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Advances in Proteolysis and Proteolytic Enzymes
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Advances in Proteolysis and Proteolytic Enzymes

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

Deadline for manuscript submissions: 20 February 2025 | Viewed by 8734

Special Issue Editor

Dr. Mikhail M. Vorob'ev

E-Mail Website
Guest Editor
A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 ul. Vavilova, 119991 Moscow, Russia
Interests: proteolysis; proteolytic enzymes; kinetics; enzyme specificity; hydrolysis of peptide bonds; bioactive peptides; demasking of peptide bonds; peptide release; modeling

Special Issue Information

Dear Colleagues,

The hydrolysis of proteins by proteolytic enzymes (proteolysis) is widespread, mainly for the implementation of degradative and regulatory functions in vivo. Proteolysis is also used in various biotechnological processes, proteomics, and food processing, etc. A wide range of protein substrates, proteolytic enzymes, and proteolysis conditions have been tested. Variation in these conditions, the use of engineered enzymes, or exposure of the reaction mixture to radiation of various origins significantly changes the course of proteolysis, which is often difficult to explain. Progress was made recently in the use of spectroscopic methods (fluorescence, FTIR, ultrasonic) to quantify changes in the conformation of polypeptide chains during proteolysis. Additionally, modern HPLC methods in combination with MS identification of peptides made it possible to reliably determine the kinetics of peptide release.

Since the first Linderstrom–Lang model of proteolysis, several have been proposed, aiming to identify kinetic patterns in specific proteolytic systems. However, there is no general model of proteolysis that can predict the rate of cleavage of any amino acid sequence, taking into account its conformation and other hydrolysis conditions. We invite authors to submit original research and review articles related to the study of various aspects of proteolysis and the prospects for the general modeling of this phenomenon.

Dr. Mikhail M. Vorob'ev
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

  • proteolysis
  • proteolytic enzymes
  • kinetics
  • enzyme specificity
  • hydrolysis of peptide bonds
  • bioactive peptides
  • demasking of peptide bonds
  • peptide release
  • modeling

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Published Papers (4 papers)

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Research

27 pages, 3207 KiB  
Article
First Insight into the Degradome of Aspergillus ochraceus: Novel Secreted Peptidases and Their Inhibitors
by Anna Shestakova, Artem Fatkulin, Daria Surkova, Alexander Osmolovskiy and Elizaveta Popova
Int. J. Mol. Sci. 2024, 25(13), 7121; https://doi.org/10.3390/ijms25137121 - 28 Jun 2024
Viewed by 1320
Abstract
Aspergillus fungi constitute a pivotal element within ecosystems, serving as both contributors of biologically active compounds and harboring the potential to cause various diseases across living organisms. The organism’s proteolytic enzyme complex, termed the degradome, acts as an intermediary in its dynamic interaction [...] Read more.
Aspergillus fungi constitute a pivotal element within ecosystems, serving as both contributors of biologically active compounds and harboring the potential to cause various diseases across living organisms. The organism’s proteolytic enzyme complex, termed the degradome, acts as an intermediary in its dynamic interaction with the surrounding environment. Using techniques such as genome and transcriptome sequencing, alongside protein prediction methodologies, we identified putative extracellular peptidases within Aspergillus ochraceus VKM-F4104D. Following manual annotation procedures, a total of 11 aspartic, 2 cysteine, 2 glutamic, 21 serine, 1 threonine, and 21 metallopeptidases were attributed to the extracellular degradome of A. ochraceus VKM-F4104D. Among them are enzymes with promising applications in biotechnology, potential targets and agents for antifungal therapy, and microbial antagonism factors. Thus, additional functionalities of the extracellular degradome, extending beyond mere protein substrate digestion for nutritional purposes, were demonstrated. Full article
(This article belongs to the Special Issue Advances in Proteolysis and Proteolytic Enzymes)
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12 pages, 1874 KiB  
Article
Phytaspase Does Not Require Proteolytic Activity for Its Stress-Induced Internalization
by Tatevik A. Torosian, Anastasia I. Barsukova, Nina V. Chichkova and Andrey B. Vartapetian
Int. J. Mol. Sci. 2024, 25(12), 6729; https://doi.org/10.3390/ijms25126729 - 19 Jun 2024
Viewed by 1114
Abstract
Phytaspases differ from other members of the plant subtilisin-like protease family by having rare aspartate cleavage specificity and unusual localization dynamics. Phytaspases are secreted from healthy plant cells but are re-internalized upon perception of death-inducing stresses. Although proteolytic activity is required for the [...] Read more.
Phytaspases differ from other members of the plant subtilisin-like protease family by having rare aspartate cleavage specificity and unusual localization dynamics. Phytaspases are secreted from healthy plant cells but are re-internalized upon perception of death-inducing stresses. Although proteolytic activity is required for the secretion of plant subtilases, its requirement for the retrograde transportation of phytaspases is currently unknown. To address this issue, we employed an approach to complement in trans the externalization of a prodomain-less form of Nicotiana tabacum phytaspase (NtPhyt) with the free prodomain in Nicotiana benthamiana leaf cells. Using this approach, the generation of the proteolytically active NtPhyt and its transport to the extracellular space at a level comparable to that of the native NtPhyt (synthesized as a canonical prodomain-containing precursor protein) were achieved. The application of this methodology to NtPhyt with a mutated catalytic Ser537 residue resulted in the secretion of the inactive, although processed (prodomain-free), protein as well. Notably, the externalized NtPhyt Ser537Ala mutant was still capable of retrograde transportation into plant cells upon the induction of oxidative stress. Our data thus indicate that the proteolytic activity of NtPhyt is dispensable for stress-induced retrograde transport of the enzyme. Full article
(This article belongs to the Special Issue Advances in Proteolysis and Proteolytic Enzymes)
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15 pages, 1366 KiB  
Article
Modeling of the Peptide Release during Proteolysis of β-Lactoglobulin by Trypsin with Consideration of Peptide Bond Demasking
by Mikhail M. Vorob’ev
Int. J. Mol. Sci. 2023, 24(15), 11929; https://doi.org/10.3390/ijms241511929 - 25 Jul 2023
Cited by 3 | Viewed by 1547
Abstract
Prospects for predicting the fragmentation of polypeptide chains during their enzymatic hydrolysis using proteolysis models are considered. The opening of the protein substrate during proteolysis and the exposure of its internal peptide bonds for a successful enzymatic attack, the so-called demasking process, were [...] Read more.
Prospects for predicting the fragmentation of polypeptide chains during their enzymatic hydrolysis using proteolysis models are considered. The opening of the protein substrate during proteolysis and the exposure of its internal peptide bonds for a successful enzymatic attack, the so-called demasking process, were taken into account. The two-step proteolysis model was used, including the parameters of demasking and the rate constants of hydrolysis of enzyme-specific peptide bonds. Herein, we have presented an algorithm for calculating the concentrations of intermediate and final peptide fragments depending on the time of hydrolysis or the degree of hydrolysis. The intermediate peptide fragments with two or one internal specific peptide bond were considered. The fragmentation of β-lactoglobulin (β-LG) by trypsin was predicted, and the calculated concentration curves for peptide fragments were compared with the experimental dependences of the concentrations on the degree of hydrolysis. Numerical parameters were proposed that characterize the concentration curves for intermediate and final peptide fragments, and they were used to compare the calculated and experimental dependences. The predicted distribution of the peptide fragments corresponded to the experimental data on the peptide release during the proteolysis of β-LG by trypsin. Full article
(This article belongs to the Special Issue Advances in Proteolysis and Proteolytic Enzymes)
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16 pages, 3791 KiB  
Article
Proteolysis of Micellar β-Casein by Trypsin: Secondary Structure Characterization and Kinetic Modeling at Different Enzyme Concentrations
by Mikhail M. Vorob’ev, Burçin Dersu Açıkgöz, Günnur Güler, Andrey V. Golovanov and Olga V. Sinitsyna
Int. J. Mol. Sci. 2023, 24(4), 3874; https://doi.org/10.3390/ijms24043874 - 15 Feb 2023
Cited by 4 | Viewed by 3217
Abstract
Tryptic proteolysis of protein micelles was studied using β-casein (β-CN) as an example. Hydrolysis of specific peptide bonds in β-CN leads to the degradation and rearrangement of the original micelles and the formation of new nanoparticles from their fragments. Samples of these nanoparticles [...] Read more.
Tryptic proteolysis of protein micelles was studied using β-casein (β-CN) as an example. Hydrolysis of specific peptide bonds in β-CN leads to the degradation and rearrangement of the original micelles and the formation of new nanoparticles from their fragments. Samples of these nanoparticles dried on a mica surface were characterized by atomic force microscopy (AFM) when the proteolytic reaction had been stopped by tryptic inhibitor or by heating. The changes in the content of β-sheets, α-helices, and hydrolysis products during proteolysis were estimated by using Fourier-transform infrared (FTIR) spectroscopy. In the current study, a simple kinetic model with three successive stages is proposed to predict the rearrangement of nanoparticles and the formation of proteolysis products, as well as changes in the secondary structure during proteolysis at various enzyme concentrations. The model determines for which steps the rate constants are proportional to the enzyme concentration, and in which intermediate nano-components the protein secondary structure is retained and in which it is reduced. The model predictions were in agreement with the FTIR results for tryptic hydrolysis of β-CN at different concentrations of the enzyme. Full article
(This article belongs to the Special Issue Advances in Proteolysis and Proteolytic Enzymes)
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