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Crystal Structure and Function of Biological Macromolecules

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Structure".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 4728

Special Issue Editor

Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Interests: structural biology; biomacromolecule; crystal structure; molecular function and mechanism; gut microbiota; drug development

Special Issue Information

Dear Colleagues,

All biological functions depend on biomacromolecules such as proteins, nucleic acid, carbohydrates, lipids, and complexes thereof. Additionally, proteins compose structural and motor elements in the microorganism, and they serve as catalysts for virtually every biochemical reaction that occurs in living things. A study of the three-dimensional structure of proteins revealed their molecular function, as well as their relationship with normal biological functions and abnormal physiological phenomena, thus revealing the life phenomenon essential to the discipline. This is the cornerstone of biology.

In recent years, research on the gut microbiota has been very active. Additionally, the gut microbiota plays a crucial role in the maintenance of human colon health and, when altered, contributes to emerging diseases, such as ulcerative colitis and type II diabetes. However, the pathogenic mechanism of gut microbiota remains unknown, and the studies on pathogenic proteins are few. Therefore, in combination with X-ray diffraction technique, etc., the molecular function and mechanism of pathogenic proteins are revealed at the atomic and molecular levels. Growing knowledge of these pathogenic proteins has already contributed significantly to a molecular understanding of disease. In addition, based on the crystal structure of these proteins, the inhibitors can be developed. These studies show promise as a treatment for disease and may lead to the development of a new drug. In a word, these studies have laid the foundation for us to expound their molecular function and mechanism and new drug development.

The focus of this Special Issue includes, but is not limited to, the study of crystal structure and the function of biological macromolecules. We are pleased to invite experts in the field to publish their latest developments and concepts in this Special Issue in the form of short communications, full-length papers, and reviews. We hope that this acquired knowledge will provide further insight and a solid pool of data for future developments in crystal structure and the function of biological macromolecules.

Dr. Yongbin Xu
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. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • structural biology
  • biomacromolecule
  • crystal structure
  • molecular function and mechanism
  • gut microbiota
  • drug development

Published Papers (2 papers)

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Research

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12 pages, 2572 KiB  
Article
Structural Basis for (2R,3R)-Taxifolin Binding and Reaction Products to the Bacterial Chalcone Isomerase of Eubacterium ramulus
by Gottfried J. Palm, Maren Thomsen, Leona Berndt and Winfried Hinrichs
Molecules 2022, 27(22), 7909; https://doi.org/10.3390/molecules27227909 - 16 Nov 2022
Viewed by 1322
Abstract
The bacterial chalcone isomerase (CHI) from Eubacterium ramulus catalyses the first step in a flavanone-degradation pathway by a reverse Michael addition. The overall fold and the constitution of the active site of the enzyme completely differ from the well-characterised chalcone isomerase of plants. [...] Read more.
The bacterial chalcone isomerase (CHI) from Eubacterium ramulus catalyses the first step in a flavanone-degradation pathway by a reverse Michael addition. The overall fold and the constitution of the active site of the enzyme completely differ from the well-characterised chalcone isomerase of plants. For (+)-taxifolin, CHI catalyses the intramolecular ring contraction to alphitonin. In this study, Fwe perform crystal structure analyses of CHI and its active site mutant His33Ala in the presence of the substrate taxifolin at 2.15 and 2.8 Å resolution, respectively. The inactive enzyme binds the substrate (+)-taxifolin as well defined, whereas the electron density maps of the native CHI show a superposition of substrate, product alphitonin, and most probably also the reaction intermediate taxifolin chalcone. Evidently, His33 mediates the stereospecific acid-base reaction by abstracting a proton from the flavonoid scaffold. The stereospecificity of the product is discussed. Full article
(This article belongs to the Special Issue Crystal Structure and Function of Biological Macromolecules)
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Review

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16 pages, 1703 KiB  
Review
General Strategies for RNA X-ray Crystallography
by Ryland W. Jackson, Claire M. Smathers and Aaron R. Robart
Molecules 2023, 28(5), 2111; https://doi.org/10.3390/molecules28052111 - 23 Feb 2023
Cited by 9 | Viewed by 2990
Abstract
An extremely small proportion of the X-ray crystal structures deposited in the Protein Data Bank are of RNA or RNA–protein complexes. This is due to three main obstacles to the successful determination of RNA structure: (1) low yields of pure, properly folded RNA; [...] Read more.
An extremely small proportion of the X-ray crystal structures deposited in the Protein Data Bank are of RNA or RNA–protein complexes. This is due to three main obstacles to the successful determination of RNA structure: (1) low yields of pure, properly folded RNA; (2) difficulty creating crystal contacts due to low sequence diversity; and (3) limited methods for phasing. Various approaches have been developed to address these obstacles, such as native RNA purification, engineered crystallization modules, and incorporation of proteins to assist in phasing. In this review, we will discuss these strategies and provide examples of how they are used in practice. Full article
(This article belongs to the Special Issue Crystal Structure and Function of Biological Macromolecules)
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