1
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Maruyama Y, Mitsutake A. Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein. ACS OMEGA 2023; 8:43827-43835. [PMID: 38027385 PMCID: PMC10666239 DOI: 10.1021/acsomega.3c05809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/19/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Proteins that do not fold into their functional native state have been linked to diseases. In this study, the influence of the main and side chains of individual amino acids on the folding of the tryptophan cage (Trp-cage), a designed 20-residue miniprotein, was analyzed. For this purpose, we calculated the solvation free energy (SFE) contributions of individual atoms by using the 3D-reference interaction site model with the atomic decomposition method. The mechanism by which the Trp-cage is stabilized during the folding process was examined by calculating the total energy, which is the sum of the conformational energy and SFE. The folding process of the Trp-cage resulted in a stable native state, with a total energy that was 62.4 kcal/mol lower than that of the unfolded state. The solvation entropy, which is considered to be responsible for the hydrophobic effect, contributed 31.3 kcal/mol to structural stabilization. In other words, the contribution of the solvation entropy accounted for approximately half of the total contribution to Trp-cage folding. The hydrophobic core centered on Trp6 contributed 15.6 kcal/mol to the total energy, whereas the solvation entropy contribution was 6.3 kcal/mol. The salt bridge formed by the hydrophilic side chains of Asp9 and Arg16 contributed 10.9 and 5.0 kcal/mol, respectively. This indicates that not only the hydrophobic core but also the salt bridge of the hydrophilic side chains gain solvation entropy and contribute to stabilizing the native structure of the Trp-cage.
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Affiliation(s)
- Yutaka Maruyama
- Data
Science Center for Creative Design and Manufacturing, The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, Japan
- Department
of Physics, School of Science and Technology, Meiji University, 1-1-1
Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
| | - Ayori Mitsutake
- Department
of Physics, School of Science and Technology, Meiji University, 1-1-1
Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
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2
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Maruyama Y, Igarashi R, Ushiku Y, Mitsutake A. Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation. J Chem Inf Model 2023; 63:1529-1541. [PMID: 36821519 PMCID: PMC10015464 DOI: 10.1021/acs.jcim.2c01444] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We apply moving root-mean-square deviation (mRMSD), which does not require a reference structure, as a method for analyzing protein dynamics. This method can be used to calculate the root-mean-square deviation (RMSD) of structure between two specified time points and to analyze protein dynamics behavior through time series analysis. We applied this method to the Trp-cage trajectory calculated by the Anton supercomputer and found that it shows regions of stable states as well as the conventional RMSD. In addition, we extracted a characteristic structure in which the side chains of Asp1 and Arg16 form hydrogen bonds near the most stable structure of the Trp-cage. We also determined that ≥20 ns is an appropriate time interval to investigate protein dynamics using mRMSD. Applying this method to NuG2 protein, we found that mRMSD can be used to detect regions of metastable states in addition to the stable state. This method can be applied to molecular dynamics simulations of proteins whose stable structures are unknown.
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Affiliation(s)
- Yutaka Maruyama
- OMRON SINIC X Corporation, Tokyo 113-0033, Japan.,Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
| | - Ryo Igarashi
- OMRON SINIC X Corporation, Tokyo 113-0033, Japan
| | | | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
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3
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Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach. J 2022. [DOI: 10.3390/j5010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The stability of a protein is determined from its properties and surrounding solvent. In our previous study, the total energy as a sum of the conformational and solvation free energies was demonstrated to be an appropriate energy function for evaluating the stability of a protein in a protein folding system. We plotted the various energies against the root mean square deviation, required as a reference structure. Herein, we replotted the various energies against the end-to-end distance between the N- and C-termini, which is not a required reference and is experimentally measurable. The solvation free energies for all proteins tend to be low as the end-to-end distance increases, whereas the conformational energies tend to be low as the end-to-end distance decreases. The end-to-end distance is one of interesting measures to study the behavior of proteins.
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4
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Yablonskaya OI, Voeikov VL, Novikov KN, Buravleva EV, Menshov VA, Trofimov AV. Effect of Humid Air Exposed to IR Radiation on Enzyme Activity. Int J Mol Sci 2022; 23:ijms23020601. [PMID: 35054784 PMCID: PMC8775401 DOI: 10.3390/ijms23020601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022] Open
Abstract
Water vapor absorbs well in the infra-red region of the electromagnetic spectrum. Absorption of radiant energy by water or water droplets leads to formation of exclusion zone water that possesses peculiar physico-chemical properties. In the course of this study, normally functioning and damaged alkaline phosphatase, horseradish peroxidase and catalase were treated with humid air irradiated with infrared light with a wavelength in the range of 1270 nm and referred to as coherent humidity (CoHu). One-minute long treatment with CoHu helped to partially protect enzymes from heat inactivation, mixed function oxidation, and loss of activity due to partial unfolding. Authors suggest that a possible mechanism underlying the observed effects involves altering the physicochemical properties of aqueous media while treatment of the objects with CoHu where CoHu acts as an intermediary.
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Affiliation(s)
- Olga I. Yablonskaya
- Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119334 Moscow, Russia; (V.A.M.); (A.V.T.)
- Correspondence:
| | - Vladimir L. Voeikov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.L.V.); (K.N.N.); (E.V.B.)
| | - Kirill N. Novikov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.L.V.); (K.N.N.); (E.V.B.)
| | - Ekaterina V. Buravleva
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.L.V.); (K.N.N.); (E.V.B.)
| | - Valeriy A. Menshov
- Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119334 Moscow, Russia; (V.A.M.); (A.V.T.)
| | - Aleksei V. Trofimov
- Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119334 Moscow, Russia; (V.A.M.); (A.V.T.)
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5
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Sumi T, Imamura H. Water-mediated interactions destabilize proteins. Protein Sci 2021; 30:2132-2143. [PMID: 34382697 PMCID: PMC8442971 DOI: 10.1002/pro.4168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/29/2023]
Abstract
Proteins are folded to avoid exposure of the nonpolar groups to water because water-mediated interactions between nonpolar groups are a promising factor in the thermodynamic stabilities of proteins-which is a well-accepted view as one of the unique effects of hydrophobic interactions. This article poses a critical question for this classical view by conducting an accurate solvation free-energy calculation for a thermodynamic cycle of a protein folding using a liquid-state density functional theory. Here, the solvation-free energy for a leucine zipper formation was examined in the coiled-coil protein GCN4-p1, a typical model for hydrophobic interactions, which demonstrated that water-mediated interactions were unfavorable for the association of nonpolar groups in the native state, while the dispersion forces between them were, instead, responsible for the association. Furthermore, the present analysis well predicted the isolated helical state stabilized by pressure, which was previously observed in an experiment. We reviewed the problems in the classical concept and semiempirical presumption that the energetic cost of the hydration of nonpolar groups is a driving force of folding.
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Affiliation(s)
- Tomonari Sumi
- Research Institute for Interdisciplinary ScienceOkayama UniversityKita‐kuJapan
- Department of Chemistry, Faculty of ScienceOkayama UniversityKita‐kuJapan
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life SciencesRitsumeikan UniversityKusatsuJapan
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6
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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7
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Maruyama Y, Koroku S, Imai M, Takeuchi K, Mitsutake A. Mutation-induced change in chignolin stability from π-turn to α-turn. RSC Adv 2020; 10:22797-22808. [PMID: 35514567 PMCID: PMC9054626 DOI: 10.1039/d0ra01148g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/20/2020] [Indexed: 11/21/2022] Open
Abstract
A mutation from threonine to proline at the eighth residue in chignolin changes π-turn to α-turn.
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Affiliation(s)
- Yutaka Maruyama
- Architecture Development Team
- FLAGSHIP 2020 Project
- RIKEN Center for Computational Science
- Kobe 650-0047
- Japan
| | - Shunpei Koroku
- Department of Physics
- School of Science and Technology
- Meiji University
- Kawasaki-shi
- Japan
| | - Misaki Imai
- Cellular and Molecular Biotechnology Research Institute
- National Institute of Advanced Industrial Science and Technology
- Koto
- Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute
- National Institute of Advanced Industrial Science and Technology
- Koto
- Japan
| | - Ayori Mitsutake
- Department of Physics
- School of Science and Technology
- Meiji University
- Kawasaki-shi
- Japan
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8
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Mallamace D, Fazio E, Mallamace F, Corsaro C. The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results. Int J Mol Sci 2018; 19:ijms19123825. [PMID: 30513664 PMCID: PMC6321052 DOI: 10.3390/ijms19123825] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 02/07/2023] Open
Abstract
The biological activity of proteins depends on their three-dimensional structure, known as the native state. The main force driving the correct folding mechanism is the hydrophobic effect and when this folding kinetics is altered, aggregation phenomena intervene causing the occurrence of illnesses such as Alzheimer and Parkinson’s diseases. The other important effect is performed by water molecules and by their ability to form a complex network of hydrogen bonds whose dynamics influence the mobility of protein amino acids. In this work, we review the recent results obtained by means of spectroscopic techniques, such as Fourier Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopies, on hydrated lysozyme. In particular, we explore the Energy Landscape from the thermal region of configurational stability up to that of the irreversible denaturation. The importance of the coupling between the solute and the solvent will be highlighted as well as the different behaviors of hydrophilic and hydrophobic moieties of protein amino acid residues.
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Affiliation(s)
- Domenico Mallamace
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra (MIFT), Università di Messina, 98166 Messina, Italy.
| | - Enza Fazio
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra (MIFT), Università di Messina, 98166 Messina, Italy.
| | - Francesco Mallamace
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
- Istituto dei Sistemi Complessi (ISC)-CNR, 00185 Rome, Italy.
| | - Carmelo Corsaro
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra (MIFT), Università di Messina, 98166 Messina, Italy.
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9
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Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA. Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput 2018; 14:2784-2796. [PMID: 29570286 DOI: 10.1021/acs.jctc.8b00097] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water is essential in many biological processes, and the hydration structure plays a critical role in facilitating protein folding, dynamics, and ligand binding. A variety of biophysical spectroscopic techniques have been used to probe the water solvating proteins, often complemented with molecular dynamics (MD) simulations to resolve the spatial and dynamic features of the hydration shell, but comparing relative water structure is challenging. In this study 1 μs MD simulations were performed to identify and characterize hydration sites around HIV-1 protease bound to an inhibitor, darunavir (DRV). The water density, hydration site occupancy, extent and anisotropy of fluctuations, coordinated water molecules, and hydrogen bonds were characterized and compared to the properties of bulk water. The water density of the principal hydration shell was found to be higher than bulk, dependent on the topology and physiochemical identity of the biomolecular surface. The dynamics of water molecules occupying principal hydration sites was highly dependent on the number of water-water interactions and inversely correlated with hydrogen bonds to the protein-inhibitor complex. While many waters were conserved following the symmetry of homodimeric HIV protease, the asymmetry induced by DRV resulted in asymmetric lower-occupancy hydration sites at the concave surface of the active site. Key interactions between water molecules and the protease, that stabilize the protein in the inhibited form, were altered in a drug resistant variant of the protease indicating that modulation of solvent-solute interactions might play a key role in conveying drug resistance. Our analysis provides insights into the interplay between an enzyme inhibitor complex and the hydration shell and has implications in elucidating water structure in a variety of biological processes and applications including ligand binding, inhibitor design, and resistance.
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Affiliation(s)
- Florian Leidner
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Janet Paulsen
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Yves A Muller
- Division of Biotechnology , Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen 91052 , Germany
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
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10
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Abstract
We discuss the stability of an entire protein and the influence of main chains and side chains of individual amino acids to investigate the protein-folding mechanism. For this purpose, we calculated the solvation free-energy contribution of individual atoms using the three-dimensional reference interaction site model with the atomic decomposition method. We generated structures of chignolin miniprotein by a molecular dynamics simulation and classified them into six types: native 1, native 2, misfolded 1, misfolded 2, intermediate, and unfolded states. The total energies of the native (-171.1 kcal/mol) and misfolded (-171.2 kcal/mol) states were almost the same and lower than those of the intermediate (-158.5 kcal/mol) and unfolded (-148.1 kcal/mol) states; however, their components were different. In the native state, the side-chain interaction between Thr6 and Thr8 is important for the formation of π-turn. On the other hand, the hydrogen bonds between the atoms of the main chains in the misfolded state become stronger than those in the intermediate state.
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Affiliation(s)
- Yutaka Maruyama
- Co-Design Team, FLAGSHIP 2020 Project , RIKEN Advanced Institute for Computational Science , Kobe 650-0047 , Japan
| | - Ayori Mitsutake
- Department of Physics , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
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11
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Durec M, Marek R, Kozelka J. Water-Tryptophan Interactions: Lone-pair⋅⋅⋅π or O−H⋅⋅⋅π? Molecular Dynamics Simulations of β-Galactosidase Suggest that Both Modes Can Co-exist. Chemistry 2018; 24:5849-5859. [DOI: 10.1002/chem.201705364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Matúš Durec
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 625 00 Brno Czech Republic
- Department of Condensed Matter Physics, Faculty of Science; Masaryk University; Kotlářská 2 611 37 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 625 00 Brno Czech Republic
- National Center for Biomolecular Research, Faculty of Science; Masaryk University; Kamenice 5/A4 625 00 Brno Czech Republic
| | - Jiří Kozelka
- Department of Condensed Matter Physics, Faculty of Science; Masaryk University; Kotlářská 2 611 37 Brno Czech Republic
- Biologie Intégrée du Globule Rouge, UMR S1134, Inserm; Université Paris Diderot, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles; 75739 Paris France
- Institut National de la Transfusion Sanguine (INTS); 75739 Paris France
- Laboratoire d'Excellence GR-Ex; 75739 Paris France
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12
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Sumi T, Maruyama Y, Mitsutake A, Mochizuki K, Koga K. Application of reference‐modified density functional theory: Temperature and pressure dependences of solvation free energy. J Comput Chem 2017; 39:202-217. [DOI: 10.1002/jcc.25101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Tomonari Sumi
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
- Department of Chemistry, Faculty of ScienceOkayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
| | - Yutaka Maruyama
- Co‐Design Team, FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science, 7‐1‐26, Minatojima‐minami‐machiKobe650‐0047 Japan
| | - Ayori Mitsutake
- Department of PhysicsKeio University, 3‐14‐1 Hiyoshi, Kohoku‐kuYokohama Kanagawa223–8522 Japan
| | - Kenji Mochizuki
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
| | - Kenichiro Koga
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
- Department of Chemistry, Faculty of ScienceOkayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
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13
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Maruyama Y, Mitsutake A. Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT. J Phys Chem B 2017; 121:9881-9885. [DOI: 10.1021/acs.jpcb.7b08487] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yutaka Maruyama
- Co-Design Team,
FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science, Kobe 650-0047, Japan
| | - Ayori Mitsutake
- Department
of Physics, Keio University, Yokohama, Kanagawa 223-8522, Japan
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14
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Chong Y, Kleinhammes A, Wu Y. Protein dynamics and thermodynamics crossover at 10 °C: Different roles of hydration at hydrophilic and hydrophobic groups. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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16
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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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17
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Biedermannová L, Schneider B. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2192-202. [PMID: 26527137 PMCID: PMC4631476 DOI: 10.1107/s1399004715015679] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/20/2015] [Indexed: 12/22/2022]
Abstract
Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon-donor hydrogen bonds, OH-π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.
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Affiliation(s)
- Lada Biedermannová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic
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18
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Wang X, Ye X, Zhang G. Investigation of pH-induced conformational change and hydration of poly(methacrylic acid) by analytical ultracentrifugation. SOFT MATTER 2015; 11:5381-5388. [PMID: 26059391 DOI: 10.1039/c5sm00806a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Analytical ultracentrifugation was performed on poly(methacrylic acid) (PMAA) with a series of weight average molar masses (Mw) in aqueous solutions as a function of pH. The scales of the sedimentation coefficient (s) and the diffusion coefficient (D) to Mw at infinite dilutions were obtained at different pH values, indicating that PMAA chains adopt a collapsed structure at low pH values, and stretch at pH higher than 5.2. Our results show that the sedimentation coefficient exhibits a minimum at pH ∼ 6.0, presumably due to the effect of the conformational change and the hydration state of PMAA chains. When pH increases from 6.0 to 8.5, PMAA chains with high molar mass shrink a little bit, presumably because the sodium ions act as a bridging agent between nonadjacent carboxylate groups. Furthermore, the weight average molar mass of PMAA at pH 8.5 increases by one fold than that at pH 4.0, indicating the condensation of sodium ions and the increase in the number of hydration water molecules around carboxylate groups at high pH values.
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Affiliation(s)
- Xiaoyan Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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Sumi T, Mitsutake A, Maruyama Y. A solvation-free-energy functional: A reference-modified density functional formulation. J Comput Chem 2015; 36:1359-69. [DOI: 10.1002/jcc.23942] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/26/2015] [Accepted: 03/29/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Tomonari Sumi
- Department of Chemistry; Faculty of Science, Okayama University; 3-1-1 Tsushima-Naka Kita-ku Okayama 700-8530 Japan
| | - Ayori Mitsutake
- Department of Physics; Keio University; 3-14-1, Hiyoshi Kohoku-ku, Yokohama Kanagawa 223-8522 Japan
- JST, PREST; 3-14-1 Hiyoshi Kohoku-ku, Yokohama Kanagawa 223-8522 Japan
| | - Yutaka Maruyama
- Department of Physics; Keio University; 3-14-1, Hiyoshi Kohoku-ku, Yokohama Kanagawa 223-8522 Japan
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Rahaman O, Kalimeri M, Melchionna S, Hénin J, Sterpone F. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. J Phys Chem B 2014; 119:8939-49. [PMID: 25317828 DOI: 10.1021/jp507571u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, we address the question of whether the enhanced stability of thermophilic proteins has a direct connection with internal hydration. Our model systems are two homologous G domains of different stability: the mesophilic G domain of the elongation factor thermal unstable protein from E. coli and the hyperthermophilic G domain of the EF-1α protein from S. solfataricus. Using molecular dynamics simulation at the microsecond time scale, we show that both proteins host water molecules in internal cavities and that these molecules exchange with the external solution in the nanosecond time scale. The hydration free energy of these sites evaluated via extensive calculations is found to be favorable for both systems, with the hyperthermophilic protein offering a slightly more favorable environment to host water molecules. We estimate that, under ambient conditions, the free energy gain due to internal hydration is about 1.3 kcal/mol in favor of the hyperthermophilic variant. However, we also find that, at the high working temperature of the hyperthermophile, the cavities are rather dehydrated, meaning that under extreme conditions other molecular factors secure the stability of the protein. Interestingly, we detect a clear correlation between the hydration of internal cavities and the protein conformational landscape. The emerging picture is that internal hydration is an effective observable to probe the conformational landscape of proteins. In the specific context of our investigation, the analysis confirms that the hyperthermophilic G domain is characterized by multiple states and it has a more flexible structure than its mesophilic homologue.
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Affiliation(s)
- Obaidur Rahaman
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Maria Kalimeri
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Simone Melchionna
- ‡CNR-IPCF, Consiglio Nazionale delle Ricerche, Physics Dept., Univ. La Sapienza, P.le A. Moro 2, 00185, Rome, Italy
| | - Jérôme Hénin
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
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Chong SH, Ham S. Protein Folding Thermodynamics: A New Computational Approach. J Phys Chem B 2014; 118:5017-25. [DOI: 10.1021/jp500269m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Song-Ho Chong
- Department of Chemistry, Sookmyung Women’s University, Cheongpa-ro
47-gil 100, Yongsan-Ku, Seoul 140-742, Korea
| | - Sihyun Ham
- Department of Chemistry, Sookmyung Women’s University, Cheongpa-ro
47-gil 100, Yongsan-Ku, Seoul 140-742, Korea
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Ksenofontova OI. Investigation of conformational mobility of insulin superfamily peptides: Use of SPC/E and TIP4P water models. Mol Biol 2014. [DOI: 10.1134/s0026893314030121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Maruyama Y, Yoshida N, Tadano H, Takahashi D, Sato M, Hirata F. Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT. J Comput Chem 2014; 35:1347-55. [PMID: 24771232 DOI: 10.1002/jcc.23619] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/26/2014] [Accepted: 04/06/2014] [Indexed: 01/19/2023]
Abstract
A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems.
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Affiliation(s)
- Yutaka Maruyama
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, 223-8522, Japan
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