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Naito H, Sumi T, Koga K. How do water-mediated interactions and osmotic second virial coefficients vary with particle size? Faraday Discuss 2024; 249:440-452. [PMID: 37791511 DOI: 10.1039/d3fd00104k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
We examine quantitatively the solute-size dependences of the effective interactions between nonpolar solutes in water and in a simple liquid. The potential w(r) of mean force and the osmotic second virial coefficients B are calculated with high accuracy from molecular dynamics simulations. As the solute diameter increases from methane's to C60's with the solute-solute and solute-solvent attractive interaction parameters fixed to those for the methane-methane and methane-water interactions, the first minimum of w(r) lowers from -1.1 to -4.7 in units of the thermal energy kT. Correspondingly, the magnitude of B (<0) increases proportional to σα with some power close to 6 or 7, which reinforces the solute-size dependence of B found earlier for a smaller range of σ [H. Naito, R. Okamoto, T. Sumi and K. Koga, J. Chem. Phys., 2022, 156, 221104]. We also demonstrate that the strength of the attractive interactions between solute and solvent molecules can qualitatively change the characteristics of the effective pair interaction between solute particles, both in water and in a simple liquid. If the solute-solvent attractive force is set to be weaker (stronger) than a threshold, the effective interaction becomes increasingly attractive (repulsive) with increasing solute size.
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Affiliation(s)
- Hidefumi Naito
- Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan.
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Tomonari Sumi
- Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan.
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Kenichiro Koga
- Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan.
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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2
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In Silico Study: Combination of α-Mangostin and Chitosan Conjugated with Trastuzumab against Human Epidermal Growth Factor Receptor 2. Polymers (Basel) 2022; 14:polym14132747. [PMID: 35808792 PMCID: PMC9268814 DOI: 10.3390/polym14132747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 12/10/2022] Open
Abstract
Breast cancer is a type of cancer with the highest prevalence worldwide. Almost 10–30% of breast cancer cases are diagnosed as positive for HER2 (human epidermal growth factor receptor 2). The currently available treatment methods still exhibit many shortcomings such as a high incidence of side effects and treatment failure due to resistance. This in silico study aims to simulate α-mangostin and chitosan combination conjugated to trastuzumab formulation against HER2 as an effort to improve breast cancer patient therapy. This molecular docking simulation was done through using PatchDock Server. The materials used including the two-dimensional structure of α-mangostin, chitosan, and sodium tripolyphosphate from the PubChem database; trastuzumab FASTA sequence from the DrugBank database; and HER2 structure obtained from a crystal complex with PDB ID: 1N8Z. The results indicated that the particle of α-mangostin and chitosan combinations interacted mostly with the crystallizable fragment (Fc region) of trastuzumab in the conjugation process. The conjugation of trastuzumab to the particle of a combination of α-mangostin and chitosan resulted in the greatest increase in the binding score of the smallest-sized particles (50 Å) with an increase in the score of 3828 and also gave the most similar mode of interaction with trastuzumab. However, the conjugation of trastuzumab eliminated the similarity of the mode of interaction and increased the value of atomic contact energy. Thus, a cominbation of α-mangostin and chitosan conjugated to a trastuzumab formulation was predicted can increase the effectiveness of breast cancer therapy at a relatively small particle size but with the consequence of decreasing atomic contact energy.
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3
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Robinson VN, Ghosh R, Egan CK, Riera M, Knight C, Paesani F, Hassanali A. The behavior of methane-water mixtures under elevated pressures from simulations using many-body potentials. J Chem Phys 2022; 156:194504. [PMID: 35597630 DOI: 10.1063/5.0089773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane-water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane-water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane-water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. We find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.
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Affiliation(s)
- Victor Naden Robinson
- The 'Abdus Salam' International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Raja Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Colin K Egan
- The 'Abdus Salam' International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Christopher Knight
- Computational Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Ali Hassanali
- The 'Abdus Salam' International Centre for Theoretical Physics, I-34151 Trieste, Italy
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4
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Baul U, Bley M, Dzubiella J. Thermal Compaction of Disordered and Elastin-like Polypeptides: A Temperature-Dependent, Sequence-Specific Coarse-Grained Simulation Model. Biomacromolecules 2020; 21:3523-3538. [DOI: 10.1021/acs.biomac.0c00546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Upayan Baul
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Michael Bley
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Joachim Dzubiella
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
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5
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6
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Zieba K, Czaplewski C, Liwo A, Graziano G. Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models. Phys Chem Chem Phys 2020; 22:4758-4771. [PMID: 32064469 DOI: 10.1039/c9cp06627f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study provides a deep computational analysis of the thermodynamic and structural features associated with the hydration of xenon, Xe, and its pairwise hydrophobic interaction (i.e., the potential of mean force, PMF), over a large temperature range. Xe is described both as a Lennard-Jones particle, LJ-Xe, and as a Mie particle, Mie-Xe (pseudo hard sphere). Three different water models are used: TIP3P-Ew, SPCE and TIP4P-2005. Mie-Xe is more hydrophobic than LJ-Xe due to the lack of the attractive energetic interactions with water molecules; its hydration, around room temperature, is opposed by a large and negative entropy change and a positive enthalpy change. The PMF of Mie-Xe is characterized by a deep minimum at contact distance whose depth increases with temperature, and whose magnitude is significantly larger than that obtained for LJ-Xe. The contact minimum configuration of Mie-Xe is favoured by a large positive entropy change and contrasted by a positive enthalpy change. These results are qualitatively the same regardless of the water model used. There is no clear connection between the values determined for the thermodynamic functions and the structural features of the hydration shells surrounding the single Mie-Xe and the couple of Mie-Xe particles in the contact minimum configuration. This confirms that the structural reorganization of water associated with such processes is characterized by an almost complete enthalpy-entropy compensation.
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Affiliation(s)
- Karolina Zieba
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy.
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7
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Abstract
Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent-solvent and solute-solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.
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8
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Barnett JW, Ashbaugh HS. Evaluation of second osmotic virial coefficients from molecular simulation following scaled-particle theory. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1639698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- J. Wesley Barnett
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
| | - Henry S. Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
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9
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Mukhija A, Kishore N. Thermodynamic insights into interaction of protein coated gold nanoclusters with DNA and influence of coating on drug binding. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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10
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Jiang Z, Remsing RC, Rego NB, Patel AJ. Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes. J Phys Chem B 2019; 123:1650-1661. [PMID: 30682885 DOI: 10.1021/acs.jpcb.8b11423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to important insights into these processes. Although techniques such as the indirect umbrella sampling (INDUS) method can be used to characterize solvent fluctuations in static observation volumes of various sizes and shapes, characterizing how the solvent mediates inherently dynamic processes, such as self-assembly or conformational change, remains a challenge. In this work, we generalize the INDUS method to facilitate the enhanced sampling of solvent fluctuations in dynamical observation volumes, whose positions and shapes can evolve. We illustrate the usefulness of this generalization by characterizing water density fluctuations in dynamical volumes pertaining to the hydration of flexible solutes, the assembly of small hydrophobes, and conformational transitions in a model peptide. We also use the method to probe the dynamics of hard spheres.
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Affiliation(s)
| | - Richard C Remsing
- Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
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11
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Islam N, Flint M, Rick SW. Water hydrogen degrees of freedom and the hydrophobic effect. J Chem Phys 2019; 150:014502. [DOI: 10.1063/1.5053239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Naeyma Islam
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Mahalia Flint
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Steven W. Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
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12
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Drug partitioning in individual and mixed micelles and interaction with protein upon delivery form micellar media. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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13
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Okamoto R, Onuki A. Theory of nonionic hydrophobic solutes in mixture solvent: Solvent-mediated interaction and solute-induced phase separation. J Chem Phys 2018; 149:014501. [DOI: 10.1063/1.5037673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ryuichi Okamoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Akira Onuki
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
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14
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Gao A, Tan L, Chaudhari MI, Asthagiri D, Pratt LR, Rempe SB, Weeks JD. Role of Solute Attractive Forces in the Atomic-Scale Theory of Hydrophobic Effects. J Phys Chem B 2018; 122:6272-6276. [DOI: 10.1021/acs.jpcb.8b01711] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ang Gao
- Institute for Physical Science and Technology, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Liang Tan
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Mangesh I. Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - D. Asthagiri
- Chemical and Biomolecular Engineering Rice University, Houston, Texas 77005, United States
| | - Lawrence R. Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Susan B. Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - John D. Weeks
- Institute for Physical Science and Technology, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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15
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Ashbaugh HS, Barnett JW, Saltzman A, Langrehr M, Houser H. Connections between the Anomalous Volumetric Properties of Alcohols in Aqueous Solution and the Volume of Hydrophobic Association. J Phys Chem B 2018; 122:3242-3250. [PMID: 28968101 DOI: 10.1021/acs.jpcb.7b08728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The partial molar volumes of alcohols in water exhibit a non-monotonic dependence on concentration at room temperature, initially decreasing with increasing concentration before passing through a minimum and rising to the pure liquid plateau. This anomalous behavior is associated with hydrophobic interactions. We report molecular simulations of short chain alcohols and alkanes in water to examine the volumetric properties of these mixtures at infinite dilution over a range of temperatures. Our simulations find this anomaly disappears at a crossover temperature, above which the solute volume only varies monotonically with concentration. A Voronoi volume analysis of solution configurations finds that solutes in clusters take up less space than individual solutes at low temperature and more space at elevated temperatures. These changes in cluster volumes are subsequently shown to correlate with the derivative of the solute partial molar volume with respect to solute concentration. The changes in solute volume upon nonpolar solute association impact the response of molecular-scale hydrophobic interactions for assembly with increasing pressure.
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Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - J Wesley Barnett
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Alexander Saltzman
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Mae Langrehr
- Department of Chemical and Biomolecular Engineering , University of Delaware , Newark , Delaware 19716 , United States
| | - Hayden Houser
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
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16
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Judy E, Pagariya D, Kishore N. Drug Partitioning in Micellar Media and Its Implications in Rational Drug Design: Insights with Streptomycin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:3467-3484. [PMID: 29482319 DOI: 10.1021/acs.langmuir.7b04346] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Oral bioavailability of a drug molecule requires its effective delivery to the target site. In general, majority of synthetically developed molecular entities have high hydrophobic nature as well as low bioavailability, therefore the need for suitable delivery vehicles arises. Self-assembled structures such as micelles, niosomes, and liposomes have been used as effective delivery vehicles and studied extensively. However, the information available in literature is mostly qualitative in nature. We have quantitatively investigated the partitioning of antibiotic drug streptomycin into cationic, nonionic, and a mixture of cationic and nonionic surfactant micelles and its interaction with the transport protein serum albumin upon subsequent delivery. A combination of calorimetry and spectroscopy has been used to obtain the thermodynamic signatures associated with partitioning and interaction with the protein and the resulting conformational changes in the latter. The results have been correlated with other class of drugs of different nature to understand the role of molecular features in the partitioning process. These studies are oriented toward understanding the physical chemistry of partitioning of a variety of drug molecules into suitable delivery vehicles and hence establishing structure-property-energetics relationships. Such studies provide general guidelines toward a broader goal of rational drug design.
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Affiliation(s)
- Eva Judy
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400 076 , India
| | - Darshna Pagariya
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400 076 , India
| | - Nand Kishore
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400 076 , India
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17
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Tang D, Delpo C, Blackmon O, Ashbaugh HS. Note: Second osmotic virial coefficients of short alkanes and their alcohol counterparts in water as a function of temperature. J Chem Phys 2018; 148:016101. [DOI: 10.1063/1.5008573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Du Tang
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
| | - Courtney Delpo
- Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, USA
| | - Odella Blackmon
- Department of Chemistry, William Carey University, Hattiesburg, Mississippi 39401, USA
| | - Henry S. Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
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18
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Abstract
This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.
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Affiliation(s)
- Matthew B Hillyer
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
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19
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Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context. Proc Natl Acad Sci U S A 2017; 114:13345-13350. [PMID: 29158409 DOI: 10.1073/pnas.1700092114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobic interactions drive many important biomolecular self-assembly phenomena. However, characterizing hydrophobicity at the nanoscale has remained a challenge due to its nontrivial dependence on the chemistry and topography of biomolecular surfaces. Here we use molecular simulations coupled with enhanced sampling methods to systematically displace water molecules from the hydration shells of nanostructured solutes and calculate the free energetics of interfacial water density fluctuations, which quantify the extent of solute-water adhesion, and therefore solute hydrophobicity. In particular, we characterize the hydrophobicity of curved graphene sheets, self-assembled monolayers (SAMs) with chemical patterns, and mutants of the protein hydrophobin-II. We find that water density fluctuations are enhanced near concave nonpolar surfaces compared with those near flat or convex ones, suggesting that concave surfaces are more hydrophobic. We also find that patterned SAMs and protein mutants, having the same number of nonpolar and polar sites but different geometrical arrangements, can display significantly different strengths of adhesion with water. Specifically, hydroxyl groups reduce the hydrophobicity of methyl-terminated SAMs most effectively not when they are clustered together but when they are separated by one methyl group. Hydrophobin-II mutants show that a charged amino acid reduces the hydrophobicity of a large nonpolar patch when placed at its center, rather than at its edge. Our results highlight the power of water density fluctuations-based measures to characterize the hydrophobicity of nanoscale surfaces and caution against the use of additive approximations, such as the commonly used surface area models or hydropathy scales for characterizing biomolecular hydrophobicity and the associated driving forces of assembly.
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21
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Resolving solvophobic interactions inferred from experimental solvation free energies and evaluated from molecular simulations. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2016.11.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Cerdeiriña CA, Widom B. Osmotic Second Virial Coefficients of Aqueous Solutions from Two-Component Equations of State. J Phys Chem B 2016; 120:13144-13151. [DOI: 10.1021/acs.jpcb.6b09912] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claudio A. Cerdeiriña
- Departamento
de Física Aplicada, Universidad de Vigo, Campus del Agua, Ourense 32004, Spain
- Department
of Chemistry, Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, United States
| | - B. Widom
- Department
of Chemistry, Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, United States
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23
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Hatano I, Mochizuki K, Sumi T, Koga K. Hydrophobic Polymer Chain in Water That Undergoes a Coil-to-Globule Transition Near Room Temperature. J Phys Chem B 2016; 120:12127-12134. [DOI: 10.1021/acs.jpcb.6b08347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- I. Hatano
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
| | - K. Mochizuki
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
| | - T. Sumi
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
| | - K. Koga
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
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24
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Synergistic Inhibition of Protein Fibrillation by Proline and Sorbitol: Biophysical Investigations. PLoS One 2016; 11:e0166487. [PMID: 27870861 PMCID: PMC5117683 DOI: 10.1371/journal.pone.0166487] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/28/2016] [Indexed: 11/19/2022] Open
Abstract
We report here interesting synergistic effects of proline and sorbitol, two well-known chemical chaperones, in the inhibition of fibrillation of two proteins, insulin and lysozyme. A combination of many biophysical techniques has been used to understand the structural morphology and modes of interaction of the chaperones with the proteins during fibrillation. Both the chaperones establish stronger polar interactions in the elongation and saturation stages of fibrillation compared to that in the native stage. However, when presented as a mixture, we also see contribution of hydrophobic interactions. Thus, a co-operative adjustment of polar and hydrophobic interactions between the chaperones and the protein surface seems to drive the synergistic effects in the fibrillation process. In insulin, this synergy is quantitatively similar in all the stages of the fibrillation process. These observations would have significant implications for understanding protein folding concepts, in general, and for designing combination therapies against protein fibrillation, in particular.
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25
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Pratt LR, Chaudhari MI, Rempe SB. Statistical Analyses of Hydrophobic Interactions: A Mini-Review. J Phys Chem B 2016; 120:6455-60. [PMID: 27258151 DOI: 10.1021/acs.jpcb.6b04082] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review focuses on the striking recent progress in solving for hydrophobic interactions between small inert molecules. We discuss several new understandings. First, the inverse temperature phenomenology of hydrophobic interactions, i.e., strengthening of hydrophobic bonds with increasing temperature, is decisively exhibited by hydrophobic interactions between atomic-scale hard sphere solutes in water. Second, inclusion of attractive interactions associated with atomic-size hydrophobic reference cases leads to substantial, nontrivial corrections to reference results for purely repulsive solutes. Hydrophobic bonds are weakened by adding solute dispersion forces to treatment of reference cases. The classic statistical mechanical theory for those corrections is not accurate in this application, but molecular quasi-chemical theory shows promise. Finally, because of the masking roles of excluded volume and attractive interactions, comparisons that do not discriminate the different possibilities face an interpretive danger.
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Affiliation(s)
- Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University , New Orleans, Louisiana 70118, United States
| | - Mangesh I Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
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Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907;
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Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation. Proc Natl Acad Sci U S A 2016; 113:E2224-30. [PMID: 26957607 DOI: 10.1073/pnas.1513659113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005)Nature437(7059):640-647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air-water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces.
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Chaudhari MI, Rempe SB, Asthagiri D, Tan L, Pratt LR. Molecular Theory and the Effects of Solute Attractive Forces on Hydrophobic Interactions. J Phys Chem B 2016; 120:1864-70. [DOI: 10.1021/acs.jpcb.5b09552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Susan B. Rempe
- Center
for Biological and Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - D. Asthagiri
- Department
of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - L. Tan
- 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
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Choudhary S, Talele P, Kishore N. Thermodynamic insights into drug–surfactant interactions: Study of the interactions of naporxen, diclofenac sodium, neomycin, and lincomycin with hexadecytrimethylammonium bromide by using isothermal titration calorimetry. Colloids Surf B Biointerfaces 2015; 132:313-21. [DOI: 10.1016/j.colsurfb.2015.05.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/06/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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Ashbaugh HS, Weiss K, Williams SM, Meng B, Surampudi LN. Temperature and Pressure Dependence of Methane Correlations and Osmotic Second Virial Coefficients in Water. J Phys Chem B 2015; 119:6280-94. [DOI: 10.1021/acs.jpcb.5b02056] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henry S. Ashbaugh
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Katie Weiss
- Alfred University, Alfred, New York 14802, United States
| | - Steven M. Williams
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bin Meng
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Lalitanand N. Surampudi
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
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Abstract
Processes ranging from oil-water phase separation to the formation of solid clathrate hydrates send mixed messages regarding whether oil molecules hate or love to be surrounded by water. Recent experimental and theoretical results help decipher these mixed messages by illuminating the conditions under which the stability of a hydrophobic contact is expected to exceed thermal energy fluctuations - thus facilitating hydrophobic self-assembly and the emergence of structure from randomness. Important open questions remain regarding the dependence of hydrophobic interactions on molecular size and temperature, as well as the balance of direct and water-mediated interactions.
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Affiliation(s)
- Dor Ben-Amotz
- Purdue University, Department of Chemistry, West Lafayette, Indiana 47907, United States
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Palmer JC, Debenedetti PG. Recent advances in molecular simulation: A chemical engineering perspective. AIChE J 2015. [DOI: 10.1002/aic.14706] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jeremy C. Palmer
- Dept. of Chemical and Biomolecular Engineering; University of Houston; Houston TX 77204
| | - Pablo G. Debenedetti
- Dept. of Chemical and Biological Engineering; Princeton University; Princeton NJ 08544
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Chaudhari MI, Sabo D, Pratt LR, Rempe SB. Hydration of Kr(aq) in Dilute and Concentrated Solutions. J Phys Chem B 2014; 119:9098-102. [DOI: 10.1021/jp508866h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and
Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Dubravko Sabo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Lawrence R. Pratt
- Department of Chemical
and
Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Susan B. Rempe
- Center for Biological and
Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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