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Life
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Biomolecular Dynamics Explored by Incoherent Neutron Spectroscopy
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Biomolecular Dynamics Explored by Incoherent Neutron Spectroscopy

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".

Deadline for manuscript submissions: closed (15 March 2023) | Viewed by 8728

Special Issue Editors

Dr. Tatsuhito Matsuo

E-Mail Website
Guest Editor
1. Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai 319-1106, Ibaraki, Japan
2. Department of Physics, Universaty of Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
3. Institut Laue-Langevin, 71 Avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
Interests: biophysics; biochemistry; protein structure; protein dynamics; small-angle X-ray scattering; small-angle neutron scattering; quasielastic neutron scattering
Prof. Dr. Judith Peters

E-Mail Website
Guest Editor
Univ. Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique (LiPhy) France and Institut Laue Langevin, 38402 Saint-Martin-d'Hères, France
Interests: biophysics; molecular dynamics; extreme conditions; origin of life; high pressure; neutron scattering

Special Issue Information

Dear Colleagues,

In living organisms, including us humans, a diverse range of biomolecules express specific biological functions to maintain life. Malfunction of some biomolecules can cause various types of diseases. In either case, biological functions are closely related to conformational changes and intramolecular motional changes within biomolecules.

As detailed atomic structures have been solved by powerful techniques such as X-ray/neutron diffraction, cryo-electron microscopy, and nuclear magnetic resonance, deeper knowledge of their dynamical pictures is needed. In terms of the dynamics of biomolecules, there is a temporal and spatial hierarchy ranging from atomic vibrations at femto-second timescale to large-scale motions such as domain motions of proteins, flip-flop motions of lipids in biomembranes, and bending motions of nucleic acids. Among this hierarchy, atomic motions occurring at pico- and nano-second timescales at an Ångstrom length scale are considered to be the “driving force” for larger conformational changes that take place at a much slower timescale. These motions correspond to side-chain fluctuations and segmental motions. The only way to directly measure these kinds of motions is incoherent neutron scattering (iNS). iNS has widely been used to study the dynamics of proteins, lipids, and nucleic acids to elucidate the role of molecular dynamics in their biological functions, sometimes combined with molecular dynamics (MD) simulation, which gives complementary information to iNS. This Special Issue of Life aims to provide a forum to discuss how the molecular dynamics resolved by iNS is related to biological functions or malfunctions, e.g., various diseases. Original research papers and review articles dealing with dynamical properties of biomolecules by iNS or those by iNS combined with relevant experimental/theoretical techniques are welcome.

We, Guest Editors, cordially invite researchers working in this field to contribute to this Special Issue of Life.

Dr. Tatsuhito Matsuo
Prof. Dr. Judith Peters
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular dynamics
  • incoherent neutron scattering
  • biology
  • protein, lipid, DNA, cells
  • dynamics–function relationship
  • phenomenological model of biomolecules
  • modeling and simulations

Published Papers (5 papers)

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Research

Jump to: Review

9 pages, 3787 KiB  
Article
Data Collection for Dilute Protein Solutions via a Neutron Backscattering Spectrometer
by Taiki Tominaga, Hiroshi Nakagawa, Masae Sahara, Takashi Oda, Rintaro Inoue and Masaaki Sugiyama
Life 2022, 12(5), 675; https://doi.org/10.3390/life12050675 - 02 May 2022
Cited by 1 | Viewed by 1583
Abstract
Understanding protein functions requires not only static but also dynamic structural information. Incoherent quasi-elastic neutron scattering (QENS), which utilizes the highly incoherent scattering ability of hydrogen, is a powerful technique for revealing the dynamics of proteins in deuterium oxide (D2O) buffer [...] Read more.
Understanding protein functions requires not only static but also dynamic structural information. Incoherent quasi-elastic neutron scattering (QENS), which utilizes the highly incoherent scattering ability of hydrogen, is a powerful technique for revealing the dynamics of proteins in deuterium oxide (D2O) buffer solutions. The background scattering of sample cells suitable for aqueous protein solution samples, conducted with a neutron backscattering spectrometer, was evaluated. It was found that the scattering intensity of an aluminum sample cell coated with boehmite using D2O was lower than that of a sample cell coated with regular water (H2O). The D2O-Boehmite coated cell was used for the QENS measurement of a 0.8 wt.% aqueous solution of an intrinsically disordered protein in an intrinsically disordered region of a helicase-associated endonuclease for a fork-structured type of DNA. The cell was inert against aqueous samples at 283–363 K. In addition, meticulous attention to cells with small individual weight differences and the positional reproducibility of the sample cell relative to the spectrometer neutron beam position enabled the accurate subtraction of the scattering profiles of the D2O buffer and the sample container. Consequently, high-quality information on protein dynamics could be extracted from dilute protein solutions. Full article
(This article belongs to the Special Issue Biomolecular Dynamics Explored by Incoherent Neutron Spectroscopy)
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17 pages, 8142 KiB  
Article
Alkanes as Membrane Regulators of the Response of Early Membranes to Extreme Temperatures
by Loreto Misuraca, Antonino Caliò, Josephine G. LoRicco, Ingo Hoffmann, Roland Winter, Bruno Demé, Judith Peters and Philippe M. Oger
Life 2022, 12(3), 445; https://doi.org/10.3390/life12030445 - 17 Mar 2022
Cited by 6 | Viewed by 1956
Abstract
One of the first steps in the origin of life was the formation of a membrane, a physical boundary that allowed the retention of molecules in concentrated solutions. The proto-membrane was likely formed by self-assembly of simple readily available amphiphiles, such as short-chain [...] Read more.
One of the first steps in the origin of life was the formation of a membrane, a physical boundary that allowed the retention of molecules in concentrated solutions. The proto-membrane was likely formed by self-assembly of simple readily available amphiphiles, such as short-chain fatty acids and alcohols. In the commonly accepted scenario that life originated near hydrothermal systems, how these very simple membrane bilayers could be stable enough in time remains a debated issue. We used various complementary techniques such as dynamic light scattering, small angle neutron scattering, neutron spin-echo spectroscopy, and Fourier-transform infrared spectroscopy to explore the stability of a novel protomembrane system in which the insertion of alkanes in the midplane is proposed to shift membrane stability to higher temperatures, pH, and hydrostatic pressures. We show that, in absence of alkanes, protomembranes transition into lipid droplets when temperature increases; while in presence of alkanes, membranes persist for longer times in a concentration-dependent manner. Proto-membranes containing alkanes are stable at higher temperatures and for longer times, have a higher bending rigidity, and can revert more easily to their initial state upon temperature variations. Hence, the presence of membrane intercalating alkanes could explain how the first membranes could resist the harsh and changing environment of the hydrothermal systems. Furthermore, modulating the quantity of alkanes in the first membranes appears as a possible strategy to adapt the proto-membrane behavior according to temperature fluctuations, and it offers a first glimpse into the evolution of the first membranes. Full article
(This article belongs to the Special Issue Biomolecular Dynamics Explored by Incoherent Neutron Spectroscopy)
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Review

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15 pages, 1337 KiB  
Review
Incoherent Neutron Scattering and Terahertz Time-Domain Spectroscopy on Protein and Hydration Water
by Hiroshi Nakagawa and Naoki Yamamoto
Life 2023, 13(2), 318; https://doi.org/10.3390/life13020318 - 23 Jan 2023
Cited by 2 | Viewed by 1387
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), [...] Read more.
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. Full article
(This article belongs to the Special Issue Biomolecular Dynamics Explored by Incoherent Neutron Spectroscopy)
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21 pages, 4379 KiB  
Review
Sub-Nanosecond Dynamics of Pathologically Relevant Bio-Macromolecules Observed by Incoherent Neutron Scattering
by Tatsuhito Matsuo and Judith Peters
Life 2022, 12(8), 1259; https://doi.org/10.3390/life12081259 - 17 Aug 2022
Cited by 3 | Viewed by 1365
Abstract
Incoherent neutron scattering (iNS) is one of the most powerful techniques to study the dynamical behavior of bio-macromolecules such as proteins and lipid molecules or whole cells. This technique has widely been used to elucidate the fundamental aspects of molecular motions that manifest [...] Read more.
Incoherent neutron scattering (iNS) is one of the most powerful techniques to study the dynamical behavior of bio-macromolecules such as proteins and lipid molecules or whole cells. This technique has widely been used to elucidate the fundamental aspects of molecular motions that manifest in the bio-macromolecules in relation to their intrinsic molecular properties and biological functions. Furthermore, in the last decade, iNS studies focusing on a possible relationship between molecular dynamics and biological malfunctions, i.e., human diseases and disorders, have gained importance. In this review, we summarize recent iNS studies on pathologically relevant proteins and lipids and discuss how the findings are of importance to elucidate the molecular mechanisms of human diseases and disorders that each study targets. Since some diseases such as amyloidosis have become more relevant in the aging society, research in this field will continue to develop further and be more important in the current increasing trend for longevity worldwide. Full article
(This article belongs to the Special Issue Biomolecular Dynamics Explored by Incoherent Neutron Spectroscopy)
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13 pages, 1226 KiB  
Review
Exploring the Limits of Biological Complexity Amenable to Studies by Incoherent Neutron Spectroscopy
by Eugene Mamontov
Life 2022, 12(8), 1219; https://doi.org/10.3390/life12081219 - 11 Aug 2022
Viewed by 1446
Abstract
The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been [...] Read more.
The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms. Full article
(This article belongs to the Special Issue Biomolecular Dynamics Explored by Incoherent Neutron Spectroscopy)
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