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Zhang M, Xiao W, Zhang C, Zhang L. Terahertz Kerr Effect of Liquids. SENSORS (BASEL, SWITZERLAND) 2022; 22:9424. [PMID: 36502125 PMCID: PMC9739268 DOI: 10.3390/s22239424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
In recent years, tremendous advancements have been made in various technologies such as far-infrared, low-frequency Raman, and two-dimensional (2D) Raman terahertz (THz) spectroscopies. A coherent method has emerged from numerous experimental and theoretical investigations of molecular dynamics in liquids by comparing linear and non-linear spectroscopic techniques. Intermolecular hydrogen bond vibration, molecular reorientation motion, and interaction between molecule/ionic solute and hydrogen bonds have been demonstrated to occur in the THz region, which are closely related to their physical/chemical properties and structural dynamics. However, precise probing of various modes of motion is difficult because of the complexity of the collective and cooperative motion of molecules and spectral overlap of related modes. With the development of THz science and technology, current state-of-the-art THz sources can generate pulsed electric fields with peak intensities of the order of microvolts per centimeter (MV/cm). Such strong fields enable the use of THz waves as the light source for non-linear polarization of the medium and in turn leads to the development of the emerging THz Kerr effect (TKE) technique. Many low-frequency molecular motions, such as the collective directional motion of molecules and cooperative motion under the constraint of weak intermolecular interactions, are resonantly excited by an intense THz electric field. Thus, the TKE technique provides an interesting prospect for investigating low-frequency dynamics of different media. In view of this, this paper first summarizes the research work on TKE spectroscopy by taking a solid material without low-frequency molecular motions as an example. Starting from the principle of TKE technology and its application in investigating the properties of solid matter, we have explored the low-frequency molecular dynamics of liquid water and aqueous solutions using TKE. Liquid water is a core of life and possesses many extraordinary physical and biochemical properties. The hydrogen bond network plays a crucial role in these properties and is the main reason for its various kinetic and thermodynamic properties, which differ from those of other liquids. However, the structure of the hydrogen bond network between water and solutes is not well known. Therefore, evaluating the hydrogen bond-related kinetic properties of liquid water is important.
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2
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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4
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Becher M, Lichtinger A, Minikejew R, Vogel M, Rössler EA. NMR Relaxometry Accessing the Relaxation Spectrum in Molecular Glass Formers. Int J Mol Sci 2022; 23:ijms23095118. [PMID: 35563506 PMCID: PMC9105706 DOI: 10.3390/ijms23095118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 12/10/2022] Open
Abstract
It is a longstanding question whether universality or specificity characterize the molecular dynamics underlying the glass transition of liquids. In particular, there is an ongoing debate to what degree the shape of dynamical susceptibilities is common to various molecular glass formers. Traditionally, results from dielectric spectroscopy and light scattering have dominated the discussion. Here, we show that nuclear magnetic resonance (NMR), primarily field-cycling relaxometry, has evolved into a valuable method, which provides access to both translational and rotational motions, depending on the probe nucleus. A comparison of 1H NMR results indicates that translation is more retarded with respect to rotation for liquids with fully established hydrogen-bond networks; however, the effect is not related to the slow Debye process of, for example, monohydroxy alcohols. As for the reorientation dynamics, the NMR susceptibilities of the structural (α) relaxation usually resemble those of light scattering, while the dielectric spectra of especially polar liquids have a different broadening, likely due to contributions from cross correlations between different molecules. Moreover, NMR relaxometry confirms that the excess wing on the high-frequency flank of the α-process is a generic relaxation feature of liquids approaching the glass transition. However, the relevance of this feature generally differs between various methods, possibly because of their different sensitivities to small-amplitude motions. As a major advantage, NMR is isotope specific; hence, it enables selective studies on a particular molecular entity or a particular component of a liquid mixture. Exploiting these possibilities, we show that the characteristic Cole-Davidson shape of the α-relaxation is retained in various ionic liquids and salt solutions, but the width parameter may differ for the components. In contrast, the low-frequency flank of the α-relaxation can be notably broadened for liquids in nanoscopic confinements. This effect also occurs in liquid mixtures with a prominent dynamical disparity in their components.
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Affiliation(s)
- Manuel Becher
- Nordbayerisches NMR Zentrum, Universität Bayreuth, 95440 Bayreuth, Germany; (M.B.); (A.L.); (R.M.)
| | - Anne Lichtinger
- Nordbayerisches NMR Zentrum, Universität Bayreuth, 95440 Bayreuth, Germany; (M.B.); (A.L.); (R.M.)
| | - Rafael Minikejew
- Nordbayerisches NMR Zentrum, Universität Bayreuth, 95440 Bayreuth, Germany; (M.B.); (A.L.); (R.M.)
| | - Michael Vogel
- Institut für Physik Kondensierter Materie, Technische Universität Darmstadt, 64289 Darmstadt, Germany;
| | - Ernst A. Rössler
- Nordbayerisches NMR Zentrum, Universität Bayreuth, 95440 Bayreuth, Germany; (M.B.); (A.L.); (R.M.)
- Correspondence:
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5
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Waibl F, Kraml J, Fernández-Quintero ML, Loeffler JR, Liedl KR. Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. J Comput Aided Mol Des 2022; 36:101-116. [PMID: 35031880 PMCID: PMC8907097 DOI: 10.1007/s10822-021-00429-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/28/2021] [Indexed: 12/03/2022]
Abstract
Hydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist to predict solvation thermodynamics of compounds ranging from small molecules to large biomolecules. Arguably the most precise methods are those based on molecular dynamics (MD) simulations in explicit solvent. One theory that has seen increased use is inhomogeneous solvation theory (IST). However, while many applications require accurate description of salt-water mixtures, no implementation of IST is currently able to estimate solvation properties involving more than one solvent species. Here, we present an extension to grid inhomogeneous solvation theory (GIST) that can take salt contributions into account. At the example of carbazole in 1 M NaCl solution, we compute the solvation energy as well as first and second order entropies. While the effect of the first order ion entropy is small, both the water-water and water-ion entropies contribute strongly. We show that the water-ion entropies are efficiently approximated using the Kirkwood superposition approximation. However, this approach cannot be applied to the water-water entropy. Furthermore, we test the quantitative validity of our method by computing salting-out coefficients and comparing them to experimental data. We find a good correlation to experimental salting-out constants, while the absolute values are overpredicted due to the approximate second order entropy. Since ions are frequently used in MD, either to neutralize the system or as a part of the investigated process, our method greatly extends the applicability of GIST. The use-cases range from biopharmaceuticals, where many assays require high salt concentrations, to environmental research, where solubility in sea water is important to model the fate of organic substances.
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Affiliation(s)
- Franz Waibl
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Johannes Kraml
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Johannes R Loeffler
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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6
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Sousa AA, Schuck P, Hassan SA. Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters. NANOSCALE ADVANCES 2021; 3:2995-3027. [PMID: 34124577 PMCID: PMC8168927 DOI: 10.1039/d1na00086a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/16/2021] [Indexed: 05/03/2023]
Abstract
The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.
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Affiliation(s)
- Alioscka A Sousa
- Department of Biochemistry, Federal University of São Paulo São Paulo SP 04044 Brazil
| | - Peter Schuck
- National Institute of Biomedical Imaging and Bioengineering, NIH Bethesda MD 20892 USA
| | - Sergio A Hassan
- BCBB, National Institute of Allergy and Infectious Diseases, NIH Bethesda MD 20892 USA
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7
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Characterization of the Features of Water Inside the SecY Translocon. J Membr Biol 2021; 254:133-139. [PMID: 33811496 DOI: 10.1007/s00232-021-00178-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Despite extended experimental and computational studies, the mechanism regulating membrane protein folding and stability in cell membranes is not fully understood. In this review, I will provide a personal and partial account of the scientific efforts undertaken by Dr. Stephen White to shed light on this topic. After briefly describing the role of water and the hydrophobic effect on cellular processes, I will discuss the physical chemistry of water confined inside the SecY translocon pore. I conclude with a review of recent literature that attempts to answer fundamental questions on the pathway and energetics of translocon-guided membrane protein insertion.
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8
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Päslack C, Schäfer LV, Heyden M. Protein flexibility reduces solvent-mediated friction barriers of ligand binding to a hydrophobic surface patch. Phys Chem Chem Phys 2021; 23:5665-5672. [PMID: 33656505 DOI: 10.1039/d1cp00181g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Solvent fluctuations have been explored in detail for idealized and rigid hydrophobic model systems, but so far it has remained unclear how internal protein motions and their coupling to the surrounding solvent affect the dynamics of ligand binding to biomolecular surfaces. Here, molecular dynamics simulations were used to elucidate the solvent-mediated binding of a model ligand to the hydrophobic surface patch of ubiquitin. The ligand's friction profiles reveal pronounced long-time correlations and enhanced friction in the vicinity of the protein, similar to idealized hydrophobic surfaces. Interestingly, these effects are shaped by internal protein motions. Protein flexibility modulates water density fluctuations near the hydrophobic surface patch and smooths out the friction profile of ligand binding.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Lars V Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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9
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Di Rienzo L, Miotto M, Bò L, Ruocco G, Raimondo D, Milanetti E. Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. Front Mol Biosci 2021; 8:626837. [PMID: 33718433 PMCID: PMC7954116 DOI: 10.3389/fmolb.2021.626837] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.
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Affiliation(s)
- Lorenzo Di Rienzo
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mattia Miotto
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy.,Department of Physics, Sapienza University, Rome, Italy
| | - Leonardo Bò
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy.,Department of Physics, Sapienza University, Rome, Italy
| | | | - Edoardo Milanetti
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy.,Department of Physics, Sapienza University, Rome, Italy
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10
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Stasiulewicz M, Panuszko A, Śmiechowski M, Bruździak P, Maszota P, Stangret J. Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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11
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Tan P, Huang J, Mamontov E, García Sakai V, Merzel F, Liu Z, Ye Y, Hong L. Decoupling between the translation and rotation of water in the proximity of a protein molecule. Phys Chem Chem Phys 2020; 22:18132-18140. [PMID: 32761039 DOI: 10.1039/d0cp02416c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction between water and biomacromolecules is of fundamental interest in biophysics, biochemistry and physical chemistry. By combining neutron scattering and molecular dynamics simulations on a perdeuterated protein at a series of hydration levels, we demonstrated that the translational motion of water is slowed down more significantly than its rotation, when water molecules approach the protein molecule. Further analysis of the simulation trajectories reveals that the observed decoupling results from the fact that the translational motion of water is more correlated over space and more retarded by the charged/polar residues and spatial confinement on the protein surface, than the rotation. Moreover, around the stable protein residues (with smaller atomic fluctuations), water exhibits more decoupled dynamics, indicating a connection between the observed translation-rotation decoupling in hydration water and the local stability of the protein molecule.
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Affiliation(s)
- Pan Tan
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Victoria García Sakai
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, UK
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, SI 1000 Ljubljana, Slovenia
| | - Zhuo Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiyang Ye
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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12
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Gadolinium Complexes as Contrast Agent for Cellular NMR Spectroscopy. Int J Mol Sci 2020; 21:ijms21114042. [PMID: 32516957 PMCID: PMC7312942 DOI: 10.3390/ijms21114042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Aqua Gd3+ and Gd-DOTA (gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacete) complexes were studied as a contrast agent in cellular NMR (nuclear magnetic resonance) spectroscopy for distinguishing between intracellular and extracellular spaces. The contrast agents for this purpose should provide strong paramagnetic relaxation enhancement and localize in the extracellular space without disturbing biological functions. Cell membrane permeability to Gd complexes was evaluated from the concentrations of gadolinium complexes in the inside and outside of E. coli cells measured by the 1H-NMR relaxation. The site-specific binding of the complexes to E. coli cells was also analyzed by high-resolution solid-state 13C-NMR. The aqua Gd3+ complex did not enhance T1 relaxation in proportion to the amount of added Gd3+. This Gd3+ concentration dependence and the 13C-NMR indicated that its strong cytotoxicity should be due to the binding of the paramagnetic ions to cellular components especially at the lipid membranes. In contrast, Gd-DOTA stayed in the solution states and enhanced relaxation in proportion to the added amount. This agent exhibited strong T1 contrast between the intra- and extracellular spaces by a factor of ten at high concentrations under which the cells were viable over a long experimental time of days. These properties make Gd-DOTA suitable for selectively contrasting the living cellular space in NMR spectroscopy primarily owing to its weak interaction with cellular components.
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Zhang X, Wang Z, Chen Z, Li H, Zhang L, Ye J, Zhang Q, Zhuang W. Molecular Mechanism of Water Reorientation Dynamics in Dimethyl Sulfoxide Aqueous Mixtures. J Phys Chem B 2020; 124:1806-1816. [PMID: 32022564 DOI: 10.1021/acs.jpcb.0c00717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonmonotonic composition dependence is often observed for numerous properties in the aqueous mixtures of small amphiphilic molecules. The molecular picture underlying this structure-activity relationship, however, remains largely elusive. We herein studied water reorientation dynamics in the aqueous mixture of dimethyl sulfoxide (DMSO), which has a significant nonmonotonic composition dependence, using molecular dynamic simulation and an extended molecular jump model. The analysis indicates that this nonideal behavior is driven by the collective frame diffusion component of water reorientation, which decelerates in the water-rich regime because of the strengthened hydrogen bonds and accelerates in the water-poor regime as the hydrogen bonding network is broken into smaller aggregates. The current work therefore connects the microheterogeneity in the solvation structure of DMSO-water with its nonmonotonic hydration dynamics and sheds new light on how microsegregation leads to the multiscale hydration nonideality in general.
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Affiliation(s)
- Xia Zhang
- College of Chemistry and Materials Science, Inner Mongolia University for Nationlities, Tongliao Inner Mongolia 028043, China
| | - Zhangtao Wang
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou, Liaoning 121013, China
| | - Zhening Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Hui Li
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou, Liaoning 121013, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Jinting Ye
- College of Chemistry and Materials Science, Inner Mongolia University for Nationlities, Tongliao Inner Mongolia 028043, China
| | - Qiang Zhang
- College of Chemistry and Materials Science, Inner Mongolia University for Nationlities, Tongliao Inner Mongolia 028043, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
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14
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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Rezaei-Ghaleh N, Munari F, Becker S, Assfalg M, Griesinger C. A facile oxygen-17 NMR method to determine effective viscosity in dilute, molecularly crowded and confined aqueous media. Chem Commun (Camb) 2019; 55:12404-12407. [PMID: 31566648 DOI: 10.1039/c9cc06124j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We present an NMR method based on natural abundance 17O relaxation of water to determine effective viscosity in biological aqueous samples. The method accurately captures viscosity of dilute and crowded protein solutions and offers a fairly simple way to quantify the internal fluidity of biological condensates formed through phase separation.
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Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany. and Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Francesca Munari
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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16
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Maurer M, Oostenbrink C. Water in protein hydration and ligand recognition. J Mol Recognit 2019; 32:e2810. [PMID: 31456282 PMCID: PMC6899928 DOI: 10.1002/jmr.2810] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022]
Abstract
This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.
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Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
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17
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Wang P, Wang X, Liu L, Zhao H, Qi W, He M. The Hydration Shell of Monomeric and Dimeric Insulin Studied by Terahertz Time-Domain Spectroscopy. Biophys J 2019; 117:533-541. [PMID: 31326108 DOI: 10.1016/j.bpj.2019.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is believed to be a significant biological mechanism related to neurodegenerative disease, which makes the early-stage detection of aggregates a major concern. We demonstrated the use of terahertz (THz) time-domain spectroscopy to study protein-water interaction of monomeric and dimeric bovine insulin in aqueous samples. Regulated by changing pH and verified by size-exclusion chromatography and dynamic light scattering, we then measured their concentration-dependent changes in THz absorption between 0.5 and 3.0 THz and quantitatively deduced the extended hydration shell thickness by cubic distribution model and random distribution model. Under a random distribution assumption, the extended hydration thickness is 15.4 ± 0.4 Å for monomeric insulin and 17.5 ± 0.5 Å for dimeric insulin, with the hydration number of 6700 and 11,000, respectively. The hydration number of dimeric insulin is not twice but 1.64 times that of monomeric insulin, further supported by the ratio of solvent-accessible surface area. This "1.64-times" relation probably originates from the structural and conformational changes accompanied with dimerization. Combined with the investigations on insulin samples with different single amino acid mutations, residue B24 is believed to play an important role in the dimerization process. It is demonstrated that THz time-domain spectroscopy is a useful tool and has the sensitivity to provide the hydration information of different protein aggregates at an early stage.
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Affiliation(s)
- Pengfei Wang
- State Key Laboratory of Precision Measuring Technology and Instruments
| | | | - Liyuan Liu
- Key Laboratory of Optoelectronic Information Technology, Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
| | - Hongwei Zhao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering
| | - Mingxia He
- State Key Laboratory of Precision Measuring Technology and Instruments.
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18
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Capponi S, White SH, Tobias DJ, Heyden M. Structural Relaxation Processes and Collective Dynamics of Water in Biomolecular Environments. J Phys Chem B 2019; 123:480-486. [PMID: 30566356 DOI: 10.1021/acs.jpcb.8b12052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this simulation study, we investigate the influence of biomolecular confinement on dynamical processes in water. We compare water confined in a membrane protein nanopore at room temperature to pure liquid water at low temperatures with respect to structural relaxations, intermolecular vibrations, and the propagation of collective modes. We observe distinct potential energy landscapes experienced by water molecules in the two environments, which nevertheless result in comparable hydrogen bond lifetimes and sound propagation velocities. Hence, we show that a viscoelastic argument that links slow rearrangements of the water-hydrogen bond network to ice-like collective properties applies to both, the pure liquid and biologically confined water, irrespective of differences in the microscopic structure.
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Affiliation(s)
| | | | | | - Matthias Heyden
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287-1604 , United States
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19
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Heid E, Braun D. Fundamental limitations of the time-dependent Stokes shift for investigating protein hydration dynamics. Phys Chem Chem Phys 2019; 21:4435-4443. [DOI: 10.1039/c8cp07623e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the TDSS measured in protein systems, large protein contributions fully obscure hydration dynamics.
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Affiliation(s)
- Esther Heid
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - Daniel Braun
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
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20
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Gagkaeva ZV, Zhukova ES, Grinenko V, Grebenko AK, Sidoruk KV, Voeikova TA, Dressel M, Gorshunov BP. Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix. J Biol Phys 2018; 44:401-417. [PMID: 29732506 PMCID: PMC6082806 DOI: 10.1007/s10867-018-9497-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/13/2018] [Indexed: 01/30/2023] Open
Abstract
Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000 cm-1 in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm-1 and mainly determine the terahertz absorption. When cooled down to liquid helium temperatures, the bands in Shewanella oneidensis MR-1 and cytochrome c reveal a distinct fine structure. In all three materials, we identify the presence of liquid bound water in the form of librational and translational absorption bands at ≈ 200 and ≈ 600 cm-1, respectively. The sharp excitations seen above 1000 cm-1 are assigned to intramolecular vibrations.
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Affiliation(s)
- Z V Gagkaeva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - E S Zhukova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - V Grinenko
- Institute for Metallic Materials, IFW Dresden, Dresden, Germany
| | - A K Grebenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - K V Sidoruk
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - T A Voeikova
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - M Dressel
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Physikalisches Institut, Universität Stuttgart, Stuttgart, Germany
| | - B P Gorshunov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
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21
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Abstract
Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by 17O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for 17O MRD. By contrast, we find that the 17O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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22
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Jungwirth P, Laage D. Ion-Induced Long-Range Orientational Correlations in Water: Strong or Weak, Physiologically Relevant or Unimportant, and Unique to Water or Not? J Phys Chem Lett 2018; 9:2056-2057. [PMID: 29669422 DOI: 10.1021/acs.jpclett.8b01027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2 , 16610 Prague 6 , Czech Republic
| | - Damien Laage
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
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23
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Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results. Int J Pharm 2018; 540:65-77. [PMID: 29412151 DOI: 10.1016/j.ijpharm.2018.01.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/20/2022]
Abstract
The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules.
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24
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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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25
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Laage D, Elsaesser T, Hynes JT. Perspective: Structure and ultrafast dynamics of biomolecular hydration shells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044018. [PMID: 28470026 PMCID: PMC5398927 DOI: 10.1063/1.4981019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 05/25/2023]
Abstract
The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.
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Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Départment de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
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26
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Lanza G, Chiacchio MA. Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine. Chemphyschem 2017; 18:1586-1596. [PMID: 28371186 DOI: 10.1002/cphc.201700149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/11/2022]
Abstract
A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H2 O, Ala2 H+ ⋅18 H2 O, and Ala2 ⋅18 H2 O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy
| | - Maria A Chiacchio
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy
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27
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Protein hydration: Investigation of globular protein crystal structures. Int J Biol Macromol 2017; 99:160-165. [DOI: 10.1016/j.ijbiomac.2017.02.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/10/2017] [Indexed: 01/06/2023]
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28
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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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29
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Leo N, Liu J, Archbold I, Tang Y, Zeng X. Ionic Strength, Surface Charge, and Packing Density Effects on the Properties of Peptide Self-Assembled Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:2050-2058. [PMID: 28135097 DOI: 10.1021/acs.langmuir.6b04038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The various environmental parameters of packing density, ionic strength, and solution charge were examined for their effects on the properties of the immobilized peptide mimotope CH19 (CGSGSGSQLGPYELWELSH) that binds with the therapeutic antibody Trastuzumab (Herceptin) on a gold substrate. The immobilization of CH19 onto gold was examined with a quartz crystal microbalance (QCM). The QCM data showed the presence of intermolecular interactions resulting in the increase of viscoelastic properties of the peptide self-assembled monolayer (SAM). The CH19 SAM was diluted with CS7 (CGSGSGS) to decrease the packing density as CH19/CS7. The packing density and ionic strength parameters were evaluated by atomic force microscopy (AFM), ellipsometry, and QCM. AFM and ellipsometry showed a distinct conformational difference between CH19 and CH19/CS7, indicating a relationship between packing density and conformational state of the immobilized peptide. The CH19 SAM thickness was 40 Å with a rough topology, while the CH19/CS7 SAM thickness was 20 Å with a smooth topology. The affinity studies showed that the affinity of CH19 and CH19/CS7 to Trastuzumab were both on the order of 107 M-1 in undiluted PBS buffer, while the dilution of the buffer by 1000× increased both SAMs affinities to Trastuzumab to the order of 1015 M-2 and changed the binding behavior from noncooperative to cooperative binding. This indicated that ionic strength had a more pronounced effect on binding properties of the CH19 SAM than packing density. Electrochemical impedance spectroscopy (EIS) was conducted on the CH19/CS7 SAM, which showed an increase in impedance after each EIS measurement cycle. Cyclic voltammetry on the CH19/CS7 SAM decreased impedance to near initial values. The impact of the packing density, buffer ionic strength, and local charge perturbation of the peptide SAM properties was interpreted based on the titratable sites in CH19 that could participate in the proton transfer and water equilibrium.
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Affiliation(s)
- Norman Leo
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Juan Liu
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ian Archbold
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Yongan Tang
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Xiangqun Zeng
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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30
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Marques MPM, Batista de Carvalho ALM, Sakai VG, Hatter L, Batista de Carvalho LAE. Intracellular water – an overlooked drug target? Cisplatin impact in cancer cells probed by neutrons. Phys Chem Chem Phys 2017; 19:2702-2713. [DOI: 10.1039/c6cp05198g] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Intracellular water as a secondary pharmacological target?
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Affiliation(s)
- M. P. M. Marques
- Unidade de I&D Química-Física Molecular
- Dep. of Chemistry
- R. Larga
- Univ. Coimbra
- 3004-535 Coimbra
| | | | - V. Garcia Sakai
- ISIS Facility
- STFC Rutherford Appleton Laboratory
- Chilton
- Didcot
- UK
| | - L. Hatter
- Research Complex at Harwell
- STFC Rutherford Appleton Laboratory
- Chilton
- Didcot
- UK
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31
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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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32
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Zhang R, Zhang Y, Antila HS, Lutkenhaus JL, Sammalkorpi M. Role of Salt and Water in the Plasticization of PDAC/PSS Polyelectrolyte Assemblies. J Phys Chem B 2016; 121:322-333. [DOI: 10.1021/acs.jpcb.6b12315] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ran Zhang
- State
Key Laboratory of Polymer Physics and Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Yanpu Zhang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Hanne S. Antila
- Department
of Chemistry, School of Chemical Technology, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Jodie L. Lutkenhaus
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Maria Sammalkorpi
- Department
of Chemistry, School of Chemical Technology, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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33
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Stachura M, Chakraborty S, Gottberg A, Ruckthong L, Pecoraro VL, Hemmingsen L. Direct Observation of Nanosecond Water Exchange Dynamics at a Protein Metal Site. J Am Chem Soc 2016; 139:79-82. [PMID: 27973778 DOI: 10.1021/jacs.6b11525] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanosecond ligand exchange dynamics at metal sites within proteins is essential in catalysis, metal ion transport, and regulatory metallobiochemistry. Herein we present direct observation of the exchange dynamics of water at a Cd2+ binding site within two de novo designed metalloprotein constructs using 111mCd perturbed angular correlation (PAC) of γ-rays and 113Cd NMR spectroscopy. The residence time of the Cd2+-bound water molecule is tens of nanoseconds at 20 °C in both proteins. This constitutes the first direct experimental observation of the residence time of Cd2+ coordinated water in any system, including the simple aqua ion. A Leu to Ala amino acid substitution ∼10 Å from the Cd2+ site affects both the equilibrium constant and the residence time of water, while, surprisingly, the metal site structure, as probed by PAC spectroscopy, remains essentially unaltered. This implies that remote mutations may affect metal site dynamics, even when structure is conserved.
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Affiliation(s)
- Monika Stachura
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, 2100 København Ø, Denmark
| | - Saumen Chakraborty
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States
| | | | - Leela Ruckthong
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109-1055, United States
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, 2100 København Ø, Denmark
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34
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Biswas S, Mukherjee SK, Chowdhury PK. Crowder-Induced Rigidity in a Multidomain Protein: Insights from Solvation. J Phys Chem B 2016; 120:12501-12510. [DOI: 10.1021/acs.jpcb.6b10478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saikat Biswas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sanjib Kumar Mukherjee
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit Kumar Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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35
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Tuszynski JA, Wenger C, Friesen DE, Preto J. An Overview of Sub-Cellular Mechanisms Involved in the Action of TTFields. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:E1128. [PMID: 27845746 PMCID: PMC5129338 DOI: 10.3390/ijerph13111128] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 10/23/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022]
Abstract
Long-standing research on electric and electromagnetic field interactions with biological cells and their subcellular structures has mainly focused on the low- and high-frequency regimes. Biological effects at intermediate frequencies between 100 and 300 kHz have been recently discovered and applied to cancer cells as a therapeutic modality called Tumor Treating Fields (TTFields). TTFields are clinically applied to disrupt cell division, primarily for the treatment of glioblastoma multiforme (GBM). In this review, we provide an assessment of possible physical interactions between 100 kHz range alternating electric fields and biological cells in general and their nano-scale subcellular structures in particular. This is intended to mechanistically elucidate the observed strong disruptive effects in cancer cells. Computational models of isolated cells subject to TTFields predict that for intermediate frequencies the intracellular electric field strength significantly increases and that peak dielectrophoretic forces develop in dividing cells. These findings are in agreement with in vitro observations of TTFields' disruptive effects on cellular function. We conclude that the most likely candidates to provide a quantitative explanation of these effects are ionic condensation waves around microtubules as well as dielectrophoretic effects on the dipole moments of microtubules. A less likely possibility is the involvement of actin filaments or ion channels.
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Affiliation(s)
- Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Cornelia Wenger
- The Institute of Biophysics and Biomedical Engineering, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal.
| | - Douglas E Friesen
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Jordane Preto
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
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36
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Fisette O, Päslack C, Barnes R, Isas JM, Langen R, Heyden M, Han S, Schäfer LV. Hydration Dynamics of a Peripheral Membrane Protein. J Am Chem Soc 2016; 138:11526-35. [PMID: 27548572 DOI: 10.1021/jacs.6b07005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Water dynamics in the hydration shell of the peripheral membrane protein annexin B12 were studied using MD simulations and Overhauser DNP-enhanced NMR. We show that retardation of water motions near phospholipid bilayers is extended by the presence of a membrane-bound protein, up to around 10 Å above that protein. Near the membrane surface, electrostatic interactions with the lipid head groups strongly slow down water dynamics, whereas protein-induced water retardation is weaker and dominates only at distances beyond 10 Å from the membrane surface. The results can be understood from a simple model based on additive contributions from the membrane and the protein to the activation free energy barriers of water diffusion next to the biomolecular surfaces. Furthermore, analysis of the intermolecular vibrations of the water network reveals that retarded water motions near the membrane shift the vibrational modes to higher frequencies, which we used to identify an entropy gradient from the membrane surface toward the bulk water. Our results have implications for processes that take place at lipid membrane surfaces, including molecular recognition, binding, and protein-protein interactions.
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Affiliation(s)
- Olivier Fisette
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
| | - Christopher Päslack
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany.,Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Ryan Barnes
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - J Mario Isas
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Ralf Langen
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Matthias Heyden
- Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Songi Han
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
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37
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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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38
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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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39
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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: 528] [Impact Index Per Article: 66.0] [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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40
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Dopfer O, Fujii M. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level. Chem Rev 2016; 116:5432-63. [DOI: 10.1021/acs.chemrev.5b00610] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Otto Dopfer
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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41
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Nickels JD, Atkinson J, Papp-Szabo E, Stanley C, Diallo SO, Perticaroli S, Baylis B, Mahon P, Ehlers G, Katsaras J, Dutcher JR. Structure and Hydration of Highly-Branched, Monodisperse Phytoglycogen Nanoparticles. Biomacromolecules 2016; 17:735-43. [DOI: 10.1021/acs.biomac.5b01393] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jonathan D. Nickels
- Joint
Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Physics, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John Atkinson
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Erzsebet Papp-Szabo
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Christopher Stanley
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Souleymane O. Diallo
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | | | - Benjamin Baylis
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Perry Mahon
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Georg Ehlers
- Quantum Condensed
Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Joint
Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Physics, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John R. Dutcher
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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42
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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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43
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Martin DR, Matyushov DV. Hydration shells of proteins probed by depolarized light scattering and dielectric spectroscopy: orientational structure is significant, positional structure is not. J Chem Phys 2015; 141:22D501. [PMID: 25494772 DOI: 10.1063/1.4895544] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water interfacing hydrated proteins carry properties distinct from those of the bulk and is often described as a separate entity, a "biological water." We address here the question of which dynamical and structural properties of hydration water deserve this distinction. The study focuses on different aspects of the density and orientational fluctuations of hydration water and the ability to separate them experimentally by combining depolarized light scattering with dielectric spectroscopy. We show that the dynamics of the density fluctuations of the hydration shells reflect the coupled dynamics of the solute and solvent and do not require a special distinction as "biological water." The orientations of shell water molecules carry dramatically different physics and do require a separation into a sub-ensemble. Depending on the property considered, the perturbation of water's orientational structure induced by the protein propagates 3-5 hydration shells into the bulk at normal temperature.
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Affiliation(s)
- Daniel R Martin
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA
| | - Dmitry V Matyushov
- Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA
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44
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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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45
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Cravens SL, Schonhoft JD, Rowland MM, Rodriguez AA, Anderson BG, Stivers JT. Molecular crowding enhances facilitated diffusion of two human DNA glycosylases. Nucleic Acids Res 2015; 43:4087-97. [PMID: 25845592 PMCID: PMC4417188 DOI: 10.1093/nar/gkv301] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/22/2022] Open
Abstract
Intracellular space is at a premium due to the high concentrations of biomolecules and is expected to have a fundamental effect on how large macromolecules move in the cell. Here, we report that crowded solutions promote intramolecular DNA translocation by two human DNA repair glycosylases. The crowding effect increases both the efficiency and average distance of DNA chain translocation by hindering escape of the enzymes to bulk solution. The increased contact time with the DNA chain provides for redundant damage patrolling within individual DNA chains at the expense of slowing the overall rate of damaged base removal from a population of molecules. The significant biological implication is that a crowded cellular environment could influence the mechanism of damage recognition as much as any property of the enzyme or DNA.
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Affiliation(s)
- Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Joseph D Schonhoft
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Meng M Rowland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Alyssa A Rodriguez
- Department of Chemistry and Biochemistry, The University of San Diego, 5998 Alcalá Park, San Diego, CA 92110, USA
| | - Breeana G Anderson
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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46
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King JT, Arthur EJ, Osborne DG, Brooks CL, Kubarych KJ. Biomolecular hydration dynamics probed with 2D-IR spectroscopy: From dilute solution to a macromolecular crowd. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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47
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Sushko O, Dubrovka R, Donnan RS. Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected. J Chem Phys 2015; 142:055101. [DOI: 10.1063/1.4907271] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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48
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Jakobsen S, Bereau T, Meuwly M. Multipolar force fields and their effects on solvent dynamics around simple solutes. J Phys Chem B 2015; 119:3034-45. [PMID: 25584801 DOI: 10.1021/jp508052q] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential, which is especially important to describe key, challenging interactions, such as lone pairs, π-interactions, and hydrogen bonds. These chemical environments are probed by focusing on the hydration properties of two molecules: N-methylacetamide and phenyl bromide. Both, equilibrium and dynamical, quantities are affected by the quality of the electrostatic model. The alteration of the first solvation shell in MTP simulations is validated by comparing with lifetimes and correlation times of solute-solvent interactions from experiment. The improved dynamical behavior found in the MTP simulations—observed for molecules parametrized using very different protocols—suggests that a systematic improvement of both equilibrium and dynamical quantities when using MTP electrostatics is possible.
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Affiliation(s)
- Sofie Jakobsen
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland
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49
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Mazur K, Bonn M, Hunger J. Hydrogen bond dynamics in primary alcohols: a femtosecond infrared study. J Phys Chem B 2015; 119:1558-66. [PMID: 25531023 DOI: 10.1021/jp509816q] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-bonded liquids are excellent solvents, in part due to the highly dynamic character of the directional interaction associated with the hydrogen bond. Here we study the vibrational and reorientational dynamics of deuterated hydroxyl groups in various primary alcohols using polarization-resolved femtosecond infrared spectroscopy. We show that the relaxation of the OD stretch vibration is similar for ethanol and its higher homologues (∼0.9 ps), while it is appreciably faster for methanol (∼0.75 ps). The fast relaxation for methanol is attributed to strong coupling of the OD stretch vibration to the overtone of the CH3 rocking mode. Subsequent to excited state relaxation, the dissipation of the excess energy leads to structural relaxation of the alcohol liquid structure. We show that this relaxation of the H-bonded network depends on the alkyl chain length. We find that the anisotropy of the excitation decays by both thermal diffusion from excited OD groups to nonexcited molecules and reorientational motion. The reorientation is described well by a model employing two relaxation times that increase linearly with increasing alcohol size. The short reorientation time is assigned to the partial reorientation of molecules within the alcohol cluster, while the long reorientation times can be attributed to breaking and reforming of hydrogen bonds.
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Affiliation(s)
- Kamila Mazur
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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50
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Lanza G, Chiacchio MA. Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation. Phys Chem Chem Phys 2015; 17:17101-11. [DOI: 10.1039/c5cp00270b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco
- Università di Catania
- 95125 Catania
- Italy
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