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Structure and Function of Macromolecular Interactions
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Structure and Function of Macromolecular Interactions

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 4612

Special Issue Editor

Prof. Dr. R. Holland Cheng

E-Mail Website
Guest Editor
Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
Interests: structural biology; 3D image reconstruction; microscopy; vaccine design; virus structures; molecular medicine; genomics; proteomics; metabolomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The state-of-art biochemical/biophysical methods used in structural studies are vast, ranging from hydrodynamic to scattering techniques, and have played a fundamental role in our understanding of viral infection in recent years. Macromolecular interactions have provided insights into the complex assembles, involving quaternary dynamics, nucleotide packaging, and heterologous–molecule interactions. This Special Issue, "Structure and Function of Macromolecular Interactions", intends to gather the recently unveiled interactions that allow the elucidation of mechanistic pathways that govern biological processes at the atomic and molecular levels. The method undertaken for any particular study contributes crucial information concerning the representative visualized discrete dynamic states. With joint efforts in the field, we will publish works that structurally characterize chosen macromolecules to formulate common platforms to develop targets for therapeutic intervention and improved vector designs for gene delivery.

Prof. Dr. R. Holland Cheng
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

  • macromolecular assembly
  • conformational proteomics
  • molecular dynamics
  • structure determination
  • membrane proteins
  • Bayesian structural time series/modeling

Published Papers (3 papers)

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Research

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19 pages, 2743 KiB  
Article
The Multienzyme Complex Nature of Dehydroepiandrosterone Sulfate Biosynthesis
by Anastasiya Tumilovich, Evgeniy Yablokov, Yuri Mezentsev, Pavel Ershov, Viktoriia Basina, Oksana Gnedenko, Leonid Kaluzhskiy, Tatsiana Tsybruk, Irina Grabovec, Maryia Kisel, Polina Shabunya, Natalia Soloveva, Nikita Vavilov, Andrei Gilep and Alexis Ivanov
Int. J. Mol. Sci. 2024, 25(4), 2072; https://doi.org/10.3390/ijms25042072 - 08 Feb 2024
Viewed by 655
Abstract
Dehydroepiandrosterone (DHEA), a precursor of steroid sex hormones, is synthesized by steroid 17-alpha-hydroxylase/17,20-lyase (CYP17A1) with the participation of microsomal cytochrome b5 (CYB5A) and cytochrome P450 reductase (CPR), followed by sulfation by two cytosolic sulfotransferases, SULT1E1 and SULT2A1, for storage and transport to tissues [...] Read more.
Dehydroepiandrosterone (DHEA), a precursor of steroid sex hormones, is synthesized by steroid 17-alpha-hydroxylase/17,20-lyase (CYP17A1) with the participation of microsomal cytochrome b5 (CYB5A) and cytochrome P450 reductase (CPR), followed by sulfation by two cytosolic sulfotransferases, SULT1E1 and SULT2A1, for storage and transport to tissues in which its synthesis is not available. The involvement of CYP17A1 and SULTs in these successive reactions led us to consider the possible interaction of SULTs with DHEA-producing CYP17A1 and its redox partners. Text mining analysis, protein–protein network analysis, and gene co-expression analysis were performed to determine the relationships between SULTs and microsomal CYP isoforms. For the first time, using surface plasmon resonance, we detected interactions between CYP17A1 and SULT2A1 or SULT1E1. SULTs also interacted with CYB5A and CPR. The interaction parameters of SULT2A1/CYP17A1 and SULT2A1/CYB5A complexes seemed to be modulated by 3′-phosphoadenosine-5′-phosphosulfate (PAPS). Affinity purification, combined with mass spectrometry (AP-MS), allowed us to identify a spectrum of SULT1E1 potential protein partners, including CYB5A. We showed that the enzymatic activity of SULTs increased in the presence of only CYP17A1 or CYP17A1 and CYB5A mixture. The structures of CYP17A1/SULT1E1 and CYB5A/SULT1E1 complexes were predicted. Our data provide novel fundamental information about the organization of microsomal CYP-dependent macromolecular complexes. Full article
(This article belongs to the Special Issue Structure and Function of Macromolecular Interactions)
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Review

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16 pages, 1097 KiB  
Review
Importance of Non-Covalent Interactions in Yeast Cell Wall Molecular Organization
by Tatyana S. Kalebina, Valentina V. Rekstina, Elizaveta E. Pogarskaia and Tatiana Kulakovskaya
Int. J. Mol. Sci. 2024, 25(5), 2496; https://doi.org/10.3390/ijms25052496 - 21 Feb 2024
Viewed by 649
Abstract
This review covers a group of non-covalently associated molecules, particularly proteins (NCAp), incorporated in the yeast cell wall (CW) with neither disulfide bridges with proteins covalently attached to polysaccharides nor other covalent bonds. Most NCAp, particularly Bgl2, are polysaccharide-remodeling enzymes. Either directly contacting [...] Read more.
This review covers a group of non-covalently associated molecules, particularly proteins (NCAp), incorporated in the yeast cell wall (CW) with neither disulfide bridges with proteins covalently attached to polysaccharides nor other covalent bonds. Most NCAp, particularly Bgl2, are polysaccharide-remodeling enzymes. Either directly contacting their substrate or appearing as CW lipid-associated molecules, such as in vesicles, they represent the most movable enzymes and may play a central role in CW biogenesis. The absence of the covalent anchoring of NCAp allows them to be there where and when it is necessary. Another group of non-covalently attached to CW molecules are polyphosphates (polyP), the universal regulators of the activity of many enzymes. These anionic polymers are able to form complexes with metal ions and increase the diversity of non-covalent interactions through charged functional groups with both proteins and polysaccharides. The mechanism of regulation of polysaccharide-remodeling enzyme activity in the CW is unknown. We hypothesize that polyP content in the CW is regulated by another NCAp of the CW—acid phosphatase—which, along with post-translational modifications, may thus affect the activity, conformation and compartmentalization of Bgl2 and, possibly, some other polysaccharide-remodeling enzymes. Full article
(This article belongs to the Special Issue Structure and Function of Macromolecular Interactions)
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21 pages, 1441 KiB  
Review
The Knowns and Unknowns in Protein–Metabolite Interactions
by Ilya Kurbatov, Georgii Dolgalev, Viktoriia Arzumanian, Olga Kiseleva and Ekaterina Poverennaya
Int. J. Mol. Sci. 2023, 24(4), 4155; https://doi.org/10.3390/ijms24044155 - 19 Feb 2023
Cited by 5 | Viewed by 2934
Abstract
Increasing attention has been focused on the study of protein–metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely [...] Read more.
Increasing attention has been focused on the study of protein–metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein–protein interactions, protein–metabolite interactions are still not clearly defined. Existing assays for detecting protein–metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein–metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term “interaction” to advance the field of interactomics further. Full article
(This article belongs to the Special Issue Structure and Function of Macromolecular Interactions)
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