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Tavagnacco L, Zanatta M, Buratti E, Bertoldo M, Chiessi E, Appel M, Natali F, Orecchini A, Zaccarelli E. Water slowing down drives the occurrence of the low temperature dynamical transition in microgels. Chem Sci 2024; 15:9249-9257. [PMID: 38903230 PMCID: PMC11186305 DOI: 10.1039/d4sc02650k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 06/22/2024] Open
Abstract
The protein dynamical transition marks an increase in atomic mobility and the onset of anharmonic motions at a critical temperature (T d), which is considered relevant for protein functionality. This phenomenon is ubiquitous, regardless of protein composition, structure and biological function and typically occurs at large protein content, to avoid water crystallization. Recently, a dynamical transition has also been reported in non-biological macromolecules, such as poly(N-isopropyl acrylamide) (PNIPAM) microgels, bearing many similarities to proteins. While the generality of this phenomenon is well-established, the role of water in the transition remains a subject of debate. In this study, we use atomistic molecular dynamics (MD) simulations and elastic incoherent neutron scattering (EINS) experiments with selective deuteration to investigate the microscopic origin of the dynamical transition and distinguish water and PNIPAM roles. While a standard analysis of EINS experiments would suggest that the dynamical transition occurs in PNIPAM and water at a similar temperature, simulations reveal a different perspective, also qualitatively supported by experiments. From room temperature down to about 180 K, PNIPAM exhibits only modest changes of dynamics, while water, being mainly hydration water under the probed extreme confinement, significantly slows down and undergoes a mode-coupling transition from diffusive to activated. Our findings therefore challenge the traditional view of the dynamical transition, demonstrating that it occurs in proximity of the water mode-coupling transition, shedding light on the intricate interplay between polymer and water dynamics.
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Affiliation(s)
- Letizia Tavagnacco
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| | - Marco Zanatta
- Department of Physics, University of Trento Via Sommarive 14 38123 Trento Italy
| | - Elena Buratti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Monica Bertoldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata Via della Ricerca Scientifica I 00133 Rome Italy
| | - Markus Appel
- Institut Laue-Langevin 71 avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Francesca Natali
- CNR-IOM, Operative Group Grenoble (OGG), Institut Laue Langevin F-38042 Grenoble France
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
| | - Emanuela Zaccarelli
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
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2
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Kölbel J, Anuschek ML, Stelzl I, Santitewagun S, Friess W, Zeitler JA. Dynamical Transition in Dehydrated Proteins. J Phys Chem Lett 2024; 15:3581-3590. [PMID: 38527099 PMCID: PMC11000241 DOI: 10.1021/acs.jpclett.3c03584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
Abstract
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilized sucrose exhibited steadily increasing absorption with temperature as anharmonic excitations commenced as the system emerged from a deep minimum of the potential energy landscape where harmonic vibrations dominate. The polypeptide bacitracin and two globular proteins, lysozyme and human serum albumin, showed a more complex temperature dependence. Further analysis focused on the spectral signature below and above the boson peak. We found evidence of the onset of anharmonic motions that are characteristic for partial unfolding and molecular jamming in the dry biomolecules. The activation of modes of the protein molecules at temperatures comparable to the protein dynamical transition temperature was observed in the absence of hydration. No evidence of Fröhlich coherence, postulated to facilitate biological function, was found in our experiments.
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Affiliation(s)
- Johanna Kölbel
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
| | - Moritz L. Anuschek
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - Ivonne Stelzl
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - Supawan Santitewagun
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
| | - Wolfgang Friess
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - J. Axel Zeitler
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
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3
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Sauer MA, Heyden M. Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins. J Chem Theory Comput 2023; 19:5481-5490. [PMID: 37515568 PMCID: PMC10624555 DOI: 10.1021/acs.jctc.2c01309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2023]
Abstract
Low-frequency molecular vibrations at far-infrared frequencies are thermally excited at room temperature. As a consequence, thermal fluctuations are not limited to the immediate vicinity of local minima on the potential energy surface, and anharmonic properties cannot be ignored. The latter is particularly relevant in molecules with multiple conformations, such as proteins and other biomolecules. However, existing theoretical and computational frameworks for the analysis of molecular vibrations have so far been limited by harmonic or quasi-harmonic approximations, which are ill-suited to describe anharmonic low-frequency vibrations. Here, we introduce a fully anharmonic analysis of molecular vibrations based on a time correlation formalism that eliminates the need for harmonic or quasi-harmonic approximations. We use molecular dynamics simulations of a small protein to demonstrate that this new approach, in contrast to harmonic and quasi-harmonic normal modes, correctly identifies the collective degrees of freedom associated with molecular vibrations at any given frequency. This allows us to unambiguously characterize the anharmonic character of low-frequency vibrations in the far-infrared spectrum.
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Affiliation(s)
- Michael A Sauer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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4
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Allen JL, Sanders TJ, Horvat J, Lewis RA, Rule KC. Determination of Vibrational Modes of l-Alanine Single Crystals by a Combination of Terahertz Spectroscopy Measurements and Density Functional Calculations. PHYSICAL REVIEW LETTERS 2023; 130:226901. [PMID: 37327443 DOI: 10.1103/physrevlett.130.226901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Density-functional theory may be used to predict both the frequency and the dipole moment of the fundamental oscillations of molecular crystals. Suitably polarized photons at those frequencies excite such oscillations. Thus, in principle, terahertz spectroscopy may confirm the calculated fundamental modes of amino acids. However, reports to date have multiple shortcomings: (a) material of uncertain purity and morphology and diluted in a binder material is employed; (b) consequently, vibrations along all crystal axes are excited simultaneously; (c) data are restricted to room temperature, where resonances are broad and the background dominant; and (d) comparison with theory has been unsatisfactory (in part because the theory assumes zero temperature). Here, we overcome all four obstacles, in reporting detailed low-temperature polarized THz spectra of single-crystal l-alanine, assigning vibrational modes using density-functional theory, and comparing the calculated dipole moment vector direction to the electric field polarization of the measured spectra. Our direct and detailed comparison of theory with experiment corrects previous mode assignments for l-alanine, and reveals unreported modes, previously obscured by closely spaced spectral absorptions. The fundamental modes are thereby determined.
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Affiliation(s)
- J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - K C Rule
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
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5
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Nakagawa H, Yamamoto N. Incoherent Neutron Scattering and Terahertz Time-Domain Spectroscopy on Protein and Hydration Water. Life (Basel) 2023; 13:life13020318. [PMID: 36836676 PMCID: PMC9961865 DOI: 10.3390/life13020318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Incoherent inelastic and quasi-elastic neutron scattering (INS) and terahertz time-domain spectroscopy (THz-TDS) are spectroscopy methods that directly detect molecular dynamics, with an overlap in the measured energy regions of each method. Due to the different characteristics of their probes (i.e., neutron and light), the information obtained and the sample conditions suitable for each method differ. In this review, we introduce the differences in the quantum beam properties of the two methods and their associated advantages and disadvantages in molecular spectroscopy. Neutrons are scattered via interaction with nuclei; one characteristic of neutron scattering is a large incoherent scattering cross-section of a hydrogen atom. INS records the auto-correlation functions of atomic positions. By using the difference in neutron scattering cross-sections of isotopes in multi-component systems, some molecules can be selectively observed. In contrast, THz-TDS observes the cross-correlation function of dipole moments. In water-containing biomolecular samples, the absorption of water molecules is particularly large. While INS requires large-scale experimental facilities, such as accelerators and nuclear reactors, THz-TDS can be performed at the laboratory level. In the analysis of water molecule dynamics, INS is primarily sensitive to translational diffusion motion, while THz-TDS observes rotational motion in the spectrum. The two techniques are complementary in many respects, and a combination of the two is very useful in analyzing the dynamics of biomolecules and hydration water.
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Affiliation(s)
- Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai-mura 319-1195, Ibaraki, Japan
- J-PARC Center, Japan Atomic Energy Agency, Tokai-mura 319-1195, Ibaraki, Japan
- Correspondence: (H.N.); (N.Y.)
| | - Naoki Yamamoto
- Division of Biophysics, Department of Physiology, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan
- Correspondence: (H.N.); (N.Y.)
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6
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Komandin GA, Zaytsev KI, Dolganova IN, Nozdrin VS, Chuchupal SV, Anzin VB, Spektor IE. Quantification of solid-phase chemical reactions using the temperature-dependent terahertz pulsed spectroscopy, sum rule, and Arrhenius theory: thermal decomposition of α-lactose monohydrate. OPTICS EXPRESS 2022; 30:9208-9221. [PMID: 35299355 DOI: 10.1364/oe.453528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Transformations of the low-energy vibrational spectra are associated with structural changes in an analyte and closely related to the instability of weak chemical bounds. Terahertz (THz)/far-infrared optical spectroscopy is commonly used to probe such transformation, aimed at characterization of the underlying solid-phase chemical reactions in organic compounds. However, such studies usually provide quite qualitative information about the temperature- and time-dependent parameters of absorption peaks in dielectric spectra of an analyte. In this paper, an approach for quantitative analyses of the solid-phased chemical reactions based on the THz pulsed spectroscopy was developed. It involves studying an evolution of the sample optical properties, as a function of the analyte temperature and reaction time, and relies on the classical oscillator model, the sum rule, and the Arrhenius theory. The method allows one to determine the temperature-dependent reaction rate V1(T) and activation energy Ea. To demonstrate the practical utility of this method, it was applied to study α-lactose monohydrate during its temperature-induced molecular decomposition. Analysis of the measured THz spectra revealed the increase of the reaction rate in the range of V1 ≃ ~9 × 10-4-10-2 min-1, when the analyte temperature rises from 313 to 393 K, while the Arrhenius activation energy is Ea ≃ ~45.4 kJ/mol. Thanks to a large number of obtained physical and chemical parameters, the developed approach expands capabilities of THz spectroscopy in chemical physics, analytical chemistry, and pharmaceutical industry.
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Abstract
Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases. Several techniques are used for studying protein dynamics, e.g., magnetic resonance, fluorescence imaging techniques, mid-infrared spectroscopy and biochemical assays. Spectroscopic analysis, based on the use of terahertz (THz) radiation with frequencies between 0.1 and 15 THz (3–500 cm−1), was underestimated by the biochemical community. In recent years, however, the potential of THz spectroscopy in the analysis of both simple structures, such as polypeptide molecules, and complex structures, such as protein complexes, has been demonstrated. The THz absorption spectrum provides some information on proteins: for small molecules the THz spectrum is dominated by individual modes related to the presence of hydrogen bonds. For peptides, the spectral information concerns their secondary structure, while for complex proteins such as globular proteins and viral glycoproteins, spectra also provide information on collective modes. In this short review, we discuss the results obtained by THz spectroscopy in the protein dynamics investigations. In particular, we will illustrate advantages and applications of THz spectroscopy, pointing out the complementary information it may provide.
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8
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George DK, Chen JY, He Y, Knab JR, Markelz AG. Functional-State Dependence of Picosecond Protein Dynamics. J Phys Chem B 2021; 125:11134-11140. [PMID: 34606257 DOI: 10.1021/acs.jpcb.1c05018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E1 ∼ 0.1 kJ/mol and E2 ∼ 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent-protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.
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Affiliation(s)
- D K George
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - J Y Chen
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - Yunfen He
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - J R Knab
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
| | - A G Markelz
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
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9
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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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10
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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11
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Valzania L, Zhao Y, Rong L, Wang D, Georges M, Hack E, Zolliker P. THz coherent lensless imaging. APPLIED OPTICS 2019; 58:G256-G275. [PMID: 31873509 DOI: 10.1364/ao.58.00g256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/28/2019] [Indexed: 06/10/2023]
Abstract
Imaging with THz radiation has proved an important tool for both fundamental science and industrial use. Here we review a class of THz imaging implementations, named coherent lensless imaging, that reconstruct the coherent response of arbitrary samples with a minimized experimental setup based only on a coherent source and a camera. After discussing the appropriate sources and detectors to perform them, we detail the fundamental principles and implementations of THz digital holography and phase retrieval. These techniques owe a lot to imaging with different wavelengths, yet innovative concepts are also being developed in the THz range and are ready to be applied in other spectral ranges. This makes our review useful for both the THz and imaging communities, and we hope it will foster their interaction.
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12
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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13
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Combining Neutron Scattering, Deuteration Technique, and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-019-2312-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Aloi E, Guzzi R, Bartucci R. Unsaturated lipid bilayers at cryogenic temperature: librational dynamics of chain-labeled lipids from pulsed and CW-EPR. Phys Chem Chem Phys 2019; 21:18699-18705. [PMID: 31423504 DOI: 10.1039/c9cp03318a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fully hydrated bilayers of monounsaturated palmitoyloleoylphosphatidylcholine (POPC) and diunsaturated dioleoylphosphatidylcholine (DOPC) lipids have low main phase transition temperatures (271 K for POPC and 253 K for DOPC). Two-pulse echo detected spectra, combined with continuous wave electron paramagnetic resonance spectroscopy, are employed to study the low-temperature lamellar phases of the POPC and DOPC unsaturated bilayers that are usually studied in the fluid state. Phosphatidylcholine spin-labeled at C-5 and C-16 carbon atom positions along the acyl chain were used and the temperature varied over the range 77-270 K. Segmental chain librational oscillations of small amplitude and with correlation time in the subnanosecond to nanosecond range are found in both membranes. The mean-square angular amplitude, α2, of librations increases with temperature, is larger close to the bilayer midplane than close to the first acyl chain segments, and is larger in diunsaturated than in monounsaturated bilayers. In the inner hydrocarbon region of both lipid matrices, α2 increases first slowly and linearly with temperature and then more rapidly, and a dynamical transition is detected in the range 190-210 K. Compared to dipalmitoylphosphatidylcholine bilayers of fully saturated symmetric chain lipids, the presence of double bonds in the acyl chain enhances the intensity of librational motion which is characterized by larger angular variations at the terminal methyl ends. These findings highlight biophysical properties of unsaturated bilayers in the frozen state, including a detailed characterization of segmental chain dynamics and the evidence of a dynamical transition that appears to be a generic feature in hydrated macromolecular systems. These results can also be relevant in regulating membrane physical properties and function at higher physiological temperatures.
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Affiliation(s)
- Erika Aloi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria, 87036 Rende, Italy
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15
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Novelli F, Bernal Lopez M, Schwaab G, Roldan Cuenya B, Havenith M. Water Solvation of Charged and Neutral Gold Nanoparticles. J Phys Chem B 2019; 123:6521-6528. [DOI: 10.1021/acs.jpcb.9b02358] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Beatriz Roldan Cuenya
- Department of Interface Science, Fritz-Haber Institute of the Max Planck Society, Berlin 14195, Germany
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16
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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17
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Iorio A, Camisasca G, Gallo P. Slow dynamics of hydration water and the trehalose dynamical transition. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Pathak AK, Bandyopadhyay T. Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water. J Chem Theory Comput 2019; 15:2706-2718. [PMID: 30849227 DOI: 10.1021/acs.jctc.9b00005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters. This might have led to the present trait of discovery that DTs of biomolecules, irrespective of the potential functions for water models used, occur within a narrow band of temperature variation (30-40 K). Whereas a water molecule in a biomolecular surface and one in bulk are polarized differently, therefore explicit treatment of water polarizability would be a powerful approach toward the treatment of hydration water, believed to cause the DT manifestation. Using MD simulations, we investigated the effects of polarizable water on the DT of biomolecules and the dynamic properties of hydration water. We chose two types of solutes: globular protein (lysozyme) and more open and flexible RNAs (a hairpin and a riboswitch) with different natures of hydrophilic sites than proteins in general. We found that the characteristic temperature of DT ( TDT) for the solutes in polarizable water is always higher than that in its nonpolarizable counterpart. In particular, for RNAs, the variations are found to be ∼45 K between the two water models, whereas for the more compact lysozyme, it is only ∼4 K. The results are discussed in light of the enormous increase in relaxation times of a liquid upon cooling in the paradigm of dynamic switchover in hydration water with liquid-liquid phase transition, derived from the existence of the second critical point. Our result supports the idea that structures of biomolecules and their interactions with the hydration water determines TDT and provides evidence for the decisive role of polarizable water on the onset of DT, which has been hitherto ignored.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
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19
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Tavagnacco L, Chiessi E, Zanatta M, Orecchini A, Zaccarelli E. Water-Polymer Coupling Induces a Dynamical Transition in Microgels. J Phys Chem Lett 2019; 10:870-876. [PMID: 30735054 PMCID: PMC6416711 DOI: 10.1021/acs.jpclett.9b00190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
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Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| | - Ester Chiessi
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientica I, 00133 Rome, Italy
| | - Marco Zanatta
- Department
of Computer Science, University of Verona, Strada Le Grazie 15, 37138 Verona, Italy
| | - Andrea Orecchini
- Department
of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM
c/o Department of Physics and Geology, University
of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
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20
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Gagkaeva ZV, Zhukova ES, Grinenko V, Grebenko AK, Sidoruk KV, Voeikova TA, Dressel M, Gorshunov BP. Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix. J Biol Phys 2018; 44:401-417. [PMID: 29732506 PMCID: PMC6082806 DOI: 10.1007/s10867-018-9497-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/13/2018] [Indexed: 01/30/2023] Open
Abstract
Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000 cm-1 in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm-1 and mainly determine the terahertz absorption. When cooled down to liquid helium temperatures, the bands in Shewanella oneidensis MR-1 and cytochrome c reveal a distinct fine structure. In all three materials, we identify the presence of liquid bound water in the form of librational and translational absorption bands at ≈ 200 and ≈ 600 cm-1, respectively. The sharp excitations seen above 1000 cm-1 are assigned to intramolecular vibrations.
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Affiliation(s)
- Z V Gagkaeva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - E S Zhukova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - V Grinenko
- Institute for Metallic Materials, IFW Dresden, Dresden, Germany
| | - A K Grebenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - K V Sidoruk
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - T A Voeikova
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - M Dressel
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Physikalisches Institut, Universität Stuttgart, Stuttgart, Germany
| | - B P Gorshunov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
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21
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Zanatta M, Tavagnacco L, Buratti E, Bertoldo M, Natali F, Chiessi E, Orecchini A, Zaccarelli E. Evidence of a low-temperature dynamical transition in concentrated microgels. SCIENCE ADVANCES 2018; 4:eaat5895. [PMID: 30276264 PMCID: PMC6162076 DOI: 10.1126/sciadv.aat5895] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/21/2018] [Indexed: 05/07/2023]
Abstract
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a "protein-like" dynamical transition in nonbiological aqueous environments. To this aim, we exploit the popular colloidal system of poly-N-isopropylacrylamide (PNIPAM) microgels, extending their investigation to unprecedentedly high concentrations. Owing to the heterogeneous architecture of the microgels, water crystallization is avoided in concentrated samples, allowing us to monitor atomic dynamics at low temperatures. By elastic incoherent neutron scattering and molecular dynamics simulations, we find that a dynamical transition occurs at a temperature T d ~ 250 K, independently from PNIPAM mass fraction. However, the transition is smeared out on approaching dry conditions. The quantitative agreement between experiments and simulations provides evidence that the transition occurs simultaneously for PNIPAM and water dynamics. The similarity of these results with hydrated protein powders suggests that the dynamical transition is a generic feature in complex macromolecular systems, independently from their biological function.
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Affiliation(s)
- Marco Zanatta
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Letizia Tavagnacco
- Consiglio Nazionale delle Ricerche (CNR)–Istituto dei Sistemi Complessi, Sede Sapienza, and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy
| | - Elena Buratti
- CNR–Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Area della Ricerca, via G. Moruzzi 1, 56124 Pisa, Italy
| | - Monica Bertoldo
- CNR–Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Area della Ricerca, via G. Moruzzi 1, 56124 Pisa, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
| | - Francesca Natali
- CNR–Istituto Officina dei Materiali (IOM), Operative Group in Grenoble, c/o Institut Laue Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France
| | - Ester Chiessi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133 Rome, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
| | - Emanuela Zaccarelli
- Consiglio Nazionale delle Ricerche (CNR)–Istituto dei Sistemi Complessi, Sede Sapienza, and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
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22
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Esser A, Forbert H, Sebastiani F, Schwaab G, Havenith M, Marx D. Hydrophilic Solvation Dominates the Terahertz Fingerprint of Amino Acids in Water. J Phys Chem B 2018; 122:1453-1459. [DOI: 10.1021/acs.jpcb.7b08563] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alexander Esser
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald Forbert
- Center
for Solvation Science ZEMOS, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Federico Sebastiani
- Lehrstuhl
für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl
für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl
für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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23
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Imoto S, Forbert H, Marx D. Aqueous TMAO solutions as seen by theoretical THz spectroscopy: hydrophilic versus hydrophobic water. Phys Chem Chem Phys 2018; 20:6146-6158. [DOI: 10.1039/c7cp07003a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All THz resonances of aqueous TMAO solutions are computed and assigned based on ab initio molecular dynamics simulations.
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Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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24
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Pandey HD, Leitner DM. Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study. J Phys Chem B 2017; 121:9498-9507. [DOI: 10.1021/acs.jpcb.7b05892] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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25
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Mensink MA, Šibík J, Frijlink HW, van der Voort Maarschalk K, Hinrichs WLJ, Zeitler JA. Thermal Gradient Mid- and Far-Infrared Spectroscopy as Tools for Characterization of Protein Carbohydrate Lyophilizates. Mol Pharm 2017; 14:3550-3557. [PMID: 28874050 PMCID: PMC5627341 DOI: 10.1021/acs.molpharmaceut.7b00568] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protein
drugs play an important role in modern day medicine. Typically,
these proteins are formulated as liquids requiring cold chain processing.
To circumvent the cold chain and achieve better storage stability,
these proteins can be dried in the presence of carbohydrates. We demonstrate
that thermal gradient mid- and far-infrared spectroscopy (FTIR and
THz-TDS, respectively) can provide useful information about solid-state
protein carbohydrate formulations regarding mobility and intermolecular
interactions. A model protein (BSA) was lyophilized in the presence
of three carbohydrates with different size and protein stabilizing
capacity. A gradual increase in mobility was observed with increasing
temperature in formulations containing protein and/or larger carbohydrates
(oligo- or polysaccharides), lacking a clear onset of fast mobility
as was observed for smaller molecules. Furthermore, both techniques
are able to identify the glass transition temperatures (Tg) of the samples. FTIR provides additional information
as it can independently monitor changes in protein and carbohydrate
bands at the Tg. Lastly, THz-TDS confirms
previous findings that protein–carbohydrate interactions decrease
with increasing molecular weight of the carbohydrate, which results
in decreased protein stabilization.
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Affiliation(s)
- M A Mensink
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Janssen Vaccines and Prevention , Archimedesweg 4, 2333 CN Leiden, The Netherlands
| | - J Šibík
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom.,F. Hoffmann-La Roche A.G. , Basel 4070, Switzerland
| | - H W Frijlink
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - K van der Voort Maarschalk
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Process Technology, Corbion Purac , P.O. Box 21, 4200 AA Gorinchem, The Netherlands
| | - W L J Hinrichs
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - J A Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
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26
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Liu Z, Huang J, Tyagi M, O'Neill H, Zhang Q, Mamontov E, Jain N, Wang Y, Zhang J, Smith JC, Hong L. Dynamical Transition of Collective Motions in Dry Proteins. PHYSICAL REVIEW LETTERS 2017; 119:048101. [PMID: 29341744 DOI: 10.1103/physrevlett.119.048101] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 06/07/2023]
Abstract
Water is widely assumed to be essential for protein dynamics and function. In particular, the well-documented "dynamical" transition at ∼200 K, at which the protein changes from a rigid, nonfunctional form to a flexible, functional state, as detected in hydrogenated protein by incoherent neutron scattering, requires hydration. Here, we report on coherent neutron scattering experiments on perdeuterated proteins and reveal that a transition occurs in dry proteins at the same temperature resulting primarily from the collective heavy-atom motions. The dynamical transition discovered is intrinsic to the energy landscape of dry proteins.
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Affiliation(s)
- Zhuo Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA and Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37931, USA
| | - Qiu Zhang
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37931, USA
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Nitin Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Yujie Wang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Zhang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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27
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Pattni V, Vasilevskaya T, Thiel W, Heyden M. Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations. J Phys Chem B 2017. [PMID: 28636363 PMCID: PMC5607456 DOI: 10.1021/acs.jpcb.7b03966] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
In
this molecular dynamics simulation study, we analyze intermolecular
vibrations in the hydration shell of a solvated enyzme, the membrane
type 1–matrix metalloproteinase, with high spatial resolution.
Our approach allows us to characterize vibrational signatures of the
local hydrogen bond network, the translational mobility of water molecules,
as well as the molecular entropy, in specific local environments.
Our study demonstrates the heterogeneity of water properties within
the hydration shell of a complex biomolecule. We define a classification
scheme based on the vibrational density of states that allows us to
distinguish separate classes of hydration water species and facilitates
the description of hydration water properties at distinct hydration
sites. The results demonstrate that no single characteristic of the
protein surface is sufficient to determine the properties of nearby
water. The protein surface geometry, quantified here by the number
of protein atoms in the vicinity of a hydration water molecule, as
well as the chemical nature of a solvated protein functional group,
influences dynamic and thermodynamic properties of solvating water
molecules.
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Affiliation(s)
- Viren Pattni
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, DE-45470 Mülheim an der Ruhr, Germany
| | - Tatiana Vasilevskaya
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, DE-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, DE-45470 Mülheim an der Ruhr, Germany
| | - Matthias Heyden
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, DE-45470 Mülheim an der Ruhr, Germany
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28
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Rahaman O, Kalimeri M, Katava M, Paciaroni A, Sterpone F. Configurational Disorder of Water Hydrogen-Bond Network at the Protein Dynamical Transition. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b03888] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Obaidur Rahaman
- Institute
of Structural Mechanics, Bauhaus-Universitt Weimar, Marienstr. 15, D-99423 Weimar, Germany
| | - Maria Kalimeri
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 10, P.O. Box 692, FI-33101 Tampere, Finland
| | - Marina Katava
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alessandro Paciaroni
- Dipartimento
di Fisica e Geologia, Universite di Perugia, via A. Pascoli, 06123 Perugia, Italy
| | - Fabio Sterpone
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
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29
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Carpinteri A, Lacidogna G, Piana G, Bassani A. Terahertz mechanical vibrations in lysozyme: Raman spectroscopy vs modal analysis. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Das Mahanta D, Patra A, Samanta N, Luong TQ, Mukherjee B, Mitra RK. Non-monotonic dynamics of water in its binary mixture with 1,2-dimethoxy ethane: A combined THz spectroscopic and MD simulation study. J Chem Phys 2016; 145:164501. [DOI: 10.1063/1.4964857] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Debasish Das Mahanta
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Animesh Patra
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Nirnay Samanta
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Trung Quan Luong
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Biswaroop Mukherjee
- Thematic Unit for Excellence–Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
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31
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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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32
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Yamamoto N, Ohta K, Tamura A, Tominaga K. Broadband Dielectric Spectroscopy on Lysozyme in the Sub-Gigahertz to Terahertz Frequency Regions: Effects of Hydration and Thermal Excitation. J Phys Chem B 2016; 120:4743-55. [PMID: 27158918 DOI: 10.1021/acs.jpcb.6b01491] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have performed dielectric spectral measurements of lysozyme in a solid state to understand the effects of hydration and thermal excitation on the low-frequency dynamics of protein. Dielectric measurements were performed under changing hydration conditions at room temperature in the frequency region of 0.5 GHz to 1.8 THz. We also studied the temperature dependence (83 to 293 K) of the complex dielectric spectra in the THz frequency region (0.3 THz to 1.8 THz). Spectral analyses were performed using model functions for the complex dielectric constant. To reproduce the spectra, we found that two relaxational modes and two underdamped modes are necessary together with an ionic conductivity term in the model function. At room temperature, the two relaxational modes have relaxation times of ∼20 ps and ∼100 ps. The faster component has a major spectral intensity and is suggested to be due to coupled water-protein motion. The two underdamped modes are necessary to reproduce the temperature dependence of the spectra in the THz region satisfactorily. The protein dynamical transition is a well-known behavior in the neutron-scattering experiment for proteins, where the atomic mean-square displacement shows a sudden change in the temperature dependence at approximately 200 K, when the samples are hydrated. A similar behavior has also been observed in the temperature dependence of the absorption spectra of protein in the THz frequency region. From our broadband dielectric spectroscopic measurements, we conclude that the increase in the spectral intensities in the THz region at approximately 200 K is due to a spectral blue-shift of the fast relaxational mode.
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Affiliation(s)
- Naoki Yamamoto
- Graduate School of Science and ‡Molecular Photoscience Research Center, Kobe University , Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Kaoru Ohta
- Graduate School of Science and ‡Molecular Photoscience Research Center, Kobe University , Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Atsuo Tamura
- Graduate School of Science and ‡Molecular Photoscience Research Center, Kobe University , Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Graduate School of Science and ‡Molecular Photoscience Research Center, Kobe University , Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
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33
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Sibik J, Zeitler JA. Direct measurement of molecular mobility and crystallisation of amorphous pharmaceuticals using terahertz spectroscopy. Adv Drug Deliv Rev 2016; 100:147-57. [PMID: 26772139 DOI: 10.1016/j.addr.2015.12.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 11/26/2022]
Abstract
Despite much effort in the area, no comprehensive understanding of the formation and behaviour of amorphous solids has yet been achieved. This severely limits the industrial application of such materials, including drug delivery where, in principle, amorphous solids have demonstrated their great usefulness in increasing the bioavailability of poorly aqueous soluble active pharmaceutical ingredients. Terahertz time-domain spectroscopy is a relatively novel analytical technique that can be used to measure the fast molecular dynamics of molecules with high accuracy in a non-contact and non-destructive fashion. Over the past decade a number of applications for the characterisation of amorphous drug molecules and formulations have been developed and it has been demonstrated how this technique can be used to determine the onset and strength in molecular mobility that underpins the crystallisation of amorphous drugs. In this review we provide an overview of the history, fundamentals and future perspective of pharmaceutical applications related to the terahertz dynamics of amorphous systems.
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34
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Nilsson L. Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules. Biophys J 2016; 108:2755-6. [PMID: 26083911 DOI: 10.1016/j.bpj.2015.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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35
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Mamontov E, Sharma VK, Borreguero JM, Tyagi M. Protein-Style Dynamical Transition in a Non-Biological Polymer and a Non-Aqueous Solvent. J Phys Chem B 2016; 120:3232-9. [DOI: 10.1021/acs.jpcb.6b00866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Mamontov
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - V. K. Sharma
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Solid
State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - J. M. Borreguero
- Neutron
Data Analysis and Visualization Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - M. Tyagi
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, Maryland 20899, United States
- Department
of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
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36
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Samanta N, Luong TQ, Das Mahanta D, Mitra RK, Havenith M. Effect of Short Chain Poly(ethylene glycol)s on the Hydration Structure and Dynamics around Human Serum Albumin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:831-837. [PMID: 26720549 DOI: 10.1021/acs.langmuir.5b03884] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report the changes in the hydration dynamics around a globular protein, human serum albumin (HSA), in the presence of two short chain crowding agents, namely poly(ethylene glycol)s (PEG 200 and 400). The change in the network water structure is investigated using FTIR spectroscopy in the far-infrared (FIR) frequency range. Site specific changes are obtained by time-resolved fluorescence spectroscopic technique using the intrinsic fluorophore tryptophan (Trp214) of HSA. The collective hydration dynamics of HSA in the presence of PEG molecules are obtained using terahertz (THz) time domain spectroscopy (TTDS) and high intensity p-Ge THz measurements. Our study affirms a considerable perturbation of HSA hydration beyond a critical concentration of PEG.
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Affiliation(s)
- Nirnay Samanta
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Trung Quan Luong
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Debasish Das Mahanta
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
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37
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Pharmaceutical Terahertz Spectroscopy and Imaging. ADVANCES IN DELIVERY SCIENCE AND TECHNOLOGY 2016. [DOI: 10.1007/978-1-4939-4029-5_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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38
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Samanta N, Mahanta DD, Mitra RK. Collective hydration dynamics of guanidinium chloride solutions and its possible role in protein denaturation: a terahertz spectroscopic study. Phys Chem Chem Phys 2015; 16:23308-15. [PMID: 25259383 DOI: 10.1039/c4cp03273j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The remarkable ability of guanidinium chloride (GdmCl) to denature proteins is a well studied yet controversial phenomenon; the exact molecular mechanism is still debatable, especially the role of hydration dynamics, which has been paid less attention. In the present contribution, we have addressed the issue of whether the collective hydrogen bond dynamics of water gets perturbed in the presence of GdmCl and its possible impact on the denaturation of a globular protein human serum albumin (HSA), using terahertz (THz) time domain spectroscopy (TTDS) in the frequency range of 0.3-2.0 THz. The collective hydrogen bond dynamics is determined by fitting the obtained complex dielectric response in a multiple Debye relaxation model. To compare the results, the studies were extended to two more salts: tetramethylguanidinium chloride (TMGdmCl) and sodium chloride (NaCl). It was concluded that the change in hydration dynamics plays a definite role in the protein denaturation process.
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Affiliation(s)
- Nirnay Samanta
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700098, India.
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39
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Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
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40
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Lewandowski JR, Halse ME, Blackledge M, Emsley L. Direct observation of hierarchical protein dynamics. Science 2015; 348:578-81. [DOI: 10.1126/science.aaa6111] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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41
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Parrott EPJ, Zeitler JA. Terahertz time-domain and low-frequency Raman spectroscopy of organic materials. APPLIED SPECTROSCOPY 2015; 69:1-25. [PMID: 25506684 DOI: 10.1366/14-07707] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
With the ongoing proliferation of terahertz time-domain instrumentation from semiconductor physics into applied spectroscopy over the past decade, measurements at terahertz frequencies (1 THz ≡ 10(12) Hz ≡ 33 cm(-1)) have attracted a sustained growing interest, in particular the investigation of hydrogen-bonding interactions in organic materials. More recently, the availability of Raman spectrometers that are readily able to measure in the equivalent spectral region very close to the elastic scattering background has also grown significantly. This development has led to renewed efforts in performing spectroscopy at the interface between dielectric relaxation phenomena and vibrational spectroscopy. In this review, we briefly outline the underlying technology, the physical phenomena governing the light-matter interaction at terahertz frequencies, recent examples of spectroscopic studies, and the current state of the art in assigning spectral features to vibrational modes based on computational techniques.
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Affiliation(s)
- Edward P J Parrott
- Chinese University of Hong Kong, Department of Electronic Engineering, Shatin, New Territories, Hong Kong Sar, China
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42
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Gente R, Koch M. Monitoring leaf water content with THz and sub-THz waves. PLANT METHODS 2015; 11:15. [PMID: 25767560 PMCID: PMC4357146 DOI: 10.1186/s13007-015-0057-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/12/2015] [Indexed: 05/04/2023]
Abstract
Terahertz technology is still an evolving research field that attracts scientists with very different backgrounds working on a wide range of subjects. In the past two decades, it has been demonstrated that terahertz technology can provide a non-invasive tool for measuring and monitoring the water content of leaves and plants. In this paper we intend to review the different possibilities to perform in-vivo water status measurements on plants with the help of THz and sub-THz waves. The common basis of the different methods is the strong absorption of THz and sub-THz waves by liquid water. In contrast to simpler, yet destructive, methods THz and sub-THz waves allow for the continuous monitoring of plant water status over several days on the same sample. The technologies, which we take into focus, are THz time domain spectroscopy, THz continuous wave setups, THz quasi time domain spectroscopy and sub-THz continuous wave setups. These methods differ with respect to the generation and detection schemes, the covered frequency range, the processing and evaluation of the experimental data, and the mechanical handling of the measurements. Consequently, we explain which method fits best in which situation. Finally, we discuss recent and future technological developments towards more compact and budget-priced measurement systems for use in the field.
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Affiliation(s)
- Ralf Gente
- Faculty of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032 Marburg Germany
| | - Martin Koch
- Faculty of Physics and Material Sciences Center, Philipps-Universität Marburg, Renthof 5, 35032 Marburg Germany
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43
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Wang Z, Chiang WS, Le P, Fratini E, Li M, Alatas A, Baglioni P, Chen SH. One role of hydration water in proteins: key to the "softening" of short time intraprotein collective vibrations of a specific length scale. SOFT MATTER 2014; 10:4298-4303. [PMID: 24789017 DOI: 10.1039/c4sm00257a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
High resolution inelastic X-ray scattering (IXS) experiments show that the "phonon energy softening" and "phonon population enhancement" observed in a hydrated native protein when increasing the temperature from 200 K to physiological temperature are not directly related to the protein structure. Such phenomena were also observed in a denatured sample without a defined tertiary structure and with a limited residual secondary structure. However, in a dry sample, such "softening" is strongly suppressed. These facts suggest that the above-mentioned protein "softening" phenomenon is water-induced. In addition, increasing the hydration level can also induce "phonon energy softening" at room temperature, but not at 200 K. This change may be due to a qualitative difference in the dynamics of hydration water at 200 K and at room temperature.
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Affiliation(s)
- Zhe Wang
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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44
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Terahertz underdamped vibrational motion governs protein-ligand binding in solution. Nat Commun 2014; 5:3999. [PMID: 24893252 DOI: 10.1038/ncomms4999] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 04/29/2014] [Indexed: 11/08/2022] Open
Abstract
Low-frequency collective vibrational modes in proteins have been proposed as being responsible for efficiently directing biochemical reactions and biological energy transport. However, evidence of the existence of delocalized vibrational modes is scarce and proof of their involvement in biological function absent. Here we apply extremely sensitive femtosecond optical Kerr-effect spectroscopy to study the depolarized Raman spectra of lysozyme and its complex with the inhibitor triacetylchitotriose in solution. Underdamped delocalized vibrational modes in the terahertz frequency domain are identified and shown to blue-shift and strengthen upon inhibitor binding. This demonstrates that the ligand-binding coordinate in proteins is underdamped and not simply solvent-controlled as previously assumed. The presence of such underdamped delocalized modes in proteins may have significant implications for the understanding of the efficiency of ligand binding and protein-molecule interactions, and has wider implications for biochemical reactivity and biological function.
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45
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Cerveny S, Swenson J. Dynamics of supercooled water in a biological model system of the amino acid l-lysine. Phys Chem Chem Phys 2014; 16:22382-90. [DOI: 10.1039/c4cp02487g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lysine solutions establish a new relaxation behaviour of supercooled interfacial water.
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Affiliation(s)
- Silvina Cerveny
- Centro de Física de Materiales-Material Physics Centre (MPC)
- CSIC-Universidad del País Vasco (UPV/EHU)
- San Sebastian, Spain
- Donostia International Physics Center
- San Sebastián, Spain
| | - Jan Swenson
- Department of Applied Physics
- Chalmers University of Technology
- SE-412 96 Göteborg, Sweden
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46
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Sassi P, Perticaroli S, Comez L, Giugliarelli A, Paolantoni M, Fioretto D, Morresi A. Volume properties and spectroscopy: A terahertz Raman investigation of hen egg white lysozyme. J Chem Phys 2013; 139:225101. [DOI: 10.1063/1.4838355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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47
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Kuo YH, Tseng YR, Chiang YW. Concurrent observation of bulk and protein hydration water by spin-label ESR under nanoconfinement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:13865-13872. [PMID: 24138087 DOI: 10.1021/la403002t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Under nanoconfinement the formation of crystalline ice is suppressed, allowing the study of water dynamics at subfreezing temperatures. Here we report a temperature-dependent investigation (170-260 K) of the behavior of hydration water under nanoconfinement by ESR techniques. A 26-mer-long peptide and the Bax protein are studied. This study provides site-specific information about the different local hydrations concurrently present in the protein/peptide solution, enabling a decent comparison of the hydration molecules-those that are buried inside, in contact with, and detached from the protein surface. Such a comparison is not possible without employing ESR under nanoconfinement. Though the confined bulk and surface hydrations behave differently, they both possess a transition similar to the reported fragile-to-strong crossover transition around 220 K. On the contrary, this transition is absent for the hydration near the buried sites of the protein. The activation energy determined under nanoconfinement is found to be lower in surface hydration than in bulk hydration. The protein structural flexibility, derived from the interspin distance distributions P(r) at different temperatures, is obtained by dipolar ESR spectroscopy. The P(r) result demonstrates that the structural flexibility is strongly correlated with the transition in the surface water, corroborating the origin of the protein dynamical transition at subfreezing temperatures.
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Affiliation(s)
- Yun-Hsuan Kuo
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University , Hsinchu 30013, Taiwan
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48
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Polley D, Patra A, Mitra RK. Dielectric relaxation of the extended hydration sheathe of DNA in the THz frequency region. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Chen NN, Liang J, Ren LY. High-birefringence, low-loss porous fiber for single-mode terahertz-wave guidance. APPLIED OPTICS 2013; 52:5297-5302. [PMID: 23872779 DOI: 10.1364/ao.52.005297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 06/28/2013] [Indexed: 06/02/2023]
Abstract
A new kind of polymer porous fiber with elliptical air-holes is designed for obtaining high birefringence in the terahertz (THz) frequency range in this paper. Using the finite element method, the properties of this kind of fiber are simulated in detail including the single-mode propagation condition, the birefringence, and the loss. Theoretical results indicate that the single-mode THz wave in the frequency range from 0.73 to 1.22 THz can be guided in the fiber; the birefringence can be enhanced by rotating the major axis of the elliptical air-hole and there exists an optimal rotating angle at 30°. At this optimal angle a birefringence as high as 0.0445 can be obtained in a wide frequency range. Low-loss THz guidance can be achieved owing to the effective reduction of the material absorption in such a porous fiber. This research is useful for polarization-maintaining THz-wave guidance.
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Affiliation(s)
- Na-na Chen
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China
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50
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Wang Z, Bertrand CE, Chiang WS, Fratini E, Baglioni P, Alatas A, Alp EE, Chen SH. Inelastic X-ray Scattering Studies of the Short-Time Collective Vibrational Motions in Hydrated Lysozyme Powders and Their Possible Relation to Enzymatic Function. J Phys Chem B 2013; 117:1186-95. [DOI: 10.1021/jp312842m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhe Wang
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher E. Bertrand
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wei-Shan Chiang
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emiliano Fratini
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence,
I-50019, Italy
| | - Piero Baglioni
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence,
I-50019, Italy
| | - Ahmet Alatas
- Advanced Photon
Source, Argonne National Lab, Argonne,
Illinois, 60439, United States
| | - E. Ercan Alp
- Advanced Photon
Source, Argonne National Lab, Argonne,
Illinois, 60439, United States
| | - Sow-Hsin Chen
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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