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Biocatalysis: Mechanisms of Proteolytic Enzymes

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A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 8917

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Special Issue Information

Dear Colleagues,

Proteases are traditionally among the most studied enzymes and over the decades a wealth of structural, functional and theoretical information has accumulated. However, the understanding of the molecular mechanisms underlying their activities and regulation remains incomplete. Although the basic principles of peptide bond hydrolysis were delineated a long time ago, there is a lack of experimental evidence for many aspects of substrate recognition, turnover, energetics, time course of the catalytic steps, and of the fine-tuned physiological regulation of activity. Thus, it is worth investigating and comparing the molecular mechanisms for the numerous serine, cysteine, metallo and aspartic proteases, as well as for the much rarer threonine, asparagine and glutamic type. In order to add more biological and medical relevance, we welcome articles that analyze molecular interactions of proteases with natural substrates and inhibitors or their synthetic small molecule counterparts.

The goal of this Special Issue is to present experimental, computational and comparative studies, which promote a deeper understanding of the common mechanistic principles of proteases. Also, structural and analytical data from crystallography, cryo-EM, NMR and MS that support functional and mechanistic research are welcome. Therefore, submissions to this Special Issue on the “Biocatalysis: Mechanisms of Proteolytic Enzymes” should be either original research papers, including short communications, or reviews and perspectives. Eventually, we hope to draw a topical picture of the current status and developments, which could have an impact on other fields of research, such as medicine and pharmacy.

Accepted papers are published in the joint Special Issue in Catalysts or International Journal of Molecular Sciences.

Dr. Peter Goettig
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.

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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

aspartic proteases
catalytic mechanism
conformational selection
cysteine proteases
enzyme kinetics
metalloproteases
nucleophilic attack
peptide bond hydrolysis
serine protease

Published Papers (2 papers)

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Research

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15 pages, 629 KiB

Open AccessArticle

The Evolution, Gene Expression Profile, and Secretion of Digestive Peptidases in Lepidoptera Species

by Lucas R. Lima, Renata O. Dias, Felipe Jun Fuzita, Clélia Ferreira, Walter R. Terra and Marcio C. Silva-Filho

Catalysts 2020, 10(2), 217; https://0-doi-org.brum.beds.ac.uk/10.3390/catal10020217 - 11 Feb 2020

Cited by 6 | Viewed by 2293

Abstract

Serine peptidases (SPs) are responsible for most primary protein digestion in Lepidoptera species. An expansion of the number of genes encoding trypsin and chymotrypsin enzymes and the ability to upregulate the expression of some of these genes in response to peptidase inhibitor (PI) ingestion have been associated with the adaptation of Noctuidae moths to herbivory. To investigate whether these gene family expansion events are common to other Lepidoptera groups, we searched for all genes encoding putative trypsin and chymotrypsin enzymes in 23 publicly available genomes from this taxon. Phylogenetic analysis showed that several gene family expansion events may have occurred in the taxon’s evolutionary history and that these events gave rise to a very diverse group of enzymes, including proteins lacking the canonical SP catalytic triad. The expression profile of these enzymes along the midgut and the secretion mechanisms by which these enzymes enter the luminal content were also analyzed in Spodoptera frugiperda larvae using RNA-seq and proteomics. These results support the proposal of a midgut countercurrent flux responsible for the direction of these proteins to the anterior portion of the midgut and show that these enzymes reach the midgut lumen via both exocytosis and microapocrine secretion mechanisms. Full article

(This article belongs to the Special Issue Biocatalysis: Mechanisms of Proteolytic Enzymes)

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Review

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18 pages, 4955 KiB

Open AccessFeature PaperReview

Reversed Proteolysis—Proteases as Peptide Ligases

by Peter Goettig

Catalysts 2021, 11(1), 33; https://0-doi-org.brum.beds.ac.uk/10.3390/catal11010033 - 30 Dec 2020

Cited by 8 | Viewed by 6084

Abstract

Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress. Full article

(This article belongs to the Special Issue Biocatalysis: Mechanisms of Proteolytic Enzymes)

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