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Molecular Research in Protein–Ligand Interactions

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

Deadline for manuscript submissions: 31 January 2026 | Viewed by 673

Special Issue Editor


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Guest Editor
School of Chemical Engineering, Sichuan University, Chengdu, China
Interests: protein–ligand; computer simulation; cyclodextrin; metal–organic framework; drug delivery; controlled release; target

Special Issue Information

Dear Colleagues,

Drug discovery is a process where bioactive compounds are designed and screened either on the basis of specific molecular targets or by the identification of active ingredients from traditional medicine, as well as by serendipitous discovery. Both forward and reverse pharmacology approaches not only require a deep knowledge of the molecular processes involved in each pathological condition and disease but also the specific protein targets and the effects of drug binding on the conformation and activity of the proteins involved. An understanding of how drugs can modify and modulate specific cellular pathways and functions will be helpful during the process of drug development and clinical trials.

This Special Issue focuses on recent studies that aimed to investigate protein–ligand interactions, with a special aim of elucidating the molecular mode of action and the protein targets of drugs as well as natural compounds, and the cellular pathways involved. Indeed, protein–ligand interactions may affect both protein conformation and biological activity. However, for many bioactive compounds there is a lack of knowledge of their molecular targets, their effects on protein structure, and how they can modulate different cellular pathways and functions. Studies providing such information are welcomed and will help to elucidate the molecular basis for many drugs’ activity and the development of new drugs.

Dr. Qiaomei Sun
Guest Editor

Manuscript Submission Information

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Keywords

  • interaction
  • protein–ligand
  • computer simulation
  • docking
  • molecular simulation

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Published Papers (1 paper)

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Research

17 pages, 3037 KB  
Article
Symmetric Dimeric Structure and Ligand Recognition of CutR, a LysR-Type Transcriptional Regulator from Mycobacterium sp. Strain JC1
by Hyo Je Cho, Ka Young Lee, Hyun-Shik Lee and Beom Sik Kang
Int. J. Mol. Sci. 2025, 26(21), 10533; https://doi.org/10.3390/ijms262110533 - 29 Oct 2025
Viewed by 447
Abstract
Mycobacteria possess carbon monoxide dehydrogenase (CO-DH) to utilize CO as an energy source and to resist host defense mechanisms. The expression of the CO-DH gene is regulated by CutR, a LysR-type transcriptional regulator (LTTR) that exhibits unique characteristics, suggesting that it functions as [...] Read more.
Mycobacteria possess carbon monoxide dehydrogenase (CO-DH) to utilize CO as an energy source and to resist host defense mechanisms. The expression of the CO-DH gene is regulated by CutR, a LysR-type transcriptional regulator (LTTR) that exhibits unique characteristics, suggesting that it functions as a dimer rather than the typical tetramer. Size-exclusion chromatography revealed that CutR forms a stable dimer. Electrophoretic mobility shift assays demonstrated that dimeric CutR specifically binds to an inverted repeat sequence (IR1) containing T-n12-A motifs located upstream of the cutB gene, which encodes the medium subunit of CO-DH. Crystal structure determination at 1.8 Å resolution revealed that CutR consists of an N-terminal DNA-binding domain with a winged helix-turn-helix motif and a C-terminal ligand-binding domain comprising two regulatory subdomains (RD1 and RD2), forming a unique two-fold symmetrical homodimer. This dimer is stabilized through four interfaces, including an extensive 12-stranded antiparallel β-sheet formed between RD1 subdomains via intertwining C-terminal β11 strands. This represents the first symmetric dimeric LTTR structure with tightly associated ligand-binding domains. The recognition helices are spaced closer together than they are in typical DNA-bound LTTRs, despite binding longer T-n12-A sequences, suggesting that a conformational change is required to enhance DNA-binding affinity. A putative ligand-binding site was identified between the RD1 and RD2 subdomains, where glycerol binding induced local conformational changes. Comparative genomic analysis revealed conservation of CutR and the IR1 sequence across Mycobacterium species, supporting the dimeric regulatory mechanism and providing new insights into LTTR diversity. Full article
(This article belongs to the Special Issue Molecular Research in Protein–Ligand Interactions)
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