of curvature. These results suggest that one should include charge-dependent entropic corrections to continuum models aimed at predicting the solvation free energies of large biomolecules.
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Affiliation(s)
- Tod A Pascal
- †Graduate School of EEWS (WCU), Korea Advanced Institute of Science and Technology, Daejeon, Korea
- ‡Materials and Simulation Process Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Shiang-Tai Lin
- §Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - William Goddard
- †Graduate School of EEWS (WCU), Korea Advanced Institute of Science and Technology, Daejeon, Korea
- ‡Materials and Simulation Process Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Yousung Jung
- †Graduate School of EEWS (WCU), Korea Advanced Institute of Science and Technology, Daejeon, Korea
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164
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Kienle S, Liese S, Schwierz N, Netz RR, Hugel T. The effect of temperature on single-polypeptide adsorption. Chemphyschem 2012; 13:982-9. [PMID: 22290722 DOI: 10.1002/cphc.201100776] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/19/2011] [Indexed: 11/08/2022]
Abstract
The hydrophobic attraction (HA) is believed to be one of the main driving forces for protein folding. Understanding its temperature dependence promises a deeper understanding of protein folding. Herein, we present an approach to investigate the HA with a combined experimental and simulation approach, which is complementary to previous studies on the temperature dependence of the solvation of small hydrophobic spherical particles. We determine the temperature dependence of the free-energy change and detachment length upon desorption of single polypeptides from hydrophobic substrates in aqueous environment. Both the atomic force microscopy (AFM) based experiments and the molecular dynamics (MD) simulations show only a weak dependence of the free energy change on temperature. In fact, depending on the substrate, we find a maximum or a minimum in the temperature-dependent free energy change, meaning that the entropy increases or decreases with temperature for different substrates. These observations are in contrast to the solvation of small hydrophobic particles and can be rationalized by a compensation mechanism between the various contributions to the desorption force. On the one hand this is reminiscent of the protein folding process, where large entropic and enthalpic contributions compensate each other to result in a small free energy difference between the folded and unfolded state. On the other hand, the protein folding process shows much stronger temperature dependence, pointing to a fundamental difference between protein folding and adsorption. Nevertheless such temperature dependent single molecule desorption studies open large possibilities to study equilibrium and non-equilibrium processes dominated by the hydrophobic attraction.
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Affiliation(s)
- Sandra Kienle
- Department of Physics (E22), IMETUM, CeNS, Technische Universität München, Boltzmannstr. 11, 85748 Garching, Germany
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165
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Thermo-sensitivity and triggered drug release of polysaccharide nanogels derived from pullulan-g-poly(l-lactide) copolymers. Carbohydr Polym 2012. [DOI: 10.1016/j.carbpol.2011.08.061] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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166
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Shu X, Lu Z, Li G, Tian Y, Xia S, Zhou X, Yang B, Shen H, Liu B, Zhu J. Diversified nanoparticle assembly pathways: materials architecture control beyond the amphiphilicity paradigm. J Phys Chem B 2011; 115:14416-23. [PMID: 22049989 DOI: 10.1021/jp2104159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functional versatility of a chemical system is ultimately dictated by the availability of distinctly accessible architectures. The generation of a diverse array of assembled constructs from a single type of nanoscale building block is a promising yet largely elusive goal. We report herein the utility of a monolayer-modified nanoparticle for the creation of a broad range of architectures. The versatile modes of assembly complement the conventionally used, amphiphilicity-driven strategy. We demonstrate that one can vary the nanoparticle assembly pathways within the confines of solvent media through the modulation of interactions and partitioning of nanoparticles. Merging of the molecular-scale design and higher-ordered arrangement enables diversified assembly through the manipulation of experimental parameters such as solvent, pH, affinity molecule, and temperature. Microfluidics provides an effective channel to control the monodispersity and size on all the architectures attainable in the bulk solution phase. These observations could be further explored for an understanding of diversified matter organization and order generation beyond the amphiphilicity paradigm.
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Affiliation(s)
- Xin Shu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, China
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167
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Extended surfaces modulate hydrophobic interactions of neighboring solutes. Proc Natl Acad Sci U S A 2011; 108:17678-83. [PMID: 21987795 DOI: 10.1073/pnas.1110703108] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affects hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size from subnanometer to a few nanometers. The interfaces are self-assembled monolayers with a range of chemistries, from hydrophilic to hydrophobic. We show that the driving force for assembly in the vicinity of a hydrophobic surface is weaker than that in bulk water and decreases with increasing temperature, in contrast to that in the bulk. We explain these distinct features in terms of an interplay between interfacial fluctuations and excluded volume effects--the physics encoded in Lum-Chandler-Weeks theory [Lum K, Chandler D, Weeks JD (1999) J Phys Chem B 103:4570-4577]. Our results suggest a catalytic role for hydrophobic interfaces in the unfolding of proteins, for example, in the interior of chaperonins and in amyloid formation.
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168
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Schulz EP, Alarcón LM, Appignanesi GA. Behavior of water in contact with model hydrophobic cavities and tunnels and carbon nanotubes. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:114. [PMID: 22015681 DOI: 10.1140/epje/i2011-11114-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 09/19/2011] [Indexed: 05/31/2023]
Abstract
By means of molecular dynamics simulations we analyze the behavior of water in contact with model hydrophobic cavities and tunnels. We study the hydration and filling propensity of cavities and tunnels carved in alkane monolayers and, for comparison, we also study single-walled carbon nanotubes of similar size. Our results will determine the dependence of the filling propensity as a function of cavity size while revealing the dynamical nature of the process with alternation of filled and dry states. Concerning the tunnels built across the monolayer, we shall show that the minimum diameter in order to get filled is about twice as large as that for the carbon nanotubes, thus evidencing a more hydrophobic behavior. The existence of water-water hydrogen bonds, a necessary condition for penetration, will also be made evident.
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Affiliation(s)
- E P Schulz
- Sección Fisicoquímica, INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000-Bahía Blanca, Argentina
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169
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170
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Abstract
Hydrophobicity underpins self-assembly in many natural and synthetic molecular and nanoscale systems. A signature of hydrophobicity is its temperature dependence. The first experimental evaluation of the temperature and size dependence of hydration free energy in a single hydrophobic polymer is reported, which tests key assumptions in models of hydrophobic interactions in protein folding. Herein, the hydration free energy required to extend three hydrophobic polymers with differently sized aromatic side chains was directly measured by single molecule force spectroscopy. The results are threefold. First, the hydration free energy per monomer is found to be strongly dependent on temperature and does not follow interfacial thermodynamics. Second, the temperature dependence profiles are distinct among the three hydrophobic polymers as a result of a hydrophobic size effect at the subnanometer scale. Third, the hydration free energy of a monomer on a macromolecule is different from a free monomer; corrections for the reduced hydration free energy due to hydrophobic interaction from neighboring units are required.
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171
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Alarcón L, Malaspina D, Schulz E, Frechero M, Appignanesi G. Structure and orientation of water molecules at model hydrophobic surfaces with curvature: From graphene sheets to carbon nanotubes and fullerenes. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.07.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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172
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Sumi T, Sekino H. Possible mechanism underlying high-pressure unfolding of proteins: formation of a short-period high-density hydration shell. Phys Chem Chem Phys 2011; 13:15829-32. [PMID: 21814668 DOI: 10.1039/c1cp21347d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration effects on high-pressure unfolding of a hydrophobic polymer chain are investigated through a multiscale simulation based on density-functional theory. The results strongly suggest the following: a thermodynamic origin for high-pressure denaturation, i.e., the decrease in volume due to the unfolding can be explained by the formation of a short-period high-density hydration shell.
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Affiliation(s)
- Tomonari Sumi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan.
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173
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Accordino SR, Rodriguez Fris JA, Sciortino F, Appignanesi GA. Quantitative investigation of the two-state picture for water in the normal liquid and the supercooled regime. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:48. [PMID: 21573766 DOI: 10.1140/epje/i2011-11048-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/19/2011] [Accepted: 04/06/2011] [Indexed: 05/30/2023]
Abstract
Several evidences have helped to establish the two-state nature of liquid water. Thus, within the normal liquid and supercooled regimes water has been shown to consist of a mixture of well-structured, low-density molecules and unstructured, high-density ones. However, quantitative analyses have faced the burden of unambiguously determining both the presence and the fraction of each kind of water "species". A recent approach by combining a local structure index with potential-energy minimisations allows us to overcome this difficulty. Thus, in this work we extend such study and employ it to quantitatively determine the fraction of structured molecules as a function of temperature for different densities. This enables us to validate predictions of two-state models.
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Affiliation(s)
- S R Accordino
- Sección Fisicoquımica - INQUISUR and Departamento de Quımica, Universidad Nacional del Sur, Avenida Alem, Bahıa Blanca, Argentina
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174
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Allison JR, Boguslawski K, Fraternali F, van Gunsteren WF. A Refined, Efficient Mean Solvation Force Model that Includes the Interior Volume Contribution. J Phys Chem B 2011; 115:4547-57. [DOI: 10.1021/jp2017117] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jane R. Allison
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
| | - Katharina Boguslawski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
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175
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Gazi HAR, Biswas R. Heterogeneity in Binary Mixtures of (Water + Tertiary Butanol): Temperature Dependence Across Mixture Composition. J Phys Chem A 2011; 115:2447-55. [DOI: 10.1021/jp109772h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harun Al Rasid Gazi
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700 098, India
| | - Ranjit Biswas
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700 098, India
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176
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Acevedo-Vélez C, Andre G, Dufrêne YF, Gellman SH, Abbott NL. Single-Molecule Force Spectroscopy of β-Peptides That Display Well-Defined Three-Dimensional Chemical Patterns. J Am Chem Soc 2011; 133:3981-8. [DOI: 10.1021/ja1089183] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Claribel Acevedo-Vélez
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Guillaume Andre
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université Catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium
| | - Yves F. Dufrêne
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université Catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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177
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Wang HJ, Kleinhammes A, Tang P, Xu Y, Wu Y. Temperature dependence of lysozyme hydration and the role of elastic energy. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:031924. [PMID: 21517540 PMCID: PMC3388542 DOI: 10.1103/physreve.83.031924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 02/03/2011] [Indexed: 05/30/2023]
Abstract
Water plays a critical role in protein dynamics and functions. However, the most basic property of hydration--the water sorption isotherm--remains inadequately understood. Surface adsorption is the commonly adopted picture of hydration. Since it does not account for changes in the conformational entropy of proteins, it is difficult to explain why protein dynamics and activity change upon hydration. The solution picture of hydration provides an alternative approach to describe the thermodynamics of hydration. Here, the flexibility of proteins could influence the hydration level through the change of elastic energy upon hydration. Using nuclear magnetic resonance to measure the isotherms of lysozyme in situ between 18 and 2 °C, the present work provides evidence that the part of water uptake associated with the onset of protein function is significantly reduced below 8 °C. Quantitative analysis shows that such reduction is directly related to the reduction of protein flexibility and enhanced cost in elastic energy upon hydration at lower temperature. The elastic property derived from the water isotherm agrees with direct mechanical measurements, providing independent support for the solution model. This result also implies that water adsorption at charged and polar groups occurring at low vapor pressure, which is known for softening the protein, is crucial for the later stage of water uptake, leading to the activation of protein dynamics. The present work sheds light on the mutual influence of protein flexibility and hydration, providing the basis for understanding the role of hydration on protein dynamics.
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Affiliation(s)
- Hai-Jing Wang
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255, USA
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178
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Varilly P, Patel AJ, Chandler D. An improved coarse-grained model of solvation and the hydrophobic effect. J Chem Phys 2011; 134:074109. [PMID: 21341830 PMCID: PMC3077811 DOI: 10.1063/1.3532939] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/09/2010] [Indexed: 11/14/2022] Open
Abstract
We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum-Chandler-Weeks theory [J. Phys. Chem. B 134, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and 2-3 orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation, and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations.
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Affiliation(s)
- Patrick Varilly
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
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179
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Berntsen P, Svanberg C, Swenson J. Interplay between hydration water and headgroup dynamics in lipid bilayers. J Phys Chem B 2011; 115:1825-32. [PMID: 21302948 DOI: 10.1021/jp110899j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the interplay between water and lipid dynamics has been investigated by broadband dielectric spectroscopy and modulated differential scanning calorimetry (MDSC). The multilamellar lipid bilayer system 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been studied over a broad temperature range at three different water contents: about 3, 6, and 9 water molecules per lipid molecule. The results from the dielectric relaxation measurements show that at temperatures <250 K the lipid headgroup rotation is described by a super-Arrhenius temperature dependence at the lowest hydration level and by the Arrhenius law at the highest hydration level. This difference in the temperature dependence of the lipid headgroup rotation can be explained by the increasing interaction between the headgroups with decreasing water content, which causes their rotational motion to be more cooperative in character. The main water relaxation shows an anomalous dependence on the water content in the supercooled and glassy regime. In contrast to the general behavior of interfacial water, the water dynamics is fastest in the driest sample and its temperature dependence is best described by a super-Arrhenius temperature dependence. The best explanation for this anomalous behavior is that the water relaxation becomes more determined by fast local lipid motions than by the intrinsic water dynamics at low water contents. In support for this interpretation is the finding that the relaxation time of the main water process is faster than that in most other host systems at temperatures below 180 K. Thus, the dielectric relaxation data show clearly the strong interplay between water and lipid dynamics; the water influences the lipid dynamics and vice versa. In the MDSC data, we observe a weak enthalpy relaxation at 203 K for the driest sample and at 179 K for the most hydrated sample, attributed to the freezing-in of the lipid headgroup rotation observed in the dielectric data, since this motion reaches a time scale of about 100 s at about the same temperatures.
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Affiliation(s)
- P Berntsen
- Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.
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180
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Sedlmeier F, Horinek D, Netz RR. Entropy and enthalpy convergence of hydrophobic solvation beyond the hard-sphere limit. J Chem Phys 2011; 134:055105. [DOI: 10.1063/1.3530585] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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181
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Lambeth BP, Junghans C, Kremer K, Clementi C, Site LD. Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces. J Chem Phys 2010; 133:221101. [DOI: 10.1063/1.3522773] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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182
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Study of heat of micellization and phase separation for Pluronic aqueous solutions by using a high sensitivity differential scanning calorimetry. Colloid Polym Sci 2010. [DOI: 10.1007/s00396-010-2308-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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183
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Yang Z, Yang X, Xu Z, Yang N. Molecular simulations of structures and solvation free energies of passivated gold nanoparticles in supercritical CO2. J Chem Phys 2010; 133:094702. [DOI: 10.1063/1.3469774] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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184
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Bauer BA, Patel S. Role of electrostatics in modulating hydrophobic interactions and barriers to hydrophobic assembly. J Phys Chem B 2010; 114:8107-17. [PMID: 20509706 PMCID: PMC2916683 DOI: 10.1021/jp101995d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic effects continue to be an active area of research due to implications for a wide range of physicochemical phenomena. Molecular dynamics simulations have been used extensively in the study of such effects using various water potential models, with few studies addressing the differences between models. In particular, studies considering the explicit treatment of water polarizability are underrepresented in the literature. We present results from molecular dynamics simulations that systematically compare the dependence of large-scale hydrophobic effects on the water model. We consider three common nonpolarizable models (SPC/E, TIP3P, and TIP4P) and two common polarizable models (TIP4P-FQ and SWM4-NDP). Results highlight the similarities and differences of the different water models in the vicinity of two large hydrophobic plates. In particular, profiles of average density, density fluctuations, orientation, and hydrogen bonding show only minor differences among the water models studied. However, the potential of mean force for the hydrophobe dimerization is significantly reduced in the polarizable water systems. TIP4P-FQ shows the deepest minimum of approximately -54(+/-3) kcal/mol compared to -40(+/-3), -40(+/-2), -42(+/-3), and -45(+/-5) kcal/mol for TIP4P, TIP3P, SPC/E, and SWM4-NDP (all relative to the dissociated state). We discuss the relationship between hydrophobic association and the strength of water-water interactions in the liquid phase. Results suggest that models treating polarizability (both implicitly and explicitly) influence a stronger driving force toward hydrophobic assembly. Implications of these results, as well as prospectives on future work, are discussed.
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Affiliation(s)
- Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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185
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Malaspina DC, Schulz EP, Alarcón LM, Frechero MA, Appignanesi GA. Structural and dynamical aspects of water in contact with a hydrophobic surface. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2010; 32:35-42. [PMID: 20524031 DOI: 10.1140/epje/i2010-10594-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 02/12/2010] [Accepted: 04/19/2010] [Indexed: 05/29/2023]
Abstract
By means of molecular dynamics simulations we study the structure and dynamics of water molecules in contact with a model hydrophobic surface: a planar graphene-like layer. The analysis of the distributions of a local structural index indicates that the water molecules proximal to the graphene layer are considerably more structured than the rest and, thus, than the bulk. This structuring effect is lost in a few angstroms and is basically independent of temperature for a range studied comprising parts of both the normal liquid and supercooled states (240K to 320K). In turn, such structured water molecules present a dynamics that is slower than the bulk, as a consequence of their improved interactions with their first neighbors.
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Affiliation(s)
- D C Malaspina
- Departamento de Química, Sección Fisicoquímica, INQUISUR-UNS-CONICET, Universidad Nacional del Sur, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
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186
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Sumi T, Imazaki N, Sekino H. Dewetting-induced globule-coil transitions of model polymers and possible implications high-temperature and low-pressure unfolding of proteins. J Chem Phys 2010; 132:165101. [DOI: 10.1063/1.3394864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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187
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Li ITS, Walker GC. Interfacial Free Energy Governs Single Polystyrene Chain Collapse in Water and Aqueous Solutions. J Am Chem Soc 2010; 132:6530-40. [DOI: 10.1021/ja101155h] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isaac T. S. Li
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
| | - Gilbert C. Walker
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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188
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Thermochemical study of the influence of tetraalkylammonium cation sizes on the interaction of their salts with formamide and carbamide in aqueous solutions. Russ Chem Bull 2010. [DOI: 10.1007/s11172-009-0092-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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189
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A probabilistic approach to the effect of water hydrogen bonds on the kinetics of protein folding and protein denaturation. Adv Colloid Interface Sci 2010; 154:77-90. [PMID: 20163782 DOI: 10.1016/j.cis.2010.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 01/20/2010] [Indexed: 11/23/2022]
Abstract
Previously, we presented a review of our kinetic models for the nucleation mechanism of protein folding and for the protein thermal denaturation in a barrierless way. A protein was treated as a random heteropolymer consisting of hydrophobic, hydrophilic, and neutral beads. As a crucial idea of the model, an overall potential around the cluster of native residues wherein a residue performs a chaotic motion was considered as the combination of the average dihedral, effective pairwise, and confining potentials. The overall potential as a function of the distance from the cluster has a double well shape. This allowed one to develop kinetic models for the nucleation mechanism of protein folding (NMPF) and barrierless protein denaturation (BPD) by using the mean first passage time analysis. In the original models, however, hydrogen bonding effects were taken into account only indirectly which affected the accuracy of the models because hydrogen bonding does play a crucial role in the folding, stability, and denaturation of proteins. To improve the NMPF and BPD models and explicitly take into account the hydrogen bonding "water-water" and "water-protein residue", we have developed a probabilistic hydrogen bond (PHB) model for the effect of hydrogen bond networks of water molecules around two solute particles (immersed in water) on their interaction, and have then combined the PHB model with the NMPF and BPD models. In this paper, that can be regarded as sequel of our previous review, we analyze the modified NMPF and BPD models that explicitly take into account the effect of water-water hydrogen bonding on these processes. As expected, the application of the modified models to the folding/unfolding of two model proteins (one short, consisting of 124 residues and the other large, consisting of 2500 residues) demonstrate that the hydrogen bond networks play a very important role in the protein folding/unfolding phenomena.
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190
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Quantum chemical-based drug–receptor interaction of tetrahydroimidobenzodiazepinones (HIV-1-NNRTIs) with receptor (HIV-1-NNRTI-binding pocket). Med Chem Res 2010. [DOI: 10.1007/s00044-010-9298-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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191
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Influence of the size of fixed-rigidity spheres on the structural and energy characteristics of hydrophobic hydration. Russ Chem Bull 2009. [DOI: 10.1007/s11172-008-0244-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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192
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Nakamura I, Shi AC. Study of entropy-driven self-assembly of rigid macromolecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:021112. [PMID: 19792082 DOI: 10.1103/physreve.80.021112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Indexed: 05/28/2023]
Abstract
A simple model composed of two rigid macromolecules (adsorbents) immersed in a large number of small molecules (adsorbates) is used to study entropy-driven association processes. The surfaces of the adsorbents are capable of adsorbing the smaller adsorbates. The partition function of the model is obtained analytically. The probability of dimerization and the number of adsorbed molecules are shown to depend on the enthalpy and the entropy differences between the assembled and the disassembled states. Under certain conditions, dimerization of the macromolecules occurs with increasing temperature. This entropy-driven self-assembly is originated from an overall entropy gain due to the release of the adsorbed small molecules, leading to a large peak in the heat capacity due to the dimer formation. The desorption of the adsorbates induces a sharp change in the first-order derivative of the free energy, resulting in another large peak in the heat capacity. A temperature-induced re-entrance into the dimer state is also contained in the model.
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Affiliation(s)
- Issei Nakamura
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada L8S 4L8.
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193
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Djikaev YS, Ruckenstein E. The role of hydrogen bond networks in the barrierless thermal denaturation of a native protein. J Chem Phys 2009; 131:045105. [DOI: 10.1063/1.3179688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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194
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Freddolino PL, Park S, Roux B, Schulten K. Force field bias in protein folding simulations. Biophys J 2009; 96:3772-80. [PMID: 19413983 DOI: 10.1016/j.bpj.2009.02.033] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 02/12/2009] [Accepted: 02/19/2009] [Indexed: 10/20/2022] Open
Abstract
Long timescale (>1 micros) molecular dynamics simulations of protein folding offer a powerful tool for understanding the atomic-scale interactions that determine a protein's folding pathway and stabilize its native state. Unfortunately, when the simulated protein fails to fold, it is often unclear whether the failure is due to a deficiency in the underlying force fields or simply a lack of sufficient simulation time. We examine one such case, the human Pin1 WW domain, using the recently developed deactivated morphing method to calculate free energy differences between misfolded and folded states. We find that the force field we used favors the misfolded states, explaining the failure of the folding simulations. Possible further applications of deactivated morphing and implications for force field development are discussed.
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Affiliation(s)
- Peter L Freddolino
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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195
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Guvench O, MacKerell AD. Computational fragment-based binding site identification by ligand competitive saturation. PLoS Comput Biol 2009; 5:e1000435. [PMID: 19593374 PMCID: PMC2700966 DOI: 10.1371/journal.pcbi.1000435] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 06/05/2009] [Indexed: 11/19/2022] Open
Abstract
Fragment-based drug discovery using NMR and x-ray crystallographic methods has proven utility but also non-trivial time, materials, and labor costs. Current computational fragment-based approaches circumvent these issues but suffer from limited representations of protein flexibility and solvation effects, leading to difficulties with rigorous ranking of fragment affinities. To overcome these limitations we describe an explicit solvent all-atom molecular dynamics methodology (SILCS: Site Identification by Ligand Competitive Saturation) that uses small aliphatic and aromatic molecules plus water molecules to map the affinity pattern of a protein for hydrophobic groups, aromatic groups, hydrogen bond donors, and hydrogen bond acceptors. By simultaneously incorporating ligands representative of all these functionalities, the method is an in silico free energy-based competition assay that generates three-dimensional probability maps of fragment binding (FragMaps) indicating favorable fragment∶protein interactions. Applied to the two-fold symmetric oncoprotein BCL-6, the SILCS method yields two-fold symmetric FragMaps that recapitulate the crystallographic binding modes of the SMRT and BCOR peptides. These FragMaps account both for important sequence and structure differences in the C-terminal halves of the two peptides and also the high mobility of the BCL-6 His116 sidechain in the peptide-binding groove. Such SILCS FragMaps can be used to qualitatively inform the design of small-molecule inhibitors or as scoring grids for high-throughput in silico docking that incorporate both an atomic-level description of solvation and protein flexibility. Fragment-based drug discovery is based on a simple yet powerful principle: instead of trying to screen through the vast number of possible drug-like compounds during the drug discovery process, screen representative drug-like fragments, which are far fewer in number. Once a suitable fragment is discovered, it can then be built up or linked with other fragments to give a drug-like molecule. Because such fragments are small, even “good” fragments bind weakly to their targets, therefore requiring significant time, labor, and materials costs for experimental detection and characterization of binding. In the present work, we describe a computational approach to the problem of detecting and characterizing fragment binding. Importantly, the method provides atomic-resolution results and also explicitly takes into account the effect that molecular water has on binding and the inherent flexibility of protein targets. The methodology is demonstrated by application to the BCL-6 protein, which is implicated in a variety of cancers, is conceptually easy to understand, and can yield results in a matter of days using present-day commodity computers.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland, United States of America
- * E-mail:
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196
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197
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Petersen C, Tielrooij KJ, Bakker HJ. Strong temperature dependence of water reorientation in hydrophobic hydration shells. J Chem Phys 2009; 130:214511. [DOI: 10.1063/1.3142861] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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198
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Chen H, Xu J, Voth GA. Unusual Hydrophobic Interactions in Acidic Aqueous Solutions. J Phys Chem B 2009; 113:7291-7. [DOI: 10.1021/jp9025909] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hanning Chen
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112-0850
| | - Jianqing Xu
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112-0850
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112-0850
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199
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Djikaev YS, Ruckenstein E. First passage time analysis of protein folding via nucleation and of barrierless protein denaturation. Adv Colloid Interface Sci 2009; 146:18-30. [PMID: 19006782 DOI: 10.1016/j.cis.2008.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/22/2008] [Accepted: 09/22/2008] [Indexed: 11/17/2022]
Abstract
A review of the kinetic models, recently developed by the authors for the nucleation mechanism of protein folding and for the barrierless thermal denaturation, is presented. Both models are based on the mean first passage time analysis. A protein is treated as a random heteropolymer consisting of hydrophobic, hydrophilic, or neutral beads. As a crucial idea of the model, an overall potential around the cluster of native residues wherein a residue performs a chaotic motion is considered as the combination of the average dihedral, effective pairwise, and confining potentials. The overall potential as a function of the distance from the cluster center has a double well shape which allows one to determine its emission and absorption rates by the first passage time analysis. One can thus develop a theory for the nucleation mechanism of protein folding and calculate the temperature dependence of the folding time. A kinetic model for protein denaturation occurring in a barrierless way has been also developed by using the same approach. The numerical calculations for two model proteins (one consisting of 124 amino acids and the other of 2500 amino acids) demonstrate that the models can predict folding and unfolding times consistent with experimental data.
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Affiliation(s)
- Y S Djikaev
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, United States.
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200
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Tsui HW, Hsu YH, Wang JH, Chen LJ. Novel behavior of heat of micellization of pluronics F68 and F88 in aqueous solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13858-62. [PMID: 19053637 DOI: 10.1021/la803272y] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is well understood that the heat of micellization for surfactants is monotonically decreased along with an increase in temperature. However, this behavior for polymeric surfactants has never been carefully examined. In this study, the heat of micellization of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers (Pluronics F68 and F88) in water as a function of temperature is carefully examined by using a high-sensitivity differential scanning calorimeter (HSDSC). The critical micelle temperature (CMT) decreases along with an increase in the concentration of Pluronic F68 (or F88). The heat of micellization decreases along with an increase in the temperature, as expected, when the CMT is higher than 55 and 42 degrees C for Pluronics F68 and F88, respectively. It is interesting to observe that the heat of micellization increases along with the temperature while the temperature is below 55 and 42 degrees C for Pluronics F68 and F88, respectively. The enthalpy-entropy compensation phenomenon for the micellization of Pluronics F68 and F88 in connection with the hydrophobicity is discussed.
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Affiliation(s)
- Hung-Wei Tsui
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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