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Structural Dynamics of Macromolecules
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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: 20 May 2025 | Viewed by 9062

Special Issue Editor

Prof. Dr. Ki Hyun Nam

E-Mail Website
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
Special Issues, Collections and Topics in MDPI journals

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

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Keywords

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

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Published Papers (6 papers)

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Research

10 pages, 8815 KiB  
Article
Comparative Analysis of Symmetry Parameters in the E2 Inner Core of the Pyruvate Dehydrogenase Complex
by Han-ul Kim, Myeong Seon Jeong, Mi Young An, Yoon Ho Park, Sun Hee Park, Sang J. Chung, Yoon-sun Yi, Sangmi Jun, Young Kwan Kim and Hyun Suk Jung
Int. J. Mol. Sci. 2024, 25(24), 13731; https://doi.org/10.3390/ijms252413731 - 23 Dec 2024
Abstract
Recent advances in cryo-electron microscopy (cryo-EM) have facilitated the high-resolution structural determination of macromolecular complexes in their native states, providing valuable insights into their dynamic behaviors. However, insufficient understanding or experience with the cryo-EM image processing parameters can result in the loss of [...] Read more.
Recent advances in cryo-electron microscopy (cryo-EM) have facilitated the high-resolution structural determination of macromolecular complexes in their native states, providing valuable insights into their dynamic behaviors. However, insufficient understanding or experience with the cryo-EM image processing parameters can result in the loss of biological meaning. In this paper, we investigate the dihydrolipoyl acetyltransferase (E2) inner core complex of the pyruvate dehydrogenase complex (PDC) and reconstruct the 3D maps using five different symmetry parameters. The results demonstrate that the reconstructions yield structurally identical 3D models even at a near-atomic structure. This finding underscores a crucial message for researchers engaging in single-particle analysis (SPA) with relatively user-friendly and convenient image processing software. This approach helps reduce the risk of missing critical biological details, such as the dynamic properties of macromolecules. Full article
(This article belongs to the Special Issue Structural Dynamics of Macromolecules)
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14 pages, 3722 KiB  
Article
Structure Characterization of Zinc Finger Motif 1 and 2 of GLI1 DNA Binding Region
by Mousheng Wu, Nusrat Jahan, Amanda Sharp, Anwar Ullah, Corinne E. Augelli-Szafran, Sixue Zhang and Rebecca J. Boohaker
Int. J. Mol. Sci. 2024, 25(24), 13368; https://doi.org/10.3390/ijms252413368 - 13 Dec 2024
Viewed by 560
Abstract
As a transcription factor, GLI1 plays an important role in cell cycle regulation, DNA replication, and DNA damage responses. The aberrant activation of GLI1 has been associated with cancers such as glioma, osteosarcoma, and rhabdomyosarcoma. The binding of GLI1 to a specific DNA [...] Read more.
As a transcription factor, GLI1 plays an important role in cell cycle regulation, DNA replication, and DNA damage responses. The aberrant activation of GLI1 has been associated with cancers such as glioma, osteosarcoma, and rhabdomyosarcoma. The binding of GLI1 to a specific DNA sequence was achieved by five tandem zinc finger motifs (Zif motifs) on the N-terminal part of the molecule. Here, we reported a novel homodimeric crystal structure of Zif1-2. These two Zif motifs are linearized. Namely, Zif2 does not bend and interact with Zif1 of the same molecule. Instead, Zif1 from one molecule interacts with Zif2 from another molecule. The dimer interface of Zif1-2 is unique and different from the conformation of Zif1-2 from the GLI1-DNA co-crystal structure. The dimeric conformation of Zif motifs could represent the native conformation of apo form GLI1 Zif motifs in the cell. The molecular dynamics simulation result of the homodimer, the in silico mutagenesis, and the predicted protease stability of these mutants using a large language model are also presented. Full article
(This article belongs to the Special Issue Structural Dynamics of Macromolecules)
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16 pages, 7031 KiB  
Article
Structural Insights and Catalytic Mechanism of 3-Hydroxybutyryl-CoA Dehydrogenase from Faecalibacterium Prausnitzii A2-165
by Jaewon Yang, Hyung Jin Jeon, Seonha Park, Junga Park, Seonhye Jang, Byeongmin Shin, Kyuhyeon Bang, Hye-Jin Kim Hawkes, Sungha Park, Sulhee Kim and Kwang Yeon Hwang
Int. J. Mol. Sci. 2024, 25(19), 10711; https://doi.org/10.3390/ijms251910711 - 5 Oct 2024
Viewed by 1019
Abstract
Atopic dermatitis (AD) is characterized by a T-helper cell type 2 (Th2) inflammatory response leading to skin damage with erythema and edema. Comparative fecal sample analysis has uncovered a strong correlation between AD and Faecalibacterium prausnitzii strain A2-165, specifically associated with butyrate production. [...] Read more.
Atopic dermatitis (AD) is characterized by a T-helper cell type 2 (Th2) inflammatory response leading to skin damage with erythema and edema. Comparative fecal sample analysis has uncovered a strong correlation between AD and Faecalibacterium prausnitzii strain A2-165, specifically associated with butyrate production. Therefore, understanding the functional mechanisms of crucial enzymes in the butyrate pathway, such as 3-hydroxybutyryl-CoA dehydrogenase of A2-165 (A2HBD), is imperative. Here, we have successfully elucidated the three-dimensional structure of A2HBD in complex with acetoacetyl-CoA and NAD+ at a resolution of 2.2Å using the PAL-11C beamline (third generation). Additionally, X-ray data of A2HBD in complex with acetoacetyl-CoA at a resolution of 1.9 Å were collected at PAL-XFEL (fourth generation) utilizing Serial Femtosecond Crystallography (SFX). The monomeric structure of A2HBD consists of two domains, N-terminal and C-terminal, with cofactor binding occurring at the N-terminal domain, while the C-terminal domain facilitates dimerization. Our findings elucidate the binding mode of NAD+ to A2HBD. Upon acetoacetyl-CoA binding, the crystal structure revealed a significant conformational change in the Clamp-roof domain (root-mean-square deviation of 2.202 Å). Notably, residue R143 plays a critical role in capturing the adenine phosphate ring, underlining its significance in substrate recognition and catalytic activity. The binding mode of acetoacetyl-CoA was also clarified, indicating its lower stability compared to NAD+. Furthermore, the conformational change of hydrophobic residues near the catalytic cavity upon substrate binding resulted in cavity shrinkage from an open to closed conformation. This study confirms the conformational changes of catalytic triads involved in the catalytic reaction and presents a proposed mechanism for substrate reduction based on structural observations. Full article
(This article belongs to the Special Issue Structural Dynamics of Macromolecules)
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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
Cited by 1 | Viewed by 2314
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 5 | Viewed by 2604
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 1367
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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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Anisotropic X-ray Scattering Signal of Proteins and Effect on Structure Refinement
Authors: Hyotcherl Ihee
Affiliation: Department of Chemistry and KI for the BioCentury, KAIST (Korea Advanced Institute of Science and Technology) Director, Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
Abstract: When protein molecules in solution are excited by a linearly polarized laser pulse, the molecules with their transient dipoles oriented parallel to the laser polarization are preferentially excited. This photoselective alignment results in an anisotropic X-ray scattering pattern, distinguishable from the typical isotropic X-ray scattering pattern from randomly oriented molecules in solution. Here, we introduce a new approach to simulate the anisotropic X-ray scattering signal from an ensemble of photoselectively aligned molecules. The anisotropic X-ray scattering signals of homodimeric hemoglobin (HbI) were simulated and compared with those arising from the isotropically oriented molecules. We also examined the potential errors that may arise in the refined structure obtained using anisotropic signals, if the anisotropy contribution is not properly accounted for during structural analysis.

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