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Protein Folding, towards the Comprehensive Understanding from Various Aspects
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Protein Folding, towards the Comprehensive Understanding from Various Aspects

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

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 30931

Special Issue Editor

Dr. Takeshi Kikuchi

E-Mail Website
Guest Editor
College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan
Interests: computational chemistry; biophysics; bioinformatics; protein structure
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The great progress in the 3D structural prediction of proteins has been achieved in recent years. The main issue is turning to the elucidation of the folding mechanism of a protein to it native structure. The folding mechanisms of proteins has been studied by many researchers using experimental, theoretical and computational tools, but we do not have a general and unified view on protein folding. Protein folding includes several phenomena with various time scales and does not allow for making a simple speculation. Thus, protein folding is still a challenging issue. Proteins fold into their native 3D structures according to their amino acid sequence information. It is also an interesting problem to decode the information of the 3D structure formation in the amino acid sequence of a protein. How the folding mechanism of a protein changes during its evolution is another interesting problem. Such research will also serve to clarify the various properties of intrinsically disordered proteins, including their functions.

On the other hand, protein misfolding sometimes causes diseases such as amyloidosis. For the therapy of such a disease, the understanding of protein folding mechanisms are indispensable. That is, the elucidation of the protein folding mechanism will help to develop therapeutic methods of misfolding disease.

Thus, we are planning this Special Issue for the aim of comprehensive understanding of protein folding and misfolding in the various aspects, that is, experiment, theory, computation evolution, medical issues and so on. We are also interesting to understand the relationships of folding to functions of various proteins. We are awaiting your contribution.

Dr. Takeshi Kikuchi
Guest Editor

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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

  • protein 3D structure formation
  • evolution
  • bioinformatics
  • computational and experimental techniques
  • folding disease
  • function
  • protein folding in vivo

Published Papers (22 papers)

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Research

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13 pages, 1800 KiB  
Article
Influence of Nε-Lysine Acetylation on the Formation of Protein Aggregates and Antibiotic Persistence in E. coli
by Karolina Stojowska-Swędrzyńska, Dorota Kuczyńska-Wiśnik and Ewa Laskowska
Molecules 2024, 29(2), 383; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules29020383 - 12 Jan 2024
Viewed by 900
Abstract
Numerous studies indicate that reversible Nε-lysine acetylation in bacteria may play a key role in the regulation of metabolic processes, transcription and translation, biofilm formation, virulence, and drug resistance. Using appropriate mutant strains deficient in non-enzymatic acetylation and enzymatic acetylation or [...] Read more.
Numerous studies indicate that reversible Nε-lysine acetylation in bacteria may play a key role in the regulation of metabolic processes, transcription and translation, biofilm formation, virulence, and drug resistance. Using appropriate mutant strains deficient in non-enzymatic acetylation and enzymatic acetylation or deacetylation pathways, we investigated the influence of protein acetylation on cell viability, protein aggregation, and persister formation in Escherichia coli. Lysine acetylation was found to increase protein aggregation and cell viability under the late stationary phase. Moreover, increased lysine acetylation stimulated the formation of persisters. These results suggest that acetylation-dependent aggregation may improve the survival of bacteria under adverse conditions (such as the late stationary phase) and during antibiotic treatment. Further experiments revealed that acetylation-favorable conditions may increase persister formation in Klebsiella pneumoniae clinical isolate. However, the exact mechanisms underlying the relationship between acetylation and persistence in this pathogen remain to be elucidated. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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14 pages, 5288 KiB  
Article
Influence of Amino Acid Substitutions in ApoMb on Different Stages of Unfolding of Amyloids
by Natalya Katina, Victor Marchenkov, Natalya Ryabova, Nelly Ilyina, Natalia Marchenko, Vitalii Balobanov and Alexey Finkelstein
Molecules 2023, 28(23), 7736; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28237736 - 23 Nov 2023
Viewed by 694
Abstract
To date, most research on amyloid aggregation has focused on describing the structure of amyloids and the kinetics of their formation, while the conformational stability of fibrils remains insufficiently explored. The aim of this work was to investigate the effect of amino acid [...] Read more.
To date, most research on amyloid aggregation has focused on describing the structure of amyloids and the kinetics of their formation, while the conformational stability of fibrils remains insufficiently explored. The aim of this work was to investigate the effect of amino acid substitutions on the stability of apomyoglobin (ApoMb) amyloids. A study of the amyloid unfolding of ApoMb and its six mutant variants by urea has been carried out. Changes in the structural features of aggregates during unfolding were recorded by far-UV CD and native electrophoresis. It was shown that during the initial stage of denaturation, amyloids’ secondary structure partially unfolds. Then, the fibrils undergo dissociation and form intermediate aggregates weighing approximately 1 MDa, which at the last stage of unfolding decompose into 18 kDa monomeric unfolded molecules. The results of unfolding transitions suggest that the stability of the studied amyloids relative to the intermediate aggregates and of the latter relative to unfolded monomers is higher for ApoMb variants with substitutions that increase the hydrophobicity of the residues. The results presented provide a new insight into the mechanism of stabilization of protein aggregates and can serve as a base for further investigations of the amyloids’ stability. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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21 pages, 3716 KiB  
Article
Conformational Stability of the N-Terminal Region of MDM2
by Bruno Rizzuti, Olga Abian, Adrián Velazquez-Campoy and José L. Neira
Molecules 2023, 28(22), 7578; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28227578 - 14 Nov 2023
Viewed by 668
Abstract
MDM2 is an E3 ubiquitin ligase which is crucial for the degradation and inhibition of the key tumor-suppressor protein p53. In this work, we explored the stability and the conformational features of the N-terminal region of MDM2 (N-MDM2), through which it binds to [...] Read more.
MDM2 is an E3 ubiquitin ligase which is crucial for the degradation and inhibition of the key tumor-suppressor protein p53. In this work, we explored the stability and the conformational features of the N-terminal region of MDM2 (N-MDM2), through which it binds to the p53 protein as well as other protein partners. The isolated domain possessed a native-like conformational stability in a narrow pH range (7.0 to 10.0), as shown by intrinsic and 8-anilinonapthalene-1-sulfonic acid (ANS) fluorescence, far-UV circular dichroism (CD), and size exclusion chromatography (SEC). Guanidinium chloride (GdmCl) denaturation followed by intrinsic and ANS fluorescence, far-UV CD and SEC at physiological pH, and differential scanning calorimetry (DSC) and thermo-fluorescence experiments showed that (i) the conformational stability of isolated N-MDM2 was very low; and (ii) unfolding occurred through the presence of several intermediates. The presence of a hierarchy in the unfolding intermediates was also evidenced through DSC and by simulating the unfolding process with the help of computational techniques based on constraint network analysis (CNA). We propose that the low stability of this protein is related to its inherent flexibility and its ability to interact with several molecular partners through different routes. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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12 pages, 11110 KiB  
Article
AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology
by Pawel Dabrowski-Tumanski and Andrzej Stasiak
Molecules 2023, 28(22), 7462; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28227462 - 7 Nov 2023
Cited by 2 | Viewed by 1160
Abstract
AlphaFold is a groundbreaking deep learning tool for protein structure prediction. It achieved remarkable accuracy in modeling many 3D structures while taking as the user input only the known amino acid sequence of proteins in question. Intriguingly though, in the early steps of [...] Read more.
AlphaFold is a groundbreaking deep learning tool for protein structure prediction. It achieved remarkable accuracy in modeling many 3D structures while taking as the user input only the known amino acid sequence of proteins in question. Intriguingly though, in the early steps of each individual structure prediction procedure, AlphaFold does not respect topological barriers that, in real proteins, result from the reciprocal impermeability of polypeptide chains. This study aims to investigate how this failure to respect topological barriers affects AlphaFold predictions with respect to the topology of protein chains. We focus on such classes of proteins that, during their natural folding, reproducibly form the same knot type on their linear polypeptide chain, as revealed by their crystallographic analysis. We use partially artificial test constructs in which the mutual non-permeability of polypeptide chains should not permit the formation of complex composite knots during natural protein folding. We find that despite the formal impossibility that the protein folding process could produce such knots, AlphaFold predicts these proteins to form complex composite knots. Our study underscores the necessity for cautious interpretation and further validation of topological features in protein structures predicted by AlphaFold. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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21 pages, 16913 KiB  
Article
Einstein Model of a Graph to Characterize Protein Folded/Unfolded States
by Steve Tyler, Christophe Laforge, Adrien Guzzo, Adrien Nicolaï, Gia G. Maisuradze and Patrick Senet
Molecules 2023, 28(18), 6659; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28186659 - 16 Sep 2023
Viewed by 1155
Abstract
The folded structures of proteins can be accurately predicted by deep learning algorithms from their amino-acid sequences. By contrast, in spite of decades of research studies, the prediction of folding pathways and the unfolded and misfolded states of proteins, which are intimately related [...] Read more.
The folded structures of proteins can be accurately predicted by deep learning algorithms from their amino-acid sequences. By contrast, in spite of decades of research studies, the prediction of folding pathways and the unfolded and misfolded states of proteins, which are intimately related to diseases, remains challenging. A two-state (folded/unfolded) description of protein folding dynamics hides the complexity of the unfolded and misfolded microstates. Here, we focus on the development of simplified order parameters to decipher the complexity of disordered protein structures. First, we show that any connected, undirected, and simple graph can be associated with a linear chain of atoms in thermal equilibrium. This analogy provides an interpretation of the usual topological descriptors of a graph, namely the Kirchhoff index and Randić resistance, in terms of effective force constants of a linear chain. We derive an exact relation between the Kirchhoff index and the average shortest path length for a linear graph and define the free energies of a graph using an Einstein model. Second, we represent the three-dimensional protein structures by connected, undirected, and simple graphs. As a proof of concept, we compute the topological descriptors and the graph free energies for an all-atom molecular dynamics trajectory of folding/unfolding events of the proteins Trp-cage and HP-36 and for the ensemble of experimental NMR models of Trp-cage. The present work shows that the local, nonlocal, and global force constants and free energies of a graph are promising tools to quantify unfolded/disordered protein states and folding/unfolding dynamics. In particular, they allow the detection of transient misfolded rigid states. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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18 pages, 4895 KiB  
Article
Fibrillization Process of Human Amyloid-Beta Protein (1–40) under a Molecular Crowding Environment Mimicking the Interior of Living Cells Using Cell Debris
by Mitsuhiro Hirai, Shigeki Arai and Hiroki Iwase
Molecules 2023, 28(18), 6555; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28186555 - 10 Sep 2023
Cited by 1 | Viewed by 979
Abstract
Molecular crowding environments play a crucial role in understanding the mechanisms of biological reactions. Inside living cells, a diverse array of molecules coexists within a volume fraction ranging from 10% to 30% v/v. However, conventional spectroscopic methods often face difficulties [...] Read more.
Molecular crowding environments play a crucial role in understanding the mechanisms of biological reactions. Inside living cells, a diverse array of molecules coexists within a volume fraction ranging from 10% to 30% v/v. However, conventional spectroscopic methods often face difficulties in selectively observing the structures of particular proteins or membranes within such molecularly crowded environments due to the presence of high background signals. Therefore, it is crucial to establish in vitro measurement conditions that closely resemble the intracellular environment. Meanwhile, the neutron scattering method offers a significant advantage in selectively observing target biological components, even within crowded environments. Recently, we have demonstrated a novel scattering method capable of selectively detecting the structures of targeted proteins or membranes in a closely mimicking intracellular milieu achieved utilizing whole-cell contents (deuterated-cell debris). This method relies on the inverse contrast matching technique in neutron scattering. By employing this method, we successfully observed the fibrillization process of human amyloid beta-protein (Aβ 1–40) under a molecular crowding environment (13.1% w/v cell debris, Aβ/cell debris = ~1/25 w/w) that closely mimics the interior of living cells. Aβ protein is well known as a major pathogenic component of Alzheimer’s disease. The present results combining model simulation analyses clearly show that the intracellular environment facilitates the potential formation of even more intricate higher-order aggregates of Aβ proteins than those previously reported. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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23 pages, 4299 KiB  
Article
Does a Similar 3D Structure Mean a Similar Folding Pathway? The Presence of a C-Terminal α-Helical Extension in the 3D Structure of MAX60 Drastically Changes the Folding Pathway Described for Other MAX-Effectors from Magnaporthe oryzae
by Mounia Lahfa, Assia Mouhand, Karine de Guillen, Philippe Barthe, Thomas Kroj, André Padilla and Christian Roumestand
Molecules 2023, 28(16), 6068; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28166068 - 15 Aug 2023
Cited by 1 | Viewed by 1047
Abstract
Does a similar 3D structure mean a similar folding pathway? This question is particularly meaningful when it concerns proteins sharing a similar 3D structure, but low sequence identity or homology. MAX effectors secreted by the phytopathogenic fungus Magnaporthe oryzae present such characteristics. They [...] Read more.
Does a similar 3D structure mean a similar folding pathway? This question is particularly meaningful when it concerns proteins sharing a similar 3D structure, but low sequence identity or homology. MAX effectors secreted by the phytopathogenic fungus Magnaporthe oryzae present such characteristics. They share a common 3D structure, a ß-sandwich with the same topology for all the family members, but an extremely low sequence identity/homology. In a previous study, we have investigated the folding of two MAX effectors, AVR-Pia and AVR-Pib, using High-Hydrostatic-Pressure NMR and found that they display a similar folding pathway, with a common folding intermediate. In the present work, we used a similar strategy to investigate the folding conformational landscape of another MAX effector, MAX60, and found a very different folding intermediate. Our analysis strongly supports that the presence of a C-terminal α-helical extension in the 3D structure of MAX60 could be responsible for its different folding pathway. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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22 pages, 6172 KiB  
Article
Inhibitor Design Strategy for Myostatin: Dynamics and Interaction Networks Define the Affinity and Release Mechanisms of the Inhibited Complexes
by Dóra Nagy-Fazekas, Zsolt Fazekas, Nóra Taricska, Pál Stráner, Dóra Karancsiné Menyhárd and András Perczel
Molecules 2023, 28(15), 5655; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28155655 - 26 Jul 2023
Cited by 1 | Viewed by 1274
Abstract
Myostatin, an important negative regulator of muscle mass, is a therapeutic target for muscle atrophic disorders such as muscular dystrophy. Thus, the inhibition of myostatin presents a strategy to treat these disorders. It has long been established that the myostatin prodomain is a [...] Read more.
Myostatin, an important negative regulator of muscle mass, is a therapeutic target for muscle atrophic disorders such as muscular dystrophy. Thus, the inhibition of myostatin presents a strategy to treat these disorders. It has long been established that the myostatin prodomain is a strong inhibitor of the mature myostatin, and the minimum peptide of the prodomain—corresponding to the α1-helix of its lasso-region—responsible for the inhibitory efficiency was defined and characterized as well. Here we show that the minimum peptide segment based on the growth differentiation factor 11 (GDF11), which we found to be more helical in its stand-alone solvated stfate than the similar segment of myostatin, is a promising new base scaffold for inhibitor design. The proposed inhibitory peptides in their solvated state and in complex with the mature myostatin were analyzed by in silico molecule modeling supplemented with the electronic circular dichroism spectroscopy measurements. We defined the Gaussian–Mahalanobis mean score to measure the fraction of dihedral angle-pairs close to the desired helical region of the Ramachandran-plot, carried out RING analysis of the peptide-protein interaction networks and characterized the internal motions of the complexes using our rigid-body segmentation protocol. We identified a variant—11m2—that is sufficiently ordered both in solvent and within the inhibitory complex, forms a high number of contacts with the binding-pocket and induces such changes in its internal dynamics that lead to a rigidified, permanently locked conformation that traps this peptide in the binding site. We also showed that the naturally evolved α1-helix has been optimized to simultaneously fulfill two very different roles: to function as a strong binder as well as a good leaving group. It forms an outstanding number of non-covalent interactions with the mature core of myostatin and maintains the most ordered conformation within the complex, while it induces independent movement of the gate-keeper β-hairpin segment assisting the dissociation and also results in the least-ordered solvated form which provides extra stability for the dissociated state and discourages rebinding. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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9 pages, 426 KiB  
Article
Polymer Dynamics in Glycerol–Water Mixtures
by Janez Stepišnik
Molecules 2023, 28(14), 5506; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28145506 - 19 Jul 2023
Viewed by 719
Abstract
Velocity correlation spectra (VAS) in binary mixtures of water and glycerol (G/W), obtained by measurements using the modulated gradient spin echo (MGSE) NMR method, were explained by the interactions of water molecules with clusters formed around the hydrophilic glycerol molecule, which drastically change [...] Read more.
Velocity correlation spectra (VAS) in binary mixtures of water and glycerol (G/W), obtained by measurements using the modulated gradient spin echo (MGSE) NMR method, were explained by the interactions of water molecules with clusters formed around the hydrophilic glycerol molecule, which drastically change the molecular dynamics and rheology of the mixture. It indicates a thickening of the shear viscosity, which could affect the dynamics of submerged macromolecules. The calculation of the polymer dynamics with the Langevin equations according to the Rouse model, where the friction was replaced by the memory function of the retarded friction, gave the dependence of the dynamics of the polymer on the rate of shear viscous properties of the solvent. The obtained formula was used to calculate the segmental VAS of the polymer when immersed in pure water and in a G/W mixture with 33 vol% glycerol content, taking into account the inverse proportionality between the solvent VAS and friction. The spectrum shows that in the G/W mixture, the fast movements of the polymer segments are strongly inhibited, which creates the conditions for slow processes caused by the internal interaction between the polymer segments, such as interactions that cause disordered polypeptides to spontaneously fold into biologically active protein molecules when immersed in such a solvent. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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25 pages, 4387 KiB  
Article
The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
by Qiang Sun, Xian He and Yanfang Fu
Molecules 2023, 28(13), 5164; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28135164 - 2 Jul 2023
Viewed by 2272
Abstract
Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular [...] Read more.
Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular hydrogen bondings. During folding, hydrophobic interactions are regarded to be the driving forces, especially in the initial structural collapse of a protein. Additionally, folding is guided by the strong interactions within proteins, such as intramolecular hydrogen bondings related to the α-helices and β-sheets of proteins. Therefore, a protein is divided into the folding key (FK) regions related to intramolecular hydrogen bondings and the non-folding key (non-FK) regions. Various conformations are expected for FK and non-FK regions. Different from non-FK regions, it is necessary for FK regions to form the specific conformations in folding, which are regarded as the necessary folding pathways (or “beacons”). Additionally, sequential folding is expected for the FK regions, and the intermediate state is found during folding. They are reflected on the local basins in the free energy landscape (FEL) of folding. To demonstrate the structural model, molecular dynamics (MD) simulations are conducted on the folding pathway of the TRP-cage in water. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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19 pages, 3068 KiB  
Article
L-Proline Prevents Endoplasmic Reticulum Stress in Microglial Cells Exposed to L-azetidine-2-carboxylic Acid
by Jordan Allan Piper, Nour Al Hammouri, Margo Iris Jansen, Kenneth J. Rodgers, Giuseppe Musumeci, Amolika Dhungana, Sahar Masoumeh Ghorbanpour, Laura A. Bradfield and Alessandro Castorina
Molecules 2023, 28(12), 4808; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28124808 - 16 Jun 2023
Cited by 2 | Viewed by 1614
Abstract
L-Azetidine-2-carboxylic acid (AZE) is a non-protein amino acid that shares structural similarities with its proteogenic L-proline amino acid counterpart. For this reason, AZE can be misincorporated in place of L-proline, contributing to AZE toxicity. In previous work, we have shown that AZE induces [...] Read more.
L-Azetidine-2-carboxylic acid (AZE) is a non-protein amino acid that shares structural similarities with its proteogenic L-proline amino acid counterpart. For this reason, AZE can be misincorporated in place of L-proline, contributing to AZE toxicity. In previous work, we have shown that AZE induces both polarization and apoptosis in BV2 microglial cells. However, it is still unknown if these detrimental effects involve endoplasmic reticulum (ER) stress and whether L-proline co-administration prevents AZE-induced damage to microglia. Here, we investigated the gene expression of ER stress markers in BV2 microglial cells treated with AZE alone (1000 µM), or co-treated with L-proline (50 µM), for 6 or 24 h. AZE reduced cell viability, nitric oxide (NO) secretion and caused a robust activation of the unfolded protein response (UPR) genes (ATF4, ATF6, ERN1, PERK, XBP1, DDIT3, GADD34). These results were confirmed by immunofluorescence in BV2 and primary microglial cultures. AZE also altered the expression of microglial M1 phenotypic markers (increased IL-6, decreased CD206 and TREM2 expression). These effects were almost completely prevented upon L-proline co-administration. Finally, triple/quadrupole mass spectrometry demonstrated a robust increase in AZE-bound proteins after AZE treatment, which was reduced by 84% upon L-proline co-supplementation. This study identified ER stress as a pathogenic mechanism for AZE-induced microglial activation and death, which is reversed by co-administration of L-proline. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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10 pages, 2370 KiB  
Article
Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations
by Elena Ermakova, Olga Makshakova, Rauf Kurbanov, Ilya Ibraev, Yuriy Zuev and Igor Sedov
Molecules 2023, 28(10), 4070; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28104070 - 13 May 2023
Cited by 1 | Viewed by 1372
Abstract
Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of [...] Read more.
Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of its mutants, in which the positively charged residues Arg7 and Lys8 have been replaced by alanine. All three peptides rapidly underwent spontaneous aggregation and conformational transition from random coils to beta-rich structures. The simulations reveal that the initial and essential step of the aggregation process involves peptide dimerization and the formation of small beta-sheets. A decrease in positive charge and an increase in the number of hydrophobic residues in the mutant peptides lead to an increase in the rate of their aggregation. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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Review

Jump to: Research

34 pages, 6405 KiB  
Review
Organic Synthesis and Current Understanding of the Mechanisms of CFTR Modulator Drugs Ivacaftor, Tezacaftor, and Elexacaftor
by Filipa C. Ferreira, Camilla D. Buarque and Miquéias Lopes-Pacheco
Molecules 2024, 29(4), 821; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules29040821 - 10 Feb 2024
Cited by 1 | Viewed by 2996
Abstract
The monogenic rare disease Cystic Fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance (CFTR) protein, an anion channel expressed at the apical plasma membrane of epithelial cells. The discovery and subsequent development of CFTR modulators—small molecules acting [...] Read more.
The monogenic rare disease Cystic Fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance (CFTR) protein, an anion channel expressed at the apical plasma membrane of epithelial cells. The discovery and subsequent development of CFTR modulators—small molecules acting on the basic molecular defect in CF—have revolutionized the standard of care for people with CF (PwCF), thus drastically improving their clinical features, prognosis, and quality of life. Currently, four of these drugs are approved for clinical use: potentiator ivacaftor (VX-770) alone or in combination with correctors lumacaftor, (VX-809), tezacaftor (VX-661), and elexacaftor (VX-445). Noteworthily, the triple combinatorial therapy composed of ivacaftor, tezacaftor, and elexacaftor constitutes the most effective modulator therapy nowadays for the majority of PwCF. In this review, we exploit the organic synthesis of ivacaftor, tezacaftor, and elexacaftor by providing a retrosynthetic drug analysis for these CFTR modulators. Furthermore, we describe the current understanding of the mechanisms of action (MoA’s) of these compounds by discussing several studies that report the key findings on the molecular mechanisms underlying their action on the CFTR protein. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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32 pages, 3004 KiB  
Review
Protein Misfolding in Pregnancy: Current Insights, Potential Mechanisms, and Implications for the Pathogenesis of Preeclampsia
by Bani Medegan Fagla and Irina Alexandra Buhimschi
Molecules 2024, 29(3), 610; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules29030610 - 26 Jan 2024
Viewed by 1644
Abstract
Protein misfolding disorders are a group of diseases characterized by supra-physiologic accumulation and aggregation of pathogenic proteoforms resulting from improper protein folding and/or insufficiency in clearance mechanisms. Although these processes have been historically linked to neurodegenerative disorders, such as Alzheimer’s disease, evidence linking [...] Read more.
Protein misfolding disorders are a group of diseases characterized by supra-physiologic accumulation and aggregation of pathogenic proteoforms resulting from improper protein folding and/or insufficiency in clearance mechanisms. Although these processes have been historically linked to neurodegenerative disorders, such as Alzheimer’s disease, evidence linking protein misfolding to other pathologies continues to emerge. Indeed, the deposition of toxic protein aggregates in the form of oligomers or large amyloid fibrils has been linked to type 2 diabetes, various types of cancer, and, in more recent years, to preeclampsia, a life-threatening pregnancy-specific disorder. While extensive physiological mechanisms are in place to maintain proteostasis, processes, such as aging, genetic factors, or environmental stress in the form of hypoxia, nutrient deprivation or xenobiotic exposures can induce failure in these systems. As such, pregnancy, a natural physical state that already places the maternal body under significant physiological stress, creates an environment with a lower threshold for aberrant aggregation. In this review, we set out to discuss current evidence of protein misfolding in pregnancy and potential mechanisms supporting a key role for this process in preeclampsia pathogenesis. Improving our understanding of this emerging pathophysiological process in preeclampsia can lead to vital discoveries that can be harnessed to create better diagnoses and treatment modalities for the disorder. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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19 pages, 4007 KiB  
Review
Structural Fluctuation, Relaxation, and Folding of Protein: An Approach Based on the Combined Generalized Langevin and RISM/3D-RISM Theories
by Fumio Hirata
Molecules 2023, 28(21), 7351; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28217351 - 30 Oct 2023
Viewed by 730
Abstract
In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto [...] Read more.
In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto the two dynamic variables: the structural fluctuation defined by the displacement of atoms from their equilibrium positions, and the solvent density fluctuation. The equation has an expression similar to the classical Langevin equation (CLE) for a harmonic oscillator, possessing terms corresponding to the restoring force proportional to the structural fluctuation, as well as the frictional and random forces. However, there is a distinct difference between the two expressions that touches on the essential physics of the structural fluctuation, that is, the force constant, or Hessian, in the restoring force. In the CLE, this is given by the second derivative of the potential energy among atoms in a protein. So, the quadratic nature or the harmonicity is only valid at the minimum of the potential surface. On the contrary, the linearity of the restoring force in the GLE originates from the projection of the water’s degrees of freedom onto the protein’s degrees of freedom. Taking this into consideration, Kim and Hirata proposed an ansatz for the Hessian matrix. The ansatz is used to equate the Hessian matrix with the second derivative of the free-energy surface or the potential of the mean force of a protein in water, defined by the sum of the potential energy among atoms in a protein and the solvation free energy. Since the free energy can be calculated from the molecular mechanics and the RISM/3D-RISM theory, one can perform an analysis similar to the normal mode analysis (NMA) just by diagonalizing the Hessian matrix of the free energy. This method is referred to as the Generalized Langevin Mode Analysis (GLMA). This theory may be realized to explore a variety of biophysical processes, including protein folding, spectroscopy, and chemical reactions. The present article is devoted to reviewing the development of this theory, and to providing perspective in exploring life phenomena. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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13 pages, 4480 KiB  
Review
Recent Computational Advances Regarding Amyloid-β and Tau Membrane Interactions in Alzheimer’s Disease
by Phuong H. Nguyen and Philippe Derreumaux
Molecules 2023, 28(20), 7080; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28207080 - 13 Oct 2023
Viewed by 1445
Abstract
The interactions of amyloid proteins with membranes have been subject to many experimental and computational studies, as these interactions contribute in part to neurodegenerative diseases. In this review, we report on recent simulations that have focused on the adsorption and insertion modes of [...] Read more.
The interactions of amyloid proteins with membranes have been subject to many experimental and computational studies, as these interactions contribute in part to neurodegenerative diseases. In this review, we report on recent simulations that have focused on the adsorption and insertion modes of amyloid-β and tau proteins in membranes. The atomistic-resolution characterization of the conformational changes of these amyloid proteins upon lipid cell membrane and free lipid interactions is of interest to rationally design drugs targeting transient oligomers in Alzheimer’s disease. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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20 pages, 4227 KiB  
Review
The Hybrid Nano-Biointerface between Proteins/Peptides and Two-Dimensional Nanomaterials
by Giuseppe Forte, Diego La Mendola and Cristina Satriano
Molecules 2023, 28(20), 7064; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28207064 - 13 Oct 2023
Viewed by 1176
Abstract
In typical protein–nanoparticle surface interactions, the biomolecule surface binding and consequent conformational changes are intermingled with each other and are pivotal to the multiple functional properties of the resulting hybrid bioengineered nanomaterial. In this review, we focus on the peculiar properties of the [...] Read more.
In typical protein–nanoparticle surface interactions, the biomolecule surface binding and consequent conformational changes are intermingled with each other and are pivotal to the multiple functional properties of the resulting hybrid bioengineered nanomaterial. In this review, we focus on the peculiar properties of the layer formed when biomolecules, especially proteins and peptides, face two-dimensional (2D) nanomaterials, to provide an overview of the state-of-the-art knowledge and the current challenges concerning the biomolecule coronas and, in general, the 2D nano-biointerface established when peptides and proteins interact with the nanosheet surface. Specifically, this review includes both experimental and simulation studies, including some recent machine learning results of a wide range of nanomaterial and peptide/protein systems. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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20 pages, 2806 KiB  
Review
Ubiquitin-Dependent and Independent Proteasomal Degradation in Host-Pathogen Interactions
by Wojciech Bialek, James F. Collawn and Rafal Bartoszewski
Molecules 2023, 28(18), 6740; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28186740 - 21 Sep 2023
Cited by 1 | Viewed by 1272
Abstract
Ubiquitin, a small protein, is well known for tagging target proteins through a cascade of enzymatic reactions that lead to protein degradation. The ubiquitin tag, apart from its signaling role, is paramount in destabilizing the modified protein. Here, we explore the complex role [...] Read more.
Ubiquitin, a small protein, is well known for tagging target proteins through a cascade of enzymatic reactions that lead to protein degradation. The ubiquitin tag, apart from its signaling role, is paramount in destabilizing the modified protein. Here, we explore the complex role of ubiquitin-mediated protein destabilization in the intricate proteolysis process by the 26S proteasome. In addition, the significance of the so-called ubiquitin-independent pathway and the role of the 20S proteasome are considered. Next, we discuss the ubiquitin–proteasome system’s interplay with pathogenic microorganisms and how the microorganisms manipulate this system to establish infection by a range of elaborate pathways to evade or counteract host responses. Finally, we focus on the mechanisms that rely either on (i) hijacking the host and on delivering pathogenic E3 ligases and deubiquitinases that promote the degradation of host proteins, or (ii) counteracting host responses through the stabilization of pathogenic effector proteins. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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15 pages, 1226 KiB  
Review
Liquid–Liquid Phase Separation and Protective Protein Aggregates in Bacteria
by Dorota Kuczyńska-Wiśnik, Karolina Stojowska-Swędrzyńska and Ewa Laskowska
Molecules 2023, 28(18), 6582; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28186582 - 12 Sep 2023
Cited by 3 | Viewed by 1642
Abstract
Liquid–liquid phase separation (LLPS) and the formation of membraneless organelles (MLOs) contribute to the spatiotemporal organization of various physiological processes in the cell. These phenomena have been studied and characterized mainly in eukaryotic cells. However, increasing evidence indicates that LLPS-driven protein condensation may [...] Read more.
Liquid–liquid phase separation (LLPS) and the formation of membraneless organelles (MLOs) contribute to the spatiotemporal organization of various physiological processes in the cell. These phenomena have been studied and characterized mainly in eukaryotic cells. However, increasing evidence indicates that LLPS-driven protein condensation may also occur in prokaryotes. Recent studies indicate that aggregates formed during proteotoxic stresses may also play the role of MLOs and increase the fitness of bacteria under stress. The beneficial effect of aggregates may result from the sequestration and protection of proteins against irreversible inactivation or degradation, activation of the protein quality control system and induction of dormancy. The most common stress that bacteria encounter in the natural environment is water loss. Therefore, in this review, we focus on protein aggregates formed in E. coli upon desiccation–rehydration stress. In silico analyses suggest that various mechanisms and interactions are responsible for their formation, including LLPS, disordered sequences and aggregation-prone regions. These data support findings that intrinsically disordered proteins and LLPS may contribute to desiccation tolerance not only in eukaryotic cells but also in bacteria. LLPS-driven aggregation may be a strategy used by pathogens to survive antibiotic treatment and desiccation stress in the hospital environment. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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18 pages, 1012 KiB  
Review
Unveiling the Effects of Copper Ions in the Aggregation of Amyloidogenic Proteins
by Valentina Oliveri
Molecules 2023, 28(18), 6446; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28186446 - 5 Sep 2023
Cited by 1 | Viewed by 1445
Abstract
Amyloid diseases have become a global concern due to their increasing prevalence. Transition metals, including copper, can affect the aggregation of the pathological proteins involved in these diseases. Copper ions play vital roles in organisms, but the disruption of their homeostasis can negatively [...] Read more.
Amyloid diseases have become a global concern due to their increasing prevalence. Transition metals, including copper, can affect the aggregation of the pathological proteins involved in these diseases. Copper ions play vital roles in organisms, but the disruption of their homeostasis can negatively impact neuronal function and contribute to amyloid diseases with toxic protein aggregates, oxidative stress, mitochondrial dysfunction, impaired cellular signaling, inflammation, and cell death. Gaining insight into the imbalance of copper ions and its impact on protein folding and aggregation is crucial for developing focused therapies. This review examines the influence of copper ions on significant amyloid proteins/peptides, offering a comprehensive overview of the current understanding in this field. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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19 pages, 18692 KiB  
Review
Ultrafast Transient Absorption Spectra and Kinetics of Rod and Cone Visual Pigments
by Arjun Krishnamoorthi, Keyvan Khosh Abady, Dinesh Dhankhar and Peter M. Rentzepis
Molecules 2023, 28(15), 5829; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28155829 - 2 Aug 2023
Viewed by 1441
Abstract
Rods and cones are the photoreceptor cells containing the visual pigment proteins that initiate visual phototransduction following the absorption of a photon. Photon absorption induces the photochemical transformation of a visual pigment, which results in the sequential formation of distinct photo-intermediate species on [...] Read more.
Rods and cones are the photoreceptor cells containing the visual pigment proteins that initiate visual phototransduction following the absorption of a photon. Photon absorption induces the photochemical transformation of a visual pigment, which results in the sequential formation of distinct photo-intermediate species on the femtosecond to millisecond timescales, whereupon a visual electrical signal is generated and transmitted to the brain. Time-resolved spectroscopic studies of the rod and cone photo-intermediaries enable the detailed understanding of initial events in vision, namely the key differences that underlie the functionally distinct scotopic (rod) and photopic (cone) visual systems. In this paper, we review our recent ultrafast (picoseconds to milliseconds) transient absorption studies of rod and cone visual pigments with a detailed comparison of the transient molecular spectra and kinetics of their respective photo-intermediaries. Key results include the characterization of the porphyropsin (carp fish rhodopsin) and human green-cone opsin photobleaching sequences, which show significant spectral and kinetic differences when compared against that of bovine rhodopsin. These results altogether reveal a rather strong interplay between the visual pigment structure and its corresponding photobleaching sequence, and relevant outstanding questions that will be further investigated through a forthcoming study of the human blue-cone visual pigment are discussed. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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13 pages, 2663 KiB  
Review
Non-Native Structures of Apomyoglobin and Apoleghemoglobin in Folding Intermediates Related to the Protein Misfolding
by Chiaki Nishimura and Takeshi Kikuchi
Molecules 2023, 28(9), 3970; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28093970 - 8 May 2023
Viewed by 1369
Abstract
Protein folding is essential for a polypeptide chain to acquire its proper structure and function. Globins are a superfamily of ubiquitous heme-binding α-helical proteins whose function is principally to regulate oxygen homoeostasis. In this review, we explore the hierarchical helical formation in the [...] Read more.
Protein folding is essential for a polypeptide chain to acquire its proper structure and function. Globins are a superfamily of ubiquitous heme-binding α-helical proteins whose function is principally to regulate oxygen homoeostasis. In this review, we explore the hierarchical helical formation in the globin proteins apomyoglobin and leghemoglobin, and we discuss the existence of non-native and misfolded structures occurring during the course of folding to its native state. This review summarizes the research aimed at characterizing and comparing the equilibrium and kinetic intermediates, as well as delineating the complete folding pathway at a molecular level, in order to answer the following questions: “What is the mechanism of misfolding via a folding intermediate? Does the non-native structure stabilize the contemporary intermediate structure? Does the non-native structure induce slower folding?” The role of the non-native structures in the folding intermediate related to misfolding is also discussed. Full article
(This article belongs to the Special Issue Protein Folding, towards the Comprehensive Understanding from Various Aspects)
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