1
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Khan T, Das N, Negi KS, Bhowmik S, Sen P. Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability. Int J Biol Macromol 2023; 253:127100. [PMID: 37778586 DOI: 10.1016/j.ijbiomac.2023.127100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.
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Affiliation(s)
- Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Kuldeep Singh Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Suman Bhowmik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India.
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2
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The Hydrophobic Effect Studied by Using Interacting Colloidal Suspensions. Int J Mol Sci 2023; 24:ijms24032003. [PMID: 36768326 PMCID: PMC9916416 DOI: 10.3390/ijms24032003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Interactions between nanoparticles (NPs) determine their self-organization and dynamic processes. In these systems, a quantitative description of the interparticle forces is complicated by the presence of the hydrophobic effect (HE), treatable only qualitatively, and due to the competition between the hydrophobic and hydrophilic forces. Recently, instead, a sort of crossover of HE from hydrophilic to hydrophobic has been experimentally observed on a local scale, by increasing the temperature, in pure confined water and studying the occurrence of this crossover in different water-methanol solutions. Starting from these results, we then considered the idea of studying this process in different nanoparticle solutions. By using photon correlation spectroscopy (PCS) experiments on dendrimer with OH terminal groups (dissolved in water and methanol, respectively), we show the existence of this hydrophobic-hydrophilic crossover with a well defined temperature and nanoparticle volume fraction dependence. In this frame, we have used the mode coupling theory extended model to evaluate the measured time-dependent density correlation functions (ISFs). In this context we will, therefore, show how the measured spectra are strongly dependent on the specificity of the interactions between the particles in solution. The observed transition demonstrates that just the HE, depending sensitively on the system thermodynamics, determines the hydrophobic and hydrophilic interaction properties of the studied nanostructures surface.
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3
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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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4
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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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5
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Jiao S, Rivera Mirabal DM, DeStefano AJ, Segalman RA, Han S, Shell MS. Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics. Biomacromolecules 2022; 23:1745-1756. [PMID: 35274944 DOI: 10.1021/acs.biomac.1c01687] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. We also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Daniela M Rivera Mirabal
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemical Engineering, University of Puerto Rico, Mayagüez, Puerto Rico 00681, United States
| | - Audra J DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A Segalman
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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6
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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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7
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Cho Y, Christoff-Tempesta T, Kaser SJ, Ortony JH. Dynamics in supramolecular nanomaterials. SOFT MATTER 2021; 17:5850-5863. [PMID: 34114584 DOI: 10.1039/d1sm00047k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Self-assembly of amphiphilic small molecules in water leads to nanostructures with customizable structure-property relationships arising from their tunable chemistries. Characterization of these assemblies is generally limited to their static structures -e.g. their geometries and dimensions - but the implementation of tools that provide a deeper understanding of molecular motions has recently emerged. Here, we summarize recent reports showcasing dynamics characterization tools and their application to small molecule assemblies, and we go on to highlight supramolecular systems whose properties are substantially affected by their conformational, exchange, and water dynamics. This review illustrates the importance of considering dynamics in rational amphiphile design.
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Affiliation(s)
- Yukio Cho
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ty Christoff-Tempesta
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Samuel J Kaser
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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8
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Bilodeau CL, Lau EY, Roush DJ, Snyder MA, Cramer SM. Behavior of Water Near Multimodal Chromatography Ligands and Its Consequences for Modulating Protein-Ligand Interactions. J Phys Chem B 2021; 125:6112-6120. [PMID: 34097423 DOI: 10.1021/acs.jpcb.1c01549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multimodal chromatography is a powerful approach for purifying proteins that uses ligands containing multiple modes of interaction. Recent studies have shown that selectivity in multimodal chromatographic separations is a function of the ligand structure and geometry. Here, we performed molecular dynamics simulations to explore how the ligand structure and geometry affect ligand-water interactions and how these differences in solution affect the nature of protein-ligand interactions. Our investigation focused on three chromatography ligands: Capto MMC, Nuvia cPrime, and Prototype 4, a structural variant of Nuvia cPrime. First, the solvation characteristics of each ligand were quantified via three metrics: average water density, fluctuations, and residence time. We then explored how solvation was perturbed when the ligand was bound to the protein surface and found that the probability of the phenyl ring dewetting followed the order: Capto MMC > Prototype 4 > Nuvia cPrime. To explore how these differences in dewetting affect protein-ligand interactions, we calculated the probability of each ligand binding to different types of residues on the protein surface and found that the probability of binding to a hydrophobic residue followed the same order as the dewetting behavior. This study illustrates the role that wetting and dewetting play in modulating protein-ligand interactions.
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Affiliation(s)
- Camille L Bilodeau
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Edmond Y Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - David J Roush
- Biologics Process R&D, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mark A Snyder
- Process Chromatography Division, Bio-Rad Laboratories, 6000 James Watson Drive, Hercules, California 94547, United States
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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9
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Belousov R, Qaisrani MN, Hassanali A, Roldán É. First-passage fingerprints of water diffusion near glutamine surfaces. SOFT MATTER 2020; 16:9202-9216. [PMID: 32510065 DOI: 10.1039/d0sm00541j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their proximity to biological interfaces and can play an important role in processes such as protein folding and aggregation. In this work, we study the dynamics of water near glutamine surfaces-a system of interest in studies of neurodegenerative diseases. Combining molecular-dynamics simulations and stochastic modelling, we study how the mean first-passage time and related statistics of water molecules escaping subnanometer-sized regions vary from the interface to the bulk. Our analysis reveals a dynamical complexity that reflects underlying chemical and geometrical properties of the glutamine surfaces. From the first-passage time statistics of water molecules, we infer their space-dependent diffusion coefficient in directions normal to the surfaces. Interestingly, our results suggest that the mobility of water varies over a longer length scale than the chemical potential associated with the water-protein interactions. The synergy of molecular dynamics and first-passage techniques opens the possibility for extracting space-dependent diffusion coefficients in more complex, inhomogeneous environments that are commonplace in living matter.
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Affiliation(s)
- Roman Belousov
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
| | - Muhammad Nawaz Qaisrani
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy. and SISSA - International School for Advanced Studies, Via Bonomea 265, 34136 Trieste, Italy
| | - Ali Hassanali
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
| | - Édgar Roldán
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
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10
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Qaisrani MN, Grisanti L, Gebauer R, Hassanali A. Structural and dynamical heterogeneities at glutamine-water interfaces. Phys Chem Chem Phys 2019; 21:16083-16094. [PMID: 31298261 DOI: 10.1039/c9cp02259g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The behavior of water at the surfaces of solid amino acid crystals has received little attention despite its importance in nucleation processes. In this work, we take a first step to fill this gap by using molecular dynamics simulations to study the structural and dynamical properties of water near the (100), (010) and (001) surfaces of l-glutamine crystals. These highly hydrophilic surfaces serve as excellent model systems for interrogating the behavior of water. Despite having the same molecular composition, water at each surface displays characteristic structural, orientational and dynamical correlations. This behavior is tuned by how the different chemical groups of amino acids make contact with the liquid phase. All three surfaces yield a glassy layer of interfacial water which is reflected in different ways such as the presence of a rotationally arrested layer of water molecules and substantial slow down of the diffusion of water near the interface. By increasing the concentration of molecules in solution, we show that the binding of glutamine molecules to the crystal surface creates a crowded environment involving pockets of trapped water molecules altering the water dynamics in a highly non-trivial manner suggesting that the solvent dynamics may have important implications on crystal nucleation.
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Affiliation(s)
- Muhammad Nawaz Qaisrani
- International School for Advanced Studies, Via Bonomea 265, 34136 Trieste, Italy and The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy.
| | - Luca Grisanti
- Divison of Theoretical Physics - Institut Ruer Bošković (IRB), Bijenička cesta 54, 10000, Zagreb, Croatia.
| | - Ralph Gebauer
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy.
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy.
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11
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Dynamics Properties of Photosynthetic Microorganisms Probed by Incoherent Neutron Scattering. Biophys J 2019; 116:1759-1768. [PMID: 31003761 DOI: 10.1016/j.bpj.2019.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 01/06/2023] Open
Abstract
Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Hence, a more flexible environment in the PQ-binding niche has been associated to a less efficient ET. A similar function/dynamics relationship was also demonstrated in Rhodobacter sphaeroides reaction centers having inhibited ET, indicating that flexibility at the quinones region plays a crucial role in evolutionarily distant organisms. Instead, a different functional/dynamical correlation was observed in algal mutants hosting a single amino acid replacement residing in a D1 domain far from the PQ-binding niche. Noteworthy, this mutant displayed the highest degree of flexibility, and besides having a nativelike ET efficiency in physiological conditions, it acquired novel, to our knowledge, phenotypic traits enabling it to preserve a high maximal quantum yield of photosystem II photochemistry in extreme habitats. Overall, in the nanosecond timescale, the degree of the observed flexibility is related to the mutation site; in the picosecond timescale, we highlighted the presence of a more pronounced dynamic heterogeneity in all mutants compared to the native cells, which could be related to a marked chemically heterogeneous environment.
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12
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Pluhařová E, Jungwirth P, Matubayasi N, Marsalek O. Structure and Dynamics of the Hydration Shell: Spatially Decomposed Time Correlation Approach. J Chem Theory Comput 2019; 15:803-812. [PMID: 30537825 DOI: 10.1021/acs.jctc.8b00111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular simulations provide insight into solvation structures and dynamics with unparalleled spatial and temporal resolution. Here, we take advantage of this fact and develop a set of generally applicable computational tools for a detailed analysis of the hydration shell around an ionic or molecular solute. These tools allow us to quantify and visualize orientationally resolved radial distribution functions as well as distance-resolved orientational time-correlation functions of water molecules surrounding the solute. Such a detailed view of the hydration shells allows us to unravel important structural and dynamical features, which are not accessible when employing standard analysis techniques.
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Affiliation(s)
- Eva Pluhařová
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 2155/3 , 18223 Prague 8 , Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Prague 6 , Czech Republic
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , Toyonaka, Osaka 560-8531 , Japan.,Elements Strategy Initiative for Catalysts and Batteries , Kyoto University , Katsura, Kyoto 615-8520 , Japan
| | - Ondrej Marsalek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Prague 6 , Czech Republic.,Charles University , Faculty of Mathematics and Physics , Ke Karlovu 3 , 12116 Prague 2 , Czech Republic
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13
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Jackson GL, Mantha S, Kim SA, Diallo SO, Herwig KW, Yethiraj A, Mahanthappa MK. Ion-Specific Confined Water Dynamics in Convex Nanopores of Gemini Surfactant Lyotropic Liquid Crystals. J Phys Chem B 2018; 122:10031-10043. [PMID: 30251848 DOI: 10.1021/acs.jpcb.8b05942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The impact of pore geometry and functionality on the dynamics of water nanoconfined in porous media are the subject of some debate. We report the synthesis and small-angle X-ray scattering (SAXS) characterization of a series of perdeuterated gemini surfactant lyotropic liquid crystals (LLCs), in which convex, water-filled nanopores of well-defined dimensions are lined with carboxylate functionalities. Quasielastic neutron scattering (QENS) measurements of the translational water dynamics in these dicarboxylate LLC nanopores as functions of the surfactant hydration state and the charge compensating counterion (Na+, K+, NMe4+) reveal that the measured dynamics depend primarily on surfactant hydration, with an unexpected counterion dependence that varies with hydration number. We rationalize these trends in terms of a balance between counterion-water attractions and the nanopore volume excluded by the counterions. On the basis of electron density maps derived from SAXS analyses of these LLCs, we directly show that the volume excluded by the counterions depends on both their size and spatial distribution in the water-filled channels. The translational water dynamics in the convex pores of these LLCs are also slower than those reported in the concave pores of AOT reverse micelles, implying that water dynamics also depend on the nanopore curvature.
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Affiliation(s)
- Grayson L Jackson
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Sriteja Mantha
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Sung A Kim
- Department of Chemical Engineering & Materials Science , University of Minnesota , 421 Washington Avenue, S.E. , Minneapolis , Minnesota 55455 , United States
| | | | | | - Arun Yethiraj
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Mahesh K Mahanthappa
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States.,Department of Chemical Engineering & Materials Science , University of Minnesota , 421 Washington Avenue, S.E. , Minneapolis , Minnesota 55455 , United States
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14
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Mohanta D, Jana M. Effects of ethanol on the secondary structure specific hydration properties of Chymotrypsin Inhibitor 2 in its folded and unfolded forms. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1496246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Dayanidhi Mohanta
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
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15
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Computational discovery of chemically patterned surfaces that effect unique hydration water dynamics. Proc Natl Acad Sci U S A 2018; 115:8093-8098. [PMID: 30038028 DOI: 10.1073/pnas.1807208115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The interactions of water with solid surfaces govern their apparent hydrophobicity/hydrophilicity, influenced at the molecular scale by surface coverage of chemical groups of varied nonpolar/polar character. Recently, it has become clear that the precise patterning of surface groups, and not simply average surface coverage, has a significant impact on the structure and thermodynamics of hydration layer water, and, in turn, on macroscopic interfacial properties. Here we show that patterning also controls the dynamics of hydration water, a behavior frequently thought to be leveraged by biomolecules to influence functional dynamics, but yet to be generalized. To uncover the role of surface heterogeneities, we couple a genetic algorithm to iterative molecular dynamics simulations to design the patterning of surface functional groups, at fixed coverage, to either minimize or maximize proximal water diffusivity. Optimized surface configurations reveal that clustering of hydrophilic groups increases hydration water mobility, while dispersing them decreases it, but only if hydrophilic moieties interact with water through directional, hydrogen-bonding interactions. Remarkably, we find that, across different surfaces, coverages, and patterns, both the chemical potential for inserting a methane-sized hydrophobe near the interface and, in particular, the hydration water orientational entropy serve as strong predictors for hydration water diffusivity, suggesting that these simple thermodynamic quantities encode the way surfaces control water dynamics. These results suggest a deep and intriguing connection between hydration water thermodynamics and dynamics, demonstrating that subnanometer chemical surface patterning is an important design parameter for engineering solid-water interfaces with applications spanning separations to catalysis.
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16
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Srivastava A, Debnath A. Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations. J Chem Phys 2018. [DOI: 10.1063/1.5011803] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
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17
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Sharma S, Biswas P. Hydration water dynamics around a protein surface: a first passage time approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:035101. [PMID: 29192889 DOI: 10.1088/1361-648x/aa9eab] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A stochastic noise-driven dynamic model is proposed to study the diffusion of water molecules around a protein surface, under the effect of thermal fluctuations that arise due to the collision of water molecules with the surrounding environment. The underlying dynamics of such a system may be described in the framework of the generalized Langevin equation, where the thermal fluctuations are assumed to be algebraically correlated in time, which governs the non-Markovian behavior of the system. Results of the calculations of mean-square displacement and the velocity autocorrelation function reveal that the hydration water around the protein surface follows subdiffusive dynamics at long times. Analytical expressions for the first passage time distribution, survival probability, mean residence time and mean first passage time of water molecules are derived for different boundary conditions, to analyze hydration water dynamics under the effect of thermally correlated noise. The results depict a unimodal distribution of the first passage time unlike Brownian motion. The survival probability of hydration water follows a stretched exponential decay for both boundary conditions. The mean residence time of the hydration water molecule for different initial positions increases with increase in the complexity/heterogeneity of the surrounding environment for both boundary conditions. The mean first passage time of the water molecule to reach the absorbing/reflecting boundary follows an asymptotic power law with respect to the thickness of the hydration layer, and increases with increase in the complexity/heterogeneity of the environment.
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Affiliation(s)
- Shivangi Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
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18
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Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
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19
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Barnes R, Sun S, Fichou Y, Dahlquist FW, Heyden M, Han S. Spatially Heterogeneous Surface Water Diffusivity around Structured Protein Surfaces at Equilibrium. J Am Chem Soc 2017; 139:17890-17901. [PMID: 29091442 PMCID: PMC6021025 DOI: 10.1021/jacs.7b08606] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hydration water on the surface of a protein is thought to mediate the thermodynamics of protein-ligand interactions. For hydration water to play a role beyond modulating global protein solubility or stability, the thermodynamic properties of hydration water must reflect on the properties of the heterogeneous protein surface and thus spatially vary over the protein surface. A potent read-out of local variations in thermodynamic properties of hydration water is its equilibrium dynamics spanning picosecond to nanosecond time scales. In this study, we employ Overhauser dynamic nuclear polarization (ODNP) to probe the equilibrium hydration water dynamics at select sites on the surface of Chemotaxis Y (CheY) in dilute solution. ODNP reports on site-specific hydration water dynamics within 5-10 Å of a label tethered to the biomolecular surface on two separate time scales of motion, corresponding to diffusive water (DW) and protein-water coupled motions, referred to as bound water (BW). We find DW dynamics to be highly heterogeneous across the surface of CheY. We identify a significant correlation between DW dynamics and the local hydropathy of the CheY protein surface, empirically determined by molecular dynamics (MD) simulations, and find the more hydrophobic sites to be hydrated with slower diffusing water. Furthermore, we compare the hydration water dynamics on different polypeptides and liposome surfaces and find the DW dynamics on globular proteins to be significantly more heterogeneous than on intrinsically disordered proteins (IDPs), peptides, and liposomes. The heterogeneity in the hydration water dynamics suggests that structured proteins have the capacity to encode information into the surrounding hydration shell.
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Affiliation(s)
- Ryan Barnes
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Sheng Sun
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Yann Fichou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Matthias Heyden
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85281, United States
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
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20
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21
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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22
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Atamas N, Bardik V, Bannikova A, Grishina O, Lugovskoi E, Lavoryk S, Makogonenko Y, Korolovych V, Nerukh D, Paschenko V. The effect of water dynamics on conformation changes of albumin in pre-denaturation state: photon correlation spectroscopy and simulation. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Yang J, Wang Y, Wang L, Zhong D. Mapping Hydration Dynamics around a β-Barrel Protein. J Am Chem Soc 2017; 139:4399-4408. [DOI: 10.1021/jacs.6b12463] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jin Yang
- Department of Physics, Department
of Chemistry and Biochemistry, and Programs of Biophysics, Chemical
Physics and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yafang Wang
- Department of Physics, Department
of Chemistry and Biochemistry, and Programs of Biophysics, Chemical
Physics and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lijuan Wang
- Department of Physics, Department
of Chemistry and Biochemistry, and Programs of Biophysics, Chemical
Physics and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dongping Zhong
- Department of Physics, Department
of Chemistry and Biochemistry, and Programs of Biophysics, Chemical
Physics and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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24
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Gavrilov Y, Leuchter JD, Levy Y. On the coupling between the dynamics of protein and water. Phys Chem Chem Phys 2017; 19:8243-8257. [DOI: 10.1039/c6cp07669f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Jessica D. Leuchter
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yaakov Levy
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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25
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Dhindsa GK, Bhowmik D, Goswami M, O’Neill H, Mamontov E, Sumpter BG, Hong L, Ganesh P, Chu XQ. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study. J Phys Chem B 2016; 120:10059-10068. [DOI: 10.1021/acs.jpcb.6b07511] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gurpreet K. Dhindsa
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Debsindhu Bhowmik
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Monojoy Goswami
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O’Neill
- Biology and
Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Bobby G. Sumpter
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Liang Hong
- Institute of Natural Science & Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Panchapakesan Ganesh
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiang-qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
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26
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Comez L, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. SOFT MATTER 2016; 12:5501-5514. [PMID: 27280176 DOI: 10.1039/c5sm03119b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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27
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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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28
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Wilkins DM, Manolopoulos DE, Dang LX. Nuclear quantum effects in water exchange around lithium and fluoride ions. J Chem Phys 2016; 142:064509. [PMID: 25681925 DOI: 10.1063/1.4907554] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell is found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.
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Affiliation(s)
- David M Wilkins
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Liem X Dang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 93352, USA
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29
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Franck JM, Ding Y, Stone K, Qin PZ, Han S. Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces. J Am Chem Soc 2015; 137:12013-23. [PMID: 26256693 PMCID: PMC4656248 DOI: 10.1021/jacs.5b05813] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emerging Overhauser effect dynamic nuclear polarization (ODNP) technique measures the translational mobility of water within the vicinity (5-15 Å) of preselected sites. The work presented here expands the capabilities of the ODNP technique and illuminates an important, previously unseen, property of the translational diffusion dynamics of water at the surface of DNA duplexes. We attach nitroxide radicals (i.e., spin labels) to multiple phosphate backbone positions of DNA duplexes, allowing ODNP to measure the hydration dynamics at select positions along the DNA surface. With a novel approach to ODNP analysis, we isolate the contributions of water molecules at these sites that undergo free translational diffusion from water molecules that either loosely bind to or exchange protons with the DNA. The results reveal that a significant population of water in a localized volume adjacent to the DNA surface exhibits fast, bulk-like characteristics and moves unusually rapidly compared to water found in similar probe volumes near protein and membrane surfaces. Control studies show that the observation of these characteristics are upheld even when the DNA duplex is tethered to streptavidin or the mobility of the nitroxides is altered. This implies that, as compared to protein or lipid surfaces, it is an intrinsic feature of the DNA duplex surface that it interacts only weakly with a significant fraction of the surface hydration water network. The displacement of this translationally mobile water is energetically less costly than that of more strongly bound water by up to several kBT and thus can lower the activation barrier for interactions involving the DNA surface.
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Affiliation(s)
- John M. Franck
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
- National Biomedical Center for Advanced ESR Technology, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, CA
| | - Katherine Stone
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
- Pacira Pharmaceuticals, Inc, San Diego, CA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
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30
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Garanger E, MacEwan SR, Sandre O, Brûlet A, Bataille L, Chilkoti A, Lecommandoux S. Structural Evolution of a Stimulus-Responsive Diblock Polypeptide Micelle by Temperature Tunable Compaction of its Core. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01371] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Elisabeth Garanger
- Laboratoire
de Chimie des Polymères Organiques (LCPO), CNRS UMR 5629, Université de Bordeaux, Bordeaux-INP, Pessac 33607 Cedex, France
- Institut Européen de Chimie et Biologie (IECB), Pessac 33607, France
| | - Sarah R. MacEwan
- Department
of Biomedical Engineering, Duke University, Campus Box 90281, Durham, North Carolina 27708, United States
| | - Olivier Sandre
- Laboratoire
de Chimie des Polymères Organiques (LCPO), CNRS UMR 5629, Université de Bordeaux, Bordeaux-INP, Pessac 33607 Cedex, France
| | - Annie Brûlet
- Laboratoire
Léon Brillouin (LLB), CEA-CNRS UMR 12, CEA-Saclay, Gif-sur-Yvette 91191, France
| | - Laure Bataille
- Laboratoire
de Chimie des Polymères Organiques (LCPO), CNRS UMR 5629, Université de Bordeaux, Bordeaux-INP, Pessac 33607 Cedex, France
- Institut Européen de Chimie et Biologie (IECB), Pessac 33607, France
| | - Ashutosh Chilkoti
- Department
of Biomedical Engineering, Duke University, Campus Box 90281, Durham, North Carolina 27708, United States
| | - Sébastien Lecommandoux
- Laboratoire
de Chimie des Polymères Organiques (LCPO), CNRS UMR 5629, Université de Bordeaux, Bordeaux-INP, Pessac 33607 Cedex, France
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31
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Saha D, Supekar S, Mukherjee A. Distribution of Residence Time of Water around DNA Base Pairs: Governing Factors and the Origin of Heterogeneity. J Phys Chem B 2015; 119:11371-81. [DOI: 10.1021/acs.jpcb.5b03553] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debasis Saha
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
| | - Shreyas Supekar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
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32
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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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33
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Dutta P, Botlani M, Varma S. Water Dynamics at Protein–Protein Interfaces: Molecular Dynamics Study of Virus–Host Receptor Complexes. J Phys Chem B 2014; 118:14795-807. [DOI: 10.1021/jp5089096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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34
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Lu C, Prada-Gracia D, Rao F. Structure and dynamics of water in crowded environments slows down peptide conformational changes. J Chem Phys 2014; 141:045101. [DOI: 10.1063/1.4891465] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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35
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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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36
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Enami S, Colussi AJ. Ion-Specific Long-Range Correlations on Interfacial Water Driven by Hydrogen Bond Fluctuations. J Phys Chem B 2014; 118:1861-6. [DOI: 10.1021/jp411385u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shinichi Enami
- The Hakubi
Center for Advanced Research, Kyoto University, Kyoto 606-8302, Japan
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Agustín J. Colussi
- Linde Center for Global Environmental
Science, California Institute of Technology, Pasadena, California 91125, United States
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37
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Krylov NA, Pentkovsky VM, Efremov RG. Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations. ACS NANO 2013; 7:9428-9442. [PMID: 24070369 DOI: 10.1021/nn4042392] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized via unconstrained molecular dynamics (MD) simulations. Although the overall water dynamics corresponds well to literature data, namely, the efficient braking near polar head groups of lipids, a number of interesting and biologically relevant details observed in this work have not been sufficiently discussed so far; for instance, the fact that waters "sense" the membrane unexpectedly early, before water density begins to decrease. In this "transitional zone" the velocity distributions of water and their H-bonding patterns deviate from those in the bulk solution. The boundaries of this zone are well preserved even despite the local (<1 nm size) perturbation of the lipid bilayer, thus indicating a decoupling of the surface and bulk dynamics of water. This is in excellent agreement with recent experimental data. Near the membrane surface, water movement becomes anisotropic, that is, solvent molecules preferentially move outward the bilayer. Deep in the membrane interior, the velocities can even exceed those in the bulk solvent and undergo large-scale fluctuations. The analysis of MD trajectories of individual waters in the middle part of the acyl chain region of lipids reveals a number of interesting rare phenomena, such as the fast (ca. 50 ps) breakthrough across the membrane or long-time (up to 750 ps) "roaming" between lipid leaflets. The analysis of these events was accomplished to delineate the mechanisms of spontaneous water permeation inside the hydrophobic membrane core. It was shown that such nontrivial dynamics of water in an "alien" environment is driven by the dynamic heterogeneities of the local bilayer structure and the formation of transient atomic-scale "defects" in it. The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed.
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Affiliation(s)
- Nikolay A Krylov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia
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38
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D'Cunha C, Morozov AN, Chatfield DC. Theoretical study of HOCl-catalyzed keto-enol tautomerization of β-cyclopentanedione in an explicit water environment. J Phys Chem A 2013; 117:8437-48. [PMID: 23902476 DOI: 10.1021/jp401409y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of acid-catalyzed keto-enol tautomerization of β-cyclopentanedione (CPD) in solution is studied computationally. Reaction profiles are first calculated for a limited solvation environment using ab initio and density functional methods. Barrier heights for systems including up to one hydration shell of explicit water molecules depend strongly on the number of waters involved in proton transfer and to a lesser but significant extent on the number of waters forming hydrogen bonds with waters in the proton-transfer chain (each such water reduces the barrier by 4.4 kcal/mol on average). Barriers of 8-13 kcal/mol were obtained when a full or nearly full hydration shell was present, consistent with calculations for nonacid-catalyzed keto-enol tautomerization of related molecules. The presence of HOCl reduced the barrier by 4.5 kcal/mol in relation to the gas phase, consistent with the well-known principle that keto-enol tautomerization can be acid- or base-catalyzed. The reaction was also modeled beginning with snapshots of reactant conformations taken from a 300 K molecular dynamics simulation of CPD, HOCl, and 324 explicit waters. Reaction profiles were calculated at a QM/MM level with waters in the first hydration shell either fixed or energy-minimized at each step along the reaction coordinate. A substantial variation in barrier height was observed in both cases, depending primarily on electrostatic interactions (hydrogen bonding) with first-hydration-shell waters and, to a lesser extent, on electrostatic interactions with more distant waters and geometric distortion effects. For the lowest barriers, the extent of barrier reduction by waters involved in proton transfer is consistent with the limited solvation results, but further barrier reduction due to hydrogen bonding to waters involved in proton transfer is not observed. It is postulated that this is because highly flexible structures such as extensive hydrogen bonding networks optimal for reaction are entropically disfavored and so may not contribute significantly to the observed reaction rate.
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Affiliation(s)
- Cassian D'Cunha
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, USA
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39
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Pal S, Bandyopadhyay S. Effects of protein conformational motions in the native form and non-uniform distribution of electrostatic interaction sites on interfacial water. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Pal S, Bandyopadhyay S. Effects of Protein Conformational Flexibilities and Electrostatic Interactions on the Low-Frequency Vibrational Spectrum of Hydration Water. J Phys Chem B 2013; 117:5848-56. [DOI: 10.1021/jp402662v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Somedatta Pal
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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41
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Franck JM, Scott JA, Han S. Nonlinear scaling of surface water diffusion with bulk water viscosity of crowded solutions. J Am Chem Soc 2013; 135:4175-8. [PMID: 23347324 PMCID: PMC3785640 DOI: 10.1021/ja3112912] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The translational hydration dynamics within 0.5-1.5 nm of the surface of a DPPC liposome, a model biomacromolecular surface, is analyzed by the recently developed Overhauser dynamic nuclear polarization (ODNP) technique. We find that dramatic changes to the bulk solvent cause only weak changes in the surface hydration dynamics. Specifically, both a >10-fold increase in bulk viscosity and the restriction of diffusion by confinement on a multiple nm length-scale change the local translational diffusion coefficient of the surface water surrounding the lipid bilayer by <2.5-fold. By contrast, previous ODNP studies have shown that changes to the biomacromolecular surface induced by folding, binding, or aggregation can cause local hydration dynamics to vary by factors of up to 30. We suggest that the surface topology and chemistry at the ≤1.5 nm scale, rather than the characteristics of the solvent, nearly exclusively determine the macromolecule's surface hydration dynamics.
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Affiliation(s)
- John M. Franck
- Dept. of Chemistry and Biochemistry, University of California, Santa Barbara
| | - John A. Scott
- Dept. of Chemistry and Biochemistry, University of California, Santa Barbara
| | - Songi Han
- Dept. of Chemistry and Biochemistry, University of California, Santa Barbara
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42
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Boopathi S, Kolandaivel P. Molecular dynamics simulations and density functional theory studies of NALMA and NAGMA dipeptides. J Biomol Struct Dyn 2013; 31:158-73. [DOI: 10.1080/07391102.2012.698380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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43
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Development of ions-TIP4P-Ew force fields for molecular processes in bulk and at the aqueous interface using molecular simulations. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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44
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Hu L, Joshi SB, Andra KK, Thakkar SV, Volkin DB, Bann JG, Middaugh CR. Comparison of the structural stability and dynamic properties of recombinant anthrax protective antigen and its 2-fluorohistidine-labeled analogue. J Pharm Sci 2012; 101:4118-28. [PMID: 22911632 DOI: 10.1002/jps.23294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/19/2012] [Accepted: 07/31/2012] [Indexed: 01/15/2023]
Abstract
Protective antigen (PA) is the primary protein antigenic component of both the currently used anthrax vaccine and related recombinant vaccines under development. An analogue of recombinant PA (2-FHis rPA) has been recently shown to block the key steps of pore formation in the process of inducing cytotoxicity in cells, and thus can potentially be used as an antitoxin or a vaccine. This rPA analogue was produced by fermentation to incorporate the unnatural amino acid 2-fluorohistidine (2-FHis). In this study, the effects of 2-FHis labeling on rPA antigen's conformational stability and dynamic properties were investigated by various biophysical techniques. Temperature/pH stability profiles of rPA and 2-FHis rPA were analyzed by the empirical phase diagram (EPD) approach, and physical stability differences between them were identified. Results showed that rPA and 2-FHis rPA had similar stability at pH 7-8. With decreasing solution pH, however, 2-FHis rPA was found to be more stable. Dynamic sensitive measurements of the two proteins at pH 5 found that 2-FHis rPA was more dynamic and/or differentially hydrated under acidic pH conditions. The biophysical characterization and stability data provide information useful for the potential development of 2-FHis rPA as a more stable rPA vaccine candidate.
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Affiliation(s)
- Lei Hu
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
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45
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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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46
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47
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Sinha SK, Bandyopadhyay S. Polar solvation dynamics of lysozyme from molecular dynamics studies. J Chem Phys 2012; 136:185102. [DOI: 10.1063/1.4712036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Xie M, Li H, Ye M, Zhang Y, Hu J. Peptide Self-Assembly on Mica under Ethanol-Containing Atmospheres: Effects of Ethanol on Epitaxial Growth of Peptide Nanofilaments. J Phys Chem B 2012; 116:2927-33. [DOI: 10.1021/jp2089438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Muyun Xie
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
- Graduate School of the Chinese Academy of Sciences
| | - Hai Li
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
| | - Ming Ye
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
| | - Yi Zhang
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
| | - Jun Hu
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
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49
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Yoshida K, Yamaguchi T, Kittaka S, Bellissent-Funel MC, Fouquet P. Neutron spin echo measurements of monolayer and capillary condensed water in MCM-41 at low temperatures. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:064101. [PMID: 22277165 DOI: 10.1088/0953-8984/24/6/064101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Neutron spin echo measurements of monolayer and capillary condensed heavy water (D(2)O) confined in MCM-41 C10 (pore diameter 2.10 nm) were performed in a temperature range of 190-298 K. The intermediate scattering functions were analyzed by the Kohlrausch-Williams-Watts stretched exponential function. The relaxation times of confined D(2)O in the capillary condensed state follow remarkably well the Vogel-Fulcher-Tammann equation between 298 and 220 K, whereas below 220 K they show an Arrhenius type behavior. That is, the fragile-to-strong (FTS) dynamic crossover occurs, which has never been seen in experiments on bulk water. On the other hand, for monolayer D(2)O, the FTS dynamic crossover was not observed in the temperature range measured. The FTS dynamic crossover observed in capillary condensed water would take place in the central region of the pore, not near the pore surface. Because the tetrahedral-like water structure in the central region of the pore is more preserved than that near the pore surface, the FTS dynamic crossover would be concerned with the tetrahedral-like water structure.
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Affiliation(s)
- K Yoshida
- Advanced Materials Institute and Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan
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50
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Sinha SK, Bandyopadhyay S. Local heterogeneous dynamics of water around lysozyme: a computer simulation study. Phys Chem Chem Phys 2012; 14:899-913. [DOI: 10.1039/c1cp22575h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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