1
|
Eberhardt J, Forli S. WaterKit: Thermodynamic Profiling of Protein Hydration Sites. J Chem Theory Comput 2023; 19:2535-2556. [PMID: 37094087 PMCID: PMC10732097 DOI: 10.1021/acs.jctc.2c01087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Water desolvation is one of the key components of the free energy of binding of small molecules to their receptors. Thus, understanding the energetic balance of solvation and desolvation resulting from individual water molecules can be crucial when estimating ligand binding, especially when evaluating different molecules and poses as done in High-Throughput Virtual Screening (HTVS). Over the most recent decades, several methods were developed to tackle this problem, ranging from fast approximate methods (usually empirical functions using either discrete atom-atom pairwise interactions or continuum solvent models) to more computationally expensive and accurate ones, mostly based on Molecular Dynamics (MD) simulations, such as Grid Inhomogeneous Solvation Theory (GIST) or Double Decoupling. On one hand, MD-based methods are prohibitive to use in HTVS to estimate the role of waters on the fly for each ligand. On the other hand, fast and approximate methods show an unsatisfactory level of accuracy, with low agreement with results obtained with the more expensive methods. Here we introduce WaterKit, a new grid-based sampling method with explicit water molecules to calculate thermodynamic properties using the GIST method. Our results show that the discrete placement of water molecules is successful in reproducing the position of crystallographic waters with very high accuracy, as well as providing thermodynamic estimates with accuracy comparable to more expensive MD simulations. Unlike these methods, WaterKit can be used to analyze specific regions on the protein surface, (such as the binding site of a receptor), without having to hydrate and simulate the whole receptor structure. The results show the feasibility of a general and fast method to compute thermodynamic properties of water molecules, making it well-suited to be integrated in high-throughput pipelines such as molecular docking.
Collapse
Affiliation(s)
- Jerome Eberhardt
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Prediction of local thermodynamics of water in and around endo-functionalized molecular tube receptors: An approach using grid inhomogeneous solvation theory. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Zhou H, Li Y, Yang Y, Liu S, Yang Z. Lanosterol reduces the aggregation propensity of ultraviolet-damaged human γD-crystallins: a molecular dynamics study. Phys Chem Chem Phys 2021; 23:13696-13704. [PMID: 34128026 DOI: 10.1039/d1cp00132a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ultraviolet (UV) radiation-induced oxidation of tryptophan (Trp) to kynurenine (KN) (TRP > KN) in human γD-crystallins (HγD-Crys) promotes the conversion of proteins into partially unfolded species that act as important precursors for sequential large-scale aggregation. Herein, we report that lanosterol shows protective activity to the structure of the TRP > KN mutant HγD-Crys, particularly its N-terminal domain (N-td), by using all-atom molecular dynamics simulations. The Trp68 > KN mutation significantly destabilizes the originally highly stable "Tyr55-Trp68-Tyr62" cluster, thereby causing loop2, where the mutation occurs, to become very flexible. The large fluctuation of loop2 induces cracks, which appear on the protein surface, resulting in the intrusion of water molecules into the hydrophobic core of the N-td. This event eventually triggers the unfolding of the N-td. However, lanosterol can suppress the large fluctuation of loop2 to protect the structural stability of the mutant N-td, thus reducing the aggregation propensity of the TRP > KN mutant HγD-Crys. This structure protective activity of lanosterol arises from its capability to preferentially bind to the hydrophobic regions near loop2. Thus, lanosterol acts as a "water blocker" to prevent the invasion of solvent molecules into the hydrophobic core. These findings provide some valuable insights into the development of potential lanosterol-based drugs for cataract prevention and treatment.
Collapse
Affiliation(s)
- Hong Zhou
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Youyun Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Ying Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Shengtang Liu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Zaixing Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| |
Collapse
|
5
|
Computational study of pomegranate peel extract polyphenols as potential inhibitors of SARS-CoV-2 virus internalization. Mol Cell Biochem 2020; 476:1179-1193. [PMID: 33200379 PMCID: PMC7668668 DOI: 10.1007/s11010-020-03981-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/06/2020] [Indexed: 01/02/2023]
Abstract
The search for effective coronavirus disease (COVID-19) therapy has attracted a great deal of scientific interest due to its unprecedented health care system overload worldwide. We have carried out a study to investigate the in silico effects of the most abundant pomegranate peel extract constituents on the multi-step process of serious acute respiratory syndrome coronavirus 2 (SARS-CoV-2) internalization in the host cells. Binding affinities and interactions of ellagic acid, gallic acid, punicalagin and punicalin were studied on four selected protein targets with a significant and confirmed role in the process of the entry of virus into a host cell. The protein targets used in this study were: SARS-CoV-2 spike glycoprotein, angiotensin-converting enzyme 2, furin and transmembrane serine protease 2. The results showed that the constituents of pomegranate peel extracts, namely punicalagin and punicalin had very promising potential for significant interactions with the selected protein targets and were therefore deemed good candidates for further in vitro and in vivo evaluation.
Collapse
|
6
|
Setny P. Conserved internal hydration motifs in protein kinases. Proteins 2020; 88:1578-1591. [DOI: 10.1002/prot.25977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/18/2020] [Accepted: 07/05/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Piotr Setny
- Centre of New Technologies University of Warsaw Warsaw Poland
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Projective mechanisms subtending real world phenomena wipe away cause effect relationships. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 151:1-13. [PMID: 31838044 DOI: 10.1016/j.pbiomolbio.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/16/2019] [Accepted: 12/10/2019] [Indexed: 01/11/2023]
Abstract
Causal relationships lie at the very core of scientific description of biophysical phenomena. Nevertheless, observable facts involving changes in system shape, dimension and symmetry may elude simple cause and effect inductive explanations. Here we argue that numerous physical and biological phenomena such as chaotic dynamics, symmetry breaking, long-range collisionless neural interactions, zero-valued energy singularities, and particle/wave duality can be accounted for in terms of purely topological mechanisms devoid of causality. We illustrate how simple topological claims, seemingly far away from scientific inquiry (e.g., "given at least some wind on Earth, there must at all times be a cyclone or anticyclone somewhere"; "if one stirs to dissolve a lump of sugar in a cup of coffee, it appears there is always a point without motion"; "at any moment, there is always a pair of antipodal points on the Earth's surface with equal temperatures and barometric pressures") reflect the action of non-causal topological rules. To do so, we introduce some fundamental topological tools and illustrate how phenomena such as double slit experiments, cellular mechanisms and some aspects of brain function can be explained in terms of geometric projections and mappings, rather than local physical effects. We conclude that unavoidable, passive, spontaneous topological modifications may lead to novel functional biophysical features, independent of exerted physical forces, thermodynamic constraints, temporal correlations and probabilistic a priori knowledge of previous cases.
Collapse
|
9
|
Arturo T. Towards dewetting monoclonal antibodies for therapeutical purposes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:153-159. [PMID: 31525385 DOI: 10.1016/j.pbiomolbio.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/22/2019] [Accepted: 09/07/2019] [Indexed: 12/30/2022]
Abstract
Dewetting transition - a concept borrowed from fluid mechanics - is a physiological process that takes place inside the hydrophobic pores of ion channels. This transient phenomenon causes a metastable state that forbids water molecules to cross microscopic receptor cavities. This leads to a decreased conductance, a closure of the pore and, subsequently, severe impairment of cellular performance. We suggest that artificially-provoked dewetting transition in ion channel hydrophobic pores might stand for a molecular candidate to erase detrimental organisms, such as viruses, bacteria, and cancer cells. We describe a novel type of high-affinity monoclonal antibody, that: a) targets specific trans-membrane receptor structures of harmful or redundant cells; b) is equipped with lipophilic and/or hydrophobic fragments that prevent physiological water flow inside ion channels. Therefore, we achieve an artificial dewetting transition inside receptor cavities, that causes discontinuity within transmembrane ionic flows, channel blockage, and subsequent damage of morbid cells. As an example, we describe dewetting monoclonal antibodies that target the M2 channel of the Influenza A virus: they might prevent water from entering pores thus leading to virion impairment.
Collapse
Affiliation(s)
- Tozzi Arturo
- Center for Nonlinear Science, Department of Physics, University of North Texas, 1155 Union Circle, #311427, Denton, TX, 76203-5017, USA.
| |
Collapse
|
10
|
Collective Transformation of Water between Hyperactive Antifreeze Proteins: RiAFPs. CRYSTALS 2019. [DOI: 10.3390/cryst9040188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We demonstrate, by molecular dynamics simulations, that water confined between a pair of insect hyperactive antifreeze proteins from the longhorn beetle Rhagium inquisitor is discontinuously expelled as the two proteins approach each other at a certain distance. The extensive striped hydrophobic–hydrophilic pattern on the surface, comprising arrays of threonine residues, enables water to form three independent ice channels through the assistance of hydroxyl groups, even at 300 K. The transformation is reminiscent of a freezing–melting transition rather than a drying transition and governs the stable protein–protein separation in the evaluation of the potential of mean force. The collectivity of water penetration or expulsion and the hysteresis in the time scale of ten nanoseconds predict a potential first-order phase transition at the limit of infinite size and provide a new framework for the water-mediated interaction between solutes.
Collapse
|
11
|
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
| |
Collapse
|
12
|
Pantsar T, Poso A. Binding Affinity via Docking: Fact and Fiction. Molecules 2018; 23:molecules23081899. [PMID: 30061498 PMCID: PMC6222344 DOI: 10.3390/molecules23081899] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/03/2023] Open
Abstract
In 1982, Kuntz et al. published an article with the title “A Geometric Approach to Macromolecule-Ligand Interactions”, where they described a method “to explore geometrically feasible alignment of ligands and receptors of known structure”. Since then, small molecule docking has been employed as a fast way to estimate the binding pose of a given compound within a specific target protein and also to predict binding affinity. Remarkably, the first docking method suggested by Kuntz and colleagues aimed to predict binding poses but very little was specified about binding affinity. This raises the question as to whether docking is the right tool to estimate binding affinity. The short answer is no, and this has been concluded in several comprehensive analyses. However, in this opinion paper we discuss several critical aspects that need to be reconsidered before a reliable binding affinity prediction through docking is realistic. These are not the only issues that need to be considered, but they are perhaps the most critical ones. We also consider that in spite of the huge efforts to enhance scoring functions, the accuracy of binding affinity predictions is perhaps only as good as it was 10–20 years ago. There are several underlying reasons for this poor performance and these are analyzed. In particular, we focus on the role of the solvent (water), the poor description of H-bonding and the lack of the systems’ true dynamics. We hope to provide readers with potential insights and tools to overcome the challenging issues related to binding affinity prediction via docking.
Collapse
Affiliation(s)
- Tatu Pantsar
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Sullivan MR, Yao W, Tang D, Ashbaugh HS, Gibb BC. The Thermodynamics of Anion Complexation to Nonpolar Pockets. J Phys Chem B 2018; 122:1702-1713. [PMID: 29373793 PMCID: PMC10668596 DOI: 10.1021/acs.jpcb.7b12259] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The interactions between nonpolar surfaces and polarizable anions lie in a gray area between the hydrophobic and Hofmeister effects. To assess the affinity of these interactions, NMR and ITC were used to probe the thermodynamics of eight anions binding to four different hosts whose pockets each consist primarily of hydrocarbon. Two classes of host were examined: cavitands and cyclodextrins. For all hosts, anion affinity was found to follow the Hofmeister series, with associations ranging from 1.6-5.7 kcal mol-1. Despite the fact that cavitand hosts 1 and 2 possess intrinsic negative electrostatic fields, it was determined that these more enveloping hosts generally bound anions more strongly. The observation that the four hosts each possess specific anion affinities that cannot be readily explained by their structures, points to the importance of counter cations and the solvation of the "empty" hosts, free guests, and host-guest complexes, in defining the affinity.
Collapse
Affiliation(s)
- Matthew R. Sullivan
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Wei Yao
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Du Tang
- Department of Chemical and Biomolecular Engineering, 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
| |
Collapse
|
15
|
Bai L, Jang J, Zhang Z, Jang J. Dewetting transition of water confined between atomically rough surfaces: A lattice gas Monte Carlo simulation study. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
16
|
Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. Nat Chem 2017; 10:8-16. [DOI: 10.1038/nchem.2894] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/20/2017] [Indexed: 12/19/2022]
|
17
|
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.
Collapse
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;
| |
Collapse
|
18
|
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
| |
Collapse
|
19
|
AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking. Molecules 2016; 21:molecules21111604. [PMID: 27886114 PMCID: PMC6274120 DOI: 10.3390/molecules21111604] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 11/27/2022] Open
Abstract
Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.
Collapse
|
20
|
Inuki S, Aiba T, Hirata N, Ichihara O, Yoshidome D, Kita S, Maenaka K, Fukase K, Fujimoto Y. Isolated Polar Amino Acid Residues Modulate Lipid Binding in the Large Hydrophobic Cavity of CD1d. ACS Chem Biol 2016; 11:3132-3139. [PMID: 27648599 DOI: 10.1021/acschembio.6b00674] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The CD1d protein is a nonpolymorphic MHC class I-like protein that controls the activation of natural killer T (NKT) cells through the presentation of self- and foreign-lipid ligands, glycolipids, or phospholipids, leading to the secretion of various cytokines. The CD1d contains a large hydrophobic lipid binding pocket: the A' pocket of CD1d, which recognizes hydrophobic moieties of the ligands, such as long fatty acyl chains. Although lipid-protein interactions typically rely on hydrophobic interactions between lipid chains and the hydrophobic sites of proteins, we showed that the small polar regions located deep inside the hydrophobic A' pocket could be used for the modulation of the lipid binding. A series of the ligands, α-galactosyl ceramide (α-GalCer) derivatives containing polar groups in the acyl chain, was synthesized, and the structure-activity relationship studies demonstrated that simple modification from a methylene to an amide group in the long fatty acyl chain, when introduced at optimal positions, enhanced the CD1d recognition of the glycolipid ligands. Formation of hydrogen bonds between the amide group and the polar residues was supported by molecular dynamics (MD) simulations and WaterMap calculations. The computational studies suggest that localized hydrating water molecules may play an important role in the ligand recognition. Here, the results showed that confined polar residues in the large hydrophobic lipid binding pockets of the proteins could be potential targets to modulate the affinity for its ligands.
Collapse
Affiliation(s)
- Shinsuke Inuki
- Graduate
School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Toshihiko Aiba
- Graduate
School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Natsumi Hirata
- Graduate
School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Osamu Ichihara
- Schrödinger K. K., 17F Marunouchi
Trust Tower North, 1-8-1 Marunouchi Chiyoda-ku, Tokyo 100-0005, Japan
| | - Daisuke Yoshidome
- Schrödinger K. K., 17F Marunouchi
Trust Tower North, 1-8-1 Marunouchi Chiyoda-ku, Tokyo 100-0005, Japan
| | - Shunsuke Kita
- Graduate
School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Katsumi Maenaka
- Graduate
School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Koichi Fukase
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yukari Fujimoto
- Graduate
School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| |
Collapse
|
21
|
Schneider S, Provasi D, Filizola M. How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways. Biochemistry 2016; 55:6456-6466. [PMID: 27778501 DOI: 10.1021/acs.biochem.6b00948] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Substantial attention has recently been devoted to G protein-biased agonism of the μ-opioid receptor (MOR) as an ideal new mechanism for the design of analgesics devoid of serious side effects. However, designing opioids with appropriate efficacy and bias is challenging because it requires an understanding of the ligand binding process and of the allosteric modulation of the receptor. Here, we investigated these phenomena for TRV-130, a G protein-biased MOR small-molecule agonist that has been shown to exert analgesia with less respiratory depression and constipation than morphine and that is currently being evaluated in human clinical trials for acute pain management. Specifically, we carried out multimicrosecond, all-atom molecular dynamics (MD) simulations of the binding of this ligand to the activated MOR crystal structure. Analysis of >50 μs of these MD simulations provides insights into the energetically preferred binding pathway of TRV-130 and its stable pose at the orthosteric binding site of MOR. Information transfer from the TRV-130 binding pocket to the intracellular region of the receptor was also analyzed, and was compared to a similar analysis carried out on the receptor bound to the classical unbiased agonist morphine. Taken together, these studies lead to a series of testable hypotheses of ligand-receptor interactions that are expected to inform the structure-based design of improved opioid analgesics.
Collapse
Affiliation(s)
- Sebastian Schneider
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| |
Collapse
|
22
|
Zhu Z, Sheng N, Fang H, Wan R. Colored spectrum characteristics of thermal noise on the molecular scale. Phys Chem Chem Phys 2016; 18:30189-30195. [PMID: 27779258 DOI: 10.1039/c6cp04433f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Thermal noise is of fundamental importance to many processes. Traditionally, thermal noise has been treated as white noise on the macroscopic scale. Using molecular dynamics simulations and power spectrum analysis, we show that the thermal noise of solute molecules in water is non-white on the molecular scale, which is in contrast to the conventional theory. In the frequency domain from 2 × 1011 Hz to 1013 Hz, the power spectrum of thermal noise for polar solute molecules resembles the spectrum of 1/f noise. The power spectrum of thermal noise for non-polar solute molecules deviates only slightly from the spectrum of white noise. The key to this phenomenon is the existence of hydrogen bonds between polar solute molecules and solvent water molecules. Furthermore, for polar solute molecules, the degree of power spectrum deviation from that of white noise is associated with the average lifetime of the hydrogen bonds between the solute and the solvent molecules.
Collapse
Affiliation(s)
- Zhi Zhu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Sheng
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
| | - Rongzheng Wan
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
| |
Collapse
|
23
|
Zhou S, Sun H, Cheng LT, Dzubiella J, Li B, McCammon JA. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations. J Chem Phys 2016; 145:054114. [PMID: 27497546 PMCID: PMC4975753 DOI: 10.1063/1.4959971] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/05/2016] [Indexed: 12/29/2022] Open
Abstract
Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of fluctuations into the VISM and understanding the impact of interfacial fluctuations on biomolecular solvation with an implicit-solvent approach.
Collapse
Affiliation(s)
- Shenggao Zhou
- Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Jiangsu, Suzhou 215006, China
| | - Hui Sun
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, USA
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, USA
| | - Joachim Dzubiella
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany and Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Bo Li
- Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, La Jolla, California 92093-0112, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA
| |
Collapse
|
24
|
Changes in hydration structure are necessary for collective motions of a multi-domain protein. Sci Rep 2016; 6:26302. [PMID: 27193111 PMCID: PMC4872039 DOI: 10.1038/srep26302] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/25/2016] [Indexed: 01/27/2023] Open
Abstract
Conformational motions of proteins are necessary for their functions. To date, experimental studies measuring conformational fluctuations of a whole protein structure have revealed that water molecules hydrating proteins are necessary to induce protein functional motions. However, the underlying microscopic mechanism behind such regulation remains unsolved. To clarify the mechanism, multi-domain proteins are good targets because it is obvious that water molecules between domains play an important role in domain motions. Here, we show how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, through molecular dynamics simulation supported by structural analyses and biochemical experiments. We first identified collective domain motions of the protein, which open/close an active-site cleft between domains. The analyses on changes in hydration structure revealed that changes in local hydration in the depth of the cleft are necessary for the domain motion and vice versa. In particular, ‘wetting’/‘drying’ at a hydrophobic pocket and ‘adsorption’/‘dissociation’ of a few water molecules at a hydrophilic crevice in the cleft were induced by dynamic rearrangements of hydrogen-bond networks, and worked as a switch for the domain motions. Our results microscopically demonstrated the importance of hydrogen-bond networks of water molecules in understanding energy landscapes of protein motions.
Collapse
|
25
|
Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
Collapse
Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
| |
Collapse
|
26
|
Tozzi A, Flå T, Peters JF. Building a minimum frustration framework for brain functions over long time scales. J Neurosci Res 2016; 94:702-16. [PMID: 27114266 DOI: 10.1002/jnr.23748] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/14/2016] [Accepted: 03/28/2016] [Indexed: 01/02/2023]
Abstract
The minimum frustration principle (MFP) is a computational approach stating that, over the long time scales of evolution, proteins' free energy decreases more than expected by thermodynamical constraints as their amino acids assume conformations progressively closer to the lowest energetic state. This Review shows that this general principle, borrowed from protein folding dynamics, can also be fruitfully applied to nervous function. Highlighting the foremost role of energetic requirements, macromolecular dynamics, and above all intertwined time scales in brain activity, the MFP elucidates a wide range of mental processes from sensations to memory retrieval. Brain functions are compared with trajectories that, over long nervous time scales, are attracted toward the low-energy bottom of funnel-like structures characterized by both robustness and plasticity. We discuss how the principle, derived explicitly from evolution and selection of a funneling structure from microdynamics of contacts, is unlike other brain models equipped with energy landscapes, such as the Bayesian and free energy principles and the Hopfield networks. In summary, we make available a novel approach to brain function cast in a biologically informed fashion, with the potential to be operationalized and assessed empirically. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Arturo Tozzi
- Center for Nonlinear Science, University of North Texas, Denton, Texas
| | - Tor Flå
- Department of Mathematics and Statistics, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, Tromsø, Norway
| | - James F Peters
- Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Mathematics, Adıyaman University, Adıyaman, Turkey
| |
Collapse
|
27
|
Martin L, Bilek MM, Weiss AS, Kuyucak S. Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus 2016; 6:20150045. [PMID: 26855748 PMCID: PMC4686237 DOI: 10.1098/rsfs.2015.0045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide-surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.
Collapse
Affiliation(s)
- Lewis Martin
- Department of Applied Physics, University of Sydney, Sydney, New South Wales, Australia
| | - Marcela M. Bilek
- Department of Applied Physics, University of Sydney, Sydney, New South Wales, Australia
| | - Anthony S. Weiss
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
- Department of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
- Bosch Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Serdar Kuyucak
- Department of Applied Physics, University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
28
|
Liu J, Yang Z, Li H, Gu Z, Garate JA, Zhou R. Dewetting transition assisted clearance of (NFGAILS) amyloid fibrils from cell membranes by graphene. J Chem Phys 2015; 141:22D520. [PMID: 25494791 DOI: 10.1063/1.4901113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clearance of partially ordered oligomers and monomers deposited on cell membrane surfaces is believed to be an effective route to alleviate many potential protein conformational diseases (PCDs). With large-scale all-atom molecular dynamics simulations, here we show that graphene nanosheets can easily and quickly win a competitive adsorption of human islet amyloid polypeptides (hIAPP22-28) NFGAILS and associated fibrils against cell membrane, due to graphene's unique two-dimensional, highly hydrophobic surface with its all-sp(2) hybrid structure. A nanoscale dewetting transition was observed at the interfacial region between the fibril (originally deposited on the membrane) and the graphene nanosheet, which significantly assisted the adsorption of fibrils onto graphene from the membrane. The π-π stacking interaction between Phe23 and graphene played a crucial role, providing the driving force for the adsorption at the graphene surface. This study renders new insight towards the importance of water during the interactions between amyloid peptides, the phospholipidic membrane, and graphene, which might shed some light on future developments of graphene-based nanomedicine for preventing/curing PCDs like type II diabetes mellitus.
Collapse
Affiliation(s)
- Jiajia Liu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Haotian Li
- Bio-X Lab, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Zonglin Gu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | | | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| |
Collapse
|
29
|
Altabet YE, Debenedetti PG. The role of material flexibility on the drying transition of water between hydrophobic objects: a thermodynamic analysis. J Chem Phys 2015; 141:18C531. [PMID: 25399196 DOI: 10.1063/1.4898366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Liquid water confined between hydrophobic objects of sufficient size becomes metastable with respect to its vapor at separations smaller than a critical drying distance. Macroscopic thermodynamic arguments predicting this distance have been restricted to the limit of perfectly rigid confining materials. However, no material is perfectly rigid and it is of interest to account for this fact in the thermodynamic analysis. We present a theory that combines the current macroscopic theory with the thermodynamics of elasticity to derive an expression for the critical drying distance for liquids confined between flexible materials. The resulting expression is the sum of the well-known drying distance for perfectly rigid confining materials and a new term that accounts for flexibility. Thermodynamic arguments show that this new term is necessarily positive, meaning that flexibility increases the critical drying distance. To study the expected magnitude and scaling behavior of the flexible term, we consider the specific case of water and present an example of drying between thin square elastic plates that are simply supported along two opposite edges and free at the remaining two. We find that the flexible term can be the same order of magnitude or greater than the rigid solution for materials of biological interest at ambient conditions. In addition, we find that when the rigid solution scales with the characteristic size of the immersed objects, the flexible term is independent of size and vice versa. Thus, the scaling behavior of the overall drying distance will depend on the relative weights of the rigid and flexible contributions.
Collapse
Affiliation(s)
- Y Elia Altabet
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
30
|
Sim AYL, Verma C. How does a hydrocarbon staple affect peptide hydrophobicity? J Comput Chem 2015; 36:773-84. [DOI: 10.1002/jcc.23859] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/06/2015] [Accepted: 01/19/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Adelene Y. L. Sim
- Bioinformatics Institute (A*STAR); 30 Biopolis Street #07-01 Matrix 138671 Singapore
| | - Chandra Verma
- Bioinformatics Institute (A*STAR); 30 Biopolis Street #07-01 Matrix 138671 Singapore
- School of Biological Sciences, Nanyang Technological University; 60 Nanyang Drive 637551 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543
| |
Collapse
|
31
|
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]
|
32
|
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.
Collapse
Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
| | | | | |
Collapse
|
33
|
Michel J, Henchman RH, Gerogiokas G, Southey MWY, Mazanetz MP, Law RJ. Evaluation of Host–Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory. J Chem Theory Comput 2014; 10:4055-68. [DOI: 10.1021/ct500368p] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Julien Michel
- EaStCHEM
School of Chemistry, Joseph Black Building, King’s Buildings, Edinburgh EH9 3JJ, United Kingdom
| | - Richard H. Henchman
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Georgios Gerogiokas
- EaStCHEM
School of Chemistry, Joseph Black Building, King’s Buildings, Edinburgh EH9 3JJ, United Kingdom
| | - Michelle W. Y. Southey
- Evotec (U.K.) Limited, Innovation
Drive 114 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Michael P. Mazanetz
- Evotec (U.K.) Limited, Innovation
Drive 114 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Richard J. Law
- Evotec (U.K.) Limited, Innovation
Drive 114 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| |
Collapse
|
34
|
Abstract
Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg(2+) ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg(2+) or Na(+), benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg(2+) bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.
Collapse
Affiliation(s)
- Weifeng Li
- Institute of Quantitative Biology and Medicine, School for Radiological & Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, China 215123
| | | | | | | |
Collapse
|
35
|
Guo Z, Streu K, Krilov G, Mohanty U. Probing the Origin of Structural Stability of Single and Double Stapled p53 Peptide Analogs Bound to MDM2. Chem Biol Drug Des 2014; 83:631-42. [DOI: 10.1111/cbdd.12284] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/06/2013] [Accepted: 01/06/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Zuojun Guo
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
- Genomics Institute of the Novartis Research Foundation; 10675 John Jay Hopkins Dr. San Diego CA 92121 USA
| | - Kristina Streu
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Goran Krilov
- Schrödinger, Inc.; 120 W 45th Street, 17th Fl. New York NY 10036 USA
| | - Udayan Mohanty
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| |
Collapse
|
36
|
Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput 2014; 10:1454-1467. [PMID: 24803864 PMCID: PMC3985794 DOI: 10.1021/ct401058w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Indexed: 12/26/2022]
Abstract
We incorporate the Poisson-Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also apply our VISM-PB theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host-guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host-guest system. We finally discuss several issues for further improvement of VISM.
Collapse
Affiliation(s)
- Shenggao Zhou
- Department
of Mathematics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Li-Tien Cheng
- Department
of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Joachim Dzubiella
- Soft
Matter and Functional Materials, Helmholtz-Center Berlin, 14109 Berlin,
Germany, and Physics Department, Humboldt-University
of Berlin, 12489 Berlin, Germany
| | - Bo Li
- Department
of Mathematics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, Department of Pharmacology, Center
for Theoretical Biological Physics, and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, United States
| |
Collapse
|
37
|
Nguyen CN, Cruz A, Gilson MK, Kurtzman T. Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. J Chem Theory Comput 2014; 10:2769-2780. [PMID: 25018673 PMCID: PMC4089914 DOI: 10.1021/ct401110x] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 01/04/2023]
Abstract
Water molecules in the active site of an enzyme occupy a complex, heterogeneous environment, and the thermodynamic properties of active-site water are functions of position. As a consequence, it is thought that an enzyme inhibitor can gain affinity by extending into a region occupied by unfavorable water or lose affinity by displacing water from a region where it was relatively stable. Recent advances in the characterization of binding-site water, based on the analysis of molecular simulations with explicit water molecules, have focused largely on simplified representations of water as occupying well-defined hydration sites. Our grid-based treatment of hydration, GIST, offers a more complete picture of the complex distributions of water properties, but it has not yet been applied to proteins. This first application of GIST to protein-ligand modeling, for the case of Coagulation Factor Xa, shows that ligand scoring functions based on GIST perform at least as well as scoring functions based on a hydration-site approach (HSA), when applied to exactly the same simulation data. Interestingly, the displacement of energetically unfavorable water emerges as the dominant factor in the fitted scoring functions, for both GIST and HSA methods, while water entropy plays a secondary role, at least in the present context.
Collapse
Affiliation(s)
- Crystal N Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Anthony Cruz
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Blvd. West, Bronx, New York 10468, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Blvd. West, Bronx, New York 10468, United States
| |
Collapse
|
38
|
Guo C, Luo Y, Zhou R, Wei G. Triphenylalanine peptides self-assemble into nanospheres and nanorods that are different from the nanovesicles and nanotubes formed by diphenylalanine peptides. NANOSCALE 2014; 6:2800-2811. [PMID: 24468750 DOI: 10.1039/c3nr02505e] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding the nature of the self-assembly of peptide nanostructures at the molecular level is critical for rational design of functional bio-nanomaterials. Recent experimental studies have shown that triphenylalanine(FFF)-based peptides can self-assemble into solid plate-like nanostructures and nanospheres, which are different from the hollow nanovesicles and nanotubes formed by diphenylalanine(FF)-based peptides. In spite of extensive studies, the assembly mechanism and the molecular basis for the structural differences between FFF and FF nanostructures remain poorly understood. In this work, we first investigate the assembly process and the structural features of FFF nanostructures using coarse-grained molecular dynamics simulations, and then compare them with FF nanostructures. We find that FFF peptides spontaneously assemble into solid nanometer-sized nanospheres and nanorods with substantial β-sheet contents, consistent with the structural properties of hundred-nanometer-sized FFF nano-plates characterized by FT-IR spectroscopy. Distinct from the formation mechanism of water-filled FF nanovesicles and nanotubes reported in our previous study, intermediate bilayers are not observed during the self-assembly process of FFF nanospheres and nanorods. The peptides in FFF nanostructures are predominantly anti-parallel-aligned, which can form larger sizes of β-sheet-like structures than the FF counterparts. In contrast, FF peptides exhibit lipid-like assembly behavior and assemble into bilayered nanostructures. Furthermore, although the self-assembly of FF and FFF peptides is mostly driven by side chain-side chain (SC-SC) aromatic stacking interactions, the main chain-main chain (MC-MC) interactions also play an important role in the formation of fine structures of the assemblies. The delicate interplay between MC-MC and SC-SC interactions results in the different nanostructures formed by the two peptides. These findings provide new insights into the structure and self-assembly pathway of di-/tri-phenylalanine peptide assemblies, which might be helpful for the design of bioinspired nanostructures.
Collapse
Affiliation(s)
- Cong Guo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), 220 Handan Road, Shanghai, 200433, China
| | | | | | | |
Collapse
|
39
|
Yang Z, Xia Z, Huynh T, King JA, Zhou R. Dissecting the contributions of β-hairpin tyrosine pairs to the folding and stability of long-lived human γD-crystallins. NANOSCALE 2014; 6:1797-807. [PMID: 24352614 PMCID: PMC3976203 DOI: 10.1039/c3nr03782g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ultraviolet-radiation-induced damage to and aggregation of human lens crystallin proteins are thought to be a significant pathway to age-related cataract. The aromatic residues within the duplicated Greek key domains of γ- and β-crystallins are the main ultraviolet absorbers and are susceptible to direct and indirect ultraviolet damage. The previous site-directed mutagenesis studies have revealed a striking difference for two highly conserved homologous β-hairpin Tyr pairs, at the N-terminal domain (N-td) and C-terminal domain (C-td), respectively, in their contribution to the overall stability of HγD-Crys, but why they behave so differently still remains a mystery. In this paper, we systematically investigated the underlying molecular mechanism and detailed contributions of these two Tyr pairs with large scale molecular dynamics simulations. A series of different tyrosine-to-alanine pair(s) substitutions were performed in either the N-td, the C-td, or both. Our results suggest that the Y45A/Y50A pair substitution in the N-td mainly affects the stability of the N-td itself, while the Y133A/Y138A pair substitution in the C-td leads to a more cooperative unfolding of both N-td and C-td. The stability of motif 2 in the N-td is mainly determined by the interdomain interface, while motif 1 in the N-td or motifs 3 and 4 in the C-td are mainly stabilized by the intradomain hydrophobic core. The damage to any tyrosine pair(s) can directly introduce some apparent water leakage to the hydrophobic core at the interface, which in turn causes a serious loss in the stability of the N-td. However, for the C-td substitutions, it may further impair the stable "sandwich-like" Y133-R167-Y138 cluster (through cation-π interactions) in the wild-type, thus causing the loop regions near the residue A138 to undergo large fluctuations, which in turn results in the intrusion of water into the hydrophobic core of the C-td and induces the C-td to lose its stability. These findings help resolve the "mystery" on why these two Tyr pairs display such a striking difference in their contributions to the overall protein stability despite their highly homologous nature.
Collapse
Affiliation(s)
- Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X & Collaborative Innovation Center of Suzhou Nano Science and Technology, Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China.
| | | | | | | | | |
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Stephen F Martin
- Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
| | | |
Collapse
|
41
|
UV-radiation induced disruption of dry-cavities in human γD-crystallin results in decreased stability and faster unfolding. Sci Rep 2013; 3:1560. [PMID: 23532089 PMCID: PMC3609025 DOI: 10.1038/srep01560] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022] Open
Abstract
Age-onset cataracts are believed to be expedited by the accumulation of UV-damaged human γD-crystallins in the eye lens. Here we show with molecular dynamics simulations that the stability of γD-crystallin is greatly reduced by the conversion of tryptophan to kynurenine due to UV-radiation, consistent with previous experimental evidences. Furthermore, our atomic-detailed results reveal that kynurenine attracts more waters and other polar sidechains due to its additional amino and carbonyl groups on the damaged tryptophan sidechain, thus breaching the integrity of nearby dry center regions formed by the two Greek key motifs in each domain. The damaged tryptophan residues cause large fluctuations in the Tyr-Trp-Tyr sandwich-like hydrophobic clusters, which in turn break crucial hydrogen-bonds bridging two β-strands in the Greek key motifs at the “tyrosine corner”. Our findings may provide new insights for understanding of the molecular mechanism of the initial stages of UV-induced cataractogenesis.
Collapse
|
42
|
Affiliation(s)
- Riccardo Baron
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820;
| | - J. Andrew McCammon
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0365;
| |
Collapse
|
43
|
Kang SG, Huynh T, Xia Z, Zhang Y, Fang H, Wei G, Zhou R. Hydrophobic interaction drives surface-assisted epitaxial assembly of amyloid-like peptides. J Am Chem Soc 2013; 135:3150-7. [PMID: 23360070 DOI: 10.1021/ja310989u] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The molecular mechanism of epitaxial fibril formation has been investigated for GAV-9 (NH(3)(+)-VGGAVVAGV-CONH(2)), an amyloid-like peptide extracted from a consensus sequence of amyloidogenic proteins, which assembles with very different morphologies, "upright" on mica and "flat" on the highly oriented pyrolytic graphite (HOPG). Our all-atom molecular dynamics simulations reveal that the strong electrostatic interaction induces the "upright" conformation on mica, whereas the hydrophobic interaction favors the "flat" conformation on HOPG. We also show that the epitaxial pattern on mica is ensured by the lattice matching between the anisotropic binding sites of the basal substrate and the molecular dimension of GAV-9, accompanied with a long-range order of well-defined β-strands. Furthermore, the binding free energy surfaces indicate that the longitudinal assembly growth is predominantly driven by the hydrophobic interaction along the longer crystallographic unit cell direction of mica. These findings provide a molecular basis for the surface-assisted molecular assembly, which might also be useful for the design of de novo nanodevices.
Collapse
Affiliation(s)
- Seung-gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | | | | | | | | | | | | |
Collapse
|
44
|
Das P, Kapoor D, Halloran KT, Zhou R, Matthews CR. Interplay between drying and stability of a TIM barrel protein: a combined simulation-experimental study. J Am Chem Soc 2013; 135:1882-90. [PMID: 23293932 PMCID: PMC3637939 DOI: 10.1021/ja310544t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent molecular dynamics simulations have suggested important roles for nanoscale dewetting in the stability, function, and folding dynamics of proteins. Using a synergistic simulation-experimental approach on the αTS TIM barrel protein, we validated this hypothesis by revealing the occurrence of drying inside hydrophobic amino acid clusters and its manifestation in experimental measures of protein stability and structure. Cavities created within three clusters of branched aliphatic amino acids [isoleucine, leucine, and valine (ILV) clusters] were found to experience strong water density fluctuations or intermittent dewetting transitions in simulations. Individually substituting 10 residues in the large ILV cluster at the N-terminus with less hydrophobic alanines showed a weakening or diminishing effect on dewetting that depended on the site of the mutation. Our simulations also demonstrated that replacement of buried leucines with isosteric, polar asparagines enhanced the wetting of the N- and C-terminal clusters. The experimental results on the stability, secondary structure, and compactness of the native and intermediate states for the asparagine variants are consistent with the preferential drying of the large N-terminal cluster in the intermediate. By contrast, the region encompassing the small C-terminal cluster experiences only partial drying in the intermediate, and its structure and stability are unaffected by the asparagine substitution. Surprisingly, the structural distortions required to accommodate the replacement of leucine by asparagine in the N-terminal cluster revealed the existence of alternative stable folds in the native basin. This combined simulation-experimental study demonstrates the critical role of drying within hydrophobic ILV clusters in the folding and stability of the αTS TIM barrel.
Collapse
Affiliation(s)
- Payel Das
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598
| | - Divya Kapoor
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Kevin T. Halloran
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598
- Department of Chemistry, Columbia University, New York, NY 10027
| | - C. Robert Matthews
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| |
Collapse
|
45
|
Solvent fluctuations in hydrophobic cavity-ligand binding kinetics. Proc Natl Acad Sci U S A 2013; 110:1197-202. [PMID: 23297241 DOI: 10.1073/pnas.1221231110] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Water plays a crucial part in virtually all protein-ligand binding processes in and out of equilibrium. Here, we investigate the role of water in the binding kinetics of a ligand to a prototypical hydrophobic pocket by explicit-water molecular dynamics (MD) simulations and implicit diffusional approaches. The concave pocket in the unbound state exhibits wet/dry hydration oscillations whose magnitude and time scale are significantly amplified by the approaching ligand. In turn, the ligand's stochastic motion intimately couples to the slow hydration fluctuations, leading to a sixfold-enhanced friction in the vicinity of the pocket entrance. The increased friction considerably decelerates association in the otherwise barrierless system, indicating the importance of molecular-scale hydrodynamic effects in cavity-ligand binding arising due to capillary fluctuations. We derive and analyze the diffusivity profile and show that the mean first passage time distribution from the MD simulation can be accurately reproduced by a standard Brownian dynamics simulation if the appropriate position-dependent friction profile is included. However, long-time decays in the water-ligand (random) force autocorrelation demonstrate violation of the Markovian assumption, challenging standard diffusive approaches for rate prediction. Remarkably, the static friction profile derived from the force correlations strongly resembles the profile derived on the Markovian assumption apart from a simple shift in space, which can be rationalized by a time-space retardation in the ligand's downhill dynamics toward the pocket. The observed spatiotemporal hydrodynamic coupling may be of biological importance providing the time needed for conformational receptor-ligand adjustments, typical of the induced-fit paradigm.
Collapse
|
46
|
Nguyen CN, Young TK, Gilson MK. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem Phys 2012; 137:044101. [PMID: 22852591 DOI: 10.1063/1.4733951] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.
Collapse
Affiliation(s)
- Crystal N Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA
| | | | | |
Collapse
|
47
|
Rogers KE, Ortiz-Sánchez JM, Baron R, Fajer M, de Oliveira CAF, McCammon JA. On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. J Chem Theory Comput 2012; 9:46-53. [PMID: 23316123 PMCID: PMC3541752 DOI: 10.1021/ct300515n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Indexed: 12/19/2022]
Abstract
![]()
We use thermodynamic integration (TI) and explicit solvent
molecular
dynamics (MD) simulation to estimate the absolute free energy of host–guest
binding. In the unbound state, water molecules visit all of the internally
accessible volume of the host, which is fully hydrated on all sides.
Upon binding of an apolar guest, the toroidal host cavity is fully
dehydrated; thus, during the intermediate λ stages along the
integration, the hydration of the host fluctuates between hydrated
and dehydrated states. Estimating free energies by TI can be especially
challenging when there is a considerable difference in hydration between
the two states of interest. We investigate these aspects using the
popular TIP3P and TIP4P water models. TI free energy estimates through
MD largely depend on water-related interactions, and water dynamics
significantly affect the convergence of binding free energy calculations.
Our results indicate that wetting/dewetting transitions play a major
role in slowing the convergence of free energy estimation. We employ
two alternative approaches—one analytical and the other empirically
based on actual MD sampling—to correct for the standard state
free energy. This correction is sizable (up to 4 kcal/mol), and the
two approaches provide corrections that differ by about 1 kcal/mol.
For the system considered here, the TIP4P water model combined with
an analytical correction for the standard state free energy provides
higher overall accuracy. This observation might be transferable to
other systems in which water-related contributions dominate the binding
process.
Collapse
Affiliation(s)
- Kathleen E Rogers
- Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California 92093-0365, United States ; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California 92093, United States
| | | | | | | | | | | |
Collapse
|
48
|
Ferguson AL, Giovambattista N, Rossky PJ, Panagiotopoulos AZ, Debenedetti PG. A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates. J Chem Phys 2012; 137:144501. [DOI: 10.1063/1.4755750] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
49
|
Huggins DJ. Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules. Phys Chem Chem Phys 2012; 14:15106-17. [PMID: 23037989 DOI: 10.1039/c2cp42631e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures of biomolecules and the strengths of association between them depend critically on interactions with water molecules. Thus, understanding these interactions is a prerequisite for understanding the structure and function of all biomolecules. Inhomogeneous fluid solvation theory provides a framework to derive thermodynamic properties of individual water molecules from a statistical mechanical analysis. In this work, two biomolecules are analysed to probe the distribution and thermodynamics of surrounding water molecules. The great majority of hydration sites are predicted to contribute favourably to the total free energy with respect to bulk water, though hydration sites close to non-polar regions of the solute do not contribute significantly. Analysis of a biomolecule with a positively and negatively charged functional group predicts that a charged species perturbs the free energy of water molecules to a distance of approximately 6.0 Å. Interestingly, short simulations are found to provide converged predictions if samples are taken with sufficient frequency, a finding that has the potential to significantly reduce the required computational cost of such analysis. In addition, the predicted thermodynamic properties of hydration sites with the potential for direct hydrogen bonding interactions are found to disagree significantly for two different water models. This study provides important information on how inhomogeneous fluid solvation theory can be employed to understand the structures and intermolecular interactions of biomolecules.
Collapse
Affiliation(s)
- David J Huggins
- University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge, CB2 0XZ, UK.
| |
Collapse
|
50
|
Cozzi R, Nuccitelli A, D'Onofrio M, Necchi F, Rosini R, Zerbini F, Biagini M, Norais N, Beier C, Telford JL, Grandi G, Assfalg M, Zacharias M, Maione D, Rinaudo CD. New insights into the role of the glutamic acid of the E‐box motif in group B
Streptococcus
pilus 2a assembly. FASEB J 2012; 26:2008-18. [DOI: 10.1096/fj.11-196378] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Mariapina D'Onofrio
- Nuclear Magnetic Resonance LaboratoryDepartment of BiotechnologyUniversity of VeronaVeronaItaly
| | | | | | | | | | | | | | | | | | - Michael Assfalg
- Nuclear Magnetic Resonance LaboratoryDepartment of BiotechnologyUniversity of VeronaVeronaItaly
| | | | | | | |
Collapse
|