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Structural Dynamics of Macromolecules

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: closed (25 April 2024) | Viewed by 5527

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Guest Editor
Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
Interests: serial crystallography; serial femtosecond crystallography; room temperature structure; X-ray crystallography; molecular dynamics; macromolecular crystallography
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Special Issue Information

Dear Colleagues,

Structural information on macromolecules provides useful information to understand molecular mechanisms at atomic resolutions for life systems. Unlike the understanding of molecular mechanisms based on static structural information in the past, it has recently become possible to observe the structural dynamics of macromolecules using serial crystallography (SX) or Cryo-EM techniques. The SX technique enables the determination of the room temperature structure with minimized radiation damage. In addition, SX with pump-probe or mix-and-inject experiments enables us to visualize the time-resolved molecular dynamics. The Cryo-EM technique enables the provision of the various conformations of target macromolecules. Moreover, recent computational studies provide highly accurate structural models and information for molecular dynamics. In this Special Issue, we collect research on the structural changes of macromolecules to gain a deeper understanding of the molecular mechanisms.

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 the “Structural dynamics of macromolecules”.

Dr. Ki Hyun Nam
Guest Editor

Manuscript Submission Information

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Keywords

  • Structural biology
  • Structural dynamics
  • Serial crystallography
  • X-ray crystallography
  • Cryo-EM time-resolved studies
  • Molecular dynamics

Published Papers (3 papers)

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Research

16 pages, 2872 KiB  
Article
Structural and Biochemical Analyses of the Butanol Dehydrogenase from Fusobacterium nucleatum
by Xue Bai, Jing Lan, Shanru He, Tingting Bu, Jie Zhang, Lulu Wang, Xiaoling Jin, Yuanchao Mao, Wanting Guan, Liying Zhang, Ming Lu, Hailong Piao, Inseong Jo, Chunshan Quan, Ki Hyun Nam and Yongbin Xu
Int. J. Mol. Sci. 2023, 24(3), 2994; https://doi.org/10.3390/ijms24032994 - 3 Feb 2023
Viewed by 1718
Abstract
Butanol dehydrogenase (BDH) plays a significant role in the biosynthesis of butanol in bacteria by catalyzing butanal conversion to butanol at the expense of the NAD(P)H cofactor. BDH is an attractive enzyme for industrial application in butanol production; however, its molecular function remains [...] Read more.
Butanol dehydrogenase (BDH) plays a significant role in the biosynthesis of butanol in bacteria by catalyzing butanal conversion to butanol at the expense of the NAD(P)H cofactor. BDH is an attractive enzyme for industrial application in butanol production; however, its molecular function remains largely uncharacterized. In this study, we found that Fusobacterium nucleatum YqdH (FnYqdH) converts aldehyde into alcohol by utilizing NAD(P)H, with broad substrate specificity toward aldehydes but not alcohols. An in vitro metal ion substitution experiment showed that FnYqdH has higher enzyme activity in the presence of Co2+. Crystal structures of FnYqdH, in its apo and complexed forms (with NAD and Co2+), were determined at 1.98 and 2.72 Å resolution, respectively. The crystal structure of apo- and cofactor-binding states of FnYqdH showed an open conformation between the nucleotide binding and catalytic domain. Key residues involved in the catalytic and cofactor-binding sites of FnYqdH were identified by mutagenesis and microscale thermophoresis assays. The structural conformation and preferred optimal metal ion of FnYqdH differed from that of TmBDH (homolog protein of FnYqdH). Overall, we proposed an alternative model for putative proton relay in FnYqdH, thereby providing better insight into the molecular function of BDH. Full article
(This article belongs to the Special Issue Structural Dynamics of Macromolecules)
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15 pages, 5798 KiB  
Article
Structural Basis of the Inhibition of L-Methionine γ-Lyase from Fusobacterium nucleatum
by Tingting Bu, Jing Lan, Inseong Jo, Jie Zhang, Xue Bai, Shanru He, Xiaoling Jin, Lulu Wang, Yu Jin, Xiaoyu Jin, Liying Zhang, Hailong Piao, Nam-Chul Ha, Chunshan Quan, Ki Hyun Nam and Yongbin Xu
Int. J. Mol. Sci. 2023, 24(2), 1651; https://doi.org/10.3390/ijms24021651 - 13 Jan 2023
Cited by 3 | Viewed by 1916
Abstract
Fusobacterium nucleatum is a lesion-associated obligate anaerobic pathogen of destructive periodontal disease; it is also implicated in the progression and severity of colorectal cancer. Four genes (FN0625, FN1055, FN1220, and FN1419) of F. nucleatum are involved in producing [...] Read more.
Fusobacterium nucleatum is a lesion-associated obligate anaerobic pathogen of destructive periodontal disease; it is also implicated in the progression and severity of colorectal cancer. Four genes (FN0625, FN1055, FN1220, and FN1419) of F. nucleatum are involved in producing hydrogen sulfide (H2S), which plays an essential role against oxidative stress. The molecular functions of Fn1419 are known, but their mechanisms remain unclear. We determined the crystal structure of Fn1419 at 2.5 Å, showing the unique conformation of the PLP-binding site when compared with L-methionine γ-lyase (MGL) proteins. Inhibitor screening for Fn1419 with L-cysteine showed that two natural compounds, gallic acid and dihydromyricetin, selectively inhibit the H2S production of Fn1419. The chemicals of gallic acid, dihydromyricetin, and its analogs containing trihydroxybenzene, were potentially responsible for the enzyme-inhibiting activity on Fn1419. Molecular docking and mutational analyses suggested that Gly112, Pro159, Val337, and Arg373 are involved in gallic acid binding and positioned close to the substrate and pyridoxal-5′-phosphate-binding site. Gallic acid has little effect on the other H2S-producing enzymes (Fn1220 and Fn1055). Overall, we proposed a molecular mechanism underlying the action of Fn1419 from F. nucleatum and found a new lead compound for inhibitor development. Full article
(This article belongs to the Special Issue Structural Dynamics of Macromolecules)
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10 pages, 1135 KiB  
Article
Peculiarities of Scattering of Ultrashort Laser Pulses on DNA and RNA Trinucleotides
by Dmitry Makarov and Anastasia Kharlamova
Int. J. Mol. Sci. 2022, 23(23), 15417; https://doi.org/10.3390/ijms232315417 - 6 Dec 2022
Cited by 2 | Viewed by 1022
Abstract
Currently, X-ray diffraction analysis (XRD) with high spatial and time resolution (TR-XRD) is based on the known theory of X-ray scattering, where the main parameter of USP—its duration—is not taken into account. In the present work, it is shown that, for scattering of [...] Read more.
Currently, X-ray diffraction analysis (XRD) with high spatial and time resolution (TR-XRD) is based on the known theory of X-ray scattering, where the main parameter of USP—its duration—is not taken into account. In the present work, it is shown that, for scattering of attosecond USPs on DNA and RNA trinucleotides, the pulse length is the most important scattering parameter. The diffraction pattern changes considerably in comparison with the previously known scattering theory. The obtained results are extremely important in TR-XRD when using attosecond pulses to study trinucleotides of DNA and RNA, because with the previously known scattering theory, which does not take into account the duration of USP, one cannot correctly interpret, and therefore “decode”, DNA and RNA structures. Full article
(This article belongs to the Special Issue Structural Dynamics of Macromolecules)
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