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Biomolecules
Special Issues
Supramolecular Protein Structures
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Supramolecular Protein Structures

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (22 January 2022) | Viewed by 15782

Special Issue Editor

Prof. Dr. Victoria Bunik

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Guest Editor
1. Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
2. Department of Biochemistry, Sechenov University, 105043 Moscow, Russia
3. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
Interests: interplay between metabolism and signaling; intracellular compartmentation; metabolic regulation; multienzyme complexes of 2-oxo acid dehydrogenases; organization of metabolic pathways; protein structure–function relationship; supramolecular structures
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, the biological sciences have faced tremendous progress in the development of different analytic and genetic techniques to thoroughly identify and characterize the molecular components of different biosystems. Reductionistic approaches continue to provide biologists with deciphered genomes and tools for their manipulation, resolved structures of varied proteins, and functional parameters of biological catalysts. To use all the knowledge accumulated by the analysis, for our holistic understanding of a biosystem, particularly in determining our ability to direct its regulation, a synthesis of the current knowledge on particular cellular components is required. Understanding the principles and regulation of the homo- and hetero-oligomerization of proteins in vitro and in vivo, and the role of these processes in the formation of supramolecular structures paving the way to cellular compartmentation and metabolic regulation, represents a significant step in this synthesis.

We would like to promote this step by collecting contributions for this Special Issue from different specialists, thus supporting an interface for the exchange of methods and opinions between the related scientific fields, employing their specific approaches and backgrounds. This Special Issue intends to consider: (i) molecular mechanisms of the protein interactions with other cellular components, such as proteins, lipids, and nucleic acids; (2) multienzyme complexes and metabolomes (i.e., associates of the enzymes of a certain pathway); (3) regulatory complexes and mechanisms of their transient formation and reorganization in response to specific stimuli; (4) methodical and bioinformatics approaches to characterize the multiprotein complexes and supramolecular structures; and (5) the significance of protein interactions with other molecular components of a cell in heath and disease.

This Special Issue of Biomolecules invites your contributions on these and related topics, either in the form of original research articles or reviews.

Prof. Dr. Victoria Bunik
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. Biomolecules 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 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

  • isoenzyme- and isoform-specific protein complexes
  • metabolite compartmentation
  • microreactors
  • microcompartments
  • multienzyme complexes
  • protein–protein interactions
  • protein–lipid interactions
  • protein–nucleic-acid interactions
  • protein complexes in signaling
  • supramolecular organization

Published Papers (5 papers)

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Research

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12 pages, 2970 KiB  
Communication
Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen
by Olivier Nicolas Lemaire, Marie-Caroline Müller, Jörg Kahnt and Tristan Wagner
Biomolecules 2021, 11(11), 1679; https://doi.org/10.3390/biom11111679 - 11 Nov 2021
Cited by 3 | Viewed by 1650
Abstract
Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable [...] Read more.
Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg2+-site, the Mg2+-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs. Full article
(This article belongs to the Special Issue Supramolecular Protein Structures)
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Review

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22 pages, 3054 KiB  
Review
Regulation of p53 Function by Formation of Non-Nuclear Heterologous Protein Complexes
by Lev Zavileyskiy and Victoria Bunik
Biomolecules 2022, 12(2), 327; https://doi.org/10.3390/biom12020327 - 18 Feb 2022
Cited by 6 | Viewed by 4425
Abstract
A transcription factor p53 is activated upon cellular exposure to endogenous and exogenous stresses, triggering either homeostatic correction or cell death. Depending on the stress level, often measurable as DNA damage, the dual outcome is supported by p53 binding to a number of [...] Read more.
A transcription factor p53 is activated upon cellular exposure to endogenous and exogenous stresses, triggering either homeostatic correction or cell death. Depending on the stress level, often measurable as DNA damage, the dual outcome is supported by p53 binding to a number of regulatory and metabolic proteins. Apart from the nucleus, p53 localizes to mitochondria, endoplasmic reticulum and cytosol. We consider non-nuclear heterologous protein complexes of p53, their structural determinants, regulatory post-translational modifications and the role in intricate p53 functions. The p53 heterologous complexes regulate the folding, trafficking and/or action of interacting partners in cellular compartments. Some of them mainly sequester p53 (HSP proteins, G6PD, LONP1) or its partners (RRM2B, PRKN) in specific locations. Formation of other complexes (with ATP2A2, ATP5PO, BAX, BCL2L1, CHCHD4, PPIF, POLG, SOD2, SSBP1, TFAM) depends on p53 upregulation according to the stress level. The p53 complexes with SIRT2, MUL1, USP7, TXN, PIN1 and PPIF control regulation of p53 function through post-translational modifications, such as lysine acetylation or ubiquitination, cysteine/cystine redox transformation and peptidyl-prolyl cis-trans isomerization. Redox sensitivity of p53 functions is supported by (i) thioredoxin-dependent reduction of p53 disulfides, (ii) inhibition of the thioredoxin-dependent deoxyribonucleotide synthesis by p53 binding to RRM2B and (iii) changed intracellular distribution of p53 through its oxidation by CHCHD4 in the mitochondrial intermembrane space. Increasing knowledge on the structure, function and (patho)physiological significance of the p53 heterologous complexes will enable a fine tuning of the settings-dependent p53 programs, using small molecule regulators of specific protein–protein interactions of p53. Full article
(This article belongs to the Special Issue Supramolecular Protein Structures)
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16 pages, 2455 KiB  
Review
The Assembly of Super-Complexes in the Plant Chloroplast
by Kezhen Qin, Alisdair R. Fernie and Youjun Zhang
Biomolecules 2021, 11(12), 1839; https://doi.org/10.3390/biom11121839 - 7 Dec 2021
Cited by 5 | Viewed by 3581
Abstract
Increasing evidence has revealed that the enzymes of several biological pathways assemble into larger supramolecular structures called super-complexes. Indeed, those such as association of the mitochondrial respiratory chain complexes play an essential role in respiratory activity and promote metabolic fitness. Dynamically assembled super-complexes [...] Read more.
Increasing evidence has revealed that the enzymes of several biological pathways assemble into larger supramolecular structures called super-complexes. Indeed, those such as association of the mitochondrial respiratory chain complexes play an essential role in respiratory activity and promote metabolic fitness. Dynamically assembled super-complexes are able to alternate between participating in large complexes and existing in a free state. However, the functional significance of the super-complexes is not entirely clear. It has been proposed that the organization of respiratory enzymes into super-complexes could reduce oxidative damage and increase metabolism efficiency. There are several protein complexes that have been revealed in the plant chloroplast, yet little research has been focused on the formation of super-complexes in this organelle. The photosystem I and light-harvesting complex I super-complex’s structure suggests that energy absorbed by light-harvesting complex I could be efficiently transferred to the PSI core by avoiding concentration quenching. Here, we will discuss in detail core complexes of photosystem I and II, the chloroplast ATPase the chloroplast electron transport chain, the Calvin–Benson cycle and a plastid localized purinosome. In addition, we will also describe the methods to identify these complexes. Full article
(This article belongs to the Special Issue Supramolecular Protein Structures)
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13 pages, 1420 KiB  
Review
Modification of Glyceraldehyde-3-Phosphate Dehydrogenase with Nitric Oxide: Role in Signal Transduction and Development of Apoptosis
by Vladimir I. Muronetz, Maria V. Medvedeva, Irina A. Sevostyanova and Elena V. Schmalhausen
Biomolecules 2021, 11(11), 1656; https://doi.org/10.3390/biom11111656 - 8 Nov 2021
Cited by 9 | Viewed by 2336
Abstract
This review focuses on the consequences of GAPDH S-nitrosylation at the catalytic cysteine residue. The widespread hypothesis according to which S-nitrosylation causes a change in GAPDH structure and its subsequent binding to the Siah1 protein is considered in detail. It is [...] Read more.
This review focuses on the consequences of GAPDH S-nitrosylation at the catalytic cysteine residue. The widespread hypothesis according to which S-nitrosylation causes a change in GAPDH structure and its subsequent binding to the Siah1 protein is considered in detail. It is assumed that the GAPDH complex with Siah1 is transported to the nucleus by carrier proteins, interacts with nuclear proteins, and induces apoptosis. However, there are several conflicting and unproven elements in this hypothesis. In particular, there is no direct confirmation of the interaction between the tetrameric GAPDH and Siah1 caused by S-nitrosylation of GAPDH. The question remains as to whether the translocation of GAPDH into the nucleus is caused by S-nitrosylation or by some other modification of the catalytic cysteine residue. The hypothesis of the induction of apoptosis by oxidation of GAPDH is considered. This oxidation leads to a release of the coenzyme NAD+ from the active center of GAPDH, followed by the dissociation of the tetramer into subunits, which move to the nucleus due to passive transport and induce apoptosis. In conclusion, the main tasks are summarized, the solutions to which will make it possible to more definitively establish the role of nitric oxide in the induction of apoptosis. Full article
(This article belongs to the Special Issue Supramolecular Protein Structures)
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20 pages, 2242 KiB  
Review
Update on Thiamine Triphosphorylated Derivatives and Metabolizing Enzymatic Complexes
by Lucien Bettendorff
Biomolecules 2021, 11(11), 1645; https://doi.org/10.3390/biom11111645 - 7 Nov 2021
Cited by 13 | Viewed by 2693
Abstract
While the cellular functions of the coenzyme thiamine (vitamin B1) diphosphate (ThDP) are well characterized, the triphosphorylated thiamine derivatives, thiamine triphosphate (ThTP) and adenosine thiamine triphosphate (AThTP), still represent an intriguing mystery. They are present, generally in small amounts, in nearly all organisms, [...] Read more.
While the cellular functions of the coenzyme thiamine (vitamin B1) diphosphate (ThDP) are well characterized, the triphosphorylated thiamine derivatives, thiamine triphosphate (ThTP) and adenosine thiamine triphosphate (AThTP), still represent an intriguing mystery. They are present, generally in small amounts, in nearly all organisms, bacteria, fungi, plants, and animals. The synthesis of ThTP seems to require ATP synthase by a mechanism similar to ATP synthesis. In E. coli, ThTP is synthesized during amino acid starvation, while in plants, its synthesis is dependent on photosynthetic processes. In E. coli, ThTP synthesis probably requires oxidation of pyruvate and may play a role at the interface between energy and amino acid metabolism. In animal cells, no mechanism of regulation is known. Cytosolic ThTP levels are controlled by a highly specific cytosolic thiamine triphosphatase (ThTPase), coded by thtpa, and belonging to the ubiquitous family of the triphosphate tunnel metalloenzymes (TTMs). While members of this protein family are found in nearly all living organisms, where they bind organic and inorganic triphosphates, ThTPase activity seems to be restricted to animals. In mammals, THTPA is ubiquitously expressed with probable post-transcriptional regulation. Much less is known about the recently discovered AThTP. In E. coli, AThTP is synthesized by a high molecular weight protein complex from ThDP and ATP or ADP in response to energy stress. A better understanding of these two thiamine derivatives will require the use of transgenic models. Full article
(This article belongs to the Special Issue Supramolecular Protein Structures)
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