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Protein Folding and Protein Engineering by Combination of Domains: When One plus One Is More than Two

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 6696

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Special Issue Editors

Prof. Dr. Alexei V. Finkelstein

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Guest Editor

Laboratory of Protein Physics, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
Interests: protein physics; protein structure; protein folding; protein folding intermediates; protein design; phase transitions; phase transition kinetics; transition states; antifreeze proteins; amyloids; protein bioinformatics
Special Issues, Collections and Topics in MDPI journals

Dr. Vitalii Balobanov

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Guest Editor

Institute of Protein Research, Pushchino, 142290 Moscow, Russia
Interests: protein engineering; protein physics; protein structure; phase transitions; amyloids

Special Issue Information

Dear Colleagues,

The combination and rearrangement of domains is one of the main pathways for protein evolution. The combination of several domains can yield results that exceed the sum of their properties. It is not surprising that this pathway is also attractive for protein engineering. Combining domains as building blocks provides an amazing variety of function combinations. Domain combinations can increase the specificity of enzymes; act as links between domains that have functional roles; mutually regulate activities; combine functions in a single chain that can act independently, consistently, or in a new context, and provide a structural basis for the development of entirely new functions.

We invite colleagues whose work is devoted to the design and engineering of proteins to participate in this Special Issue. We are seeking original research articles and reviews that describe advances in protein engineering through a combination of functional and structural domains, as well as articles and reviews devoted to the analysis of these achievements and the search for prospects for the application of this approach.

We look forward to receiving your contributions!

Prof. Dr. Alexei V. Finkelstein
Dr. Vitalii Balobanov
Guest Editors

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. Molecules is an international peer-reviewed open access semimonthly 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 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

protein design
protein engineering
protein structure
protein folding
phase transitions
antifreeze proteins
amyloids

Published Papers (4 papers)

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Research

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10 pages, 2903 KiB

Open AccessArticle

The New Functional Hybrid Chaperone Protein ADGroEL–SacSm

by Alisa Mikhaylina, Natalia Lekontseva, Victor Marchenkov, Viktoria Kolesnikova, Albina Khairetdinova, Oleg Nikonov and Vitalii Balobanov

Molecules 2023, 28(17), 6196; https://doi.org/10.3390/molecules28176196 - 23 Aug 2023

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Abstract

The creation of new proteins by combining natural domains is a commonly used technique in protein engineering. In this work, we have tested the possibilities and limitations of using circular homo-oligomeric Sm-like proteins as a basis for attaching other domains. Attachment to such a stable base should bring target domains together and keep them in the correct mutual orientation. We chose a circular homoheptameric Sm-like protein from Sulfolobus acidocaldarius as a stable backbone and the apical domain of the GroEL chaperone protein as the domain of study. This domain by itself, separated from the rest of the GroEL molecule, does not form an oligomeric ring. In our design, the hyperstable SacSm held the seven ADGroELs together and forced them to oligomerize. The designed hybrid protein was obtained and studied with various physical and chemical methods. Stepwise assembly and self-organization of this protein have been shown. First, the SacSm base was assembled, and then ADGroEL was folded on it. Functional testing showed that the obtained fusion protein was able to bind the same non-native proteins as the full-length GroEL chaperone. It also reduced the aggregation of a number of proteins when they were heated, which confirms its chaperone activity. Thus, the engineering path we chose made it possible to create an efficient thermostable chaperone. The result obtained shows the productivity of the way we chose for the creation and stabilization of oligomeric proteins. Full article

(This article belongs to the Special Issue Protein Folding and Protein Engineering by Combination of Domains: When One plus One Is More than Two)

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16 pages, 8757 KiB

Open AccessArticle

In Vivo Incorporation of Photoproteins into GroEL Chaperonin Retaining Major Structural and Functional Properties

by Victor Marchenkov, Tanya Ivashina, Natalia Marchenko, Natalya Ryabova, Olga Selivanova, Alexander Timchenko, Hiroshi Kihara, Vladimir Ksenzenko and Gennady Semisotnov

Molecules 2023, 28(4), 1901; https://doi.org/10.3390/molecules28041901 - 16 Feb 2023

Cited by 2 | Viewed by 1296

Abstract

The incorporation of photoproteins into proteins of interest allows the study of either their localization or intermolecular interactions in the cell. Here we demonstrate the possibility of in vivo incorporating the photoprotein Aequorea victoria enhanced green fluorescent protein (EGFP) or Gaussia princeps luciferase (GLuc) into the tetradecameric quaternary structure of GroEL chaperonin and describe some physicochemical properties of the labeled chaperonin. Using size-exclusion and affinity chromatography, electrophoresis, fluorescent and electron transmission microscopy (ETM), small-angle X-ray scattering (SAXS), and bioluminescence resonance energy transfer (BRET), we show the following: (i) The GroEL₁₄-EGFP is evenly distributed within normally divided E. coli cells, while gigantic undivided cells are characterized by the uneven distribution of the labeled GroEL₁₄ which is mainly localized close to the cellular periplasm; (ii) EGFP and likely GLuc are located within the inner cavity of one of the two GroEL chaperonin rings and do not essentially influence the protein oligomeric structure; (iii) GroEL₁₄ containing either EGFP or GLuc is capable of interacting with non-native proteins and the cochaperonin GroES. Full article

(This article belongs to the Special Issue Protein Folding and Protein Engineering by Combination of Domains: When One plus One Is More than Two)

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8 pages, 1584 KiB

Open AccessCommunication

Enzymatic Protein Immobilization on Amino-Functionalized Nanoparticles

by Qun Ma, Boqiang He, Guojin Tang, Ran Xie and Peng Zheng

Molecules 2023, 28(1), 379; https://doi.org/10.3390/molecules28010379 - 02 Jan 2023

Cited by 1 | Viewed by 1803

Abstract

The immobilization of proteins on nanoparticles has received much attention in recent years. Among different approaches, enzymatic protein immobilization shows unique advantages because of its site-specific connection. OaAEP1 is a recently engineered peptide ligase which can specifically recognize an N-terminal GL residue (NH₂–Gly–Leu) and a C-terminal NGL amino acid residue (Asn–Gly–Leu–COOH) and ligates them efficiently. Herein, we report OaAEP1-mediated protein immobilization on synthetic magnetic nanoparticles. Our work showed that OaAEP1 could mediate C-terminal site-specific protein immobilization on the amino-functionalized Fe₃O₄ nanoparticles. Our work demonstrates a new method for site-specific protein immobilization on nanoparticles. Full article

(This article belongs to the Special Issue Protein Folding and Protein Engineering by Combination of Domains: When One plus One Is More than Two)

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Review

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13 pages, 1938 KiB

Open AccessReview

Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics

by Anton A. Komar

Molecules 2023, 28(5), 2383; https://doi.org/10.3390/molecules28052383 - 05 Mar 2023

Viewed by 2155

Abstract

The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure–activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation. Full article

(This article belongs to the Special Issue Protein Folding and Protein Engineering by Combination of Domains: When One plus One Is More than Two)

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