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Special Issue "Molecular Dynamics from Macromolecule to Small Molecules"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 30 April 2022.

Special Issue Editor

Dr. Ki Hyun Nam
E-Mail
Guest Editor
Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
Interests: serial crystallography; applied crystallography; radiation damage; industrial enzyme; directed evolution; fluorescence
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Macromolecules and small molecules exhibit certain structural conformation in chemical, biological and physical reactions or specific environments. Observing the structural changes of these molecules has become an important research area for the deeper understanding of target molecules. To observe structural dynamics, various techniques such as spectroscopy, X-ray crystallography, electron microscopy, and computer-based molecular dynamics are applied. These techniques provide collection of several different static structural information to provide insights into the dynamics of a molecule, or structural information at certain time-delay through time-resolved studies. These observations of structural changes not only provide fundamental information to understand the molecular mechanisms, but also to provide insight into industrial and medical applications. 

This Special Issue covers comprehensive topics such as theory, technology development, and original research for molecular dynamics, and is intended to contribute to the molecular dynamics research community. I warmly welcome your contributions to this Special Issue on “Molecular dynamics from macromolecule to small molecules.”

Dr. Ki Hyun Nam
Guest Editor

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 papers will be 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • conformational change
  • structural change
  • collection of static structures
  • technique development
  • time-resolved spectroscopy
  • time-resolved crystallography
  • time-resolved cryo-electron microscopy

Published Papers (7 papers)

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Editorial

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Editorial
Molecular Dynamics—From Small Molecules to Macromolecules
Int. J. Mol. Sci. 2021, 22(7), 3761; https://doi.org/10.3390/ijms22073761 - 05 Apr 2021
Cited by 4 | Viewed by 789
Abstract
All molecular systems, from small molecules to macromolecules, exhibit specific characteristics for a specific environment and time. In order to gain an accurate understanding of the functions of all types of molecules, studies of their structure and dynamics are essential. Through dynamic studies, [...] Read more.
All molecular systems, from small molecules to macromolecules, exhibit specific characteristics for a specific environment and time. In order to gain an accurate understanding of the functions of all types of molecules, studies of their structure and dynamics are essential. Through dynamic studies, using techniques such as spectroscopy, structure determination, and computer analysis, it is possible to collect functional information on molecules at specific times and in specific environments. Such information not only reveals the properties and mechanisms of action of molecules but also provides insights that can be applied to various industries, such as the development of new materials and drugs. Herein, I discuss the importance of molecular dynamics studies, present the time scale of molecular motion, and review techniques for analyzing molecular dynamics. Full article
(This article belongs to the Special Issue Molecular Dynamics from Macromolecule to Small Molecules)
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Research

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Article
Anti-Kasha Behavior of 3-Hydroxyflavone and Its Derivatives
Int. J. Mol. Sci. 2021, 22(20), 11103; https://doi.org/10.3390/ijms222011103 - 14 Oct 2021
Viewed by 362
Abstract
Excited state intramolecular proton transfer (ESIPT) in 3-hydroxyflavone (3HF) has been known for its dependence on excitation wavelength. Such a behavior violates Kasha’s rule, which states that the emission and photochemistry of a compound would only take place from its lowest excited state. [...] Read more.
Excited state intramolecular proton transfer (ESIPT) in 3-hydroxyflavone (3HF) has been known for its dependence on excitation wavelength. Such a behavior violates Kasha’s rule, which states that the emission and photochemistry of a compound would only take place from its lowest excited state. The photochemistry of 3HF was studied using femtosecond transient absorption spectroscopy at a shorter wavelength excitation (266 nm), and these new experimental findings were interpreted with the aid of computational studies. These new results were compared with those from previous studies that were obtained with a longer wavelength excitation and show that there exists a pathway of proton transfer that bypasses the normal first excited state from the higher excited state to the tautomer from first excited state. The experimental data correlate with the electron density difference calculations such that the proton transfer process is faster on the longer excitation wavelength than compared to the shorter excitation wavelength. Full article
(This article belongs to the Special Issue Molecular Dynamics from Macromolecule to Small Molecules)
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Article
Structural Dynamics of C2F4I2 in Cyclohexane Studied via Time-Resolved X-ray Liquidography
Int. J. Mol. Sci. 2021, 22(18), 9793; https://doi.org/10.3390/ijms22189793 - 10 Sep 2021
Viewed by 621
Abstract
The halogen elimination of 1,2-diiodoethane (C2H4I2) and 1,2-diiodotetrafluoroethane (C2F4I2) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute–solvent interactions in solution-phase reactions. While the [...] Read more.
The halogen elimination of 1,2-diiodoethane (C2H4I2) and 1,2-diiodotetrafluoroethane (C2F4I2) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute–solvent interactions in solution-phase reactions. While the kinetics and reaction pathways of the halogen elimination reaction of C2H4I2 were reported to vary substantially depending on the solvent, the solvent effects on the photodissociation of C2F4I2 remain to be explored, as its reaction dynamics have only been studied in methanol. Here, to investigate the solvent dependence, we conducted a time-resolved X-ray liquidography (TRXL) experiment on C2F4I2 in cyclohexane. The data revealed that (ⅰ) the solvent dependence of the photoreaction of C2F4I2 is not as strong as that observed for C2H4I2, and (ⅱ) the nongeminate recombination leading to the formation of I2 is slower in cyclohexane than in methanol. We also show that the molecular structures of the relevant species determined from the structural analysis of TRXL data provide an excellent benchmark for DFT calculations, especially for investigating the relevance of exchange-correlation functionals used for the structural optimization of haloalkanes. This study demonstrates that TRXL is a powerful technique to study solvent dependence in the solution phase. Full article
(This article belongs to the Special Issue Molecular Dynamics from Macromolecule to Small Molecules)
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Article
Tunneling Quantum Dynamics in Ammonia
Int. J. Mol. Sci. 2021, 22(15), 8282; https://doi.org/10.3390/ijms22158282 - 31 Jul 2021
Viewed by 909
Abstract
Ammonia is a well-known example of a two-state system and must be described in quantum-mechanical terms. In this article, we will explain the tunneling phenomenon that occurs in ammonia molecules from the perspective of trajectory-based quantum dynamics, rather than the usual quantum probability [...] Read more.
Ammonia is a well-known example of a two-state system and must be described in quantum-mechanical terms. In this article, we will explain the tunneling phenomenon that occurs in ammonia molecules from the perspective of trajectory-based quantum dynamics, rather than the usual quantum probability perspective. The tunneling of the nitrogen atom through the potential barrier in ammonia is not merely a probability problem; there are underlying reasons and mechanisms explaining why and how the tunneling in ammonia can happen. Under the framework of quantum Hamilton mechanics, the tunneling motion of the nitrogen atom in ammonia can be described deterministically in terms of the quantum trajectories of the nitrogen atom and the quantum forces applied. The vibrations of the nitrogen atom about its two equilibrium positions are analyzed in terms of its quantum trajectories, which are solved from the Hamilton equations of motion. The vibration periods are then computed by the quantum trajectories and compared with the experimental measurements. Full article
(This article belongs to the Special Issue Molecular Dynamics from Macromolecule to Small Molecules)
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Article
Room-Temperature Structure of Xylitol-Bound Glucose Isomerase by Serial Crystallography: Xylitol Binding in the M1 Site Induces Release of Metal Bound in the M2 Site
Int. J. Mol. Sci. 2021, 22(8), 3892; https://doi.org/10.3390/ijms22083892 - 09 Apr 2021
Cited by 7 | Viewed by 600
Abstract
Glucose isomerase (GI) is an important enzyme that is widely used in industrial applications, such as in the production of high-fructose corn syrup or bioethanol. Studying inhibitor effects on GI is important to deciphering GI-specific molecular functions, as well as potential industrial applications. [...] Read more.
Glucose isomerase (GI) is an important enzyme that is widely used in industrial applications, such as in the production of high-fructose corn syrup or bioethanol. Studying inhibitor effects on GI is important to deciphering GI-specific molecular functions, as well as potential industrial applications. Analysis of the existing xylitol-bound GI structure revealed low metal occupancy at the M2 site; however, it remains unknown why this phenomenon occurs. This study reports the room-temperature structures of native and xylitol-bound GI from Streptomyces rubiginosus (SruGI) determined by serial millisecond crystallography. The M1 site of native SruGI exhibits distorted octahedral coordination; however, xylitol binding results in the M1 site exhibit geometrically stable octahedral coordination. This change results in the rearrangement of metal-binding residues for the M1 and M2 sites, the latter of which previously displayed distorted metal coordination, resulting in unstable coordination of Mg2+ at the M2 site and possibly explaining the inducement of low metal-binding affinity. These results enhance the understanding of the configuration of the xylitol-bound state of SruGI and provide insights into its future industrial application. Full article
(This article belongs to the Special Issue Molecular Dynamics from Macromolecule to Small Molecules)
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Article
Unfolding and Aggregation of Lysozyme under the Combined Action of Dithiothreitol and Guanidine Hydrochloride: Optical Studies
Int. J. Mol. Sci. 2021, 22(5), 2710; https://doi.org/10.3390/ijms22052710 - 08 Mar 2021
Cited by 3 | Viewed by 702
Abstract
Using a number of optical techniques (interferometry, dynamic light scattering, and spectroscopy), denaturation of hen egg white lysozyme (HEWL) by treatment with a combination of dithiothreitol (DTT) and guanidine hydrochloride (GdnHCl) has been investigated. The denaturing solutions were selected so that protein denaturation [...] Read more.
Using a number of optical techniques (interferometry, dynamic light scattering, and spectroscopy), denaturation of hen egg white lysozyme (HEWL) by treatment with a combination of dithiothreitol (DTT) and guanidine hydrochloride (GdnHCl) has been investigated. The denaturing solutions were selected so that protein denaturation occurred with aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM) or without aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM, GdnHCl 6 M) and can be evaluated after 60 min of treatment. It has been found that denatured by solution with 6 M GdnHCl lysozyme completely loses its enzymatic activity after 30 min and the size of the protein molecule increases by 1.5 times, from 3.8 nm to 5.7 nm. Denaturation without of GdnHCl led to aggregation with preserving about 50% of its enzymatic activity. Denaturation of HEWL was examined using interferometry. Previously, it has been shown that protein denaturation that occurs without subsequent aggregation leads to an increase in the refractive index (Δn ~ 4.5 × 10−5). This is most likely due to variations in the HEWL–solvent interface area. By applying modern optical techniques conjointly, it has been possible to obtain information on the nature of time-dependent changes that occur inside a protein and its hydration shell as it undergoes denaturation. Full article
(This article belongs to the Special Issue Molecular Dynamics from Macromolecule to Small Molecules)
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Article
Lard Injection Matrix for Serial Crystallography
Int. J. Mol. Sci. 2020, 21(17), 5977; https://doi.org/10.3390/ijms21175977 - 19 Aug 2020
Cited by 12 | Viewed by 1365
Abstract
Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation damage. Moreover, it allows for the study of structural dynamics of macromolecules using a time-resolved pump-probe, as well as mix-and-inject [...] Read more.
Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation damage. Moreover, it allows for the study of structural dynamics of macromolecules using a time-resolved pump-probe, as well as mix-and-inject experiments. Delivering a crystal sample using a viscous medium decreases sample consumption by lowering the flow rate while being extruded from the injector or syringe as compared to a liquid jet injector. Since the environment of crystal samples varies, continuous development of the delivery medium is important for extended SX applications. Herein, I report the preparation and characterization of a lard-based sample delivery medium for SX. This material was obtained using heat treatment, and then the soluble impurities were removed through phase separation. The lard injection medium was highly stable and could be injected via a syringe needle extruded at room temperature with a flow rate < 200 nL/min. Serial millisecond crystallography experiments were performed using lard, and the room temperature structures of lysozyme and glucose isomerase embedded in lard at 1.75 and 1.80 Å, respectively, were determined. The lard medium showed X-ray background scattering similar or relatively lower than shortenings and lipidic cubic phase; therefore, it can be used as sample delivery medium in SX experiments. Full article
(This article belongs to the Special Issue Molecular Dynamics from Macromolecule to Small Molecules)
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