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Structure and Function of Proteins: From Bioinformatics Insights
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Structure and Function of Proteins: From Bioinformatics Insights

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

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 9238

Special Issue Editor

Dr. Jianwen Fang

E-Mail Website
Guest Editor
Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20850, USA
Interests: data-mining algorithms; systems biology; protein bioinformatics; software and database development; computational drug discovery; integrated data analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In complex biological systems, there are different levels of orchestration of agency and function: organs and cells work in concert to perform complex operations, and they are composed of a variety of proteins that play fundamental roles in internal and external interactions. At the same time, bioinformatics has become essential for elucidating the links between protein structure, dynamics, and function, as well as for understanding target-based drug discovery approaches. It is therefore clear that an integrated approach combining different computational and experimental techniques will provide more comprehensive and mechanistic insights into protein structure and function.

In this Special Issue, we will explore the application of bioinformatics in key areas such as prediction of 3D structures of unstructured proteins, prediction of gene expression, identification of transposable elements, and prediction of interactions between biologically important proteins (e.g., druggable proteins) and ligands.

In addition, reports are encouraged to propose new experimental or computational methods for the interpretation and understanding of biophysical-chemical data, structural studies of proteins and macromolecular assemblies, modification of protein structure and function via molecular biology and genetics techniques, conditions for functional analysis under physiology, and protein interactions with receptors, nucleic acids, or other specific ligands or substrates. Protein and peptide biochemistry studies aimed at synthesizing or characterizing molecules that mimic active aspects of proteins or act as inhibitors of protein function are also welcome.

Dr. Jianwen Fang
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

  • biomedical application
  • DNA sequencing
  • bioinformatics
  • structural bioinformatics
  • protein dynamics
  • allostery
  • drug discovery
  • computational approaches

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Published Papers (5 papers)

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Research

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33 pages, 13466 KiB  
Article
Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements
by Yahaira de J. Tamayo-Ordóñez, Ninfa M. Rosas-García, Francisco A. Tamayo-Ordoñez, Benjamín A. Ayil-Gutiérrez, Juan M. Bello-López, Gerardo de J. Sosa-Santillán, Erika Acosta-Cruz, Francisco Anguebes-Franseschi, Siprian Damas-Damas, Angel V. Domínguez-May, Atl Victor Córdova-Quiroz and María Concepción Tamayo-Ordóñez
Curr. Issues Mol. Biol. 2024, 46(6), 5744-5776; https://doi.org/10.3390/cimb46060344 - 9 Jun 2024
Viewed by 1492
Abstract
In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the [...] Read more.
In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies. Full article
(This article belongs to the Special Issue Structure and Function of Proteins: From Bioinformatics Insights)
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21 pages, 3927 KiB  
Article
In Silico Analysis of Protein–Protein Interactions of Putative Endoplasmic Reticulum Metallopeptidase 1 in Schizosaccharomyces pombe
by Dalia González-Esparragoza, Alan Carrasco-Carballo, Nora H. Rosas-Murrieta, Lourdes Millán-Pérez Peña, Felix Luna and Irma Herrera-Camacho
Curr. Issues Mol. Biol. 2024, 46(5), 4609-4629; https://doi.org/10.3390/cimb46050280 - 12 May 2024
Viewed by 1560
Abstract
Ermp1 is a putative metalloprotease from Schizosaccharomyces pombe and a member of the Fxna peptidases. Although their function is unknown, orthologous proteins from rats and humans have been associated with the maturation of ovarian follicles and increased ER stress. This study focuses on [...] Read more.
Ermp1 is a putative metalloprotease from Schizosaccharomyces pombe and a member of the Fxna peptidases. Although their function is unknown, orthologous proteins from rats and humans have been associated with the maturation of ovarian follicles and increased ER stress. This study focuses on proposing the first prediction of PPI by comparison of the interologues between humans and yeasts, as well as the molecular docking and dynamics of the M28 domain of Ermp1 with possible target proteins. As results, 45 proteins are proposed that could interact with the metalloprotease. Most of these proteins are related to the transport of Ca2+ and the metabolism of amino acids and proteins. Docking and molecular dynamics suggest that the M28 domain of Ermp1 could hydrolyze leucine and methionine residues of Amk2, Ypt5 and Pex12. These results could support future experimental investigations of other Fxna peptidases, such as human ERMP1. Full article
(This article belongs to the Special Issue Structure and Function of Proteins: From Bioinformatics Insights)
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18 pages, 5284 KiB  
Article
Targeting CDK9 in Cancer: An Integrated Approach of Combining In Silico Screening with Experimental Validation for Novel Degraders
by Mahesh Koirala and Mario DiPaola
Curr. Issues Mol. Biol. 2024, 46(3), 1713-1730; https://doi.org/10.3390/cimb46030111 - 22 Feb 2024
Cited by 1 | Viewed by 1530
Abstract
The persistent threat of cancer remains a significant hurdle for global health, prompting the exploration of innovative approaches in the quest for successful therapeutic interventions. Cyclin-dependent kinase 9 (CDK9), a central player in transcription regulation and cell cycle progression, has emerged as a [...] Read more.
The persistent threat of cancer remains a significant hurdle for global health, prompting the exploration of innovative approaches in the quest for successful therapeutic interventions. Cyclin-dependent kinase 9 (CDK9), a central player in transcription regulation and cell cycle progression, has emerged as a promising target to combat cancer. Its pivotal role in oncogenic pathways and the pressing need for novel cancer treatments has propelled CDK9 into the spotlight of drug discovery efforts. This article presents a comprehensive study that connects a multidisciplinary approach, combining computational methodologies, experimental validation, and the transformative Proteolysis-Targeting Chimera (PROTAC) technology. By uniting these diverse techniques, we aim to identify, characterize, and optimize a new class of degraders targeting CDK9. We explore these compounds for targeted protein degradation, offering a novel and potentially effective approach to cancer therapy. This cohesive strategy utilizes the combination of computational predictions and experimental insights, with the goal of advancing the development of effective anticancer therapeutics, targeting CDK9. Full article
(This article belongs to the Special Issue Structure and Function of Proteins: From Bioinformatics Insights)
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23 pages, 6402 KiB  
Article
In Silico Evaluation of Coding and Non-Coding nsSNPs in the Thrombopoietin Receptor (MPL) Proto-Oncogene: Assessing Their Influence on Protein Stability, Structure, and Function
by Hakeemah H. Al-nakhle, Hind S. Yagoub, Sadin H. Anbarkhan, Ghadah A. Alamri and Norah M. Alsubaie
Curr. Issues Mol. Biol. 2023, 45(12), 9390-9412; https://doi.org/10.3390/cimb45120589 - 23 Nov 2023
Cited by 1 | Viewed by 1566
Abstract
The thrombopoietin receptor (MPL) gene is a critical regulator of hematopoiesis, and any alterations in its structure or function can result in a range of hematological disorders. Non-synonymous single nucleotide polymorphisms (nsSNPs) in MPL have the potential to disrupt normal protein [...] Read more.
The thrombopoietin receptor (MPL) gene is a critical regulator of hematopoiesis, and any alterations in its structure or function can result in a range of hematological disorders. Non-synonymous single nucleotide polymorphisms (nsSNPs) in MPL have the potential to disrupt normal protein function, prompting our investigation into the most deleterious MPL SNPs and the associated structural changes affecting protein–protein interactions. We employed a comprehensive suite of bioinformatics tools, including PredictSNP, InterPro, ConSurf, I-Mutant2.0, MUpro, Musitedeep, Project HOPE, STRING, RegulomeDB, Mutpred2, CScape, and CScape Somatic, to analyze 635 nsSNPs within the MPL gene. Among the analyzed nsSNPs, PredictSNP identified 28 as significantly pathogenic, revealing three critical functional domains within MPL. Ten of these nsSNPs exhibited high conservation scores, indicating potential effects on protein structure and function, while 14 were found to compromise MPL protein stability. Although the most harmful nsSNPs did not directly impact post-translational modification sites, 13 had the capacity to substantially alter the protein’s physicochemical properties. Some mutations posed a risk to vital protein–protein interactions crucial for hematological functions, and three non-coding region nsSNPs displayed significant regulatory potential with potential implications for hematopoiesis. Furthermore, 13 out of 21 nsSNPs evaluated were classified as high-risk pathogenic variants by Mutpred2. Notably, amino acid alterations such as C291S, T293N, D295G, and W435C, while impactful on protein stability and function, were deemed non-oncogenic “passenger” mutations. Our study underscores the substantial impact of missense nsSNPs on MPL protein structure and function. Given MPL’s central role in hematopoiesis, these mutations can significantly disrupt hematological processes, potentially leading to a variety of disorders. The identified high-risk pathogenic nsSNPs may hold promise as potential biomarkers or therapeutic targets for hematological diseases. This research lays the foundation for future investigations into the MPL gene’s role in the realm of hematological health and diseases. Full article
(This article belongs to the Special Issue Structure and Function of Proteins: From Bioinformatics Insights)
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Review

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27 pages, 4220 KiB  
Review
ADAR Family Proteins: A Structural Review
by Carolyn N. Ashley, Emmanuel Broni and Whelton A. Miller III
Curr. Issues Mol. Biol. 2024, 46(5), 3919-3945; https://doi.org/10.3390/cimb46050243 - 26 Apr 2024
Cited by 2 | Viewed by 2316
Abstract
This review aims to highlight the structures of ADAR proteins that have been crucial in the discernment of their functions and are relevant to future therapeutic development. ADAR proteins can correct or diversify genetic information, underscoring their pivotal contribution to protein diversity and [...] Read more.
This review aims to highlight the structures of ADAR proteins that have been crucial in the discernment of their functions and are relevant to future therapeutic development. ADAR proteins can correct or diversify genetic information, underscoring their pivotal contribution to protein diversity and the sophistication of neuronal networks. ADAR proteins have numerous functions in RNA editing independent roles and through the mechanisms of A-I RNA editing that continue to be revealed. Provided is a detailed examination of the ADAR family members—ADAR1, ADAR2, and ADAR3—each characterized by distinct isoforms that offer both structural diversity and functional variability, significantly affecting RNA editing mechanisms and exhibiting tissue-specific regulatory patterns, highlighting their shared features, such as double-stranded RNA binding domains (dsRBD) and a catalytic deaminase domain (CDD). Moreover, it explores ADARs’ extensive roles in immunity, RNA interference, and disease modulation, demonstrating their ambivalent nature in both the advancement and inhibition of diseases. Through this comprehensive analysis, the review seeks to underline the potential of targeting ADAR proteins in therapeutic strategies, urging continued investigation into their biological mechanisms and health implications. Full article
(This article belongs to the Special Issue Structure and Function of Proteins: From Bioinformatics Insights)
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