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Conti Nibali V, Sacchetti F, Paciaroni A, Petrillo C, Tarek M, D'Angelo G. Intra-protein interacting collective modes in the terahertz frequency region. J Chem Phys 2023; 159:161101. [PMID: 37870134 DOI: 10.1063/5.0142381] [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: 01/13/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Understanding how proteins work requires a thorough understanding of their internal dynamics. Proteins support a wide range of motions, from the femtoseconds to seconds time scale, relevant to crucial biological functions. In this context, the term "protein collective dynamics" refers to the complex patterns of coordinated motions of numerous atoms throughout the protein in the sub-picosecond time scale (terahertz frequency region). It is hypothesized that these dynamics have a substantial impact on the regulation of functional dynamical mechanisms, including ligand binding and allosteric signalling, charge transport direction, and the regulation of thermodynamic and thermal transport properties. Using the theoretical framework of hydrodynamics, the collective dynamics of proteins had previously been described in a manner akin to that of simple liquids, i.e. in terms of a single acoustic-like excitation, related to intra-protein vibrational motions. Here, we employ an interacting-mode model to analyse the results from molecular dynamics simulations and we unveil that the vibrational landscape of proteins is populated by multiple acoustic-like and low-frequency optic-like modes, with mixed symmetry and interfering with each other. We propose an interpretation at the molecular level of the observed scenario that we relate to the side-chains and the hydrogen-bonded networks dynamics. The present insights provide a perspective for understanding the molecular mechanisms underlying the energy redistribution processes in the interior of proteins.
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Affiliation(s)
- Valeria Conti Nibali
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, Messina University, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Mounir Tarek
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Giovanna D'Angelo
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, Messina University, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
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2
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Yoshida K, Uchiyama H, Yamaguchi T. Structure and dynamical properties of hydrated F-actin investigated by X-ray scattering. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Shrestha UR, Bhowmik D, Van Delinder KW, Mamontov E, O’Neill H, Zhang Q, Alatas A, Chu XQ. Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity. J Phys Chem B 2017; 121:923-930. [DOI: 10.1021/acs.jpcb.6b10245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Utsab R. Shrestha
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
| | - Debsindhu Bhowmik
- Computational
Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Kurt W. Van Delinder
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Hugh O’Neill
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Qiu Zhang
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Ahmet Alatas
- Advanced
Photon Source, Argonne National laboratory, Argonne, IL 60439, United States
| | - Xiang-Qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
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4
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Yoshida K, Tashiro A, Yamaguchi T. Thermal properties and hydration structure of poly-l-lysine, polyglycine, and lysozyme. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.08.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Yoshida K, Baron AQR, Uchiyama H, Tsutsui S, Yamaguchi T. Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering. J Chem Phys 2016; 144:134505. [PMID: 27059578 DOI: 10.1063/1.4944987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.
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Affiliation(s)
- Koji Yoshida
- Department of Chemistry, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Alfred Q R Baron
- Materials Dynamics Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroshi Uchiyama
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Satoshi Tsutsui
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Toshio Yamaguchi
- Department of Chemistry, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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6
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Longo M, Marconi M, Orecchini A, Petrillo C, Monaco G, Calvitti M, Pirisinu I, Romani R, Sacchetti F, Sebastiani F, Zanatta M, Paciaroni A. Terahertz Dynamics in Human Cells and Their Chromatin. J Phys Chem Lett 2014; 5:2177-2181. [PMID: 26279530 DOI: 10.1021/jz500918w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The terahertz dynamics of human cells of the U937 line and their chromatin has been investigated by high-resolution inelastic X-ray scattering. To highlight its dynamical features in situ, nuclear DNA has been stained by uranyl-acetate salt. The general behavior of the collective dynamics of the whole cell is quite similar to that of bulk water, with a nearly wavevector-independent branch located at about 5 meV and a propagating mode with a linear trend corresponding to a speed of sound of 2900 ± 100 m/s. We provide the first experimental evidence for the existence of two branches also in the dispersion curves of chromatin. The high-energy mode displays an acoustic-like behavior with a sound velocity similar to unstained cells, but in this case the branch likely originates from the superposition of intramolecular DNA optic modes. A low-energy optic-like branch, distinctive of the chromatin moiety, is found at about 2.5 meV.
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Affiliation(s)
- M Longo
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ‡Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - M Marconi
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - A Orecchini
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - C Petrillo
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - G Monaco
- §Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, I-38123 Povo, Trento, Italy
| | - M Calvitti
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - I Pirisinu
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - R Romani
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - F Sacchetti
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ⊥CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - F Sebastiani
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ⊥CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - M Zanatta
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - A Paciaroni
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
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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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8
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Conti Nibali V, D'Angelo G, Paciaroni A, Tobias DJ, Tarek M. On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water. J Phys Chem Lett 2014; 5:1181-1186. [PMID: 26274468 DOI: 10.1021/jz500023e] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Picosecond time scale dynamics of hydrated proteins has been connected with the onset of biological activity as it coincides with solvent-solute hydrogen bond rearrangements and amino acid rotational relaxation time scales. The presence and fluctuations of protein hydration water (PHW) largely influence protein motions that are believed to be slaved to those of the solvent, yet to date, how protein and hydration water dynamics are coupled remains unclear. Here, we provide a significant advance in characterizing this coupling; we present the first full study of both the longitudinal and transverse coherent collective motions in a protein-solvent system. The data show unexpectedly the presence in the water dynamics of collective modes belonging to the protein. The properties of these modes, in particular, their propagation velocities and amplitudes, indicate a strengthening of the interactions and a higher rigidity of the network of solvent molecules close to the protein surface. Accordingly, the present study presents the most compelling and clear evidence of a very strong dynamical coupling between a protein and its hydration water, previously suggested by studies using various experimental techniques.
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Affiliation(s)
| | - Giovanna D'Angelo
- †Dipartimento di Fisica, Università degli Studi di Messina, Messina, Italy
| | | | - Douglas J Tobias
- ¶Department of Chemistry, University of California, Irvine, California 92697-2025 United States
| | - Mounir Tarek
- §CNRS, UMR Structure et Réactivité des Systèmes Moléculaires Complexes, University of Lorraine, Nancy, France
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9
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Sebastiani F, Orecchini A, Paciaroni A, Jasnin M, Zaccai G, Moulin M, Haertlein M, De Francesco A, Petrillo C, Sacchetti F. Collective THz dynamics in living Escherichia coli cells. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.06.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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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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11
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Paciaroni A, Orecchini A, Haertlein M, Moulin M, Conti Nibali V, De Francesco A, Petrillo C, Sacchetti F. Vibrational Collective Dynamics of Dry Proteins in the Terahertz Region. J Phys Chem B 2012; 116:3861-5. [DOI: 10.1021/jp211190q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandro Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
- Institut Laue Langevin, 6 rue J. Horowitz, F-38042 Grenoble, France
| | | | - Martine Moulin
- Institut Laue Langevin, 6 rue J. Horowitz, F-38042 Grenoble, France
| | - Valeria Conti Nibali
- Dipartimento di Fisica, Università degli Studi di Messina, via Salita Sperone, I-98166 Messina, Italy
| | - Alessio De Francesco
- CNR, Istituto Officina dei Materiali, Unità di Grenoble, Institut Laue Langevin, 6 rue J. Horowitz, F-38042 Grenoble, France
| | - Caterina Petrillo
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
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