1
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Jenney FE, Wang H, George SJ, Xiong J, Guo Y, Gee LB, Marizcurrena JJ, Castro-Sowinski S, Staskiewicz A, Yoda Y, Hu MY, Tamasaku K, Nagasawa N, Li L, Matsuura H, Doukov T, Cramer SP. Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'. Sci Rep 2024; 14:12197. [PMID: 38806591 PMCID: PMC11133467 DOI: 10.1038/s41598-024-62261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
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Affiliation(s)
- Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | | | | | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leland B Gee
- LCLS, SLAC National Laboratory, Stanford, CA, 94025, USA
| | | | | | - Anna Staskiewicz
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Nobumoto Nagasawa
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo, 679-5165, Japan
| | | | - Tzanko Doukov
- SSRL, SLAC National Laboratory, Stanford, CA, 94025, USA
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2
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Borah B, Acharya GR, Grajeda D, Emerson MS, Harris MA, Milinda Abeykoon AM, Sangoro J, Baker GA, Nieuwkoop AJ, Margulis CJ. Do Ionic Liquids Slow Down in Stages? J Am Chem Soc 2023; 145:25518-25522. [PMID: 37963184 PMCID: PMC10691361 DOI: 10.1021/jacs.3c08639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
High impact recent articles have reported on the existence of a liquid-liquid (L-L) phase transition as a function of both pressure and temperature in ionic liquids (ILs) containing the popular trihexyltetradecylphosphonium cation (P666,14+), sometimes referred to as the "universal liquifier". The work presented here reports on the structural-dynamic pathway from liquid to glass of the most well-studied IL comprising the P666,14+ cation. We present experimental and computational evidence that, on cooling, the path from the room-temperature liquid to the glass state is one of separate structural-dynamic changes. The first stage involves the slowdown of the charge network, while the apolar subcomponent is fully mobile. A second, separate stage entails the slowdown of the apolar domain. Whereas it is possible that these processes may be related to the liquid-liquid and glass transitions, more research is needed to establish this conclusively.
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Affiliation(s)
- Bichitra Borah
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Gobin Raj Acharya
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Diana Grajeda
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Matthew S. Emerson
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Matthew A. Harris
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - AM Milinda Abeykoon
- National
Synchrotron Light Source II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Joshua Sangoro
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gary A. Baker
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Andrew J. Nieuwkoop
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Claudio J. Margulis
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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3
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Clark JA, Prabhu VM, Douglas JF. Molecular Dynamics Simulation of the Influence of Temperature and Salt on the Dynamic Hydration Layer in a Model Polyzwitterionic Polymer PAEDAPS. J Phys Chem B 2023; 127:8185-8198. [PMID: 37668318 PMCID: PMC10578162 DOI: 10.1021/acs.jpcb.3c03654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
We investigate the hydration of poly(3-[2-(acrylamido) ethyldimethylammonio] propanesulfonate) over a range of temperatures in pure water and with the inclusion of 0.1 mol/L NaCl using atomistic molecular dynamics simulation. Drawing on concepts drawn from the field of glass-forming liquids, we use the Debye-Waller parameter () for describing the water mobility gradient around the polybetaine backbone extending to an overall distance ≈18 Å. The water mobility in this layer is defined through the mean-square water molecule displacement at a time on the order of water's β-relaxation time. The brushlike topology of polybetaines leads to two regions in the dynamic hydration layer. The inner region of ≈10.5 Å is explored by pendant group conformational motions, and the outer region of ≈7.5 Å represents an extended layer of reduced water mobility relative to bulk water. The dynamic hydration layer extends far beyond the static hydration layer, adjacent to the polymer.
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Affiliation(s)
- Jennifer A. Clark
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Vivek M. Prabhu
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Jack F. Douglas
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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4
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Syryamina VN, Astvatsaturov DA, Dzuba SA, Chumakova NA. Glass-like behavior of intercalated organic solvents in graphite oxide detected by spin-probe EPR. Phys Chem Chem Phys 2023; 25:25720-25727. [PMID: 37721717 DOI: 10.1039/d3cp03253a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Membranes based on graphite oxide (GO) are promising materials for the separation of polar liquids and gases. Understanding the properties of solvents immersed in GO is important for the development of various technological applications. Here, the molecular motions of the TEMPO nitroxide spin probe in acetonitrile intercalated into the GO inter-plane space were studied using electron paramagnetic resonance (EPR), including its pulsed version, and electron spin echo (ESE). For a sample containing 75% acetonitrile relative to equilibrium sorption at room temperature, ESE-detected stochastic librations were observed for TEMPO molecules above 135 K. Since these librations are an inherent property of molecular glasses, this fact indicates that intercalated acetonitrile forms a two-dimensional glass state. Above 225 K, an acceleration of stochastic librations was observed, indicating the manifestation of a glass-like dynamical cross-over. Continuous wave (CW) EPR spectra of TEMPO showed the absence of overall tumbling motions in the entire investigated temperature range of up to 340 K, indicating that the intercalated acetonitrile does not behave as a bulk liquid (the melting point of acetonitrile is 229 K). Dynamical librations of TEMPO molecules detected by CW EPR were found to accelerate above 240 K.
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Affiliation(s)
- Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk, 630090, Russian Federation.
| | - Dmitry A Astvatsaturov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Science, Kosygin St. 4, Moscow, 119991, Russian Federation
- M.V. Lomonosov Moscow State University, Chemistry Department, Leninskiye Gory, 1/3, Moscow, 119991, Russian Federation
| | - Sergei A Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk, 630090, Russian Federation.
- Department of Physics, Novosibirsk State University, 630090, Novosibirsk, Russian Federation
| | - Natalia A Chumakova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Science, Kosygin St. 4, Moscow, 119991, Russian Federation
- M.V. Lomonosov Moscow State University, Chemistry Department, Leninskiye Gory, 1/3, Moscow, 119991, Russian Federation
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5
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Khan RAA, Luo M, Alsaad AM, Qattan IA, Abedrabbo S, Hua D, Zulfqar A. The Role of Polymer Chain Stiffness and Guest Nanoparticle Loading in Improving the Glass Transition Temperature of Polymer Nanocomposites. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1896. [PMID: 37446412 DOI: 10.3390/nano13131896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
The impact of polymer chain stiffness characterized by the bending modulus (kθ) on the glass transition temperature (Tg) of pure polymer systems, as well as polymer nanocomposites (PNCs), is investigated using molecular dynamics simulations. At small kθ values, the pure polymer system and respective PNCs are in an amorphous state, whereas at large kθ values, both systems are in a semicrystalline state with a glass transition at low temperature. For the pure polymer system, Tg initially increases with kθ and does not change obviously at large kθ. However, the Tg of PNCs shows interesting behaviors with the increasing volume fraction of nanoparticles (fNP) at different kθ values. Tg tends to increase with fNP at small kθ, whereas it becomes suppressed at large kθ.
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Affiliation(s)
- Raja Azhar Ashraaf Khan
- Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Mengbo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ahmad M Alsaad
- Department of Physics, Jordan University of Science & Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Issam A Qattan
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi 127788, United Arab Emirates
| | - Sufian Abedrabbo
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi 127788, United Arab Emirates
| | - Daoyang Hua
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Afsheen Zulfqar
- Department of Physics, Zhejiang Normal University, Jinhua 321004, China
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6
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Abstract
The theory of electron transfer reactions establishes the conceptual foundation for redox solution chemistry, electrochemistry, and bioenergetics. Electron and proton transfer across the cellular membrane provide all energy of life gained through natural photosynthesis and mitochondrial respiration. Rates of biological charge transfer set kinetic bottlenecks for biological energy storage. The main system-specific parameter determining the activation barrier for a single electron-transfer hop is the reorganization energy of the medium. Both harvesting of light energy in natural and artificial photosynthesis and efficient electron transport in biological energy chains require reduction of the reorganization energy to allow fast transitions. This review article discusses mechanisms by which small values of the reorganization energy are achieved in protein electron transfer and how similar mechanisms can operate in other media, such as nonpolar and ionic liquids. One of the major mechanisms of reorganization energy reduction is through non-Gibbsian (nonergodic) sampling of the medium configurations on the reaction time. A number of alternative mechanisms, such as electrowetting of active sites of proteins, give rise to non-parabolic free energy surfaces of electron transfer. These mechanisms, and nonequilibrium population of donor-acceptor vibrations, lead to a universal phenomenology of separation between the Stokes shift and variance reorganization energies of electron transfer.
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Affiliation(s)
- Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA.
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7
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Mostajabi Sarhangi S, Matyushov DV. Effect of Water Deuteration on Protein Electron Transfer. J Phys Chem Lett 2023; 14:723-729. [PMID: 36648391 DOI: 10.1021/acs.jpclett.2c03690] [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: 06/17/2023]
Abstract
Traditional theories of long-range protein electron transfer describe the reaction rate in terms of the tunneling distance and the reaction free energy. They do not recognize two physical effects: (i) local wetting of the active site by hydration water and (ii) protein identity affecting the rate through dynamics and flexibility. We find, by molecular dynamics simulations, a significant, ∼25 times, slowing down of the rate of protein electron transfer upon deuteration. H/D substitution changes the rate constant pre-exponential factor in the regime of electron transfer controlled by medium dynamics. Switching from light to heavy water increases the effective medium relaxation time. The effect is caused by both a global change in the flexibility of the protein backbone and locally stronger hydrogen bonds to charged residues.
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Affiliation(s)
- Setare Mostajabi Sarhangi
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
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8
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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9
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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.
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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
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10
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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.
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11
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Li W, Nforneh B, Whitcomb KL, Warncke K. Resolution and characterization of confinement- and temperature-dependent dynamics in solvent phases that surround proteins in frozen aqueous solution by using spin-probe EPR spectroscopy. Methods Enzymol 2022; 666:25-57. [PMID: 35465922 DOI: 10.1016/bs.mie.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Spin probe electron paramagnetic resonance spectroscopy is applied to characterize the dynamics of concentric hydration and mesophase solvent domains that surround proteins within the ice boundary in frozen aqueous solutions. The solvent dynamics are tuned by variation of temperature (190-265K) and by the degree of ice boundary confinement, which is modulated by the volume of added cryosolvent (0-~50Å separation distance from protein surface). Goals are to: (1) characterize the protein-coupled solvent dynamics on correlation time scales of ~10-10<τ<10-7s, and spatial scales from protein surface to periphery of the surrounding solution, from the perspective of a free, small-molecule (~7Å diameter) probe, and (2) reveal properties of the solvent-protein coupling that can be correlated with protein functions, that are measureable under the same conditions. Rotational mobility of the nitroxide spin probe, TEMPOL, resolves and tracks two solvent components, the protein-associated domain (PAD; akin to hydration layer) and surrounding mesodomain, through their distinct temperature- and confinement-dependent values of τ and normalized weight. Detailed protocols are described for simulation of two-component nitroxide EPR spectra, which are categorized by line shape regime and guided by a library of template spectra and simulation parameters derived from two model soluble globular proteins. The order-disorder transition in the PAD, which is a universal feature of protein-coupled solvent dynamics, provides a well-defined, tunable property for elucidating mechanism in solvent-protein-function dynamical coupling. The low-temperature mesodomain system and EPR spin probe method are generally applicable to reveal solvent contributions to a broad range of macromolecule-mediated biological processes.
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Affiliation(s)
- Wei Li
- Department of Physics, Emory University, Atlanta, GA, United States
| | - Benjamen Nforneh
- Department of Physics, Emory University, Atlanta, GA, United States
| | - Katie L Whitcomb
- Department of Physics, Emory University, Atlanta, GA, United States
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, GA, United States.
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12
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Bock LV, Grubmüller H. Effects of cryo-EM cooling on structural ensembles. Nat Commun 2022; 13:1709. [PMID: 35361752 PMCID: PMC8971465 DOI: 10.1038/s41467-022-29332-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/10/2022] [Indexed: 01/01/2023] Open
Abstract
Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures. The rapid temperature drop during plunge-freezing affects the structural ensembles obtained by cryo-EM. To quantify the extent of perturbation, Bock and Grubmüller combined continuum calculations, MD simulations, and kinetic models.
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Affiliation(s)
- Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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13
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Probing Small-Angle Molecular Motions with EPR Spectroscopy: Dynamical Transition and Molecular Packing in Disordered Solids. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8020019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Disordered molecular solids present a rather broad class of substances of different origin—amorphous polymers, materials for photonics and optoelectronics, amorphous pharmaceutics, simple molecular glass formers, and others. Frozen biological media in many respects also may be referred to this class. Theoretical description of dynamics and structure of disordered solids still does not exist, and only some phenomenological models can be developed to explain results of particular experiments. Among different experimental approaches, electron paramagnetic resonance (EPR) applied to spin probes and labels also can deliver useful information. EPR allows probing small-angle orientational molecular motions (molecular librations), which intrinsically are inherent to all molecular solids. EPR is employed in its conventional continuous wave (CW) and pulsed—electron spin echo (ESE)—versions. CW EPR spectra are sensitive to dynamical librations of molecules while ESE probes stochastic molecular librations. In this review, different manifestations of small-angle motions in EPR of spin probes and labels are discussed. It is shown that CW-EPR-detected dynamical librations provide information on dynamical transition in these media, similar to that explored with neutron scattering, and ESE-detected stochastic librations allow elucidating some features of nanoscale molecular packing. The possible EPR applications are analyzed for gel-phase lipid bilayers, for biological membranes interacting with proteins, peptides and cryoprotectants, for supercooled ionic liquids (ILs) and supercooled deep eutectic solvents (DESs), for globular proteins and intrinsically disordered proteins (IDPs), and for some other molecular solids.
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14
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Clinger JA, Moreau DW, McLeod MJ, Holyoak T, Thorne RE. Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection. IUCRJ 2021; 8:784-792. [PMID: 34584739 PMCID: PMC8420759 DOI: 10.1107/s2052252521007053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/08/2021] [Indexed: 05/28/2023]
Abstract
Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and the complex experimental infrastructure that are required remain serious obstacles to its widespread application. Here, millisecond mix-and-quench crystallography (MMQX) has been developed, which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxy-kinase (PEPCK) is observed with a time resolution of 40 ms. By lowering the entry barrier to time-resolved crystallography, MMQX should enable a broad expansion in structural studies of protein dynamics.
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Affiliation(s)
- Jonathan A. Clinger
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
| | - David W. Moreau
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
| | - Matthew J. McLeod
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert E. Thorne
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
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15
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Abstract
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins (RFP) mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy show in all cases an increase in the turn-on temperature in the bleached state. The result is surprising given that there is little change in the protein surface, and thus, the solvent dynamics held responsible for the transition should not change. A spectral analysis of the measurements guided by quasiharmonic calculations of the protein absorbance reveals that indeed the solvent dynamical turn-on temperature is independent of the thermal stability/photostate however the protein dynamical turn-on temperature shifts to higher temperatures. This is the first demonstration of switching the protein dynamical turn-on temperature with protein functional state. The observed shift in protein dynamical turn-on temperature relative to the solvent indicates an increase in the required mobile waters necessary for the protein picosecond motions, that is, these motions are more collective. Melting-point measurements reveal that the photobleached state is more thermally stable, and structural analysis of related RFP’s shows that there is an increase in internal water channels as well as a more uniform atomic root mean squared displacement. These observations are consistent with previous suggestions that water channels form with extended light excitation providing O2 access to the chromophore and subsequent fluorescence loss. We report that these same channels increase internal coupling enhancing thermal stability and collectivity of the picosecond protein motions. The terahertz spectroscopic characterization of the protein and solvent dynamical onsets can be applied generally to measure changes in collectivity of protein motions.
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Capaccioli S, Zheng L, Kyritsis A, Paciaroni A, Vogel M, Ngai KL. The Dynamics of Hydrated Proteins Are the Same as Those of Highly Asymmetric Mixtures of Two Glass-Formers. ACS OMEGA 2021; 6:340-347. [PMID: 33458485 PMCID: PMC7807739 DOI: 10.1021/acsomega.0c04655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/08/2020] [Indexed: 05/31/2023]
Abstract
Customarily, the studies of dynamics of hydrated proteins are focused on the fast hydration water ν-relaxation, the slow structural α-relaxation responsible for a single glass transition, and the protein dynamic transition (PDT). Guided by the analogy with the dynamics of highly asymmetric mixtures of molecular glass-formers, we explore the possibility that the dynamics of hydrated proteins are richer than presently known. By providing neutron scattering, dielectric relaxation, calorimetry, and deuteron NMR data in two hydrated globular proteins, myoglobin and BSA, and the fibrous elastin, we show the presence of two structural α-relaxations, α1 and α2, and the hydration water ν-relaxation, all coupled together with interconnecting properties. There are two glass transition temperatures T g α1and T g α2 corresponding to vitrification of the α1 and α2 processes. Relaxation time τα2(T) of the α2-relaxation changes its Arrhenius temperature dependence to super-Arrhenius on crossing T g α1 from below. The ν-relaxation responds to the two vitrifications by changing the T-dependence of its relaxation time τν(T) on crossing consecutively T g α2 and T g α1. It generates the PDT at T d where τν(T d) matches about five times the experimental instrument timescale τexp, provided that T d > T g α1. This condition is satisfied by the hydrated globular proteins considered in this paper, and the ν-relaxation is in the liquid state with τν(T) having the super-Arrhenius temperature dependence. However, if T d < T g α1, the ν-relaxation fails to generate the PDT because it is in the glassy state and τν(T) has Arrhenius T-dependence, as in the case of hydrated elastin. Overall, the dynamics of hydrated proteins are the same as the dynamics of highly asymmetric mixtures of glass-formers. The results from this study have expanded the knowledge of the dynamic processes and their properties in hydrated proteins, and impact on research in this area is expected.
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Affiliation(s)
- Simone Capaccioli
- Dipartimento
di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - Lirong Zheng
- School
of Physics and Astronomy, Shanghai Jiao
Tong University, Shanghai 200240, China
- Institute
of Natural Sciences, Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Apostolos Kyritsis
- Department
of Physics, National Technical University
of Athens, 157 80 Athens, Greece
| | | | - Michael Vogel
- Institute
of Condensed Matter Physics, Technische
Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Kia L. Ngai
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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17
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Stripp ST, Mebs S, Haumann M. Temperature Dependence of Structural Dynamics at the Catalytic Cofactor of [FeFe]-hydrogenase. Inorg Chem 2020; 59:16474-16488. [PMID: 33147959 DOI: 10.1021/acs.inorgchem.0c02316] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[FeFe]-hydrogenases are nature's blueprint for efficient hydrogen turnover. Understanding their enzymatic mechanism may improve technological H2 fuel generation. The active-site cofactor (H-cluster) consists of a [4Fe-4S] cluster ([4Fe]H), cysteine-linked to a diiron site ([2Fe]H) carrying an azadithiolate (adt) group, terminal cyanide and carbon monoxide ligands, and a bridging carbon monoxide (μCO) in the oxidized protein (Hox). Recently, the debate on the structure of reduced H-cluster states was intensified by the assignment of new species under cryogenic conditions. We investigated temperature effects (4-280 K) in infrared (IR) and X-ray absorption spectroscopy (XAS) data of [FeFe]-hydrogenases using fit analyses and quantum-chemical calculations. IR data from our laboratory and literature sources were evaluated. At ambient temperatures, reduced H-cluster states with a bridging hydride (μH-, in Hred and Hsred) or with an additional proton at [4Fe]H (Hred') or at the distal iron of [2Fe]H (Hhyd) prevail. At cryogenic temperatures, these species are largely replaced by states that hold a μCO, lack [4Fe]H protonation, and bind an additional proton at the adt nitrogen (HredH+ and HsredH+). XAS revealed the atomic coordinate dispersion (i.e., the Debye-Waller parameter, 2σ2) of the iron-ligand bonds and Fe-Fe distances in the oxidized and reduced H-cluster. 2σ2 showed a temperature dependence typical for the so-called protein-glass transition, with small changes below ∼200 K and a pronounced increase above this "breakpoint". This behavior is attributed to the freezing-out of larger-scale anharmonic motions of amino acid side chains and water species. We propose that protonation at [4Fe]H as well as ligand rearrangement and μH- binding at [2Fe]H are impaired because of restricted molecular mobility at cryogenic temperatures so that protonation can be biased toward adt. We conclude that a H-cluster with a μCO, selective [4Fe]H or [2Fe]H protonation, and catalytic proton transfer via adt facilitates efficient H2 conversion in [FeFe]-hydrogenase.
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Affiliation(s)
- Sven T Stripp
- Physics Department, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany
| | - Stefan Mebs
- Physics Department, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany
| | - Michael Haumann
- Physics Department, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany
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18
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Kadantsev VN, Goltsov A. Collective excitations in α-helical protein structures interacting with the water environment. Electromagn Biol Med 2020; 39:419-432. [PMID: 33023315 DOI: 10.1080/15368378.2020.1826961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Low-frequency vibrational excitations of protein macromolecules in the terahertz frequency region are suggested to contribute to many biological processes such as enzymatic catalysis, intra-protein energy/charge transport, recognition, and allostery. To explain high effectiveness of these processes, two possible mechanisms of the long-lived excitation were proposed by H. Fröhlich and A.S. Davydov, which relate to either vibrational modes or solitary waves, respectively. In this paper, we developed a quantum dynamic model of vibrational excitation in α-helical proteins interacting with the aqueous environment. In the model, we distinguished three coupled subsystems, i.e., (i) a chain of hydrogen-bonded peptide groups (PGs), interacting with (ii) the subsystem of the side-chain residuals which in turn interact with (iii) the environment, surrounding water responsible for dissipation and fluctuation in the system. It was shown that the equation of motion for phonon variables of the PG chain can be transformed to nonlinear Schrodinger equation which admits bifurcation into the solution corresponding to the weak-damped vibrational modes (Fröhlich-type regime) and Davydov solitons. A bifurcation parameter is derived through the strength of phonon-phonon interaction between the side-chains and hydration-shell water molecules. As shown, the energy of these excited states is pumped through the interaction of the side-chains with fluctuating water environment of the proteins. The suggested mechanism of the collective vibrational mode excitation is discussed in connection with the recent experiments on the long-lived collective protein excitations in the terahertz frequency region and vibrational energy transport pathways in proteins.
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Affiliation(s)
| | - Alexey Goltsov
- Russian Technological University (MIREA) , Moscow, Russia
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19
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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]
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20
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Gorka M, Cherepanov DA, Semenov AY, Golbeck JH. Control of electron transfer by protein dynamics in photosynthetic reaction centers. Crit Rev Biochem Mol Biol 2020; 55:425-468. [PMID: 32883115 DOI: 10.1080/10409238.2020.1810623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Trehalose and glycerol are low molecular mass sugars/polyols that have found widespread use in the protection of native protein states, in both short- and long-term storage of biological materials, and as a means of understanding protein dynamics. These myriad uses are often attributed to their ability to form an amorphous glassy matrix. In glycerol, the glass is formed only at cryogenic temperatures, while in trehalose, the glass is formed at room temperature, but only upon dehydration of the sample. While much work has been carried out to elucidate a mechanistic view of how each of these matrices interact with proteins to provide stability, rarely have the effects of these two independent systems been directly compared to each other. This review aims to compile decades of research on how different glassy matrices affect two types of photosynthetic proteins: (i) the Type II bacterial reaction center from Rhodobacter sphaeroides and (ii) the Type I Photosystem I reaction center from cyanobacteria. By comparing aggregate data on electron transfer, protein structure, and protein dynamics, it appears that the effects of these two distinct matrices are remarkably similar. Both seem to cause a "tightening" of the solvation shell when in a glassy state, resulting in severely restricted conformational mobility of the protein and associated water molecules. Thus, trehalose appears to be able to mimic, at room temperature, nearly all of the effects on protein dynamics observed in low temperature glycerol glasses.
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
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21
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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.
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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
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22
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Krah A, Huber RG, Bond PJ. How Ligand Binding Affects the Dynamical Transition Temperature in Proteins. Chemphyschem 2020; 21:916-926. [DOI: 10.1002/cphc.201901221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Krah
- School of Computational SciencesKorea Institute for Advanced Study 85 Hoegiro, Dongdaemun-gu Seoul 02455 Republic of Korea
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Roland G. Huber
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Peter J. Bond
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
- National University of SingaporeDepartment of Biological Sciences 14 Science Drive 4 Singapore 117543
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23
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Siemer AB. Advances in studying protein disorder with solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 106:101643. [PMID: 31972419 PMCID: PMC7202078 DOI: 10.1016/j.ssnmr.2020.101643] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/26/2023]
Abstract
Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Univeristy of Southern California, 1501 San Pablo Street, Los Angeles, CA, 90033, USA.
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24
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Hollingsworth WR, Williams V, Ayzner AL. Semiconducting Eggs and Ladders: Understanding Exciton Landscape Formation in Aqueous π-Conjugated Inter-Polyelectrolyte Complexes. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- William R. Hollingsworth
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Vanessa Williams
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Alexander L. Ayzner
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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25
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Abstract
Human hemoglobin is the textbook example of the stereochemistry of an allosteric protein and of the exquisite control that a protein can exert over ligand binding. However, the fundamental basis by which the protein facilitates the ligand movement remains unknown. In this study, we used cryogenic X-ray crystallography and a high-repetition pulsed laser irradiation technique to elucidate the atomic details of ligand migration processes in hemoglobin after photolysis of the bound CO. Our data clarify the distinct CO migration pathways in the individual subunits of hemoglobin and unravel the functional roles of the internal cavities and neighboring amino acid residues in ligand exit and entry. Our results also demonstrate the high gas permeability and porosity of hemoglobin, facilitating O2 delivery. Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and β subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), β15Trp(A12), and β71Phe(E15). We also observe electron density evidence for the distal histidine [α58/β63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in β subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or β subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.
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26
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Glass transitions as affected by food compositions and by conventional and novel freezing technologies: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.09.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Martin DR, Dinpajooh M, Matyushov DV. Polarizability of the Active Site in Enzymatic Catalysis: Cytochrome c. J Phys Chem B 2019; 123:10691-10699. [DOI: 10.1021/acs.jpcb.9b09236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Mohammadhasan Dinpajooh
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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28
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Moreau DW, Atakisi H, Thorne RE. Solvent flows, conformation changes and lattice reordering in a cold protein crystal. Acta Crystallogr D Struct Biol 2019; 75:980-994. [PMID: 31692472 PMCID: PMC6834080 DOI: 10.1107/s2059798319013822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 10/10/2019] [Indexed: 11/10/2022] Open
Abstract
When protein crystals are abruptly cooled, the unit-cell, protein and solvent-cavity volumes all contract, but the volume of bulk-like internal solvent may expand. Outflow of this solvent from the unit cell and its accumulation in defective interior crystal regions has been suggested as one cause of the large increase in crystal mosaicity on cooling. It is shown that when apoferritin crystals are abruptly cooled to temperatures between 220 and 260 K, the unit cell contracts, solvent is pushed out and the mosaicity grows. On temperature-dependent timescales of 10 to 200 s, the unit-cell and solvent-cavity volume then expand, solvent flows back in, and the mosaicity and B factor both drop. Expansion and reordering at fixed low temperature are associated with small-amplitude but large-scale changes in the conformation and packing of apoferritin. These results demonstrate that increases in mosaicity on cooling arise due to solvent flows out of or into the unit cell and to incomplete, arrested relaxation of protein conformation. They indicate a critical role for time in variable-temperature crystallographic studies, and the feasibility of probing interactions and cooperative conformational changes that underlie cold denaturation in the presence of liquid solvent at temperatures down to ∼200 K.
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Affiliation(s)
- David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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29
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Aloi E, Bartucci R. Interdigitated lamellar phases in the frozen state: Spin-label CW- and FT-EPR. Biophys Chem 2019; 253:106229. [DOI: 10.1016/j.bpc.2019.106229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
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30
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Golysheva EA, Dzuba SA. Lipid chain mobility and packing in DOPC bilayers at cryogenic temperatures. Chem Phys Lipids 2019; 226:104817. [PMID: 31525380 DOI: 10.1016/j.chemphyslip.2019.104817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/07/2019] [Accepted: 09/03/2019] [Indexed: 11/30/2022]
Abstract
Low-temperature molecular mobility and packing in biological tissues are important for their survival upon cryopreservation. Electron paramagnetic resonance (EPR) in its pulsed version of electron spin echo (ESE) allows studying stochastic librations of spin-labeled molecules, the type of motion which dominates at low temperatures. These librations are characterized by the parameter <α2>τc where <α2> is the mean squared angular amplitude and τc is the correlation time for the motion. This parameter is known to be larger for higher temperature and for looser intermolecular structure. In this work, ESE data for the bilayers comprised of doubly-unsaturated DOPC (dioleoyl-glycero-phosphocholine) lipids and mono-unsaturated POPC (palmitoyl-oleoyl-glycero-phosphocholine) lipids with spin-labeled stearic acids added were obtained in the temperature range between 80 and 210 K; the results were compared also with the previously obtained data for fully-saturated DPPC (dipalmitoyl-glycero-phosphocholine) lipid bilayers [J. Phys. Chem. B2014, 118, 12,478-12,485; Appl. Magn. Reson. 2018, 49, 1369-1383]. It turned out that for DOPC bilayers the <α2>τc values are of intermediate magnitude between those for POPC and DPPC bilayers, which implies an intermediate density of lipid packing. A possible explanation of this result could be rearrangement at cryogenic temperatures of the DOPC lipid tails, with their terminal segments folding cooperatively. This interpretation is also in agreement with the known thermodynamic properties of gel-fluid transition for DOPC bilayer.
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Affiliation(s)
- Elena A Golysheva
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation; Department of Physics, Novosibirsk State University, Novosibirsk, 630090, Russian Federation
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation; Department of Physics, Novosibirsk State University, Novosibirsk, 630090, Russian Federation.
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31
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Capaccioli S, Ngai KL, Ancherbak S, Bertoldo M, Ciampalini G, Thayyil MS, Wang LM. The JG β-relaxation in water and impact on the dynamics of aqueous mixtures and hydrated biomolecules. J Chem Phys 2019; 151:034504. [DOI: 10.1063/1.5100835] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S. Capaccioli
- CNR-IPCF, Dipartimento di Fisica, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
- Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
| | - K. L. Ngai
- CNR-IPCF, Dipartimento di Fisica, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
- State Key Lab of Metastable Materials Science and Technology, and College of Materials Science and Engineering, Yanshan University, Qinhuangdao, Hebei, 066004, China
| | - S. Ancherbak
- Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
| | - M. Bertoldo
- ISOF - CNR Area della Ricerca di Bologna, Via P. Gobetti 101, 40129 Bologna, Italy
| | - G. Ciampalini
- Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
| | | | - Li-Min Wang
- State Key Lab of Metastable Materials Science and Technology, and College of Materials Science and Engineering, Yanshan University, Qinhuangdao, Hebei, 066004, China
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32
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Ballesteros D, Walters C. Solid-State Biology and Seed Longevity: A Mechanical Analysis of Glasses in Pea and Soybean Embryonic Axes. FRONTIERS IN PLANT SCIENCE 2019; 10:920. [PMID: 31379902 PMCID: PMC6646689 DOI: 10.3389/fpls.2019.00920] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/28/2019] [Indexed: 05/15/2023]
Abstract
The cytoplasm of anhydrobiotes (organisms that persist in the absence of water) solidifies during drying. Despite this stabilization, anhydrobiotes vary in how long they persist while dry. In this paper, we call upon concepts currently used to explain stability of amorphous solids (also known as glasses) in synthetic polymers, foods, and pharmaceuticals to the understand variation in longevity of biological systems. We use embryonic axes of pea (Pisum sativum) and soybean (Glycine max) seeds as test systems that have relatively long and short survival times, respectively, but similar geometries and water sorption behaviors. We used dynamic mechanical analysis to gain insights on structural and mobility properties that relate to stability of other organic systems with controlled composition. Changes of elastic and loss moduli, and the dissipation function, tan δ, in response to moisture and temperature were compared in pea and soybean axes containing less than 0.2 g H2O g-1 dry mass. The work shows high complexity of structure-regulated molecular mobility within dried seed matrices. As was previously observed for pea cotyledons, there were multiple relaxations of structural constraints to molecular movement, which demonstrate substantial localized, "fast" motions within solidified cytoplasm. There was detected variation in the coordination among long-range slow, diffusive and short-range fast, vibrational motions in glasses of pea compared to soybean, which suggest higher constraints to motion in pea and greater "fragility" in soybean. We are suggesting that differences in fragility contribute to variation of seed longevity. Indeed, fragility and coordination of short and long range motions are linked to stability and physical aging of synthetic polymers.
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Affiliation(s)
| | - Christina Walters
- National Laboratory for Genetic Resources Preservation, USDA-ARS, Fort Collins, CO, United States
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Moreau DW, Atakisi H, Thorne RE. Ice formation and solvent nanoconfinement in protein crystals. IUCRJ 2019; 6:346-356. [PMID: 31098016 PMCID: PMC6503922 DOI: 10.1107/s2052252519001878] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/31/2019] [Indexed: 05/06/2023]
Abstract
Ice formation within protein crystals is a major obstacle to the cryocrystallographic study of protein structure, and has limited studies of how the structural ensemble of a protein evolves with temperature in the biophysically interesting range from ∼260 K to the protein-solvent glass transition near 200 K. Using protein crystals with solvent cavities as large as ∼70 Å, time-resolved X-ray diffraction was used to study the response of protein and internal solvent during rapid cooling. Solvent nanoconfinement suppresses freezing temperatures and ice-nucleation rates so that ice-free, low-mosaicity diffraction data can be reliably collected down to 200 K without the use of cryoprotectants. Hexagonal ice (Ih) forms in external solvent, but internal crystal solvent forms stacking-disordered ice (Isd) with a near-random stacking of cubic and hexagonal planes. Analysis of powder diffraction from internal ice and single-crystal diffraction from the host protein structure shows that the maximum crystallizable solvent fraction decreases with decreasing crystal solvent-cavity size, and that an ∼6 Å thick layer of solvent adjacent to the protein surface cannot crystallize. These results establish protein crystals as excellent model systems for the study of nanoconfined solvent. By combining fast cooling, intense X-ray beams and fast X-ray detectors, complete structural data sets for high-value targets, including membrane proteins and large complexes, may be collected at ∼220-240 K that have much lower mosaicities and comparable B factors, and that may allow more confident identification of ligand binding than in current cryocrystallographic practice.
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Affiliation(s)
- David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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Combarro Palacios I, Olsson C, Kamma-Lorger CS, Swenson J, Cerveny S. Motions of water and solutes-Slaving versus plasticization phenomena. J Chem Phys 2019; 150:124902. [PMID: 30927900 DOI: 10.1063/1.5030064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It is well-accepted that hydration water is crucial for the structure, dynamics, and function of proteins. However, the exact role of water for the motions and functions of proteins is still debated. Experiments have shown that protein and water dynamics are strongly coupled but with water motions occurring on a considerably faster time scale (the so-called slaving behavior). On the other hand, water also reduces the conformational entropy of proteins and thereby acts as a plasticizer of them. In this work, we analyze the dynamics (using broadband dielectric spectroscopy) of some specific non-biological water solutions in a broad concentration range to elucidate the role of water in the dynamics of the solutes. Our results demonstrate that at low water concentrations (less than 5 wt. %), the plasticization phenomenon prevails for all the materials analyzed. However, at higher water concentrations, two different scenarios can be observed: the slaving phenomenon or plasticization, depending on the solute analyzed. These results generalize the slaving phenomenon to some, but not all, non-biological solutions and allow us to analyze the key factors for observing the slaving behavior in protein solutions as well as to reshaping the slaving concept.
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Affiliation(s)
- Izaskun Combarro Palacios
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Christoffer Olsson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | | | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Silvina Cerveny
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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Golysheva EA, Shevelev GY, Dzuba SA. Dynamical transition in molecular glasses and proteins observed by spin relaxation of nitroxide spin probes and labels. J Chem Phys 2018; 147:064501. [PMID: 28810753 DOI: 10.1063/1.4997035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In glassy substances and biological media, dynamical transitions are observed in neutron scattering that manifests itself as deviations of the translational mean-squared displacement, 〈x2〉, of hydrogen atoms from harmonic dynamics. In biological media, the deviation occurs at two temperature intervals, at ∼100-150 K and at ∼170-230 K, and it is attributed to the motion of methyl groups in the former case and to the transition from harmonic to anharmonic or diffusive motions in the latter case. In this work, electron spin echo (ESE) spectroscopy-a pulsed version of electron paramagnetic resonance-is applied to study the spin relaxation of nitroxide spin probes and labels introduced in molecular glass former o-terphenyl and in protein lysozyme. The anisotropic contribution to the rate of the two-pulse ESE decay, ΔW, is induced by spin relaxation appearing because of restricted orientational stochastic molecular motion; it is proportional to 〈α2〉τc, where 〈α2〉 is the mean-squared angle of reorientation of the nitroxide molecule around the equilibrium position and τc is the correlation time of reorientation. The ESE time window allows us to study motions with τc < 10-7 s. For glassy o-terphenyl, the 〈α2〉τc temperature dependence shows a transition near 240 K, which is in agreement with the literature data on 〈x2〉. For spin probes of essentially different size, the obtained data were found to be close, which evidences that motion is cooperative, involving a nanocluster of several neighboring molecules. For the dry lysozyme, the 〈α2〉τc values below 260 K were found to linearly depend on the temperature in the same way as it was observed in neutron scattering for 〈x2〉. As spin relaxation is influenced only by stochastic motion, the harmonic motions seen in ESE must be overdamped. In the hydrated lysozyme, ESE data show transitions near 130 K for all nitroxides, near 160 K for the probe located in the hydration layer, and near 180 K for the label in the protein interior. For this system, the two latter transitions are not observed in neutron scattering. The ESE-detected transitions are suggested to be related with water dynamics in the nearest hydration shell: with water glass transition near 130 K and with the onset of overall water molecular reorientations near 180 K; the disagreement with neutron scattering is ascribed to the larger time window for ESE-detected motions.
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Affiliation(s)
- Elena A Golysheva
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Georgiy Yu Shevelev
- Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
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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
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37
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Abstract
Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed.
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Affiliation(s)
- Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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38
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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.
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Affiliation(s)
- Salman Seyedi
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287, USA
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39
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Grille Coronel L, Acierno JP, Ermácora MR. Ultracompact states of native proteins. Biophys Chem 2017; 230:36-44. [DOI: 10.1016/j.bpc.2017.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
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40
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Aloi E, Oranges M, Guzzi R, Bartucci R. Low-Temperature Dynamics of Chain-Labeled Lipids in Ester- and Ether-Linked Phosphatidylcholine Membranes. J Phys Chem B 2017; 121:9239-9246. [PMID: 28892381 DOI: 10.1021/acs.jpcb.7b07386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Continuous wave electron paramagnetic resonance spectroscopy and two-pulse echo detected spectra of chain-labeled lipids are used to study the dynamics of frozen lipid membranes over the temperature range 77-260 K. Bilayers of ester-linked dihexadecanoylphosphatidylcholine (DPPC) with noninterdigitated chains and ether-linked dihexadecyl phosphatidylcholine (DHPC) with interdigitated chains are considered. Rapid stochastic librations of small angular amplitude are found in both lipid matrices. In noninterdigitated DPPC bilayers, the mean-square angular amplitude, [Formula: see text], of the motion increases with temperature and it is larger close to the chain termini than close to the polar/apolar interface. In contrast, in interdigitated DHPC lamellae, [Formula: see text] is small and temperature and label-position independent at low temperature and increases steeply at high temperature. The rotational correlation time, τc, of librations lies in the subnanosecond range for DPPC and in the nanosecond range for DHPC. In all membrane samples, the temperature dependence of [Formula: see text] resembles that of the mean-square atomic displacement revealed by neutron scattering and a dynamical transition is detected in the range 210-240 K. The results highlight the librational oscillations and the glass-like behavior in bilayer and interdigitated lipid membranes.
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Affiliation(s)
- Erika Aloi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Maria Oranges
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Rita Guzzi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Rosa Bartucci
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
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41
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Frontzek (neé Svanidze) AV, Embs JP, Paccou L, Guinet Y, Hédoux A. Low-Frequency Dynamics of BSA Complementarily Studied by Raman and Inelastic Neutron Spectroscopy. J Phys Chem B 2017; 121:5125-5132. [DOI: 10.1021/acs.jpcb.7b01395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna V. Frontzek (neé Svanidze)
- Jülich
Center for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, Outstation
at MLZ, Lichtenbergstraße 1, 85747 Garching, Germany
- A.F. Ioffe Physical Technical Institute, ul. Politekhnicheskaya 26, 194021 St. Petersburg, Russian Federation
| | - Jan Peter Embs
- Laboratory
for Neutron Scattering and Imaging, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | | | - Yannick Guinet
- Université Lille Nord de France, F-59000 Lille, France
- USTL UMET UMR CNRS 8207, F-59655 Villeneuve d’Ascq, France
| | - Alain Hédoux
- Université Lille Nord de France, F-59000 Lille, France
- USTL UMET UMR CNRS 8207, F-59655 Villeneuve d’Ascq, France
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42
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Draganski AR, Friedman JM, Ludescher RD. Solvent-Slaved Dynamic Processes Observed by Tryptophan Phosphorescence of Human Serum Albumin. Biophys J 2017; 112:881-891. [PMID: 28297647 DOI: 10.1016/j.bpj.2016.12.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/16/2016] [Accepted: 12/23/2016] [Indexed: 10/20/2022] Open
Abstract
Despite extensive experimental and computational efforts to understand the nature of the hierarchy of protein fluctuations and the modulating role of the protein hydration shell, a detailed microscopic description of the dynamics of the protein-solvent system has yet to be achieved. By using single tryptophan protein phosphorescence, we follow site-specific internal protein dynamics over a broad temperature range and demonstrate three independent dynamic processes. Process I is seen at temperatures below the bulk solvent Tg, has low activation energy, and is likely due to fast vibrations that may be enabled by water mobility on the protein surface. Process II is observed above 170 K, with activation energy typical of β relaxations in a glass; it has the same temperature dependence as fluctuations of hydration shell waters. Process III is observed at T > 200 K; it has super-Arrhenius temperature dependence and closely follows the primary relaxation of the bulk. The fluorescence of pyranine bound to the protein reports on the mobility of water in the hydration shell; it reveals a shift in emission spectra with increasing temperature, indicative of a changing H-bond network at the surface of the protein. These results support a model of solvent-slaved protein dynamics.
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Affiliation(s)
- Andrew R Draganski
- Department of Food Science, Rutgers University, New Brunswick, New Jersey
| | - Joel M Friedman
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York.
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43
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Clayton JA, Qi M, Godt A, Goldfarb D, Han S, Sherwin MS. Gd 3+-Gd 3+ distances exceeding 3 nm determined by very high frequency continuous wave electron paramagnetic resonance. Phys Chem Chem Phys 2017; 19:5127-5136. [PMID: 28139788 PMCID: PMC5394103 DOI: 10.1039/c6cp07119h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling is a very powerful tool for elucidating the structure and organization of biomolecules. Gd3+ complexes have recently emerged as a new class of spin labels for distance determination by pulsed EPR spectroscopy at Q- and W-band. We present CW EPR measurements at 240 GHz (8.6 Tesla) on a series of Gd-rulers of the type Gd-PyMTA-spacer-Gd-PyMTA, with Gd-Gd distances ranging from 1.2 nm to 4.3 nm. CW EPR measurements of these Gd-rulers show that significant dipolar broadening of the central |-1/2〉 → |1/2〉 transition occurs at 30 K for Gd-Gd distances up to ∼3.4 nm with Gd-PyMTA as the spin label. This represents a significant extension for distances accessible by CW EPR, as nitroxide-based spin labels at X-band frequencies can typically only access distances up to ∼2 nm. We show that this broadening persists at biologically relevant temperatures above 200 K, and that this method is further extendable up to room temperature by immobilizing the sample in glassy trehalose. We show that the peak-to-peak broadening of the central transition follows the expected 1/r3 dependence for the electron-electron dipolar interaction, from cryogenic temperatures up to room temperature. A simple procedure for simulating the dependence of the lineshape on interspin distance is presented, in which the broadening of the central transition is modeled as an S = 1/2 spin whose CW EPR lineshape is broadened through electron-electron dipolar interactions with a neighboring S = 7/2 spin.
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Affiliation(s)
- Jessica A Clayton
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA. and Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Bielefeld, Germany
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Songi Han
- Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA and Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA and Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Mark S Sherwin
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA. and Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA
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44
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Syryamina VN, Dzuba SA. Dynamical Transitions at Low Temperatures in the Nearest Hydration Shell of Phospholipid Bilayers. J Phys Chem B 2017; 121:1026-1032. [DOI: 10.1021/acs.jpcb.6b10133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. N. Syryamina
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - S. A. Dzuba
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
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45
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Nandi PK, English NJ. Role of Hydration Layer in Dynamical Transition in Proteins: Insights from Translational Self-Diffusivity. J Phys Chem B 2016; 120:12031-12039. [PMID: 27933939 DOI: 10.1021/acs.jpcb.6b06683] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elucidation of the role of hydration water underpinning dynamical crossover in proteins has proven challenging. Indeed, many contradictory findings in the literature seek to establish either causal or correlative links between water and protein behavior. Here, via molecular dynamics, we compute the temperature dependence of mean-square displacement and translational self-diffusivities for both hen egg white lysozyme and its hydration layer from 190 to 300 K. We find that the protein's mobility increases sharply at ∼230 K, indicating dynamical onset; concerted motion with hydration-water molecules is evident up to ∼285 K, confirming dynamical correlation between them. Exploring underlying mechanisms of such concerted motion, we scrutinize the water-protein hydrogen-bonding network as a function of temperature, noting sharp deviation from linearity of the hydrogen bond number's profile with temperature originating near the protein dynamical transition. Our studies reveal a common temperature profile/dependence of self-diffusivity values of the protein, hydration water, and the bulk solvent, originating from a common dependence on the bulk solvent viscosity, ηS. The key mechanistic role adopted by the protein-water hydrogen bond network in relation to the onset of proteins' dynamical transition is also discussed.
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Affiliation(s)
- Prithwish K Nandi
- School of Chemical and Bioprocess Engineering, University College Dublin , Belfield, Dublin 4, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin , Belfield, Dublin 4, Ireland
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46
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Gupta M, Chakravarty C, Bandyopadhyay S. Sensitivity of Protein Glass Transition to the Choice of Water Model. J Chem Theory Comput 2016; 12:5643-5655. [DOI: 10.1021/acs.jctc.6b00825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madhulika Gupta
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology-Kharagpur, Kharagpur 721302, India
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47
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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.
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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
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48
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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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49
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Ngai KL, Capaccioli S, Paciaroni A. Dynamics of hydrated proteins and bio-protectants: Caged dynamics, β-relaxation, and α-relaxation. Biochim Biophys Acta Gen Subj 2016; 1861:3553-3563. [PMID: 27155356 DOI: 10.1016/j.bbagen.2016.04.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The properties of the three dynamic processes, α-relaxation, ν-relaxation, and caged dynamics in aqueous mixtures and hydrated proteins are analogous to corresponding processes found in van der Waals and polymeric glass-formers apart from minor differences. METHODS Collection of various experimental data enables us to characterize the structural α-relaxation of the protein coupled to hydration water (HW), the secondary or ν-relaxation of HW, and the caged HW process. RESULTS From the T-dependence of the ν-relaxation time of hydrated myoglobin, lysozyme, and bovine serum albumin, we obtain Ton at which it enters the experimental time windows of Mössbauer and neutron scattering spectroscopies, coinciding with protein dynamical transition (PDT) temperature Td. However, for all systems considered, the α-relaxation time at Ton or Td is many orders of magnitude longer. The other step change of the mean-square-displacement (MSD) at Tg_alpha originates from the coupling of the nearly constant loss (NCL) of caged HW to density. The coupling of the NCL to density is further demonstrated by another step change at the secondary glass temperature Tg_beta in two bio-protectants, trehalose and sucrose. CONCLUSIONS The structural α-relaxation plays no role in PDT. Since PDT is simply due to the ν-relaxation of HW, the term PDT is a misnomer. NCL of caged dynamics is coupled to density and show transitions at lower temperature, Tg_beta and Tg_alpha. GENERAL SIGNIFICANCE The so-called protein dynamical transition (PDT) of hydrated proteins is not caused by the structural α-relaxation of the protein but by the secondary ν-relaxation of hydration water. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".
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Affiliation(s)
- K L Ngai
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy.
| | - S Capaccioli
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy; Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - A Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia, Via A Pascoli 1, 06123 Perugia, Italy
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Khodadadi S, Sokolov AP. Atomistic details of protein dynamics and the role of hydration water. Biochim Biophys Acta Gen Subj 2016; 1861:3546-3552. [PMID: 27155577 DOI: 10.1016/j.bbagen.2016.04.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND The importance of protein dynamics for their biological activity is now well recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. Yet, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. SCOOP OF REVIEW Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. MAJOR CONCLUSIONS Internal protein dynamics spread over a wide time range from faster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10-100ps time scale. This process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape. GENERAL SIGNIFICANCE The proposed atomistic picture of protein dynamics provides deeper understanding of various relaxation processes and their hierarchy, similarity and differences between various biological macromolecules, including proteins, DNA and RNA. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".
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Affiliation(s)
- Sheila Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands; Delft Project management B.V., Delft University of Technology, Delft, The Netherlands
| | - Alexei P Sokolov
- Joint Institute for Neutron Sciences, University of Tennessee, Knoxville, TN, USA.
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