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Protein Domains: Structure and Molecular Function
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Protein Domains: Structure and Molecular Function

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Biochemistry, Molecular and Cellular Biology".

Deadline for manuscript submissions: closed (20 April 2025) | Viewed by 6804

Special Issue Editor

Dr. Guangfeng Zhou

E-Mail Website
Guest Editor
Institute for Protein Design, Biochemistry Department, University of Washington, Seattle, WA 98195, USA
Interests: small-molecule drug discovery; deep learning; computational biophysics; molecular dynamics simulation; protein design

Special Issue Information

Dear Colleagues,

Protein domains, which are unique autonomous folding units, possess distinct structural and functional characteristics. These domains typically determine a protein’s biological role by contributing to a specific function or interaction. The identification of these protein domains is often a crucial step in understanding the structure and function of the protein.

Over the past decades, a variety of experimental and computational techniques have been developed and utilized to identify and characterize protein domains. These techniques include X-ray crystallography, cryo-electron microscopy (cryo-EM), and molecular dynamics simulations. In recent years, deep learning models have emerged as powerful tools in this field. They have been particularly effective in predicting domain boundaries and functions based on sequence and structure information.

Furthermore, protein domains can serve as essential building blocks in protein engineering, allowing for the design of proteins with desired functions. This capability has significant implications for various fields, including drug design and synthetic biology.

This Special Issue of CIMB welcomes both original research and comprehensive review papers on the study of the molecular structure and function of protein domains. We look forward to receiving your contributions.

Dr. Guangfeng Zhou
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. Current Issues in Molecular Biology is an international peer-reviewed open access monthly 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 2200 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

  • protein structure
  • protein domains
  • domain classification
  • protein engineering
  • protein design
  • protein modeling
  • machine learning
  • deep learning
  • protein structure prediction
  • protein function prediction

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Published Papers (3 papers)

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Research

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11 pages, 2102 KiB  
Communication
Exercise-Induced Shear Stress Drives mRNA Translation In Vitro
by Daniel Conde, Mario A. Garcia, Manuel Gomez and Alvaro N. Gurovich
Curr. Issues Mol. Biol. 2024, 46(9), 9895-9905; https://doi.org/10.3390/cimb46090589 - 5 Sep 2024
Cited by 1 | Viewed by 1504
Abstract
The vascular endothelium is the first line of defense to prevent cardiovascular disease. Its optimal functioning and health are maintained by the interaction of the proteins—endothelial nitric oxide synthase (eNOS), sirtuin 1 (SIRT1), and endothelin 1 (ET1)—and the genes that encode them—NOS3 [...] Read more.
The vascular endothelium is the first line of defense to prevent cardiovascular disease. Its optimal functioning and health are maintained by the interaction of the proteins—endothelial nitric oxide synthase (eNOS), sirtuin 1 (SIRT1), and endothelin 1 (ET1)—and the genes that encode them—NOS3, SIRT1, and EDN1, respectively. Aerobic exercise improves endothelial function by allegedly increasing endothelial shear stress (ESS). However, there are no current data exploring the acute effects of specific exercise-induced ESS intensities on these regulatory proteins and genes that are associated with endothelial function. The purpose of this study was to assess the acute changes in endothelial proteins and gene expression after exposure to low-, moderate-, and high-intensity exercise-induced ESS. Human umbilical vein endothelial cells (HUVECs) were exposed to resting ESS (18 dynes/cm2, 60 pulses per minute (PPM)), low ESS (35 dynes/cm2, 100 PPM), moderate ESS (50 dynes/cm2, 120 PPM), and high ESS (70 dynes/cm2, 150 PPM). Protein and gene expression were quantified by fluorescent Western blot and RTqPCR, respectively. All exercise conditions showed an increase in eNOS and SIRT1 expression and a decrease in NOS3 and SIRT1 gene expression when compared to resting conditions. In addition, there was no expression of ET1 and an increase in EDN1 gene expression when compared to resting conditions. These results show that (1) exercise-induced ESS increases the expressions of vascular protective proteins and (2) there is an inverse relationship between the proteins and their encoding genes immediately after exercise-induced ESS, suggesting that exercise has a previously unexplored translational role catalyzing mRNA to proteins. Full article
(This article belongs to the Special Issue Protein Domains: Structure and Molecular Function)
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Review

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22 pages, 3236 KiB  
Review
YBX1: A Multifunctional Protein in Senescence and Immune Regulation
by Wenze Zhang, Ying Liu, Zhe Zhao, Yizhi Zhang, Yujuan Liang and Wanxia Wang
Curr. Issues Mol. Biol. 2024, 46(12), 14058-14079; https://doi.org/10.3390/cimb46120841 - 13 Dec 2024
Viewed by 2176
Abstract
The Y-box binding protein 1 (YBX1) is a multifunctional protein with a wide range of roles in cell biology. It plays a crucial role in immune modulation, senescence, and disease progression. This review presents a comprehensive analysis of the specific functions and mechanisms [...] Read more.
The Y-box binding protein 1 (YBX1) is a multifunctional protein with a wide range of roles in cell biology. It plays a crucial role in immune modulation, senescence, and disease progression. This review presents a comprehensive analysis of the specific functions and mechanisms of YBX1 in these areas. Initially, YBX1 is shown to be closely associated with cellular senescence and impacts significant biological processes, including cell proliferation, damage repair, and metabolism. This suggests potential applications in the prevention and treatment of senescence-related diseases. Additionally, YBX1 regulates the immune response by controlling the function of immune cells and the expression of immune molecules. It is essential in maintaining immune system homeostasis and impacts the pathological process of various diseases, including tumors. Lastly, the diverse functions of the YBX1 protein make it a promising candidate for the development of innovative therapeutic strategies for diseases. Comprehensive research on its mechanisms could provide novel insights and approaches for the prevention, diagnosis, and treatment of related diseases. Full article
(This article belongs to the Special Issue Protein Domains: Structure and Molecular Function)
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25 pages, 925 KiB  
Review
Conformational Alterations of the Cell Surface of Monomeric and Dimeric β2m-Free HLA-I (Proto-HLA) May Enable Novel Immune Functions in Health and Disease
by Mepur H. Ravindranath, Narendranath M. Ravindranath, Carly J. Amato-Menker, Fatiha El Hilali and Edward J. Filippone
Curr. Issues Mol. Biol. 2024, 46(7), 6961-6985; https://doi.org/10.3390/cimb46070416 - 4 Jul 2024
Cited by 1 | Viewed by 2572
Abstract
Human leukocyte antigens (HLAs) are polymorphic glycoproteins expressed on the cell surface of nucleated cells and consist of two classes, HLA class I and HLA class II. In contrast, in mice, these molecules, known as H-2, are expressed on both nucleated cells and [...] Read more.
Human leukocyte antigens (HLAs) are polymorphic glycoproteins expressed on the cell surface of nucleated cells and consist of two classes, HLA class I and HLA class II. In contrast, in mice, these molecules, known as H-2, are expressed on both nucleated cells and erythrocytes. HLA-I molecules (Face-1) are heterodimers consisting of a polypeptide heavy chain (HC) and a light chain, B2-microglobulin (B2m). The heterodimers bind to antigenic peptides and present them to the T-cell receptors of CD8+ cytotoxic T lymphocytes. The HCs can also independently emerge on the cell surface as B2m-free HC monomers without peptides (Face-2). Early investigators suggested that the occurrence of B2m-free HCs on the cell surface resulted from the dissociation of B2m from Face-1. However, others documented the independent emergence of B2m-free HCs (Face-2) from the endoplasmic reticulum (ER) to the cell surface. The clustering of such HC molecules on either the cell surface or on exosomes resulted in the dimerization of B2m-free HCs to form homodimers (if the same allele, designated as Face-3) or heterodimers (if different alleles, designated as Face-4). Face-2 occurs at low levels on the cell surface of several normal cells but is upregulated on immune cells upon activation by proinflammatory cytokines and other agents such as anti-CD3 antibodies, phytohemagglutinin, and phorbol myristate acetate. Their density on the cell surface remains high as long as the cells remain activated. After activation-induced upregulation, Face-2 molecules undergo homo- and heterodimerization (Face-3 and Face-4). Observations made on the structural patterns of HCs and their dimerization in sharks, fishes, and tetrapod species suggest that the formation of B2m-free HC monomers and dimers is a recapitalization of a phylogenetically conserved event, befitting the term Proto-HLA for the B2m-free HCs. Spontaneous arthritis occurs in HLA-B27+ mice lacking B2m (HLA-B27+ B2m−/−) but not in HLA-B27+ B2m+/+ mice. Anti-HC-specific monoclonal antibodies (mAbs) delay disease development. Some HLA-I polyreactive mAbs (MEM series) used for immunostaining confirm the existence of B2m-free variants in several cancer cells. The conformational alterations that occur in the B2m-free HCs enable them to interact with several inhibitory and activating receptors of cellular components of the innate (natural killer (NK) cells) and adaptive (T and B cells) immune systems. The NK cells express killer immunoglobulin-like receptors (KIRs), whereas leukocytes (T and B lymphocytes, monocytes/macrophages, and dendritic cells) express leukocyte immunoglobulin-like receptors (LILRs). The KIRs and LILRs include activating and inhibitory members within their respective groups. This review focuses on the interaction of KIRs and LILRs with B2m-free HC monomers and dimers in patients with spondylarthritis. Several investigations reveal that the conformational alterations occurring in the alpha-1 and alpha-2 domains of B2m-free HCs may facilitate immunomodulation by their interaction with KIR and LILR receptors. This opens new avenues to immunotherapy of autoimmune diseases and even human cancers that express B2m-free HCs. Full article
(This article belongs to the Special Issue Protein Domains: Structure and Molecular Function)
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