101
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Bhore N, Wang BJ, Chen YW, Liao YF. Critical Roles of Dual-Specificity Phosphatases in Neuronal Proteostasis and Neurological Diseases. Int J Mol Sci 2017; 18:ijms18091963. [PMID: 28902166 PMCID: PMC5618612 DOI: 10.3390/ijms18091963] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/01/2017] [Accepted: 09/07/2017] [Indexed: 12/31/2022] Open
Abstract
Protein homeostasis or proteostasis is a fundamental cellular property that encompasses the dynamic balancing of processes in the proteostasis network (PN). Such processes include protein synthesis, folding, and degradation in both non-stressed and stressful conditions. The role of the PN in neurodegenerative disease is well-documented, where it is known to respond to changes in protein folding states or toxic gain-of-function protein aggregation. Dual-specificity phosphatases have recently emerged as important participants in maintaining balance within the PN, acting through modulation of cellular signaling pathways that are involved in neurodegeneration. In this review, we will summarize recent findings describing the roles of dual-specificity phosphatases in neurodegeneration and offer perspectives on future therapeutic directions.
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Affiliation(s)
- Noopur Bhore
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang-Ming University and Academia Sinica, Taipei 11529, Taiwan.
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Bo-Jeng Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Yun-Wen Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Yung-Feng Liao
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang-Ming University and Academia Sinica, Taipei 11529, Taiwan.
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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102
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Kyne C, Crowley PB. Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm. Biochemistry 2017; 56:5026-5032. [DOI: 10.1021/acs.biochem.7b00731] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ciara Kyne
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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103
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Cohen RD, Pielak GJ. Quinary interactions with an unfolded state ensemble. Protein Sci 2017; 26:1698-1703. [PMID: 28571108 PMCID: PMC5563149 DOI: 10.1002/pro.3206] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/21/2017] [Accepted: 05/26/2017] [Indexed: 01/10/2023]
Abstract
Anfinsen's thermodynamic hypothesis states that the native three-dimensional fold of a protein represents the structure with the lowest Gibbs free energy. Changes in the free energy of denaturation can arise from changes to the folded state, the unfolded state, or both. It has been recently recognized that quinary interactions, transient contacts that take place only in cells, can modulate protein stability through interactions involving the folded state. Here we show that the cellular environment can also remodel the unfolded state ensemble.
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Affiliation(s)
- Rachel D. Cohen
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillNorth Carolina27599
- Integrative Program for Biological and Genome SciencesUniversity of North CarolinaChapel HillNorth Carolina27599
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104
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Diniz A, Dias JS, Jiménez-Barbero J, Marcelo F, Cabrita EJ. Protein-Glycan Quinary Interactions in Crowding Environment Unveiled by NMR Spectroscopy. Chemistry 2017. [PMID: 28649731 DOI: 10.1002/chem.201702800] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein-glycan interactions as modulators for quinary structures in crowding environments were explored. The interaction between human galectin 3 (Gal-3) and distinct macromolecular crowders, such as bovine and human serum albumin (BSA and HSA), Ficoll 70 and PEG3350, was scrutinized. The molecular recognition event of the specific ligand, lactose, by Gal-3 in crowding conditions was evaluated. Gal-3 interactions were monitored by NMR analysing chemical shift perturbation (CSP) and line broadening of 1 H15 N-HSQC signals. The intensity of the Gal-3 1 H15 N-HSQC signals decreased in the presence of all crowders, due to the increase in the solution viscosity and to the formation of large protein complexes. When glycosylated containing samples of BSA and HSA were used, signal broadening was more severe than that observed in the presence of the more viscous solutions of PEG3350 and Ficoll 70. However, for the samples containing glycoproteins, the signal intensity of 1 H15 N-HSQC recovered upon addition of lactose. We show that serum proteins interact with Gal-3, through their α2,3-linked sialylgalactose moieties exposed at their surfaces, competing with lactose for the same binding site. The quinary interaction between Gal-3 and serum glycoproteins, could help to co-localize Gal-3 at the cell surface, and may play a role in adhesion and signalling functions of this protein.
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Affiliation(s)
- Ana Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jorge S Dias
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC-bioGUNE Bizkaia, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48005, Bilbao, Spain.,Departament Organic Chemistry II, EHU-UPV, 48040, Leioa, Spain
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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105
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Liu B, Åberg C, van Eerden FJ, Marrink SJ, Poolman B, Boersma AJ. Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding. Biophys J 2017; 112:1929-1939. [PMID: 28494963 DOI: 10.1016/j.bpj.2017.04.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/27/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022] Open
Abstract
Cells are highly crowded with proteins and polynucleotides. Any reaction that depends on the available volume can be affected by macromolecular crowding, but the effects of crowding in cells are complex and difficult to track. Here, we present a set of Förster resonance energy transfer (FRET)-based crowding-sensitive probes and investigate the role of the linker design. We investigate the sensors in vitro and in vivo and by molecular dynamics simulations. We find that in vitro all the probes can be compressed by crowding, with a magnitude that increases with the probe size, the crowder concentration, and the crowder size. We capture the role of the linker in a heuristic scaling model, and we find that compression is a function of size of the probe and volume fraction of the crowder. The FRET changes observed in Escherichia coli are more complicated, where FRET-increases and scaling behavior are observed solely with probes that contain the helices in the linker. The probe with the highest sensitivity to crowding in vivo yields the same macromolecular volume fractions as previously obtained from cell dry weight. The collection of new probes provides more detailed readouts on the macromolecular crowding than a single sensor.
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Affiliation(s)
- Boqun Liu
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Christoffer Åberg
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Floris J van Eerden
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
| | - Arnold J Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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106
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DeMott CM, Majumder S, Burz DS, Reverdatto S, Shekhtman A. Ribosome Mediated Quinary Interactions Modulate In-Cell Protein Activities. Biochemistry 2017; 56:4117-4126. [PMID: 28715177 DOI: 10.1021/acs.biochem.7b00613] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomes are present inside bacterial cells at micromolar concentrations and occupy up to 20% of the cell volume. Under these conditions, even weak quinary interactions between ribosomes and cytosolic proteins can affect protein activity. By using in-cell and in vitro NMR spectroscopy, and biophysical techniques, we show that the enzymes, adenylate kinase and dihydrofolate reductase, and the respective coenzymes, ATP and NADPH, bind to ribosomes with micromolar affinity, and that this interaction suppresses the enzymatic activities of both enzymes. Conversely, thymidylate synthase, which works together with dihydrofolate reductase in the thymidylate synthetic pathway, is activated by ribosomes. We also show that ribosomes impede diffusion of green fluorescent protein in vitro and contribute to the decrease in diffusion in vivo. These results strongly suggest that ribosome-mediated quinary interactions contribute to the differences between in vitro and in vivo protein activities and that ribosomes play a previously under-appreciated nontranslational role in regulating cellular biochemistry.
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Affiliation(s)
- Christopher M DeMott
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Subhabrata Majumder
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
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107
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Rotta M, Timmers LFSM, Sequeiros-Borja C, Bizarro CV, de Souza ON, Santos DS, Basso LA. Observed crowding effects on Mycobacterium tuberculosis 2-trans-enoyl-ACP (CoA) reductase enzyme activity are not due to excluded volume only. Sci Rep 2017; 7:6826. [PMID: 28754992 PMCID: PMC5533716 DOI: 10.1038/s41598-017-07266-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/23/2017] [Indexed: 11/29/2022] Open
Abstract
The cellular milieu is a complex and crowded aqueous solution. Macromolecular crowding effects are commonly studied in vitro using crowding agents. The aim of the present study was to evaluate the effects, if any, of macromolecular synthetic crowding agents on the apparent steady-state kinetic parameters (K m , k cat , and k cat /K m ) of Mycobacterium tuberculosis 2-trans-enoyl-ACP (CoA) reductase (InhA). Negligible effects on InhA activity were observed for ficoll 70, ficoll 400 and dextran 70. A complex effect was observed for PEG 6000. Glucose and sucrose showed, respectively, no effect on InhA activity and decreased k cat /K m for NADH and k cat for 2-trans-dodecenoyl-CoA. Molecular dynamics results suggest that InhA adopts a more compact conformer in sucrose solution. The effects of the crowding agents on the energy (E a and E η ), enthalpy (∆H # ), entropy (∆S # ), and Gibbs free energy (∆G # ) of activation were determined. The ∆G # values for all crowding agents were similar to buffer, suggesting that excluded volume effects did not facilitate stable activated ES # complex formation. Nonlinear Arrhenius plot for PEG 6000 suggests that "soft" interactions play a role in crowding effects. The results on InhA do not unequivocally meet the criteria for crowding effect due to exclude volume only.
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Affiliation(s)
- Mariane Rotta
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, RS, Brazil
| | - Luis F S M Timmers
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Faculdade de Informática, PUCRS, Porto Alegre, RS, Brazil
- Laboratório de FarmInformática (FarmInf), Faculdade de Farmácia, PUCRS, Porto Alegre, RS, Brazil
| | - Carlos Sequeiros-Borja
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Faculdade de Informática, PUCRS, Porto Alegre, RS, Brazil
- Laboratório de FarmInformática (FarmInf), Faculdade de Farmácia, PUCRS, Porto Alegre, RS, Brazil
| | - Cristiano V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Osmar N de Souza
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Faculdade de Informática, PUCRS, Porto Alegre, RS, Brazil
- Laboratório de FarmInformática (FarmInf), Faculdade de Farmácia, PUCRS, Porto Alegre, RS, Brazil
| | - Diogenes S Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.
| | - Luiz A Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, RS, Brazil.
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108
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Plitzko JM, Schuler B, Selenko P. Structural Biology outside the box-inside the cell. Curr Opin Struct Biol 2017; 46:110-121. [PMID: 28735108 DOI: 10.1016/j.sbi.2017.06.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/17/2017] [Accepted: 06/23/2017] [Indexed: 01/11/2023]
Abstract
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
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Affiliation(s)
- Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Philipp Selenko
- Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Laboratory, Robert-Roessle Strasse 10, D-13125 Berlin, Germany.
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109
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Kadisch M, Willrodt C, Hillen M, Bühler B, Schmid A. Maximizing the stability of metabolic engineering-derived whole-cell biocatalysts. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600170] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/22/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Marvin Kadisch
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Christian Willrodt
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Michael Hillen
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Bruno Bühler
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Andreas Schmid
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
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110
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Gorensek-Benitez AH, Smith AE, Stadmiller SS, Perez Goncalves GM, Pielak GJ. Cosolutes, Crowding, and Protein Folding Kinetics. J Phys Chem B 2017; 121:6527-6537. [PMID: 28605189 PMCID: PMC5982521 DOI: 10.1021/acs.jpcb.7b03786] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long accepted as the most important interaction, recent work shows that steric repulsions alone cannot explain the effects of macromolecular cosolutes on the equilibrium thermodynamics of protein stability. Instead, chemical interactions have been shown to modulate, and even dominate, crowding-induced steric repulsions. Here, we use 19F NMR to examine the effects of small and large cosolutes on the kinetics of protein folding and unfolding using the metastable 7 kDa N-terminal SH3 domain of the Drosophila signaling protein drk (SH3), which folds by a two-state mechanism. The small cosolutes consist of trimethylamine N-oxide and sucrose, which increase equilibrium protein stability, and urea, which destabilizes proteins. The macromolecules comprise the stabilizing sucrose polymer, Ficoll, and the destabilizing globular protein, lysozyme. We assessed the effects of these cosolutes on the differences in free energy between the folded state and the transition state and between the unfolded ensemble and the transition state. We then examined the temperature dependence to assess changes in activation enthalpy and entropy. The enthalpically mediated effects are more complicated than suggested by equilibrium measurements. We also observed enthalpic effects with the supposedly inert sucrose polymer, Ficoll, that arise from its macromolecular nature. Assessment of activation entropies shows important contributions from solvent and cosolute, in addition to the configurational entropy of the protein that, again, cannot be gleaned from equilibrium data. Comparing the effects of Ficoll to those of the more physiologically relevant cosolute lysozyme reveals that synthetic polymers are not appropriate models for understanding the kinetics of protein folding in cells.
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Affiliation(s)
| | - Austin E. Smith
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Samantha S. Stadmiller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | - Gary J. Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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111
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Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017; 121:8009-8025. [PMID: 28666087 PMCID: PMC5582368 DOI: 10.1021/acs.jpcb.7b03570] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The
effects of crowding in biological environments on biomolecular
structure, dynamics, and function remain not well understood. Computer
simulations of atomistic models of concentrated peptide and protein
systems at different levels of complexity are beginning to provide
new insights. Crowding, weak interactions with other macromolecules
and metabolites, and altered solvent properties within cellular environments
appear to remodel the energy landscape of peptides and proteins in
significant ways including the possibility of native state destabilization.
Crowding is also seen to affect dynamic properties, both conformational
dynamics and diffusional properties of macromolecules. Recent simulations
that address these questions are reviewed here and discussed in the
context of relevant experiments.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States.,Quantitative Biology Center, RIKEN , Kobe, Japan
| | - Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan
| | - Po-Hung Wang
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States
| | - Yuji Sugita
- Quantitative Biology Center, RIKEN , Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan.,Advanced Institute for Computational Science, RIKEN , Kobe, Japan
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112
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Garland J. Unravelling the complexity of signalling networks in cancer: A review of the increasing role for computational modelling. Crit Rev Oncol Hematol 2017; 117:73-113. [PMID: 28807238 DOI: 10.1016/j.critrevonc.2017.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023] Open
Abstract
Cancer induction is a highly complex process involving hundreds of different inducers but whose eventual outcome is the same. Clearly, it is essential to understand how signalling pathways and networks generated by these inducers interact to regulate cell behaviour and create the cancer phenotype. While enormous strides have been made in identifying key networking profiles, the amount of data generated far exceeds our ability to understand how it all "fits together". The number of potential interactions is astronomically large and requires novel approaches and extreme computation methods to dissect them out. However, such methodologies have high intrinsic mathematical and conceptual content which is difficult to follow. This review explains how computation modelling is progressively finding solutions and also revealing unexpected and unpredictable nano-scale molecular behaviours extremely relevant to how signalling and networking are coherently integrated. It is divided into linked sections illustrated by numerous figures from the literature describing different approaches and offering visual portrayals of networking and major conceptual advances in the field. First, the problem of signalling complexity and data collection is illustrated for only a small selection of known oncogenes. Next, new concepts from biophysics, molecular behaviours, kinetics, organisation at the nano level and predictive models are presented. These areas include: visual representations of networking, Energy Landscapes and energy transfer/dissemination (entropy); diffusion, percolation; molecular crowding; protein allostery; quinary structure and fractal distributions; energy management, metabolism and re-examination of the Warburg effect. The importance of unravelling complex network interactions is then illustrated for some widely-used drugs in cancer therapy whose interactions are very extensive. Finally, use of computational modelling to develop micro- and nano- functional models ("bottom-up" research) is highlighted. The review concludes that computational modelling is an essential part of cancer research and is vital to understanding network formation and molecular behaviours that are associated with it. Its role is increasingly essential because it is unravelling the huge complexity of cancer induction otherwise unattainable by any other approach.
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Affiliation(s)
- John Garland
- Manchester Interdisciplinary Biocentre, Manchester University, Manchester, UK.
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113
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Abriata LA, Spiga E, Peraro MD. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics. Biophys J 2017; 111:743-755. [PMID: 27558718 DOI: 10.1016/j.bpj.2016.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/06/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022] Open
Abstract
Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Enrico Spiga
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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114
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Li C, Zhao J, Cheng K, Ge Y, Wu Q, Ye Y, Xu G, Zhang Z, Zheng W, Zhang X, Zhou X, Pielak G, Liu M. Magnetic Resonance Spectroscopy as a Tool for Assessing Macromolecular Structure and Function in Living Cells. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:157-182. [PMID: 28301750 DOI: 10.1146/annurev-anchem-061516-045237] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Investigating the structure, modification, interaction, and function of biomolecules in their native cellular environment leads to physiologically relevant knowledge about their mechanisms, which will benefit drug discovery and design. In recent years, nuclear and electron magnetic resonance (NMR) spectroscopy has emerged as a useful tool for elucidating the structure and function of biomacromolecules, including proteins, nucleic acids, and carbohydrates in living cells at atomic resolution. In this review, we summarize the progress and future of in-cell NMR as it is applied to proteins, nucleic acids, and carbohydrates.
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Affiliation(s)
- Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Yuwei Ge
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Yansheng Ye
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Zeting Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Wenwen Zheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Gary Pielak
- Department of Chemistry, Department of Biochemistry and Biophysics, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
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115
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Luo Y, Raso SW, Gallant J, Steinmeyer C, Mabuchi Y, Lu Z, Entrican C, Rouse JC. Evidence for intermolecular domain exchange in the Fab domains of dimer and oligomers of an IgG1 monoclonal antibody. MAbs 2017; 9:916-926. [PMID: 28590212 DOI: 10.1080/19420862.2017.1331803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Recombinant protein therapeutics have become increasingly useful in combating human diseases, such as cancer and those of genetic origin. One quality concern for protein therapeutics is the content and the structure of the aggregated proteins in the product, due to the potential immunogenicity of these aggregates. Collective efforts have led to a better understanding of some types of protein aggregates, and have revealed the diversity in the structure and cause of protein aggregation. In this work we used a broad range of analytical techniques to characterize the quinary structure (complexes in which each composing unit maintains native quaternary structure) of the stable non-covalent dimer and oligomers of a monoclonal IgG1λ antibody. The results supported a mechanism of intermolecular domain exchange involving the Fab domains of 2 or more IgG molecules. This mechanism can account for the native-like higher order (secondary, tertiary and disulfide bonding) structure, the stability of the non-covalent multimers, and the previously observed partial loss of the antigen-binding sites without changing the antigen-binding affinity and kinetics of the remaining sites (Luo et al., 2009, mAbs 1:491). Furthermore, the previously observed increase in the apparent affinity to various Fcγ receptors (ibid), which may potentially promote immunogenicity, was also explained by the quinary structure proposed here. Several lines of evidence indicated that the formation of multimers by the mechanism of intermolecular domain exchange took place mostly during expression, not in the purified materials. The findings in this work will advance our knowledge of the mechanisms for aggregation in therapeutic monoclonal antibodies.
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Affiliation(s)
- Yin Luo
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Stephen W Raso
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Judith Gallant
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Colleen Steinmeyer
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Yasuko Mabuchi
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Zhaojiang Lu
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Clifford Entrican
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
| | - Jason C Rouse
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences , Pfizer Inc. , Andover , USA
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116
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Protein hydration: Investigation of globular protein crystal structures. Int J Biol Macromol 2017; 99:160-165. [DOI: 10.1016/j.ijbiomac.2017.02.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/10/2017] [Indexed: 01/06/2023]
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117
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Physicochemical code for quinary protein interactions in Escherichia coli. Proc Natl Acad Sci U S A 2017; 114:E4556-E4563. [PMID: 28536196 DOI: 10.1073/pnas.1621227114] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How proteins sense and navigate the cellular interior to find their functional partners remains poorly understood. An intriguing aspect of this search is that it relies on diffusive encounters with the crowded cellular background, made up of protein surfaces that are largely nonconserved. The question is then if/how this protein search is amenable to selection and biological control. To shed light on this issue, we examined the motions of three evolutionary divergent proteins in the Escherichia coli cytoplasm by in-cell NMR. The results show that the diffusive in-cell motions, after all, follow simplistic physical-chemical rules: The proteins reveal a common dependence on (i) net charge density, (ii) surface hydrophobicity, and (iii) the electric dipole moment. The bacterial protein is here biased to move relatively freely in the bacterial interior, whereas the human counterparts more easily stick. Even so, the in-cell motions respond predictably to surface mutation, allowing us to tune and intermix the protein's behavior at will. The findings show how evolution can swiftly optimize the diffuse background of protein encounter complexes by just single-point mutations, and provide a rational framework for adjusting the cytoplasmic motions of individual proteins, e.g., for rescuing poor in-cell NMR signals and for optimizing protein therapeutics.
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118
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Rusinga FI, Weis DD. Soft interactions and volume exclusion by polymeric crowders can stabilize or destabilize transient structure in disordered proteins depending on polymer concentration. Proteins 2017; 85:1468-1479. [PMID: 28425679 DOI: 10.1002/prot.25307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 01/19/2023]
Abstract
The effects of macromolecular crowding on the transient structure of intrinsically disordered proteins is not well-understood. Crowding by biological molecules inside cells could modulate transient structure and alter IDP function. Volume exclusion theory and observations of structured proteins suggest that IDP transient structure would be stabilized by macromolecular crowding. Amide hydrogen exchange (HX) of IDPs in highly concentrated polymer solutions would provide valuable insights into IDP transient structure under crowded conditions. Here, we have used mass spectrometry to measure HX by a transiently helical random coil domain of the activator of thyroid and retinoid receptor (ACTR) in solutions containing 300 g L-1 and 400 g L-1 of Ficoll, a synthetic polysaccharide, using a recently-developed strong cation exchange-based cleanup method [Rusinga, et al., Anal Chem 2017;89:1275-1282]. Transiently helical regions of ACTR exchanged faster in 300 g L-1 Ficoll than in dilute buffer. In contrast, one transient helix exchanged more slowly in 400 g L-1 Ficoll. Nonspecific interactions destabilize ACTR helicity in 300 g L-1 Ficoll because ACTR engages with the Ficoll polymer mesh. In contrast, 400 g L-1 Ficoll is a semi-dilute solution where ACTR cannot engage the Ficoll mesh. At this higher concentration, volume exclusion stabilizes ACTR helicity because ACTR is compacted in interstitial spaces between Ficoll molecules. Our results suggest that the interplay between nonspecific interactions and volume exclusion in different cellular compartments could modulate IDP function by altering the stability of IDP transient structures. Proteins 2017; 85:1468-1479. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Farai I Rusinga
- Department of Chemistry and R. N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - David D Weis
- Department of Chemistry and R. N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas, USA
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119
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Gibbs EB, Cook EC, Showalter SA. Application of NMR to studies of intrinsically disordered proteins. Arch Biochem Biophys 2017; 628:57-70. [PMID: 28502465 DOI: 10.1016/j.abb.2017.05.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/20/2022]
Abstract
The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role in enhancing not only our understanding of the intrinsically disordered native state, but also how that state contributes to biological function. While pathological functions associated with protein aggregation are well established, it has recently become clear that disordered regions also mediate functionally advantageous assembly into high-order structures that promote the formation of membrane-less sub-cellular compartments and even hydrogels. Across the range of functional assembly states accessed by disordered regions, post-translational modifications and regulatory macromolecular interactions, which can also be investigated by NMR spectroscopy, feature prominently. Here we will explore the many ways in which NMR has advanced our understanding of the physical-chemical phase space occupied by disordered protein regions and provide prospectus for the future role of NMR in this emerging and exciting field.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik C Cook
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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120
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Stadmiller SS, Gorensek-Benitez AH, Guseman AJ, Pielak GJ. Osmotic Shock Induced Protein Destabilization in Living Cells and Its Reversal by Glycine Betaine. J Mol Biol 2017; 429:1155-1161. [PMID: 28263768 PMCID: PMC5985519 DOI: 10.1016/j.jmb.2017.03.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 12/18/2022]
Abstract
Many organisms can adapt to changes in the solute content of their surroundings (i.e., the osmolarity). Hyperosmotic shock causes water efflux and a concomitant reduction in cell volume, which is countered by the accumulation of osmolytes. This volume reduction increases the crowded nature of the cytoplasm, which is expected to affect protein stability. In contrast to traditional theory, which predicts that more crowded conditions can only increase protein stability, recent work shows that crowding can destabilize proteins through transient attractive interactions. Here, we quantify protein stability in living Escherichia coli cells before and after hyperosmotic shock in the presence and absence of the osmolyte, glycine betaine. The 7-kDa N-terminal src-homology 3 domain of Drosophila signal transduction protein drk is used as the test protein. We find that hyperosmotic shock decreases SH3 stability in cells, consistent with the idea that transient attractive interactions are important under physiologically relevant crowded conditions. The subsequent uptake of glycine betaine returns SH3 to the stability observed without osmotic shock. These results highlight the effect of transient attractive interactions on protein stability in cells and provide a new explanation for why stressed cells accumulate osmolytes.
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Affiliation(s)
- Samantha S Stadmiller
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | | | - Alex J Guseman
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27514, USA.
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121
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Luchinat E, Banci L. In-cell NMR: a topical review. IUCRJ 2017; 4:108-118. [PMID: 28250949 PMCID: PMC5330521 DOI: 10.1107/s2052252516020625] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/29/2016] [Indexed: 05/18/2023]
Abstract
Classical structural biology approaches allow structural characterization of biological macromolecules in vitro, far from their physiological context. Nowadays, thanks to the wealth of structural data available and to technological and methodological advances, the interest of the research community is gradually shifting from pure structural determination towards the study of functional aspects of biomolecules. Therefore, a cellular structural approach is ideally needed to characterize biological molecules, such as proteins, in their native cellular environment and the functional processes that they are involved in. In-cell NMR is a new application of high-resolution nuclear magnetic resonance spectroscopy that allows structural and dynamical features of proteins and other macromolecules to be analyzed directly in living cells. Owing to its challenging nature, this methodology has shown slow, but steady, development over the past 15 years. To date, several in-cell NMR approaches have been successfully applied to both bacterial and eukaryotic cells, including several human cell lines, and important structural and functional aspects have been elucidated. In this topical review, the major advances of in-cell NMR are summarized, with a special focus on recent developments in eukaryotic and mammalian cells.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center – CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Biomedical, Clinical and Experimental Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center – CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
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122
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Towards understanding cellular structure biology: In-cell NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:547-557. [PMID: 28257994 DOI: 10.1016/j.bbapap.2017.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biological processes and for structural analysis in cellular environments.
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123
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Cohen RD, Pielak GJ. A cell is more than the sum of its (dilute) parts: A brief history of quinary structure. Protein Sci 2017; 26:403-413. [PMID: 27977883 PMCID: PMC5326556 DOI: 10.1002/pro.3092] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
Most knowledge of protein structure and function is derived from experiments performed with purified protein resuspended in dilute, buffered solutions. However, proteins function in the crowded, complex cellular environment. Although the first four levels of protein structure provide important information, a complete understanding requires consideration of quinary structure. Quinary structure comprises the transient interactions between macromolecules that provides organization and compartmentalization inside cells. We review the history of quinary structure in the context of several metabolic pathways, and the technological advances that have yielded recent insight into protein behavior in living cells. The evidence demonstrates that protein behavior in isolated solutions deviates from behavior in the physiological environment.
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Affiliation(s)
- Rachel D. Cohen
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillNorth Carolina27599
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124
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Abstract
The effects of small (∼102 Da) and larger (>103 Da) cosolutes on the equilibrium stability of monomeric globular proteins are broadly understood, excluding volume stabilizes proteins and chemical interactions are stabilizing when repulsive, but destabilizing when attractive. Proteins, however, rarely work alone. Here, we investigate the effects of small and large cosolutes on the equilibrium stability of the simplest defined protein-protein interactions, the side-by-side homodimer formed by the A34F variant of the 56-residue B1 domain of protein G. We used 19F nuclear magnetic resonance spectroscopy to quantify the effects of urea, trimethylamine oxide, Ficoll, and more physiologically relevant cosolutes on the dimer dissociation constant. The data reveal the same stabilizing and destabilizing influences from chemical interactions as observed in studies of protein stability. Results with more physiologically relevant molecules such as bovine serum albumin, lysozyme, and reconstituted Escherichia coli cytosol reflect the importance of chemical interactions between these cosolutes and the test protein. Our study serves as a stepping-stone to a more complete understanding of crowding effects on protein-protein interactions.
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Affiliation(s)
- Alex J. Guseman
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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125
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Ligand-promoted protein folding by biased kinetic partitioning. Nat Chem Biol 2017; 13:369-371. [PMID: 28218913 PMCID: PMC5362304 DOI: 10.1038/nchembio.2303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/12/2016] [Indexed: 01/03/2023]
Abstract
Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems.
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126
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Kyne C, Jordon K, Filoti DI, Laue TM, Crowley PB. Protein charge determination and implications for interactions in cell extracts. Protein Sci 2017; 26:258-267. [PMID: 27813264 PMCID: PMC5275725 DOI: 10.1002/pro.3077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/24/2016] [Accepted: 10/27/2016] [Indexed: 01/30/2023]
Abstract
Decades of dilute-solution studies have revealed the influence of charged residues on protein stability, solubility and stickiness. Similar characterizations are now required in physiological solutions to understand the effect of charge on protein behavior under native conditions. Toward this end, we used free boundary and native gel electrophoresis to explore the charge of cytochrome c in buffer and in Escherichia coli extracts. We find that the charge of cytochrome c was ∼2-fold lower than predicted from primary structure analysis. Cytochrome c charge was tuned by sulfate binding and was rendered anionic in E. coli extracts due to interactions with macroanions. Mutants in which three or four cationic residues were replaced with glutamate were charge-neutral and "inert" in extracts. A comparison of the interaction propensities of cytochrome c and the mutants emphasizes the role of negative charge in stabilizing physiological environments. Charge-charge repulsion and preferential hydration appear to prevent aggregation. The implications for molecular organization in vivo are discussed.
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Affiliation(s)
- Ciara Kyne
- School of ChemistryNational University of IrelandGalway, University RoadGalwayIreland
| | - Kiara Jordon
- Spin Analytical468 Portland StreetBerwickMaine03901
| | - Dana I. Filoti
- Centre to Advance Macromolecular Interaction Sciences University of New HampshireDurhamNew Hampshire03824
| | - Thomas M. Laue
- Spin Analytical468 Portland StreetBerwickMaine03901
- Centre to Advance Macromolecular Interaction Sciences University of New HampshireDurhamNew Hampshire03824
| | - Peter B. Crowley
- School of ChemistryNational University of IrelandGalway, University RoadGalwayIreland
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127
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Danielsson J, Oliveberg M. Comparing protein behaviour in vitro and in vivo , what does the data really tell us? Curr Opin Struct Biol 2017; 42:129-135. [DOI: 10.1016/j.sbi.2017.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
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128
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Zhang N, An L, Li J, Liu Z, Yao L. Quinary Interactions Weaken the Electric Field Generated by Protein Side-Chain Charges in the Cell-like Environment. J Am Chem Soc 2017; 139:647-654. [DOI: 10.1021/jacs.6b11058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ning Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Jingwen Li
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijun Liu
- National
Center for Protein Science Shanghai, Institute of Biochemistry and
Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201210, China
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129
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Emergence of Life on Earth: A Physicochemical Jigsaw Puzzle. J Mol Evol 2016; 84:1-7. [PMID: 27995274 DOI: 10.1007/s00239-016-9775-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
Abstract
We review physicochemical factors and processes that describe how cellular life can emerge from prebiotic chemical matter; they are: (1) prebiotic Earth is a multicomponent and multiphase reservoir of chemical compounds, to which (2) Earth-Moon rotations deliver two kinds of regular cycling energies: diurnal electromagnetic radiation and seawater tides. (3) Emerging colloidal phases cyclically nucleate and agglomerate in seawater and consolidate as geochemical sediments in tidal zones, creating a matrix of microspaces. (4) Some microspaces persist and retain memory from past cycles, and others re-dissolve and re-disperse back into the Earth's chemical reservoir. (5) Proto-metabolites and proto-biopolymers coevolve with and within persisting microspaces, where (6) Macromolecular crowding and other non-covalent molecular forces govern the evolution of hydrophilic, hydrophobic, and charged molecular surfaces. (7) The matrices of microspaces evolve into proto-biofilms of progenotes with rudimentary but evolving replication, transcription, and translation, enclosed in unstable cell envelopes. (8) Stabilization of cell envelopes 'crystallizes' bacteria-like genetics and metabolism with low horizontal gene transfer-life 'as we know it.' These factors and processes constitute the 'working pieces' of the jigsaw puzzle of life's emergence. They extend the concept of progenotes as the first proto-cellular life, connected backward in time to the cycling chemistries of the Earth-Moon planetary system, and forward to the ancient cell cycle of first bacteria-like organisms. Supra-macromolecular models of 'compartments first' are preferred: they facilitate macromolecular crowding-a key abiotic/biotic transition toward living states. Evolutionary models of metabolism or genetics 'first' could not have evolved in unconfined and uncrowded environments because of the diffusional drift to disorder mandated by the second law of thermodynamics.
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130
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Bhattacharyya S, Bershtein S, Yan J, Argun T, Gilson AI, Trauger SA, Shakhnovich EI. Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity. eLife 2016; 5. [PMID: 27938662 PMCID: PMC5176355 DOI: 10.7554/elife.20309] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/09/2016] [Indexed: 12/31/2022] Open
Abstract
Gene dosage toxicity (GDT) is an important factor that determines optimal levels of protein abundances, yet its molecular underpinnings remain unknown. Here, we demonstrate that overexpression of DHFR in E. coli causes a toxic metabolic imbalance triggered by interactions with several functionally related enzymes. Though deleterious in the overexpression regime, surprisingly, these interactions are beneficial at physiological concentrations, implying their functional significance in vivo. Moreover, we found that overexpression of orthologous DHFR proteins had minimal effect on all levels of cellular organization - molecular, systems, and phenotypic, in sharp contrast to E. coli DHFR. Dramatic difference of GDT between 'E. coli's self' and 'foreign' proteins suggests the crucial role of evolutionary selection in shaping protein-protein interaction (PPI) networks at the whole proteome level. This study shows how protein overexpression perturbs a dynamic metabolon of weak yet potentially functional PPI, with consequences for the metabolic state of cells and their fitness.
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Affiliation(s)
- Sanchari Bhattacharyya
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jin Yan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,College of Chemical Engineering, Sichuan University, Chengdu, China
| | - Tijda Argun
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Amy I Gilson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Sunia A Trauger
- Small Molecule Mass Spectrometry, Northwest Laboratories, Harvard University, Cambridge, United States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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131
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Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm. eLife 2016; 5. [PMID: 27801646 PMCID: PMC5089862 DOI: 10.7554/elife.19274] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/28/2016] [Indexed: 12/24/2022] Open
Abstract
Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.
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Affiliation(s)
- Isseki Yu
- iTHES Research Group, RIKEN, Saitama, Japan.,Theoretical Molecular Science Laboratory, RIKEN, Saitama, Japan
| | - Takaharu Mori
- iTHES Research Group, RIKEN, Saitama, Japan.,Theoretical Molecular Science Laboratory, RIKEN, Saitama, Japan
| | - Tadashi Ando
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Kobe, Japan
| | - Ryuhei Harada
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, Kobe, Japan
| | - Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, Kobe, Japan
| | - Yuji Sugita
- iTHES Research Group, RIKEN, Saitama, Japan.,Theoretical Molecular Science Laboratory, RIKEN, Saitama, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Kobe, Japan.,Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, Kobe, Japan
| | - Michael Feig
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Kobe, Japan.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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132
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Qin S, Zhou HX. Protein folding, binding, and droplet formation in cell-like conditions. Curr Opin Struct Biol 2016; 43:28-37. [PMID: 27771543 DOI: 10.1016/j.sbi.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
The many bystander macromolecules in the crowded cellular environments present both steric repulsion and weak attraction to proteins undergoing folding or binding and hence impact the thermodynamic and kinetic properties of these processes. The weak but nonrandom binding with bystander macromolecules may facilitate subcellular localization and biological function. Weak binding also leads to the emergence of a protein-rich droplet phase, which has been implicated in regulating a variety of cellular functions. All these important problems can now be addressed by realistic modeling of intermolecular interactions. Configurational sampling of concentrated protein solutions is an ongoing challenge.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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133
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Affiliation(s)
- Thomas Laue
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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134
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Cohen RD, Pielak GJ. Electrostatic Contributions to Protein Quinary Structure. J Am Chem Soc 2016; 138:13139-13142. [DOI: 10.1021/jacs.6b07323] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Rachel D. Cohen
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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135
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Majumder S, DeMott CM, Reverdatto S, Burz DS, Shekhtman A. Total Cellular RNA Modulates Protein Activity. Biochemistry 2016; 55:4568-73. [PMID: 27456029 DOI: 10.1021/acs.biochem.6b00330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA constitutes up to 20% of a cell's dry weight, corresponding to ∼20 mg/mL. This high concentration of RNA facilitates low-affinity protein-RNA quinary interactions, which may play an important role in facilitating and regulating biological processes. In the yeast Pichia pastoris, the level of ubiquitin-RNA colocalization increases when cells are grown in the presence of dextrose and methanol instead of methanol as the sole carbon source. Total RNA isolated from cells grown in methanol increases β-galactosidase activity relative to that seen with RNA isolated from cells grown in the presence of dextrose and methanol. Because the total cellular RNA content changes with growth medium, protein-RNA quinary interactions can alter in-cell protein biochemistry and may play an important role in cell adaptation, critical to many physiological and pathological states.
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Affiliation(s)
- Subhabrata Majumder
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher M DeMott
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
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136
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The Differential Response of Proteins to Macromolecular Crowding. PLoS Comput Biol 2016; 12:e1005040. [PMID: 27471851 PMCID: PMC4966950 DOI: 10.1371/journal.pcbi.1005040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/27/2016] [Indexed: 12/02/2022] Open
Abstract
The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins. Most in vitro and in silico biophysical experiments generally study proteins in an isolated environment, overlooking that their natural environment—the cell cytoplasm—is a solution that is highly populated by proteins. To address this knowledge gap, here we explored how a crowded environment alters the conformational sampling of three proteins, each with a different degree of disorder and flexibility. We simulated a crowded system composed by the three proteins and reaching a cell-like concentration and compared the protein behavior observed with that induced by PEG500, a synthetic crowding agent. Despite some similarities between the environments, protein crowders showed a number of characteristics that raise concerns about the use of diluted solutions or synthetic agents when studying protein behavior.
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137
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Müntener T, Häussinger D, Selenko P, Theillet FX. In-Cell Protein Structures from 2D NMR Experiments. J Phys Chem Lett 2016; 7:2821-5. [PMID: 27379949 DOI: 10.1021/acs.jpclett.6b01074] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells, but it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from a single set of 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (∼50 μM) measured at moderate magnetic field strengths (600 MHz), thus offering an easily accessible alternative for determining intracellular protein structures.
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Affiliation(s)
- Thomas Müntener
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Philipp Selenko
- Department of Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin) , Robert Roessle Straße 10, 13125 Berlin, Germany
| | - Francois-Xavier Theillet
- Department of Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin) , Robert Roessle Straße 10, 13125 Berlin, Germany
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138
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Simple NMR methods for evaluating higher order structures of monoclonal antibody therapeutics with quinary structure. J Pharm Biomed Anal 2016; 128:398-407. [PMID: 27344629 DOI: 10.1016/j.jpba.2016.06.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 12/31/2022]
Abstract
Monoclonal antibody (mAb) drugs constitute the largest class of protein therapeutics currently on the market. Correctly folded protein higher order structure (HOS), including quinary structure, is crucial for mAb drug quality. The quinary structure is defined as the association of quaternary structures (e.g., oligomerized mAb). Here, several commonly available analytical methods, i.e., size-exclusion-chromatography (SEC) FPLC, multi-angle light scattering (MALS), circular dichroism (CD), NMR and multivariate analysis, were combined and modified to yield a complete profile of HOS and comparable metrics. Rituximab and infliximab were chosen for method evaluation because both IgG1 molecules are known to be homologous in sequence, superimposable in Fab crystal structure and identical in Fc structure. However, herein the two are identified to be significantly different in quinary structure in addition to minor secondary structure differences. All data collectively showed rituximab was mostly monomeric while infliximab was in mono-oligomer equilibrium driven by its Fab fragment. The quinary structure differences were qualitatively inferred from the less used but more reproducible dilution-injection-SEC-FPLC curve method. Quantitative principal component analysis (PCA) was performed on NMR spectra of either the intact or the in-situ enzymatic-digested mAb samples. The cleavage reactions happened directly in NMR tubes without further separation, which greatly enhanced NMR spectra quality and resulted in larger inter- and intra-lot variations based on PCA. The new in-situ enzymatic digestion method holds potential in identifying structural differences on larger therapeutic molecules using NMR.
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139
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Abstract
In-cell NMR spectroscopy is a unique tool for characterizing biological macromolecules in their physiological environment at atomic resolution. Recent progress in NMR instruments and sample preparation methods allows functional processes, such as metal uptake, disulfide-bond formation and protein folding, to be analyzed by NMR in living, cultured human cells. This protocol describes the necessary steps to overexpress one or more proteins of interest inside human embryonic kidney 293T (HEK293T) cells, and it explains how to set up in-cell NMR experiments. The cDNA is transiently transfected as a complex with a cationic polymer (DNA:PEI (polyethylenimine)), and protein expression is carried on for 2-3 d, after which the NMR sample is prepared. (1)H and (1)H-(15)N correlation NMR experiments (for example, using band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence (SOFAST-HMQC)) can be carried out in <2 h, ensuring cell viability. Uniform (15)N labeling and amino-acid-specific (e.g., cysteine, methionine) labeling schemes are possible. The entire procedure takes 4 d from cell culture seeding to NMR data collection.
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140
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Tai J, Dave K, Hahn V, Guzman I, Gruebele M. Subcellular modulation of protein VlsE stability and folding kinetics. FEBS Lett 2016; 590:1409-16. [PMID: 27129718 DOI: 10.1002/1873-3468.12193] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/16/2016] [Accepted: 04/19/2016] [Indexed: 01/29/2023]
Abstract
The interior of a cell interacts differently with proteins than a dilute buffer because of a wide variety of macromolecules, chaperones, and osmolytes that crowd and interact with polypeptide chains. We compare folding of fluorescent constructs of protein VlsE among three environments inside cells. The nucleus increases the stability of VlsE relative to the cytoplasm, but slows down folding kinetics. VlsE is also more stable in the endoplasmic reticulum, but unlike PGK, tends to aggregate there. Although fluorescent-tagged VlsE and PGK show opposite stability trends from in vitro to the cytoplasm, their trends from cytoplasm to nucleus are similar.
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Affiliation(s)
- Jonathan Tai
- Department of Biochemistry, University of Illinois, Urbana, IL, USA
| | - Kapil Dave
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL, USA
| | - Vincent Hahn
- Karlsruher Institut für Technologie, Institut für Angewandte Physik, Karlsruhe, Germany
| | | | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL, USA.,Departments of Chemistry and Physics, University of Illinois, Urbana, IL, USA
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141
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Kyne C, Crowley PB. Grasping the nature of the cell interior: fromPhysiological ChemistrytoChemical Biology. FEBS J 2016; 283:3016-28. [DOI: 10.1111/febs.13744] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/09/2016] [Accepted: 04/18/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Ciara Kyne
- School of Chemistry; National University of Ireland Galway; Ireland
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; Ireland
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142
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Bille A, Mohanty S, Irbäck A. Peptide folding in the presence of interacting protein crowders. J Chem Phys 2016; 144:175105. [PMID: 27155657 DOI: 10.1063/1.4948462] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.
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Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Sandipan Mohanty
- Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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143
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Huang KY, Kingsley CN, Sheil R, Cheng CY, Bierma JC, Roskamp KW, Khago D, Martin RW, Han S. Stability of Protein-Specific Hydration Shell on Crowding. J Am Chem Soc 2016; 138:5392-402. [PMID: 27052457 PMCID: PMC7849722 DOI: 10.1021/jacs.6b01989] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate that the effect of protein crowding is critically dependent on the stability of the protein's hydration shell, which can dramatically vary between different proteins. In the human eye lens, γS-crystallin (γS-WT) forms a densely packed transparent hydrogel with a high refractive index, making it an ideal system for studying the effects of protein crowding. A single point mutation generates the cataract-related variant γS-G18V, dramatically altering the optical properties of the eye lens. This system offers an opportunity to explore fundamental questions regarding the effect of protein crowding, using γS-WT and γS-G18V: (i) how do the diffusion dynamics of hydration water change as a function of protein crowding?; and (ii) upon hydrogel formation of γS-WT, has a dynamic transition occurred generating a single population of hydration water, or do populations of bulk and hydration water coexist? Using localized spin probes, we separately probe the local translational diffusivity of both surface hydration and interstitial water of γS-WT and γS-G18V in solution. Surprisingly, we find that under the influence of hydrogel formation at highly crowded γS-WT concentrations up to 500 mg/mL, the protein hydration shell remains remarkably dynamic, slowing by less than a factor of 2, if at all, compared to that in dilute protein solutions of ∼5 mg/mL. Upon self-crowding, the population of this robust surface hydration water increases, while a significant bulk-like water population coexists even at ∼500 mg/mL protein concentrations. In contrast, surface water of γS-G18V irreversibly dehydrates with moderate concentration increases or subtle alterations to the solution conditions, demonstrating that the effect of protein crowding is highly dependent on the stability of the protein-specific hydration shell. The core function of γS-crystallin in the eye lens may be precisely its capacity to preserve a robust hydration shell, whose stability is abolished by a single G18V mutation.
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Affiliation(s)
- Kuo-Ying Huang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | | | - Ryan Sheil
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Jan C. Bierma
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Domarin Khago
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
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144
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Protein folding alterations in amyotrophic lateral sclerosis. Brain Res 2016; 1648:633-649. [PMID: 27064076 DOI: 10.1016/j.brainres.2016.04.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 02/07/2023]
Abstract
Protein misfolding leads to the formation of aggregated proteins and protein inclusions, which are associated with synaptic loss and neuronal death in neurodegenerative diseases. Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that targets motor neurons in the brain, brainstem and spinal cord. Several proteins misfold and are associated either genetically or pathologically in ALS, including superoxide dismutase 1 (SOD1), Tar DNA binding protein-43 (TDP-43), Ubiquilin-2, p62, VCP, and dipeptide repeat proteins produced by unconventional repeat associated non-ATG translation of the repeat expansion in C9ORF72. Chaperone proteins, including heat shock proteins (Hsp׳s) and the protein disulphide isomerase (PDI) family, assist in protein folding and therefore can prevent protein misfolding, and have been implicated as being protective in ALS. In this review we provide an overview of the current literature regarding the molecular mechanisms of protein misfolding and aggregation in ALS, and the role of chaperones as potential targets for therapeutic intervention. This article is part of a Special Issue entitled SI:ER stress.
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145
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Dave K, Gelman H, Thu CTH, Guin D, Gruebele M. The Effect of Fluorescent Protein Tags on Phosphoglycerate Kinase Stability Is Nonadditive. J Phys Chem B 2016; 120:2878-85. [PMID: 26923443 DOI: 10.1021/acs.jpcb.5b11915] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is frequently assumed that fluorescent protein tags used in biological imaging experiments are minimally perturbing to their host protein. As in-cell experiments become more quantitative and measure rates and equilibrium constants, rather than just "on-off" activity or the presence of a protein, it becomes more important to understand such perturbations. One criterion for a protein modification to be a perturbation is additivity of two perturbations (a linear effect on the protein free energy). Here we show that adding fluorescent protein tags to a host protein in vitro has a large nonadditive effect on its folding free energy. We compare an unlabeled, three singly labeled, and a doubly labeled enzyme (phosphoglycerate kinase). We propose two mechanisms for nonadditivity. In the "quinary interaction" mechanism, two tags interact transiently with one another, relieving the host protein from unfavorable tag-protein interactions. In the "crowding" mechanism, adding two tags provides the minimal crowding necessary to overcome destabilizing interactions of individual tags with the host protein. Both of these mechanisms affect protein stability in cells; we show here that they must also be considered for tagged proteins used for reference in vitro.
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Affiliation(s)
| | | | - Chu Thi Hien Thu
- Department of Chemistry, Hanoi University of Science, Vietnam National University , Hanoi, Vietnam
| | | | - Martin Gruebele
- Department of Chemistry, Hanoi University of Science, Vietnam National University , Hanoi, Vietnam
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146
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Sequential protein expression and selective labeling for in-cell NMR in human cells. Biochim Biophys Acta Gen Subj 2016; 1860:527-33. [DOI: 10.1016/j.bbagen.2015.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/23/2022]
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147
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Gao M, Gnutt D, Orban A, Appel B, Righetti F, Winter R, Narberhaus F, Müller S, Ebbinghaus S. Faltung einer RNA-Haarnadel in der dicht gedrängten Zelle. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mimi Gao
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - David Gnutt
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Axel Orban
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Bettina Appel
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Francesco Righetti
- Biologie der Mikroorganismen; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Roland Winter
- Lehrstuhl für Physikalische Chemie I; TU Dortmund; Otto-Hahn-Str. 4a 44227 Dortmund Deutschland
| | - Franz Narberhaus
- Biologie der Mikroorganismen; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Sabine Müller
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Simon Ebbinghaus
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
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148
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Gao M, Gnutt D, Orban A, Appel B, Righetti F, Winter R, Narberhaus F, Müller S, Ebbinghaus S. RNA Hairpin Folding in the Crowded Cell. Angew Chem Int Ed Engl 2016; 55:3224-8. [PMID: 26833452 PMCID: PMC4762321 DOI: 10.1002/anie.201510847] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 12/02/2022]
Abstract
Precise secondary and tertiary structure formation is critically important for the cellular functionality of ribonucleic acids (RNAs). RNA folding studies were mainly conducted in vitro, without the possibility of validating these experiments inside cells. Here, we directly resolve the folding stability of a hairpin‐structured RNA inside live mammalian cells. We find that the stability inside the cell is comparable to that in dilute physiological buffer. On the contrary, the addition of in vitro artificial crowding agents, with the exception of high‐molecular‐weight PEG, leads to a destabilization of the hairpin structure through surface interactions and reduction in water activity. We further show that RNA stability is highly variable within cell populations as well as within subcellular regions of the cytosol and nucleus. We conclude that inside cells the RNA is subject to (localized) stabilizing and destabilizing effects that lead to an on average only marginal modulation compared to diluted buffer.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - David Gnutt
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Axel Orban
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Bettina Appel
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Francesco Righetti
- Microbial Biology, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Roland Winter
- Physical Chemistry I, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Sabine Müller
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Simon Ebbinghaus
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
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149
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Structural disorder of monomeric α-synuclein persists in mammalian cells. Nature 2016; 530:45-50. [PMID: 26808899 DOI: 10.1038/nature16531] [Citation(s) in RCA: 624] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/14/2015] [Indexed: 12/22/2022]
Abstract
Intracellular aggregation of the human amyloid protein α-synuclein is causally linked to Parkinson's disease. While the isolated protein is intrinsically disordered, its native structure in mammalian cells is not known. Here we use nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy to derive atomic-resolution insights into the structure and dynamics of α-synuclein in different mammalian cell types. We show that the disordered nature of monomeric α-synuclein is stably preserved in non-neuronal and neuronal cells. Under physiological cell conditions, α-synuclein is amino-terminally acetylated and adopts conformations that are more compact than when in buffer, with residues of the aggregation-prone non-amyloid-β component (NAC) region shielded from exposure to the cytoplasm, which presumably counteracts spontaneous aggregation. These results establish that different types of crowded intracellular environments do not inherently promote α-synuclein oligomerization and, more generally, that intrinsic structural disorder is sustainable in mammalian cells.
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150
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Macdonald B, McCarley S, Noeen S, van Giessen AE. β-Hairpin Crowding Agents Affect α-Helix Stability in Crowded Environments. J Phys Chem B 2016; 120:650-9. [DOI: 10.1021/acs.jpcb.5b10575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bryanne Macdonald
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Shannon McCarley
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Sundus Noeen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Alan E. van Giessen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
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