1
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Azizi K, Laio A, Hassanali A. Solvation thermodynamics from cavity shapes of amino acids. PNAS NEXUS 2023; 2:pgad239. [PMID: 37545648 PMCID: PMC10400782 DOI: 10.1093/pnasnexus/pgad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.
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Affiliation(s)
- Khatereh Azizi
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Alessandro Laio
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- SISSA, Via Bonomea 265, I-34136 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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2
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Dongmo Foumthuim CJ, Giacometti A. Solvent quality and solvent polarity in polypeptides. Phys Chem Chem Phys 2023; 25:4839-4853. [PMID: 36692363 DOI: 10.1039/d2cp05214h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Using molecular dynamics and thermodynamic integration, we report on the solvation process of seven polypeptides (GLY, ALA, ILE, ASN, LYS, ARG, GLU) in water and in cyclohexane. The polypeptides are selected to cover the full hydrophobic scale while varying their chain length from tri- to undeca-homopeptides, providing indications on possible non-additivity effects as well as the role of the peptide backbone in the overall stability of the polypeptides. The use of different solvents and different polypeptides allows us to investigate the relation between solvent quality - the capacity of a given solvent to fold/unfold a given biopolymer often described on a scale ranging from "good" to "poor"; and solvent polarity - related to the specific interactions of any solvent with respect to a reference solvent. Undeca-glycine is found to be the only polypeptide to have a stable collapse in water (polar solvent), with the other hydrophobic polypeptides displaying repeated folding and unfolding events in water, with polar polypeptides presenting even more complex behavior. By contrast, all polypeptides are found to keep an extended conformation in cyclohexane, irrespective of their polarity. All considered polypeptides are also found to have favorable solvation free energy independent of the solvent polarity and their intrinsic hydrophobicity, clearly highlighting the prominent stabilizing role of the peptide backbone - with the solvation process largely enthalpically dominated in polar polypeptides and partially entropically driven for hydrophobic polypeptides. Our study thus reveals the complexity of the solvation process of polypeptides defying the common view "like dissolves like", with the solute polarity playing the most prominent role. The absence of mirror symmetry upon the inversion of polarities of both the solvent and the polypeptides is confirmed.
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Affiliation(s)
- Cedrix J Dongmo Foumthuim
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30172 Venezia Mestre, Italy.
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30172 Venezia Mestre, Italy. .,European Centre for Living Technology (ECLT) Ca Bottacin, Dorsoduro 3911, Calle Crosera 30123 Venice, Italy
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3
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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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4
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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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5
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Tomar DS, Paulaitis ME, Pratt LR, Asthagiri DN. Hydrophilic Interactions Dominate the Inverse Temperature Dependence of Polypeptide Hydration Free Energies Attributed to Hydrophobicity. J Phys Chem Lett 2020; 11:9965-9970. [PMID: 33170720 DOI: 10.1021/acs.jpclett.0c02972] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We address the association of the hydrophobic driving forces in protein folding with the inverse temperature dependence of protein hydration, wherein stabilizing hydration effects strengthen with increasing temperature in a physiological range. All-atom calculations of the free energy of hydration of aqueous deca-alanine conformers, holistically including backbone and side-chain interactions together, show that attractive peptide-solvent interactions and the thermal expansion of the solvent dominate the inverse temperature signatures that have been interpreted traditionally as the hydrophobic stabilization of proteins in aqueous solution. Equivalent calculations on a methane solute are also presented as a benchmark for comparison. The present study calls for a reassessment of the forces that stabilize folded protein conformations in aqueous solutions and of the additivity of hydrophobic/hydrophilic contributions.
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Affiliation(s)
- Dheeraj S Tomar
- Xilio Therapeutics Inc., Waltham, Massachusetts 02451, 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
| | - Dilipkumar N Asthagiri
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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6
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Asthagiri D, Tomar DS. System Size Dependence of Hydration-Shell Occupancy and Its Implications for Assessing the Hydrophobic and Hydrophilic Contributions to Hydration. J Phys Chem B 2020; 124:798-806. [DOI: 10.1021/acs.jpcb.9b11200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Dilipkumar Asthagiri
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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7
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Muralidharan A, Pratt L, Chaudhari M, Rempe S. Quasi-chemical theory for anion hydration and specific ion effects: Cl-(aq) vs. F-(aq). ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cpletx.2019.100037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Ou SC, Pettitt BM. Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles. J Chem Theory Comput 2019; 15:2649-2658. [PMID: 30768893 DOI: 10.1021/acs.jctc.8b01157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Techniques to calculate the free energy changes of a system are very useful in the study of biophysical and biochemical properties. In practice, free energy changes can be described with thermodynamic cycles, and the free energy change of an individual process can be computed by sufficiently sampling the corresponding configurations. However, this is still time-consuming especially for large biomolecular systems. Previously, we have shown that by utilizing precomputed solute-solvent correlations, so-called proximal distribution functions (pDF), we are capable of reconstructing the solvent environment near solute atoms, thus estimating the solute-solvent interactions and solvation free energies of molecules. In this contribution, we apply the technique of pDF-reconstructions to calculate chemical potentials and use this information in thermodynamic cycles. This illustrates how free energy changes of nontrivial chemical processes in aqueous solution systems can be rapidly estimated.
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Affiliation(s)
- Shu-Ching Ou
- Sealy Center for Structural Biology and Molecular Biophysics , University of Texas Medical Branch , 301 University Boulevard , Galveston , Texas 77555-0304 , United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics , University of Texas Medical Branch , 301 University Boulevard , Galveston , Texas 77555-0304 , United States
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9
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Muralidharan A, Pratt LR, Chaudhari MI, Rempe SB. Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F -) Anion Hydration. J Phys Chem A 2018; 122:9806-9812. [PMID: 30475612 DOI: 10.1021/acs.jpca.8b08474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Accurate predictions of the hydration free energy for anions typically has been more challenging than that for cations. Hydrogen bond donation to the anion in hydrated clusters such as F(H2O) n - can lead to delicate structures. Consequently, the energy landscape contains many local minima, even for small clusters, and these minima present a challenge for computational optimization. Utilization of cluster experimental results for the free energies of gas-phase clusters shows that even though anharmonic effects are interesting they need not be of troublesome magnitudes for careful applications of quasi-chemical theory to ion hydration. Energy-optimized cluster structures for anions can leave the central ion highly exposed, and application of implicit solvation models to these structures can incur more serious errors than those for metal cations. Utilizing cluster structures sampled from ab initio molecular dynamics simulations substantially fixes those issues.
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Affiliation(s)
- A Muralidharan
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - L R Pratt
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - M I Chaudhari
- Center for Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
| | - S B Rempe
- Center for Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
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10
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Tomar DS, Ramesh N, Asthagiri D. Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides. J Chem Phys 2018; 148:222822. [DOI: 10.1063/1.5022465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Dheeraj S. Tomar
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21208, USA
| | - Niral Ramesh
- Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005-1892, USA
| | - D. Asthagiri
- Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005-1892, USA
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11
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Asthagiri D, Karandur D, Tomar DS, Pettitt BM. Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly 15. J Phys Chem B 2017; 121:8078-8084. [PMID: 28774177 DOI: 10.1021/acs.jpcb.7b05469] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simulations and experiments show oligo-glycines, polypeptides lacking any side chains, can collapse in water. We assess the hydration thermodynamics of this collapse by calculating the hydration free energy at each of the end points of the reaction coordinate, here taken as the end-to-end distance (r) in the chain. To examine the role of the various conformations for a given r, we study the conditional distribution, P(Rg|r), of the radius of gyration for a given value of r. The free energy change versus Rg, -kBT ln P(Rg|r), is found to vary more gently compared to the corresponding variation in the excess hydration free energy. Using this observation within a multistate generalization of the potential distribution theorem, we calculate a tight upper bound for the hydration free energy of the peptide for a given r. On this basis, we find that peptide hydration greatly favors the expanded state of the chain, despite primitive hydrophobic effects favoring chain collapse. The net free energy of collapse is seen to be a delicate balance between opposing intrapeptide and hydration effects, with intrapeptide contributions favoring collapse.
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Affiliation(s)
- D Asthagiri
- Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas, United States.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas, United States
| | - Deepti Karandur
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine , Houston, Texas, United States
| | - Dheeraj S Tomar
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland, United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas, United States.,Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine , Houston, Texas, United States
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12
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Drake JA, Harris RC, Pettitt BM. Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility. Biophys J 2017; 111:756-767. [PMID: 27558719 DOI: 10.1016/j.bpj.2016.07.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/30/2016] [Accepted: 07/06/2016] [Indexed: 01/24/2023] Open
Abstract
Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains.
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Affiliation(s)
- Justin A Drake
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Robert C Harris
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas.
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13
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Kumar A, Bisht M, Venkatesu P. Exploring the structure and stability of amino acids and glycine peptides in biocompatible ionic liquids. RSC Adv 2016. [DOI: 10.1039/c5ra26690d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amino acids (AAs) are vital components for a variety of biological systems and can be linked through covalent bonds (or peptide bonds) to form a protein structure.
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Affiliation(s)
- Awanish Kumar
- Department of Chemistry
- University of Delhi
- Delhi-110 007
- India
| | - Meena Bisht
- Department of Chemistry
- University of Delhi
- Delhi-110 007
- India
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14
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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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15
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Govinda V, Venkatesu P. A Comprehensive Experimental Study to Understand the Hofmeister Series of Anions of Aqueous Imidazolium-Based Ionic Liquids on Glycine Peptides. Ind Eng Chem Res 2014. [DOI: 10.1021/ie503736g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Varadhi Govinda
- Department of Chemistry, University of Delhi, Delhi 110 007, India
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16
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Shao Q. Methanol Concentration Dependent Protein Denaturing Ability of Guanidinium/Methanol Mixed Solution. J Phys Chem B 2014; 118:6175-85. [DOI: 10.1021/jp500280v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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17
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Tomar DS, Weber V, Pettitt BM, Asthagiri D. Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model. J Phys Chem B 2014; 118:4080-7. [PMID: 24650057 PMCID: PMC3993919 DOI: 10.1021/jp500727u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
![]()
The
hydration thermodynamics of the amino acid X relative to the
reference G (glycine) or the hydration thermodynamics of a small-molecule
analog of the side chain of X is often used to model the contribution
of X to protein stability and solution thermodynamics. We consider
the reasons for successes and limitations of this approach by calculating
and comparing the conditional excess free energy, enthalpy, and entropy
of hydration of the isoleucine side chain in zwitterionic isoleucine,
in extended penta-peptides, and in helical deca-peptides. Butane in
gauche conformation serves as a small-molecule analog for the isoleucine
side chain. Parsing the hydrophobic and hydrophilic contributions
to hydration for the side chain shows that both of these aspects of
hydration are context-sensitive. Furthermore, analyzing the solute–solvent
interaction contribution to the conditional excess enthalpy of the
side chain shows that what is nominally considered a property of the
side chain includes entirely nonobvious contributions of the background.
The context-sensitivity of hydrophobic and hydrophilic hydration and
the conflation of background contributions with energetics attributed
to the side chain limit the ability of a single scaling factor, such
as the fractional solvent exposure of the group in the protein, to
map the component energetic contributions of the model-compound data
to their value in the protein. But ignoring the origin of cancellations
in the underlying components the group-transfer model may appear to
provide a reasonable estimate of the free energy for a given error
tolerance.
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Affiliation(s)
- Dheeraj S Tomar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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