1
|
Tavagnacco L, Zanatta M, Buratti E, Bertoldo M, Chiessi E, Appel M, Natali F, Orecchini A, Zaccarelli E. Water slowing down drives the occurrence of the low temperature dynamical transition in microgels. Chem Sci 2024; 15:9249-9257. [PMID: 38903230 PMCID: PMC11186305 DOI: 10.1039/d4sc02650k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 06/22/2024] Open
Abstract
The protein dynamical transition marks an increase in atomic mobility and the onset of anharmonic motions at a critical temperature (T d), which is considered relevant for protein functionality. This phenomenon is ubiquitous, regardless of protein composition, structure and biological function and typically occurs at large protein content, to avoid water crystallization. Recently, a dynamical transition has also been reported in non-biological macromolecules, such as poly(N-isopropyl acrylamide) (PNIPAM) microgels, bearing many similarities to proteins. While the generality of this phenomenon is well-established, the role of water in the transition remains a subject of debate. In this study, we use atomistic molecular dynamics (MD) simulations and elastic incoherent neutron scattering (EINS) experiments with selective deuteration to investigate the microscopic origin of the dynamical transition and distinguish water and PNIPAM roles. While a standard analysis of EINS experiments would suggest that the dynamical transition occurs in PNIPAM and water at a similar temperature, simulations reveal a different perspective, also qualitatively supported by experiments. From room temperature down to about 180 K, PNIPAM exhibits only modest changes of dynamics, while water, being mainly hydration water under the probed extreme confinement, significantly slows down and undergoes a mode-coupling transition from diffusive to activated. Our findings therefore challenge the traditional view of the dynamical transition, demonstrating that it occurs in proximity of the water mode-coupling transition, shedding light on the intricate interplay between polymer and water dynamics.
Collapse
Affiliation(s)
- Letizia Tavagnacco
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| | - Marco Zanatta
- Department of Physics, University of Trento Via Sommarive 14 38123 Trento Italy
| | - Elena Buratti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Monica Bertoldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata Via della Ricerca Scientifica I 00133 Rome Italy
| | - Markus Appel
- Institut Laue-Langevin 71 avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Francesca Natali
- CNR-IOM, Operative Group Grenoble (OGG), Institut Laue Langevin F-38042 Grenoble France
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
| | - Emanuela Zaccarelli
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Vural D, Shrestha UR, Petridis L, Smith JC. Water molecule ordering on the surface of an intrinsically disordered protein. Biophys J 2023; 122:4326-4335. [PMID: 37838830 PMCID: PMC10722392 DOI: 10.1016/j.bpj.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023] Open
Abstract
The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.
Collapse
Affiliation(s)
- Derya Vural
- Department of Physics, Marmara University, Istanbul, Türkiye; Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
| | - Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Martinez-Gonzalez JA, Nandi PK, English NJ, Gowen A. Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions. Int J Mol Sci 2022; 23:ijms232415949. [PMID: 36555590 PMCID: PMC9785973 DOI: 10.3390/ijms232415949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Classical molecular-dynamics simulations have been performed to examine the interplay between ubiquitin and its hydration-water sub-layers, chiefly from a vibrational-mode and IR viewpoint-where we analyse individual sub-layers characteristics. The vibrational Density of States (VDOS) revealed that the first solvation sub-shell indicates a confined character therein. For layers of increasing distance from the surface, the adoption of greater bulk-like spectral behaviour was evident, suggesting that vibrational harmonisation to bulk occurs within 6-7 Å of the surface.
Collapse
Affiliation(s)
- José Angel Martinez-Gonzalez
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- School of Biosystems Engineering, University College Dublin, Belfield, D04 N2E5 Dublin, Ireland
- ISIS Pulsed Neutron and Moun Source, Rutherford Appleton Laboratory, Harwell Science & Innovation Campus, Chilton, Didcot OX11 0QL, UK
- School of Pharmacy, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
- Correspondence: (J.A.M.-G.); (N.J.E.)
| | - Prithwish K. Nandi
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Niall J. English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Correspondence: (J.A.M.-G.); (N.J.E.)
| | - Aoife Gowen
- School of Biosystems Engineering, University College Dublin, Belfield, D04 N2E5 Dublin, Ireland
| |
Collapse
|
6
|
Zhang L, Liu Z, Yang C, García Sakai V, Tyagi M, Hong L. Conduction Mechanism in Graphene Oxide Membranes with Varied Water Content: From Proton Hopping Dominant to Ion Diffusion Dominant. ACS NANO 2022; 16:13771-13782. [PMID: 35993828 DOI: 10.1021/acsnano.2c00686] [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] [Indexed: 06/15/2023]
Abstract
Proton conductors, particularly hydrated solid membranes, have various applications in sensors, fuel cells, and cellular biological systems. Unraveling the intrinsic proton transfer mechanism is critical for establishing the foundation of proton conduction. Two scenarios on electrical conduction, the Grotthuss and the vehicle mechanisms, have been reported by experiments and simulations. But separating and quantifying the contributions of these two components from experiments is difficult. Here, we present the conductive behavior of a two-dimensional layered proton conductor, graphene oxide membrane (GOM), and find that proton hopping is dominant at low water content, while ion diffusion prevails with increasing water content. This change in the conduction mechanism is attributable to the layers of water molecules in GOM nanosheets. The overall conductivity is greatly improved by forming one layer of water molecules. It reaches the maximum with two layers of water molecules, resulting from creating a complete hydrogen-bond network within GOM. When more than two layers of water molecules enter the GOM nanosheets, inducing the breakage of the ordered lamellar structure, protons spread in both in-plane and out-of-plane directions inside the GOM. Our results validate the existence of two conduction mechanisms and show their distinct contributions to the overall conductivity. Furthermore, these findings provide an optimization strategy for the design of realizing the fast proton transfer in materials with water participation.
Collapse
Affiliation(s)
- Lei Zhang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chenxing Yang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Victoria García Sakai
- Rutherford Appleton Laboratory, ISIS Neutron and Muon Facility, Science and Technology Facilities Council, Didcot OX11 0QX, United Kingdom
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
7
|
Li Y, Han Z, Ma C, Hong L, Ding Y, Chen Y, Zhao J, Liu D, Sun G, Zuo T, Cheng H, Han CC. Structure and dynamics of supercooled water in the hydration layer of poly(ethylene glycol). STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054901. [PMID: 36090796 PMCID: PMC9462885 DOI: 10.1063/4.0000158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
The statics and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) (PEG) were studied by a combination of quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. Two samples, that is, hydrogenated PEG/deuterated water (h-PEG/D2O) and fully deuterated PEG/hydrogenated water (d-PEG/H2O) with the same molar ratio of ethylene glycol (EG) monomer to water, 1:1, are compared. The QENS data of h-PEG/D2O show the dynamics of PEG, and that of d-PEG/H2O reveals the motion of water. The temperature-dependent elastic scattering intensity of both samples has shown transitions at supercooled temperature, and these transition temperatures depend on the energy resolution of the instruments. Therefore, neither one is a phase transition, but undergoes dynamic process. The dynamic of water can be described as an Arrhenius to super-Arrhenius transition, and it reveals the hydrogen bonding network relaxation of hydration water around PEG at supercooled temperature. Since the PEG-water hydrogen bond structural relaxation time from MD is in good agreement with the average relaxation time from QENS (d-PEG/H2O), MD may further reveal the atomic pictures of the supercooled hydration water. It shows that hydration water molecules form a series of pools around the hydrophilic oxygen atom of PEG. At supercooled temperature, they have a more bond ordered structure than bulk water, proceed a trapping sites diffusion on the PEG surface, and facilitate the structural relaxation of PEG backbone.
Collapse
Affiliation(s)
| | | | | | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanwei Ding
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Ye Chen
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Junpeng Zhao
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Dong Liu
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | - Guangai Sun
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | | | - He Cheng
- Author to whom correspondence should be addressed: . Tel.: +86-769-8915-6445. Fax: +86-769-8915-6441
| | - Charles C. Han
- Institute for Advanced Study, Shenzhen University, Shenzhen 508060, China
| |
Collapse
|
8
|
Exploring the Limits of Biological Complexity Amenable to Studies by Incoherent Neutron Spectroscopy. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081219. [PMID: 36013398 PMCID: PMC9410259 DOI: 10.3390/life12081219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms.
Collapse
|
9
|
Stachowski TR, Vanarotti M, Seetharaman J, Lopez K, Fischer M. Water Networks Repopulate Protein-Ligand Interfaces with Temperature. Angew Chem Int Ed Engl 2022; 61:e202112919. [PMID: 35648650 PMCID: PMC9329195 DOI: 10.1002/anie.202112919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 12/14/2022]
Abstract
High-resolution crystal structures highlight the importance of water networks in protein-ligand interactions. However, as these are typically determined at cryogenic temperature, resulting insights may be structurally precise but not biologically accurate. By collecting 10 matched room-temperature and cryogenic datasets of the biomedical target Hsp90α, we identified changes in water networks that impact protein conformations at the ligand binding interface. Water repositioning with temperature repopulates protein ensembles and ligand interactions. We introduce Flipper conformational barcodes to identify temperature-sensitive regions in electron density maps. This revealed that temperature-responsive states coincide with ligand-responsive regions and capture unique binding signatures that disappear upon cryo-cooling. Our results have implications for discovering Hsp90 selective ligands, and, more generally, for the utility of hidden protein and water conformations in drug discovery.
Collapse
Affiliation(s)
- Timothy R. Stachowski
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTN 38105USA
| | - Murugendra Vanarotti
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTN 38105USA
| | - Jayaraman Seetharaman
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTN 38105USA
| | - Karlo Lopez
- School of Natural SciencesMathematicsand EngineeringCalifornia State UniversityBakersfieldCA 93311USA
| | - Marcus Fischer
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTN 38105USA
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTN 38105USA
| |
Collapse
|
10
|
Reuhl M, Vogel M. Temperature-Dependent Dynamics at Protein-Solvent Interfaces. J Chem Phys 2022; 157:074705. [DOI: 10.1063/5.0105062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We perform differential scanning calorimetry, broadband dielectric spectroscopy (BDS), and nuclear magnetic resonance (NMR) studies to ascertain the molecular dynamics in mixtures of ethylene glycol with elastin or lysozyme over broad temperature ranges. To focus on the protein-solvent interface, we use mixtures with about equal numbers of amino acids and solvent molecules. The elastin and lysozyme mixtures show similar glass transition steps, which extend over a broad temperature range of 157-185K. The BDS and NMR studies yield fully consistent results for the fastest process P1, which is caused by the structural relaxation of ethylene glycol between the protein molecules and follows an Arrhenius law with an activation energy of Ea=0.63eV. It involves quasi-isotropic reorientation and is very similar in the elastin and lysozyme matrices but different from the alpha and beta relaxations of bulk ethylene glycol. Two slower BDS processes P2 and P3 have protein-dependent time scales, but exhibit a similar Arrhenius-like temperature dependence with an activation energy of Ea~0.81eV. However, P2 and P3 do not have a clear NMR signature. In particular, the NMR results for the lysozyme mixture reveal that the protein backbone does not show isotropic alpha-like motion on the P2 and P3 time scales but only restricted beta-like reorientation. The different activation energies of the P1 and P2/P3 processes do not support an intimate coupling of protein and ethylene glycol dynamics. The present results are compared with previous findings for mixtures of proteins with water or glycerol, implying qualitatively different dynamical couplings at various protein-solvent interfaces.
Collapse
Affiliation(s)
| | - Michael Vogel
- Institute of Condensed Matter Physics, TU Darmstadt, Germany
| |
Collapse
|
11
|
Stachowski TR, Vanarotti M, Seetharaman J, Lopez K, Fischer M. Water Networks Repopulate Protein‐Ligand Interfaces With Temperature. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Timothy R Stachowski
- St Jude Children's Research Hospital Chemical Biology & Therapeutics UNITED STATES
| | - Murugendra Vanarotti
- St Jude Children's Research Hospital Chemical Biology & Therapeutics UNITED STATES
| | | | - Karlo Lopez
- California State University - Bakersfield School of Natural Sciences, Mathematics, and Engineering UNITED STATES
| | - Marcus Fischer
- St. Jude Children's Research Hospital Chemical Biology & Therapeutics 262 Danny Thomas Place 38105 Memphis UNITED STATES
| |
Collapse
|
12
|
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.
Collapse
|
13
|
Mamontov E, Bordallo HN, Delaire O, Nickels J, Peters J, Schneider GJ, Smith JC, Sokolov AP. Broadband Wide-Angle VElocity Selector (BWAVES) neutron spectrometer designed for the SNS Second Target Station. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202227202003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recently proposed wide-angle velocity selector (WAVES) device for choosing the velocity of detected neutrons after they have been scattered by the sample paves the way for inverted geometry neutron spectrometers with continuously adjustable final neutron wavelength. BWAVES broadband inverted geometry spectrometer proposed for the Second Target Station at the Spallation Neutron Source at Oak Ridge National Laboratory is designed using WAVES to simultaneously probe dynamic processes spanning 4.5 decades in time (energy transfer). This makes BWAVES a uniquely flexible instrument which can be viewed as either a quasielasitc neutron scattering (QENS) spectrometer with a practically unlimited (overlapping with the vibrational excitations) range of energy transfers, or a broadband inelastic vibrational neutron spectrometer with QENS capabilities, including a range of accessible momentum transfer (Q) and a sufficiently high energy resolution at the elastic line. The new capabilities offered by BWAVES will expand the application of neutron scattering in ways not possible with existing neutron spectrometers.
Collapse
|
14
|
Huang J, Xu Q, Liu Z, Jain N, Tyagi M, Wei DQ, Hong L. Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density. Molecules 2021; 26:5693. [PMID: 34577164 PMCID: PMC8470667 DOI: 10.3390/molecules26185693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.
Collapse
Affiliation(s)
- Juan Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Nitin Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA;
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Peng Cheng Laboratory, Shenzhen 518055, China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
15
|
Tokunaga Y, Tanaka M, Iida H, Kinoshita M, Tojima Y, Takeuchi K, Imashimizu M. Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin. Biophys J 2021; 120:2386-2393. [PMID: 33894216 PMCID: PMC8390810 DOI: 10.1016/j.bpj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 310 helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.
Collapse
Affiliation(s)
- Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hitoshi Iida
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Moto Kinoshita
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Tojima
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
| |
Collapse
|
16
|
Martínez-González JA, Nandi PK, English NJ, Gowen AA. Infrared spectra and density of states at the interface between water and protein: Insights from classical molecular dynamics. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
17
|
Li R, Liu Z, Li L, Huang J, Yamada T, Sakai VG, Tan P, Hong L. Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:054703. [PMID: 33094127 PMCID: PMC7556885 DOI: 10.1063/4.0000036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated protein powder, a concentrated protein solution, and in living Escherichia coli (E. coli) cells. Anomalous sub-diffusion of water is observed in all samples, which is alleviated upon increasing the water content. Complementary molecular dynamics simulations and coarse-grained numerical modeling demonstrated that the sub-diffusive behavior results from the heterogeneous distribution of microscopic translational mobility of interfacial water. Moreover, by comparing the experimental results measured on E. coli cells with those from a concentrated protein solution with the same amount of water, we show that water in the two samples has a similar average mobility, however the underlying distribution of motion is more heterogeneous in the living cell.
Collapse
Affiliation(s)
| | | | - Like Li
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Ibaraki 319-1106, Japan
| | - Victoria García Sakai
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Pan Tan
- Authors to whom correspondence should be addressed: and
| | - Liang Hong
- Authors to whom correspondence should be addressed: and
| |
Collapse
|
18
|
Mamontov E, Cheng Y, Daemen LL, Keum JK, Kolesnikov AI, Pajerowski D, Podlesnyak A, Ramirez-Cuesta AJ, Ryder MR, Stone MB. Effect of Hydration on the Molecular Dynamics of Hydroxychloroquine Sulfate. ACS OMEGA 2020; 5:21231-21240. [PMID: 32869009 PMCID: PMC7423024 DOI: 10.1021/acsomega.0c03091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Chloroquine and its derivative hydroxychloroquine are primarily known as antimalaria drugs. Here, we investigate the influence of hydration water on the molecular dynamics in hydroxychloroquine sulfate, a commonly used solubilized drug form. When hydration, even at a low level, results in a disordered structure, as opposed to the highly ordered structure of dry hydroxychloroquine sulfate, the activation barriers for the rotation of methyl groups in the drug molecules become randomized and, on average, significantly reduced. The facilitated stochastic motions of the methyl groups may benefit the biomolecular activity due to the more efficient sampling of the energy landscape in the disordered hydration environment experienced by the drug molecules in vivo.
Collapse
|
19
|
Kämpf K, Demuth D, Zamponi M, Wuttke J, Vogel M. Quasielastic neutron scattering studies on couplings of protein and water dynamics in hydrated elastin. J Chem Phys 2020; 152:245101. [PMID: 32610976 DOI: 10.1063/5.0011107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Performing quasielastic neutron scattering measurements and analyzing both elastic and quasielasic contributions, we study protein and water dynamics of hydrated elastin. At low temperatures, hydration-independent methyl group rotation dominates the findings. It is characterized by a Gaussian distribution of activation energies centered at about Em = 0.17 eV. At ∼195 K, coupled protein-water motion sets in. The hydration water shows diffusive motion, which is described by a Gaussian distribution of activation energies with Em = 0.57 eV. This Arrhenius behavior of water diffusion is consistent with previous results for water reorientation, but at variance with a fragile-to-strong crossover at ∼225 K. The hydration-related elastin backbone motion is localized and can be attributed to the cage rattling motion. We speculate that its onset at ∼195 K is related to a secondary glass transition, which occurs when a β relaxation of the protein has a correlation time of τβ ∼ 100 s. Moreover, we show that its temperature-dependent amplitude has a crossover at the regular glass transition Tg = 320 K of hydrated elastin, where the α relaxation of the protein obeys τα ∼ 100 s. By contrast, we do not observe a protein dynamical transition when water dynamics enters the experimental time window at ∼240 K.
Collapse
Affiliation(s)
- Kerstin Kämpf
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Dominik Demuth
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Michaela Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Joachim Wuttke
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Michael Vogel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| |
Collapse
|
20
|
Weigler M, Combarro-Palacios I, Cerveny S, Vogel M. On the microscopic origins of relaxation processes in aqueous peptide solutions undergoing a glass transition. J Chem Phys 2020; 152:234503. [PMID: 32571076 DOI: 10.1063/5.0010312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We combine broadband dielectric spectroscopy (BDS) with 1H and 2H nuclear magnetic resonance (NMR) to study molecular dynamics in mixtures of ε-polylysine with H2O or D2O. In BDS, four relaxation processes can be attributed to molecular dynamics. While the fastest process P1 obeys the Arrhenius law, the slowest process P4 shows prominent non-Arrhenius behavior typical of structural α relaxation. For the intermediate processes P2 and P3, the temperature dependence changes at the glass transition temperature Tg. The 1H and 2H NMR results yield insights into the molecular origins of these relaxation phenomena. In these NMR analyses, we exploit, in addition to the isotope selectivity of the method, the possibility to distinguish between various types of motion based on their respective line-shape effects and the capability to single out specific molecular moieties based on different spin-lattice relaxation behaviors. In this way, we reveal that process P1 results from the rotation of side and end groups of the peptide, while process P2 is caused by a reorientation of essentially all water molecules, which are quasi-isotropic and survive well below Tg. As for the peptide backbone dynamics, we find evidence that rotational motion of polar groups is involved in process P3 and that nonpolar regions show a dynamical process, which is located between P3 and P4. Thus, the NMR analyses do not yield evidence for coexisting fast peptide-decoupled and slow peptide-coupled water species, which contribute to BDS processes P2 and P3, respectively, but minor bimodality of water motion may remain undetected. Finally, it is demonstrated that the proton/deuteron exchange needs to be considered when interpreting experimental results for molecular dynamics in aqueous peptide solutions.
Collapse
Affiliation(s)
- M Weigler
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - I Combarro-Palacios
- Centro de Fisica Materiales (CSIC-UPV/EHU) - Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastian, Spain
| | - S Cerveny
- Centro de Fisica Materiales (CSIC-UPV/EHU) - Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastian, Spain
| | - M Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| |
Collapse
|
21
|
Baryiames CP, Baiz CR. Slow Oil, Slow Water: Long-Range Dynamic Coupling across a Liquid–Liquid Interface. J Am Chem Soc 2020; 142:8063-8067. [DOI: 10.1021/jacs.0c00817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christopher P. Baryiames
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| |
Collapse
|
22
|
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
| |
Collapse
|
23
|
Marques MPM, Batista de Carvalho ALM, Mamede AP, Rudić S, Dopplapudi A, García Sakai V, Batista de Carvalho LAE. Intracellular water as a mediator of anticancer drug action. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1700083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- M. P. M. Marques
- Unidade de I&D Química-Física Molecular, Department of Chemistry, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - A. P. Mamede
- Unidade de I&D Química-Física Molecular, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - S. Rudić
- STFC Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, UK
| | - A. Dopplapudi
- STFC Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, UK
| | - V. García Sakai
- STFC Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, UK
| | | |
Collapse
|
24
|
Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
Collapse
Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | | |
Collapse
|
25
|
Maurer M, Oostenbrink C. Water in protein hydration and ligand recognition. J Mol Recognit 2019; 32:e2810. [PMID: 31456282 PMCID: PMC6899928 DOI: 10.1002/jmr.2810] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022]
Abstract
This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.
Collapse
Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
26
|
Wohlfromm T, Vogel M. On the coupling of protein and water dynamics in confinement: Spatially resolved molecular dynamics simulation studies. J Chem Phys 2019; 150:245101. [DOI: 10.1063/1.5097777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Timothy Wohlfromm
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Michael Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| |
Collapse
|
27
|
Tavagnacco L, Chiessi E, Zanatta M, Orecchini A, Zaccarelli E. Water-Polymer Coupling Induces a Dynamical Transition in Microgels. J Phys Chem Lett 2019; 10:870-876. [PMID: 30735054 PMCID: PMC6416711 DOI: 10.1021/acs.jpclett.9b00190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
Collapse
Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| | - Ester Chiessi
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientica I, 00133 Rome, Italy
| | - Marco Zanatta
- Department
of Computer Science, University of Verona, Strada Le Grazie 15, 37138 Verona, Italy
| | - Andrea Orecchini
- Department
of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM
c/o Department of Physics and Geology, University
of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| |
Collapse
|
28
|
Batista de Carvalho ALM, Mamede AP, Dopplapudi A, Garcia Sakai V, Doherty J, Frogley M, Cinque G, Gardner P, Gianolio D, Batista de Carvalho LAE, Marques MPM. Anticancer drug impact on DNA – a study by neutron spectroscopy coupled with synchrotron-based FTIR and EXAFS. Phys Chem Chem Phys 2019; 21:4162-4175. [DOI: 10.1039/c8cp05881d] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Complementary information on drug–DNA interplay has been achieved for Pt/Pd anticancer agents, by a combined QENS, SR-FTIR-ATR and EXAFS approach.
Collapse
Affiliation(s)
| | - Adriana P. Mamede
- Química-Física Molecular
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
| | - Asha Dopplapudi
- ISIS Facility
- STFC Rutherford Appleton Laboratory
- Chilton
- Didcot
- UK
| | | | - James Doherty
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | - Mark Frogley
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | - Gianfelice Cinque
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | - Peter Gardner
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Diego Gianolio
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | | | - M. Paula M. Marques
- Química-Física Molecular
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
| |
Collapse
|
29
|
Entropic contribution to enhanced thermal stability in the thermostable P450 CYP119. Proc Natl Acad Sci U S A 2018; 115:E10049-E10058. [PMID: 30297413 PMCID: PMC6205451 DOI: 10.1073/pnas.1807473115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enhanced thermostability of thermophilic proteins with respect to their mesophilic counterparts is often attributed to the enthalpy effect, arising from strong interactions between protein residues. Intuitively, these strong interresidue interactions will rigidify the biomolecules. However, the present work utilizing neutron scattering and solution NMR spectroscopy measurements demonstrates a contrary example that the thermophilic cytochrome P450, CYP119, is much more flexible than its mesophilic counterpart, CYP101A1, something which is not apparent just from structural comparison of the two proteins. A mechanism to explain this apparent contradiction is that higher flexibility in the folded state of CYP119 increases its conformational entropy and thereby reduces the entropy gain during denaturation, which will increase the free energy needed for unfolding and thus stabilize the protein. This scenario is supported by thermodynamic data on the temperature dependence of unfolding free energy, which shows a significant entropic contribution to the thermostability of CYP119 and lends an added dimension to enhanced stability, previously attributed only to presence of aromatic stacking interactions and salt bridge networks. Our experimental data also support the notion that highly thermophilic P450s such as CYP119 may use a mechanism that partitions flexibility differently from mesophilic P450s between ligand binding and thermal stability.
Collapse
|
30
|
Tan P, Liang Y, Xu Q, Mamontov E, Li J, Xing X, Hong L. Gradual Crossover from Subdiffusion to Normal Diffusion: A Many-Body Effect in Protein Surface Water. PHYSICAL REVIEW LETTERS 2018; 120:248101. [PMID: 29956983 DOI: 10.1103/physrevlett.120.248101] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/12/2018] [Indexed: 06/08/2023]
Abstract
Dynamics of hydration water is essential for the function of biomacromolecules. Previous studies have demonstrated that water molecules exhibit subdiffusion on the surface of biomacromolecules; yet the microscopic mechanism remains vague. Here, by performing neutron scattering, molecular dynamics simulations, and analytic modeling on hydrated perdeuterated protein powders, we found water molecules jump randomly between trapping sites on protein surfaces, whose waiting times obey a broad distribution, resulting in subdiffusion. Moreover, the subdiffusive exponent gradually increases with observation time towards normal diffusion due to a many-body volume-exclusion effect.
Collapse
Affiliation(s)
- Pan Tan
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yihao Liang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jinglai Li
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiangjun Xing
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
31
|
Geske J, Harrach M, Heckmann L, Horstmann R, Klameth F, Müller N, Pafong E, Wohlfromm T, Drossel B, Vogel M. Molecular Dynamics Simulations of Water, Silica, and Aqueous Mixtures in Bulk and Confinement. ACTA ACUST UNITED AC 2018. [DOI: 10.1515/zpch-2017-1042] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Abstract
Aqueous systems are omnipresent in nature and technology. They show complex behaviors, which often originate in the existence of hydrogen-bond networks. Prominent examples are the anomalies of water and the non-ideal behaviors of aqueous solutions. The phenomenology becomes even richer when aqueous liquids are subject to confinement. To this day, many properties of water and its mixtures, in particular, under confinement, are not understood. In recent years, molecular dynamics simulations developed into a powerful tool to improve our knowledge in this field. Here, our simulation results for water and aqueous mixtures in the bulk and in various confinements are reviewed and some new simulation data are added to improve our knowledge about the role of interfaces. Moreover, findings for water are compared with results for silica, exploiting that both systems form tetrahedral networks.
Collapse
Affiliation(s)
- Julian Geske
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Michael Harrach
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Lotta Heckmann
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Robin Horstmann
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Felix Klameth
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Niels Müller
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Elvira Pafong
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Timothy Wohlfromm
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Barbara Drossel
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Michael Vogel
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| |
Collapse
|
32
|
Chen P, Terenzi C, Furó I, Berglund LA, Wohlert J. Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions. Biomacromolecules 2018; 19:2567-2579. [DOI: 10.1021/acs.biomac.8b00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Pan Chen
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Camilla Terenzi
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - István Furó
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Lars A. Berglund
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Jakob Wohlert
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| |
Collapse
|
33
|
Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
Collapse
|
34
|
Demuth D, Sattig M, Steinrücken E, Weigler M, Vogel M. 2H NMR Studies on the Dynamics of Pure and Mixed Hydrogen-Bonded Liquids in Confinement. Z PHYS CHEM 2018. [DOI: 10.1515/zpch-2017-1027] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
2H NMR is used to ascertain dynamical behaviors of pure and mixed hydrogen-bonded liquids in bulk and in confinement. Detailed comparisons of previous and new results in broad dynamic and temperature ranges reveal that confinement effects differ for various liquids and confinements. For water, molecular reorientation strongly depends on the confinement size, with much slower and less fragile structural relaxation under more severe geometrical restriction. Moreover, a dynamical crossover occurs when a fraction of solid water forms so that the dynamics of the fraction of liquid water becomes even more restricted and, as a consequence, changes from bulk-like to interface-dominated. For glycerol, by contrast, confinement has weak effects on the reorientation dynamics. Mixed hydrogen-bonded liquids show even more complex dynamical behaviors. For aqueous solutions, the temperature dependence of the structural relaxation becomes discontinuous when the concentration changes due to a freezing of water fractions. This tendency for partial crystallization is enhanced rather than reduced by confinement, because different liquid-matrix interactions of the molecular species induce micro-phase segregation, which facilitates ice formation in water-rich regions. In addition, dynamical couplings at solvent-protein interfaces are discussed. It is shown that, on the one hand, solvent dynamics are substantially slowed down at protein surfaces and, on the other hand, protein dynamics significantly depend on the composition and, thus, the viscosity of the solvent. Furthermore, a protein dynamical transition occurs when the amplitude of water-coupled restricted backbone dynamics vanishes upon cooling.
Collapse
Affiliation(s)
- Dominik Demuth
- Institut für Festkörperphysik , Technische Universität Darmstadt , Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Matthias Sattig
- Institut für Festkörperphysik , Technische Universität Darmstadt , Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Elisa Steinrücken
- Institut für Festkörperphysik , Technische Universität Darmstadt , Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Max Weigler
- Institut für Festkörperphysik , Technische Universität Darmstadt , Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Michael Vogel
- Institut für Festkörperphysik , Technische Universität Darmstadt , Hochschulstr. 6 , 64289 Darmstadt , Germany
| |
Collapse
|
35
|
Seyedi S, Matyushov DV. Ergodicity breaking of iron displacement in heme proteins. SOFT MATTER 2017; 13:8188-8201. [PMID: 29082406 DOI: 10.1039/c7sm01561e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.
Collapse
Affiliation(s)
- Salman Seyedi
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287, USA
| | | |
Collapse
|
36
|
Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
Collapse
Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| |
Collapse
|
37
|
Atamas N, Bardik V, Bannikova A, Grishina O, Lugovskoi E, Lavoryk S, Makogonenko Y, Korolovych V, Nerukh D, Paschenko V. The effect of water dynamics on conformation changes of albumin in pre-denaturation state: photon correlation spectroscopy and simulation. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
38
|
Mandal A, Boatz JC, Wheeler TB, van der Wel PCA. On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 67:165-178. [PMID: 28229262 PMCID: PMC5445385 DOI: 10.1007/s10858-017-0089-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/19/2017] [Indexed: 05/07/2023]
Abstract
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.
Collapse
Affiliation(s)
- Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Travis B Wheeler
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
| |
Collapse
|
39
|
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
| |
Collapse
|
40
|
Kuffel A. How water mediates the long-range interactions between remote protein molecules. Phys Chem Chem Phys 2017; 19:5441-5448. [DOI: 10.1039/c6cp05788h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mechanism of the influence of the presence of one protein molecule on the internal dynamics of another is proposed.
Collapse
Affiliation(s)
- Anna Kuffel
- Faculty of Chemistry
- Department of Physical Chemistry
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| |
Collapse
|
41
|
Gavrilov Y, Leuchter JD, Levy Y. On the coupling between the dynamics of protein and water. Phys Chem Chem Phys 2017; 19:8243-8257. [DOI: 10.1039/c6cp07669f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.
Collapse
Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Jessica D. Leuchter
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yaakov Levy
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| |
Collapse
|
42
|
Castellanos MM, McAuley A, Curtis JE. Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering. Comput Struct Biotechnol J 2016; 15:117-130. [PMID: 28138368 PMCID: PMC5257034 DOI: 10.1016/j.csbj.2016.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/10/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
In order to increase shelf life and minimize aggregation during storage, many biotherapeutic drugs are formulated and stored as either frozen solutions or lyophilized powders. However, characterizing amorphous solids can be challenging with the commonly available set of biophysical measurements used for proteins in liquid solutions. Therefore, some questions remain regarding the structure of the active pharmaceutical ingredient during freezing and drying of the drug product and the molecular role of excipients. Neutron scattering is a powerful technique to study structure and dynamics of a variety of systems in both solid and liquid phases. Moreover, neutron scattering experiments can generally be correlated with theory and molecular simulations to analyze experimental data. In this article, we focus on the use of neutron techniques to address problems of biotechnological interest. We describe the use of small-angle neutron scattering to study the solution structure of biological molecules and the packing arrangement in amorphous phases, that is, frozen glasses and freeze-dried protein powders. In addition, we discuss the use of neutron spectroscopy to measure the dynamics of glassy systems at different time and length scales. Overall, we expect that the present article will guide and prompt the use of neutron scattering to provide unique insights on many of the outstanding questions in biotechnology.
Collapse
Affiliation(s)
- Maria Monica Castellanos
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - Arnold McAuley
- Department of Drug Product Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States
| |
Collapse
|
43
|
Cerveny S, Combarro-Palacios I, Swenson J. Evidence of Coupling between the Motions of Water and Peptides. J Phys Chem Lett 2016; 7:4093-4098. [PMID: 27683955 DOI: 10.1021/acs.jpclett.6b01864] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Studies of protein dynamics at low temperatures are generally performed on hydrated powders and not in biologically realistic solutions of water because of water crystallization. However, here we avoid the problem of crystallization by reducing the size of the biomolecules. We have studied oligomers of the amino acid l-lysine, fully dissolved in water, and our dielectric relaxation data show that the glass transition-related dynamics of the oligomers is determined by the water dynamics, in a way similar to that previously observed for solvated proteins. This implies that the crucial role of water for protein dynamics can be extended to other types of macromolecular systems, where water is also able to determine their conformational fluctuations. Using the energy landscape picture of macromolecules, the thermodynamic criterion for such solvent-slaved macromolecular motions may be that the macromolecules need the entropy contribution from the solvent to overcome the enthalpy barriers between different conformational substates.
Collapse
Affiliation(s)
- Silvina Cerveny
- Centro de Fisica de Materiales (CSIC, UPV/EHU)-Materials Physics Center (MPC) , Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Donostia International Physics Center, 20018 San Sebastián, Spain
| | - Izaskun Combarro-Palacios
- Centro de Fisica de Materiales (CSIC, UPV/EHU)-Materials Physics Center (MPC) , Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Jan Swenson
- Department of Applied Physics, Chalmers University of Technology , SE-412 96 Göteborg, Sweden
| |
Collapse
|
44
|
Comez L, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. SOFT MATTER 2016; 12:5501-5514. [PMID: 27280176 DOI: 10.1039/c5sm03119b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.
Collapse
Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | | | | | | | | | | |
Collapse
|
45
|
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.
Collapse
|
46
|
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".
Collapse
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.
| |
Collapse
|
47
|
Mamontov E, O'Neill H. Microscopic relaxations in a protein sustained down to 160K in a non-glass forming organic solvent. Biochim Biophys Acta Gen Subj 2016; 1861:3513-3519. [PMID: 27154287 DOI: 10.1016/j.bbagen.2016.04.024] [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: 01/12/2016] [Revised: 04/24/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND We have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160K. METHODS We have utilized quasielastic neutron scattering. RESULTS A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamical transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. CONCLUSIONS Our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics. GENERAL SIGNIFICANCE We hypothesize that, if the long debated idea regarding the direct link between the microscopic relaxations and the biological activity in proteins is correct, then not only the microscopic relaxations, but also the activity, could be sustained in proteins all the way down to the freezing temperature of a non-glass forming solvent with a weak temperature dependence of its viscosity. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
Collapse
Affiliation(s)
- E Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - H O'Neill
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| |
Collapse
|
48
|
Nilsson L. Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules. Biophys J 2016; 108:2755-6. [PMID: 26083911 DOI: 10.1016/j.bpj.2015.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
| |
Collapse
|
49
|
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
| |
Collapse
|
50
|
Rinne KF, Schulz JCF, Netz RR. Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water. J Chem Phys 2016; 142:215104. [PMID: 26049528 DOI: 10.1063/1.4921777] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using extensive molecular dynamics simulations of a single eight-residue alanine polypeptide in explicit water, we investigate the influence of α-helix formation on the dielectric spectrum. For this, we project long equilibrium trajectories into folded and unfolded states and thereby obtain dielectric spectra representative for disordered as well α-helical conformations without the need to change any other system parameter such as pH or temperature. The absorption spectrum in the α-helical state exhibits a feature in the sub-GHz range that is significantly stronger than in the unfolded state. As we show by an additional decomposition into peptide and water contributions, this slow dielectric mode, the relaxation time of which matches the independently determined peptide rotational relaxation time, is mostly caused by peptide polarization correlations, but also contains considerable contributions from peptide-water correlations. In contrast, the peptide spectral contribution shows no features in the GHz range where bulk water absorbs, not even in the peptide-water correlation part, we conclude that hydration water around Ala8 is more influenced by peptide polarization relaxation effects than the other way around. A further decomposition into water-self and water-collective polarization correlations shows that the dielectric response of hydration water is, in contrast to electrolyte solutions, retarded and that this retardation is mostly due to collective effects, the self relaxation of hydration water molecules is only slightly slowed down compared to bulk water. We find the dynamic peptide-water polarization cross correlations to be rather long-ranged and to extend more than one nanometer away from the peptide-water interface into the water hydration shell, in qualitative agreement with previous simulation studies and recent THz absorption experiments.
Collapse
Affiliation(s)
- Klaus F Rinne
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|