1
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Suating P, Ernst NE, Alagbe BD, Skinner HA, Mague JT, Ashbaugh HS, Gibb BC. On the Nature of Guest Complexation in Water: Triggered Wetting-Water-Mediated Binding. J Phys Chem B 2022; 126:3150-3160. [PMID: 35438501 PMCID: PMC9059121 DOI: 10.1021/acs.jpcb.2c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/18/2022] [Indexed: 11/30/2022]
Abstract
The complexity of macromolecular surfaces means that there are still many open questions regarding how specific areas are solvated and how this might affect the complexation of guests. Contributing to the identification and classification of the different possible mechanisms of complexation events in aqueous solution, and as part of the recent SAMPL8 exercise, we report here on the synthesis and conformational properties of TEEtOA 2, a cavitand with conformationally flexible ethyl groups at its portal. Using a combination of ITC and NMR spectroscopy, we report the binding affinities of a series of carboxylates to 2 and compare it to a related cavitand TEMOA 1. Additionally, we report MD simulations revealing how the wetting of the pocket of 2 is controlled by the conformation of its rim ethyl groups and, correspondingly, a novel triggered wetting, guest complexation mechanism, whereby the approaching guest opens up the pocket of the host, inducing its wetting and ultimately allows the formation of a hydrated host-guest complex (H·G·H2O). A general classification of complexation mechanisms is also suggested.
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Affiliation(s)
- Paolo Suating
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Nicholas E. Ernst
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Busayo D. Alagbe
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Hannah A. Skinner
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Henry S. Ashbaugh
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bruce C. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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2
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Moon H, Collanton RP, Monroe JI, Casey TM, Shell MS, Han S, Scott SL. Evidence for Entropically Controlled Interfacial Hydration in Mesoporous Organosilicas. J Am Chem Soc 2022; 144:1766-1777. [PMID: 35041412 DOI: 10.1021/jacs.1c11342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
At aqueous interfaces, the distribution and dynamics of adsorbates are modulated by the behavior of interfacial water. Hydration of a hydrophobic surface can store entropy via the ordering of interfacial water, which contributes to the Gibbs energy of solute binding. However, there is little experimental evidence for the existence of such entropic reservoirs, and virtually no precedent for their rational design in systems involving extended interfaces. In this study, two series of mesoporous silicas were modified in distinct ways: (1) progressively deeper thermal dehydroxylation, via condensation of surface silanols, and (2) increasing incorporation of nonpolar organic linkers into the silica framework. Both approaches result in decreasing average surface polarity, manifested in a blue-shift in the fluorescence of an adsorbed dye. For the inorganic silicas, hydrogen-bonding of water becomes less extensive as the number of surface silanols decreases. Overhauser dynamic nuclear polarization (ODNP) relaxometry indicates enhanced surface water diffusivity, reflecting a loss of enthalpic hydration. In contrast, organosilicas show a monotonic decrease in surface water diffusivity with decreasing polarity, reflecting enhanced hydrophobic hydration. Molecular dynamics simulations predict increased tetrahedrality of interfacial water for the organosilicas, implying increased ordering near the nm-size organic domains (relative to inorganic silicas, which necessarily lack such domains). These findings validate the prediction that hydrophobic hydration at interfaces is controlled by the microscopic length scale of the hydrophobic regions. They further suggest that the hydration thermodynamics of structurally heterogeneous silica surfaces can be tuned to promote adsorption, which in turn tunes the selectivity in catalytic reactions.
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Affiliation(s)
- Hyunjin Moon
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Ryan P Collanton
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Thomas M Casey
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States.,Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Susannah L Scott
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States.,Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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3
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Hernandez-Cortes P. Bioinformatic Analysis of Substrate
Binding Sites in Decapod Brachyurin-C Collagenases. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Ivanov AA, Pozmogova TN, Solovieva AO, Frolova TS, Sinitsyna OI, Lundovskaya OV, Tsygankova AR, Haouas M, Landy D, Benassi E, Shestopalova LV, Falaise C, Cadot E, Shestopalov MA, Abramov PA, Sokolov MN. From Specific γ-CD/[Nb 6 Cl 12 (H 2 O) 6 ] 2+ Recognition to Biological Activity Tuning. Chemistry 2020; 26:7479-7485. [PMID: 32181923 DOI: 10.1002/chem.202000739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/12/2020] [Indexed: 11/06/2022]
Abstract
Specific molecular recognition of γ-cyclodextrin (γ-CD) by the cationic hexanuclear niobium [Nb6 Cl12 (H2 O)6 ]2+ cluster complex in aqueous solutions results in a 1:1 supramolecular assembly {[Nb6 Cl12 (H2 O)6 ]@γ-CD}2+ . NMR spectroscopy, isothermal titration calorimetry (ITC), and ESI-MS were used to study the interaction between the inorganic cluster and the organic macrocycle. Such molecular association affects the biological activity of [Nb6 Cl12 (H2 O)6 ]2+ , decreasing its cytotoxicity despite enhanced cellular uptake. The 1:1 stoichiometry is maintained in solution over a large window of the reagents' ratio, but crystallization by slow evaporation produces a 1:2 host-guest complex [Nb6 Cl12 (H2 O)6 @(γ-CD)2 ]Cl2 ⋅20 H2 O featuring the cluster encapsulated between two molecules of γ-CD. The 1:2 complex was characterized by XRD, elemental analysis, IR spectroscopy, and thermogravimetric analysis (TGA). Quantum chemical calculations were performed to model host-guest interaction.
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Affiliation(s)
- Anton A Ivanov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev ave., 630090, Novosibirsk, Russia
| | - Tatiana N Pozmogova
- Novosibirsk State University, 2 Pirogova st., 630090, Novosibirsk, Russia.,Research Institute of Clinical and Experimental Lymphology, Branch of the ICG SB RAS, 2 Timakova st., 630117, Novosibirsk, Russia
| | - Anastasiya O Solovieva
- Research Institute of Clinical and Experimental Lymphology, Branch of the ICG SB RAS, 2 Timakova st., 630117, Novosibirsk, Russia.,Federal Research Center of Fundamental and Translational Medicine, 2 Timakova st., 630117, Novosibirsk, Russia
| | - Tatiana S Frolova
- Novosibirsk State University, 2 Pirogova st., 630090, Novosibirsk, Russia.,Federal Research Center of Fundamental and Translational Medicine, 2 Timakova st., 630117, Novosibirsk, Russia.,Federal Research Center Institute of Cytology and Genetics SB RAS, 10 acad. Lavrentiev ave., 630090, Novosibirsk, Russia
| | - Olga I Sinitsyna
- Novosibirsk State University, 2 Pirogova st., 630090, Novosibirsk, Russia.,Federal Research Center Institute of Cytology and Genetics SB RAS, 10 acad. Lavrentiev ave., 630090, Novosibirsk, Russia
| | - Olga V Lundovskaya
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev ave., 630090, Novosibirsk, Russia
| | - Alphiya R Tsygankova
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev ave., 630090, Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova st., 630090, Novosibirsk, Russia
| | - Mohamed Haouas
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, 45 avenue des Etats-Unis, 78035, Versailles, France
| | - David Landy
- Unité de Chimie Environnementale et Interactions sur le Vivant, (UCEIV, EA 4492), ULCO, 145, Avenue Maurice Schumann, MREI 1, 59140, Dunkerque, France
| | - Enrico Benassi
- Novosibirsk State University, 2 Pirogova st., 630090, Novosibirsk, Russia.,Shihezi University, 280 N 4th Rd, Shihezi, 832000, Xinjiang, P. R. China
| | | | - Clément Falaise
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, 45 avenue des Etats-Unis, 78035, Versailles, France
| | - Emmanuel Cadot
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, 45 avenue des Etats-Unis, 78035, Versailles, France
| | - Michael A Shestopalov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev ave., 630090, Novosibirsk, Russia
| | - Pavel A Abramov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev ave., 630090, Novosibirsk, Russia.,South Ural State University, 76 Lenina st., 454080, Chelyabinsk, Russia
| | - Maxim N Sokolov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev ave., 630090, Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova st., 630090, Novosibirsk, Russia
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5
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Wang J, Zheng X, Wang W, Guo H, Liu R, Zong W. A study on the interaction between cadmium and α-chymotrypsin and the underlying mechanisms. J Biochem Mol Toxicol 2018; 33:e22248. [DOI: 10.1002/jbt.22248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Jing Wang
- Department of Environmental Science; School of Environmental and Material Engineering, Yantai University; Yantai China
| | - Xiaolin Zheng
- Department of Environmental Science; School of Environmental and Material Engineering, Yantai University; Yantai China
| | - Weichao Wang
- Department of Environmental Engineering, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health; Jinan China
| | - Hongli Guo
- Department of Environmental Engineering, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health; Jinan China
| | - Rutao Liu
- Department of Environmental Engineering, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health; Jinan China
| | - Wansong Zong
- College of Geography and Environment, Department of Environmental Science, College of Population, Resources and Environment, Shandong Normal University; Jinan China
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6
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Weiß RG, Chudoba R, Setny P, Dzubiella J. Affinity, kinetics, and pathways of anisotropic ligands binding to hydrophobic model pockets. J Chem Phys 2018; 149:094902. [DOI: 10.1063/1.5025118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- R. Gregor Weiß
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, D-12489 Berlin, Germany
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Richard Chudoba
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, D-12489 Berlin, Germany
- Research Group Simulations of Energy Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Straße 3, D-79104 Freiburg, Germany
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 00-927 Warsaw, Poland
| | - Joachim Dzubiella
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, D-12489 Berlin, Germany
- Research Group Simulations of Energy Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Straße 3, D-79104 Freiburg, Germany
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7
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Abstract
Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by 17O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for 17O MRD. By contrast, we find that the 17O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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8
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Abstract
Diverse structural types of natural products and their mimics have served as targets of opportunity in our laboratory to inspire the discovery and development of new methods and strategies to assemble polyfunctional and polycyclic molecular architectures. Furthermore, our efforts toward identifying novel compounds having useful biological properties led to the creation of new targets, many of which posed synthetic challenges that required the invention of new methodology. In this Perspective, selected examples of how we have exploited a diverse range of natural products and their mimics to create, explore, and solve a variety of problems in chemistry and biology will be discussed. The journey was not without its twists and turns, but the unexpected often led to new revelations and insights. Indeed, in our recent excursion into applications of synthetic organic chemistry to neuroscience, avoiding the more-traveled paths was richly rewarding.
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Affiliation(s)
- Stephen F Martin
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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9
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Weiß RG, Setny P, Dzubiella J. Principles for Tuning Hydrophobic Ligand–Receptor Binding Kinetics. J Chem Theory Comput 2017; 13:3012-3019. [DOI: 10.1021/acs.jctc.7b00216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R. Gregor Weiß
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, D-12489 Berlin, Germany
- Institut
für Weiche Materie and Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
| | - Piotr Setny
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joachim Dzubiella
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, D-12489 Berlin, Germany
- Institut
für Weiche Materie and Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
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10
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Djikaev Y, Ruckenstein E. Recent developments in the theoretical, simulational, and experimental studies of the role of water hydrogen bonding in hydrophobic phenomena. Adv Colloid Interface Sci 2016; 235:23-45. [PMID: 27312562 DOI: 10.1016/j.cis.2016.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/27/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
Abstract
Hydrophobic effects (hydrophobic hydration and hydrophobic interaction) constitute an important element of a wide variety of phenomena relevant to biological, physical, chemical, environmental, engineering, and pharmaceutical sciences, such as the immiscibility of oil and water, self-assembly of amphiphiles leading to micelle and membrane formation, folding and stability and unfolding of the native structure of a biologically active protein, gating of ion channels, wetting, froth floatation, and adhesion. On the other hand, the hydrogen bonding ability of water plays a major (if not crucial) role in hydrophobic phenomena. We present a review of most important and relatively recent experimental, simulational, and theoretical research on hydrophobic phenomena in various systems. With a particular interest we survey investigations clarifying the role of water hydrogen bonding therein, because it has been the main object of our own recent research. We have developed a probabilistic hydrogen bond (PHB) model that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of its distance to a hydrophobe, hydrophobe radius, and temperature. Knowing that function, one can explicitly identify a water hydrogen bond contribution to the external potential whereto a water molecule is subjected near a hydrophobe. Combining the PHB model with the classical density functional theory (DFT), one can examine the contribution of water hydrogen bonding to the temperature and lengthscale effects on the hydration of particles and on their solvent-mediated interactions over the entire low-to-high temperature and small-to-large lengthscale ranges. We applied the combined DFT/PHB model to study a variety of hydrophobic phenomena such as (liquid) water in contact with a hydrophobic plate, solvation of spherical solutes of various radii in associated and non-associated liquids at various temperatures, the solvent-mediated interaction of spherical solutes and its temperature dependence, interaction of C60 fullerenes in water, temperature effect on the evaporation lengthscale of water confined between two hydrophobes, temperature dependence of the effective width of the solute-solvent transition layer and average density therein. These applications demonstrated that the DFT/PHB model can serve as a valuable tool in studying hydrophobic phenomena because it constitutes a balanced combination of simplicity, accuracy, and detail. The predictions of the combined DFT/PHB approach for the solvent density profiles and thermodynamic aspects of hydrophobic phenomena are generally in good agreement with experiments and simulations. For example, it predicts the small-to-large crossover lengthscale of its mechanism to be approximately in the range from 1nm to 4nm, and decreasing with increasing temperature. It also suggests that, in terms of the average fluid density in the solute-solvent transition layer, the transition layer for small hydrophobes (of radii ≲2 nm) becomes enriched with rather than depleted of fluid when both the solvent-solute affinity and hb-energy alteration ratio become large enough. The boundary values of these parameters, needed for the depletion-to-enrichment crossover, are predicted to decrease with increasing temperature.
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11
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Maeda Y, Makhlynets OV, Matsui H, Korendovych IV. Design of Catalytic Peptides and Proteins Through Rational and Combinatorial Approaches. Annu Rev Biomed Eng 2016; 18:311-28. [PMID: 27022702 PMCID: PMC6345664 DOI: 10.1146/annurev-bioeng-111215-024421] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design.
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Affiliation(s)
- Yoshiaki Maeda
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, Syracuse, New York 13244;
| | - Hiroshi Matsui
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021
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12
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Maeda Y, Fang J, Ikezoe Y, Pike DH, Nanda V, Matsui H. Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides. PLoS One 2016; 11:e0153700. [PMID: 27116246 PMCID: PMC4846159 DOI: 10.1371/journal.pone.0153700] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 04/03/2016] [Indexed: 12/13/2022] Open
Abstract
Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β-sheets and amyloid fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. The enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality.
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Affiliation(s)
- Yoshiaki Maeda
- Department of Chemistry, Hunter College and the Graduate Center, City University of New York, New York, New York, United State of America
| | - Justin Fang
- Department of Chemistry, Hunter College and the Graduate Center, City University of New York, New York, New York, United State of America
| | - Yasuhiro Ikezoe
- Department of Chemistry, Hunter College and the Graduate Center, City University of New York, New York, New York, United State of America
| | - Douglas H. Pike
- Department of Biochemistry, Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United State of America
| | - Vikas Nanda
- Department of Biochemistry, Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United State of America
| | - Hiroshi Matsui
- Department of Chemistry, Hunter College and the Graduate Center, City University of New York, New York, New York, United State of America
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York, United State of America
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13
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 417] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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15
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Myslinski JM, Clements JH, Martin SF. Protein-ligand interactions: probing the energetics of a putative cation-π interaction. Bioorg Med Chem Lett 2014; 24:3164-7. [PMID: 24856058 DOI: 10.1016/j.bmcl.2014.04.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/01/2023]
Abstract
In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO-pTyr-Ac6c-Asn wherein the R group is varied to include different alkyl, cycloalkyl, and aryl groups. Although an indole ring is reputed to have the strongest interaction with a guanidinium ion, binding free energies, ΔG°, for derivatives of RCO-pTyr-Ac6c-Asn bearing cyclohexyl and phenyl groups were slightly more favorable than their indolyl analog. Crystallographic analysis of two complexes reveals that test ligands bind in similar poses with the notable exception of the relative orientation and proximity of the phenyl and indolyl rings relative to an arginine residue of the domain. These spatial orientations are consistent with those observed in other cation-π interactions, but there is no net energetic benefit to such an interaction in this biological system. Accordingly, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.
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Affiliation(s)
- James M Myslinski
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - John H Clements
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - Stephen F Martin
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA.
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16
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Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. Heterogeneous Hydration of p53/MDM2 Complex. J Chem Theory Comput 2014; 10:1302-1313. [PMID: 24803860 PMCID: PMC3958133 DOI: 10.1021/ct400967m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Indexed: 12/23/2022]
Abstract
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Water-mediated
interactions play critical roles in biomolecular
recognition processes. Explicit solvent molecular dynamics (MD) simulations
and the variational implicit-solvent model (VISM) are used to study
those hydration properties during binding for the biologically important
p53/MDM2 complex. Unlike simple model solutes, in such a realistic
and heterogeneous solute–solvent system with both geometrical
and chemical complexity, the local water distribution sensitively
depends on nearby amino acid properties and the geometric shape of
the protein. We show that the VISM can accurately describe the locations
of high and low density solvation shells identified by the MD simulations
and can explain them by a local coupling balance of solvent–solute
interaction potentials and curvature. In particular, capillary transitions
between local dry and wet hydration states in the binding pocket are
captured for interdomain distance between 4 to 6 Å, right at
the onset of binding. The underlying physical connection between geometry
and polarity is illustrated and quantified. Our study offers a microscopic
and physical insight into the heterogeneous hydration behavior of
the biologically highly relevant p53/MDM2 system and demonstrates
the fundamental importance of hydrophobic effects for biological binding
processes. We hope our study can help to establish new design rules
for drugs and medical substances.
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Affiliation(s)
- Zuojun Guo
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Bo Li
- Department of Mathematics and Center for Theoretical Biological Physics, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0112, United States
| | - Joachim Dzubiella
- Department of Physics, Humboldt University of Berlin , Newtonstr. 15, 12489 Berlin, Germany ; Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin , Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0112, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, and Center for Theoretical Biological Physics, University of California , San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, United States
| | - Jianwei Che
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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17
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Zhang SR, Wu HL, Zhang XH, Zhai M, Yu RQ. Quantitative study of state switching in proteins using a single probe combined with trilinear decomposition. NEW J CHEM 2014. [DOI: 10.1039/c3nj01533e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excitation–Emission Matrix fluorescence (EEM) signals from the state switching of α-chymotrypsin can be resolved and investigated quantitatively by trilinear decomposition.
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Affiliation(s)
- Shu-Rong Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082, China
| | - Hai-Long Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082, China
| | - Xi-Hua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082, China
| | - Min Zhai
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082, China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082, China
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18
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Martin SF, Clements JH. Correlating structure and energetics in protein-ligand interactions: paradigms and paradoxes. Annu Rev Biochem 2013; 82:267-93. [PMID: 23746256 DOI: 10.1146/annurev-biochem-060410-105819] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Predicting protein-binding affinities of small molecules, even closely related ones, is a formidable challenge in biomolecular recognition and medicinal chemistry. A thermodynamic approach to optimizing affinity in protein-ligand interactions requires knowledge and understanding of how altering the structure of a small molecule will be manifested in protein-binding enthalpy and entropy changes; however, there is a relative paucity of such detailed information. In this review, we examine two strategies commonly used to increase ligand potency. The first of these involves introducing a cyclic constraint to preorganize a small molecule in its biologically active conformation, and the second entails adding nonpolar groups to a molecule to increase the amount of hydrophobic surface that is buried upon binding. Both of these approaches are motivated by paradigms suggesting that protein-binding entropy changes should become more favorable, but paradoxes can emerge that defy conventional wisdom.
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Affiliation(s)
- Stephen F Martin
- Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
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19
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Kapcha LH, Rossky PJ. A simple atomic-level hydrophobicity scale reveals protein interfacial structure. J Mol Biol 2013; 426:484-98. [PMID: 24120937 DOI: 10.1016/j.jmb.2013.09.039] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
Many amino acid residue hydrophobicity scales have been created in an effort to better understand and rapidly characterize water-protein interactions based only on protein structure and sequence. There is surprisingly low consistency in the ranking of residue hydrophobicity between scales, and their ability to provide insightful characterization varies substantially across subject proteins. All current scales characterize hydrophobicity based on entire amino acid residue units. We introduce a simple binary but atomic-level hydrophobicity scale that allows for the classification of polar and non-polar moieties within single residues, including backbone atoms. This simple scale is first shown to capture the anticipated hydrophobic character for those whole residues that align in classification among most scales. Examination of a set of protein binding interfaces establishes good agreement between residue-based and atomic-level descriptions of hydrophobicity for five residues, while the remaining residues produce discrepancies. We then show that the atomistic scale properly classifies the hydrophobicity of functionally important regions where residue-based scales fail. To illustrate the utility of the new approach, we show that the atomic-level scale rationalizes the hydration of two hydrophobic pockets and the presence of a void in a third pocket within a single protein and that it appropriately classifies all of the functionally important hydrophilic sites within two otherwise hydrophobic pores. We suggest that an atomic level of detail is, in general, necessary for the reliable depiction of hydrophobicity for all protein surfaces. The present formulation can be implemented simply in a manner no more complex than current residue-based approaches.
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Affiliation(s)
- Lauren H Kapcha
- Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78712-1167, USA
| | - Peter J Rossky
- Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78712-1167, USA.
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20
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Picosecond-resolved solvent reorganization and energy transfer in biological and model cavities. Biochimie 2013; 95:1127-35. [PMID: 23376876 DOI: 10.1016/j.biochi.2012.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 12/21/2012] [Indexed: 11/22/2022]
Abstract
Water molecules in hydrophobic biological cleft/cavities are of contemporary interest for the biomolecular structure and molecular recognition of hydrophobic ligands/drugs. Here, we have explored picosecond-resolved solvation dynamics of water molecules and associated polar amino acids in the hydrophobic cleft around Cys-34 position of Endogenous Serum Albumin (ESA). While site selective acrylodan labeling to Cys-34 allows us to probe solvation in the cleft, Förster resonance energy transfer (FRET) from intrinsic fluorescent amino acid Trp 214 to the extrinsic acrylodan probes structural integrity of the protein in our experimental condition. Temperature dependent solvation in the cleft clearly shows that the dynamics follows Arrhenius type behavior up to 60 °C, after which a major structural perturbation of the protein is evident. We have also monitored polarization gated dynamics of the acrylodan probe and FRET from Trp 214 to acrylodan at various temperatures. The dynamical behavior of the immediate environments around the probe acrylodan in the cleft has been compared with a model biomimetic cavity of a reverse micelle (w0 = 5). Using same fluorescent probe of acrylodan, we have checked the structural integrity of the model cavity at various temperatures using picosecond-resolved FRET from Trp to acrylodan in the cavity. We have also estimated possible distribution of donor-acceptor distances in the protein and reverse micelles. Our studies reveal that the energetics of the water molecules in the biological cleft is comparable to that in the model cavity indicating a transition from bound state to quasibound state, closely consistent with a recent MD simulation study.
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21
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Giovambattista N, Rossky P, Debenedetti P. Computational Studies of Pressure, Temperature, and Surface Effects on the Structure and Thermodynamics of Confined Water. Annu Rev Phys Chem 2012; 63:179-200. [DOI: 10.1146/annurev-physchem-032811-112007] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- N. Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210;
| | - P.J. Rossky
- Institute for Computational Engineering and Sciences, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712;
| | - P.G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544-5263;
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22
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Myslinski JM, DeLorbe JE, Clements JH, Martin SF. Protein-ligand interactions: thermodynamic effects associated with increasing nonpolar surface area. J Am Chem Soc 2011; 133:18518-21. [PMID: 22007755 DOI: 10.1021/ja2068752] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and Ac-pTyr-Xaa-Asn derived tripeptides in which the Xaa residue is an α,α-cycloaliphatic amino acid that varies in ring size from three- to seven-membered. Although the six- and seven-membered ring analogs are approximately equipotent, binding affinities of those having three- to six-membered rings increase incrementally with ring size because increasingly more favorable binding enthalpies dominate increasingly less favorable binding entropies, a finding consistent with an enthalpy-driven hydrophobic effect. Crystallographic analysis reveals that the only significant differences in structures of the complexes are in the number of van der Waals contacts between the domain and the methylene groups in the Xaa residues. There is a positive correlation between buried nonpolar surface area and binding free energy and enthalpy, but not with ΔC(p). Displacing a water molecule from a protein-ligand interface is not necessarily reflected in a favorable change in binding entropy. These findings highlight some of the fallibilities associated with commonly held views of relationships of structure and energetics in protein-ligand interactions and have significant implications for ligand design.
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Affiliation(s)
- James M Myslinski
- Chemistry and Biochemistry Department, Institute of Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
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23
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Bhattacharjee N, Biswas P. Structure of hydration water in proteins: a comparison of molecular dynamics simulations and database analysis. Biophys Chem 2011; 158:73-80. [PMID: 21665349 DOI: 10.1016/j.bpc.2011.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 05/07/2011] [Accepted: 05/08/2011] [Indexed: 11/15/2022]
Abstract
Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compare it with those obtained from molecular dynamics simulations. Tetrahedral order parameter of water in proteins calculated from previous and present simulation studies show that the potential of bulk water overestimates the average tetrahedral order parameter compared to those calculated from crystal structures. Hydration waters are found to be more ordered at a distance between the first and second solvation shell from the protein surface. The values of the order parameter decrease sharply when the water molecules are located very near or far away from the protein surface. At small water-water distance, the values of order parameter of water are very low. The average order parameter records a maximum value at a distance equivalent to the first solvation layer with respect to the water-water radial distribution and asymptotically approaches a constant value at large distances. Results from present analysis will help to get a better insight into structure of hydration water around proteins. The analysis will also help to improve the accuracy of water models on the protein surface.
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24
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Affiliation(s)
- Caterina Bissantz
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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25
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Cheng LT, Wang Z, Setny P, Dzubiella J, Li B, McCammon JA. Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J Chem Phys 2010; 131:144102. [PMID: 19831428 DOI: 10.1063/1.3242274] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A model nanometer-sized hydrophobic receptor-ligand system in aqueous solution is studied by the recently developed level-set variational implicit solvent model (VISM). This approach is compared to all-atom computer simulations. The simulations reveal complex hydration effects within the (concave) receptor pocket, sensitive to the distance of the (convex) approaching ligand. The ligand induces and controls an intermittent switching between dry and wet states of the hosting pocket, which determines the range and magnitude of the pocket-ligand attraction. In the level-set VISM, a geometric free-energy functional of all possible solute-solvent interfaces coupled to the local dispersion potential is minimized numerically. This approach captures the distinct metastable states that correspond to topologically different solute-solvent interfaces, and thereby reproduces the bimodal hydration behavior observed in the all-atom simulation. Geometrical singularities formed during the interface relaxation are found to contribute significantly to the energy barrier between different metastable states. While the hydration phenomena can thus be explained by capillary effects, the explicit inclusion of dispersion and curvature corrections seems to be essential for a quantitative description of hydrophobically confined systems on nanoscales. This study may shed more light onto the tight connection between geometric and energetic aspects of biomolecular hydration and may represent a valuable step toward the proper interpretation of experimental receptor-ligand binding rates.
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Affiliation(s)
- Li-Tien Cheng
- Department of Mathematics, University of California San Diego, La Jolla, California 92093, USA.
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26
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Rossky PJ. Exploring nanoscale hydrophobic hydration. Faraday Discuss 2010; 146:13-8; discussion 79-101, 395-401. [DOI: 10.1039/c005270c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Setny P, Wang Z, Cheng LT, Li B, McCammon JA, Dzubiella J. Dewetting-controlled binding of ligands to hydrophobic pockets. PHYSICAL REVIEW LETTERS 2009; 103:187801. [PMID: 19905832 PMCID: PMC2832595 DOI: 10.1103/physrevlett.103.187801] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Indexed: 05/27/2023]
Abstract
We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting-dewetting transitions in the weakly solvated pocket. The transitions lead to bimodal solvent fluctuations which govern magnitude and range of the pocket-ligand attraction. A recently developed implicit water model, based on the minimization of a geometric functional, captures the sensitive aqueous interface response to the concave-convex pocket-ligand configuration semiquantitatively.
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Affiliation(s)
- P. Setny
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California 92093, USA
- Interdisciplinary Center for Mathematical and Computational Modeling, University of Warsaw, Warsaw 02-089, Poland
| | - Z. Wang
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California 92093, USA
- Department of Mathematics, UC San Diego, La Jolla, California 92093, USA
| | - L.-T. Cheng
- Department of Mathematics, UC San Diego, La Jolla, California 92093, USA
| | - B. Li
- Department of Mathematics, UC San Diego, La Jolla, California 92093, USA
- NSF Center for Theoretical Biological Physics (CTBP), UC San Diego, La Jolla, California 92093, USA
| | - J. A. McCammon
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California 92093, USA
- NSF Center for Theoretical Biological Physics (CTBP), UC San Diego, La Jolla, California 92093, USA
- Department of Pharmacology and HHMI, UC San Diego, La Jolla, California 92093, USA
| | - J. Dzubiella
- Physics Department, Technical University Munich, 85748 Garching, Germany
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28
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Giovambattista N, Debenedetti PG, Rossky PJ. Enhanced surface hydrophobicity by coupling of surface polarity and topography. Proc Natl Acad Sci U S A 2009; 106:15181-5. [PMID: 19706474 PMCID: PMC2741225 DOI: 10.1073/pnas.0905468106] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Indexed: 11/18/2022] Open
Abstract
We use atomistic computer simulation to explore the relationship between mesoscopic (liquid drop contact angle) and microscopic (surface atomic polarity) characteristics for water in contact with a model solid surface based on the structure of silica. We vary both the magnitude and direction of the solid surface polarity at the atomic scale and characterize the response of an aqueous interface in terms of the solvent molecular organization and contact angle. We show that when the topography and polarity of the surface act in concert with the asymmetric charge distribution of water, the hydrophobicity varies substantially and, further, can be maximal for a surface with significant polarity. The results suggest that patterning of a surface on several length scales, from atomic to mum lengths, can make important independent contributions to macroscopic hydrophobicity.
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Affiliation(s)
- Nicolas Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, NY 11210-2889
- Department of Chemical Engineering, Princeton University, Princeton, NJ 08544-5263; and
| | - Pablo G. Debenedetti
- Department of Chemical Engineering, Princeton University, Princeton, NJ 08544-5263; and
| | - Peter J. Rossky
- Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences, University of Texas, Austin, TX 78712
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29
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Jensen MØ, Mouritsen OG, Peters GH. The hydrophobic effect: molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces. J Chem Phys 2007; 120:9729-44. [PMID: 15267989 DOI: 10.1063/1.1697379] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C(36)H(74) or n-alcohol C(35)H(71)OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding experimental data from x-ray reflectivity measurements, reveal a uniform weak de-wetting characteristic for the extended hydrophobic surface, while the hydrophilic surface is weakly wetted. These microscopic data are consistent with macroscopic contact angle measurements. Specific water orientation is present at both surfaces. The ordering is characteristically different between the surfaces and of longer range at the hydrophilic surface. Furthermore, the dynamic properties of water are different at the two surfaces and different from the bulk behavior. In particular, at the hydrophobic surface, time-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together with a partial drying of the surfaces are more indicative of the hydrophobic effect than structural ordering, which we suggest to be independent of surface topology.
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Affiliation(s)
- Morten Ø Jensen
- Quantum Protein Center (QUP), Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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30
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Schröder C, Rudas T, Boresch S, Steinhauser O. Simulation studies of the protein-water interface. I. Properties at the molecular resolution. J Chem Phys 2007; 124:234907. [PMID: 16821953 DOI: 10.1063/1.2198802] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report molecular dynamics simulations of three globular proteins: ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1 in explicit water. The proteins differ in their overall charge and fold type and were chosen to represent to some degree the structural variability found in medium-sized proteins. The length of each simulation was at least 15 ns, and larger than usual solvent boxes were used. We computed radial distribution functions, as well as orientational correlation functions about the surface residues. Two solvent shells could be clearly discerned about charged and polar amino acids. Near apolar amino acids the water density near such residues was almost devoid of structure. The mean residence time of water molecules was determined for water shells about the full protein, as well as for water layers about individual amino acids. In the dynamic properties, two solvent shells could be characterized as well. However, by comparison to simulations of pure water it could be shown that the influence of the protein reaches beyond 6 A, i.e., beyond the first two shells. In the first shell (r < or =3.5 A), the structural and dynamical properties of solvent waters varied considerably and depended primarily on the physicochemical properties of the closest amino acid side chain, with which the waters interact. By contrast, the solvent properties seem not to depend on the specifics of the protein studied (such as the net charge) or on the secondary structure element in which an amino acid is located. While differing considerably from the neat liquid, the properties of waters in the second solvation shell (3.5< r < or =6 A) are rather uniform; a direct influence from surface amino acids are already mostly shielded.
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Affiliation(s)
- C Schröder
- Department of Biomolecular Structural Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
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31
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Affiliation(s)
- Ariel Fernández
- Indiana University School of Informatics and Center for Computational Biology and Bioinformatics, Indianapolis, Indiana 46202, USA.
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32
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Noinville S, Revault M, Quiquampoix H, Baron MH. Structural effects of drying and rehydration for enzymes in soils: a kinetics-FTIR analysis of α-chymotrypsin adsorbed on montmorillonite. J Colloid Interface Sci 2004; 273:414-25. [PMID: 15082376 DOI: 10.1016/j.jcis.2004.01.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Accepted: 01/30/2004] [Indexed: 10/26/2022]
Abstract
The effects of desiccation and rehydration cycles encountered by extracellular enzymes in soils are studied on -chymotrypsin adsorbed on montmorillonite. The controlled hygrometric FTIR cell used in this study enables to monitor drying and rehydration steps undergone by the -chymotrypsin-montmorillonite suspension or by the enzyme alone. Relative humidity (RH) determines the amount of deuterated water in the FTIR cell atmosphere. The molar water/protein ratio (W/P) as well as the conformational and solvation states of the enzyme have been determined using H/D exchange monitored by FTIR-transmission spectroscopy. When the W/P ratio decreases from 3500 to approximately 400, unfolding of beta-secondary structure in three different domains involves about 8% of the polypeptide backbone with respect to the most solvated states. Desiccation induces beta-unfolding, which opens channels allowing free vapor water molecules to diffuse into the enzyme at 15% RH. On drying to 0% RH, displacements of internal water (H2O) in the enzyme are demonstrated by reverse peptide isotopic exchanges (COND ==> CONH). Specific beta-structures, only formed in highly solvated states, sequester around 20 internal H2O molecules. Indeed, most of the unfolded secondary structures during the drying step are refolded at W/P approximately 1000 during rehydration. However, self-association hinders the recovery of the initial closed tertiary structure. The pD-dependent structural changes controlling inward and outward water diffusion are suppressed, whether the protein is initially in an adsorbed state or in solution. Changes in secondary structures encountered during desiccation/rehydration cycle are similar for the protein either free or in the adsorbed state. Thus domains that are unfolded by adsorption are not concerned by the desiccation/rehydration cycle.
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Affiliation(s)
- S Noinville
- Laboratoire de Dynamique, Interactions et Réactivité CNRS-Université Paris 6, UMR 7075, 2 rue Henri Dunant, 94320 Thiais, France.
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33
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Pichierri F. Computation of the permanent dipole moment of α-chymotrypsin from linear-scaling semiempirical quantum mechanical methods. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/j.theochem.2003.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Pal SK, Peon J, Zewail AH. Ultrafast surface hydration dynamics and expression of protein functionality: alpha -Chymotrypsin. Proc Natl Acad Sci U S A 2002; 99:15297-302. [PMID: 12427971 PMCID: PMC137710 DOI: 10.1073/pnas.242600399] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report studies of hydration dynamics at the surface of the enzyme protein bovine pancreatic alpha-chymotrypsin. The probe is the well known 1-anilinonaphthalene-8-sulfonate, which binds selectively in the native state of the protein, not the molten globule, as shown by x-ray crystallography. With femtosecond time resolution, we examined the hydration dynamics at two pHs, when the protein is physiologically in the inactive state (pH 3.6) or the active state (pH 6.7); the global structure and the binding site remain the same. The hydration correlation function, C(t), whose decay is governed by the rotational and translational motions of water molecules at the site, shows the behavior observed in this laboratory for other proteins, Subtilisin Carlsberg and Monellin, using the intrinsic amino acid tryptophan as a probe for surface hydration. However, the time scales and amplitudes vary drastically at the two pHs. For the inactive protein state, C(t) decays with an ultrafast component, close to bulk-type behavior, but 50% of the C(t) decays at a much slower rate, tau = 43 ps. In contrast, for the active state, the ultrafast component becomes dominant (90%) and the slow component changes to a faster decay, tau = 28 ps. These results indicate that in the active state water molecules in the hydration layer around the site have a high degree of mobility, whereas in the inactive state the water is more rigidly structured. For the substrate-enzyme complex, the function and dynamics at the probe site are correlated, and the relevance to the enzymatic action is clear.
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Affiliation(s)
- Samir Kumar Pal
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena 91125, USA
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Weeks JD. Connecting local structure to interface formation: a molecular scale van der Waals theory of nonuniform liquids. Annu Rev Phys Chem 2002; 53:533-62. [PMID: 11972018 DOI: 10.1146/annurev.physchem.53.100201.133929] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.
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Affiliation(s)
- John D Weeks
- Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
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Makarov V, Pettitt BM, Feig M. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res 2002; 35:376-84. [PMID: 12069622 DOI: 10.1021/ar0100273] [Citation(s) in RCA: 292] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many theoretical, computational, and experimental techniques recently have been successfully used for description of the solvent distribution around macromolecules. In this Account, we consider recent developments in the areas of protein and nucleic acid solvation and hydration as seen by experiment, theory, and simulations. We find that in most cases not only the general phenomena of solvation but even local hydration patterns are more accurately discussed in the context of water distributions rather than individual molecules of water. While a few localized or high-residency waters are often associated with macromolecules in solution (or crystals from aqueous liquors), these are readily and accurately included in this more general description. The goal of this Account is to review the theoretical models used for the description of the interfacial solvent structure on the border near DNA and protein molecules. In particular, we hope to highlight the progress in this field over the past five years with a focus on comparison of simulation and experimental results.
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Affiliation(s)
- Vladimir Makarov
- Department of Chemistry, University of Houston, Houston, Texas 77204-564, USA
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Massi F, Straub JE. Probing the origins of increased activity of the E22Q "Dutch" mutant Alzheimer's beta-amyloid peptide. Biophys J 2001; 81:697-709. [PMID: 11463618 PMCID: PMC1301546 DOI: 10.1016/s0006-3495(01)75734-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The amyloid peptide congener A beta(10--35)-NH(2) is simulated in an aqueous environment in both the wild type (WT) and E22Q "Dutch" mutant forms. The origin of the noted increase in deposition activity resulting from the Dutch mutation is investigated. Multiple nanosecond time scale molecular dynamics trajectories were performed and analyzed using a variety of measures of the peptide's average structure, hydration, conformational fluctuations, and dynamics. The results of the study support the conclusions that 1) the E22Q mutant and WT peptide are both stable in "collapsed coil" conformations consistent with the WT structure of, J. Struct. Biol. 130:130--141); 2) the E22Q peptide is more flexible in solution, supporting early claims that its equilibrium structural fluctuations are larger than those of the WT peptide; and 3) the local E22Q mutation leads to a change in the first solvation layer in the region of the peptide's "hydrophobic patch," resulting in a more hydrophobic solvation of the mutant peptide. The simulation results support the view that the noted increase in activity due to the Dutch mutation results from an enhancement of the desolvation process that is an essential step in the aggregation of the peptide.
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Affiliation(s)
- F Massi
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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