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Biophysica
Special Issues
Protein Engineering: The Present and the Future
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Protein Engineering: The Present and the Future

A special issue of Biophysica (ISSN 2673-4125).

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 15760

Special Issue Editor

Prof. Dr. Javier Sancho

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50009 Zaragoza, Spain
Interests: protein stability; protein engineering; protein folding; biocomputation; drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteins are simple polymers with extraordinary properties of enormous biological and economic value. They are widely used in biological catalysis, as key components of analytical methods, or as highly specific drugs for personalized medicine. Protein engineering uses synthetic methods that allow the application of rational physicochemical knowledge and the power of evolutionary approaches to the goal of creating, in useful quantities, novel proteins that exhibit advantageous properties. In some cases, the challenge is to stabilize a natural protein for cheaper production, easier transport and storage, and longer operational life. In others, completely new properties are sought, which requires a greater amount of design. Significant advances in the understanding of protein energetics, in computational methods for sequence and structural analysis, and in synthetic methods, combined with growing economic and social interest in proteins, claim the logical transformation of Protein Engineering into a predictive quantitative discipline, where success is guaranteed by good design. In this Special Issue we will show, with examples of their application to specific proteins, the most advanced methods that anticipate the transformation of Protein Engineering from an art for practitioners to a reliable technology.

Prof. Dr. Javier Sancho
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. Biophysica is an international peer-reviewed open access quarterly 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 1000 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
  • Computational methods 
  • Evolutionary methods 
  • Protein stabilization 
  • Protein tailoring 
  • Industrial proteins 
  • Medicinal proteins

Published Papers (4 papers)

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Editorial

Jump to: Research, Review

2 pages, 182 KiB  
Editorial
Protein Engineering: The Present and the Future
by Javier Sancho
Biophysica 2022, 2(2), 111-112; https://doi.org/10.3390/biophysica2020011 - 29 Apr 2022
Viewed by 2400
Abstract
Yes, we are made of proteins, and yes, we can profit from them [...] Full article
(This article belongs to the Special Issue Protein Engineering: The Present and the Future)

Research

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7 pages, 689 KiB  
Article
Bioluminescence Resonance Energy Transfer (BRET) Allows Monitoring the Barnase-Barstar Complex In Vivo
by Victor Marchenkov, Tanya Ivashina, Natalia Marchenko, Vladimir Ksenzenko and Gennady Semisotnov
Biophysica 2022, 2(1), 72-78; https://doi.org/10.3390/biophysica2010007 - 07 Feb 2022
Cited by 2 | Viewed by 2587
Abstract
Bioluminescence resonance energy transfer (BRET) seems to be a promising biophysical technique to study protein–protein interactions within living cells due to a very specific reaction of bioluminescence that essentially decreases the background of other cellular components and light-induced destruction of biomacromolecules. An important [...] Read more.
Bioluminescence resonance energy transfer (BRET) seems to be a promising biophysical technique to study protein–protein interactions within living cells due to a very specific reaction of bioluminescence that essentially decreases the background of other cellular components and light-induced destruction of biomacromolecules. An important direction of the development of this technique is the study of known strong protein–protein complexes in vivo and the estimation of an average distance between chromophores of the donor and acceptor. Here, we demonstrate an in vivo interaction between barnase fused with luciferase (from Renilla reniformis, RLuc) and barstar fused with EGFP (enhanced green fluorescent protein of Aequorea victoria) monitored by BRET. The distance between the luciferase and EGFP chromophores within the complex has been evaluated as equal to (56 ± 2) Å. Full article
(This article belongs to the Special Issue Protein Engineering: The Present and the Future)
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7 pages, 1383 KiB  
Communication
Old Enzyme, New Role: The β-Glucosidase BglC of Streptomyces scabiei Interferes with the Plant Defense Mechanism by Hydrolyzing Scopolin
by Benoit Deflandre and Sébastien Rigali
Biophysica 2022, 2(1), 1-7; https://doi.org/10.3390/biophysica2010001 - 22 Dec 2021
Cited by 5 | Viewed by 3256
Abstract
The beta-glucosidase BglC fulfills multiple functions in both primary metabolism and induction of pathogenicity of Streptomyces scabiei, the causative agent of common scab in root and tuber crops. Indeed, this enzyme hydrolyzes cellobiose and cellotriose to feed glycolysis with glucose directly and [...] Read more.
The beta-glucosidase BglC fulfills multiple functions in both primary metabolism and induction of pathogenicity of Streptomyces scabiei, the causative agent of common scab in root and tuber crops. Indeed, this enzyme hydrolyzes cellobiose and cellotriose to feed glycolysis with glucose directly and modifies the intracellular concentration of these cello-oligosaccharides, which are the virulence elicitors. The inactivation of bglC led to unexpected phenotypes such as the constitutive overproduction of thaxtomin A, the main virulence determinant of S. scabiei. In this work, we reveal a new target substrate of BglC, the phytoalexin scopolin. Removal of the glucose moiety of scopolin generates scopoletin, a potent inhibitor of thaxtomin A production. The hydrolysis of scopolin by BglC displayed substrate inhibition kinetics, which contrasts with the typical Michaelis–Menten saturation curve previously observed for the degradation of its natural substrate cellobiose. Our work, therefore, reveals that BglC targets both cello-oligosaccharide elicitors emanating from the hosts of S. scabiei, and the scopolin phytoalexin generated by the host defense mechanisms, thereby occupying a key position to fine-tune the production of the main virulence determinant thaxtomin A. Full article
(This article belongs to the Special Issue Protein Engineering: The Present and the Future)
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Review

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20 pages, 1370 KiB  
Review
Amyloid-β Oligomers: Multiple Moving Targets
by Dylan Shea and Valerie Daggett
Biophysica 2022, 2(2), 91-110; https://doi.org/10.3390/biophysica2020010 - 28 Apr 2022
Cited by 18 | Viewed by 6255
Abstract
Alzheimer’s Disease (AD) is a neurodegenerative disorder that is characterized clinically by progressive cognitive decline and pathologically by the β-sheet rich fibril plaque deposition of the amyloid-β (Aβ) peptide in the brain. While plaques are a hallmark of AD, plaque burden is not [...] Read more.
Alzheimer’s Disease (AD) is a neurodegenerative disorder that is characterized clinically by progressive cognitive decline and pathologically by the β-sheet rich fibril plaque deposition of the amyloid-β (Aβ) peptide in the brain. While plaques are a hallmark of AD, plaque burden is not correlated with cognitive impairment. Instead, Aβ oligomers formed during the aggregation process represent the main agents of neurotoxicity, which occurs 10–20 years before patients begin to show symptoms. These oligomers are dynamic in nature and represented by a heterogeneous distribution of aggregates ranging from low- to high-molecular weight, some of which are toxic while others are not. A major difficulty in determining the pathological mechanism(s) of Aβ, developing reliable diagnostic markers for early-stage detection, as well as effective therapeutics for AD are the differentiation and characterization of oligomers formed throughout disease propagation based on their molecular features, effects on biological function, and relevance to disease propagation and pathology. Thus, it is critical to methodically identify the mechanisms of Aβ aggregation and toxicity, as well as describe the roles of different oligomers and aggregates in disease progression and molecular pathology. Here, we describe a variety of biophysical techniques used to isolate and characterize a range of Aβ oligomer populations, as well as discuss proposed mechanisms of toxicity and therapeutic interventions aimed at specific assemblies formed during the aggregation process. The approaches being used to map the misfolding and aggregation of Aβ are like what was done during the fundamental early studies, mapping protein folding pathways using combinations of biophysical techniques in concert with protein engineering. Such information is critical to the design and molecular engineering of future diagnostics and therapeutics for AD. Full article
(This article belongs to the Special Issue Protein Engineering: The Present and the Future)
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