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Salvati Manni L, Wood K, Klapproth A, Warr GG. Inelastic neutron scattering and spectroscopy methods to characterize dynamics in colloidal and soft matter systems. Adv Colloid Interface Sci 2024; 326:103135. [PMID: 38520888 DOI: 10.1016/j.cis.2024.103135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024]
Abstract
Colloidal systems and soft materials are well suited to neutron scattering, and the community has readily adopted elastic scattering techniques to investigate their structure. Due to their unique properties, neutrons may also be used to characterize the dynamics of soft materials over a wide range of length and time scales in situ. Both static structures and an understanding of how molecules move about their equilibrium positions is essential if we are to deliver on the promise of rationally designing soft materials. In this review we introduce the basics of neutron spectroscopy and explore the ways in which inelastic neutron scattering can be used to study colloidal and soft materials. Illustrative examples are chosen that highlight the phenomena suitable for investigation using this suite of techniques.
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Affiliation(s)
- Livia Salvati Manni
- School of Chemistry, University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia; School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia; School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, NSW, Australia; Australian Synchrotron, ANSTO, 800 Blackburn Rd, Clayton, VIC 3168, Australia
| | - Kathleen Wood
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Alice Klapproth
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Gregory G Warr
- School of Chemistry, University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.
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2
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Sarkar R, Mainan A, Roy S. Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods. Chem Commun (Camb) 2024. [PMID: 38501190 DOI: 10.1039/d3cc06105a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation. In addition to investigating the RNA's ion environment, we note that the RNA's hydration environment is relatively underexplored. Our study delves into its profound interplay with the structural dynamics of RNA, employing state-of-the-art atomistic simulation techniques. Through examples, we illustrate how specific ions and water molecules are associated with RNA functions, leveraging atomistic simulations to identify preferential ion binding and hydration sites. However, understanding their impact(s) on the RNA structure remains challenging due to the involvement of large length and long time scales associated with RNA's dynamic nature. Nevertheless, our contributions and recent advances in coarse-grained simulation techniques offer insights into large-scale structural changes dynamically linked to the RNA ion atmosphere. In this connection, we also review how different cutting-edge computational simulation methods provide a microscopic lens into the influence of ions and hydration on RNA structure and dynamics, elucidating distinct ion atmospheric components and specific hydration layers and their individual and collective impacts.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
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3
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Uppuladinne MVN, Achalere A, Sonavane U, Joshi R. Probing the structure of human tRNA 3Lys in the presence of ligands using docking, MD simulations and MSM analysis. RSC Adv 2023; 13:25778-25796. [PMID: 37655355 PMCID: PMC10467029 DOI: 10.1039/d3ra03694d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023] Open
Abstract
The tRNA3Lys, which acts as a primer for human immunodeficiency virus type 1 (HIV-1) reverse transcription, undergoes structural changes required for the formation of a primer-template complex. Small molecules have been targeted against tRNA3Lys to inhibit the primer-template complex formation. The present study aims to understand the kinetics of the conformational landscape spanned by tRNA3Lys in apo form using molecular dynamics simulations and Markov state modeling. The study is taken further to investigate the effect of small molecules like 1,4T and 1,5T on structural conformations and kinetics of tRNA3Lys, and comparative analysis is presented. Markov state modeling of tRNA3Lys apo resulted in three metastable states where the conformations have shown the non-canonical structures of the anticodon loop. Based on analyses of ligand-tRNA3Lys interactions, crucial ion and water mediated H-bonds and free energy calculations, it was observed that the 1,4-triazole more strongly binds to the tRNA3Lys compared to 1,5-triazole. However, the MSM analysis suggest that the 1,5-triazole binding to tRNA3Lys has brought rigidity not only in the binding pocket (TΨC arm, D-TΨC loop) but also in the whole structure of tRNA3Lys. This may affect the easy opening of primer tRNA3Lys required for HIV-1 reverse transcription.
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Affiliation(s)
- Mallikarjunachari V N Uppuladinne
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Archana Achalere
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
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4
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Sarkar R, Singh RK, Roy S. Hierarchical Hydration Dynamics of RNA with Nano-Water-Pool at Its Core. J Phys Chem B 2023; 127:6903-6919. [PMID: 37506269 DOI: 10.1021/acs.jpcb.3c03553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Many functional RNAs fold into a compact, roughly globular shape by minimizing the electrostatic repulsion between their negatively charged phosphodiester backbone. The fold of such close, compact RNA architecture is often so designed that its outer surface and complex core both are predominately populated by phosphate groups loosely sequestering bases in the intermediate layers. A number of helical junctions maintain the RNA core and its nano-water-pool. While the folding of RNA is manifested by its counterion environment composed of mixed mono- and divalent salts, the concerted role of ion and water in maintaining an RNA fold is yet to be explored. In this work, detailed atomistic simulations of SAM-I and Add Adenine riboswitch aptamers, and subgenomic flavivirus RNA (sfRNA) have been performed in a physiological mixed mono- and divalent salt environment. All three RNA systems have compact folds with a core diameter of range 1-1.7 nm. The spatiotemporal heterogeneity of RNA hydration was probed in a layer-wise manner by distinguishing the core, the intermediate, and the outer layers. The layer-wise decomposition of hydrogen bonds and collective single-particle reorientational dynamics reveal a nonmonotonic relaxation pattern with the slowest relaxation observed at the intermediate layers that involves functionally important tertiary motifs. The slowness of this intermediate layer is attributed to two types of long-resident water molecules: (i) water from ion-hydration layers and (ii) structurally trapped water (distant from ions). The relaxation kinetics of the core and the surface water essentially exposed to the phosphate groups show well-separated time scales from the intermediate layers. In the slow intermediate layers, site-specific ions and water control the functional dynamics of important RNA motifs like kink-turn, observed in different structure-probing experiments. Most interestingly, we find that as the size of the RNA core increases (SAM1 core < sfRNAcore < Add adenine core), its hydration tends to show faster relaxation. The hierarchical hydration and the layer-wise base-phosphate composition uniquely portray the globular RNA to act like a soft vesicle with a quasi-dynamic nano-water-pool at its core.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Rishabh K Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
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5
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Bin M, Reiser M, Filianina M, Berkowicz S, Das S, Timmermann S, Roseker W, Bauer R, Öström J, Karina A, Amann-Winkel K, Ladd-Parada M, Westermeier F, Sprung M, Möller J, Lehmkühler F, Gutt C, Perakis F. Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins. J Phys Chem B 2023. [PMID: 37209106 DOI: 10.1021/acs.jpcb.3c02492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress-relaxation in hydrated lysozyme proteins stimulated and probed by X-ray Photon Correlation Spectroscopy (XPCS). This approach allows us to access the nanoscale dynamics in the deeply supercooled regime (T = 180 K), which is typically not accessible through equilibrium methods. The observed stimulated dynamic response is attributed to collective stress-relaxation as the system transitions from a jammed granular state to an elastically driven regime. The relaxation time constants exhibit Arrhenius temperature dependence upon cooling with a minimum in the Kohlrausch-Williams-Watts exponent at T = 227 K. The observed minimum is attributed to an increase in dynamical heterogeneity, which coincides with enhanced fluctuations observed in the two-time correlation functions and a maximum in the dynamic susceptibility quantified by the normalized variance χT. The amplification of fluctuations is consistent with previous studies of hydrated proteins, which indicate the key role of density and enthalpy fluctuations in hydration water. Our study provides new insights into X-ray stimulated stress-relaxation and the underlying mechanisms behind spatiotemporal fluctuations in biological granular materials.
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Affiliation(s)
- Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Mariia Filianina
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sharon Berkowicz
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sudipta Das
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Wojciech Roseker
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Bauer
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- Freiberg Water Research Center, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany
| | - Jonatan Öström
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Aigerim Karina
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Katrin Amann-Winkel
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Physics, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Marjorie Ladd-Parada
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Felix Lehmkühler
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
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6
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Rosi BP, D’Angelo A, Buratti E, Zanatta M, Tavagnacco L, Natali F, Zamponi M, Noferini D, Corezzi S, Zaccarelli E, Comez L, Sacchetti F, Paciaroni A, Petrillo C, Orecchini A. Impact of the Environment on the PNIPAM Dynamical Transition Probed by Elastic Neutron Scattering. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benedetta P. Rosi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Arianna D’Angelo
- Laboratoire de Physique des Solides, CNRS, Université Paris-Saclay, 510 Rue André Rivière, 91405 Orsay, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Elena Buratti
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Marco Zanatta
- Dipartimento di Fisica, Università di Trento, via Sommarive 14, 38123 Trento, Italy
| | - Letizia Tavagnacco
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesca Natali
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
- CNR-IOM, OGG, 71 Avenue des Martyrs, 38043 Grenoble, Cedex 9, France
| | - Michaela Zamponi
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
- European Spallation Source ERIC, Box 176, 221 00 Lund, Sweden
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Lucia Comez
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
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7
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Low-temperature librations and dynamical transition in proteins at differing hydration levels. Biomol Concepts 2022; 13:81-88. [DOI: 10.1515/bmc-2022-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Hydration of water affects the dynamics and in turn the activity of biomacromolecules. We investigated the dependence of the librational oscillations and the dynamical transition on the hydrating conditions of two globular proteins with different structure and size, namely β-lactoglobulin (βLG) and human serum albumin (HSA), by spin-label electron paramagnetic resonance (EPR) in the temperature range of 120–270 K. The proteins were spin-labeled with 5-maleimide spin-label on free cysteins and prepared in the lyophilized state, at low (h = 0.12) and full (h = 2) hydration levels in buffer. The angular amplitudes of librations are small and almost temperature independent for both lyophilized proteins. Therefore, in these samples, the librational dynamics is restricted and the dynamical transition is absent. In the small and compact beta-structured βLG, the angular librational amplitudes increase with temperature and hydrating conditions, whereas hydration-independent librational oscillations whose amplitudes rise with temperature are recorded in the large and flexible alpha-structured HSA. Both βLG and HSA at low and fully hydration levels undergo the dynamical transition at about 230 K. The overall results indicate that protein librational dynamics is activated at the low hydration level h = 0.12 and highlight biophysical properties that are common to other biosamples at cryogenic temperatures.
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8
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Aloi E, Bartucci R. Influence of hydration on segmental chain librations and dynamical transition in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183805. [PMID: 34662568 DOI: 10.1016/j.bbamem.2021.183805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/29/2021] [Accepted: 10/10/2021] [Indexed: 12/23/2022]
Abstract
Continuous wave electron paramagnetic resonance spectroscopy of chain-labeled phospholipids is used to investigate the effects of hydration on the librational oscillations and the dynamical transition of phospholipid membranes in the low-temperature range 120-270 K. Bilayers of dipalmitoylphostatidiycholine (DPPC) spin-labeled at the first acyl chain segments and at the methyl ends and prepared at full, low, and very low hydration are considered. The segmental mean-square angular amplitudes of librations, 〈α2〉, are larger in the bilayer interior than at the polar/apolar interface and larger in the fully and low hydrated than in the very low hydrated membranes. For chain segments at the beginning of the hydrocarbon region, 〈α2〉-values are markedly restricted and temperature independent in DPPC with the lowest water content, whereas they increase with temperature in the low and fully hydrated bilayers, particularly at the highest temperatures. For chain segments at the chain termini, the librational amplitudes increase progressively, first slowly and then more rapidly with temperature in bilayers at any level of hydration. From the temperature dependence of the mean-square librational amplitude, the dynamical transition is detected around 240 K at the polar/apolar interface in fully and low hydrated DPPC and at around 225 K at the inner hydrocarbon region for bilayers at any hydration condition. At the dynamical transition the bilayers cross low energy barriers of activation energy in the range 10-20 kJ/mol. The results highlight biophysical properties of DPPC bilayers at low-temperature and provide evidence of the effects of the hydration on the dynamical transition in bilayers.
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Affiliation(s)
- Erika Aloi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria, 87036 Rende, (CS), Italy
| | - Rosa Bartucci
- Department of Chemistry and Chemical Technologies, Molecular Biophysics Laboratory, University of Calabria, 87036 Rende, (CS), Italy.
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Probing Small-Angle Molecular Motions with EPR Spectroscopy: Dynamical Transition and Molecular Packing in Disordered Solids. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8020019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Disordered molecular solids present a rather broad class of substances of different origin—amorphous polymers, materials for photonics and optoelectronics, amorphous pharmaceutics, simple molecular glass formers, and others. Frozen biological media in many respects also may be referred to this class. Theoretical description of dynamics and structure of disordered solids still does not exist, and only some phenomenological models can be developed to explain results of particular experiments. Among different experimental approaches, electron paramagnetic resonance (EPR) applied to spin probes and labels also can deliver useful information. EPR allows probing small-angle orientational molecular motions (molecular librations), which intrinsically are inherent to all molecular solids. EPR is employed in its conventional continuous wave (CW) and pulsed—electron spin echo (ESE)—versions. CW EPR spectra are sensitive to dynamical librations of molecules while ESE probes stochastic molecular librations. In this review, different manifestations of small-angle motions in EPR of spin probes and labels are discussed. It is shown that CW-EPR-detected dynamical librations provide information on dynamical transition in these media, similar to that explored with neutron scattering, and ESE-detected stochastic librations allow elucidating some features of nanoscale molecular packing. The possible EPR applications are analyzed for gel-phase lipid bilayers, for biological membranes interacting with proteins, peptides and cryoprotectants, for supercooled ionic liquids (ILs) and supercooled deep eutectic solvents (DESs), for globular proteins and intrinsically disordered proteins (IDPs), and for some other molecular solids.
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10
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Zheng L, Liu Z, Zhang Q, Li S, Huang J, Zhang L, Zan B, Tyagi M, Cheng H, Zuo T, Sakai VG, Yamada T, Yang C, Tan P, Jiang F, Chen H, Zhuang W, Hong L. Universal dynamical onset in water at distinct material interfaces. Chem Sci 2022; 13:4341-4351. [PMID: 35509458 PMCID: PMC9006901 DOI: 10.1039/d1sc04650k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials. Surprisingly, while the function-related anharmonic dynamical onset in the materials exhibits diverse activation temperatures, the surface water presents a universal onset at a common temperature. Further analysis of the neutron experiment and simulation results revealed that the universal onset of water results from an intrinsic surface-independent relaxation: switching of hydrogen bonds between neighboring water molecules with a common energy barrier of ∼35 kJ mol−1. We demonstrated that the dynamical onset of interfacial water is an intrinsic property of water itself, resulting from a surface independent relaxation process in water with an approximately universal energy barrier of ∼35 kJ mol−1.![]()
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Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Zhang
- College of Chemistry and Materials Science, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028043, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Zhang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - He Cheng
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Taisen Zuo
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Chenxing Yang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Tan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, 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
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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11
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George DK, Chen JY, He Y, Knab JR, Markelz AG. Functional-State Dependence of Picosecond Protein Dynamics. J Phys Chem B 2021; 125:11134-11140. [PMID: 34606257 DOI: 10.1021/acs.jpcb.1c05018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E1 ∼ 0.1 kJ/mol and E2 ∼ 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent-protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.
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Affiliation(s)
- D K George
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - J Y Chen
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - Yunfen He
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - J R Knab
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - A G Markelz
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
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12
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Černý J, Božíková P, Malý M, Tykač M, Biedermannová L, Schneider B. Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org. Acta Crystallogr D Struct Biol 2020; 76:805-813. [PMID: 32876056 PMCID: PMC7466747 DOI: 10.1107/s2059798320009389] [Citation(s) in RCA: 12] [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: 03/09/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023] Open
Abstract
A detailed description of the dnatco.datmos.org web server implementing the universal structural alphabet of nucleic acids is presented. It is capable of processing any mmCIF- or PDB-formatted files containing DNA or RNA molecules; these can either be uploaded by the user or supplied as the wwPDB or PDB-REDO structural database access code. The web server performs an assignment of the nucleic acid conformations and presents the results for the intuitive annotation, validation, modeling and refinement of nucleic acids.
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Affiliation(s)
- Jiří Černý
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, Vestec, Czech Republic
| | - Paulína Božíková
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, Vestec, Czech Republic
| | - Michal Malý
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, Vestec, Czech Republic
| | - Michal Tykač
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, Vestec, Czech Republic
| | - Lada Biedermannová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, Vestec, Czech Republic
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, Vestec, Czech Republic
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13
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Krah A, Huber RG, Bond PJ. How Ligand Binding Affects the Dynamical Transition Temperature in Proteins. Chemphyschem 2020; 21:916-926. [DOI: 10.1002/cphc.201901221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Krah
- School of Computational SciencesKorea Institute for Advanced Study 85 Hoegiro, Dongdaemun-gu Seoul 02455 Republic of Korea
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Roland G. Huber
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Peter J. Bond
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
- National University of SingaporeDepartment of Biological Sciences 14 Science Drive 4 Singapore 117543
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14
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Tian B, Garcia Sakai V, Pappas C, van der Goot AJ, Bouwman WG. Fibre formation in calcium caseinate influenced by solvent isotope effect and drying method – A neutron spectroscopy study. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Pathak AK, Bandyopadhyay T. Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water. J Chem Theory Comput 2019; 15:2706-2718. [PMID: 30849227 DOI: 10.1021/acs.jctc.9b00005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters. This might have led to the present trait of discovery that DTs of biomolecules, irrespective of the potential functions for water models used, occur within a narrow band of temperature variation (30-40 K). Whereas a water molecule in a biomolecular surface and one in bulk are polarized differently, therefore explicit treatment of water polarizability would be a powerful approach toward the treatment of hydration water, believed to cause the DT manifestation. Using MD simulations, we investigated the effects of polarizable water on the DT of biomolecules and the dynamic properties of hydration water. We chose two types of solutes: globular protein (lysozyme) and more open and flexible RNAs (a hairpin and a riboswitch) with different natures of hydrophilic sites than proteins in general. We found that the characteristic temperature of DT ( TDT) for the solutes in polarizable water is always higher than that in its nonpolarizable counterpart. In particular, for RNAs, the variations are found to be ∼45 K between the two water models, whereas for the more compact lysozyme, it is only ∼4 K. The results are discussed in light of the enormous increase in relaxation times of a liquid upon cooling in the paradigm of dynamic switchover in hydration water with liquid-liquid phase transition, derived from the existence of the second critical point. Our result supports the idea that structures of biomolecules and their interactions with the hydration water determines TDT and provides evidence for the decisive role of polarizable water on the onset of DT, which has been hitherto ignored.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
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16
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Golysheva EA, Shevelev GY, Dzuba SA. Dynamical transition in molecular glasses and proteins observed by spin relaxation of nitroxide spin probes and labels. J Chem Phys 2018; 147:064501. [PMID: 28810753 DOI: 10.1063/1.4997035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In glassy substances and biological media, dynamical transitions are observed in neutron scattering that manifests itself as deviations of the translational mean-squared displacement, 〈x2〉, of hydrogen atoms from harmonic dynamics. In biological media, the deviation occurs at two temperature intervals, at ∼100-150 K and at ∼170-230 K, and it is attributed to the motion of methyl groups in the former case and to the transition from harmonic to anharmonic or diffusive motions in the latter case. In this work, electron spin echo (ESE) spectroscopy-a pulsed version of electron paramagnetic resonance-is applied to study the spin relaxation of nitroxide spin probes and labels introduced in molecular glass former o-terphenyl and in protein lysozyme. The anisotropic contribution to the rate of the two-pulse ESE decay, ΔW, is induced by spin relaxation appearing because of restricted orientational stochastic molecular motion; it is proportional to 〈α2〉τc, where 〈α2〉 is the mean-squared angle of reorientation of the nitroxide molecule around the equilibrium position and τc is the correlation time of reorientation. The ESE time window allows us to study motions with τc < 10-7 s. For glassy o-terphenyl, the 〈α2〉τc temperature dependence shows a transition near 240 K, which is in agreement with the literature data on 〈x2〉. For spin probes of essentially different size, the obtained data were found to be close, which evidences that motion is cooperative, involving a nanocluster of several neighboring molecules. For the dry lysozyme, the 〈α2〉τc values below 260 K were found to linearly depend on the temperature in the same way as it was observed in neutron scattering for 〈x2〉. As spin relaxation is influenced only by stochastic motion, the harmonic motions seen in ESE must be overdamped. In the hydrated lysozyme, ESE data show transitions near 130 K for all nitroxides, near 160 K for the probe located in the hydration layer, and near 180 K for the label in the protein interior. For this system, the two latter transitions are not observed in neutron scattering. The ESE-detected transitions are suggested to be related with water dynamics in the nearest hydration shell: with water glass transition near 130 K and with the onset of overall water molecular reorientations near 180 K; the disagreement with neutron scattering is ascribed to the larger time window for ESE-detected motions.
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Affiliation(s)
- Elena A Golysheva
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Georgiy Yu Shevelev
- Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
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17
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Vural D, Smith JC, Glyde HR. Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins. Biophys J 2018; 114:2397-2407. [PMID: 29580551 DOI: 10.1016/j.bpj.2018.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/26/2018] [Accepted: 02/12/2018] [Indexed: 02/04/2023] Open
Abstract
Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain. Other H are quite independent. As a result, there is a distribution of motions and MSDs of H within a protein that is denoted dynamical heterogeneity. The goal of this paper is to incorporate a distribution of MSDs into models of the H incoherent intermediate scattering function, I(Q,t), that is calculated and observed. The aim is to contribute information on the distribution as well as on the average MSD from comparison of the models with simulations and experiment. For example, we find that simulations of I(Q,t) in lysozyme are well reproduced if the distribution of MSDs is bimodal with two broad peaks rather than a single broad peak.
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Affiliation(s)
- Derya Vural
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware; Department of Physics, Giresun University, Giresun, Turkey.
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Henry R Glyde
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
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18
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Abstract
Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed.
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Affiliation(s)
- Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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19
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Aloi E, Oranges M, Guzzi R, Bartucci R. Low-Temperature Dynamics of Chain-Labeled Lipids in Ester- and Ether-Linked Phosphatidylcholine Membranes. J Phys Chem B 2017; 121:9239-9246. [PMID: 28892381 DOI: 10.1021/acs.jpcb.7b07386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Continuous wave electron paramagnetic resonance spectroscopy and two-pulse echo detected spectra of chain-labeled lipids are used to study the dynamics of frozen lipid membranes over the temperature range 77-260 K. Bilayers of ester-linked dihexadecanoylphosphatidylcholine (DPPC) with noninterdigitated chains and ether-linked dihexadecyl phosphatidylcholine (DHPC) with interdigitated chains are considered. Rapid stochastic librations of small angular amplitude are found in both lipid matrices. In noninterdigitated DPPC bilayers, the mean-square angular amplitude, [Formula: see text], of the motion increases with temperature and it is larger close to the chain termini than close to the polar/apolar interface. In contrast, in interdigitated DHPC lamellae, [Formula: see text] is small and temperature and label-position independent at low temperature and increases steeply at high temperature. The rotational correlation time, τc, of librations lies in the subnanosecond range for DPPC and in the nanosecond range for DHPC. In all membrane samples, the temperature dependence of [Formula: see text] resembles that of the mean-square atomic displacement revealed by neutron scattering and a dynamical transition is detected in the range 210-240 K. The results highlight the librational oscillations and the glass-like behavior in bilayer and interdigitated lipid membranes.
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Affiliation(s)
- Erika Aloi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Maria Oranges
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Rita Guzzi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Rosa Bartucci
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
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20
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Mamontov E. Microscopic diffusion in hydrated encysted eggs of brine shrimp. Biochim Biophys Acta Gen Subj 2017; 1861:2382-2390. [PMID: 28549919 DOI: 10.1016/j.bbagen.2017.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/07/2017] [Accepted: 05/23/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND We have studied microscopic diffusion of water in fully hydrated encysted eggs of brine shrimp (Artemia). METHODS We have utilized quasielastic neutron scattering. RESULTS Dry eggs of brine shrimp were rehydrated using (1) water without additives, (2) eutectic mixture of water and dimethyl sulfoxide, and (3) a concentrated aqueous solution of lithium chloride. Despite the complexity of the hydrated multicellular organism, measurable microscopic diffusivity of water is rather well defined. Pure hydration water in eggs exhibits freezing temperature depression, whereas hydration water in eggs mixed with dimethyl sulfoxide or lithium chloride does not crystallize at all. CONCLUSIONS The characteristic size of the voids occupied by water or aqueous solvents in hydrated brine shrimp eggs is between 2 and 10nm. Those voids are accessible to co-solvents such as dimethyl sulfoxide and lithium chloride. There is no evidence of intracellular water in the hydrated eggs. GENERAL SIGNIFICANCE The lack of intracellular water in the fully hydrated (but still under arrested development) state must be linked to the unique resilience against adverse environmental factors documented not only for the anhydrous, but also hydrated encysted eggs of brine shrimp.
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Affiliation(s)
- E Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
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21
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Syryamina VN, Dzuba SA. Dynamical Transitions at Low Temperatures in the Nearest Hydration Shell of Phospholipid Bilayers. J Phys Chem B 2017; 121:1026-1032. [DOI: 10.1021/acs.jpcb.6b10133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. N. Syryamina
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - S. A. Dzuba
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
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22
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Dhindsa GK, Bhowmik D, Goswami M, O’Neill H, Mamontov E, Sumpter BG, Hong L, Ganesh P, Chu XQ. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study. J Phys Chem B 2016; 120:10059-10068. [DOI: 10.1021/acs.jpcb.6b07511] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gurpreet K. Dhindsa
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Debsindhu Bhowmik
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Monojoy Goswami
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O’Neill
- Biology and
Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Bobby G. Sumpter
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Liang Hong
- Institute of Natural Science & Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Panchapakesan Ganesh
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiang-qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
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23
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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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24
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Comparative Structural Dynamics of tRNA(Phe) with Respect to Hinge Region Methylated Guanosine: A Computational Approach. Cell Biochem Biophys 2016; 74:157-73. [PMID: 27216172 DOI: 10.1007/s12013-016-0731-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/01/2016] [Indexed: 12/13/2022]
Abstract
Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for maintaining the structural stability of tRNAs. However, their significance for upholding the tRNA structure has not been investigated in detail at the atomic level. In this study, molecular dynamic simulations have been performed to assess the effects of methylated nucleic acid bases, N (2)-methylguanosine (m(2)G) and N (2)-N (2)-dimethylguanosine (m 2 (2) G) at position 26, i.e., the hinge region of E. coli tRNA(Phe) on its structure and dynamics. The results revealed that tRNA(Phe) having unmodified guanosine in the hinge region (G26) shows structural rearrangement in the core of the molecule, resulting in lack of base stacking interactions, U-turn feature of the anticodon loop, and TΨC loop. We show that in the presence of the unmodified guanosine, the overall fold of tRNA(Phe) is essentially not the same as that of m(2)G26 and m 2 (2) G26 containing tRNA(Phe). This structural rearrangement arises due to intrinsic factors associated with the weak hydrogen-bonding patterns observed in the base triples of the tRNA(Phe) molecule. The m(2)G26 and m 2 (2) G26 containing tRNA(Phe) retain proper three-dimensional fold through tertiary interactions. Single-point energy and molecular electrostatics potential calculation studies confirmed the structural significance of tRNAs containing m(2)G26 and m 2 (2) G26 compared to tRNA with normal G26, showing that the mono-methylated (m(2)G26) and dimethylated (m 2 (2) G26) modifications are required to provide structural stability not only in the hinge region but also in the other parts of tRNA(Phe). Thus, the present study allows us to better understand the effects of modified nucleosides and ionic environment on tRNA folding.
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25
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Khodadadi S, Sokolov AP. Atomistic details of protein dynamics and the role of hydration water. Biochim Biophys Acta Gen Subj 2016; 1861:3546-3552. [PMID: 27155577 DOI: 10.1016/j.bbagen.2016.04.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND The importance of protein dynamics for their biological activity is now well recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. Yet, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. SCOOP OF REVIEW Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. MAJOR CONCLUSIONS Internal protein dynamics spread over a wide time range from faster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10-100ps time scale. This process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape. GENERAL SIGNIFICANCE The proposed atomistic picture of protein dynamics provides deeper understanding of various relaxation processes and their hierarchy, similarity and differences between various biological macromolecules, including proteins, DNA and RNA. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".
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Affiliation(s)
- Sheila Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands; Delft Project management B.V., Delft University of Technology, Delft, The Netherlands
| | - Alexei P Sokolov
- Joint Institute for Neutron Sciences, University of Tennessee, Knoxville, TN, USA.
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26
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Mamontov E, Sharma VK, Borreguero JM, Tyagi M. Protein-Style Dynamical Transition in a Non-Biological Polymer and a Non-Aqueous Solvent. J Phys Chem B 2016; 120:3232-9. [DOI: 10.1021/acs.jpcb.6b00866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Mamontov
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - V. K. Sharma
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Solid
State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - J. M. Borreguero
- Neutron
Data Analysis and Visualization Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - M. Tyagi
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, Maryland 20899, United States
- Department
of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
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27
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Roh JH, Tyagi M, Aich P, Kim K, Briber RM, Woodson SA. Charge screening in RNA: an integral route for dynamical enhancements. SOFT MATTER 2015; 11:8741-8745. [PMID: 26430908 DOI: 10.1039/c5sm02084k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Electrostatic interactions of RNA are at the center of determining the dynamical flexibility and structural stability. By analysing neutron scattering spectroscopy, we show that fast dynamics of hydrated tRNA on ps to ns timescales increases with stronger charge screening, while its structural stability either increases or remains largely unchanged. An unprecedented electrostatic threshold for the onset of additional flexibility is induced from the correlation between the charge-screening density of counterions and the promoted dynamical properties. The results demonstrate that the enhanced dynamical flexibility of tRNA originates from local conformational relaxation coupled with stabilized charge screening rather than governed by fluctuation of hydrated counterions. The present study casts light on the specificity of electrostatic interactions in the thermodynamic balance between the dynamical flexibility and structural stability of RNA.
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Affiliation(s)
- Joon Ho Roh
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, South Korea. and Biomolecular Science, University of Science and Technology, Daejeon 34113, South Korea
| | - Madhu Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Techonology, Gaithersburg, Maryland 20899, USA and Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Pulakesh Aich
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, South Korea.
| | - Kimoon Kim
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, South Korea. and Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - R M Briber
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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28
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Roh JH. Dynamics of Biopolymers: Role of Hydration and Electrostatic Interactions. MACROMOL CHEM PHYS 2015. [DOI: 10.1002/macp.201500279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joon Ho Roh
- Institute for Basic Science; Center for Self-Assembly and Complexity; 77 Cheongam-Ro Nam-gu Pohang 790-784 South Korea
- Biomolecular Science; University of Science and Technology; 217 Gajeong-ro Yuseong-gu Daejeon 305-350 South Korea
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29
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Perticaroli S, Ehlers G, Jalarvo N, Katsaras J, Nickels JD. Elasticity and Inverse Temperature Transition in Elastin. J Phys Chem Lett 2015; 6:4018-4025. [PMID: 26722771 DOI: 10.1021/acs.jpclett.5b01890] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Elastin is a structural protein and biomaterial that provides elasticity and resilience to a range of tissues. This work provides insights into the elastic properties of elastin and its peculiar inverse temperature transition (ITT). These features are dependent on hydration of elastin and are driven by a similar mechanism of hydrophobic collapse to an entropically favorable state. Using neutron scattering, we quantify the changes in the geometry of molecular motions above and below the transition temperature, showing a reduction in the displacement of water-induced motions upon hydrophobic collapse at the ITT. We also measured the collective vibrations of elastin gels as a function of elongation, revealing no changes in the spectral features associated with local rigidity and secondary structure, in agreement with the entropic origin of elasticity.
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Affiliation(s)
- Stefania Perticaroli
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Chemical and Materials Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Georg Ehlers
- Quantum Condensed Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Niina Jalarvo
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich , D-52425 Jülich, Germany
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, and JCNS Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Jonathan D Nickels
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- The Department of Physics and Astronomy, University of Tennessee, Knoxville , Knoxville, Tennessee 37996, United States
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30
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MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery. Int J Mol Sci 2015; 16:15872-902. [PMID: 26184179 PMCID: PMC4519929 DOI: 10.3390/ijms160715872] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/07/2015] [Accepted: 07/08/2015] [Indexed: 12/21/2022] Open
Abstract
While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes.
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31
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Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
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32
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Khodadadi S, Sokolov AP. Protein dynamics: from rattling in a cage to structural relaxation. SOFT MATTER 2015; 11:4984-4998. [PMID: 26027652 DOI: 10.1039/c5sm00636h] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.
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Affiliation(s)
- S Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
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33
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Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I. Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophys J 2015; 108:2876-85. [PMID: 26083927 PMCID: PMC4472199 DOI: 10.1016/j.bpj.2015.04.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/21/2015] [Accepted: 04/21/2015] [Indexed: 12/29/2022] Open
Abstract
RNA function depends crucially on the details of its dynamics. The simplest RNA dynamical unit is a two-way interhelical junction. Here, for such a unit--the transactivation response RNA element--we present evidence from molecular dynamics simulations, supported by nuclear magnetic resonance relaxation experiments, for a dynamical transition near 230 K. This glass transition arises from the freezing out of collective interhelical motional modes. The motions, resolved with site-specificity, are dynamically heterogeneous and exhibit non-Arrhenius relaxation. The microscopic origin of the glass transition is a low-dimensional, slow manifold consisting largely of the Euler angles describing interhelical reorientation. Principal component analysis over a range of temperatures covering the glass transition shows that the abrupt slowdown of motion finds its explanation in a localization transition that traps probability density into several disconnected conformational pools over the low-dimensional energy landscape. Upon temperature increase, the probability density pools then flood a larger basin, akin to a lakes-to-sea transition. Simulations on transactivation response RNA are also used to backcalculate inelastic neutron scattering data that match previous inelastic neutron scattering measurements on larger and more complex RNA structures and which, upon normalization, give temperature-dependent fluctuation profiles that overlap onto a glass transition curve that is quasi-universal over a range of systems and techniques.
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Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of California at Irvine, Irvine, California
| | - Qi Zhang
- The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina
| | - Ioan Andricioaei
- Department of Chemistry, University of California at Irvine, Irvine, California.
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34
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Vural D, Hong L, Smith JC, Glyde HR. Motional displacements in proteins: The origin of wave-vector-dependent values. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052705. [PMID: 26066197 DOI: 10.1103/physreve.91.052705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 06/04/2023]
Abstract
The average mean-square displacement, 〈r(2)〉, of H atoms in a protein is frequently determined using incoherent neutron-scattering experiments. 〈r(2)〉 is obtained from the observed elastic incoherent dynamic structure factor, S(i)(Q,ω=0), assuming the form S(i)(Q,ω=0) =exp(-Q(2)〈r(2)〉/3). This is often referred to as the Gaussian approximation (GA) to S(i)(Q,ω=0). 〈r(2)〉 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S(i)(Q,ω=0) deviates from the GA. We investigate the origin of the Q dependence of 〈r(2)〉 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q,ω) is an accurate approximation and is not the origin of the Q dependence of 〈r(2)〉. This is demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein. Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average 〈r(2)〉. The observed Q dependence of 〈r(2)〉 can be used to provide information on the dynamical heterogeneity in proteins.
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Affiliation(s)
- Derya Vural
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA
| | - Liang Hong
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P. O. Box 2008, Tennessee 37831, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P. O. Box 2008, Tennessee 37831, USA
| | - Henry R Glyde
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA
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35
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Perticaroli S, Nickels JD, Ehlers G, Mamontov E, Sokolov AP. Dynamics and rigidity in an intrinsically disordered protein, β-casein. J Phys Chem B 2014; 118:7317-26. [PMID: 24918971 DOI: 10.1021/jp503788r] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The emergence of intrinsically disordered proteins (IDPs) as a recognized structural class has forced the community to confront a new paradigm of structure, dynamics, and mechanical properties for proteins. We present novel data on the similarities and differences in the dynamics and nanomechanical properties of IDPs and other biomacromolecules on the picosecond time scale. An IDP, β-casein (CAS), has been studied in a calcium bound and unbound state using neutron and light scattering techniques. We show that CAS partially folds and stiffens upon calcium binding, but in the unfolded state, it is softer than folded proteins such as green fluorescence protein (GFP). We also see that some localized diffusive motions in CAS have a larger amplitude than in GFP at this time scale but are still smaller than those observed in tRNA. In spite of these differences, CAS dynamics are consistent with the classes of motions seen in folded protein on this time scale.
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Affiliation(s)
- Stefania Perticaroli
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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36
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Surovtsev NV, Dzuba SA. Flexibility of phospholipids with saturated and unsaturated chains studied by Raman scattering: The effect of cholesterol on dynamical and phase transitions. J Chem Phys 2014; 140:235103. [DOI: 10.1063/1.4883237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Yoon J, Lin JC, Hyeon C, Thirumalai D. Dynamical Transition and Heterogeneous Hydration Dynamics in RNA. J Phys Chem B 2014; 118:7910-9. [DOI: 10.1021/jp500643u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jeseong Yoon
- Korea Institute for Advanced Study, 130-722 Seoul, Korea
| | - Jong-Chin Lin
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | | | - D. Thirumalai
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
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38
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Bai R, Basser PJ, Briber RM, Horkay F. NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions. J Appl Polym Sci 2014; 131:10.1002/app.40001. [PMID: 24409001 PMCID: PMC3882160 DOI: 10.1002/app.40001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca2+ and Na+. Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na+ on the mobility of water molecules was practically undetectable. By contrast, addition of Ca2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced.
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Affiliation(s)
- Ruiliang Bai
- Section on Tissue Biophysics and Biomimetics, Program in Pediatric Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20740, USA
| | - Peter J. Basser
- Section on Tissue Biophysics and Biomimetics, Program in Pediatric Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Robert M. Briber
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20740,USA
| | - Ferenc Horkay
- Section on Tissue Biophysics and Biomimetics, Program in Pediatric Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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39
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Schirò G, Vetri V, Andersen C, Natali F, Koza M, Leone M, Cupane A. The Boson Peak of Amyloid Fibrils: Probing the Softness of Protein Aggregates by Inelastic Neutron Scattering. J Phys Chem B 2014; 118:2913-23. [DOI: 10.1021/jp412277y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G. Schirò
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - V. Vetri
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - C.B. Andersen
- Department
of Diabetes Biophysics, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - F. Natali
- CNR-IOM, c/o Institut Laue Langevin, Grenoble, France
| | - M.M. Koza
- Institut Laue Langevin, Grenoble, France
| | - M. Leone
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - A. Cupane
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
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40
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Mamontov E, O’Neill H, Zhang Q, Chathoth S. Temperature dependence of the internal dynamics of a protein in an aqueous solvent: Decoupling from the solvent viscosity. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.02.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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41
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Schiró G. Anharmonic onsets in polypeptides revealed by neutron scattering: Experimental evidences and quantitative description of energy resolution dependence. Biophys Chem 2013; 180-181:29-36. [DOI: 10.1016/j.bpc.2013.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/26/2013] [Accepted: 05/26/2013] [Indexed: 10/26/2022]
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42
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Lai J, Chen K, Luthey-Schulten Z. Structural intermediates and folding events in the early assembly of the ribosomal small subunit. J Phys Chem B 2013; 117:13335-45. [PMID: 23972210 DOI: 10.1021/jp404106r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using all-atom explicit solvent molecular dynamics (MD) simulations, we investigated the early structural intermediates of the 5' domain of the 16S rRNA in Escherichia coli upon the removal of the primary binding r-proteins S4, S17, and S20 and the secondary binding r-protein S16. Removal of each r-protein corresponded to the disappearance of subdomains with correlated dynamics. Correlation-based network analysis of the MD trajectories of the naked rRNA showed that the different subdomains are connected via multiple pathways with high betweenness. These pathways cross at the internal loop of helix 17 (h17) in the five-way junction (5WJ). The structure of the internal loop is disrupted by the binding of S17 and rescued by the addition of S16, suggesting an important function of the secondary binding protein in biasing the rRNA folding landscape toward the native basin. Using structure-based Gō simulations, we investigated the folding barriers of the lower four-way junction (4WJ) with h6, which is the primary binding site of S20 and the first to be transcribed. The folding of the 4WJ is consistent with the protection patterns observed in hydroxyl radical footprinting. Results from the all-atom simulations show that the fluctuations in the 5WJ are independent of the fluctuations in the 4WJ, suggesting that the subdomains fold independently and are stabilized by primary r-proteins.
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Affiliation(s)
- Jonathan Lai
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
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43
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Nickels JD, García Sakai V, Sokolov AP. Dynamics in Protein Powders on the Nanosecond–Picosecond Time Scale Are Dominated by Localized Motions. J Phys Chem B 2013; 117:11548-55. [DOI: 10.1021/jp4058884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan D. Nickels
- Joint
Institute for Neutron Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, Knoxville, Tennessee 37996, United States
| | - Victoria García Sakai
- ISIS Neutron and Muon Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Alexei P. Sokolov
- Joint
Institute for Neutron Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, Knoxville, Tennessee 37996, United States
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44
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Ngai KL, Capaccioli S, Paciaroni A. Change of caged dynamics at Tg in hydrated proteins: Trend of mean squared displacements after correcting for the methyl-group rotation contribution. J Chem Phys 2013; 138:235102. [DOI: 10.1063/1.4810752] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Chu XQ, Mamontov E, O'Neill H, Zhang Q. Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA. J Phys Chem Lett 2013; 4:936-942. [PMID: 26291359 DOI: 10.1021/jz400128u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The dynamics of RNA within the β-relaxation region of 10 ps to 1 ns is crucial to its biological function. Because of its simpler chemical building blocks and the lack of the side methyl groups, faster relaxational dynamics of RNA compared to proteins can be expected. However, the situation is actually opposite. In this work, the relaxational dynamics of tRNA is measured by quasielastic neutron scattering and analyzed using the mode coupling theory, originally developed for glass-forming liquids. Our results reveal that the dynamics of tRNA follows a log-decay within the β-relaxation region, which is an important trait demonstrated by the dynamics of proteins. The dynamics of hydrated tRNA and lysozyme compared in the time domain further demonstrate that the slower dynamics of tRNA relative to proteins originates from the difference in the folded states of tRNA and proteins, as well as the influence of their hydration water.
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Affiliation(s)
- Xiang-Qiang Chu
- †Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- §Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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46
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Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, Sokolov AP. Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP. Biophys J 2012; 103:1566-75. [PMID: 23062349 DOI: 10.1016/j.bpj.2012.08.046] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/15/2022] Open
Abstract
We present a detailed analysis of the picosecond-to-nanosecond motions of green fluorescent protein (GFP) and its hydration water using neutron scattering spectroscopy and hydrogen/deuterium contrast. The analysis reveals that hydration water suppresses protein motions at lower temperatures (<~ 200 K), and facilitates protein dynamics at high temperatures. Experimental data demonstrate that the hydration water is harmonic at temperatures <~ 180-190 K and is not affected by the proteins' methyl group rotations. The dynamics of the hydration water exhibits changes at ~ 180-190 K that we ascribe to the glass transition in the hydrated protein. Our results confirm significant differences in the dynamics of protein and its hydration water at high temperatures: on the picosecond-to-nanosecond timescale, the hydration water exhibits diffusive dynamics, while the protein motions are localized to <~3 Å. The diffusion of the GFP hydration water is similar to the behavior of hydration water previously observed for other proteins. Comparison with other globular proteins (e.g., lysozyme) reveals that on the timescale of 1 ns and at equivalent hydration level, GFP dynamics (mean-square displacements and quasielastic intensity) are of much smaller amplitude. Moreover, the suppression of the protein dynamics by the hydration water at low temperatures appears to be stronger in GFP than in other globular proteins. We ascribe this observation to the barrellike structure of GFP.
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Affiliation(s)
- Jonathan D Nickels
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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47
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Schiró G, Natali F, Cupane A. Physical origin of anharmonic dynamics in proteins: new insights from resolution-dependent neutron scattering on homomeric polypeptides. PHYSICAL REVIEW LETTERS 2012; 109:128102. [PMID: 23005991 DOI: 10.1103/physrevlett.109.128102] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Indexed: 06/01/2023]
Abstract
Neutron scattering reveals a complex dynamics in polypeptide chains, with two main onsets of anharmonicity whose physical origin and biological role are still debated. In this study the dynamics of strategically selected homomeric polypeptides is investigated with elastic neutron scattering using different energy resolutions and compared with that of a real protein. Our data spotlight the dependence of anharmonic transition temperatures and fluctuation amplitudes on energy resolution, which we quantitatively explain in terms of a two-site model for the protein-hydration water energy landscape. Experimental data strongly suggest that the protein dynamical transition is not a mere resolution effect but is due to a real physical effect. Activation barriers and free energy values obtained for the protein dynamical transition allow us to make a connection with the two-well interaction potential of supercooled-confined water proposed to explain a low-density→high-density liquid-liquid transition.
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48
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Chu XQ, Gajapathy M, Weiss KL, Mamontov E, Ng JD, Coates L. Dynamic behavior of oligomeric inorganic pyrophosphatase explored by quasielastic neutron scattering. J Phys Chem B 2012; 116:9917-21. [PMID: 22804561 DOI: 10.1021/jp303127w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The purpose of this investigation is to determine whether a large oligomeric protein, inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens with quaternary structural complexity, would have distinguishable dynamic characteristics compared to those of the small simple monomeric model protein, lysozyme. In this study, the β-relaxational dynamics of the two proteins, IPPase and lysozyme, are compared in the 10 ps to 0.5 ns time interval using quasi-elastic neutron scattering (QENS). Both of the protein dynamics show a characteristic logarithmic-like decay in the intermediate scattering function (ISF) of the hydrogen atoms. Distinguishable dynamical behavior found between two proteins reveals local flexibility and conformational substates unique to oligomeric structures. Moreover, the temperature dependence of the mean square displacement (MSD) of the hydrogen atoms in protein molecules, which is a traditional way to determine the "softness" of the protein molecule, is measured and shows no difference for the two proteins.
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Affiliation(s)
- Xiang-qiang Chu
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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49
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Giel-Pietraszuk M, Barciszewski J. Hydrostatic and osmotic pressure study of the RNA hydration. Mol Biol Rep 2012; 39:6309-18. [PMID: 22314910 PMCID: PMC3310992 DOI: 10.1007/s11033-012-1452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 01/23/2012] [Indexed: 11/17/2022]
Abstract
The tertiary structure of nucleic acids results from an equilibrium between electrostatic interactions of phosphates, stacking interactions of bases, hydrogen bonds between polar atoms and water molecules. Water interactions with ribonucleic acid play a key role in its structure formation, stabilization and dynamics. We used high hydrostatic pressure and osmotic pressure to analyze changes in RNA hydration. We analyzed the lead catalyzed hydrolysis of tRNAPhe from S. cerevisiae as well as hydrolytic activity of leadzyme. Pb(II) induced hydrolysis of the single phosphodiester bond in tRNAPhe is accompanied by release of 98 water molecules, while other molecule, leadzyme releases 86.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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50
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Yin P, Pradeep CP, Zhang B, Li FY, Lydon C, Rosnes MH, Li D, Bitterlich E, Xu L, Cronin L, Liu T. Controllable self-assembly of organic-inorganic amphiphiles containing Dawson polyoxometalate clusters. Chemistry 2012; 18:8157-62. [PMID: 22618885 DOI: 10.1002/chem.201200362] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Indexed: 11/06/2022]
Abstract
An organic-inorganic molecular hybrid containing the Dawson polyoxometalate, ((C(4)H(9))(4)N)(5)H[P(2)V(3)W(15)O(59)(OCH(2))(3)CNHCOC(15)H(31)], was synthesized and its surfactant-like amphiphilic properties, represented by the formation of bilayer vesicles, were studied in polar solvents. The vesicle size decreases with both decreasing hybrid concentration and with increasing polarity of the solvent, independently. The self-assembly behavior of this hybrid can be controlled by introducing different counterions into the acetonitrile solutions. The addition of ZnCl(2) and NaI can cause a gradual decrease and increase of vesicular sizes, respectively. Tetraalkylammonium bromide is found to disassemble the vesicle assemblies. Moreover, the original counterions of the hybrid can be replaced with protons, resulting in pH-dependent formation of vesicles in aqueous solutions. The hybrid surfactant can further form micro-needle structures in aqueous solutions upon addition of Ca(2+) ions.
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Affiliation(s)
- Panchao Yin
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
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