1
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Omwansu W, Musembi R, Derese S. Graph-based analysis of H-bond networks and unsupervised learning reveal conformational coupling in prion peptide segments. Phys Chem Chem Phys 2024. [PMID: 39291469 DOI: 10.1039/d4cp02123a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
In this study, we employed a comprehensive computational approach to investigate the physical chemistry of the water networks surrounding hydrated peptide segments, as derived from molecular dynamics simulations. Our analysis uncovers a complex interplay of direct and water-mediated hydrogen bonds that intricately weave through the peptides. We demonstrate that these hydrogen bond networks encode critical information about the peptides' conformational behavior, with the dimensionality of these networks showing sensitivity to the peptides' conformations. Additionally, we estimated the free-energy landscape of the peptides across various conformations, revealing that their structures are predominantly characterized by unfolded, partially folded, and folded configurations, resulting in broad and rugged free-energy surfaces due to the numerous degrees of freedom contributed by the surrounding solvent. Importantly, the structured nature of this free-energy landscape becomes obscured when conventional collective variables, such as the number of hydrogen bonds, are used. Our findings provide new insights into the molecular mechanisms that couple protein and solvent degrees of freedom, highlighting their significance in the functioning of biological systems.
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Affiliation(s)
- Wycliffe Omwansu
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Robinson Musembi
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
| | - Solomon Derese
- Department of Chemistry, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
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2
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Vural D, Shrestha UR, Petridis L, Smith JC. Water molecule ordering on the surface of an intrinsically disordered protein. Biophys J 2023; 122:4326-4335. [PMID: 37838830 PMCID: PMC10722392 DOI: 10.1016/j.bpj.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023] Open
Abstract
The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.
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Affiliation(s)
- Derya Vural
- Department of Physics, Marmara University, Istanbul, Türkiye; Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
| | - Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
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3
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Li Y, Han Z, Ma C, Hong L, Ding Y, Chen Y, Zhao J, Liu D, Sun G, Zuo T, Cheng H, Han CC. Structure and dynamics of supercooled water in the hydration layer of poly(ethylene glycol). STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054901. [PMID: 36090796 PMCID: PMC9462885 DOI: 10.1063/4.0000158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
The statics and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) (PEG) were studied by a combination of quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. Two samples, that is, hydrogenated PEG/deuterated water (h-PEG/D2O) and fully deuterated PEG/hydrogenated water (d-PEG/H2O) with the same molar ratio of ethylene glycol (EG) monomer to water, 1:1, are compared. The QENS data of h-PEG/D2O show the dynamics of PEG, and that of d-PEG/H2O reveals the motion of water. The temperature-dependent elastic scattering intensity of both samples has shown transitions at supercooled temperature, and these transition temperatures depend on the energy resolution of the instruments. Therefore, neither one is a phase transition, but undergoes dynamic process. The dynamic of water can be described as an Arrhenius to super-Arrhenius transition, and it reveals the hydrogen bonding network relaxation of hydration water around PEG at supercooled temperature. Since the PEG-water hydrogen bond structural relaxation time from MD is in good agreement with the average relaxation time from QENS (d-PEG/H2O), MD may further reveal the atomic pictures of the supercooled hydration water. It shows that hydration water molecules form a series of pools around the hydrophilic oxygen atom of PEG. At supercooled temperature, they have a more bond ordered structure than bulk water, proceed a trapping sites diffusion on the PEG surface, and facilitate the structural relaxation of PEG backbone.
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Affiliation(s)
| | | | | | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanwei Ding
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Ye Chen
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Junpeng Zhao
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Dong Liu
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | - Guangai Sun
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | | | - He Cheng
- Author to whom correspondence should be addressed: . Tel.: +86-769-8915-6445. Fax: +86-769-8915-6441
| | - Charles C. Han
- Institute for Advanced Study, Shenzhen University, Shenzhen 508060, China
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4
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Gómez S, Bottari C, Egidi F, Giovannini T, Rossi B, Cappelli C. Amide Spectral Fingerprints are Hydrogen Bonding-Mediated. J Phys Chem Lett 2022; 13:6200-6207. [PMID: 35770492 PMCID: PMC9272440 DOI: 10.1021/acs.jpclett.2c01277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N-acetylglycine-N-methylamide (NAGMA) and N-acetylalanine-N-methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.
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Affiliation(s)
- Sara Gómez
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Cettina Bottari
- Elettra
Sincrotrone Trieste S.C.p.A., S. S. 14 Km 163.5 in Area Science Park, I-34149, Trieste, Italy
| | - Franco Egidi
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Tommaso Giovannini
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Barbara Rossi
- Elettra
Sincrotrone Trieste S.C.p.A., S. S. 14 Km 163.5 in Area Science Park, I-34149, Trieste, Italy
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Povo, Trento, Italy
| | - Chiara Cappelli
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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5
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Lupi L, Bracco B, Sassi P, Corezzi S, Morresi A, Fioretto D, Comez L, Paolantoni M. Hydration Dynamics of Model Peptides with Different Hydrophobic Character. Life (Basel) 2022; 12:life12040572. [PMID: 35455063 PMCID: PMC9031890 DOI: 10.3390/life12040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, 00146 Rome, Italy;
| | - Brenda Bracco
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
| | - Assunta Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
- Correspondence: (L.C.); (M.P.)
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
- Correspondence: (L.C.); (M.P.)
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6
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Laity PR, Holland C. Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020551. [PMID: 35056868 PMCID: PMC8781151 DOI: 10.3390/molecules27020551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023]
Abstract
The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.
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7
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions. Int J Mol Sci 2021; 22:ijms22179350. [PMID: 34502252 PMCID: PMC8431001 DOI: 10.3390/ijms22179350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.
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8
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Chiaoprakobkij N, Suwanmajo T, Sanchavanakit N, Phisalaphong M. Curcumin-Loaded Bacterial Cellulose/Alginate/Gelatin as A Multifunctional Biopolymer Composite Film. Molecules 2020; 25:E3800. [PMID: 32825570 PMCID: PMC7503693 DOI: 10.3390/molecules25173800] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022] Open
Abstract
Multifunctional biopolymer composites comprising mechanically-disintegrated bacterial cellulose, alginate, gelatin and curcumin plasticized with glycerol were successfully fabricated through a simple, facile, cost-effective mechanical blending and casting method. SEM images indicate a well-distributed structure of the composites. The water contact angles existed in the range of 50-70°. Measured water vapor permeability values were 300-800 g/m2/24 h, which were comparable with those of commercial dressing products. No release of curcumin from the films was observed during the immersion in PBS and artificial saliva, and the fluid uptakes were in the range of 100-700%. Films were stretchable and provided appropriate stiffness and enduring deformation. Hydrated films adhered firmly onto the skin. In vitro mucoadhesion time was found in the range of 0.5-6 h with porcine mucosa as model membrane under artificial saliva medium. The curcumin-loaded films had substantial antibacterial activity against E. coli and S. aureus. The films showed non-cytotoxicity to human keratinocytes and human gingival fibroblasts but exhibited potent anticancer activity in oral cancer cells. Therefore, these curcumin-loaded films showed their potential for use as leave-on skin applications. These versatile films can be further developed to achieve desirable characteristics for local topical patches for wound care, periodontitis and oral cancer treatment.
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Affiliation(s)
- Nadda Chiaoprakobkij
- Biomedical Engineering Program, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand;
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thapanar Suwanmajo
- Centre of Excellence in Materials Science and Technology, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Neeracha Sanchavanakit
- Center of Excellence for Regenerative Dentistry, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Muenduen Phisalaphong
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
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9
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Russo D, Pelosi C, Wurm FR, Frick B, Ollivier J, Teixeira J. Insight into Protein-Polymer Conjugate Relaxation Dynamics: The Importance of Polymer Grafting. Macromol Biosci 2020; 20:e1900410. [PMID: 32285628 DOI: 10.1002/mabi.201900410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/27/2020] [Indexed: 01/03/2023]
Abstract
The bio and chemical physics of protein-polymer conjugates are related to parameters that characterize each component. With this work, it is intended to feature the dynamical properties of the protein-polymer conjugate myoglobin (Mb)-poly(ethyl ethylene phosphate), in the ps and ns time scales, in order to understand the respective roles of the protein and of the polymer size in the dynamics of the conjugate. Elastic and quasi-elastic neutron scattering is performed on completely hydrogenated samples with variable number of polymer chains covalently attached to the protein. The role of the polymer length in the protein solvation and internal dynamics is investigated using two conjugates formed by polymers of different molecular weight. It is confirmed that the flexibility of the complex increases with the number of grafted polymer chains and that a sharp dynamical transition appears when either grafting density or polymer molecular weight are high. It is shown that protein size is crucial for the polymer structural organization and interaction on the protein surface and it is established that the glass properties of the polymer change upon conjugation. The results give a better insight of the equivalence of the polymer coating and the role of water on the surface of proteins.
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Affiliation(s)
- Daniela Russo
- Consiglio Nazionale delle Ricerche & Istituto Officina dei Materiali c/o Institut Laue Langevin, Grenoble, 38042, France.,Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW, 2234, Australia
| | - Chiara Pelosi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi, Pisa, 56124, Italy
| | - Frederik R Wurm
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, Mainz, 55128, Germany
| | | | | | - Jose Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, Gif-sur-Yvette Cedex, 91191, France
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10
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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci U S A 2019; 116:20446-20452. [PMID: 31548393 DOI: 10.1073/pnas.1907251116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.
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11
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Panuszko A, Nowak M, Bruździak P, Stasiulewicz M, Stangret J. Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Jong K, Hassanali AA. A Data Science Approach to Understanding Water Networks Around Biomolecules: The Case of Tri-Alanine in Liquid Water. J Phys Chem B 2018; 122:7895-7906. [DOI: 10.1021/acs.jpcb.8b03644] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- KwangHyok Jong
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- SISSA—Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
- Department of Physics, Kim Il Sung University, Ryongnam Dong, Taesong District, Pyongyang, D. P. R. Korea
| | - Ali A. Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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13
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Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
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Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
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14
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Zhang Q, Chen H, Wu T, Jin T, Pan Z, Zheng J, Gao Y, Zhuang W. The opposite effects of sodium and potassium cations on water dynamics. Chem Sci 2017; 8:1429-1435. [PMID: 28451283 PMCID: PMC5390786 DOI: 10.1039/c6sc03320b] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/13/2016] [Indexed: 01/05/2023] Open
Abstract
Water rotational dynamics in NaSCN and KSCN solutions at a series of concentrations are investigated using femtosecond infrared spectroscopy and theory. Femtosecond infrared measurements, consistent with previous NMR observations, detect that sodium slows down while potassium accelerates the water O-H bond rotation. Results of reported neutron scattering measurements, on the other hand, suggested that these two cations have similar structure-breaking effects on water, and therefore should both accelerate water rotation through the presumably dominating large-amplitude angular jump component. To explain this discrepancy, theoretical studies with both classical and ab initio models were carried out, which indicate that both ions indeed accelerate the large-amplitude angular jump rotation of the water molecules, while the observed cation specific effect originates from the non-negligible opposite impact of the sodium and potassium cations on the diffusive rotation of water molecules.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou , Fujian 350002 , China .
- Department of Chemistry , Bohai University , Jinzhou 121013 , China
| | - Hailong Chen
- Department of Chemistry , Rice University , Houston , TX 77005 , USA .
| | - Tianmin Wu
- Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen University , Xiamen , Fujian 361005 , China
| | - Tan Jin
- State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou , Fujian 350002 , China .
| | - Zhijun Pan
- Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Junrong Zheng
- Department of Chemistry , Rice University , Houston , TX 77005 , USA .
- College of Chemistry and Molecular Engineering , Beijing National Laboratory for Molecular Sciences , Peking University , Beijing 100871 , China .
| | - Yiqin Gao
- College of Chemistry and Molecular Engineering , Beijing National Laboratory for Molecular Sciences , Peking University , Beijing 100871 , China .
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou , Fujian 350002 , China .
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15
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Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016; 116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Affiliation(s)
| | - Ali Hassanali
- International Center for Theoretical Physics, Condensed Matter and Statistical Physics 34151 Trieste, Italy
| | - Martina Havenith
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Richard Henchman
- Manchester Institute of Biotechnology The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Pohl
- Johannes Kepler University , Gruberstrasse, 40 4020 Linz, Austria
| | - Fabio Sterpone
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Théorique 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University , 751 24 Uppsala, Sweden
| | - Yao Xu
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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16
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Rossi B, Venuti V, Mele A, Punta C, Melone L, D'Amico F, Gessini A, Crupi V, Majolino D, Trotta F, Masciovecchio C. Vibrational signatures of the water behaviour upon confinement in nanoporous hydrogels. Phys Chem Chem Phys 2016; 18:12252-9. [DOI: 10.1039/c5cp07936e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational spectroscopy is used to investigate how the hydrogen-bond dynamics of water is influenced by nano-confinement and hydrophobic/hydrophilic solvation effects.
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Affiliation(s)
- B. Rossi
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
- Department of Physics University of Trento and INSTM Local Unit
- Trento
| | - V. Venuti
- Department of Physics and Earth Sciences
- University of Messina
- 98166 Messina
- Italy
| | - A. Mele
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM local unit
- Milano
- Italy
| | - C. Punta
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM local unit
- Milano
- Italy
| | - L. Melone
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM local unit
- Milano
- Italy
| | - F. D'Amico
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
| | - A. Gessini
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
| | - V. Crupi
- Department of Physics University of Trento and INSTM Local Unit
- Trento
- Italy
| | - D. Majolino
- Department of Physics University of Trento and INSTM Local Unit
- Trento
- Italy
| | - F. Trotta
- Department of Chemistry
- University of Torino
- 10125 Torino
- Italy
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17
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Duboué-Dijon E, Laage D. Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin. J Chem Phys 2015; 141:22D529. [PMID: 25494800 DOI: 10.1063/1.4902822] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. Here, we combine molecular dynamics simulations and analytic modeling to study the hydration shell structure and dynamics of a typical globular protein, ubiquitin, and of the spruce budworm hyperactive antifreeze protein over the 230-300 K temperature range. Our results show that the average perturbation induced by both proteins on the reorientation dynamics of water remains moderate and changes weakly with temperature. The dynamical heterogeneity arises mostly from the distribution of protein surface topographies and is little affected by temperature. The ice-binding face of the antifreeze protein induces a short-ranged enhancement of water structure and a greater slowdown of water reorientation dynamics than the non-ice-binding faces whose effect is similar to that of ubiquitin. However, the hydration shell of the ice-binding face remains less tetrahedral than the bulk and is not "ice-like". We finally show that the hydrogen bonds between water and the ice-binding threonine residues are particularly strong due to a steric confinement effect, thereby contributing to the strong binding of the antifreeze protein on ice crystals.
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Affiliation(s)
- Elise Duboué-Dijon
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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18
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Comez L, Perticaroli S, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Concentration dependence of hydration water in a model peptide. Phys Chem Chem Phys 2015; 16:12433-40. [PMID: 24829171 DOI: 10.1039/c4cp00840e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular dynamics of aqueous solutions of a model amphiphilic peptide is studied as a function of concentration by broad-band light scattering experiments. Similarly to protein aqueous solutions, a considerable retardation, of about a factor 6-8, of hydration water dynamics with respect to bulk water is found, showing a slight dependence on solute concentration. Conversely, the average number of water molecules perturbed by the presence of peptide, i.e. the hydration number, appears to be strongly modified by adding solute. Its behaviour, decreasing upon increasing concentration, can be interpreted considering the random close-to-contact condition experienced by solute particles. Overall, the present findings support the view of a "long range" effect of peptides on the surrounding water, extending beyond the first two hydration shells.
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Affiliation(s)
- Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy.
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19
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D'Amico F, Rossi B, Camisasca G, Bencivenga F, Gessini A, Principi E, Cucini R, Masciovecchio C. Slow-to-fast transition of hydrogen bond dynamics in acetamide hydration shell formation. Phys Chem Chem Phys 2015; 17:10987-92. [DOI: 10.1039/c5cp00486a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The acetamide hydration shell dynamics speeds up in a remarkable way upon increasing the water amount.
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Affiliation(s)
| | - Barbara Rossi
- Elettra – Sincrotrone Trieste
- I-34149 Trieste
- Italy
- Department of Physics
- University of Trento
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica
- Università Roma Tre
- I-00146 Rome
- Italy
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20
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Perticaroli S, Russo D, Paolantoni M, Gonzalez MA, Sassi P, Nickels JD, Ehlers G, Comez L, Pellegrini E, Fioretto D, Morresi A. Painting biological low-frequency vibrational modes from small peptides to proteins. Phys Chem Chem Phys 2015; 17:11423-31. [DOI: 10.1039/c4cp05388e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We use experiments and simulation to investigate the validity of different model systems used to study the low-frequency vibrations of proteins.
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Affiliation(s)
- S. Perticaroli
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Chemical and Materials Sciences Division
| | - D. Russo
- CNR-IOM
- Italy c/o Institut Laue Langevin
- France
- Institut Lumière Matière
- Université de Lyon 1
| | - M. Paolantoni
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | | | - P. Sassi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | - J. D. Nickels
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Chemistry
| | - G. Ehlers
- Quantum Condensed Matter Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - L. Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Dipartimento di Fisica e Geologia
| | | | - D. Fioretto
- Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
| | - A. Morresi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
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21
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Fogarty A, Laage D. Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation. J Phys Chem B 2014; 118:7715-29. [PMID: 24479585 PMCID: PMC4103960 DOI: 10.1021/jp409805p] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 12/27/2013] [Indexed: 02/08/2023]
Abstract
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.
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Affiliation(s)
- Aoife
C. Fogarty
- Department
of Chemistry, UMR ENS-CNRS-UPMC 8640, École
Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Department
of Chemistry, UMR ENS-CNRS-UPMC 8640, École
Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
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22
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Zhang Q, Xie W, Bian H, Gao YQ, Zheng J, Zhuang W. Microscopic Origin of the Deviation from Stokes–Einstein Behavior Observed in Dynamics of the KSCN Aqueous Solutions: A MD Simulation Study. J Phys Chem B 2013; 117:2992-3004. [DOI: 10.1021/jp400441e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning,
People’s Republic of China
- Department of Chemistry, Bohai University, Jinzhou 121000, China
| | - Wenjun Xie
- College of Chemistry and Molecular
Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - HongTao Bian
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Yi Qin Gao
- College of Chemistry and Molecular
Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Junrong Zheng
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Wei Zhuang
- State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning,
People’s Republic of China
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23
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Russo D, Gonzalez MA, Pellegrini E, Combet J, Ollivier J, Teixeira J. Evidence of Dynamical Constraints Imposed by Water Organization around a Bio–Hydrophobic Interface. J Phys Chem B 2013; 117:2829-36. [DOI: 10.1021/jp3094885] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniela Russo
- CNR-IOM c/o Institut Laue Langevin, 6 rue J.
Horowitz BP156, F-38042 Grenoble, France
| | | | - Eric Pellegrini
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - J. Combet
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - J. Ollivier
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex France
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24
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Kucukkal TG, Stuart SJ. Polarizable Molecular Dynamics Simulations of Aqueous Dipeptides. J Phys Chem B 2012; 116:8733-40. [DOI: 10.1021/jp300528m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tugba G. Kucukkal
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634,
United States
| | - Steven J. Stuart
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634,
United States
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25
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Combet S, Zanotti JM. Further evidence that interfacial water is the main "driving force" of protein dynamics: a neutron scattering study on perdeuterated C-phycocyanin. Phys Chem Chem Phys 2012; 14:4927-34. [PMID: 22388956 DOI: 10.1039/c2cp23725c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fundamental role of hydration water (also called interfacial water) is widely recognized in protein flexibility, especially in the existence of the so-called protein "dynamical transition" at around 220 K. In the present study, we take advantage of perdeuterated C-phycocyanin (CPC) and elastic incoherent neutron scattering (EINS) to distinguish between protein dynamics and interfacial water dynamics. Powders of hydrogenated (hCPC) and perdeuterated (dCPC) CPC protein have been hydrated, respectively, with D(2)O or H(2)O and measured by EINS to separately probe protein dynamics (hCPC/D(2)O) and water dynamics (dCPC/H(2)O) at different time- and length-scales. We find that "fast" (<20 ps) local mean-square displacements (MSD) of both protein and interfacial water coincide all along the temperature range, with the same dynamical transition temperature at ~220 K. On higher resolution (<400 ps), two different types of motions can be separated: (i) localized motions with the same amplitude for CPC and hydration water and two transitions at ~170 and ~240 K for both; (ii) large scale fluctuations exhibiting for both water molecules and CPC protein a single transition at ~240 K, with a significantly higher amplitude for the interfacial water than for CPC. Moreover, by comparing these motions with bulk water MSD measured under the same conditions, we show no coupling between bulk water dynamics and protein dynamics all along the temperature range. These results show that interfacial water is the main "driving force" governing both local and large scale motions in proteins.
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Affiliation(s)
- Sophie Combet
- Laboratoire Léon-Brillouin, UMR 12 CEA/CNRS, bât. 563, CEA-Saclay, F-91191 Gif-sur-Yvette, France.
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26
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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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27
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Mamontov E, Chu XQ. Water–protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions. Phys Chem Chem Phys 2012; 14:11573-88. [DOI: 10.1039/c2cp41443k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Segura JJ, Verdaguer A, Sacha GM, Fraxedas J. Dipolar origin of water etching of amino acid surfaces. Phys Chem Chem Phys 2011; 13:21446-50. [PMID: 22048449 DOI: 10.1039/c1cp22277e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The etching induced by water on hydrophobic (001) surfaces of enantiomeric L-, D- and racemic DL-valine crystals has been characterized by means of atomic force microscopy (AFM) at ambient conditions. Well-defined chiral parallelepipedic shallow patterns, one bilayer deep, are observed for the enantiomeric crystals with sides (steps) oriented along low index crystallographic directions. Hence, chirality can be readily identified by visual inspection of an AFM image after etching. The formation of such regular patterns can be rationalized using basic concepts of electrical dipolar interactions. The key factor that determines the relative etching rate for each step and thus defines the shape of the etching patterns is the orientation of the molecular dipoles with respect to the step edge. The simplicity of the approach allows the prediction of the effect of water etching on other amino acid crystals as well as the effect of the interaction of water with amino acid molecules forming part of more complex structures.
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Affiliation(s)
- J J Segura
- Centre d' Investigació en Nanociència i Nanotecnologia, Edifici CM-7, Campus UAB, Esfera UAB, E-08193 Bellaterra, Catalunya, Spain
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29
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Russo D, Pellegrini E, Gonzalez MA, Perticaroli S, Teixeira J. In situ molecular dynamics analysis of the water hydrogen bond at biomolecular sites: Hydrophobicity enhances dynamics heterogeneity. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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30
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Perticaroli S, Comez L, Paolantoni M, Sassi P, Morresi A, Fioretto D. Extended Frequency Range Depolarized Light Scattering Study of N-Acetyl-leucine-methylamide–Water Solutions. J Am Chem Soc 2011; 133:12063-8. [DOI: 10.1021/ja202272k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefania Perticaroli
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Lucia Comez
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Universitá di Perugia, Via Pascoli, I-06123, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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31
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Ravikumar KM, Hwang W. Role of hydration force in the self-assembly of collagens and amyloid steric zipper filaments. J Am Chem Soc 2011; 133:11766-73. [PMID: 21692533 DOI: 10.1021/ja204377y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In protein self-assembly, types of surfaces determine the force between them. Yet the extent to which the surrounding water contributes to this force remains as a fundamental question. Here we study three self-assembling filament systems that respectively have hydrated (collagen), dry nonpolar, and dry polar (amyloid) interfaces. Using molecular dynamics simulations, we calculate and compare local hydration maps and hydration forces. We find that the primary hydration shells are formed all over the surface, regardless of the types of the underlying amino acids. The weakly oscillating hydration force arises from coalescence and depletion of hydration shells as two filaments approach, whereas local water diffusion, orientation, or hydrogen-bonding events have no direct effect. Hydration forces between hydrated, polar, and nonpolar interfaces differ in the amplitude and phase of the oscillation relative to the equilibrium surface separation. Therefore, water-mediated interactions between these protein surfaces, ranging in character from "hydrophobic" to "hydrophilic", have a common molecular origin based on the robustly formed hydration shells, which is likely applicable to a broad range of biomolecular assemblies whose interfacial geometry is similar in length scale to those of the present study.
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32
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Russo D, Teixeira J, Kneller L, Copley JRD, Ollivier J, Perticaroli S, Pellegrini E, Gonzalez MA. Vibrational Density of States of Hydration Water at Biomolecular Sites: Hydrophobicity Promotes Low Density Amorphous Ice Behavior. J Am Chem Soc 2011; 133:4882-8. [DOI: 10.1021/ja109610f] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniela Russo
- CNR-IOM c/o Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, 91191 Gif-sur Yvette Cedex, France
| | - Larry Kneller
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - John R. D. Copley
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
| | - Jacques Ollivier
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - Stefania Perticaroli
- Dipartimento di Chimica, Università degli Studi di Perugia, Sezione di Chimica Fisica, via Elce di sotto 8, I-06123 Perugia, Italia
| | - Eric Pellegrini
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
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33
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Ding F, Liu W, Diao JX, Sun Y. Characterization of Alizarin Red S binding sites and structural changes on human serum albumin: a biophysical study. JOURNAL OF HAZARDOUS MATERIALS 2011; 186:352-359. [PMID: 21112139 DOI: 10.1016/j.jhazmat.2010.11.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 10/29/2010] [Accepted: 11/01/2010] [Indexed: 05/30/2023]
Abstract
Alizarin Red S (ARS), is a water-soluble, widely used anthraquinone dye synthesized by sulfonation of alizarin. In this report, the binding of ARS to human serum albumin (HSA) was characterized by employing fluorescence, UV/vis absorption, circular dichroism (CD), and molecular modeling methods. The data of fluorescence spectra displayed that the binding of ARS to HSA is the formation of HSA-ARS complex at 1:1 stoichiometric proportion. Hydrophobic probe 8-anilino-1-naphthalenesulfonic acid (ANS) was employed and elucidated that the dye was located in subdomain IIIA. This phenomenon corroborates the result of site-specific probe displacement experiments, which demonstrate the dye is at indole-benzodiazepine site (Sudlow's site II); and it is also consistent with guanidine hydrochloride (GuHCl) induced HSA unfolding studies and molecular modeling simulations. The features of the dye, which led to structural perturbations of HSA, have also been studied in detail by methods of UV/vis, CD and three-dimensional fluorescence spectroscopy.
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Affiliation(s)
- Fei Ding
- Department of Chemistry, China Agricultural University, Haidian District, Beijing, China
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Perticaroli S, Comez L, Paolantoni M, Sassi P, Lupi L, Fioretto D, Paciaroni A, Morresi A. Broadband depolarized light scattering study of diluted protein aqueous solutions. J Phys Chem B 2010; 114:8262-9. [PMID: 20509696 DOI: 10.1021/jp101896f] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A broadband depolarized light scattering (DLS) study is performed on diluted lysozyme aqueous solutions as a function of temperature and concentration. The dynamical susceptibility, obtained in a wide spectral range (0.6-36000 GHz) through the coupled use of interferometric and dispersive devices, is interpreted and compared with neutron scattering and Raman-induced optical Kerr-effect literature data, thus giving a general picture of relaxation phenomena. We show that the proposed approach represents a suitable tool for investigating the hydration dynamics of protein-water solutions. A detailed analysis of the quasi-elastic scattering region evidences the existence of two distinct relaxational processes at picosecond time scales. The fast process (fractions of picosecond) is attributed to bulk water dynamics, while the slow one (few picoseconds) is attributed to dynamical rearrangements of water molecules strongly influenced by the protein (hydration water). The retardation effect here estimated of about 6-7 can be regarded as a direct measure of the increased protein-water and water-water hydrogen bond stability of the water molecules within the protein hydration shell. Interestingly, a similar effect was previously observed on small hydrophilic sugar molecules. Moreover, backbone and side chains torsional motions of the protein in the 600-5300 GHz frequency range are found to be insensitive to thermal variations and to eventual changes occurring in the premelting zone.
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Russo D, Copley JR, Ollivier J, Teixeira J. On the behaviour of water hydrogen bonds at biomolecular sites: Dependences on temperature and on network dimensionality. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jasnin M, Stadler A, Tehei M, Zaccai G. Specific cellular water dynamics observed in vivo by neutron scattering and NMR. Phys Chem Chem Phys 2010; 12:10154-60. [DOI: 10.1039/c0cp01048k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Segura JJ, Verdaguer A, Cobián M, Hernández ER, Fraxedas J. Amphiphillic Organic Crystals. J Am Chem Soc 2009; 131:17853-9. [DOI: 10.1021/ja905961h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- J. J. Segura
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - A. Verdaguer
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - M. Cobián
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - E. R. Hernández
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - J. Fraxedas
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
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Russo D, Teixeira J, Ollivier J. The impact of hydration water on the dynamics of side chains of hydrophobic peptides: from dry powder to highly concentrated solutions. J Chem Phys 2009; 130:235101. [PMID: 19548762 DOI: 10.1063/1.3154383] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Elastic and quasielastic neutron scattering experiments are used to investigate the dynamics of side chains in proteins, using hydrophobic peptides, from dry and hydrated powders up to solutions, as models. The changes of the internal dynamics of a prototypical hydrophobic amino acid, N-acetyl-leucine-methylamide, and alanine amino acids are investigated as a function of water/peptide molecular ratio. While previous results have shown that, in concentrated solution, when the hydrophobic side chains are hydrated by a single hydration water layer, the only allowed motions are confined and can be attributed to librational/rotational movements associated with the methyl groups. In the present work we observe a dynamical evolution from dry to highly hydrated powder. We also observe rotational and diffusive motions and a dynamical transition at approximately 250 K for long side chain peptides while for peptides with short side chains, there is no dynamical transition but only rotational motions. With a local measurement of the influence of hydration water dynamics on the amino acid side chains dynamics, we provide unique experimental evidence that the structural and dynamical properties of interfacial water strongly influence the side chain dynamics and the activation of diffusive motions. We also emphasize that the side chain length has a role on the onset of dynamical transition.
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Affiliation(s)
- Daniela Russo
- Institut Laue Langevin, CNR-INFM and CRS/Soft, 6 rue J. Horowitz BP156, F-38042 Grenoble, France.
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