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Adhikari RS, Parambathu AV, Chapman WG, Asthagiri DN. Hydration Free Energies of Polypeptides from Popular Implicit Solvent Models versus All-Atom Simulation Results Based on Molecular Quasichemical Theory. J Phys Chem B 2022; 126:9607-9616. [PMID: 36354351 DOI: 10.1021/acs.jpcb.2c05725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Calculating the hydration free energy of a macromolecule in all-atom simulations has long remained a challenge, necessitating the use of models wherein the effect of the solvent is captured without explicit account of solvent degrees of freedom. This situation has changed with developments in the molecular quasi-chemical theory (QCT)─an approach that enables calculation of the hydration free energy of macromolecules within all-atom simulations at the same resolution as is possible for small molecular solutes. The theory also provides a rigorous and physically transparent framework to conceptualize and model interactions in molecular solutions and thus provides a convenient framework to investigate the assumptions in implicit solvent models. In this study, we compare the results using molecular QCT versus predictions from EEF1, ABSINTH, and GB/SA implicit solvent models for polyglycine and polyalanine solutes covering a range of chain lengths and conformations. The hydration free energies or the differences in hydration free energies between conformers obtained from the implicit solvent models do not agree with explicit solvent results, with the deviations being largest for the group additive EEF1 and ABSINTH models. GB/SA does better in capturing the qualitative trends seen in explicit solvent results. Analysis founded on QCT reveals the critical importance of the cooperativity of hydration that is inherent in the hydrophilic and hydrophobic contributions to hydration─physics that is not well captured in additive models but somewhat better accounted for by means of a dielectric in the GB/SA approach.
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Affiliation(s)
- Rohan S Adhikari
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas77005, United States
| | - Arjun Valiya Parambathu
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19711, United States
| | - Walter G Chapman
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas77005, United States
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Asthagiri DN, Paulaitis ME, Pratt LR. Thermodynamics of Hydration from the Perspective of the Molecular Quasichemical Theory of Solutions. J Phys Chem B 2021; 125:8294-8304. [PMID: 34313434 DOI: 10.1021/acs.jpcb.1c04182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The quasichemical organization of the potential distribution theorem, molecular quasichemical theory (QCT), enables practical calculations and also provides a conceptual framework for molecular hydration phenomena. QCT can be viewed from multiple perspectives: (a) as a way to regularize an ill-conditioned statistical thermodynamic problem; (b) as an introduction of and emphasis on the neighborship characteristics of a solute of interest; or (c) as a way to include accurate electronic structure descriptions of near-neighbor interactions in defensible statistical thermodynamics by clearly defining neighborship clusters. The theory has been applied to solutes of a wide range of chemical complexity, ranging from ions that interact with water with both long-ranged and chemically intricate short-ranged interactions, to solutes that interact with water solely through traditional van der Waals interations, and including water itself. The solutes range in variety from monatomic ions to chemically heterogeneous macromolecules. A notable feature of QCT is that, in applying the theory to this range of solutes, the theory itself provides guidance on the necessary approximations and simplifications that can facilitate the calculations. In this Perspective, we develop these ideas and document them with examples that reveal the insights that can be extracted using the QCT formulation.
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Affiliation(s)
- Dilipkumar N Asthagiri
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Michael E Paulaitis
- Center for Nanomedicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
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Utiramerur S, Paulaitis M. Analysis of Cooperativity and Group Additivity in the Hydration of 1,2-Dimethoxyethane. J Phys Chem B 2021; 125:1660-1666. [DOI: 10.1021/acs.jpcb.0c10729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sowmi Utiramerur
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - Michael Paulaitis
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
- The Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
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Tomar DS, Weber V, Pettitt BM, Asthagiri D. Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide. J Phys Chem B 2015; 120:69-76. [PMID: 26649757 DOI: 10.1021/acs.jpcb.5b09881] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state over extended states and the paired helix bundle in the assembly of two helices. The energetic contributions of attractive protein-solvent interactions are separated into quasi-chemical components consisting of a short-range part arising from interactions with solvent in the first hydration shell and the remaining long-range part that is well described by a Gaussian. In the helix-coil transition, short-range attractive protein-solvent interactions outweigh hydrophobic hydration and favor the extended coil states. Analysis of enthalpic effects shows that it is the favorable hydration of the peptide backbone that favors the unfolded state. Protein intramolecular interactions favor the helix state and are decisive in favoring folding. In the pairing of two helices, the cavity contribution outweighs the short-range attractive protein-water interactions. However, long-range, protein-solvent attractive interactions can either enhance or reverse this trend depending on the mutual orientation of the helices. In helix-helix assembly, change in enthalpy arising from change in attractive protein-solvent interactions favors disassembly. In helix pairing as well, favorable protein intramolecular interactions are found to be as important as hydration effects. Overall, hydrophilic protein-solvent interactions and protein intramolecular interactions are found to play a significant role in the thermodynamics of folding and assembly in the system studied.
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Affiliation(s)
- Dheeraj S Tomar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Valéry Weber
- IBM Research, Zurich , CH-8803 Rüschlikon, Switzerland
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - D Asthagiri
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas 77555, United States.,Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas 77005, United States
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Tomar DS, Asthagiri D, Weber V. Solvation free energy of the peptide group: its model dependence and implications for the additive-transfer free-energy model of protein stability. Biophys J 2014; 105:1482-90. [PMID: 24048000 DOI: 10.1016/j.bpj.2013.08.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/24/2013] [Accepted: 08/08/2013] [Indexed: 11/28/2022] Open
Abstract
The group-additive decomposition of the unfolding free energy of a protein in an osmolyte solution relative to that in water poses a fundamental paradox: whereas the decomposition describes the experimental results rather well, theory suggests that a group-additive decomposition of free energies is, in general, not valid. In a step toward resolving this paradox, here we study the peptide-group transfer free energy. We calculate the vacuum-to-solvent (solvation) free energies of (Gly)n and cyclic diglycine (cGG) and analyze the data according to experimental protocol. The solvation free energies of (Gly)n are linear in n, suggesting group additivity. However, the slope interpreted as the free energy of a peptide unit differs from that for cGG scaled by a factor of half, emphasizing the context dependence of solvation. However, the water-to-osmolyte transfer free energies of the peptide unit are relatively independent of the peptide model, as observed experimentally. To understand these observations, a way to assess the contribution to the solvation free energy of solvent-mediated correlation between distinct groups is developed. We show that linearity of solvation free energy with n is a consequence of uniformity of the correlation contributions, with apparent group-additive behavior in the water-to-osmolyte transfer arising due to their cancellation. Implications for inferring molecular mechanisms of solvent effects on protein stability on the basis of the group-additive transfer model are suggested.
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Affiliation(s)
- Dheeraj S Tomar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
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Priya MH, Merchant S, Asthagiri D, Paulaitis ME. Quasi-Chemical Theory of Cosolvent Hydrophobic Preferential Interactions. J Phys Chem B 2012; 116:6506-13. [DOI: 10.1021/jp301629j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Hamsa Priya
- William G. Lowrie Department
of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Safir Merchant
- Department of Chemical and Biomolecular
Engineering, Johns Hopkins University,
Baltimore, Maryland 21218, United States
| | - Dilip Asthagiri
- Department of Chemical and Biomolecular
Engineering, Johns Hopkins University,
Baltimore, Maryland 21218, United States
| | - Michael E. Paulaitis
- William G. Lowrie Department
of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
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Priya MH, Ashbaugh HS, Paulaitis ME. Cosolvent Preferential Molecular Interactions in Aqueous Solutions. J Phys Chem B 2011; 115:13633-42. [DOI: 10.1021/jp2083067] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Hamsa Priya
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - H. S. Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - M. E. Paulaitis
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
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