1
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Wu H, Ghaani MR, Nandi PK, English NJ. Investigation of Dipolar Response of the Hydrated Hen-Egg White Lysozyme Complex under Externally Applied Electric Fields: Insights from Non-equilibrium Molecular Dynamics. J Phys Chem B 2022; 126:858-868. [PMID: 35060735 PMCID: PMC8819654 DOI: 10.1021/acs.jpcb.1c07096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- HaoLun Wu
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohammad Reza Ghaani
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Prithwish K. Nandi
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- Irish Centre for High-End Computing, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland
| | - Niall J. English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Yousefi R, Lynch GC, Galbraith M, Pettitt BM. Contributions of higher-order proximal distribution functions to solvent structure around proteins. J Chem Phys 2021; 155:104110. [PMID: 34525817 PMCID: PMC8439718 DOI: 10.1063/5.0062580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 11/14/2022] Open
Abstract
The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute-solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.
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Affiliation(s)
- Razie Yousefi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - Gillian C. Lynch
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - Madeline Galbraith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
| | - B. Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, USA
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3
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Molecular dynamics in cells: A neutron view. Biochim Biophys Acta Gen Subj 2020; 1864:129475. [DOI: 10.1016/j.bbagen.2019.129475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 11/21/2022]
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4
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Sheu SY, Liu YC, Zhou JK, Schlag EW, Yang DY. Surface Topography Effects of Globular Biomolecules on Hydration Water. J Phys Chem B 2019; 123:6917-6932. [PMID: 31282162 DOI: 10.1021/acs.jpcb.9b03734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.e., hemoglobin (Hb) and G-quadruplex DNA (GDNA). The residence time, power of long-time tail, and dipole relaxation time were found to display drastic changes within the averaged hydration shell of 3.0-5.0 Å. Compared with bulk water, in the inner hydration shell, the water dipole moment displays a slower relaxation process and is more oriented toward GDNA than toward Hb, forming a hedgehog-like structure when it surrounds GDNA. In particular, a spine water structure is observed in the GDNA narrow groove. The water isotope effect not only prolongs the dynamic time scales of libration motion in the inner hydration shell and the dipole relaxation processes in the bulk but also strengthens the DNA spine water structure. The potential of the mean force profile reflects the integrity of the hydration shell structure and enables us to obtain detailed insights into the structures formed by water, such as the caged H-bond network and the edge bridge structures; it also reveals that local hydration shell free energy (LHSFE) depends on H-bond rupture processes and ranges from 0.2 to 4.2 kcal/mol. Our results demonstrate that the surface topography of a biomolecule influences the integrity of the hydration shell structure and LHSFE. Our studies are able to identify various further applications in the areas of microfluid devices and nano-dewetting on bioinspired surfaces.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan.,Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan
| | - Edward W Schlag
- Institut für Physikalische und Theoretische Chemie , TU-München , Lichtenbergstr. 4 , 85748 Garching , Germany
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
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5
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Stefanutti E, Bove LE, Alabarse FG, Lelong G, Bruni F, Ricci MA. Vibrational dynamics of confined supercooled water. J Chem Phys 2019; 150:224504. [PMID: 31202218 DOI: 10.1063/1.5094147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quest for a possible liquid-liquid coexistence line in supercooled water below its homogeneous nucleation temperature is faced by confining water within a porous silica substrate (MCM-41). This system is investigated by synchrotron radiation infrared spectroscopy, exploring both the intramolecular and the intermolecular vibrational dynamics, in the temperature range from ambient down to ∼120 K, along several isobaric paths between 0.7 kbar and 3.0 kbar. Upon lowering the temperature, the OH-stretching band shows that the intramolecular vibrational dynamics continuously evolves from predominantly liquidlike to predominantly icelike. An abrupt change in the line shape of the intermolecular vibrational band between 220 K and 240 K, depending on the pressure, is the signature of nucleation of ice within the MCM-41 pores. These findings do not support the presence of two liquid phases and provide evidence for the coexistence of liquid water and ice in water confined in MCM-41.
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Affiliation(s)
- E Stefanutti
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - L E Bove
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - F G Alabarse
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - G Lelong
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 4 Place Jussieu, 75005 Paris, France
| | - F Bruni
- Dipartimento di Scienze, Università Degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - M A Ricci
- Dipartimento di Scienze, Università Degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
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6
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Karain WI, Qaraeen NI. The adaptive nature of protein residue networks. Proteins 2017; 85:917-923. [PMID: 28168745 DOI: 10.1002/prot.25261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/19/2017] [Accepted: 01/30/2017] [Indexed: 11/09/2022]
Abstract
Protein residue networks PRNs are used to describe proteins. These networks are usually based on an average structure for the protein. However, proteins are dynamic entities that are affected by their surroundings. In this work, we study the effect of temperatures above and below the protein dynamical transition temperature(≈200 K), on three important network parameters gleaned from weighted PRNs for the solvated β-lactamase inhibitory protein BLIP: the betweenness centrality B, the closeness centrality C, and the clustering coefficient CC. The B and C values will be extracted for each node from PRNs at six different temperatures: 150 K, 180 K, 200 K, 220 K, 250 K, and 310 K respectively. The average value for the CC for each PRN will also be calculated at each temperature, respectively. We find that at temperatures ≤200 K, the network nodes with the most significant B and C values tend to have lower relative solvent accessibility RSA values, and to fall within the protein secondary structure elements (α helices and β sheets). At temperatures >200 K, the significant nodes in terms of B and C tend to have larger RSA values, and to fall on the connecting loops in the protein. The average CC decreases in value for the PRNs up to 200 K, and then remains basically constant above 200 K. This clearly shows that any conclusions based on static PRNs should be handled with care. The dynamic nature of proteins and its coupling to the surrounding environment should be taken into consideration when using the PRN paradigm. Proteins 2017; 85:917-923. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wael I Karain
- Department of Physics, Birzeit University, Birzeit, Palestine
| | - Nael I Qaraeen
- Department of Computer Science, Birzeit University, Birzeit, Palestine
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7
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Zaccai G, Natali F, Peters J, Řihová M, Zimmerman E, Ollivier J, Combet J, Maurel MC, Bashan A, Yonath A. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering. Sci Rep 2016; 6:37138. [PMID: 27849042 PMCID: PMC5111069 DOI: 10.1038/srep37138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023] Open
Abstract
Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.
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Affiliation(s)
- Giuseppe Zaccai
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Francesca Natali
- Institut Laue Langevin, F-38042 Grenoble, France.,CNR-IOM, OGG, F-38042 Grenoble, France
| | - Judith Peters
- Institut Laue Langevin, F-38042 Grenoble, France.,Univ. Grenoble Alpes, LiPhy, F-38044 Grenoble, France
| | - Martina Řihová
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France.,Institute of Physics, Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague, Czech Republic
| | - Ella Zimmerman
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - J Ollivier
- Institut Laue Langevin, F-38042 Grenoble, France
| | - J Combet
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut Charles Sadron, CNRS-UdS, 67034 Strasbourg Cedex 2, France
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Anat Bashan
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - Ada Yonath
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
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8
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Karain W. THz frequency spectrum of protein-solvent interaction energy using a recurrence plot-based Wiener-Khinchin method. Proteins 2016; 84:1549-57. [PMID: 27357803 DOI: 10.1002/prot.25097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/05/2016] [Accepted: 06/28/2016] [Indexed: 11/10/2022]
Abstract
The dynamics of a protein and the water surrounding it are coupled via nonbonded energy interactions. This coupling can exhibit a complex, nonlinear, and nonstationary nature. The THz frequency spectrum for this interaction energy characterizes both the vibration spectrum of the water hydrogen bond network, and the frequency range of large amplitude modes of proteins. We use a Recurrence Plot based Wiener-Khinchin method RPWK to calculate this spectrum, and the results are compared to those determined using the classical auto-covariance-based Wiener-Khinchin method WK. The frequency spectra for the total nonbonded interaction energy extracted from molecular dynamics simulations between the β-Lactamase Inhibitory Protein BLIP, and water molecules within a 10 Å distance from the protein surface, are calculated at 150, 200, 250, and 310 K, respectively. Similar calculations are also performed for the nonbonded interaction energy between the residues 49ASP, 53TYR, and 142PHE in BLIP, with water molecules within 10 Å from each residue respectively at 150, 200, 250, and 310 K. A comparison of the results shows that RPWK performs better than WK, and is able to detect some frequency data points that WK fails to detect. This points to the importance of using methods capable of taking the complex nature of the protein-solvent energy landscape into consideration, and not to rely on standard linear methods. In general, RPWK can be a valuable addition to the analysis tools for protein molecular dynamics simulations. Proteins 2016; 84:1549-1557. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wael Karain
- Department of Physics, Birzeit University, Birzeit, Palestine.
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9
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Rani P, Biswas P. Shape dependence of the radial distribution function of hydration water around proteins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:335102. [PMID: 25053697 DOI: 10.1088/0953-8984/26/33/335102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The characterization of hydration water in proteins is important to understand their structure, function and folding properties. A calculation of the shape parameters reveals considerable asymmetry in the shapes of globular proteins. The present study suggests a generalized approach for the calculation of radial distribution of hydration water by accounting for the shape asymmetry in proteins. The surface and radial distribution function is analyzed for three groups of high resolution globular proteins and nonglobular proteins. This generalized approach depicts a considerable difference in the hydration water distribution pattern around aspherical proteins as compared to the earlier method and this difference is more pronounced for nonglobular proteins. The peaks for normalized RDF are found to be sharper compared to those of bulk water. The normalized RDF of hydration water exactly coincides with that of the bulk beyond 8.0 Å. The radial distribution of hydration water as a function of the water-protein distance matches with the experimentally observed distribution of hydration water around myoglobin. The results reveal that the distribution of hydration water is dependent on the shapes of proteins and hence a generalized approach should be used for the calculation of hydration water distribution around proteins, especially for nonglobular proteins.
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Affiliation(s)
- Pooja Rani
- Department of Chemistry, University of Delhi, Delhi-110007, India
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10
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Woods KN. The glassy state of crambin and the THz time scale protein-solvent fluctuations possibly related to protein function. BMC BIOPHYSICS 2014; 7:8. [PMID: 25184036 PMCID: PMC4143578 DOI: 10.1186/s13628-014-0008-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND THz experiments have been used to characterize the picosecond time scale fluctuations taking place in the model, globular protein crambin. RESULTS Using both hydration and temperature as an experimental parameter, we have identified collective fluctuations (<= 200 cm(-1)) in the protein. Observation of the protein dynamics in the THz spectrum from both below and above the glass transition temperature (Tg) has provided unique insight into the microscopic interactions and modes that permit the solvent to effectively couple to the protein thermal fluctuations. CONCLUSIONS Our findings suggest that the solvent dynamics on the picosecond time scale not only contribute to protein flexibility but may also delineate the types of fluctuations that are able to form within the protein structure.
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Affiliation(s)
- Kristina N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh 15213, PA, USA
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11
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D’Amico F, Bencivenga F, Camisasca G, Gessini A, Principi E, Cucini R, Masciovecchio C. Thermodynamic hydration shell behavior of glycine. J Chem Phys 2013; 139:015101. [DOI: 10.1063/1.4812283] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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12
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Analysis of Bulk and Hydration Water During Thermal Lysozyme Denaturation Using Raman Scattering. FOOD BIOPHYS 2013. [DOI: 10.1007/s11483-013-9294-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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D’Amico F, Bencivenga F, Gessini A, Principi E, Cucini R, Masciovecchio C. Investigation of Acetic Acid Hydration Shell Formation through Raman Spectra Line-Shape Analysis. J Phys Chem B 2012; 116:13219-27. [DOI: 10.1021/jp3088594] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Francesco D’Amico
- Sincrotrone Trieste, Strada
Statale 14 km 163.5, Area Science Park, I-34012 Trieste, Italy
| | - Filippo Bencivenga
- Sincrotrone Trieste, Strada
Statale 14 km 163.5, Area Science Park, I-34012 Trieste, Italy
| | - Alessandro Gessini
- Sincrotrone Trieste, Strada
Statale 14 km 163.5, Area Science Park, I-34012 Trieste, Italy
| | - Emiliano Principi
- Sincrotrone Trieste, Strada
Statale 14 km 163.5, Area Science Park, I-34012 Trieste, Italy
| | - Riccardo Cucini
- Sincrotrone Trieste, Strada
Statale 14 km 163.5, Area Science Park, I-34012 Trieste, Italy
| | - Claudio Masciovecchio
- Sincrotrone Trieste, Strada
Statale 14 km 163.5, Area Science Park, I-34012 Trieste, Italy
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14
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Panuszko A, Wojciechowski M, Bruździak P, Rakowska PW, Stangret J. Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation. Phys Chem Chem Phys 2012; 14:15765-73. [DOI: 10.1039/c2cp42229h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Bhattacharjee N, Biswas P. Local order and mobility of water molecules around ambivalent helices. J Phys Chem B 2011; 115:12257-65. [PMID: 21916474 DOI: 10.1021/jp2066106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water on a protein surface plays a key role in determining the structure and dynamics of proteins. Compared to the properties of bulk water, many aspects of the structure and dynamics of the water surrounding the proteins are less understood. It is interesting therefore to explore how the properties of the water within the solvation shell around the peptide molecule depend on its specific secondary structure. In this work we investigate the orientational order and residence times of the water molecules to characterize the structure, energetics, and dynamics of the hydration shell water around ambivalent peptides. Ambivalent sequences are identical sequences which display multiple secondary structures in different proteins. Molecular dynamics simulations of representative proteins containing variable helix, variable nonhelix, and conserved helix are also used to explore the local structure and mobility of water molecules in their vicinity. The results, for the first time, depict a different water distribution pattern around the conserved and variable helices. The water molecules surrounding the helical segments in variable helices are found to possess a less locally ordered structure compared to those around their corresponding nonhelical counterparts and conserved helices. The long conserved helices exhibit extremely high local residence times compared to the helical conformations of the variable helices, whereas the residence times of the nonhelical conformations of the variable helices are comparable to those of the short conserved helices. This differential pattern of the structure and dynamics of water molecules in the vicinity of conserved/variable helices may lend valuable insights for understanding the role of solvent effects in determining sequence ambivalency and help in improving the accuracy of water models used in the simulations of proteins.
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16
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Achterhold K, Ostermann A, Moulin M, Haertlein M, Unruh T, Parak FG. Dynamical properties of the hydration shell of fully deuterated myoglobin. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041930. [PMID: 22181198 DOI: 10.1103/physreve.84.041930] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 08/29/2011] [Indexed: 05/31/2023]
Abstract
Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 H(2)O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 Å(-1) and a temperature range from 4 to 297 K. We used neutrons with a wavelength of λ αE 6 Å and an energy resolution of about 65 μeV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra caused by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjölander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time τ(0) in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time τ(1) in a nonbound state followed again by the oscillatory motions for τ(0) and so forth. We used the general formulation with no simplifications as τ(0)≫τ(1) or τ(1)≫τ(0). At room temperature, we obtained τ(0) αE 104 ps and τ(1) αE 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.
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Affiliation(s)
- Klaus Achterhold
- Physik-Department E17, Technische Universität München, James-Franck-Strasse 1, D-85747 Garching, Germany
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17
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Bhattacharjee N, Biswas P. Structure of hydration water in proteins: a comparison of molecular dynamics simulations and database analysis. Biophys Chem 2011; 158:73-80. [PMID: 21665349 DOI: 10.1016/j.bpc.2011.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 05/07/2011] [Accepted: 05/08/2011] [Indexed: 11/15/2022]
Abstract
Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compare it with those obtained from molecular dynamics simulations. Tetrahedral order parameter of water in proteins calculated from previous and present simulation studies show that the potential of bulk water overestimates the average tetrahedral order parameter compared to those calculated from crystal structures. Hydration waters are found to be more ordered at a distance between the first and second solvation shell from the protein surface. The values of the order parameter decrease sharply when the water molecules are located very near or far away from the protein surface. At small water-water distance, the values of order parameter of water are very low. The average order parameter records a maximum value at a distance equivalent to the first solvation layer with respect to the water-water radial distribution and asymptotically approaches a constant value at large distances. Results from present analysis will help to get a better insight into structure of hydration water around proteins. The analysis will also help to improve the accuracy of water models on the protein surface.
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18
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Ratajska-Gadomska B, Gadomski W. Influence of confinement on solvation of ethanol in water studied by Raman spectroscopy. J Chem Phys 2010; 133:234505. [DOI: 10.1063/1.3520435] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Sheu SY, Yang DY. Determination of Protein Surface Hydration Shell Free Energy of Water Motion: Theoretical Study and Molecular Dynamics Simulation. J Phys Chem B 2010; 114:16558-66. [DOI: 10.1021/jp105164t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences and Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan, Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan, and Division of Biomolecular Sensing, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Dah-Yen Yang
- Department of Life Sciences and Institute of Genome Sciences and Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan, Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan, and Division of Biomolecular Sensing, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
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20
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D'Amico F, Bencivenga F, Gessini A, Masciovecchio C. Temperature dependence of hydrogen-bond dynamics in acetic acid-water solutions. J Phys Chem B 2010; 114:10628-33. [PMID: 20701390 DOI: 10.1021/jp103730s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An inelastic UV scattering experiment has been carried out on acetic acid-water solutions as a function of temperature and concentration. The analysis of experimental data indicates the presence of a crossover temperature (T(c) approximately 325 +/- 10 K). Above T(c), the energy of hydrogen bonds responsible for water-acetic acid and acetic acid-acetic acid interactions is strongly reduced. This leads to a reduction in the average number of water molecule interacting with acetic acid, as well as to a lower number of acetic acid clusters. The latter behavior can be mainly ascribed to a temperature change in the activation energy of carboxylic groups of acetic acid. These results may be also relevant to better understand the folding mechanism in protein-water solutions.
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Affiliation(s)
- Francesco D'Amico
- Sincrotrone Trieste, Strada Statale 14 km 163.5, Area Science Park, I-34149 Trieste, Italy.
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21
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Stafford AJ, Ensign DL, Webb LJ. Vibrational Stark Effect Spectroscopy at the Interface of Ras and Rap1A Bound to the Ras Binding Domain of RalGDS Reveals an Electrostatic Mechanism for Protein−Protein Interaction. J Phys Chem B 2010; 114:15331-44. [DOI: 10.1021/jp106974e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amy J. Stafford
- Department of Chemistry and Biochemistry and Institute for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas 78712, United States
| | - Daniel L. Ensign
- Department of Chemistry and Biochemistry and Institute for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas 78712, United States
| | - Lauren J. Webb
- Department of Chemistry and Biochemistry and Institute for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas 78712, United States
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22
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Fathima NN, Baias M, Blumich B, Ramasami T. Structure and dynamics of water in native and tanned collagen fibers: Effect of crosslinking. Int J Biol Macromol 2010; 47:590-6. [PMID: 20709097 DOI: 10.1016/j.ijbiomac.2010.08.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/28/2010] [Accepted: 08/06/2010] [Indexed: 11/19/2022]
Abstract
The influence of crosslinking on the hydration structure of collagen has been investigated. Nuclear magnetic resonance, dielectric relaxation and thermoporometry were used to investigate water structure in native and crosslinked collagen fibers on both wet and dried specimen. Measurements reveal the influence of different chemical treatments on the transverse relaxation time and polarization of the collagen fibers. The frequency dependence of dielectric constant of collagen fibers displays an induction behavior on low frequencies. Bound water constrained in collagen fibers seems to provide signatures for changes induced by crosslinking agents on the pore diameter and distribution in collagen fibers. A correlation of transverse relaxation time of water in dry and wet states presented in this study presents an experimental tool for examining the differences in efficacy of crosslinking agents. Changes in the dielectric relaxation, dynamics of water structure and hydroporometric structure of collagen are dependent on the nature of crosslinking material.
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Affiliation(s)
- N Nishad Fathima
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai, India
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23
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Jinendra B, Tamaki K, Kuroki S, Vassileva M, Yoshida S, Tsenkova R. Near infrared spectroscopy and aquaphotomics: Novel approach for rapid in vivo diagnosis of virus infected soybean. Biochem Biophys Res Commun 2010; 397:685-90. [PMID: 20570650 DOI: 10.1016/j.bbrc.2010.06.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/02/2010] [Indexed: 11/15/2022]
Abstract
Near infrared spectroscopy with aquaphotomics as a novel approach was assessed for the diagnosis of soybean plants (Glycine max) infected with soybean mosaic virus (SMV) at latent symptomless stage of the disease. Near infrared (NIR) leaf spectra (in the range of 730-1025nm) acquired from soybean plants with and without the inoculation of SMV were used. Leaf samples from all plants were assayed with enzyme-linked immunosorbent assay (ELISA) to confirm the infection. Previously reported NIR band for water at 970nm and two new bands at 910nm and 936nm in the water specific region of NIR were found to be markedly sensitive to the SMV infection 2weeks prior to the appearance of visual symptoms on infected leaves. The spectral calibration model soft independent modeling of class analogy (SIMCA), predicted the disease with 91.6% sensitivity and 95.8% specificity when the second order derivative of the individual plant averaged spectra were used. The study shows the potential of NIR spectroscopy with its novel approach to elucidate latent biochemical and biophysical information of an infection as it allowed successful discrimination of SMV infected plant from healthy at the early symptomless stage of the disease.
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Affiliation(s)
- Balasuriya Jinendra
- Department of Environmental Information and Bio Production Engineering, Kobe University, 1-1 Rokko-dai, cho, 657-8501, Japan.
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24
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Woods KN. Solvent-induced backbone fluctuations and the collective librational dynamics of lysozyme studied by terahertz spectroscopy. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:031915. [PMID: 20365778 DOI: 10.1103/physreve.81.031915] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Indexed: 05/29/2023]
Abstract
THz spectroscopy is used to investigate the dynamics of the globular protein hen egg white lysozyme under varying hydration and temperature conditions. An analysis of the experimental spectra has revealed that the amount of solvent in the hydration shell has a strong influence on the low-frequency protein conformational dynamics and also the arrangement of hydrogen bonds in the protein secondary structure. Furthermore at a hydration level >0.2 we identify collective backbone fluctuations in the protein secondary structure that are not present at low hydration. It is possible that these solvent induced modes are important for the biological function of the protein.
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Affiliation(s)
- K N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
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25
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Johnson ME, Malardier-Jugroot C, Murarka RK, Head-Gordon T. Hydration water dynamics near biological interfaces. J Phys Chem B 2009; 113:4082-92. [PMID: 19425247 DOI: 10.1021/jp806183v] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed classical molecular dynamics simulations using both fixed-charge and polarizable water and protein force fields to contrast the hydration dynamics near hydrophilic and amphiphilic peptides as a function of temperature. The high peptide concentrations we use serve as a model for the surface of folded proteins where hydration layers around each residue overlap significantly. Through simulation we determine that there are notable differences in the water dynamics analyzed from the outer and inner hydration layer regions of the amphiphilic peptide solution that explains the experimentally observed presence of two translational relaxations, while the hydrophilic peptide solution shows only a single non-Arrhenius translational process with no distinction between hydration layers. Given that water dynamics for the amphiphilic peptide system reproduces all known rotational and translational hydration dynamical anomalies exhibited by hydration water near protein surfaces, our analysis provides strong evidence that dynamical signatures near biological interfaces arises because of frustration in the hydration dynamics induced by chemical heterogeneity, as opposed to just topological roughness, of the protein surface.
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Affiliation(s)
- Margaret E Johnson
- Department of Bioengineering, University of California, Berkeley, 94720, USA
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26
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Svanberg C, Berntsen P, Johansson A, Hedlund T, Axén E, Swenson J. Structural relaxations of phospholipids and water in planar membranes. J Chem Phys 2009; 130:035101. [DOI: 10.1063/1.3054141] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Paciaroni A, Orecchini A, Cornicchi E, Marconi M, Petrillo C, Haertlein M, Moulin M, Schober H, Tarek M, Sacchetti F. Fingerprints of amorphous icelike behavior in the vibrational density of states of protein hydration water. PHYSICAL REVIEW LETTERS 2008; 101:148104. [PMID: 18851580 DOI: 10.1103/physrevlett.101.148104] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Indexed: 05/26/2023]
Abstract
The low-frequency modes of protein hydration water are investigated by inelastic neutron scattering. Experiments on both protonated and fully deuterated maltose binding protein samples allow us to unambiguously single out the contribution from water. The low-energy vibrational density of states of hydration water at 100 K is similar to the density of states of high- and low-density amorphous ice, and quite different from that of simple forms of crystalline ice. This result can be related to the picture of hydration water mass density depending on the protein surface curvature, which supports its glassy behavior.
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Affiliation(s)
- A Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia, Via A. Pascoli, I-06123 Perugia, Italy
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28
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O’Brien JT, Prell JS, Steill JD, Oomens J, Williams ER. Interactions of Mono- and Divalent Metal Ions with Aspartic and Glutamic Acid Investigated with IR Photodissociation Spectroscopy and Theory. J Phys Chem A 2008; 112:10823-30. [DOI: 10.1021/jp805787e] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeff D. Steill
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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29
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Spezia R, Bresson C, Auwer CD, Gaigeot MP. Solvation of Co(III)-Cysteinato Complexes in Water: A DFT-based Molecular Dynamics Study. J Phys Chem B 2008; 112:6490-9. [DOI: 10.1021/jp075774h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Riccardo Spezia
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
| | - Carole Bresson
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
| | - Christophe Den Auwer
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
| | - Marie-Pierre Gaigeot
- Laboratoire Analyse et Modelisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR-CNRS 8587, 91025 Evry Cedex, CEA Saclay, DEN/DPC/SECR/LSRM, 91191 Gif sur Yvette, France, CEA Marcoule, DEN/DRCP/SCPS, 3017 Bagnols sur Ceze, France, and Laboratoire de Physique Théorique de la Matiere Condensée LPTMC UMR-CNRS 7600, Université P/M Curie, 75052 Paris, France
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30
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Malardier-Jugroot C, Johnson ME, Murarka RK, Head-Gordon T. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Phys Chem Chem Phys 2008; 10:4903-8. [DOI: 10.1039/b806995f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Brovchenko I, Krukau A, Smolin N, Oleinikova A, Geiger A, Winter R. Thermal breaking of spanning water networks in the hydration shell of proteins. J Chem Phys 2007; 123:224905. [PMID: 16375508 DOI: 10.1063/1.2121708] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The presence of a spanning hydrogen-bonded network of water at the surface of biomolecules is important for their conformational stability, dynamics, and function. We have studied by computer simulations the clustering and percolation of water in the hydration shell of a small elastinlike peptide (ELP) and the medium-size protein staphylococcal nuclease (SNase), in aqueous solution. We have found that in both systems a spanning network of hydration water exists at low temperatures and breaks up with increasing temperature via a quasi-two-dimensional percolation transition. The thermal breaking of the spanning water network occurs at biologically relevant temperatures, in the temperature range, which is close to the temperature of the "inverse temperature transition" of ELP and the unfolding temperature of SNase, respectively.
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Affiliation(s)
- I Brovchenko
- Physical Chemistry, University of Dortmund, Otto-Hahn-Strasse 6, Dortmund D-44227, Germany.
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32
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Ratajska-Gadomska B, Bialkowski B, Gadomski W, Radzewicz C. Ultrafast optical Kerr effect spectroscopy of water confined in nanopores of the gelatin gel. J Chem Phys 2007; 126:184708. [PMID: 17508825 DOI: 10.1063/1.2730506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on the investigation of a short-time collective dynamics of water confined in the pores of the gelatin gel, using the femtosecond optical Kerr effect spectroscopy. The ultrafast responses of water molecules obtained in bulk liquid and in three concentrations of gelatin gels are explained theoretically, both in a long time and in a short time regime, taking into account all molecular motions. We prove that the contribution of molecules involved in tetrahedral, strongly H-bonded structures stabilizing the gel network increases with the gel concentration. On the other hand the long-time relaxation of water molecules is significantly slowed down in the gel pores.
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Affiliation(s)
- B Ratajska-Gadomska
- Laboratory of Physicochemistry of Dielectrics and Magnetics, Department of Chemistry, Warsaw University, ul. Zwirki i Wigury 101, 02-089 Warsaw, Poland.
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33
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34
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Russo D, Hura GL, Copley JRD. Effects of hydration water on protein methyl group dynamics in solution. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 75:040902. [PMID: 17500858 DOI: 10.1103/physreve.75.040902] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Indexed: 05/15/2023]
Abstract
Elastic and quasielastic neutron scattering experiments have been used to investigate the dynamics of methyl groups in a protein-model hydrophobic peptide in solution. The results suggest that, when the hydrophobic side chains are hydrated by a single hydration water layer, the only allowed motions are confined and attributed to librational and rotational movement associated with the methyl groups. They provide unique experimental evidence that the structural and dynamical properties of the interfacial water strongly influence the side-chain dynamics and the activation of diffusive motion.
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Affiliation(s)
- Daniela Russo
- CNR-INFM & CRS/SOFT, c/o Institut Laue Langevin, 6 rue J. Horowitz, BP156, F-38042 Grenoble, France
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35
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Helms V. Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules. Chemphyschem 2007; 8:23-33. [PMID: 17131430 DOI: 10.1002/cphc.200600298] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are key components of biological cells. For example, enzymes catalyze biochemical reactions, membrane transporters are responsible for uptake and release of critical and superfluous components from the cell environment, and structural proteins are responsible for the stability of the cell wall and cytoskeleton. Many of the diverse protein functions involve dynamic transitions ranging from small local atomic displacements up to large allosteric conformational changes. In any conformation, proteins are in contact with the universal solvent medium of cells, water. Water not only surrounds proteins but is often an integral part of proteins and also is involved in key mechanistic steps. This Minireview discusses recent experimental and theoretical results on the role of water for protein dynamics and function.
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Affiliation(s)
- Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany.
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36
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Buchsteiner A, Lerf A, Pieper J. Water Dynamics in Graphite Oxide Investigated with Neutron Scattering. J Phys Chem B 2006; 110:22328-38. [PMID: 17091972 DOI: 10.1021/jp0641132] [Citation(s) in RCA: 243] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Graphite oxide is an inorganic multilayer system that preserves the layered structure of graphite but not the conjugated bond structure. In the past few years, detailed studies of the static structure of graphite oxide were carried out. This was mainly done by NMR investigations and led to a new structural model of graphite oxide. The layer distance of graphite oxide increases with increasing humidity level, giving rise to different spacings of the carbon layers in the range from 6 to 12 A. As a consequence, different types of motions of water and functional groups appear. Information about the mobility of the water molecules is not yet complete but is crucial for the understanding of the structure of the carbon layers as well as the intercalation process. In this paper, the hydration- and temperature-dependent dynamic behavior of graphite oxide will be investigated by quasielastic neutron scattering using the time-of-flight spectrometer NEAT at the Hahn-Meitner-Institut Berlin. The character of the embedded water does not change over a wide range of hydration levels. Especially the interlayer water remains tightly bound and does not show any translational motion. In samples with excess water, however, the water is also distributed in noninterlayer voids, leading to the observation of additional motions of bulklike or confined water. The dynamic behavior of hydrated graphite oxide can be described by a consistent model that combines two two-site jump motions for the motions of the water molecules and the motions of OH groups.
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37
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Raschke TM. Water structure and interactions with protein surfaces. Curr Opin Struct Biol 2006; 16:152-9. [PMID: 16546375 DOI: 10.1016/j.sbi.2006.03.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 02/27/2006] [Accepted: 03/06/2006] [Indexed: 11/29/2022]
Abstract
The structure of liquid water and its interaction with biological molecules is a very active area of experimental and theoretical research. The chemically complex surfaces of protein molecules alter the structure of the surrounding layer of hydrating water molecules. The dynamics of hydration water can be detected by a series of experimental techniques, which show that hydration waters typically have slower correlation times than water in bulk. Specific water-mediated interactions in protein complexes have been studied in detail, and these interactions have been incorporated into potential energy functions for protein folding and design. The subtle changes in the structure of hydration water have been investigated by theoretical studies.
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Affiliation(s)
- Tanya M Raschke
- Bio-X, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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38
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Valle-Delgado JJ, Molina-Bolívar JA, Galisteo-González F, Gálvez-Ruiz MJ, Feiler A, Rutland MW. Existence of hydration forces in the interaction between apoferritin molecules adsorbed on silica surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:9544-54. [PMID: 16207034 DOI: 10.1021/la050825s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The atomic force microscope, together with the colloid probe technique, has become a very useful instrument to measure interaction forces between two surfaces. Its potential has been exploited in this work to study the interaction between protein (apoferritin) layers adsorbed on silica surfaces and to analyze the effect of the medium conditions (pH, salt concentration, salt type) on such interactions. It has been observed that the interaction at low salt concentrations is dominated by electrical double layer (at large distances) and steric forces (at short distances), the latter being due to compression of the protein layers. The DLVO theory fits these experimental data quite well. However, a non-DLVO repulsive interaction, prior to contact of the protein layers, is observed at high salt concentration above the isoelectric point of the protein. This behavior could be explained if the presence of hydration forces in the system is assumed. The inclusion of a hydration term in the DLVO theory (extended DLVO theory) gives rise to a better agreement between the theoretical fits and the experimental results. These results seem to suggest that the hydration forces play a very important role in the stability of the proteins in the physiological media.
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Affiliation(s)
- J J Valle-Delgado
- Biocolloid and Fluid Physics Group, Department of Applied Physics, Science Faculty, University of Granada, 18071 Granada, Spain
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39
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Low frequency enzyme dynamics as a function of temperature and hydration: A neutron scattering study. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.05.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Russo D, Murarka RK, Copley JRD, Head-Gordon T. Molecular view of water dynamics near model peptides. J Phys Chem B 2005; 109:12966-75. [PMID: 16852609 PMCID: PMC2684815 DOI: 10.1021/jp051137k] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.
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Affiliation(s)
- Daniela Russo
- Authors to whom correspondence should be addressed. E-mail: ;
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41
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Kurkal V, Daniel RM, Finney JL, Tehei M, Dunn RV, Smith JC. Enzyme activity and flexibility at very low hydration. Biophys J 2005; 89:1282-7. [PMID: 15894640 PMCID: PMC1366612 DOI: 10.1529/biophysj.104.058677] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent measurements have demonstrated enzyme activity at hydrations as low as 3%. This raises the question of whether hydration-induced enzyme flexibility is important for activity. Here, to address this, picosecond dynamic neutron scattering experiments are performed on pig liver esterase powders at 0%, 3%, 12%, and 50% hydration by weight and at temperatures ranging from 120 to 300 K. At all temperatures and hydrations, significant quasielastic scattering intensity is found in the protein, indicating the presence of anharmonic, diffusive motion. As the hydration increases, a temperature-dependent dynamical transition appears and strengthens involving additional diffusive motion. The implication of these results is that, although the additional hydration-induced diffusive motion in the protein detected here may be related to increased activity, it is not required for the enzyme to function.
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Affiliation(s)
- V Kurkal
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Germany
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Gadomski W, Ratajska-Gadomska B. Evolution of water structure in biopolymer solutions during the gelation process. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.10.055] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Russo D, Murarka RK, Hura G, Verschell E, Copley JRD, Head-Gordon T. Evidence for Anomalous Hydration Dynamics near a Model Hydrophobic Peptide. J Phys Chem B 2004. [DOI: 10.1021/jp046847p] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniela Russo
- Department of Bioengineering and Graduate Group in Biophysics, University of California, Berkeley, California 94720, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562
| | - Rajesh K. Murarka
- Department of Bioengineering and Graduate Group in Biophysics, University of California, Berkeley, California 94720, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562
| | - Greg Hura
- Department of Bioengineering and Graduate Group in Biophysics, University of California, Berkeley, California 94720, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562
| | - Elizabeth Verschell
- Department of Bioengineering and Graduate Group in Biophysics, University of California, Berkeley, California 94720, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562
| | - John R. D. Copley
- Department of Bioengineering and Graduate Group in Biophysics, University of California, Berkeley, California 94720, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562
| | - Teresa Head-Gordon
- Department of Bioengineering and Graduate Group in Biophysics, University of California, Berkeley, California 94720, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562
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Abstract
The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulation for both the completely deuterated and completely hydrogenated leucine monomer. The NALMA-water system and the QENS data together provide a unique study for characterizing the dynamics of different hydration layers near a prototypical hydrophobic side chain and the backbone of which it is attached. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational and rotational water dynamics at the highest solute concentrations are found to be highly suppressed as characterized by long residential time and slow diffusion coefficients. The analysis of the more dilute concentration solutions models the first hydration shell with the 2.0 M spectra. We find that for outer layer hydration dynamics that the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis of the first hydration shell water dynamics shows spatially heterogeneous water dynamics, with fast water motions near the hydrophobic side chain, and much slower water motions near the hydrophilic backbone. We discuss the hydration dynamics results of this model protein system in the context of protein function and protein-protein recognition.
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Affiliation(s)
- Daniela Russo
- Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA
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45
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Kríz Z, Otyepka M, Bártová I, Koca J. Analysis of CDK2 active-site hydration: a method to design new inhibitors. Proteins 2004; 55:258-74. [PMID: 15048820 DOI: 10.1002/prot.20026] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X-ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side-chain is buried. Exchange of active-site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine complex simulation, two water molecules that arrange interaction between the inhibitor and the enzyme via an H-bond were observed. Two stable water molecules in the trajectory of the free CDK2 were found that occupy the same position as the nitrogens N3 and N9 of the isopentenyladenine or N1 and N6 nitrogens of the adenosine triphosphate (ATP). The positions of structural water molecules were compared with the positions of substrate polar groups and crystallographic water molecules found in the Brookhaven Protein Data Bank for various CDK2 complexes. It was concluded that tracing tightly bound water molecules may substantially help in designing new inhibitors.
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Affiliation(s)
- Zdenek Kríz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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46
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Noinville S, Revault M, Quiquampoix H, Baron MH. Structural effects of drying and rehydration for enzymes in soils: a kinetics-FTIR analysis of α-chymotrypsin adsorbed on montmorillonite. J Colloid Interface Sci 2004; 273:414-25. [PMID: 15082376 DOI: 10.1016/j.jcis.2004.01.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Accepted: 01/30/2004] [Indexed: 10/26/2022]
Abstract
The effects of desiccation and rehydration cycles encountered by extracellular enzymes in soils are studied on -chymotrypsin adsorbed on montmorillonite. The controlled hygrometric FTIR cell used in this study enables to monitor drying and rehydration steps undergone by the -chymotrypsin-montmorillonite suspension or by the enzyme alone. Relative humidity (RH) determines the amount of deuterated water in the FTIR cell atmosphere. The molar water/protein ratio (W/P) as well as the conformational and solvation states of the enzyme have been determined using H/D exchange monitored by FTIR-transmission spectroscopy. When the W/P ratio decreases from 3500 to approximately 400, unfolding of beta-secondary structure in three different domains involves about 8% of the polypeptide backbone with respect to the most solvated states. Desiccation induces beta-unfolding, which opens channels allowing free vapor water molecules to diffuse into the enzyme at 15% RH. On drying to 0% RH, displacements of internal water (H2O) in the enzyme are demonstrated by reverse peptide isotopic exchanges (COND ==> CONH). Specific beta-structures, only formed in highly solvated states, sequester around 20 internal H2O molecules. Indeed, most of the unfolded secondary structures during the drying step are refolded at W/P approximately 1000 during rehydration. However, self-association hinders the recovery of the initial closed tertiary structure. The pD-dependent structural changes controlling inward and outward water diffusion are suppressed, whether the protein is initially in an adsorbed state or in solution. Changes in secondary structures encountered during desiccation/rehydration cycle are similar for the protein either free or in the adsorbed state. Thus domains that are unfolded by adsorption are not concerned by the desiccation/rehydration cycle.
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Affiliation(s)
- S Noinville
- Laboratoire de Dynamique, Interactions et Réactivité CNRS-Université Paris 6, UMR 7075, 2 rue Henri Dunant, 94320 Thiais, France.
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47
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Valle-Delgado JJ, Molina-Bolívar JA, Galisteo-González F, Gálvez-Ruiz MJ, Feiler A, Rutland MW. Interaction Forces between BSA Layers Adsorbed on Silica Surfaces Measured with an Atomic Force Microscope. J Phys Chem B 2004. [DOI: 10.1021/jp0374197] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Abstract
Protein-water interactions are key to biological function. They have an underlying dynamic component that pervades the functional roles associated both with particular systems and with the properties of proteins in general. This article focuses on the specific ways in which the dynamics of water are important to protein structure, motion and adaptability to changes in the protein environment.
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Affiliation(s)
- Carla Mattos
- Dept Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, NC 27695-7622, USA.
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49
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Róg T, Murzyn K, Pasenkiewicz-Gierula M. The dynamics of water at the phospholipid bilayer surface: a molecular dynamics simulation study. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00002-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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50
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Abstract
Freeze-substitution is a physicochemical process in which biological specimens are immobilized and stabilized for microscopy. Water frozen within cells is replaced by organic solvents at subzero temperatures. Freeze-substitution is widely used for ultrastructural and immunocytochemical analyses of cells by transmission and scanning electron microscopy. Less well recognized is its superiority over conventional chemical fixation in preserving labile and rare tissue antigens for immunocytochemistry by light microscopy. In the postgenome era, the focus of molecular genetics will shift from analyzing DNA sequence structure to elucidating the function of gene networks, the intercellular effects of polygenetic diseases, and the conformational rearrangements of proteins in situ. Novel strategies will be needed to integrate knowledge of chemical structures of normal and abnormal macromolecules with the physiology and developmental biology of cells and tissues from whole organisms. This review summarizes the progress and future prospects of freeze-substitution for such explorations.
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Affiliation(s)
- R Shiurba
- Misato Inc., Satte-shi, Saitama, Japan
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