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Biomolecular Structures, Dynamics, and Functions
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Biomolecular Structures, Dynamics, and Functions

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 (20 October 2024) | Viewed by 2436

Special Issue Editor

Prof. Dr. Ray Luo

E-Mail Website
Guest Editor
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
Interests: computational analysis of biomolecular sequence, structure, dynamics, and function
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Understanding biomolecular structures and functions is fundamental to unveiling the mysteries of life and has profound implications for drug discovery, disease understanding, and biotechnology. Although the significance was recognized decades ago and many efforts were devoted into this field, owing to the complexity of biomolecules and limitations of experimental technologies, structures under some cases are still hard to be resolved. The central dogma connecting biomolecular sequences to structures and functions enables direct prediction from sequences and greatly facilitates the development of computational biology. Recently, machine learning methods boomed in various fields and a breakthrough is AlphaFold and its extensions that have gained significant attention for their remarkable success in predicting protein structures with unprecedented accuracy. More comprehensive understanding of biomolecular structures and functions could be achieved with combination of multiple experimental techniques and computational methods. Thus, we have decided to launch a special issue focusing on Biomolecular Structures and Functions and warmly welcome all types of submissions including both original scientific findings and methodology advancements for better understanding the relations between biomolecular structures and functions. 

This special issue is supervised by Dr. Ray Luo and assisted by our Topical Advisory Panel Member Dr. Qiang Zhu.

Prof. Dr. Ray Luo
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 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. 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

  • biomolecular structures and functions
  • biomolecular recognition
  • structural biology
  • molecular dynamics
  • machine learning
  • NMR
  • crystallography

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Published Papers (2 papers)

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Research

18 pages, 7104 KiB  
Article
Role of Non-Binding T63 Alteration in IL-18 Binding
by Chariya Peeyatu, Napat Prompat, Supayang Piyawan Voravuthikunchai, Niran Roongsawang, Surasak Sangkhathat, Pasarat Khongkow, Jirakrit Saetang and Varomyalin Tipmanee
Int. J. Mol. Sci. 2024, 25(23), 12992; https://doi.org/10.3390/ijms252312992 - 3 Dec 2024
Viewed by 481
Abstract
Engineered interleukin-18 (IL-18) has attracted interest as a cytokine-based treatment. However, knowledge-based mutagenesis of IL-18 has been reported for only a few regions of the protein structures, including binding sites I and II. When coupled with the binding region mutant (E6K), the non-binding [...] Read more.
Engineered interleukin-18 (IL-18) has attracted interest as a cytokine-based treatment. However, knowledge-based mutagenesis of IL-18 has been reported for only a few regions of the protein structures, including binding sites I and II. When coupled with the binding region mutant (E6K), the non-binding residue of IL-18, Thr63 (T63), has been shown to increase the flexibility of the binding loop. Nevertheless, the function of Thr63 in conformational regulation is still unknown. Using homology modeling, molecular dynamics simulation, and structural analysis, we investigated the effects of Thr63 alteration coupling with E6K on conformational change pattern, binding loop flexibility, and the hydrogen bond network. The results indicate that the 63rd residue was significantly associated with hydrogen-bond relaxation at the core β-barrel binding sites I and II Glu85-Ile100 loop. This result provided conformational and flexible effects to binding sites I and III by switching their binding loops and stabilizing the 63rd residue cavity. These findings may pave the way for the conceptualization of a new design for IL-18 proteins by modifying non-binding residues for structure-based drug development. Full article
(This article belongs to the Special Issue Biomolecular Structures, Dynamics, and Functions)
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13 pages, 3287 KiB  
Article
Cleavage of DNA Substrate Containing Nucleotide Mismatch in the Complementary Region to sgRNA by Cas9 Endonuclease: Thermodynamic and Structural Features
by Svetlana V. Baranova, Polina V. Zhdanova, Anastasia D. Koveshnikova, Pavel E. Pestryakov, Ivan P. Vokhtantsev, Alexander A. Chernonosov and Vladimir V. Koval
Int. J. Mol. Sci. 2024, 25(19), 10862; https://doi.org/10.3390/ijms251910862 - 9 Oct 2024
Viewed by 1085
Abstract
The non-ideal accuracy and insufficient selectivity of CRISPR/Cas9 systems is a serious problem for their use as a genome editing tool. It is important to select the target sequence correctly so that the CRISPR/Cas9 system does not cut similar sequences. This requires an [...] Read more.
The non-ideal accuracy and insufficient selectivity of CRISPR/Cas9 systems is a serious problem for their use as a genome editing tool. It is important to select the target sequence correctly so that the CRISPR/Cas9 system does not cut similar sequences. This requires an understanding of how and why mismatches in the target sequence can affect the efficiency of the Cas9/sgRNA complex. In this work, we studied the catalytic activity of the Cas9 enzyme to cleave DNA substrates containing nucleotide mismatch at different positions relative to the PAM in the “seed” sequence. We show that mismatches in the complementarity of the sgRNA/DNA duplex at different positions relative to the protospacer adjacent motif (PAM) sequence tend to decrease the cleavage efficiency and increase the half-maximal reaction time. However, for two mismatches at positions 11 and 20 relative to the PAM, an increase in cleavage efficiency was observed, both with and without an increase in half-reaction time. Thermodynamic parameters were obtained from molecular dynamics results, which showed that mismatches at positions 8, 11, and 20 relative to the PAM thermodynamically stabilize the formed complex, and a mismatch at position 2 of the PAM fragment exerts the greatest stabilization compared to the original DNA sequence. The weak correlation of the thermodynamic binding parameters of the components of the Cas9/sgRNA:dsDNA complex with the cleavage data of DNA substrates containing mismatches indicates that the efficiency of Cas9 operation is mainly affected by the conformational changes in Cas9 and the mutual arrangement of sgRNA and substrates. Full article
(This article belongs to the Special Issue Biomolecular Structures, Dynamics, and Functions)
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