1
|
Iorio A, Perin L, Gallo P. Structure and slow dynamics of protein hydration water with cryopreserving DMSO and trehalose upon cooling. J Chem Phys 2024; 160:244502. [PMID: 38912631 DOI: 10.1063/5.0205569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
We study, through molecular dynamics simulations, three aqueous solutions with one lysozyme protein and three different concentrations of trehalose and dimethyl sulfoxide (DMSO). We analyze the structural and dynamical properties of the protein hydration water upon cooling. We find that trehalose plays a major role in modifying the structure of the network of HBs between water molecules in the hydration layer of the protein. The dynamics of hydration water presents, in addition to the α-relaxation, typical of glass formers, a slower long-time relaxation process, which greatly slows down the dynamics of water, particularly in the systems with trehalose, where it becomes dominant at low temperatures. In all the solutions, we observe, from the behavior of the α-relaxation times, a shift of the Mode Coupling Theory crossover temperature and the fragile-to-strong crossover temperature toward higher values with respect to bulk water. We also observe a strong-to-strong crossover from the temperature behavior of the long-relaxation times. In the aqueous solution with only DMSO, the transition shifts to a lower temperature than in the case with only lysozyme reported in the literature. We observe that the addition of trehalose to the mixture has the opposite effect of restoring the original location of the strong-to-strong crossover. In all the solutions analyzed in this work, the observed temperature of the protein dynamical transition is slightly shifted at lower temperatures than that of the strong-to-strong crossover, but their relative order is the same, showing a correlation between the motion of the protein and that of the hydration water.
Collapse
Affiliation(s)
- Antonio Iorio
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| | - Leonardo Perin
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| | - Paola Gallo
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| |
Collapse
|
2
|
Tavagnacco L, Zanatta M, Buratti E, Bertoldo M, Chiessi E, Appel M, Natali F, Orecchini A, Zaccarelli E. Water slowing down drives the occurrence of the low temperature dynamical transition in microgels. Chem Sci 2024; 15:9249-9257. [PMID: 38903230 PMCID: PMC11186305 DOI: 10.1039/d4sc02650k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 06/22/2024] Open
Abstract
The protein dynamical transition marks an increase in atomic mobility and the onset of anharmonic motions at a critical temperature (T d), which is considered relevant for protein functionality. This phenomenon is ubiquitous, regardless of protein composition, structure and biological function and typically occurs at large protein content, to avoid water crystallization. Recently, a dynamical transition has also been reported in non-biological macromolecules, such as poly(N-isopropyl acrylamide) (PNIPAM) microgels, bearing many similarities to proteins. While the generality of this phenomenon is well-established, the role of water in the transition remains a subject of debate. In this study, we use atomistic molecular dynamics (MD) simulations and elastic incoherent neutron scattering (EINS) experiments with selective deuteration to investigate the microscopic origin of the dynamical transition and distinguish water and PNIPAM roles. While a standard analysis of EINS experiments would suggest that the dynamical transition occurs in PNIPAM and water at a similar temperature, simulations reveal a different perspective, also qualitatively supported by experiments. From room temperature down to about 180 K, PNIPAM exhibits only modest changes of dynamics, while water, being mainly hydration water under the probed extreme confinement, significantly slows down and undergoes a mode-coupling transition from diffusive to activated. Our findings therefore challenge the traditional view of the dynamical transition, demonstrating that it occurs in proximity of the water mode-coupling transition, shedding light on the intricate interplay between polymer and water dynamics.
Collapse
Affiliation(s)
- Letizia Tavagnacco
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| | - Marco Zanatta
- Department of Physics, University of Trento Via Sommarive 14 38123 Trento Italy
| | - Elena Buratti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Monica Bertoldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata Via della Ricerca Scientifica I 00133 Rome Italy
| | - Markus Appel
- Institut Laue-Langevin 71 avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Francesca Natali
- CNR-IOM, Operative Group Grenoble (OGG), Institut Laue Langevin F-38042 Grenoble France
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
| | - Emanuela Zaccarelli
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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.)
| |
Collapse
|
5
|
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.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Mahmud Ankan I, Mollah MA, Sultana J, Islam MS. Negative curvature hollow-core anti-resonant fiber for terahertz sensing. APPLIED OPTICS 2020; 59:8519-8525. [PMID: 33104530 DOI: 10.1364/ao.395914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Hollow-core fibers are advantageous for chemical sensing as they facilitate liquid infiltration into the core over conventional porous core fiber. In addition, the requirement of less bulk material significantly decreases the effective material loss (EML). In this paper, a six circular cladding tube negative curvature hollow-core fiber (NC-HCF) is proposed for chemical sensing. Five different chemicals including chloroform, polylactic acid, CCL3, glycerin, and benzene are proposed to fill the core of the NC-HCF, and sensitivities are evaluated by full vector finite element method-based COMSOL software. Numerical results reveal that the proposed sensor exhibits very high relative sensitivity in a wide range of frequency. The fabrication of the proposed fiber is feasible by existing fabrication facilities as it contains realistic fabrication parameters. Hence, the proposed sensor can potentially be used as a chemical sensor especially in the medical, food, and industrial sectors as the five chemicals mentioned above carry great medical and food significance.
Collapse
|
8
|
Feng CH, Otani C. Terahertz spectroscopy technology as an innovative technique for food: Current state-of-the-Art research advances. Crit Rev Food Sci Nutr 2020; 61:2523-2543. [PMID: 32584169 DOI: 10.1080/10408398.2020.1779649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
With the dramatic development of source and detector components, terahertz (THz) spectroscopy technology has recently shown a renaissance in various fields such as medical, material, biosensing and pharmaceutical industry. As a rapid and noninvasive technology, it has been extensively exploited to evaluate food quality and ensure food safety. In this review, the principles and processes of THz spectroscopy are first discussed. The current state-of-the-art applications of THz and imaging technologies focused on foodstuffs are then discussed. The advantages and challenges are also covered. This review offers detailed information for recent efforts dedicated to THz for monitoring the quality and safety of various food commodities and the feasibility of its widespread application. THz technology, as an emerging and unique method, is potentially applied for detecting food processing and maintaining quality and safety.
Collapse
Affiliation(s)
- Chao-Hui Feng
- RIKEN Centre for Advanced Photonics, RIKEN, Sendai, Japan
| | - Chiko Otani
- RIKEN Centre for Advanced Photonics, RIKEN, Sendai, Japan.,Department of Physics, Tohoku University, Sendai, Miyagi, Japan
| |
Collapse
|
9
|
Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
Collapse
Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | | |
Collapse
|
10
|
Observation of high-temperature macromolecular confinement in lyophilised protein formulations using terahertz spectroscopy. INTERNATIONAL JOURNAL OF PHARMACEUTICS-X 2019; 1:100022. [PMID: 31517287 PMCID: PMC6733290 DOI: 10.1016/j.ijpx.2019.100022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Structural dynamics in lyophilised protein formulations can be probed with terahertz spectroscopy and two glass transition processes, Tg,α and Tg,β, are observed. Vibrational confinement upon thermal activation is observed resulting in no detectable changes in secondary structure but strongly reduced the molecular mobility at temperatures above Tg,α. The confinement was found to be strongly dependent on the formulation. We hypothesise that confinement is linked to conformational states with potential effects on physical and chemical stability of the biomolecule during storage.
Characterising the structural dynamics of proteins and the effects of excipients are critical for optimising the design of formulations. In this work we investigated four lyophilised formulations containing bovine serum albumin (BSA) and three formulations containing a monoclonal antibody (mAb, here mAb1), and explored the role of the excipients polysorbate 80, sucrose, trehalose, and arginine on stabilising proteins. By performing temperature variable terahertz time-domain spectroscopy (THz-TDS) experiments it is possible to study the vibrational dynamics of these formulations. The THz-TDS measurements reveal two distinct glass transition processes in all tested formulations. The lower temperature transition, Tg,β, is associated with the onset of local motion due to the secondary relaxation whilst the higher temperature transition, Tg,α, marks the onset of the α-relaxation. For some of the formulations, containing globular BSA as well as mAb1, the absorption at terahertz frequencies does not increase further at temperatures above Tg,α. Such behaviour is in contrast to our previous observations for small organic molecules as well as linear polymers where absorption is always observed to steadily increase with temperature due to the stronger absorption of terahertz radiation by more mobile dipoles. The absence of such further increase in absorption with higher temperatures therefore suggests a localised confinement of the protein/excipient matrix at high temperatures that hinders any further increase in mobility. We found that subtle changes in excipient composition had an effect on the transition temperatures Tg,α and Tg,β as well as the vibrational confinement in the solid state. Further work is required to establish the potential significance of the vibrational confinement in the solid state on formulation stability and chemical degradation as well as what role the excipients play in achieving such confinement.
Collapse
|
11
|
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.
Collapse
|
12
|
Tavagnacco L, Chiessi E, Zanatta M, Orecchini A, Zaccarelli E. Water-Polymer Coupling Induces a Dynamical Transition in Microgels. J Phys Chem Lett 2019; 10:870-876. [PMID: 30735054 PMCID: PMC6416711 DOI: 10.1021/acs.jpclett.9b00190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
Collapse
Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| | - Ester Chiessi
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientica I, 00133 Rome, Italy
| | - Marco Zanatta
- Department
of Computer Science, University of Verona, Strada Le Grazie 15, 37138 Verona, Italy
| | - Andrea Orecchini
- Department
of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM
c/o Department of Physics and Geology, University
of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Cherepanov DA, Milanovsky GE, Gopta OA, Balasubramanian R, Bryant DA, Semenov AY, Golbeck JH. Electron–Phonon Coupling in Cyanobacterial Photosystem I. J Phys Chem B 2018; 122:7943-7955. [DOI: 10.1021/acs.jpcb.8b03906] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitry A. Cherepanov
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 117977 Moscow, Russia
| | - Georgy E. Milanovsky
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
| | - Oksana A. Gopta
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Ramakrishnan Balasubramanian
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
- Department of Chemistry and Biochemistry, Montana State University, 103 Chemistry and Biochemistry Building, PO Box 173400, Bozeman, Montana 59717, United States
| | - Alexey Yu. Semenov
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 117977 Moscow, Russia
| | - John H. Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Camisasca G, De Marzio M, Corradini D, Gallo P. Two structural relaxations in protein hydration water and their dynamic crossovers. J Chem Phys 2016; 145:044503. [DOI: 10.1063/1.4959286] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
|
20
|
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]
|
21
|
Sushko O, Dubrovka R, Donnan RS. Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected. J Chem Phys 2015; 142:055101. [DOI: 10.1063/1.4907271] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
|
22
|
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.
Collapse
Affiliation(s)
- Edward P J Parrott
- Chinese University of Hong Kong, Department of Electronic Engineering, Shatin, New Territories, Hong Kong Sar, China
| | | |
Collapse
|
23
|
Yudasari N, Anthony J, Leonhardt R. Terahertz pulse propagation in 3D-printed waveguide with metal wires component. OPTICS EXPRESS 2014; 22:26042-26054. [PMID: 25401638 DOI: 10.1364/oe.22.026042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report on the characterization of 3D-printed hollow core Terahertz waveguides with metal wire inclusions over a frequency range of 0.2-1.0 THz using standard THz time-domain spectroscopy. We observe single-mode broadband THz propagation in these waveguides, and measure the loss coefficient and the mode effective phase index. Our measurement data agree well with predicted values obtained from numerical simulations.
Collapse
|
24
|
Woods KN. The glassy state of crambin and the THz time scale protein-solvent fluctuations possibly related to protein function. BMC BIOPHYSICS 2014; 7:8. [PMID: 25184036 PMCID: PMC4143578 DOI: 10.1186/s13628-014-0008-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND THz experiments have been used to characterize the picosecond time scale fluctuations taking place in the model, globular protein crambin. RESULTS Using both hydration and temperature as an experimental parameter, we have identified collective fluctuations (<= 200 cm(-1)) in the protein. Observation of the protein dynamics in the THz spectrum from both below and above the glass transition temperature (Tg) has provided unique insight into the microscopic interactions and modes that permit the solvent to effectively couple to the protein thermal fluctuations. CONCLUSIONS Our findings suggest that the solvent dynamics on the picosecond time scale not only contribute to protein flexibility but may also delineate the types of fluctuations that are able to form within the protein structure.
Collapse
Affiliation(s)
- Kristina N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh 15213, PA, USA
| |
Collapse
|
25
|
Woods KN. Using THz time-scale infrared spectroscopy to examine the role of collective, thermal fluctuations in the formation of myoglobin allosteric communication pathways and ligand specificity. SOFT MATTER 2014; 10:4387-4402. [PMID: 24801988 DOI: 10.1039/c3sm53229a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this investigation we use THz time-scale spectroscopy to conduct an initial set of studies on myoglobin with the aim of providing further insight into the global, collective thermal fluctuations in the protein that have been hypothesized to play a prominent role in the dynamic formation of transient ligand channels as well as in shaping the molecular level basis for ligand discrimination. Using the two ligands O2 and CO, we have determined that the perturbation from the heme-ligand complex has a strong influence on the characteristics of the myoglobin collective dynamics that are excited upon binding. Further, the differences detected in the collective protein motions in Mb-O2 compared with those in Mb-CO appear to be intimately tied with the pathways of long-range allosteric communication in the protein, which ultimately determine the trajectories selected by the respective ligands on the path to and from the heme-binding cavity.
Collapse
Affiliation(s)
- K N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| |
Collapse
|
26
|
Lipps F, Levy S, Markelz AG. Hydration and temperature interdependence of protein picosecond dynamics. Phys Chem Chem Phys 2012; 14:6375-81. [DOI: 10.1039/c2cp23760a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
27
|
Ding T, Li R, Zeitler JA, Huber TL, Gladden LF, Middelberg APJ, Falconer RJ. Terahertz and far infrared spectroscopy of alanine-rich peptides having variable ellipticity. OPTICS EXPRESS 2010; 18:27431-44. [PMID: 21197019 DOI: 10.1364/oe.18.027431] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Terahertz spectra of four alanine-rich peptides with known secondary structures were studied by terahertz time domain spectroscopy (THz-TDS) and by Fourier transform infrared spectroscopy (FTIR) using a synchrotron light source and a liquid-helium cooled bolometer. At ambient temperatures the usable bandwidth was restricted to 0.2-1.5 THz by the absorbance of water. The existence of a solvation shell around the peptide in solution was observed and its size estimated to be between 11 and 17 Å. By cooling the peptide solution to 80 K in order to reduce the water absorbance the bandwidth was increased to 0.1-3.0 THz for both THz-TDS and FTIR. Spectra were consistent with monotonic absorbance of the peptide and the existence of a solid amorphous low density solvation shell.
Collapse
Affiliation(s)
- Tao Ding
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | | | | | | | | | | | | |
Collapse
|
28
|
Wang C, Gong J, Xing Q, Li Y, Liu F, Zhao X, Chai L, Wang C, Zheltikov AM. Application of terahertz time-domain spectroscopy in intracellular metabolite detection. JOURNAL OF BIOPHOTONICS 2010; 3:641-645. [PMID: 20533431 DOI: 10.1002/jbio.201000043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Using terahertz time-domain spectroscopy (THz-TDS), we have investigated the THz spectra of astaxanthin and riboflavin and the spectra of two kinds of cell, haenatcoccus plusivalis and bacillus subtilis, which could produce astaxanthin and riboflavin, respectively, during their metabolite process. Riboflavin was found to be much more absorptive to THz radiation and have richer spectral characteristics than astaxanthin. As an intracellular metabolite, riboflavin could be distinguished from the cells by using THz-TDS. The technique has potential applications in high-throughput screening of industrial strains.
Collapse
Affiliation(s)
- Changlei Wang
- Centre for THz Waves, Ultrafast Laser Laboratory, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, P.R. China.
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Servantie J, Atilgan C, Atilgan AR. Depth dependent dynamics in the hydration shell of a protein. J Chem Phys 2010; 133:085101. [DOI: 10.1063/1.3481089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
|
31
|
Walther M, Fischer BM, Ortner A, Bitzer A, Thoman A, Helm H. Chemical sensing and imaging with pulsed terahertz radiation. Anal Bioanal Chem 2010; 397:1009-17. [DOI: 10.1007/s00216-010-3672-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 03/18/2010] [Accepted: 03/21/2010] [Indexed: 10/19/2022]
|
32
|
Kawaguchi S, Kambara O, Shibata M, Kandori H, Tominaga K. Low-frequency dynamics of bacteriorhodopsin studied by terahertz time-domain spectroscopy. Phys Chem Chem Phys 2010; 12:10255-62. [DOI: 10.1039/b927397b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
33
|
Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics. Biophys J 2009; 97:2080-8. [PMID: 19804740 DOI: 10.1016/j.bpj.2009.07.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 06/16/2009] [Accepted: 07/23/2009] [Indexed: 11/21/2022] Open
Abstract
We elucidate the physics of protein dynamical transition via 10-100-ns molecular dynamics simulations at temperatures spanning 160-300 K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a crossover from nonstationary to stationary processes that underlie the dynamics of protein motions. A two-timescale function captures the nonexponential character of backbone structural relaxations. One timescale is attributed to the collective segmental motions and the other to local relaxations. The former is well defined by a single-exponential, nanosecond decay, operative at all temperatures. The latter is described by a set of processes that display a distribution of timescales. Although their average remains on the picosecond timescale, the distribution is markedly contracted at the onset of the transition. It is shown that the collective motions impose bounds on timescales spanned by local dynamical processes. The nonstationary character below the transition implicates the presence of a collection of substates whose interactions are restricted. At these temperatures, a wide distribution of local-motion timescales, extending beyond that of nanoseconds, is observed. At physiological temperatures, local motions are confined to timescales faster than nanoseconds. This relatively narrow window makes possible the appearance of multiple channels for the backbone dynamics to operate.
Collapse
|
34
|
Dutta P, Tominaga K. Dependence of low frequency spectra on solute and solvent in solutions studied by terahertz time-domain spectroscopy. Mol Phys 2009. [DOI: 10.1080/00268970902744334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
35
|
Png GM, Falconer RJ, Fischer BM, Zakaria HA, Mickan SP, Middelberg APJ, Abbott D. Terahertz spectroscopic differentiation of microstructures in protein gels. OPTICS EXPRESS 2009; 17:13102-15. [PMID: 19654715 DOI: 10.1364/oe.17.013102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We demonstrate that terahertz (THz) spectroscopy can be used to differentiate soft protein microstructures. Differentiation of soft microstructures in gels has to date been performed using optical imaging techniques (e.g. electron microscope), but a non-destructive differentiation tool is lacking. Particulate and fine-stranded (fibrillar) soft protein microstructures are of interest, particularly to medical researchers, because they form from naturally occurring proteins that are thought to be involved in several human diseases, such as Alzheimer's disease. In this study, globular beta-lactoglobulin structures with diameters of 2 microm, and fibrillar structures with diameters less than 0.03 microm are observed between 0.8 and 1.5 THz. Results show that the globular structures have a decline in THz transmission when compared to the fibrillar ones. The cause of this decline is possibly due to Rayleigh scattering from the globular microstructures.
Collapse
Affiliation(s)
- Gretel M Png
- Centre for Biomedical Engineering, School of Electrical and Electronic Engineering, University of Adelaide, Adelaide, SA 5005, Australia.
| | | | | | | | | | | | | |
Collapse
|
36
|
Cooksey CC, Greer BJ, Heilweil EJ. Terahertz spectroscopy of l-proline in reverse aqueous micelles. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.11.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
37
|
Leu BM, Zhang Y, Bu L, Straub JE, Zhao J, Sturhahn W, Alp EE, Sage JT. Resilience of the iron environment in heme proteins. Biophys J 2008; 95:5874-89. [PMID: 18835904 PMCID: PMC2599821 DOI: 10.1529/biophysj.108.138198] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 07/22/2008] [Indexed: 11/18/2022] Open
Abstract
Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.
Collapse
Affiliation(s)
- Bogdan M Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Leitner DM, Gruebele M, Havenith M. Solvation dynamics of biomolecules: modeling and terahertz experiments. HFSP JOURNAL 2008; 2:314-23. [PMID: 19436490 PMCID: PMC2645579 DOI: 10.2976/1.2976661] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 06/22/2008] [Indexed: 11/19/2022]
Abstract
The role of water in biomolecule dynamics has attracted much interest over the past decade, due in part to new probes of biomolecule-water interactions and developments in molecular simulations. Terahertz (THz) spectroscopy, among the most recent experimental methods brought to bear on this problem, is able to detect even small solute induced changes of the collective water network dynamics at the biomolecule-water interface. THz measurements reveal that proteins influence up to 1000 water molecules in their surroundings, and that even small saccharides influence the dynamics of hundreds of surrounding water molecules. The THz spectrum of a protein is sensitive to mutation and depends on the surface charge and flexibility of the protein. Influence on the solvation shell appears most pronounced for native wildtype proteins and decreases upon partial unfolding or mutation. THz spectra of solvated saccharides reveal that the number of water molecules coupled dynamically to a saccharide, forming a dynamical hydration shell around it, is related to the number of exposed oxygen atoms on the solute. The thickness of this layer appears correlated with the bioprotection efficiency of the saccharide. All findings support the thesis of a long-range dynamic coupling between biomolecule and solvent.
Collapse
Affiliation(s)
- David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Martin Gruebele
- Department of Chemistry, Department of Physics and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum, Germany
| |
Collapse
|
39
|
Zhang H, Zukowski E, Balu R, Gregurick SK. A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis. J Mol Graph Model 2008; 27:655-63. [PMID: 19095477 DOI: 10.1016/j.jmgm.2008.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 10/21/2008] [Accepted: 10/22/2008] [Indexed: 11/27/2022]
Abstract
We studied the terahertz (THz) spectroscopy and low frequency normal modes of both apo- and holo- (adenosine monophosphate (AMP)-bound) ricin-A-chain (RTA) as a means to understand the dynamical changes that RTA undergoes upon substrate binding. The calculated THz spectra of apo- and holo-RTAs demonstrated a general intensity suppression upon substrate binding, which is attributed to the reduced number of collective motion in THz region. In normal mode analysis of RTA we find a shearing motion that is shared by both the apo- and holo-RTAs, whereas a breathing motion, and an upward hinge rising and an alpha-G bending characteristic motion are dampened significantly upon AMP binding, suggesting these motions are involved in the necessary flexibility of the active site. In contrast, we find a normal mode motion that separates domains I and II of RTA at the interface that is more common in the holo-protein. We hypothesized that the flexibility of the entrance of RTA can facilitate the entry of rRNA and allow the substrate to adjust its conformation and orientation prior to depurination. This process suggests an rRNA binding pathway which is supplemental the current RTA depurination mechanism.
Collapse
Affiliation(s)
- Hailiang Zhang
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 100 Hilltop Circle, Baltimore, MD 21250, USA
| | | | | | | |
Collapse
|
40
|
He Y, Ku PI, Knab JR, Chen JY, Markelz AG. Protein dynamical transition does not require protein structure. PHYSICAL REVIEW LETTERS 2008; 101:178103. [PMID: 18999790 DOI: 10.1103/physrevlett.101.178103] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Indexed: 05/14/2023]
Abstract
Terahertz time domain spectroscopy shows that the protein dynamical transition, the rapid increase in protein dynamics occurring at approximately 200 K, needs neither tertiary nor secondary structure. Further, short chain alanine studies find a dynamical transition down to penta-alanine, with no transition observed for di-alanine or tri-alanine. These results reveal the temperature dependence arises strictly from the side-chain interaction with the solvent. The lack of a transition for shorter chain peptides may indicate a qualitative change in this interaction occurs at a specific peptide chain length.
Collapse
Affiliation(s)
- Yunfen He
- Physics Department, University at Buffalo, Buffalo, NY 14260, USA
| | | | | | | | | |
Collapse
|
41
|
LeBard DN, Kapko V, Matyushov DV. Energetics and kinetics of primary charge separation in bacterial photosynthesis. J Phys Chem B 2008; 112:10322-42. [PMID: 18636767 DOI: 10.1021/jp8016503] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report the results of molecular dynamics (MD) simulations and formal modeling of the free-energy surfaces and reaction rates of primary charge separation in the reaction center of Rhodobacter sphaeroides. Two simulation protocols were used to produce MD trajectories. Standard force-field potentials were employed in the first protocol. In the second protocol, the special pair was made polarizable to reproduce a high polarizability of its photoexcited state observed by Stark spectroscopy. The charge distribution between covalent and charge-transfer states of the special pair was dynamically adjusted during the simulation run. We found from both protocols that the breadth of electrostatic fluctuations of the protein/water environment far exceeds previous estimates, resulting in about 1.6 eV reorganization energy of electron transfer in the first protocol and 2.5 eV in the second protocol. Most of these electrostatic fluctuations become dynamically frozen on the time scale of primary charge separation, resulting in much smaller solvation contributions to the activation barrier. While water dominates solvation thermodynamics on long observation times, protein emerges as the major thermal bath coupled to electron transfer on the picosecond time of the reaction. Marcus parabolas were obtained for the free-energy surfaces of electron transfer by using the first protocol, while a highly asymmetric surface was obtained in the second protocol. A nonergodic formulation of the diffusion-reaction electron-transfer kinetics has allowed us to reproduce the experimental results for both the temperature dependence of the rate and the nonexponential decay of the population of the photoexcited special pair.
Collapse
Affiliation(s)
- David N LeBard
- Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | | |
Collapse
|
42
|
LeBard DN, Matyushov DV. Glassy Protein Dynamics and Gigantic Solvent Reorganization Energy of Plastocyanin. J Phys Chem B 2008; 112:5218-27. [DOI: 10.1021/jp709586e] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David N. LeBard
- Center for Biological Physics, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604
| | - Dmitry V. Matyushov
- Center for Biological Physics, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604
| |
Collapse
|
43
|
Protein Dynamics - I. Biophys J 2008. [DOI: 10.1016/s0006-3495(08)79003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|