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Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022; 7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023] Open
Abstract
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
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Affiliation(s)
- C. Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - F. Cecconi
- CNR - Istituto dei Sistemi Complessi, Rome, Italy and Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
| | - L. Chiodo
- Department of Engineering, Campus Bio-Medico University, Rome, Italy
| | - G. Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Palermo, Italy
| | - P. Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
| | - L. Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, and Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. L. Barabash
- Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA
| | - G. Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
- Dipartimento di Fisica, Università Roma Tre, Rome, Italy
| | - M. Ceccarelli
- Department of Physics and CNR-IOM, University of Cagliari, Monserrato 09042-IT, Italy
| | - B. Corry
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - R. Roth
- Institut Für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - A. Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - B. Roux
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago IL, USA
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van Dijk M, Visscher KM, Kastritis PL, Bonvin AMJJ. Solvated protein-DNA docking using HADDOCK. JOURNAL OF BIOMOLECULAR NMR 2013; 56:51-63. [PMID: 23625455 DOI: 10.1007/s10858-013-9734-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/20/2013] [Indexed: 06/02/2023]
Abstract
Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.
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Affiliation(s)
- Marc van Dijk
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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3
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Denning EJ, MacKerell AD. Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. J Am Chem Soc 2012; 134:2800-6. [PMID: 22242623 DOI: 10.1021/ja211328g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Canonical duplex RNA assumes only the A-form conformation at the secondary structure level while, in contrast, a wide range of noncanonical, tertiary conformations of RNA occur. Here, we show how the 2'-hydroxyl controls RNA conformational properties. Quantum mechanical calculations reveal that the orientation of the 2'-hydroxyl significantly alters the intrinsic flexibility of the phosphodiester backbone, favoring the A-form in duplex RNA when it is in the base orientation and facilitating sampling of a wide range of noncanonical, tertiary structures when it is in the O3' orientation. Influencing the orientation of the 2'-hydroxyl are interactions with the environment, as evidenced by crystallographic survey data, indicating the 2'-hydroxyl to sample more of the O3' orientation in noncanonical RNA structures. These results indicate that the 2'-hydroxyl acts as a "switch", both limiting the conformation of RNA to the A-form at the secondary structure level and allowing RNA to sample a wide range of noncanonical tertiary conformations.
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Affiliation(s)
- Elizabeth J Denning
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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4
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Structural characteristics of hydration sites in lysozyme. Biophys Chem 2011; 156:31-42. [DOI: 10.1016/j.bpc.2011.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/17/2011] [Accepted: 02/17/2011] [Indexed: 11/17/2022]
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5
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Virtanen JJ, Makowski L, Sosnick TR, Freed KF. Modeling the hydration layer around proteins: HyPred. Biophys J 2010; 99:1611-9. [PMID: 20816074 DOI: 10.1016/j.bpj.2010.06.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 06/14/2010] [Accepted: 06/15/2010] [Indexed: 11/25/2022] Open
Abstract
Protein hydration plays an integral role in determining protein function and stability. We develop a simple method with atomic level precision for predicting the solvent density near the surface of a protein. A set of proximal radial distribution functions are defined and calculated for a series of different atom types in proteins using all-atom, explicit solvent molecular dynamic simulations for three globular proteins. A major improvement in predicting the hydration layer is found when the protein is held immobile during the simulations. The distribution functions are used to develop a model for predicting the hydration layer with sub-1-Angstrom resolution without the need for additional simulations. The model and the distribution functions for a given protein are tested in their ability to reproduce the hydration layer from the simulations for that protein, as well as those for other proteins and for simulations in which the protein atoms are mobile. Predictions for the density of water in the hydration shells are then compared with high occupancy sites observed in crystal structures. The accuracy of both tests demonstrates that the solvation model provides a basis for quantitatively understanding protein solvation and thereby predicting the hydration layer without additional simulations.
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Affiliation(s)
- Jouko J Virtanen
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
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6
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Dolenc J, Baron R, Missimer JH, Steinmetz MO, van Gunsteren WF. Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study. Chembiochem 2008; 9:1749-56. [PMID: 18553323 DOI: 10.1002/cbic.200800096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The solvent structure and dynamics around ccbeta-p, a 17-residue peptide that forms a parallel three-stranded alpha-helical coiled coil in solution, was analysed through 10 ns explicit solvent molecular dynamics (MD) simulations at 278 and 330 K. Comparison with two corresponding simulations of the monomeric form of ccbeta-p was used to investigate the changes of hydration upon coiled-coil formation. Pronounced peaks in the solvent density distribution between residues Arg8 and Glu13 of neighbouring helices show the presence of water bridges between the helices of the ccbeta-p trimer; this is in agreement with the water sites observed in X-ray crystallography experiments. Interestingly, this water site is structurally conserved in many three-stranded coiled coils and, together with the Arg and Glu residues, forms part of a motif that determines three-stranded coiled-coil formation. Our findings show that little direct correlation exists between the solvent density distribution and the temporal ordering of water around the trimeric coiled coil. The MD-calculated effective residence times of up to 40 ps show rapid exchange of surface water molecules with the bulk phase, and indicate that the solvent distribution around biomolecules requires interpretation in terms of continuous density distributions rather than in terms of discrete molecules of water. Together, our study contributes to understanding the principles of three-stranded coiled-coil formation.
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Affiliation(s)
- Jozica Dolenc
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093 Zürich, Switzerland
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7
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Kankia BI. Inner-sphere complexes of divalent cations with single-stranded poly(rA) and poly(rU). Biopolymers 2004; 74:232-9. [PMID: 15150798 DOI: 10.1002/bip.20082] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A combination of ultrasound velocimetry, density, and UV spectroscopy has been employed to study the hydration effects of binding of Mn(2+) and alkaline-earth cations to poly(rA) and poly(rU) single strands. The hydration effects, obtained from volume and compressibility measurements, are positive due to overlapping the hydration shells of interacting molecules and consequently releasing the water molecules to bulk state. The volume effects of the binding to poly(rA), calculated per mole of cations, range from 30.6 to 40.6 cm(3) mol(-1) and the compressibility effects range from 59.2 x 10(-4) to 73.6 x 10(-4) cm(3) mol(-1) bar(-1). The volume and compressibility effects for poly(rU) are approximately 17 cm(3) mol(-1) and approximately 50 x 10(-4) cm(3) mol(-1) bar(-1), respectively. The comparative analysis of the dehydration effects suggests that the divalent cations bind to the polynucleotides in inner-sphere manner. In the case of poly(rU) the dehydration effects correspond to two direct coordination, probably between adjacent phosphate groups. The optical study did not reveal any effects of cation on the secondary structure or aggregation of poly(rU). In the case of single-helical poly(rA) binding is more specific: dehydration effects correspond to three to five direct contacts and must involve atomic groups of adenines, and the divalent cations stabilize and aggregate the polynucleotide.
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Affiliation(s)
- Besik I Kankia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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8
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Lee SL, Debenedetti PG, Errington JR, Pethica BA, Moore DJ. A Calorimetric and Spectroscopic Study of DNA at Low Hydration. J Phys Chem B 2004. [DOI: 10.1021/jp0311409] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sau Lawrence Lee
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Pablo G. Debenedetti
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Jeffrey R. Errington
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Brian A. Pethica
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - David J. Moore
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
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9
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Taraphder S, Hummer G. Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam. J Am Chem Soc 2003; 125:3931-40. [PMID: 12656628 DOI: 10.1021/ja016860c] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton-transfer reactions form an integral part of bioenergetics and enzymatic catalysis. The identification of proton-conducting pathways inside a protein is a key to understanding the mechanisms of biomolecular proton transfer. Proton pathways are modeled here as hydrogen bonded networks of proton-conducting groups, including proton-exchanging groups of amino acid side chains and bound water molecules. We focus on the identification of potential proton-conducting pathways inside a protein of known structure. However, consideration of the static structure alone is often not sufficient to detect suitable proton-transfer paths, leading, for example, from the protein surface to the active site buried inside the protein. We include dynamic fluctuations of amino acid side chains and water molecules into our analysis. To illustrate the method, proton transfer into the active site of cytochrome P450cam is studied. The cooperative rotation of amino acids and motion of water molecules are found to connect the protein surface to the molecular oxygen. Our observations emphasize the intrinsic dynamical nature of proton pathways where critical connections in the network may be transiently provided by mobile groups.
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Affiliation(s)
- Srabani Taraphder
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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10
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Abstract
With the availability of accurate methods to treat the electrostatic long-range interactions, molecular dynamics simulations have resulted in refined dynamical models of the structure of the hydration shell around RNA motifs. The models reviewed here range from basic Watson-Crick to more specific noncanonical base pairs, from "simple" double helices to RNA molecules displaying more complex tertiary folds, and from DNA/RNA hybrid double helices to RNA hybrids formed with a chemically modified strand.
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Affiliation(s)
- P Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, 67084 Strasbourg Cedex, France
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11
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Meister WV, Bohley C, Lindau S, Gromann U, Naumann S, Herrmann B, Kargov SI, Martini T, Barthel J, Hoffmann S. Mesophase-derived nucleic acid (peptide) self-organizations visualized by scanning force microscopy. SURF INTERFACE ANAL 2002. [DOI: 10.1002/sia.1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Auffinger P, Westhof E. Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes. J Mol Biol 2001; 305:1057-72. [PMID: 11162114 DOI: 10.1006/jmbi.2000.4360] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The structural and dynamic properties of the water and ion first coordination shell of the r(A-U) and d(A-T) base-pairs embedded within the r(UpA)12 and d(TpA)12 duplexes are described on the basis of two 2.4 ns molecular dynamics simulations performed in a neutralizing aqueous environment with 0.25 M added KCl. The results are compared to previous molecular dynamics simulations of the r(CpG)12 and d(CpG)12 structures performed under similar conditions. It can be concluded that: (i) RNA helices are more rigid than DNA helices of identical sequence, as reflected by the fact that RNA duplexes keep their initial A-form shape while DNA duplexes adopt more sequence-specific shapes. (ii) Around these base-pairs, the water molecules occupy 21 to 22 well-defined hydration sites, some of which are partially occupied by potassium ions. (iii) These hydration sites are occupied by an average of 21.9, 21.0, 20.1, and 19.8 solvent molecules (water and ions) around the r(G=C), r(A-U), d(G=C), and d(A-T) pairs, respectively. (iv) From a dynamic point of view, the stability of the hydration shell is the strongest for the r(G=C) pairs and the weakest for the d(A-T) pairs. (v) For RNA, the observed long-lived hydration patterns are essentially non-sequence dependent and involve water bridges located in the deep groove and linking OR atoms of adjacent phosphate groups. Maximum lifetimes are close to 400 ps. (vi) In contrast, for DNA, long-lived hydration patterns are sequence dependent and located in the minor groove. For d(CpG)12, water bridges linking the (G)N3 and (C)O2 with the O4' atoms of adjacent nucleotides with 400 ps maximum lifetimes are characterized while no such bridges are observed for d(TpA)12. (vii) Potassium ions are observed to bind preferentially to deep/major groove atoms at RpY steps, essentially d(GpC), r(GpC), and r(ApU), by forming ion-bridges between electronegative atoms of adjacent base-pairs. On average, about half an ion is observed per base-pair. Positive ion-binding determinants are related to the proximity of two or more electronegative atoms. Negative binding determinants are associated with the electrostatic and steric hindrance due to the proximity of electropositive amino groups and neutral methyl groups. Potassium ions form only transient contacts with phosphate groups.
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Affiliation(s)
- P Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes 67084, Strasbourg Cedex, France.
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13
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Makarov VA, Andrews BK, Smith PE, Pettitt BM. Residence times of water molecules in the hydration sites of myoglobin. Biophys J 2000; 79:2966-74. [PMID: 11106604 PMCID: PMC1301175 DOI: 10.1016/s0006-3495(00)76533-7] [Citation(s) in RCA: 221] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.
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Affiliation(s)
- V A Makarov
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:87-152. [PMID: 10751944 DOI: 10.1016/s0065-3233(00)53003-4] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- J N Onuchic
- Department of Physics, University of California at San Diego, La Jolla 92093-0319, USA
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15
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Kankia BI. Interaction of alkaline-earth metal ions with calf thymus DNA. Volume and compressibility effects in diluted aqueous solutions. Biophys Chem 2000; 84:227-37. [PMID: 10852310 DOI: 10.1016/s0301-4622(00)00125-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of Mg2+, Ca2+, Sr2+ and Ba2+ ions to calf thymus DNA in solutions has been investigated by ultrasonic and densimetric techniques. The obtained parameters, the apparent molar volume, phiV, and the apparent molar adiabatic compressibility, phiK(S), are very sensitive to hydration of investigated molecules. The interaction between the cations and DNA is accompanied by overlapping their hydration shells and consequently releasing the water molecules from hydration shells to bulk state. The change in the hydration is reflected in the measured parameters, phiV and phiK(S). The magnitude of these hydration changes is determined by the position of the cation relative to DNA atomic groups involved in the binding, and thus can characterize the structure of cation-DNA complexes. The values of the dehydration effects of the binding, deltaphiV and deltaphiK(S), correspond to two direct or higher number of indirect contacts between calf thymus DNA and the cations.
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Affiliation(s)
- B I Kankia
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha 68198-6025, USA.
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16
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MacKerell AD, Banavali NK. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 2000. [DOI: 10.1002/(sici)1096-987x(20000130)21:2<105::aid-jcc3>3.0.co;2-p] [Citation(s) in RCA: 622] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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MacKerell AD, Banavali NK. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 2000. [DOI: 10.1002/(sici)1096-987x(20000130)21:2%3c105::aid-jcc3%3e3.0.co;2-p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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19
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Moore DB, Martínez TJ. Ab Initio Study of Coupled Electron Transfer/Proton Transfer in Cytochrome c Oxidase. J Phys Chem A 1999. [DOI: 10.1021/jp992559v] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dana B. Moore
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Todd J. Martínez
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801
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Gonzalez-Jiménez E, Castro-Valdez I, López-Apresa E, Filippov S, Teplukhin A, Poltev V. Computer study of the role of hydration in the accuracy of nucleic acid biosynthesis. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(99)00251-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Ashbaugh HS, Garde S, Hummer G, Kaler EW, Paulaitis ME. Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes. Biophys J 1999; 77:645-54. [PMID: 10423414 PMCID: PMC1300360 DOI: 10.1016/s0006-3495(99)76920-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Conformational free energies of butane, pentane, and hexane in water are calculated from molecular simulations with explicit waters and from a simple molecular theory in which the local hydration structure is estimated based on a proximity approximation. This proximity approximation uses only the two nearest carbon atoms on the alkane to predict the local water density at a given point in space. Conformational free energies of hydration are subsequently calculated using a free energy perturbation method. Quantitative agreement is found between the free energies obtained from simulations and theory. Moreover, free energy calculations using this proximity approximation are approximately four orders of magnitude faster than those based on explicit water simulations. Our results demonstrate the accuracy and utility of the proximity approximation for predicting water structure as the basis for a quantitative description of n-alkane conformational equilibria in water. In addition, the proximity approximation provides a molecular foundation for extending predictions of water structure and hydration thermodynamic properties of simple hydrophobic solutes to larger clusters or assemblies of hydrophobic solutes.
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Affiliation(s)
- H S Ashbaugh
- Department of Chemical Engineering and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716, USA
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22
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Hummer G. Hydrophobic Force Field as a Molecular Alternative to Surface-Area Models. J Am Chem Soc 1999. [DOI: 10.1021/ja984414s] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Hummer
- Contribution from the Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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23
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Coste F, Malinge JM, Serre L, Shepard W, Roth M, Leng M, Zelwer C. Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site. Nucleic Acids Res 1999; 27:1837-46. [PMID: 10101191 PMCID: PMC148391 DOI: 10.1093/nar/27.8.1837] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently. In both models the double-helix is bent and unwound but with significantly different angle values. We solved the crystal structure at 100K of a double-stranded DNA decamer containing a single cisplatin ICL, using the anomalous scattering (MAD) of platinum as a unique source of phase information. We found 47 degrees for double-helix bending and 70 degrees for unwinding in agreement with previous electrophoretic assays. The crystals are stabilized by intermolecular contacts involving two cytosines extruded from the double-helix, one of which makes a triplet with a terminal G.C pair. The platinum coordination is nearly square and the platinum residue is embedded into a cage of nine water molecules linked to the cross-linked guanines, to the two amine groups, and to the phosphodiester backbone through other water molecules. This water molecule organization is discussed in relation with the chemical stability of the ICL.
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Affiliation(s)
- F Coste
- Centre de Biophysique Moléculaire, Centre de National de la Recherche Scientifique, affiliated to the Université d'Orléans, rue Charles Sadron, 45071 Orleans Cedex, France
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24
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Barciszewski J, Jurczak J, Porowski S, Specht T, Erdmann VA. The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 260:293-307. [PMID: 10095763 DOI: 10.1046/j.1432-1327.1999.00184.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This review describes and summarizes data on the structure and properties of water under normal conditions, at high salt concentration and under high pressure. We correlate the observed conformational changes in nucleic acids with changes in water structure and activity, and suggest a mechanism of conformational transitions of nucleic acids which accounts for changes in the water structure. From the biophysical, biochemical and crystallographic data we conclude that the Z-DNA form can be induced only at low water activity produced by high salt concentrations or high pressure, and accompanied by the stabilizing conjugative effect of the cytidine O4' electrons of the CG base pairs.
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Affiliation(s)
- J Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego, Poznan, Poland.
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25
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Abstract
Water distributions around phosphate groups in 59 B-, A-, and Z-DNA crystal structures were analyzed. It is shown that the waters are concentrated in six hydration sites per phosphate and that the positions and occupancies of these sites are dependent on the conformation and type of nucleotide. The patterns of hydration that are characteristic of the backbone of the three DNA helical types can be attributed in part to the interactions of these hydration sites.
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Affiliation(s)
- B Schneider
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
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26
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Bonvin AM, Sunnerhagen M, Otting G, van Gunsteren WF. Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. J Mol Biol 1998; 282:859-73. [PMID: 9743632 DOI: 10.1006/jmbi.1998.2034] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure and hydration of the DNA duplex d-(AGCGTACTAGTACGCT)2 corresponding to the trp operator fragment used in the crystal structure of the half site complex (PDB entry 1TRR) was studied by a 1.4 ns molecular dynamics simulation in water. The simulation, starting from a B-DNA conformation, used a non-bonded cutoff of 1.4 nm with a reaction field correction and resulted in a stable trajectory. The average DNA conformation obtained was closer to the ones found in the crystal structures of the complexes (PDB entries 1TRO and 1TRR) than to the crystal structure of unbound trp operator (Nucleic Acid Database entry BDJ061). The DNA hydration was characterized in terms of hydrogen bond percentages and corresponding residence times. The residence times of water molecules within 0.35 nm of the DNA non-exchangeable protons were calculated for comparison with NMR measurements of intermolecular water-DNA NOEs and nuclear magnetic relaxation dispersion measurements. No significant difference was found between major and minor groove hydration. The DNA donors and acceptors were hydrogen bonded to water molecules for 77(+/-19)% of the time on average. The average residence time of the hydrogen bonded water molecules was 11(+/-11) ps with a maximum of 223 ps. When all water molecules within NOE distance (0.35 nm) of non-exchangeable protons were considered, the average residence times increased to an average of 100(+/-4) ps and a maximum of 608 ps. These results agree with the experimental NMR results of Sunnerhagen et al. which did not show any evidence for water molecules bound with more than 1 ns residence time on the DNA surface. The exchange of hydration water from the DNA occurred in the major groove primarily through direct exchange with the bulk solvent, while access to and from the minor groove frequently proceeded via pathways involving ribose O3' and O4' and phosphate O2P oxygen atoms. The most common water diffusion pathways in the minor groove were perpendicular to the groove direction. In general, water molecules visited only a limited number of sites in the DNA grooves before exiting. The hydrogen bonding sites, where hydrogen bonds could be formed with donor and acceptor groups of the DNA, were filled with water molecules with an average B-factor value of 0.58 mn2. No special values were observed at any of the sites, where water molecules were observed both in the trp repressor/operator co-crystals and in the crystal structure of unbound DNA.
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Affiliation(s)
- A M Bonvin
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, CH-8092, Switzerland
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27
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Tikhonov DA, Polozov RV, Timoshenko EG, Kuznetsov YA, Gorelov AV, Dawson KA. Hydration of a B–DNA fragment in the method of atom–atom correlation functions with the reference interaction site model approximation. J Chem Phys 1998. [DOI: 10.1063/1.476704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Pettitt BM, Makarov VA, Andrews BK. Protein hydration density: theory, simulations and crystallography. Curr Opin Struct Biol 1998; 8:218-21. [PMID: 9631296 DOI: 10.1016/s0959-440x(98)80042-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Models of protein hydration are becoming increasingly more accurate in comparison with experimental data. The recent success of these models implies that the major features of the solvation layers are dominated by local correlations and that such correlations are universal. The excellent agreement between theoretical and experimental solvent electron density radial distributions marks a significant success in our ability to accurately model macromolecular hydration.
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Affiliation(s)
- B M Pettitt
- Department of Chemistry, University of Houston, TX 77024-5641, USA.
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29
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Verkhovskaya ML, Garcìa-Horsman A, Puustinen A, Rigaud JL, Morgan JE, Verkhovsky MI, Wikström M. Glutamic acid 286 in subunit I of cytochrome bo3 is involved in proton translocation. Proc Natl Acad Sci U S A 1997; 94:10128-31. [PMID: 9294174 PMCID: PMC23326 DOI: 10.1073/pnas.94.19.10128] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/1997] [Indexed: 02/05/2023] Open
Abstract
Glutamic acid 286 (E286; Escherichia coli cytochrome bo3 numbering) in subunit I of the respiratory heme-copper oxidases is highly conserved and has been suggested to be involved in proton translocation. We report a technique of enzyme reconstitution that yields essentially unidirectionally oriented cytochrome bo3 vesicles in which proton translocation can be measured. Such experiments are not feasible in the E286Q mutant due to strong inhibition of respiration, but this is not the case for the mutants E286D and E286C. The reconstituted E286D mutant enzyme readily translocates protons whereas E286C does not. Loss of proton translocation in the D135N mutant, but not in D135E or D407N, also is verified using proteoliposomes. Stopped-flow experiments show that the peroxy intermediate accumulates in the reaction of the E286Q and E286C mutant enzymes with O2. We conclude that an acidic function of the 286 locus is essential for the mechanism of proton translocation.
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Affiliation(s)
- M L Verkhovskaya
- Helsinki Bioenergetics Group and Biocentrum Helsinki, Department of Medical Chemistry, Institute of Biomedical Sciences, P.O. Box 8, 00014-University of Helsinki, Helsinki, Finland
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30
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Soumpasis DM, Georgalis Y. Potential of mean force treatment of salt-mediated protein crystallization. Biophys J 1997; 72:2770-4. [PMID: 9168051 PMCID: PMC1184473 DOI: 10.1016/s0006-3495(97)78919-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In the initial stages of crystallization of proteins, monomers aggregate rapidly and form nuclei and large fractal clusters, as previously shown by dynamic light scattering experiments (Georgalis, Y., J. Schüler, J. Frank, D. M. Soumpasis, and W. Saenger. 1995. Protein crystallization screening through scattering techniques. Adv. Colloid Interface Sci. 58:57-86). In this communication we initiate an effort to understand the effective interactions controlling charged protein aggregation and crystallization using the potential of mean force (PMF) theory. We compute the PMFs of the system lysozyme-water-NaCl within the framework of the hypernetted chain approximation for a wide range of protein and salt concentrations. We show that the computed effective interactions can rationalize the experimentally observed aggregation behavior of lysozyme under crystallization conditions.
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Affiliation(s)
- D M Soumpasis
- Max-Planck-Institut für Biophysikalische Chemie, Biocomputation Group,Göttingen, Germany.
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31
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Oprea TI, Hummer G, Garcia AE. Identification of a functional water channel in cytochrome P450 enzymes. Proc Natl Acad Sci U S A 1997; 94:2133-8. [PMID: 9122160 PMCID: PMC20053 DOI: 10.1073/pnas.94.6.2133] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/1995] [Accepted: 12/06/1996] [Indexed: 02/04/2023] Open
Abstract
Cytochrome P450 enzymes are monooxygenases that contain a functional heme b group linked to a conserved cysteine with a thiolate bond. In the native state, the central iron atom is hexacoordinated with a covalently bound water molecule. The exclusion of solvent molecules from the active site is essential for efficient enzymatic function. Upon substrate binding, water has to be displaced from the active site to prevent electron uncoupling that results in hydrogen peroxide or water. In contrast to typical hemoproteins, the protein surface is not directly accessible from the heme of cytochromes P450. We postulate a two-state model in which a conserved arginine, stabilizing the heme propionate in all known cytochrome P450 crystal structures, changes from the initial, stable side-chain conformation to another rotamer (metastable). In this new state, a functional water channel (aqueduct) is formed from the active site to a water cluster located on the thiolate side of the heme, close to the protein surface. This water cluster communicates with the surface in the closed state and is partly replaced by the flipping arginine side chain in the open state, allowing water molecules to exit to the surface or to reaccess the active site. This two-state model suggests the presence of an exit pathway for water between the active site and the protein surface.
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Affiliation(s)
- T I Oprea
- Theoretical Biology and Biophysics Group (T-10), Los Alamos National Laboratory, NM 87545, USA
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34
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Resat H, Mezei M. Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate. Biophys J 1996; 71:1179-90. [PMID: 8873992 PMCID: PMC1233585 DOI: 10.1016/s0006-3495(96)79322-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations.
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Affiliation(s)
- H Resat
- Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029-6574, USA
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35
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Garde S, Hummer G, García AE, Pratt LR, Paulaitis ME. Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1996; 53:R4310-R4313. [PMID: 9964911 DOI: 10.1103/physreve.53.r4310] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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36
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Hummer G, García AE, Soumpasis DM. A statistical mechanical description of biomolecular hydration. Faraday Discuss 1996:175-89. [PMID: 9136638 DOI: 10.1039/fd9960300175] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An efficient and accurate theoretical description of the structural hydration of biological macromolecules is presented. The hydration of molecules of almost arbitrary size (tRNA, antibody-antigen complexes, photosynthetic reaction centre) can be studied in solution and in the crystalline environment. The biomolecular structure obtained from X-ray crystallography, NMR or modelling is required as input information. The structural arrangement of water molecules near a biomolecular surface is represented by the local water density, analogous to the corresponding electron density in an X-ray diffraction experiment. The water-density distribution is approximated in terms of two- and three-particle correlation functions of solute atoms with water using a potentials-of-mean-force expansion.
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Affiliation(s)
- G Hummer
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545, USA
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37
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Garcia AE, Hummer G, Soumpasis DM. Theoretical description of biomolecular hydration. Application to A-DNA. BASIC LIFE SCIENCES 1996; 64:299-308. [PMID: 9031515 DOI: 10.1007/978-1-4615-5847-7_26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG)5]2 and [d(C5G5)]2. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers (P. Langan et al. J. Biomol. Struct. Dyn., 10, 489 (1992)).
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Affiliation(s)
- A E Garcia
- Theoretical Biology and Biophysics Group, New Mexico 87545, USA
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38
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Schoenborn BP, Garcia A, Knott R. Hydration in protein crystallography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1995; 64:105-19. [PMID: 8987380 DOI: 10.1016/0079-6107(95)00012-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Water in close proximity to the protein surface is fundamental to protein folding, stability, recognition and activity. Protein structures studied by diffraction methods show ordered water molecules around some charged, polar, and non-polar (hydrophobic) amino acids, although the later are only observed when they are at the interface between symmetry related molecules in the crystal. Water networks surrounding the protein have been observed for small proteins. Crystallographically observed water molecules are referred to as bound structural water molecules. During crystallographic data analysis, bound water molecules are often treated as though they belong to the protein. Recent developments in the treatment of the bulk solvent contribution to the low order diffraction data allow a better evaluation of the surface structure of the protein and a better localization of bound waters. The mobility of bound waters is studied by means of temperature and occupancy factors. The bulk solvent has relatively large disorder (liquid like) which is represented by liquidity factors. Within this context water layers surrounding the protein have little mobility.
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