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Biomedicines
Special Issues
Protein Structure, Function and Dynamics in Diseases and Therapeutics
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Protein Structure, Function and Dynamics in Diseases and Therapeutics

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 28762

Special Issue Editor

Dr. Gerald F. Audette

E-Mail Website
Guest Editor
Department of Chemistry, Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada
Interests: protein structure & function; bacterial secretion systems; protein dynamics; protein engineering

Special Issue Information

Dear Colleagues,

This Special Issue of Biomedicines will focus on the role of protein structure and function on the progression and treatment of disease. For many years, the role that a protein’s structure plays in its biological function has been well appreciated, and indeed, it is this correlation of structure and function that has led to significant advances in structurally-based drug design and therapeutic approaches. In recent years, the role of a protein’s dynamics has become more deeply appreciated in terms of function in relation to health and disease, as well as proteins that do not natively contain a single well-defined state, the so-called intrinsically disordered proteins (IDPs). The dynamic protein and the interactions made within the cellular context remain central issues of biomedicine.

We cordially invite authors in the field to submit original research or review articles highlighting the importance of protein structure and function, including novel approaches to study protein dynamics and IDPs in the progression and treatment of disease.

Dr. Gerald F. Audette
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. Biomedicines 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 2600 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.

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (4 papers)

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Research

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13 pages, 3587 KiB  
Article
Highlighting Human Enzymes Active in Different Metabolic Pathways and Diseases: The Case Study of EC 1.2.3.1 and EC 2.3.1.9
by Giulia Babbi, Davide Baldazzi, Castrense Savojardo, Pier Luigi Martelli and Rita Casadio
Biomedicines 2020, 8(8), 250; https://doi.org/10.3390/biomedicines8080250 - 29 Jul 2020
Cited by 6 | Viewed by 3179
Abstract
Enzymes are key proteins performing the basic functional activities in cells. In humans, enzymes can be also responsible for diseases, and the molecular mechanisms underlying the genotype to phenotype relationship are under investigation for diagnosis and medical care. Here, we focus on highlighting [...] Read more.
Enzymes are key proteins performing the basic functional activities in cells. In humans, enzymes can be also responsible for diseases, and the molecular mechanisms underlying the genotype to phenotype relationship are under investigation for diagnosis and medical care. Here, we focus on highlighting enzymes that are active in different metabolic pathways and become relevant hubs in protein interaction networks. We perform a statistics to derive our present knowledge on human metabolic pathways (the Kyoto Encyclopaedia of Genes and Genomes (KEGG)), and we found that activity aldehyde dehydrogenase (NAD(+)), described by Enzyme Commission number EC 1.2.1.3, and activity acetyl-CoA C-acetyltransferase (EC 2.3.1.9) are the ones most frequently involved. By associating functional activities (EC numbers) to enzyme proteins, we found the proteins most frequently involved in metabolic pathways. With our analysis, we found that these proteins are endowed with the highest numbers of interaction partners when compared to all the enzymes in the pathways and with the highest numbers of predicted interaction sites. As specific enzyme protein test cases, we focus on Alpha-Aminoadipic Semialdehyde Dehydrogenase (ALDH7A1, EC 2.3.1.9) and Acetyl-CoA acetyltransferase, cytosolic and mitochondrial (gene products of ACAT2 and ACAT1, respectively; EC 2.3.1.9). With computational approaches we show that it is possible, by starting from the enzyme structure, to highlight clues of their multiple roles in different pathways and of putative mechanisms promoting the association of genes to disease. Full article
(This article belongs to the Special Issue Protein Structure, Function and Dynamics in Diseases and Therapeutics)
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Review

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30 pages, 3650 KiB  
Review
Protein Dynamics in F-like Bacterial Conjugation
by Nicholas Bragagnolo, Christina Rodriguez, Naveed Samari-Kermani, Alice Fours, Mahboubeh Korouzhdehi, Rachel Lysenko and Gerald F. Audette
Biomedicines 2020, 8(9), 362; https://doi.org/10.3390/biomedicines8090362 - 19 Sep 2020
Cited by 16 | Viewed by 7685
Abstract
Efficient in silico development of novel antibiotics requires high-resolution, dynamic models of drug targets. As conjugation is considered the prominent contributor to the spread of antibiotic resistance genes, targeted drug design to disrupt vital components of conjugative systems has been proposed to lessen [...] Read more.
Efficient in silico development of novel antibiotics requires high-resolution, dynamic models of drug targets. As conjugation is considered the prominent contributor to the spread of antibiotic resistance genes, targeted drug design to disrupt vital components of conjugative systems has been proposed to lessen the proliferation of bacterial antibiotic resistance. Advancements in structural imaging techniques of large macromolecular complexes has accelerated the discovery of novel protein-protein interactions in bacterial type IV secretion systems (T4SS). The known structural information regarding the F-like T4SS components and complexes has been summarized in the following review, revealing a complex network of protein-protein interactions involving domains with varying degrees of disorder. Structural predictions were performed to provide insight on the dynamicity of proteins within the F plasmid conjugative system that lack structural information. Full article
(This article belongs to the Special Issue Protein Structure, Function and Dynamics in Diseases and Therapeutics)
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20 pages, 5599 KiB  
Review
HDX-MS: An Analytical Tool to Capture Protein Motion in Action
by Dominic Narang, Cristina Lento and Derek J. Wilson
Biomedicines 2020, 8(7), 224; https://doi.org/10.3390/biomedicines8070224 - 17 Jul 2020
Cited by 39 | Viewed by 10109
Abstract
Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange [...] Read more.
Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) provides valuable information about protein dynamics, which is highly complementary to the static picture provided by conventional high-resolution structural tools (i.e., X-ray crystallography and structural NMR). The amount of protein required to carry out HDX-MS experiments is a fraction of the amount required by alternative biophysical techniques, which are also usually lower resolution. Use of HDX-MS is growing quickly both in industry and academia, and it has been successfully used in numerous drug and vaccine development efforts, with important roles in understanding allosteric effects and mapping binding sites. Full article
(This article belongs to the Special Issue Protein Structure, Function and Dynamics in Diseases and Therapeutics)
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23 pages, 2262 KiB  
Review
The Nuclear Lamina: Protein Accumulation and Disease
by Carla Almendáriz-Palacios, Zoe E. Gillespie, Matthew Janzen, Valeria Martinez, Joanna M. Bridger, Troy A. A. Harkness, Darrell D. Mousseau and Christopher H. Eskiw
Biomedicines 2020, 8(7), 188; https://doi.org/10.3390/biomedicines8070188 - 1 Jul 2020
Cited by 12 | Viewed by 6628
Abstract
Cellular health is reliant on proteostasis—the maintenance of protein levels regulated through multiple pathways modulating protein synthesis, degradation and clearance. Loss of proteostasis results in serious disease and is associated with aging. One proteinaceous structure underlying the nuclear envelope—the nuclear lamina—coordinates essential processes [...] Read more.
Cellular health is reliant on proteostasis—the maintenance of protein levels regulated through multiple pathways modulating protein synthesis, degradation and clearance. Loss of proteostasis results in serious disease and is associated with aging. One proteinaceous structure underlying the nuclear envelope—the nuclear lamina—coordinates essential processes including DNA repair, genome organization and epigenetic and transcriptional regulation. Loss of proteostasis within the nuclear lamina results in the accumulation of proteins, disrupting these essential functions, either via direct interactions of protein aggregates within the lamina or by altering systems that maintain lamina structure. Here we discuss the links between proteostasis and disease of the nuclear lamina, as well as how manipulating specific proteostatic pathways involved in protein clearance could improve cellular health and prevent/reverse disease. Full article
(This article belongs to the Special Issue Protein Structure, Function and Dynamics in Diseases and Therapeutics)
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