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Protein Folding and Quality Control Mechanisms - In Memory of...
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Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999)

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

Deadline for manuscript submissions: closed (30 November 2019) | Viewed by 80366

Special Issue Editor

Prof. Dr. Alexei V. Finkelstein

E-Mail Website
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

Special Issue Information

Dear Colleagues,

The mysterious ability of protein chains, initially disordered, to spontaneously form their unique 3D structures has long served as an exciting puzzle for molecular biologists, physicists, and chemists. Now, when this puzzle is solved in its basics for in vitro folding of small globular proteins, and when it has been demonstrated that in vivo folding of such proteins is similar to their in vitro folding (that is, they remain unstructured during biosynthesis and get their native fold only when the entire sequence is available), the main interest is, in my opinion, shifted to folding, unfolding, and misfolding of larger globular and to non-globular (especially membrane) proteins. In particular: how long should the “unfinished” protein chain emerging at a ribosome be to form a definite 3D structure? Is this first-formed structure a native-like one? Are there thermodynamically stable but kinetically unattainable folds of protein chains? Are these rare exceptions or the main body of the protein fold space? Do chaperones actively form protein structures, and if so, how? Or do they only “passively” eliminate “unwanted” association of protein chains? What is the difference between chaperones dealing with water-soluble and membrane proteins? How does the protein structure control in vivo look like? Further, an overview of achievements of protein engineering and design, especially on intriguing “chameleon” proteins, is highly desirable. This Special Issue will focus on the various aspects of protein folding, misfolding, and unfolding.

We look forward to reading your contributions.

 

Prof. Dr. Alexei V. Finkelstein
Guest Editor

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Keywords

  • Protein folding
  • protein unfolding
  • protein misfolding
  • co-translational folding
  • protein structure
  • protein structure control
  • structural transformations
  • protein physics
  • protein engineering
  • chaperones

Published Papers (18 papers)

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Editorial

Jump to: Research, Review

4 pages, 1655 KiB  
Editorial
How A Novel Scientific Concept Was Coined the “Molten Globule State”
by Yutaka Kuroda, Shigeru Endo and Haruki Nakamura
Biomolecules 2020, 10(2), 269; https://doi.org/10.3390/biom10020269 - 10 Feb 2020
Cited by 12 | Viewed by 1878
Abstract
As a tribute to Professor Oleg B. Ptitsyn, we organized an interview with Professor Akiyoshi Wada held in Tokyo in the middle of September 2019. Both Professor A. Wada and the late Professor O. B. Ptitsyn greatly contributed to the field of protein [...] Read more.
As a tribute to Professor Oleg B. Ptitsyn, we organized an interview with Professor Akiyoshi Wada held in Tokyo in the middle of September 2019. Both Professor A. Wada and the late Professor O. B. Ptitsyn greatly contributed to the field of protein biophysics, and they played leading roles in establishing the concept of the “Molten Globule state” 35–40 years ago. This editorial is intended to recount, as accurately as possible, some episodes during the early days of protein research that led to the discovery of this state, and how this concept was coined the “Molten Globule state” and came to be widely accepted by biophysicists, biochemists, and molecular biologists. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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Research

Jump to: Editorial, Review

16 pages, 5139 KiB  
Article
The Kinetics of Amyloid Fibril Formation by de Novo Protein Albebetin and Its Mutant Variants
by Vitalii Balobanov, Rita Chertkova, Anna Egorova, Dmitry Dolgikh, Valentina Bychkova and Mikhail Kirpichnikov
Biomolecules 2020, 10(2), 241; https://doi.org/10.3390/biom10020241 - 05 Feb 2020
Cited by 4 | Viewed by 2846
Abstract
Engineering of amyloid structures is one of the new perspective areas of protein engineering. Studying the process of amyloid formation can help find ways to manage it in the interests of medicine and biotechnology. One of the promising candidates for the structural basis [...] Read more.
Engineering of amyloid structures is one of the new perspective areas of protein engineering. Studying the process of amyloid formation can help find ways to manage it in the interests of medicine and biotechnology. One of the promising candidates for the structural basis of artificial functional amyloid fibrils is albebetin (ABB), an artificial protein engineered under the leadership of O.B. Ptitsyn. Various aspects of the amyloid formation of this protein and some methods for controlling this process are investigated in this paper. Four stages of amyloid fibrils formation by this protein from the first non-fibrillar aggregates to mature fibrils and large micron-sized complexes have been described in detail. Dependence of albebetin amyloids formation on external conditions and some mutations also have been described. The introduction of similar point mutations in the two structurally identical α-β-β motifs of ABB lead to different amiloidogenesis kinetics. The inhibitory effect of a disulfide bond and high pH on amyloid fibrils formation, that can be used to control this process, was shown. The results of this work are a good basis for the further design and use of ABB-based amyloid constructs. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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12 pages, 2037 KiB  
Article
Back to GroEL-Assisted Protein Folding: GroES Binding-Induced Displacement of Denatured Proteins from GroEL to Bulk Solution
by Victor Marchenkov, Andrey Gorokhovatsky, Natalia Marchenko, Tanya Ivashina and Gennady Semisotnov
Biomolecules 2020, 10(1), 162; https://doi.org/10.3390/biom10010162 - 20 Jan 2020
Cited by 5 | Viewed by 3662
Abstract
The main events in chaperone-assisted protein folding are the binding and ligand-induced release of substrate proteins. Here, we studied the location of denatured proteins previously bound to the GroEL chaperonin resulting from the action of the GroES co-chaperonin in the presence of Mg-ATP. [...] Read more.
The main events in chaperone-assisted protein folding are the binding and ligand-induced release of substrate proteins. Here, we studied the location of denatured proteins previously bound to the GroEL chaperonin resulting from the action of the GroES co-chaperonin in the presence of Mg-ATP. Fluorescein-labeled denatured proteins (α-lactalbumin, lysozyme, serum albumin, and pepsin in the presence of thiol reagents at neutral pH, as well as an early refolding intermediate of malate dehydrogenase) were used to reveal the effect of GroES on their interaction with GroEL. Native electrophoresis has demonstrated that these proteins tend to be released from the GroEL-GroES complex. With the use of biotin- and fluorescein-labeled denatured proteins and streptavidin fused with luciferase aequorin (the so-called streptavidin trap), the presence of denatured proteins in bulk solution after GroES and Mg-ATP addition has been confirmed. The time of GroES-induced dissociation of a denatured protein from the GroEL surface was estimated using the stopped-flow technique and found to be much shorter than the proposed time of the GroEL ATPase cycle. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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17 pages, 4073 KiB  
Article
Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein
by Kyung Rok Kim, Kyung A. Kim, Joon Sung Park, Jun Young Jang, Yuri Choi, Hyung Ho Lee, Dong Chul Lee, Kyung Chan Park, Young Il Yeom, Hyun-Jung Kim and Byung Woo Han
Biomolecules 2020, 10(1), 90; https://doi.org/10.3390/biom10010090 - 06 Jan 2020
Cited by 6 | Viewed by 3426
Abstract
The N-Myc downstream-regulated gene (NDRG) family belongs to the α/β-hydrolase fold and is known to exert various physiologic functions in cell proliferation, differentiation, and hypoxia-induced cancer metabolism. In particular, NDRG3 is closely related to proliferation and migration of prostate cancer cells, and recent [...] Read more.
The N-Myc downstream-regulated gene (NDRG) family belongs to the α/β-hydrolase fold and is known to exert various physiologic functions in cell proliferation, differentiation, and hypoxia-induced cancer metabolism. In particular, NDRG3 is closely related to proliferation and migration of prostate cancer cells, and recent studies reported its implication in lactate-triggered hypoxia responses or tumorigenesis. However, the underlying mechanism for the functions of NDRG3 remains unclear. Here, we report the crystal structure of human NDRG3 at 2.2 Å resolution, with six molecules in an asymmetric unit. While NDRG3 adopts the α/β-hydrolase fold, complete substitution of the canonical catalytic triad residues to non-reactive residues and steric hindrance around the pseudo-active site seem to disable the α/β-hydrolase activity. While NDRG3 shares a high similarity to NDRG2 in terms of amino acid sequence and structure, NDRG3 exhibited remarkable structural differences in a flexible loop corresponding to helix α6 of NDRG2 that is responsible for tumor suppression. Thus, this flexible loop region seems to play a distinct role in oncogenic progression induced by NDRG3. Collectively, our studies could provide structural and biophysical insights into the molecular characteristics of NDRG3. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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18 pages, 4891 KiB  
Article
Intrinsic Disorder-Based Design of Stable Globular Proteins
by Galina S. Nagibina, Ksenia A. Glukhova, Vladimir N. Uversky, Tatiana N. Melnik and Bogdan S. Melnik
Biomolecules 2020, 10(1), 64; https://doi.org/10.3390/biom10010064 - 30 Dec 2019
Cited by 9 | Viewed by 3068
Abstract
Directed stabilization of globular proteins via substitution of a minimal number of amino acid residues is one of the most complicated experimental tasks. This work summarizes our research on the effect of amino acid substitutions on the protein stability utilizing the outputs of [...] Read more.
Directed stabilization of globular proteins via substitution of a minimal number of amino acid residues is one of the most complicated experimental tasks. This work summarizes our research on the effect of amino acid substitutions on the protein stability utilizing the outputs of the analysis of intrinsic disorder predisposition of target proteins. This allowed us to formulate the basis of one of the possible approaches to the stabilization of globular proteins. The idea is quite simple. To stabilize a protein as a whole, one needs to find its "weakest spot" and stabilize it, but the question is how this weak spot can be found in a query protein. Our approach is based on the utilization of the computational tools for the per-residue evaluation of intrinsic disorder predisposition to search for the "weakest spot" of a query protein (i.e., the region(s) with the highest local predisposition for intrinsic disorder). When such "weakest spot" is found, it can be stabilized through a limited number of point mutations by introducing order-promoting residues at hot spots, thereby increasing structural stability of a protein as a whole. Using this approach, we were able to obtain stable mutant forms of several globular proteins, such as Gαo, GFP, ribosome protein L1, and circular permutant of apical domain of GroEL. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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15 pages, 4508 KiB  
Article
Exploration of the Misfolding Mechanism of Transthyretin Monomer: Insights from Hybrid-Resolution Simulations and Markov State Model Analysis
by Shuangyan Zhou, Jie Cheng, Ting Yang, Mingyue Ma, Wenying Zhang, Shuai Yuan, Glenn V. Lo and Yusheng Dou
Biomolecules 2019, 9(12), 889; https://doi.org/10.3390/biom9120889 - 17 Dec 2019
Cited by 4 | Viewed by 3247
Abstract
Misfolding and aggregation of transthyretin (TTR) is widely known to be responsible for a progressive systemic disorder called amyloid transthyretin (ATTR) amyloidosis. Studies suggest that TTR aggregation is initiated by a rate-limiting dissociation of the homo-tetramer into its monomers, which can rapidly misfold [...] Read more.
Misfolding and aggregation of transthyretin (TTR) is widely known to be responsible for a progressive systemic disorder called amyloid transthyretin (ATTR) amyloidosis. Studies suggest that TTR aggregation is initiated by a rate-limiting dissociation of the homo-tetramer into its monomers, which can rapidly misfold and self-assemble into amyloid fibril. Thus, exploring conformational change involved in TTR monomer misfolding is of vital importance for understanding the pathogenesis of ATTR amyloidosis. In this work, microsecond timescale hybrid-resolution molecular dynamics (MD) simulations combined with Markov state model (MSM) analysis were performed to investigate the misfolding mechanism of the TTR monomer. The results indicate that a macrostate with partially unfolded conformations may serve as the misfolded state of the TTR monomer. This misfolded state was extremely stable with a very large equilibrium probability of about 85.28%. With secondary structure analysis, we found the DAGH sheet in this state to be significantly destroyed. The CBEF sheet was relatively stable and sheet structure was maintained. However, the F-strand in this sheet was likely to move away from E-strand and reform a new β-sheet with the H-strand. This observation is consistent with experimental finding that F and H strands in the outer edge drive the misfolding of TTR. Finally, transition pathways from a near native state to this misfolded macrostate showed that the conformational transition can occur either through a native-like β-sheet intermediates or through partially unfolded intermediates, while the later appears to be the main pathway. As a whole, we identified a potential misfolded state of the TTR monomer and elucidated the misfolding pathway for its conformational transition. This work can provide a valuable theoretical basis for understanding of TTR aggregation and the pathogenesis of ATTR amyloidosis at the atomic level. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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13 pages, 1906 KiB  
Article
Thermal Inactivation of a Cold-Active Esterase PMGL3 Isolated from the Permafrost Metagenomic Library
by M.V. Kryukova, L.E. Petrovskaya, E.A. Kryukova, G.Yu. Lomakina, S.A. Yakimov, E.G. Maksimov, K.M. Boyko, V.O. Popov, D.A. Dolgikh and M.P. Kirpichnikov
Biomolecules 2019, 9(12), 880; https://doi.org/10.3390/biom9120880 - 16 Dec 2019
Cited by 11 | Viewed by 2577
Abstract
PMGL3 is a cold-adapted esterase which was recently isolated from the permafrost metagenomic library. It exhibits maximum activity at 30 °C and low stability at elevated temperatures (40 °C and higher). Sequence alignment has revealed that PMGL3 is a member of the hormone-sensitive [...] Read more.
PMGL3 is a cold-adapted esterase which was recently isolated from the permafrost metagenomic library. It exhibits maximum activity at 30 °C and low stability at elevated temperatures (40 °C and higher). Sequence alignment has revealed that PMGL3 is a member of the hormone-sensitive lipase (HSL) family. In this work, we demonstrated that incubation at 40 °C led to the inactivation of the enzyme (t1/2 = 36 min), which was accompanied by the formation of tetramers and higher molecular weight aggregates. In order to increase the thermal stability of PMGL3, its two cysteines Cys49 and Cys207 were substituted by the hydrophobic residues, which are found at the corresponding positions of thermostable esterases from the HSL family. One of the obtained mutants, C207F, possessed improved stability at 40 °C (t1/2 = 169 min) and increased surface hydrophobicity, whereas C49V was less stable in comparison with the wild type PMGL3. Both mutants exhibited reduced values of Vmax and kcat, while C207F demonstrated increased affinity to the substrate, and improved catalytic efficiency. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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8 pages, 2350 KiB  
Article
The Reverse Side of a Coin: “Factor-Free” Ribosomal Protein Synthesis In Vitro is a Consequence of the In Vivo Proofreading Mechanism
by Alexei V. Finkelstein
Biomolecules 2019, 9(10), 588; https://doi.org/10.3390/biom9100588 - 08 Oct 2019
Viewed by 2490
Abstract
This paper elucidates a close connection between two well-known facts that until now have seemed independent: (i) the quality control (“proofreading”) of the emerging amino acid sequence, occurring during the normal, elongation-factor-dependent ribosomal biosynthesis, which is performed by removing those Aa-tRNAs (aminoacyl tRNAs) [...] Read more.
This paper elucidates a close connection between two well-known facts that until now have seemed independent: (i) the quality control (“proofreading”) of the emerging amino acid sequence, occurring during the normal, elongation-factor-dependent ribosomal biosynthesis, which is performed by removing those Aa-tRNAs (aminoacyl tRNAs) whose anticodons are not complementary to the exhibited mRNA codons, and (ii) the in vitro discovered existence of the factor-free ribosomal synthesis of polypeptides. It is shown that a biological role of proofreading is played by a process that is exactly opposite to the step of factor-free binding of Aa-tRNA to the ribosome-exposed mRNA: a factor-free removal of that Aa-tRNA whose anticodon is not complementary to the ribosome-exhibited mRNA codon. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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Graphical abstract

16 pages, 6363 KiB  
Article
Folding of the Ig-Like Domain of the Dengue Virus Envelope Protein Analyzed by High-Hydrostatic-Pressure NMR at a Residue-Level Resolution
by Tomonori Saotome, Maxime Doret, Manjiri Kulkarni, Yin-Shan Yang, Philippe Barthe, Yutaka Kuroda and Christian Roumestand
Biomolecules 2019, 9(8), 309; https://doi.org/10.3390/biom9080309 - 26 Jul 2019
Cited by 7 | Viewed by 4323
Abstract
Dengue fever is a mosquito-borne endemic disease in tropical and subtropical regions, causing a significant public health problem in Southeast Asia. Domain III (ED3) of the viral envelope protein contains the two dominant putative epitopes and part of the heparin sulfate receptor binding [...] Read more.
Dengue fever is a mosquito-borne endemic disease in tropical and subtropical regions, causing a significant public health problem in Southeast Asia. Domain III (ED3) of the viral envelope protein contains the two dominant putative epitopes and part of the heparin sulfate receptor binding region that drives the dengue virus (DENV)’s fusion with the host cell. Here, we used high-hydrostatic-pressure nuclear magnetic resonance (HHP-NMR) to obtain residue-specific information on the folding process of domain III from serotype 4 dengue virus (DEN4-ED3), which adopts the classical three-dimensional (3D) ß-sandwich structure known as the Ig-like fold. Interestingly, the folding pathway of DEN4-ED3 shares similarities with that of the Titin I27 module, which also adopts an Ig-like fold, but is functionally unrelated to ED3. For both proteins, the unfolding process starts by the disruption of the N- and C-terminal strands on one edge of the ß-sandwich, yielding a folding intermediate stable over a substantial pressure range (from 600 to 1000 bar). In contrast to this similarity, pressure-jump kinetics indicated that the folding transition state is considerably more hydrated in DEN4-ED3 than in Titin I27. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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11 pages, 896 KiB  
Article
Misfolding of a Single Disulfide Bonded Globular Protein into a Low-Solubility Species Conformationally and Biophysically Distinct from the Native One
by Tomonori Saotome, Toshio Yamazaki and Yutaka Kuroda
Biomolecules 2019, 9(6), 250; https://doi.org/10.3390/biom9060250 - 25 Jun 2019
Cited by 7 | Viewed by 4072
Abstract
In practice and despite Anfinsen’s dogma, the refolding of recombinant multiple SS-bonded proteins is famously difficult because misfolded species with non-native SS-bonds appear upon the oxidization of their cysteine residues. On the other hand, single SS-bond proteins are thought to be simple to [...] Read more.
In practice and despite Anfinsen’s dogma, the refolding of recombinant multiple SS-bonded proteins is famously difficult because misfolded species with non-native SS-bonds appear upon the oxidization of their cysteine residues. On the other hand, single SS-bond proteins are thought to be simple to refold because their cysteines have only one SS-bond partner. Here, we report that dengue 4 envelope protein domain 3 (DEN4 ED3), a single SS-bonded protein can be irreversibly trapped into a misfolded species through the formation of its sole intramolecular SS-bond. The misfolded species had a much lower solubility than the native one at pHs higher than about 7, and circular dichroism measurements clearly indicated that its secondary structure content was different from the native species. Furthermore, the peaks in the Heteronuclear Single Quantum Correlation spectroscopy (HSQC) spectrum of DEN4 ED3 from the supernatant fraction were sharp and well dispersed, reflecting the beta-sheeted native structure, whereas the spectrum of the precipitated fraction showed broad signals clustered near its center suggesting no or little structure and a strong tendency to aggregate. The two species had distinct biophysical properties and could interconvert into each other only by cleaving and reforming the SS-bond, strongly suggesting that they are topologically different. This phenomenon can potentially happen with any single SS-bonded protein, and our observation emphasizes the need for assessing the conformation and biophysical properties of bacterially produced therapeutic proteins in addition to their chemical purities. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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Review

Jump to: Editorial, Research

14 pages, 3716 KiB  
Review
The Future of Protein Secondary Structure Prediction Was Invented by Oleg Ptitsyn
by Daniel Rademaker, Jarek van Dijk, Willem Titulaer, Joanna Lange, Gert Vriend and Li Xue
Biomolecules 2020, 10(6), 910; https://doi.org/10.3390/biom10060910 - 16 Jun 2020
Cited by 3 | Viewed by 3497
Abstract
When Oleg Ptitsyn and his group published the first secondary structure prediction for a protein sequence, they started a research field that is still active today. Oleg Ptitsyn combined fundamental rules of physics with human understanding of protein structures. Most followers in this [...] Read more.
When Oleg Ptitsyn and his group published the first secondary structure prediction for a protein sequence, they started a research field that is still active today. Oleg Ptitsyn combined fundamental rules of physics with human understanding of protein structures. Most followers in this field, however, use machine learning methods and aim at the highest (average) percentage correctly predicted residues in a set of proteins that were not used to train the prediction method. We show that one single method is unlikely to predict the secondary structure of all protein sequences, with the exception, perhaps, of future deep learning methods based on very large neural networks, and we suggest that some concepts pioneered by Oleg Ptitsyn and his group in the 70s of the previous century likely are today’s best way forward in the protein secondary structure prediction field. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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17 pages, 2036 KiB  
Review
The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins
by Kunihiro Kuwajima
Biomolecules 2020, 10(3), 407; https://doi.org/10.3390/biom10030407 - 06 Mar 2020
Cited by 22 | Viewed by 5686
Abstract
From experimental studies of protein folding, it is now clear that there are two types of folding behavior, i.e., two-state folding and non-two-state folding, and understanding the relationships between these apparently different folding behaviors is essential for fully elucidating the molecular mechanisms of [...] Read more.
From experimental studies of protein folding, it is now clear that there are two types of folding behavior, i.e., two-state folding and non-two-state folding, and understanding the relationships between these apparently different folding behaviors is essential for fully elucidating the molecular mechanisms of protein folding. This article describes how the presence of the two types of folding behavior has been confirmed experimentally, and discusses the relationships between the two-state and the non-two-state folding reactions, on the basis of available data on the correlations of the folding rate constant with various structure-based properties, which are determined primarily by the backbone topology of proteins. Finally, a two-stage hierarchical model is proposed as a general mechanism of protein folding. In this model, protein folding occurs in a hierarchical manner, reflecting the hierarchy of the native three-dimensional structure, as embodied in the case of non-two-state folding with an accumulation of the molten globule state as a folding intermediate. The two-state folding is thus merely a simplified version of the hierarchical folding caused either by an alteration in the rate-limiting step of folding or by destabilization of the intermediate. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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19 pages, 1600 KiB  
Review
Solution of Levinthal’s Paradox and a Physical Theory of Protein Folding Times
by Dmitry N. Ivankov and Alexei V. Finkelstein
Biomolecules 2020, 10(2), 250; https://doi.org/10.3390/biom10020250 - 06 Feb 2020
Cited by 22 | Viewed by 7354
Abstract
“How do proteins fold?” Researchers have been studying different aspects of this question for more than 50 years. The most conceptual aspect of the problem is how protein can find the global free energy minimum in a biologically reasonable time, without exhaustive enumeration [...] Read more.
“How do proteins fold?” Researchers have been studying different aspects of this question for more than 50 years. The most conceptual aspect of the problem is how protein can find the global free energy minimum in a biologically reasonable time, without exhaustive enumeration of all possible conformations, the so-called “Levinthal’s paradox.” Less conceptual but still critical are aspects about factors defining folding times of particular proteins and about perspectives of machine learning for their prediction. We will discuss in this review the key ideas and discoveries leading to the current understanding of folding kinetics, including the solution of Levinthal’s paradox, as well as the current state of the art in the prediction of protein folding times. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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16 pages, 24116 KiB  
Review
Exploring Protein Fold Space
by William R. Taylor
Biomolecules 2020, 10(2), 193; https://doi.org/10.3390/biom10020193 - 27 Jan 2020
Cited by 5 | Viewed by 3372
Abstract
The model of protein folding proposed by Ptitsyn and colleagues involves the accretion of secondary structures around a nucleus. As developed by Efimov, this model also provides a useful way to view the relationships among structures. Although somewhat eclipsed by later databases based [...] Read more.
The model of protein folding proposed by Ptitsyn and colleagues involves the accretion of secondary structures around a nucleus. As developed by Efimov, this model also provides a useful way to view the relationships among structures. Although somewhat eclipsed by later databases based on the pairwise comparison of structures, Efimov’s approach provides a guide for the more automatic comparison of proteins based on an encoding of their topology as a string. Being restricted to layers of secondary structures based on beta sheets, this too has limitations which are partly overcome by moving to a more generalised secondary structure lattice that can encompass both open and closed (barrel) sheets as well as helical packing of the type encoded by Murzin and Finkelstein on small polyhedra. Regular (crystalline) lattices, such as close-packed hexagonals, were found to be too limited so pseudo-latticses were investigated including those found in quasicrystals and the Bernal tetrahedron-based lattice that he used to represent liquid water. The Bernal lattice was considered best and used to generate model protein structures. These were much more numerous than those seen in Nature, posing the open question of why this might be. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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15 pages, 2995 KiB  
Review
Cotranslational Folding of Proteins on the Ribosome
by Marija Liutkute, Ekaterina Samatova and Marina V. Rodnina
Biomolecules 2020, 10(1), 97; https://doi.org/10.3390/biom10010097 - 07 Jan 2020
Cited by 62 | Viewed by 9691
Abstract
Many proteins in the cell fold cotranslationally within the restricted space of the polypeptide exit tunnel or at the surface of the ribosome. A growing body of evidence suggests that the ribosome can alter the folding trajectory in many different ways. In this [...] Read more.
Many proteins in the cell fold cotranslationally within the restricted space of the polypeptide exit tunnel or at the surface of the ribosome. A growing body of evidence suggests that the ribosome can alter the folding trajectory in many different ways. In this review, we summarize the recent examples of how translation affects folding of single-domain, multiple-domain and oligomeric proteins. The vectorial nature of translation, the spatial constraints of the exit tunnel, and the electrostatic properties of the ribosome-nascent peptide complex define the onset of early folding events. The ribosome can facilitate protein compaction, induce the formation of intermediates that are not observed in solution, or delay the onset of folding. Examples of single-domain proteins suggest that early compaction events can define the folding pathway for some types of domain structures. Folding of multi-domain proteins proceeds in a domain-wise fashion, with each domain having its role in stabilizing or destabilizing neighboring domains. Finally, the assembly of protein complexes can also begin cotranslationally. In all these cases, the ribosome helps the nascent protein to attain a native fold and avoid the kinetic traps of misfolding. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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40 pages, 7038 KiB  
Review
Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions
by Vladimir N. Uversky and Alexei V. Finkelstein
Biomolecules 2019, 9(12), 842; https://doi.org/10.3390/biom9120842 - 08 Dec 2019
Cited by 49 | Viewed by 7507
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. [...] Read more.
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid–liquid or liquid–gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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20 pages, 5870 KiB  
Review
The Link That Binds: The Linker of Hsp70 as a Helm of the Protein’s Function
by Graham Chakafana, Tawanda Zininga and Addmore Shonhai
Biomolecules 2019, 9(10), 543; https://doi.org/10.3390/biom9100543 - 27 Sep 2019
Cited by 18 | Viewed by 4766
Abstract
The heat shock 70 (Hsp70) family of molecular chaperones plays a central role in maintaining cellular proteostasis. Structurally, Hsp70s are composed of an N-terminal nucleotide binding domain (NBD) which exhibits ATPase activity, and a C-terminal substrate binding domain (SBD). The binding of ATP [...] Read more.
The heat shock 70 (Hsp70) family of molecular chaperones plays a central role in maintaining cellular proteostasis. Structurally, Hsp70s are composed of an N-terminal nucleotide binding domain (NBD) which exhibits ATPase activity, and a C-terminal substrate binding domain (SBD). The binding of ATP at the NBD and its subsequent hydrolysis influences the substrate binding affinity of the SBD through allostery. Similarly, peptide binding at the C-terminal SBD stimulates ATP hydrolysis by the N-terminal NBD. Interdomain communication between the NBD and SBD is facilitated by a conserved linker segment. Hsp70s form two main subgroups. Canonical Hsp70 members generally suppress protein aggregation and are also capable of refolding misfolded proteins. Hsp110 members are characterized by an extended lid segment and their function tends to be largely restricted to suppression of protein aggregation. In addition, the latter serve as nucleotide exchange factors (NEFs) of canonical Hsp70s. The linker of the Hsp110 family is less conserved compared to that of the canonical Hsp70 group. In addition, the linker plays a crucial role in defining the functional features of these two groups of Hsp70. Generally, the linker of Hsp70 is quite small and varies in size from seven to thirteen residues. Due to its small size, any sequence variation that Hsp70 exhibits in this motif has a major and unique influence on the function of the protein. Based on sequence data, we observed that canonical Hsp70s possess a linker that is distinct from similar segments present in Hsp110 proteins. In addition, Hsp110 linker motifs from various genera are distinct suggesting that their unique features regulate the flexibility with which the NBD and SBD of these proteins communicate via allostery. The Hsp70 linker modulates various structure-function features of Hsp70 such as its global conformation, affinity for peptide substrate and interaction with co-chaperones. The current review discusses how the unique features of the Hsp70 linker accounts for the functional specialization of this group of molecular chaperones. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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17 pages, 943 KiB  
Review
Partners in Mischief: Functional Networks of Heat Shock Proteins of Plasmodium falciparum and Their Influence on Parasite Virulence
by Michael O. Daniyan, Jude M. Przyborski and Addmore Shonhai
Biomolecules 2019, 9(7), 295; https://doi.org/10.3390/biom9070295 - 23 Jul 2019
Cited by 28 | Viewed by 6058
Abstract
The survival of the human malaria parasite Plasmodium falciparum under the physiologically distinct environments associated with their development in the cold-blooded invertebrate mosquito vectors and the warm-blooded vertebrate human host requires a genome that caters to adaptability. To this end, a robust stress [...] Read more.
The survival of the human malaria parasite Plasmodium falciparum under the physiologically distinct environments associated with their development in the cold-blooded invertebrate mosquito vectors and the warm-blooded vertebrate human host requires a genome that caters to adaptability. To this end, a robust stress response system coupled to an efficient protein quality control system are essential features of the parasite. Heat shock proteins constitute the main molecular chaperone system of the cell, accounting for approximately two percent of the malaria genome. Some heat shock proteins of parasites constitute a large part (5%) of the ‘exportome’ (parasite proteins that are exported to the infected host erythrocyte) that modify the host cell, promoting its cyto-adherence. In light of their importance in protein folding and refolding, and thus the survival of the parasite, heat shock proteins of P. falciparum have been a major subject of study. Emerging evidence points to their role not only being cyto-protection of the parasite, as they are also implicated in regulating parasite virulence. In undertaking their roles, heat shock proteins operate in networks that involve not only partners of parasite origin, but also potentially functionally associate with human proteins to facilitate parasite survival and pathogenicity. This review seeks to highlight these interplays and their roles in parasite pathogenicity. We further discuss the prospects of targeting the parasite heat shock protein network towards the developments of alternative antimalarial chemotherapies. Full article
(This article belongs to the Special Issue Protein Folding and Quality Control Mechanisms - In Memory of Prof. Oleg B. Ptitsyn (1929-1999))
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