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Melo RLF, Freire TM, Valério RBR, Neto FS, de Castro Bizerra V, Fernandes BCC, de Sousa Junior PG, da Fonseca AM, Soares JM, Fechine PBA, Dos Santos JCS. Enhancing biocatalyst performance through immobilization of lipase (Eversa® Transform 2.0) on hybrid amine-epoxy core-shell magnetic nanoparticles. Int J Biol Macromol 2024; 264:130730. [PMID: 38462111 DOI: 10.1016/j.ijbiomac.2024.130730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Magnetic nanoparticles were functionalized with polyethylenimine (PEI) and activated with epoxy. This support was used to immobilize Lipase (Eversa® Transform 2.0) (EVS), optimization using the Taguchi method. XRF, SEM, TEM, XRD, FTIR, TGA, and VSM performed the characterizations. The optimal conditions were immobilization yield (I.Y.) of 95.04 ± 0.79 %, time of 15 h, ionic load of 95 mM, protein load of 5 mg/g, and temperature of 25 °C. The maximum loading capacity was 25 mg/g, and its stability in 60 days of storage showed a negligible loss of only 9.53 % of its activity. The biocatalyst demonstrated better stability at varying temperatures than free EVS, maintaining 28 % of its activity at 70 °C. It was feasible to esterify free fatty acids (FFA) from babassu oil with the best reaction of 97.91 % and ten cycles having an efficiency above 50 %. The esterification of produced biolubricant was confirmed by NMR, and it displayed kinematic viscosity and density of 6.052 mm2/s and 0.832 g/cm3, respectively, at 40 °C. The in-silico study showed a binding affinity of -5.8 kcal/mol between EVS and oleic acid, suggesting a stable substrate-lipase combination suitable for esterification.
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Affiliation(s)
- Rafael Leandro Fernandes Melo
- Departamento de Engenharia Metalúrgica e de Materiais, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE CEP 60440-554, Brazil; Grupo de Química de Materiais Avançados (GQMat), Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE CEP 60451-970, Brazil
| | - Tiago Melo Freire
- Grupo de Química de Materiais Avançados (GQMat), Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE CEP 60451-970, Brazil
| | - Roberta Bussons Rodrigues Valério
- Grupo de Química de Materiais Avançados (GQMat), Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE CEP 60451-970, Brazil
| | - Francisco Simão Neto
- Departamento de Engenharia Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE CEP 60455-760, Brazil
| | - Viviane de Castro Bizerra
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Campus das Auroras, Redenção, CE CEP 62790-970, Brazil
| | - Bruno Caio Chaves Fernandes
- Departamento de Agronomia e Ciência Vegetais, Universidade Federal Rural do Semi-Árido, Campus Mossoró, Mossoró, RN CEP 59625-900, Brazil
| | - Paulo Gonçalves de Sousa Junior
- Departamento de Química Orgânica e Inorgânica, Centro de Ciências, Universidade Federal do Ceará, Campus Pici, Fortaleza, CE CEP 60455760, Brazil
| | - Aluísio Marques da Fonseca
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Campus das Auroras, Redenção, CE CEP 62790-970, Brazil
| | - João Maria Soares
- Departamento de Física, Universidade do Estado do Rio Grande do Norte, Campus Mossoró, Mossoró, RN CEP 59610-090, Brazil
| | - Pierre Basílio Almeida Fechine
- Grupo de Química de Materiais Avançados (GQMat), Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE CEP 60451-970, Brazil
| | - José Cleiton Sousa Dos Santos
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Campus das Auroras, Redenção, CE CEP 62790-970, Brazil.
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2
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Gardner S, Darrow MC, Lukoyanova N, Thalassinos K, Saibil HR. Structural basis of substrate progression through the bacterial chaperonin cycle. Proc Natl Acad Sci U S A 2023; 120:e2308933120. [PMID: 38064510 PMCID: PMC10723157 DOI: 10.1073/pnas.2308933120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/20/2023] [Indexed: 12/17/2023] Open
Abstract
The bacterial chaperonin GroEL-GroES promotes protein folding through ATP-regulated cycles of substrate protein binding, encapsulation, and release. Here, we have used cryoEM to determine structures of GroEL, GroEL-ADP·BeF3, and GroEL-ADP·AlF3-GroES all complexed with the model substrate Rubisco. Our structures provide a series of snapshots that show how the conformation and interactions of non-native Rubisco change as it proceeds through the GroEL-GroES reaction cycle. We observe specific charged and hydrophobic GroEL residues forming strong initial contacts with non-native Rubisco. Binding of ATP or ADP·BeF3 to GroEL-Rubisco results in the formation of an intermediate GroEL complex displaying striking asymmetry in the ATP/ADP·BeF3-bound ring. In this ring, four GroEL subunits bind Rubisco and the other three are in the GroES-accepting conformation, suggesting how GroEL can recruit GroES without releasing bound substrate. Our cryoEM structures of stalled GroEL-ADP·AlF3-Rubisco-GroES complexes show Rubisco folding intermediates interacting with GroEL-GroES via different sets of residues.
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Affiliation(s)
- Scott Gardner
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, LondonWC1E 7HX, United Kingdom
| | | | - Natalya Lukoyanova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, LondonWC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, LondonWC1E 7HX, United Kingdom
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Helen R. Saibil
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, LondonWC1E 7HX, United Kingdom
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3
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Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023; 11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.
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Affiliation(s)
- Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - John E. Stone
- NVIDIA Corporation, Santa Clara, CA, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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4
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Liebermann DG, Jungwirth J, Riven I, Barak Y, Levy D, Horovitz A, Haran G. From Microstates to Macrostates in the Conformational Dynamics of GroEL: A Single-Molecule Förster Resonance Energy Transfer Study. J Phys Chem Lett 2023:6513-6521. [PMID: 37440608 PMCID: PMC10388350 DOI: 10.1021/acs.jpclett.3c01281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The chaperonin GroEL is a multisubunit molecular machine that assists in protein folding in the Escherichia coli cytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. Here, we report single-molecule Förster resonance energy transfer measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions. We find that four microstates span the conformational manifold of the protein and interconvert on the submillisecond time scale. A unique set of relative populations of these microstates, termed a macrostate, is obtained by varying solution conditions, e.g., adding different nucleotides or the cochaperone GroES. Strikingly, ATP titration studies demonstrate that the partition between the apo and ATP-ligated conformational macrostates traces a sigmoidal response with a Hill coefficient similar to that obtained in bulk experiments of ATP hydrolysis. These coinciding results from bulk measurements for an entire ring and single-molecule measurements for a single subunit provide new evidence for the concerted allosteric transition of all seven subunits.
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5
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Son A, Huizar Cabral V, Huang Z, Litberg TJ, Horowitz S. G-quadruplexes rescuing protein folding. Proc Natl Acad Sci U S A 2023; 120:e2216308120. [PMID: 37155907 PMCID: PMC10194009 DOI: 10.1073/pnas.2216308120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Maintaining the health of the proteome is a critical cellular task. Recently, we found G-quadruplex (G4) nucleic acids are especially potent at preventing protein aggregation in vitro and could at least indirectly improve the protein folding environment of Escherichia coli. However, the roles of G4s in protein folding were not yet explored. Here, through in vitro protein folding experiments, we discover that G4s can accelerate protein folding by rescuing kinetically trapped intermediates to both native and near-native folded states. Time-course folding experiments in E. coli further demonstrate that these G4s primarily improve protein folding quality in E. coli as opposed to preventing protein aggregation. The ability of a short nucleic acid to rescue protein folding opens up the possibility of nucleic acids and ATP-independent chaperones to play considerable roles in dictating the ultimate folding fate of proteins.
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Affiliation(s)
- Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Veronica Huizar Cabral
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Zijue Huang
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Theodore J. Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
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6
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Taguchi H, Koike-Takeshita A. In vivo client proteins of the chaperonin GroEL-GroES provide insight into the role of chaperones in protein evolution. Front Mol Biosci 2023; 10:1091677. [PMID: 36845542 PMCID: PMC9950496 DOI: 10.3389/fmolb.2023.1091677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Protein folding is often hampered by intermolecular protein aggregation, which can be prevented by a variety of chaperones in the cell. Bacterial chaperonin GroEL is a ring-shaped chaperone that forms complexes with its cochaperonin GroES, creating central cavities to accommodate client proteins (also referred as substrate proteins) for folding. GroEL and GroES (GroE) are the only indispensable chaperones for bacterial viability, except for some species of Mollicutes such as Ureaplasma. To understand the role of chaperonins in the cell, one important goal of GroEL research is to identify a group of obligate GroEL/GroES clients. Recent advances revealed hundreds of in vivo GroE interactors and obligate chaperonin-dependent clients. This review summarizes the progress on the in vivo GroE client repertoire and its features, mainly for Escherichia coli GroE. Finally, we discuss the implications of the GroE clients for the chaperone-mediated buffering of protein folding and their influences on protein evolution.
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Affiliation(s)
- Hideki Taguchi
- Cell Biology Center, Tokyo Institute of Technology, Yokohama, Japan,*Correspondence: Hideki Taguchi,
| | - Ayumi Koike-Takeshita
- Department of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
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7
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Whitelam S, Schmit JD. Low-dissipation self-assembly protocols of active sticky particles. JOURNAL OF CRYSTAL GROWTH 2022; 600:126912. [PMID: 36968622 PMCID: PMC10035568 DOI: 10.1016/j.jcrysgro.2022.126912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We use neuroevolutionary learning to identify time-dependent protocols for low-dissipation self-assembly in a model of generic active particles with interactions. When the time allotted for assembly is sufficiently long, low-dissipation protocols use only interparticle attractions, producing an amount of entropy that scales as the number of particles. When time is too short to allow assembly to proceed via diffusive motion, low-dissipation assembly protocols instead require particle self-propulsion, producing an amount of entropy that scales with the number of particles and the swim length required to cause assembly. Self-propulsion therefore provides an expensive but necessary mechanism for inducing assembly when time is of the essence.
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Affiliation(s)
- Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
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8
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Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo. Proc Natl Acad Sci U S A 2022; 119:e2209422119. [PMID: 36442111 PMCID: PMC9894238 DOI: 10.1073/pnas.2209422119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
CYT-19 is a DEAD-box protein whose adenosine-triphosphate (ATP)-dependent helicase activity facilitates the folding of group I introns in precursor RNA (pre-RNA) of Neurospora crassa (N. crassa). In the process, they consume a substantial amount of ATP. While much of the mechanistic insight into CYT-19 activity has been gained through the studies on the folding of Tetrahymena group I intron ribozyme, the more biologically relevant issue, namely the effect of CYT-19 on the self-splicing of pre-RNA, remains largely unexplored. Here, we employ a kinetic network model, based on the generalized iterative annealing mechanism (IAM), to investigate the relation between CYT-19 activity, rate of ribozyme folding, and the kinetics of the self-splicing reaction. The network rate parameters are extracted by analyzing the recent biochemical data for CYT-19-facilitated folding of Tetrahymena ribozyme. We then build extended models to explore the metabolism of pre-RNA. We show that the timescales of chaperone-mediated folding of group I ribozyme and self-splicing reaction compete with each other. As a consequence, in order to maximize the self-splicing yield of group I introns in pre-RNA, the chaperone activity must be sufficiently large to unfold the misfolded structures, but not too large to unfold the native structures prior to the self-splicing event. We discover that despite the promiscuous action on structured RNAs, the helicase activity of CYT-19 on group I ribozyme gives rise to self-splicing yields that are close to the maximum.
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9
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Finkelstein AV, Bogatyreva NS, Ivankov DN, Garbuzynskiy SO. Protein folding problem: enigma, paradox, solution. Biophys Rev 2022; 14:1255-1272. [PMID: 36659994 PMCID: PMC9842845 DOI: 10.1007/s12551-022-01000-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/19/2022] [Indexed: 01/22/2023] Open
Abstract
The ability of protein chains to spontaneously form their three-dimensional structures is a long-standing mystery in molecular biology. The most conceptual aspect of this mystery is how the protein chain can find its native, "working" spatial structure (which, for not too big protein chains, corresponds to the global free energy minimum) in a biologically reasonable time, without exhaustive enumeration of all possible conformations, which would take billions of years. This is the so-called "Levinthal's paradox." In this review, we discuss the key ideas and discoveries leading to the current understanding of protein folding kinetics, including folding landscapes and funnels, free energy barriers at the folding/unfolding pathways, and the solution of Levinthal's paradox. A special role here is played by the "all-or-none" phase transition occurring at protein folding and unfolding and by the point of thermodynamic (and kinetic) equilibrium between the "native" and the "unfolded" phases of the protein chain (where the theory obtains the simplest form). The modern theory provides an understanding of key features of protein folding and, in good agreement with experiments, it (i) outlines the chain length-dependent range of protein folding times, (ii) predicts the observed maximal size of "foldable" proteins and domains. Besides, it predicts the maximal size of proteins and domains that fold under solely thermodynamic (rather than kinetic) control. Complementarily, a theoretical analysis of the number of possible protein folding patterns, performed at the level of formation and assembly of secondary structures, correctly outlines the upper limit of protein folding times.
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Affiliation(s)
- Alexei V. Finkelstein
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Biotechnology Department of the Lomonosov Moscow State University, 4 Institutskaya Str, 142290 Pushchino, Moscow Region, Russia
- Biology Department of the Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Natalya S. Bogatyreva
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Dmitry N. Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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10
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England JL. Self-organized computation in the far-from-equilibrium cell. BIOPHYSICS REVIEWS 2022; 3:041303. [PMID: 38505518 PMCID: PMC10903489 DOI: 10.1063/5.0103151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/12/2022] [Indexed: 03/21/2024]
Abstract
Recent progress in our understanding of the physics of self-organization in active matter has pointed to the possibility of spontaneous collective behaviors that effectively compute things about the patterns in the surrounding patterned environment. Here, we describe this progress and speculate about its implications for our understanding of the internal organization of the living cell.
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Affiliation(s)
- Jeremy L England
- School of Physics, Georgia Institute of Technology, 837 State St NW, Atlanta, Georgia 30332, USA and GSK.ai, GlaxoSmithKline, 46 Menachem Begin, Ninth Floor, Tel Aviv, Israel
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11
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A diminished hydrophobic effect inside the GroEL/ES cavity contributes to protein substrate destabilization. Proc Natl Acad Sci U S A 2022; 119:e2213170119. [PMID: 36409898 PMCID: PMC9860310 DOI: 10.1073/pnas.2213170119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Confining compartments are ubiquitous in biology, but there have been few experimental studies on the thermodynamics of protein folding in such environments. Recently, we reported that the stability of a model protein substrate in the GroEL/ES chaperonin cage is reduced dramatically by more than 5 kcal mol-1 compared to that in bulk solution, but the origin of this effect remained unclear. Here, we show that this destabilization is caused, at least in part, by a diminished hydrophobic effect in the GroEL/ES cavity. This reduced hydrophobic effect is probably caused by water ordering due to the small number of hydration shells between the cavity and protein substrate surfaces. Hence, encapsulated protein substrates can undergo a process similar to cold denaturation in which unfolding is promoted by ordered water molecules. Our findings are likely to be relevant to encapsulated substrates in chaperonin systems, in general, and are consistent with the iterative annealing mechanism of action proposed for GroEL/ES.
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12
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Stan G, Lorimer GH, Thirumalai D. Friends in need: How chaperonins recognize and remodel proteins that require folding assistance. Front Mol Biosci 2022; 9:1071168. [PMID: 36479385 PMCID: PMC9720267 DOI: 10.3389/fmolb.2022.1071168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/07/2022] [Indexed: 08/19/2023] Open
Abstract
Chaperonins are biological nanomachines that help newly translated proteins to fold by rescuing them from kinetically trapped misfolded states. Protein folding assistance by the chaperonin machinery is obligatory in vivo for a subset of proteins in the bacterial proteome. Chaperonins are large oligomeric complexes, with unusual seven fold symmetry (group I) or eight/nine fold symmetry (group II), that form double-ring constructs, enclosing a central cavity that serves as the folding chamber. Dramatic large-scale conformational changes, that take place during ATP-driven cycles, allow chaperonins to bind misfolded proteins, encapsulate them into the expanded cavity and release them back into the cellular environment, regardless of whether they are folded or not. The theory associated with the iterative annealing mechanism, which incorporated the conformational free energy landscape description of protein folding, quantitatively explains most, if not all, the available data. Misfolded conformations are associated with low energy minima in a rugged energy landscape. Random disruptions of these low energy conformations result in higher free energy, less folded, conformations that can stochastically partition into the native state. Two distinct mechanisms of annealing action have been described. Group I chaperonins (GroEL homologues in eubacteria and endosymbiotic organelles), recognize a large number of misfolded proteins non-specifically and operate through highly coordinated cooperative motions. By contrast, the less well understood group II chaperonins (CCT in Eukarya and thermosome/TF55 in Archaea), assist a selected set of substrate proteins. Sequential conformational changes within a CCT ring are observed, perhaps promoting domain-by-domain substrate folding. Chaperonins are implicated in bacterial infection, autoimmune disease, as well as protein aggregation and degradation diseases. Understanding the chaperonin mechanism and the specific proteins they rescue during the cell cycle is important not only for the fundamental aspect of protein folding in the cellular environment, but also for effective therapeutic strategies.
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Affiliation(s)
- George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - George H. Lorimer
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Austin, TX, United States
- Department of Physics, University of Texas, Austin, TX, United States
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13
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Liu Y, Zhou L, Xu Y, Li K, Zhao Y, Qiao H, Xu Q, Zhao J. Heat Shock Proteins and Ferroptosis. Front Cell Dev Biol 2022; 10:864635. [PMID: 35478955 PMCID: PMC9035830 DOI: 10.3389/fcell.2022.864635] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/23/2022] [Indexed: 01/08/2023] Open
Abstract
Ferroptosis is a new form of regulatory cell death named by Dixon in 2012, which is characterized by the accumulation of lipid peroxides and iron ions. Molecular chaperones are a class of evolutionarily conserved proteins in the cytoplasm. They recognize and bind incompletely folded or assembled proteins to help them fold, transport or prevent their aggregation, but they themselves do not participate in the formation of final products. As the largest number of molecular chaperones, heat shock proteins can be divided into five families: HSP110 (HSPH), HSP90 (HSPC), HSP70 (HSPA), HSP40 (DNAJ) and small heat shock proteins (HSPB). Different heat shock proteins play different roles in promoting or inhibiting ferroptosis in different diseases. It is known that ferroptosis is participated in tumors, nervous system diseases, renal injury and ischemia-reperfusion injury. However, there are few reviews about the relationship of heat shock proteins and ferroptosis. In this study, we systematically summarize the roles of heat shock proteins in the occurrence of ferroptosis, and predict the possible mechanisms of different families of heat shock proteins in the development of ferroptosis.
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Affiliation(s)
- Ying Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
- *Correspondence: Ying Liu, ; Jie Zhao,
| | - Lin Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Yunfei Xu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Kexin Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Yao Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Haoduo Qiao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Qing Xu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
- Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Jie Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Ying Liu, ; Jie Zhao,
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14
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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15
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Karamanos TK, Clore GM. Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy. Annu Rev Biophys 2022; 51:223-246. [PMID: 35044800 DOI: 10.1146/annurev-biophys-090921-120150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular chaperones are the guardians of the proteome inside the cell. Chaperones recognize and bind unfolded or misfolded substrates, thereby preventing further aggregation; promoting correct protein folding; and, in some instances, even disaggregating already formed aggregates. Chaperones perform their function by means of an array of weak protein-protein interactions that take place over a wide range of timescales and are therefore invisible to structural techniques dependent upon the availability of highly homogeneous samples. Nuclear magnetic resonance (NMR) spectroscopy, however, is ideally suited to study dynamic, rapidly interconverting conformational states and protein-protein interactions in solution, even if these involve a high-molecular-weight component. In this review, we give a brief overview of the principles used by chaperones to bind their client proteins and describe NMR methods that have emerged as valuable tools to probe chaperone-substrate and chaperone-chaperone interactions. We then focus on a few systems for which the application of these methods has greatly increased our understanding of the mechanisms underlying chaperone functions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom;
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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16
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Horovitz A, Reingewertz TH, Cuéllar J, Valpuesta JM. Chaperonin Mechanisms: Multiple and (Mis)Understood? Annu Rev Biophys 2022; 51:115-133. [DOI: 10.1146/annurev-biophys-082521-113418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The chaperonins are ubiquitous and essential nanomachines that assist in protein folding in an ATP-driven manner. They consist of two back-to-back stacked oligomeric rings with cavities in which protein (un)folding can take place in a shielding environment. This review focuses on GroEL from Escherichia coli and the eukaryotic chaperonin-containing t-complex polypeptide 1, which differ considerably in their reaction mechanisms despite sharing a similar overall architecture. Although chaperonins feature in many current biochemistry textbooks after being studied intensively for more than three decades, key aspects of their reaction mechanisms remain under debate and are discussed in this review. In particular, it is unclear whether a universal reaction mechanism operates for all substrates and whether it is passive, i.e., aggregation is prevented but the folding pathway is unaltered, or active. It is also unclear how chaperonin clients are distinguished from nonclients and what are the precise roles of the cofactors with which chaperonins interact. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Tali Haviv Reingewertz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Jorge Cuéllar
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - José María Valpuesta
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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17
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Wälti MA, Canagarajah B, Schwieters CD, Clore GM. Visualization of Sparsely-populated Lower-order Oligomeric States of Human Mitochondrial Hsp60 by Cryo-electron Microscopy. J Mol Biol 2021; 433:167322. [PMID: 34688687 PMCID: PMC8627483 DOI: 10.1016/j.jmb.2021.167322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022]
Abstract
Human mitochondrial Hsp60 (mtHsp60) is a class I chaperonin, 51% identical in sequence to the prototypical E. coli chaperonin GroEL. mtHsp60 maintains the proteome within the mitochondrion and is associated with various neurodegenerative diseases and cancers. The oligomeric assembly of mtHsp60 into heptameric ring structures that enclose a folding chamber only occurs upon addition of ATP and is significantly more labile than that of GroEL, where the only oligomeric species is a tetradecamer. The lability of the mtHsp60 heptamer provides an opportunity to detect and visualize lower-order oligomeric states that may represent intermediates along the assembly/disassembly pathway. Using cryo-electron microscopy we show that, in addition to the fully-formed heptamer and an "inverted" tetradecamer in which the two heptamers associate via their apical domains, thereby blocking protein substrate access, well-defined lower-order oligomeric species, populated at less than 6% of the total particles, are observed. Specifically, we observe open trimers, tetramers, pentamers and hexamers (comprising ∼4% of the total particles) with rigid body rotations from one subunit to the next within ∼1.5-3.5° of that for the heptamer, indicating that these may lie directly on the assembly/disassembly pathway. We also observe a closed-ring hexamer (∼2% of the particles) which may represent an off-pathway species in the assembly/disassembly process in so far that conversion to the mature heptamer would require the closed-ring hexamer to open to accept an additional subunit. Lastly, we observe several classes of tetramers where additional subunits characterized by fuzzy electron density are caught in the act of oligomer extension.
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Affiliation(s)
- Marielle A Wälti
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Bertram Canagarajah
- Laboratory of Cell and Molecular Biology, and National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Charles D Schwieters
- Computational Biomolecular Nuclear Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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18
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Nassar R, Dignon GL, Razban RM, Dill KA. The Protein Folding Problem: The Role of Theory. J Mol Biol 2021; 433:167126. [PMID: 34224747 PMCID: PMC8547331 DOI: 10.1016/j.jmb.2021.167126] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 10/20/2022]
Abstract
The protein folding problem was first articulated as question of how order arose from disorder in proteins: How did the various native structures of proteins arise from interatomic driving forces encoded within their amino acid sequences, and how did they fold so fast? These matters have now been largely resolved by theory and statistical mechanics combined with experiments. There are general principles. Chain randomness is overcome by solvation-based codes. And in the needle-in-a-haystack metaphor, native states are found efficiently because protein haystacks (conformational ensembles) are funnel-shaped. Order-disorder theory has now grown to encompass a large swath of protein physical science across biology.
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Affiliation(s)
- Roy Nassar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Gregory L Dignon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rostam M Razban
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA.
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19
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Macro N, Chen L, Yang Y, Mondal T, Wang L, Horovitz A, Zhong D. Slowdown of Water Dynamics from the Top to the Bottom of the GroEL Cavity. J Phys Chem Lett 2021; 12:5723-5730. [PMID: 34129341 PMCID: PMC8687601 DOI: 10.1021/acs.jpclett.1c01216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
The GroE molecular chaperone system is a critical protein machine that assists the folding of substrate proteins in its cavity. Water in the cavity is suspected to play a role in substrate protein folding, but the mechanism is currently unknown. Herein, we report measurements of water dynamics in the equatorial and apical domains of the GroEL cavity in the apo and football states, using site-specific tryptophanyl mutagenesis as an intrinsic optical probe with femtosecond resolution combined with molecular dynamics simulations. We observed clearly different water dynamics in the two domains with a slowdown of the cavity water from the apical to equatorial region in the football state. The results suggest that the GroEL cavity provides a unique water environment that may facilitate substrate protein folding.
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Affiliation(s)
- Nicolas Macro
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Long Chen
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yushan Yang
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tridib Mondal
- Department
of Structural Biology, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Lijuan Wang
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amnon Horovitz
- Department
of Structural Biology, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Dongping Zhong
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, Programs of Biophysics, Program of
Chemical Physics, and Program of Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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20
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Moore AT, de Victoria AL, Koculi E. Interactions of the C-Terminal Truncated DEAD-Box Protein DDX3X With RNA and Nucleotide Substrates. ACS OMEGA 2021; 6:12640-12646. [PMID: 34056415 PMCID: PMC8154130 DOI: 10.1021/acsomega.1c00700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
DDX3X is a human DEAD-box RNA helicase implicated in many important cellular processes. In addition to the RecA-like catalytic core, DDX3X contains N- and C-terminal domains. The ancillary domains of DEAD-box RNA helicases have been shown to modulate their interactions with RNA and nucleotide substrates. Here, with the goal of understanding the role of N- and C-terminal domains of DDX3X on the DDX3X catalytic activity, we examined the interactions of RNA substrates and nucleotides with a DDX3X construct possessing the entire N-terminal domain and the catalytic core but lacking 80 residues from its C-terminal domain. Next, we compared our results with previously investigated DDX3X constructs. Our data show that the C-terminal truncated DDX3X does not bind to a blunt-ended double-helix RNA. This conclusion agrees with the data obtained on the wild-type LAF-1 protein, the DDX3X ortholog in Caenorhabditis elegans, and disagrees with the data obtained on the minimally active DDX3X construct, which misses 131 residues from its N-terminal domain and 80 residues from its C-terminal domain. The minimally active DDX3X construct was able to bind to the blunt-ended RNA construct. Combined, the previous studies and our results indicate that the N-terminal of DDX3X modulates the choice of DDX3X-RNA substrates. Furthermore, a previous study showed that the wild-type DDX3X construct hydrolyzes all four nucleotides and deoxynucleotides, both in the presence and absence of RNA. The C-terminal truncated DDX3X investigated here hydrolyzes only cytidine triphosphate (CTP) in the absence of RNA and CTP, adenosine triphosphate (ATP), and deoxyribose adenosine triphosphate (dATP) in the presence of RNA. Hence, the C-terminal truncated DDX3X has a more stringent nucleotide specificity than wild-type DDX3X.
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Affiliation(s)
- Anthony
F. T. Moore
- Department
of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | | | - Eda Koculi
- Department
of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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21
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On the Emergence of Orientational Order in Folded Proteins with Implications for Allostery. Symmetry (Basel) 2021. [DOI: 10.3390/sym13050770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The beautiful structures of single- and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein structures are considered to be aperiodic, and may have evolved this way for functional purposes, especially in instances that require a combination of softness and rigidity within the same molecule. By analyzing the solved protein structures, we show that orientational symmetry is broken in the aperiodic arrangement of the secondary structure elements (SSEs), which we deduce by calculating the nematic order parameter, P2. We find that the folded structures are nematic droplets with a broad distribution of P2. We argue that a non-zero value of P2, leads to an arrangement of the SSEs that can resist external forces, which is a requirement for allosteric proteins. Such proteins, which resist mechanical forces in some regions while being flexible in others, transmit signals from one region of the protein to another (action at a distance) in response to binding of ligands (oxygen, ATP, or other small molecules).
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22
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Koculi E, Thirumalai D. Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL. Biochemistry 2021; 60:460-464. [PMID: 33464880 DOI: 10.1021/acs.biochem.0c00903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Escherichia coli ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nanocage for a short duration. If confinement of the SPs is the mechanism by which GroEL/ES facilitates folding, it follows that the assisted folding rate, relative to the bulk value, should always be enhanced. Here, we show that this is not the case for the folding of rhodanese in the presence of the full machinery of GroEL/ES and ATP. The assisted folding rate of rhodanese decreases. On the basis of our finding and those reported in other studies, we suggest that the ATP-consuming chaperonin machinery has evolved to optimize the product of the folding rate and the yield of the folded SPs on the biological time scale. Neither the rate nor the yield is separately maximized.
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Affiliation(s)
- Eda Koculi
- Department of Biology, Johns Hopkins University, 144 Mudd Hall, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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23
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Korobko I, Mazal H, Haran G, Horovitz A. Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization. eLife 2020; 9:56511. [PMID: 32716842 PMCID: PMC7440923 DOI: 10.7554/elife.56511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/25/2020] [Indexed: 01/29/2023] Open
Abstract
The thermodynamics of protein folding in bulk solution have been thoroughly investigated for decades. By contrast, measurements of protein substrate stability inside the GroEL/ES chaperonin cage have not been reported. Such measurements require stable encapsulation, that is no escape of the substrate into bulk solution during experiments, and a way to perturb protein stability without affecting the chaperonin system itself. Here, by establishing such conditions, we show that protein stability in the chaperonin cage is reduced dramatically by more than 5 kcal mol-1 compared to that in bulk solution. Given that steric confinement alone is stabilizing, our results indicate that hydrophobic and/or electrostatic effects in the cavity are strongly destabilizing. Our findings are consistent with the iterative annealing mechanism of action proposed for the chaperonin GroEL.
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Affiliation(s)
- Ilia Korobko
- Departments of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Haran
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Amnon Horovitz
- Departments of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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24
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Balchin D, Hayer-Hartl M, Hartl FU. Recent advances in understanding catalysis of protein folding by molecular chaperones. FEBS Lett 2020; 594:2770-2781. [PMID: 32446288 DOI: 10.1002/1873-3468.13844] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022]
Abstract
Molecular chaperones are highly conserved proteins that promote proper folding of other proteins in vivo. Diverse chaperone systems assist de novo protein folding and trafficking, the assembly of oligomeric complexes, and recovery from stress-induced unfolding. A fundamental function of molecular chaperones is to inhibit unproductive protein interactions by recognizing and protecting hydrophobic surfaces that are exposed during folding or following proteotoxic stress. Beyond this basic principle, it is now clear that chaperones can also actively and specifically accelerate folding reactions in an ATP-dependent manner. We focus on the bacterial Hsp70 and chaperonin systems as paradigms, and review recent work that has advanced our understanding of how these chaperones act as catalysts of protein folding.
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Affiliation(s)
- David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London, UK
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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25
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Thirumalai D, Lorimer GH, Hyeon C. Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones. Protein Sci 2019; 29:360-377. [PMID: 31800116 DOI: 10.1002/pro.3795] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022]
Abstract
Molecular chaperones are ATP-consuming machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states. Unassisted folding occurs by the kinetic partitioning mechanism according to which folding to the native state, with low probability as well as misfolding to one of the many metastable states, with high probability, occur rapidly. GroEL is an all-purpose stochastic machine that assists misfolded substrate proteins to fold. The RNA chaperones such as CYT-19, which are ATP-consuming enzymes, help the folding of ribozymes that get trapped in metastable states for long times. GroEL does not interact with the folded proteins but CYT-19 disrupts both the folded and misfolded ribozymes. The structures of GroEL and RNA chaperones are strikingly different. Despite these differences, the iterative annealing mechanism (IAM) quantitatively explains all the available experimental data for assisted folding of proteins and ribozymes. Driven by ATP binding and hydrolysis and GroES binding, GroEL undergoes a catalytic cycle during which it samples three allosteric states, T (apo), R (ATP bound), and R″ (ADP bound). Analyses of the experimental data show that the efficiency of the GroEL-GroES machinery and mutants is determined by the resetting rate k R ″ → T , which is largest for the wild-type (WT) GroEL. Generalized IAM accurately predicts the folding kinetics of Tetrahymena ribozyme and its variants. Chaperones maximize the product of the folding rate and the steady-state native state fold by driving the substrates out of equilibrium. Neither the absolute yield nor the folding rate is optimized.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
| | - George H Lorimer
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland
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