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Pesce G, Gondelaud F, Ptchelkine D, Nilsson JF, Bignon C, Cartalas J, Fourquet P, Longhi S. Experimental Evidence of Intrinsic Disorder and Amyloid Formation by the Henipavirus W Proteins. Int J Mol Sci 2022; 23:ijms23020923. [PMID: 35055108 PMCID: PMC8780864 DOI: 10.3390/ijms23020923] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Henipaviruses are severe human pathogens within the Paramyxoviridae family. Beyond the P protein, the Henipavirus P gene also encodes the V and W proteins which share with P their N-terminal, intrinsically disordered domain (NTD) and possess a unique C-terminal domain. Henipavirus W proteins antagonize interferon (IFN) signaling through NTD-mediated binding to STAT1 and STAT4, and prevent type I IFN expression and production of chemokines. Structural and molecular information on Henipavirus W proteins is lacking. By combining various bioinformatic approaches, we herein show that the Henipaviruses W proteins are predicted to be prevalently disordered and yet to contain short order-prone segments. Using limited proteolysis, differential scanning fluorimetry, analytical size exclusion chromatography, far-UV circular dichroism and small-angle X-ray scattering, we experimentally confirmed their overall disordered nature. In addition, using Congo red and Thioflavin T binding assays and negative-staining transmission electron microscopy, we show that the W proteins phase separate to form amyloid-like fibrils. The present study provides an additional example, among the few reported so far, of a viral protein forming amyloid-like fibrils, therefore significantly contributing to enlarge our currently limited knowledge of viral amyloids. In light of the critical role of the Henipavirus W proteins in evading the host innate immune response and of the functional role of phase separation in biology, these studies provide a conceptual asset to further investigate the functional impact of the phase separation abilities of the W proteins.
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Affiliation(s)
- Giulia Pesce
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Frank Gondelaud
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Denis Ptchelkine
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Juliet F. Nilsson
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Christophe Bignon
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Jérémy Cartalas
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Patrick Fourquet
- INSERM, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS), Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille University, 27 Bvd Leï Roure, CS 30059, 13273 Marseille, France;
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
- Correspondence:
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Henry L, Panman MR, Isaksson L, Claesson E, Kosheleva I, Henning R, Westenhoff S, Berntsson O. Real-time tracking of protein unfolding with time-resolved x-ray solution scattering. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:054702. [PMID: 32984436 PMCID: PMC7511240 DOI: 10.1063/4.0000013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/17/2020] [Indexed: 05/14/2023]
Abstract
The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.
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Affiliation(s)
- L. Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - M. R. Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - L. Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - E. Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - I. Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - R. Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - S. Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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Majorina MA, Balobanov VA, Uversky VN, Melnik BS. Loops linking secondary structure elements affect the stability of the molten globule intermediate state of apomyoglobin. FEBS Lett 2020; 594:3293-3304. [PMID: 32770670 DOI: 10.1002/1873-3468.13905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/29/2020] [Accepted: 08/06/2020] [Indexed: 11/11/2022]
Abstract
Apomyoglobin is a widely used model for studying the molecular mechanisms of globular protein folding. This work aimed to analyze the effects of rigidity and length of loops linking protein secondary structure elements on the stability of the molten globule intermediate state. For this purpose, we studied folding/unfolding of mutant apomyoglobin forms with substitutions of loop-located proline residues to glycine and with loop extension by three or six glycine residues. The kinetic and equilibrium experiments performed gave an opportunity to calculate free energies of different apomyoglobin states. Our analysis revealed that the mutations introduced into the apomyoglobin loops have a noticeable effect on the stability of the intermediate state compared to the unfolded state.
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Affiliation(s)
| | | | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region, Russia
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Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
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Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
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Fleming PJ, Fleming KG. HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties. Biophys J 2018; 114:856-869. [PMID: 29490246 PMCID: PMC5984988 DOI: 10.1016/j.bpj.2018.01.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022] Open
Abstract
Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.
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Affiliation(s)
- Patrick J Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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Katina NS, Suvorina MY, Grigorashvili EI, Marchenkov VV, Ryabova NA, Nikulin AD, Surin AK. Identification of Regions in Apomyoglobin that Form Intermolecular Interactions in Amyloid Aggregates Using High-Performance Mass Spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1134/s1061934817130056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Katina NS, Balobanov VA, Ilyina NB, Vasiliev VD, Marchenkov VV, Glukhov AS, Nikulin AD, Bychkova VE. sw ApoMb Amyloid Aggregation under Nondenaturing Conditions: The Role of Native Structure Stability. Biophys J 2017; 113:991-1001. [PMID: 28877500 DOI: 10.1016/j.bpj.2017.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
Investigation of the molecular mechanisms underlying amyloid-related human diseases attracts close attention. These diseases, the number of which currently is above 40, are characterized by formation of peptide or protein aggregates containing a cross-β structure. Most of the amyloidogenesis mechanisms described so far are based on experimental studies of aggregation of short peptides, intrinsically disordered proteins, or proteins under denaturing conditions, and studies of amyloid aggregate formations by structured globular proteins under conditions close to physiological ones are still in the initial stage. We investigated the effect of amino acid substitutions on propensity of the completely helical protein sperm whale apomyoglobin (sw ApoMb) for amyloid formation from its structured state in the absence of denaturing agents. Stability and aggregation of mutated sw ApoMb were studied using circular dichroism, Fourier transform infrared spectroscopy, x-ray diffraction, native electrophoresis, and electron microscopy techniques. Here, we demonstrate that stability of the protein native state determines both protein aggregation propensity and structural peculiarities of formed aggregates. Specifically, structurally stable mutants show low aggregation propensity and moderately destabilized sw ApoMb variants form amyloids, whereas their strongly destabilized mutants form both amyloids and nonamyloid aggregates.
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Affiliation(s)
- Natalya S Katina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vitalii A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nelly B Ilyina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor D Vasiliev
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor V Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anatoly S Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina E Bychkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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Crystal Structure and Thermostability Characterization of Enterovirus D68 3D pol. J Virol 2017; 91:JVI.00876-17. [PMID: 28659472 DOI: 10.1128/jvi.00876-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022] Open
Abstract
Enterovirus D68 (EV-D68) is one of the many nonpolio enteroviruses that cause mild to severe respiratory illness. The nonstructural protein 3Dpol is an RNA-dependent RNA polymerase (RdRP) of EV-D68 which plays a critical role in the replication of the viral genome and represents a promising drug target. Here, we report the first three-dimensional crystal structure of the RdRP from EV-D68 in complex with the substrate GTP to 2.3-Å resolution. The RdRP structure is similar to structures of other viral RdRPs, where the three domains, termed the palm, fingers, and thumb, form a structure resembling a cupped right hand. Particularly, an N-terminal fragment (Gly1 to Phe30) bridges the fingers and the thumb domains, which accounts for the enhanced stability of the full-length enzyme over the truncation mutant, as assessed by our thermal shift assays and the dynamic light scattering studies. Additionally, the GTP molecule bound proximal to the active site interacts with both the palm and fingers domains to stabilize the core structure of 3Dpol Interestingly, using limited proteolysis assays, we found that different nucleoside triphosphates (NTPs) stabilize the polymerase structure by various degrees, with GTP and CTP being the most and least stabilizing nucleosides, respectively. Lastly, we derived a model of the core structure of 3Dpol stabilized by GTP, according to our proteolytic studies. The biochemical and biophysical characterizations conducted in this study help us to understand the stability of EV-D68-3Dpol, which may extend to other RdRPs as well.IMPORTANCE Enterovirus D68 (EV-D68) is an emerging viral pathogen, which caused sporadic infections around the world. In recent years, epidemiology studies have reported an increasing number of patients with respiratory diseases globally due to the EV-D68 infection. Moreover, the infection has been associated with acute flaccid paralysis and cranial nerve dysfunction in children. However, there are no vaccines and antiviral treatments specifically targeting the virus to date. In this study, we solved the crystal structure of the RNA-dependent RNA polymerase of EV-D68 and carried out systematic biophysical and biochemical characterizations on the overall and local structural stability of the wild-type (WT) enzyme and several variants, which yields a clear view on the structure-activity relationship of the EV-D68 RNA polymerase.
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Mukherjee S, Mukherjee M, Bandyopadhyay S, Dey A. Three phases in pH dependent heme abstraction from myoglobin. J Inorg Biochem 2017; 172:80-87. [DOI: 10.1016/j.jinorgbio.2017.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 04/04/2017] [Accepted: 04/08/2017] [Indexed: 10/19/2022]
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Mendes LFS, Garcia AF, Kumagai PS, de Morais FR, Melo FA, Kmetzsch L, Vainstein MH, Rodrigues ML, Costa-Filho AJ. New structural insights into Golgi Reassembly and Stacking Protein (GRASP) in solution. Sci Rep 2016; 6:29976. [PMID: 27436376 PMCID: PMC4951691 DOI: 10.1038/srep29976] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
Among all proteins localized in the Golgi apparatus, a two-PDZ (PSD95/DlgA/Zo-1) domain protein plays an important role in the assembly of the cisternae. This Golgi Reassembly and Stacking Protein (GRASP) has puzzled researchers due to its large array of functions and relevance in Golgi functionality. We report here a biochemical and biophysical study of the GRASP55/65 homologue in Cryptococcus neoformans (CnGRASP). Bioinformatic analysis, static fluorescence and circular dichroism spectroscopies, calorimetry, small angle X-ray scattering, solution nuclear magnetic resonance, size exclusion chromatography and proteolysis assays were used to unravel structural features of the full-length CnGRASP. We detected the coexistence of regular secondary structures and large amounts of disordered regions. The overall structure is less compact than a regular globular protein and the high structural flexibility makes its hydrophobic core more accessible to solvent. Our results indicate an unusual behavior of CnGRASP in solution, closely resembling a class of intrinsically disordered proteins called molten globule proteins. To the best of our knowledge, this is the first structural characterization of a full-length GRASP and observation of a molten globule-like behavior in the GRASP family. The possible implications of this and how it could explain the multiple facets of this intriguing class of proteins are discussed.
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Affiliation(s)
- Luís F. S. Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Assuero F. Garcia
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Patricia S. Kumagai
- Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Fabio R. de Morais
- Departamento de Física, Centro Multiusuário de Inovação Biomolecular, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio Mesquita, São José do Rio Preto, Brazil
| | - Fernando A. Melo
- Departamento de Física, Centro Multiusuário de Inovação Biomolecular, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio Mesquita, São José do Rio Preto, Brazil
| | - Livia Kmetzsch
- Centro de Biotecnologia, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Marilene H. Vainstein
- Centro de Biotecnologia, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcio L. Rodrigues
- Fundação Oswaldo Cruz - Fiocruz, Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Antonio J. Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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Cao LC, Chen R, Xie W, Liu YH. Enhancing the Thermostability of Feruloyl Esterase EstF27 by Directed Evolution and the Underlying Structural Basis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:8225-33. [PMID: 26329893 DOI: 10.1021/acs.jafc.5b03424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
To improve the thermostability of EstF27, two rounds of random mutagenesis were performed. A thermostable mutant, M6, with six amino acid substitutions was obtained. The half-life of M6 at 55 °C is 1680 h, while that of EstF27 is 0.5 h. The Kcat/Km value of M6 is 1.9-fold higher than that of EstF27. The concentrations of ferulic acid released from destarched wheat bran by EstF27 and M6 at their respective optimal temperatures were 223.2 ± 6.8 and 464.8 ± 11.9 μM, respectively. To further understand the structural basis of the enhanced thermostability, the crystal structure of M6 is determined at 2.0 Å. Structural analysis shows that a new disulfide bond and hydrophobic interactions formed by the mutations may play an important role in stabilizing the protein. This study not only provides us with a robust catalyst, but also enriches our knowledge about the structure-function relationship of feruloyl esterase.
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Affiliation(s)
- Li-chuang Cao
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
| | - Ran Chen
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
| | - Wei Xie
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
| | - Yu-huan Liu
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
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Insights into the Hendra virus N TAIL –XD complex: Evidence for a parallel organization of the helical MoRE at the XD surface stabilized by a combination of hydrophobic and polar interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1038-53. [DOI: 10.1016/j.bbapap.2015.04.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 11/20/2022]
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13
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van Dijk E, Hoogeveen A, Abeln S. The hydrophobic temperature dependence of amino acids directly calculated from protein structures. PLoS Comput Biol 2015; 11:e1004277. [PMID: 26000449 PMCID: PMC4441443 DOI: 10.1371/journal.pcbi.1004277] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/12/2015] [Indexed: 12/26/2022] Open
Abstract
The hydrophobic effect is the main driving force in protein folding. One can estimate the relative strength of this hydrophobic effect for each amino acid by mining a large set of experimentally determined protein structures. However, the hydrophobic force is known to be strongly temperature dependent. This temperature dependence is thought to explain the denaturation of proteins at low temperatures. Here we investigate if it is possible to extract this temperature dependence directly from a large set of protein structures determined at different temperatures. Using NMR structures filtered for sequence identity, we were able to extract hydrophobicity propensities for all amino acids at five different temperature ranges (spanning 265-340 K). These propensities show that the hydrophobicity becomes weaker at lower temperatures, in line with current theory. Alternatively, one can conclude that the temperature dependence of the hydrophobic effect has a measurable influence on protein structures. Moreover, this work provides a method for probing the individual temperature dependence of the different amino acid types, which is difficult to obtain by direct experiment. In general, proteins become functional once they fold into a specific globular structure. On folding, hydrophobic amino acids get buried inside the protein such that they are shielded from the water; this hydrophobic effect makes a protein fold stable. However, the strength of the hydrophobicity is known to be strongly temperature dependent, leading for example to lower stability at lower temperatures (cold denaturation). Nevertheless, it is difficult to quantify the temperature dependence for hydrophobic amino acids. Here we are able to estimate the strength of the hydrophobic effect, by analysing the positions of a large number of amino acids from protein structures experimentally determined at different temperatures. For each amino acid type, we use the ratio between the number of residues at the inside and at the surface of the folded structures as a measure for its hydrophobicity. This approach shows that the hydrophobic effect becomes weaker at lower temperatures, as expected from theoretical predictions. Understanding the temperature dependence for amino acids, can help to make proteins (or enzymes) stable at a specific temperature range. For example, the design of enzymes that are stable and functional at low temperatures may benefit from this work.
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Affiliation(s)
- Erik van Dijk
- Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands
| | - Arlo Hoogeveen
- Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands
| | - Sanne Abeln
- Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands
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Lopes FC, Dobrovolska O, Real-Guerra R, Broll V, Zambelli B, Musiani F, Uversky VN, Carlini CR, Ciurli S. Pliable natural biocide: Jaburetox is an intrinsically disordered insecticidal and fungicidal polypeptide derived from jack bean urease. FEBS J 2015; 282:1043-64. [DOI: 10.1111/febs.13201] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Fernanda C. Lopes
- Graduate Program in Cellular and Molecular Biology - Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
| | - Olena Dobrovolska
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
| | - Rafael Real-Guerra
- Department of Biophysics and Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
| | - Valquiria Broll
- Graduate Program in Cellular and Molecular Biology - Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa USA
- Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino Moscow Region Russia
- Department of Biological Science; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Célia R. Carlini
- Graduate Program in Cellular and Molecular Biology - Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
- Department of Biophysics and Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
- Instituto do Cérebro; Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre Brazil
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
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15
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Bychkova VE, Basova LV, Balobanov VA. How membrane surface affects protein structure. BIOCHEMISTRY (MOSCOW) 2015; 79:1483-514. [DOI: 10.1134/s0006297914130045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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Melnik TN, Majorina MA, Larina DS, Kashparov IA, Samatova EN, Glukhov AS, Melnik BS. Independent of their localization in protein the hydrophobic amino acid residues have no effect on the molten globule state of apomyoglobin and the disulfide bond on the surface of apomyoglobin stabilizes this intermediate state. PLoS One 2014; 9:e98645. [PMID: 24892675 PMCID: PMC4043776 DOI: 10.1371/journal.pone.0098645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/06/2014] [Indexed: 01/07/2023] Open
Abstract
At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to “strengthen” the protein) can result in destabilization of the protein native state of apomyoglobin.
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Affiliation(s)
- Tatiana N. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Maria A. Majorina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Daria S. Larina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ivan A. Kashparov
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ekaterina N. Samatova
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Bogdan S. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- * E-mail:
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17
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Nakagawa K, Yamada Y, Matsumura Y, Tsukamoto S, Yamamoto-Ohtomo M, Ohtomo H, Okabe T, Fujiwara K, Ikeguchi M. Relationship between chain collapse and secondary structure formation in a partially folded protein. Biopolymers 2014; 101:651-8. [DOI: 10.1002/bip.22433] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 08/13/2013] [Accepted: 10/28/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Kanako Nakagawa
- Department of Bioinformatics; Soka University; 1-236 Tangi-cho Hachioji Tokyo 192-8577 Japan
| | - Yoshiteru Yamada
- Japan Synchrotron Radiation Research Institute; Sayo Hyogo 679-5198 Japan
| | - Yoshitaka Matsumura
- Department of Physics; Kansai Medical University; 18-89 Uyama-Higashi Hirakata 573-1136 Japan
| | - Seiichi Tsukamoto
- Department of Bioinformatics; Soka University; 1-236 Tangi-cho Hachioji Tokyo 192-8577 Japan
| | - Mio Yamamoto-Ohtomo
- Department of Bioinformatics; Soka University; 1-236 Tangi-cho Hachioji Tokyo 192-8577 Japan
| | - Hideaki Ohtomo
- Department of Bioinformatics; Soka University; 1-236 Tangi-cho Hachioji Tokyo 192-8577 Japan
| | - Takahiro Okabe
- Department of Bioinformatics; Soka University; 1-236 Tangi-cho Hachioji Tokyo 192-8577 Japan
| | - Kazuo Fujiwara
- Department of Bioinformatics; Soka University; 1-236 Tangi-cho Hachioji Tokyo 192-8577 Japan
| | - Masamichi Ikeguchi
- Department of Bioinformatics; Soka University; 1-236 Tangi-cho Hachioji Tokyo 192-8577 Japan
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18
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Unfolding simulations of holomyoglobin from four mammals: identification of intermediates and β-sheet formation from partially unfolded states. PLoS One 2013; 8:e80308. [PMID: 24386077 PMCID: PMC3873898 DOI: 10.1371/journal.pone.0080308] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/11/2013] [Indexed: 01/15/2023] Open
Abstract
Myoglobin (Mb) is a centrally important, widely studied mammalian protein. While much work has investigated multi-step unfolding of apoMb using acid or denaturant, holomyoglobin unfolding is poorly understood despite its biological relevance. We present here the first systematic unfolding simulations of holoMb and the first comparative study of unfolding of protein orthologs from different species (sperm whale, pig, horse, and harbor seal). We also provide new interpretations of experimental mean molecular ellipticities of myoglobin intermediates, notably correcting for random coil and number of helices in intermediates. The simulated holoproteins at 310 K displayed structures and dynamics in agreement with crystal structures (R g ~1.48-1.51 nm, helicity ~75%). At 400 K, heme was not lost, but some helix loss was observed in pig and horse, suggesting that these helices are less stable in terrestrial species. At 500 K, heme was lost within 1.0-3.7 ns. All four proteins displayed exponentially decaying helix structure within 20 ns. The C- and F-helices were lost quickly in all cases. Heme delayed helix loss, and sperm whale myoglobin exhibited highest retention of heme and D/E helices. Persistence of conformation (RMSD), secondary structure, and ellipticity between 2-11 ns was interpreted as intermediates of holoMb unfolding in all four species. The intermediates resemble those of apoMb notably in A and H helices, but differ substantially in the D-, E- and F-helices, which interact with heme. The identified mechanisms cast light on the role of metal/cofactor in poorly understood holoMb unfolding. We also observed β-sheet formation of several myoglobins at 500 K as seen experimentally, occurring after disruption of helices to a partially unfolded, globally disordered state; heme reduced this tendency and sperm-whale did not display any sheet propensity during the simulations.
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19
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de Carvalho RV, Lopez-Ferrer D, Guimarães KS, Lins RD. IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol. J Comput Chem 2013; 34:1707-18. [PMID: 23609240 DOI: 10.1002/jcc.23299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/17/2013] [Accepted: 03/25/2013] [Indexed: 11/06/2022]
Abstract
Introduction of ion mobility mass spectrometry (IMS/MS) into the proteomic workflow provides an orthogonal separation to the widely used LC-MS platforms. IMS also provides structural information that could facilitate peptide identification. However, the lack of tools capable of predictive power in a high-throughput fashion makes peptide global profiling quite challenging. To target this issue, a computational workflow was developed based on biophysical principles to predict the collision cross-section area (CCS) of peptides as measured from IMS/MS experiments. Hosted on a web server, it allows the user to input a primary sequence (query) and retrieve information on peptide structure, sequence, and corresponding CCS. The current version is designed to identify peptide sequences up to 23 residues in length, in its higher charge state, based on a match of the molecule m/z and CCS. The protocol was validated against a 128-sequences-dataset and CCS predicted within 2.8% average error.
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Affiliation(s)
- Ranieri V de Carvalho
- Center of Informatics, Federal University of Pernambuco, Recife, PE, 50740-560, Brazil
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20
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Mukaiyama A, Nakamura T, Makabe K, Maki K, Goto Y, Kuwajima K. The Molten Globule of β2-Microglobulin Accumulated at pH 4 and Its Role in Protein Folding. J Mol Biol 2013; 425:273-91. [DOI: 10.1016/j.jmb.2012.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 01/06/2023]
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21
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Devarakonda S, Gupta K, Chalmers MJ, Hunt JF, Griffin PR, Van Duyne GD, Spiegelman BM. Disorder-to-order transition underlies the structural basis for the assembly of a transcriptionally active PGC-1α/ERRγ complex. Proc Natl Acad Sci U S A 2011; 108:18678-83. [PMID: 22049338 PMCID: PMC3219099 DOI: 10.1073/pnas.1113813108] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peroxisome proliferator activated receptor (PPAR) γ coactivator-1α (PGC-1α) is a potent transcriptional coactivator of oxidative metabolism and is induced in response to a variety of environmental cues. It regulates a broad array of target genes by coactivating a whole host of transcription factors. The estrogen-related receptor (ERR) family of nuclear receptors are key PGC-1α partners in the regulation of mitochondrial and tissue-specific oxidative metabolic pathways; these receptors also demonstrate strong physical and functional interactions with this coactivator. Here we perform comprehensive biochemical, biophysical, and structural analyses of the complex formed between PGC-1α and ERRγ. PGC-1α activation domain (PGC-1α(2-220)) is intrinsically disordered with limited secondary and no defined tertiary structure. Complex formation with ERRγ induces significant changes in the conformational mobility of both partners, highlighted by significant stabilization of the ligand binding domain (ERRγLBD) as determined by HDX (hydrogen/deuterium exchange) and an observed disorder-to-order transition in PGC-1α(2-220). Small-angle X-ray scattering studies allow for modeling of the solution structure of the activation domain in the absence and presence of ERRγLBD, revealing a stable and compact binary complex. These data show that PGC-1α(2-220) undergoes a large-scale conformational change when binding to the ERRγLBD, leading to substantial compaction of the activation domain. This change results in stable positioning of the N-terminal part of the activation domain of PGC-1α, favorable for assembly of an active transcriptional complex. These data also provide structural insight into the versatile coactivation profile of PGC-1α and can readily be extended to understand other transcriptional coregulators.
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Affiliation(s)
- Srikripa Devarakonda
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Kushol Gupta
- Department of Biochemistry and Biophysics and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Michael J. Chalmers
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458; and
| | - John F. Hunt
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
| | - Patrick R. Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458; and
| | - Gregory D. Van Duyne
- Department of Biochemistry and Biophysics and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Bruce M. Spiegelman
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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22
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Fedyukina DV, Rajagopalan S, Sekhar A, Fulmer EC, Eun YJ, Cavagnero S. Contribution of long-range interactions to the secondary structure of an unfolded globin. Biophys J 2010; 99:L37-9. [PMID: 20816043 DOI: 10.1016/j.bpj.2010.06.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/07/2010] [Accepted: 06/14/2010] [Indexed: 11/19/2022] Open
Abstract
This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins.
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Affiliation(s)
- Daria V Fedyukina
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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23
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Modeling of Hemodialysis Operation. Ann Biomed Eng 2010; 38:3347-62. [DOI: 10.1007/s10439-010-0147-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 03/17/2010] [Indexed: 11/26/2022]
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24
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Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Q Rev Biophys 2010; 43:295-332. [DOI: 10.1017/s0033583510000119] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractEnergy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein – the native landscape – is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a ‘topographical map’ of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, ‘preexisting equilibrium’ and ‘induced fit’, are interpreted within the energy landscape paradigm as extreme points of a continuum of transition mechanisms. Some experimental evidence illustrating each of these two models, as well as intermediate mechanisms, is presented and discussed.
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25
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Samatova EN, Melnik BS, Balobanov VA, Katina NS, Dolgikh DA, Semisotnov GV, Finkelstein AV, Bychkova VE. Folding intermediate and folding nucleus for I-->N and U-->I-->N transitions in apomyoglobin: contributions by conserved and nonconserved residues. Biophys J 2010; 98:1694-702. [PMID: 20409491 DOI: 10.1016/j.bpj.2009.12.4326] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Revised: 12/22/2009] [Accepted: 12/30/2009] [Indexed: 11/19/2022] Open
Abstract
Kinetic investigation on the wild-type apomyoglobin and its 12 mutants with substitutions of hydrophobic residues by Ala was performed using stopped-flow fluorescence. Characteristics of the kinetic intermediate I and the folding nucleus were derived solely from kinetic data, namely, the slow-phase folding rate constants and the burst-phase amplitudes of Trp fluorescence intensity. This allowed us to pioneer the phi-analysis for apomyoglobin. As shown, these mutations drastically destabilized the native state N and produced minor (for conserved residues of G, H helices) or even negligible (for nonconserved residues of B, C, D, E helices) destabilizing effect on the state I. On the other hand, conserved residues of A, G, H helices made a smaller contribution to stability of the folding nucleus at the rate-limiting I-->N transition than nonconserved residues of B, D, E helices. Thus, conserved side chains of the A-, G-, H-residues become involved in the folding nucleus before crossing the main barrier, whereas nonconserved side chains of the B-, D-, E-residues join the nucleus in the course of the I-->N transition.
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Affiliation(s)
- Ekaterina N Samatova
- Institute of Protein Research, Russian Academy of Sciences, Moscow, Russian Federation
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26
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Foucault M, Mayol K, Receveur-Bréchot V, Bussat MC, Klinguer-Hamour C, Verrier B, Beck A, Haser R, Gouet P, Guillon C. UV and X-ray structural studies of a 101-residue long Tat protein from a HIV-1 primary isolate and of its mutated, detoxified, vaccine candidate. Proteins 2010; 78:1441-56. [PMID: 20034112 DOI: 10.1002/prot.22661] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The 101-residue long Tat protein of primary isolate 133 of the human immunodeficiency virus type 1 (HIV-1), wt-Tat(133) displays a high transactivation activity in vitro, whereas the mutant thereof, STLA-Tat(133), a vaccine candidate for HIV-1, has none. These two proteins were chemically synthesized and their biological activity was validated. Their structural properties were characterized using circular dichroism (CD), fluorescence emission, gel filtration, dynamic light scattering, and small angle X-ray scattering (SAXS) techniques. SAXS studies revealed that both proteins were extended and belong to the family of intrinsically unstructured proteins. CD measurements showed that wt-Tat(133) or STLA-Tat(133) underwent limited structural rearrangements when complexed with specific fragments of antibodies. Crystallization trials have been performed on the two forms, assuming that the Tat(133) proteins might have a better propensity to fold in supersaturated conditions, and small crystals have been obtained. These results suggest that biologically active Tat protein is natively unfolded and requires only a limited gain of structure for its function.
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27
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Samatova EN, Katina NS, Balobanov VA, Melnik BS, Dolgikh DA, Bychkova VE, Finkelstein AV. How strong are side chain interactions in the folding intermediate? Protein Sci 2009; 18:2152-9. [PMID: 19693934 DOI: 10.1002/pro.229] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Influence of 12 nonpolar amino acids residues from the hydrophobic core of apomyoglobin on stability of its native state and folding intermediate was studied. Six of the selected residues are from the A, G and H helices; these are conserved in structure of the globin family, although nonfunctional, that is, not involved in heme binding. The rest are nonconserved hydrophobic residues that belong to the B, C, D, and E helices. Each residue was substituted by alanine, and equilibrium pH-induced transitions in apomyoglobin and its mutants were studied by circular dichroism and fluorescent spectroscopy. The obtained results allowed estimating changes in their free energy during formation of the intermediate state. It was first shown that the strength of side chain interactions in the apomyoglobin intermediate state amounts to 15-50% of that in its native state for conserved residues, and practically to 0% for nonconserved residues. These results allow a better understanding of interactions occurring in the intermediate state and shed light on involvement of certain residues in protein folding at different stages.
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Affiliation(s)
- Ekaterina N Samatova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
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28
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Kohn JE, Gillespie B, Plaxco KW. Non-sequence-specific interactions can account for the compaction of proteins unfolded under "native" conditions. J Mol Biol 2009; 394:343-50. [PMID: 19751743 DOI: 10.1016/j.jmb.2009.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 07/31/2009] [Accepted: 09/01/2009] [Indexed: 10/20/2022]
Abstract
Proteins unfolded by high concentrations of chemical denaturants adopt expanded, largely structure-free ensembles of conformations that are well approximated as random coils. In contrast, globular proteins unfolded under less denaturing conditions (via mutations, or transiently unfolded after a rapid jump to native conditions) and molten globules (arising due to mutations or cosolvents) are often compact. Here we explore the origins of this compaction using a truncated equilibrium-unfolded variant of the 57-residue FynSH3 domain. As monitored by far-UV circular dichroism, NMR spectroscopy, and hydrogen-exchange kinetics, CDelta4 (a 4-residue carboxy-terminal deletion variant of FynSH3) appears to be largely unfolded even in the absence of denaturant. Nevertheless, CDelta4 is quite compact under these conditions, with a hydrodynamic radius only slightly larger than that of the native protein. In order to understand the origins of this molten-globule-like compaction, we have characterized a random sequence polypeptide of identical amino acid composition to CDelta4. Notably, we find that the hydrodynamic radius of this random sequence polypeptide also approaches that of the native protein. Thus, while native-like interactions may contribute to the formation of compact "unfolded" states, it appears that non-sequence-specific monomer-monomer interactions can also account for the dramatic compaction observed for molten globules and the "physiological" unfolded state.
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Affiliation(s)
- Jonathan E Kohn
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
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29
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Zhuravlev PI, Materese CK, Papoian GA. Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins. J Phys Chem B 2009; 113:8800-12. [PMID: 19453123 DOI: 10.1021/jp810659u] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Proteins are highly complex molecules with features exquisitely selected by nature to carry out essential biological functions. Physical chemistry and polymer physics provide us with the tools needed to make sense of this complexity. Upon translation, many proteins fold to a thermodynamically stable form known as the native state. The native state is not static, but consists of a hierarchy of conformations, that are continuously explored through dynamics. In this review we provide a brief introduction to some of the core concepts required in the discussion of the protein native dynamics using energy landscapes ideas. We first discuss recent works which have challenged the structure-function paradigm by demonstrating function in disordered proteins. Next we examine the hierarchical organization in the energy landscapes using atomistic molecular dynamics simulations and principal component analysis. In particular, the role of direct and water-mediated contacts in sculpting the landscape is elaborated. Another approach to studying the native state ensemble is based on choosing high-resolution order parameters for computing one- or two-dimensional free energy surfaces. We demonstrate that 2D free energy surfaces provide rich thermodynamic and kinetic information about the native state ensemble. Brownian dynamics simulations on such a surface indicate that protein conformational dynamics is weakly activated. Finally, we briefly discuss implicit and coarse-grained protein models and emphasize the solvent role in determining native state structure and dynamics.
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Affiliation(s)
- Pavel I Zhuravlev
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
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30
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Baryshnikova (Samatova) EN, Melnik BS, Balobanov VA, Katina NS, Finkelshtein AV, Semisotnov GV, Bychkova VE. On the role of some conserved and nonconserved amino acid residues in the transitional state and intermediate of apomyoglobin folding. Mol Biol 2009. [DOI: 10.1134/s0026893309010178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Dametto M, Cárdenas AE. Computer simulations of the refolding of sperm whale apomyoglobin from high-temperature denaturated state. J Phys Chem B 2008; 112:9501-6. [PMID: 18616314 DOI: 10.1021/jp804300w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The refolding mechanism of apomyoglobin (apoMb) subsequent to high-temperature unfolding has been examined using computer simulations with atomic level detail. The folding of this protein has been extensively studied experimentally, providing a large database of folding parameters which can be probed using simulations. In the present study, 4-folding trajectories of apoMb were computed starting from coiled structures. A crystal structure of sperm whale myoglobin taken from the Protein Data Bank was used to construct the final native conformation by removal of the heme group followed by energy optimization. The initial unfolded conformations were obtained from high-temperature molecular dynamics simulations. Room-temperature refolding trajectories at neutral pH were obtained using the stochastic difference equation in length algorithm. The folding trajectories were compared with experimental results and two previous molecular dynamics studies at low pH. In contrast to the previous simulations, an extended intermediate with large helical content was not observed. In the present study, a structural collapse occurs without formation of helices or native contacts. Once the protein structure is more compact (radius of gyration<18 A) secondary and tertiary structures appear. These results suggest that apoMb follows a different folding pathway after high-temperature denaturation.
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Affiliation(s)
- Mariangela Dametto
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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32
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Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev 2008; 108:946-1051. [PMID: 18335973 PMCID: PMC2740730 DOI: 10.1021/cr050262p] [Citation(s) in RCA: 561] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vijay M. Krishnamurthy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George K. Kaufman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Adam R. Urbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Douglas B. Weibel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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33
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Gerard FCA, Ribeiro EDA, Albertini AAV, Gutsche I, Zaccai G, Ruigrok RWH, Jamin M. Unphosphorylated rhabdoviridae phosphoproteins form elongated dimers in solution. Biochemistry 2007; 46:10328-38. [PMID: 17705401 DOI: 10.1021/bi7007799] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phosphoprotein (P) is an essential component of the replication machinery of rabies virus (RV) and vesicular stomatitis virus (VSV), and the oligomerization of P, potentially controlled by phosphorylation, is required for its function. Up to now the stoichiometry of phosphoprotein oligomers has been controversial. Size exclusion chromatography combined with detection by multiangle laser light scattering shows that the recombinant unphosphorylated phosphoproteins from VSV and from RV exist as dimers in solution. Hydrodynamic analysis indicates that the dimers are highly asymmetric, with a Stokes radius of 4.8-5.3 nm and a frictional ratio larger than 1.7. Small-angle neutron scattering experiments confirm the dimeric state and the asymmetry of the structure and yield a radius of gyration of about 5.3 nm and a cross-sectional radius of gyration of about 1.6-1.8 nm. Similar hydrodynamic properties and molecular dimensions were obtained with a variant of VSV phosphoprotein in which Ser60 and Thr62 are substituted by Asp residues and which has been reported previously to mimic phosphorylation by inducing oligomerization and activating transcription. Here, we show that this mutant also forms a dimer with hydrodynamic properties and molecular dimensions similar to those of the wild type protein. However, incubation at 30 degrees C for several hours induced self-assembly of both wild type and mutant proteins, leading to the formation of irregular filamentous structures.
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Affiliation(s)
- Francine C A Gerard
- Unit of Virus Host Cell Interactions, UMR 5233 UJF-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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34
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Sedlak E, Wittung-Stafshede P. Discrete Roles of Copper Ions in Chemical Unfolding of Human Ceruloplasmin. Biochemistry 2007; 46:9638-44. [PMID: 17661447 DOI: 10.1021/bi700715e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human ceruloplasmin (CP) is a multicopper oxidase essential for normal iron homeostasis. The protein has six beta-barrel domains with one type 1 copper in each of domains 2, 4, and 6; the remaining copper ions form a catalytic trinuclear cluster, one type 2 and two type 3 coppers, at the interface between domains 1 and 6. We have characterized urea-induced unfolding of holo- and apo-forms of CP by far-UV circular dichroism, intrinsic fluorescence, 8-anilinonaphthalene-1-sulfonic acid binding, visible absorption, copper content, and oxidase activity probes (pH 7, 23 degrees C). We find that holo-CP unfolds in a complex reaction with at least one intermediate. The formation of the intermediate correlates with decreased secondary structure, exposure of aromatics, loss of two coppers, and reduced oxidase activity; this step is reversible, indicating that the trinuclear cluster remains intact. Further additions of urea trigger complete protein unfolding and loss of all coppers. Attempts to refold this species result in an inactive apoprotein with molten-globule characteristics. The apo-form of CP also unfolds in a multistep reaction, albeit the intermediate appears at a slightly lower urea concentration. Again, correct refolding is possible from the intermediate but not the unfolded state. Our study demonstrates that in vitro equilibrium unfolding of CP involves intermediates and that the copper ions are removed in stages. When the catalytic site is finally destroyed, refolding is not possible at neutral pH. This implies a mechanistic role for the trinuclear metal cluster as a nucleation point, aligning domains 1 and 6, during CP folding in vivo.
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Affiliation(s)
- Erik Sedlak
- Department of Biochemistry and Cell Biology, Keck Center for Structural Computational Biology, Texas, USA
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35
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Dev S, Surolia A. Dynamic light scattering study of peanut agglutinin: size, shape and urea denaturation. J Biosci 2007; 31:551-6. [PMID: 17301492 DOI: 10.1007/bf02708406] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Peanut agglutinin (PNA)is a homotetrameric protein with a unique open quaternary structure. PNA shows non-two state profile in chaotrope induced denaturation. It passes through a monomeric molten globule like state before complete denaturation (Reddy et al 1999). This denaturation profile is associated with the change in hydrodynamic radius of the native protein. Though the molten globule-like state is monomeric in nature it expands in size due to partial denaturation. The size and shape of the native PNA as well as the change in hydrodynamic radius of the protein during denaturation has been studied by dynamic light scattering (DLS). The generation of two species is evident from the profile of hydrodynamic radii. This study also reveals the extent of compactness of the intermediate state.
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Affiliation(s)
- Sagarika Dev
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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36
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Unfolding of apomyoglobin studied with two-dimensional correlations of tryptophan, 8-anilino-1-naphthalenesulfonate, and pyrene fluorescence. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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37
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Baden N, Terazima M. Intermolecular Interaction of Myoglobin with Water Molecules along the pH Denaturation Curve. J Phys Chem B 2006; 110:15548-55. [PMID: 16884278 DOI: 10.1021/jp0602171] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method of diffusion coefficient (D) measurement for proteins based on the pulsed laser-induced transient grating method using a photosensitive cross-linker was applied to the characterization of the pH denaturation process of holo- and apo-myoglobin (Mb) from the viewpoint of protein-water interaction. It was found that the pH denaturation curve monitored by D agrees quite well with that determined by the circular dichroism intensity for holo-Mb. This fact indicates that the changes in intermolecular interaction and the alpha-helix content occur simultaneously during the unfolding process. However, the pH dependence of D for apo-Mb was different from that of alpha-helix content. This different behavior can be explained in terms of the different denaturation steps for the secondary structure and the hydrogen bonding network of the intermediate species around pH 4; i.e., this intermediate is partially unfolded, but the hydrogen bonding network is dominantly an intramolecular one. Taking previously reported properties of this species into account, we conclude that water molecules are trapped in the hydrophobic core of the apo-Mb pH 4 intermediate. This fact suggests that the kinetic intermediate state of the protein folding process is a swollen state without water molecular exchange with the bulk phase.
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Affiliation(s)
- Naoki Baden
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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38
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Khan JS, Imamoto Y, Harigai M, Kataoka M, Terazima M. Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal alpha-helices. Biophys J 2006; 90:3686-93. [PMID: 16500975 PMCID: PMC1440749 DOI: 10.1529/biophysj.105.078196] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Conformational changes in the light illuminated intermediate (pB) of photoactive yellow protein (PYP) were studied from a viewpoint of the diffusion coefficient (D) change of several N-truncated PYPs, which lacked the N-terminal 6, 15, or 23 amino acid residues (T6, T15, and T23, respectively). For intact PYP (i-PYP), D of pB (D(pB)) was approximately 11% lower than that (D(pG)) of the ground state (pG) species. The difference in D (D(pG) - D(pB)) decreased upon cleavage of the N-terminal region in the order of i-PYP>T6>T15>T23. This trend clearly showed that conformational change in the N-terminal group is the main reason for the slower diffusion of pB. This slower diffusion was interpreted in terms of the unfolding of the two alpha-helices in the N-terminal region, increasing the intermolecular interactions due to hydrogen bonding with water molecules. The increase in friction per one residue by the unfolding of the alpha-helix was estimated to be 0.3 x 10(-12) kg/s. The conformational change in the N-terminal group upon photoillumination is discussed.
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Affiliation(s)
- Javaid Shahbaz Khan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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39
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Receveur-Bréchot V, Bourhis JM, Uversky VN, Canard B, Longhi S. Assessing protein disorder and induced folding. Proteins 2005; 62:24-45. [PMID: 16287116 DOI: 10.1002/prot.20750] [Citation(s) in RCA: 337] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Intrinsically disordered proteins (IDPs) defy the structure-function paradigm as they fulfill essential biological functions while lacking well-defined secondary and tertiary structures. Conformational and spectroscopic analyses showed that IDPs do not constitute a uniform family, and can be divided into subfamilies as a function of their residual structure content. Residual intramolecular interactions are thought to facilitate binding to a partner and then induced folding. Comprehensive information about experimental approaches to investigate structural disorder and induced folding is still scarce. We herein provide hints to readily recognize features typical of intrinsic disorder and review the principal techniques to assess structural disorder and induced folding. We describe their theoretical principles and discuss their respective advantages and limitations. Finally, we point out the necessity of using different approaches and show how information can be broadened by the use of multiples techniques.
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Affiliation(s)
- Véronique Receveur-Bréchot
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Universités Aix-Marseille I et II, Campus de Luminy, Marseille Cedex 09, France
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40
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Kurt N, Rajagopalan S, Cavagnero S. Effect of hsp70 chaperone on the folding and misfolding of polypeptides modeling an elongating protein chain. J Mol Biol 2005; 355:809-20. [PMID: 16309705 PMCID: PMC1570398 DOI: 10.1016/j.jmb.2005.10.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2005] [Revised: 10/10/2005] [Accepted: 10/11/2005] [Indexed: 11/16/2022]
Abstract
Virtually nothing is known about the interaction of co-translationally active chaperones with nascent polypeptides and the resulting effects on peptide conformation and folding. We have explored this issue by NMR analysis of apomyoglobin N-terminal fragments of increasing length, taken as models for different stages of protein biosynthesis, in the absence and presence of the substrate binding domain of Escherichia coli Hsp70, DnaK-beta. The incomplete polypeptides misfold and self-associate under refolding conditions. In the presence of DnaK-beta, however, formation of the original self-associated species is completely or partially prevented. Chaperone interaction with incomplete protein chains promotes a globally unfolded dynamic DnaK-beta-bound state, which becomes folding-competent only upon incorporation of the residues corresponding to the C-terminal H helix. The chaperone does not bind the full-length protein at equilibrium. However, its presence strongly disfavors the kinetic accessibility of misfolding side-routes available to the full-length chain. This work supports the role of DnaK as a "holder" for incomplete N-terminal polypeptides. However, as the chain approaches its full-length status, the tendency to intramolecularly bury non-polar surface efficiently outcompetes chaperone binding. Under these conditions, DnaK serves as a "folding enhancer" by supporting folding of a population of otherwise folding-incompetent full-length protein chains.
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Affiliation(s)
- Neşe Kurt
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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41
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Chow C, Kurt N, Murphy RM, Cavagnero S. Structural characterization of apomyoglobin self-associated species in aqueous buffer and urea solution. Biophys J 2005; 90:298-309. [PMID: 16214860 PMCID: PMC1367028 DOI: 10.1529/biophysj.105.070227] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biophysical characterization of nonfunctional protein aggregates at physiologically relevant temperatures is much needed to gain deeper insights into the kinetic and thermodynamic relationships between protein folding and misfolding. Dynamic and static laser light scattering have been employed for the detection and detailed characterization of apomyoglobin (apoMb) soluble aggregates populated at room temperature upon dissolving the purified protein in buffer at pH 6.0, both in the presence and absence of high concentrations of urea. Unlike the beta-sheet self-associated aggregates previously reported for this protein at high temperatures, the soluble aggregates detected here have either alpha-helical or random coil secondary structure, depending on solvent and solution conditions. Hydrodynamic diameters range from 80 to 130 nm, with semiflexible chain-like morphology. The combined use of low pH and high urea concentration leads to structural unfolding and complete elimination of the large aggregates. Even upon starting from this virtually monomeric unfolded state, however, protein refolding leads to the formation of severely self-associated species with native-like secondary structure. Under these conditions, kinetic apoMb refolding proceeds via two parallel routes: one leading to native monomer, and the other leading to a misfolded and heavily self-associated state bearing native-like secondary structure.
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Affiliation(s)
- Charles Chow
- Department of Chemistry, and Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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42
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Paliwal A, Asthagiri D, Bossev DP, Paulaitis ME. Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation. Biophys J 2004; 87:3479-92. [PMID: 15347583 PMCID: PMC1304814 DOI: 10.1529/biophysj.104.050526] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 09/01/2004] [Indexed: 11/18/2022] Open
Abstract
We studied the pressure-induced folding/unfolding transition of staphylococcal nuclease (SN) over a pressure range of approximately 1-3 kilobars at 25 degrees C by small-angle neutron scattering and molecular dynamics simulations. We find that applying pressure leads to a twofold increase in the radius of gyration derived from the small-angle neutron scattering spectra, and P(r), the pair distance distribution function, broadens and shows a transition from a unimodal to a bimodal distribution as the protein unfolds. The results indicate that the globular structure of SN is retained across the folding/unfolding transition although this structure is less compact and elongated relative to the native structure. Pressure-induced unfolding is initiated in the molecular dynamics simulations by inserting water molecules into the protein interior and applying pressure. The P(r) calculated from these simulations likewise broadens and shows a similar unimodal-to-bimodal transition with increasing pressure. The simulations also reveal that the bimodal P(r) for the pressure-unfolded state arises as the protein expands and forms two subdomains that effectively diffuse apart during initial stages of unfolding. Hydrophobic contact maps derived from the simulations show that water insertions into the protein interior and the application of pressure together destabilize hydrophobic contacts between these two subdomains. The findings support a mechanism for the pressure-induced unfolding of SN in which water penetration into the hydrophobic core plays a central role.
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Affiliation(s)
- Amit Paliwal
- Department of Chemical and Biomolecular Engineering, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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43
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Bourhis JM, Johansson K, Receveur-Bréchot V, Oldfield CJ, Dunker KA, Canard B, Longhi S. The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinsically disordered proteins that fold upon binding to their physiological partner. Virus Res 2004; 99:157-67. [PMID: 14749181 DOI: 10.1016/j.virusres.2003.11.007] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The nucleoprotein of measles virus consists of an N-terminal domain, N(CORE) (aa 1-400), resistant to proteolysis, and a C-terminal domain, N(TAIL) (aa 401-525), hypersensitive to proteolysis and not visible by electron microscopy. Using two complementary computational approaches, we predict that N(TAIL) belongs to the class of natively unfolded proteins. Using different biochemical and biophysical approaches, we show that N(TAIL) is indeed unstructured in solution. In particular, the spectroscopic and hydrodynamic properties of N(TAIL) indicate that this protein domain belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The isolated N(TAIL) domain was shown to be able to bind to its physiological partner, the phosphoprotein (P), and to undergo an induced folding upon binding to the C-terminal moiety of P [J. Biol. Chem. 278 (2003) 18638]. Using a computational analysis, we have identified within N(TAIL) a putative alpha-helical molecular recognition element (alpha-MoRE, aa 488-499), which could be involved in binding to P via induced folding. We report the bacterial expression and purification of a truncated form of N(TAIL) (N(TAIL2), aa 401-488) devoid of the alpha-MoRE. We show that N(TAIL2) has lost the ability to bind to P, thus supporting the hypothesis that the alpha-MoRE may play a role in binding to P. We have further analyzed the alpha-helical propensities of N(TAIL2) and N(TAIL) using circular dichroism in the presence of 2,2,2-trifluoroethanol. We show that N(TAIL2) has a lower alpha-helical potential compared to N(TAIL), thus suggesting that the alpha-MoRE may be indeed involved in the induced folding of N(TAIL).
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Affiliation(s)
- Jean-Marie Bourhis
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, Cedex 09 13288, Marseille, France
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44
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Dyson HJ, Wright PE. Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance. ADVANCES IN PROTEIN CHEMISTRY 2004; 62:311-40. [PMID: 12418108 DOI: 10.1016/s0065-3233(02)62012-1] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- H Jane Dyson
- Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
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45
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Ramboarina S, Redfield C. Structural characterisation of the human alpha-lactalbumin molten globule at high temperature. J Mol Biol 2003; 330:1177-88. [PMID: 12860137 DOI: 10.1016/s0022-2836(03)00639-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molten globules are partially folded forms of proteins thought to be general intermediates in protein folding. The 15N-1H HSQC NMR spectrum of the human alpha-lactalbumin (alpha-LA) molten globule at pH 2 and 20 degrees C is characterised by broad lines which make direct study by NMR methods difficult; this broadening arises from conformational fluctuations throughout the protein on a millisecond to microsecond timescale. Here, we find that an increase in temperature to 50 degrees C leads to a dramatic sharpening of peaks in the 15N-1H HSQC spectrum of human alpha-LA at pH 2. Far-UV CD and ANS fluorescence experiments demonstrate that under these conditions human alpha-LA maintains a high degree of helical secondary structure and the exposed hydrophobic surfaces that are characteristic of a molten globule. Analysis of the H(alpha), H(N) and 15N chemical shifts of the human alpha-LA molten globule at 50 degrees C leads to the identification of regions of native-like helix in the alpha-domain and of non-native helical propensity in the beta-domain. The latter may be responsible for the observed overshoot in ellipticity at 222 nm in kinetic refolding experiments.
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Affiliation(s)
- Stephanié Ramboarina
- Oxford Centre for Molecular Sciences, Central Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QH, UK
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46
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Longhi S, Receveur-Bréchot V, Karlin D, Johansson K, Darbon H, Bhella D, Yeo R, Finet S, Canard B. The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein. J Biol Chem 2003; 278:18638-48. [PMID: 12621042 DOI: 10.1074/jbc.m300518200] [Citation(s) in RCA: 230] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nucleoprotein of measles virus consists of an N-terminal moiety, N(CORE), resistant to proteolysis and a C-terminal moiety, N(TAIL), hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purification, and characterization of measles virus N(TAIL). Using nuclear magnetic resonance, circular dichroism, gel filtration, dynamic light scattering, and small angle x-ray scattering, we show that N(TAIL) is not structured in solution. Its sequence and spectroscopic and hydrodynamic properties indicate that N(TAIL) belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The same epitopes are exposed in N(TAIL) and within the nucleoprotein, which rules out dramatic conformational changes in the isolated N(TAIL) domain compared with the full-length nucleoprotein. Most unstructured proteins undergo some degree of folding upon binding to their partners, a process termed "induced folding." We show that N(TAIL) is able to bind its physiological partner, the phosphoprotein, and that it undergoes such an unstructured-to-structured transition upon binding to the C-terminal moiety of the phosphoprotein. The presence of flexible regions at the surface of the viral nucleocapsid would enable plastic interactions with several partners, whereas the gain of structure arising from induced folding would lead to modulation of these interactions. These results contribute to the study of the emerging field of natively unfolded proteins.
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Affiliation(s)
- Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille Cedex 09, France.
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47
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Abramov VM, Vasiliev AM, Khlebnikov VS, Vasilenko RN, Kulikova NL, Kosarev IV, Ishchenko AT, Gillespie JR, Millett IS, Fink AL, Uversky VN. Structural and functional properties of Yersinia pestis Caf1 capsular antigen and their possible role in fulminant development of primary pneumonic plague. J Proteome Res 2002; 1:307-15. [PMID: 12645886 DOI: 10.1021/pr025511u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yersinia pestis capsular antigen Caf1 is shown to be a beta-structural protein that in polymeric form possesses very high conformational stability. Different approaches show that a dimer is the minimal cooperative block of Caf1 adhesin. Caf1 dimer interacts effectively with IL-1 receptors of human macrophage and epithelial cells. The specificity of such interaction is confirmed by the inhibition of IL-1alpha binding by Caf1. The Caf1 role in pneumonic plague pathogenesis is discussed.
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Affiliation(s)
- Vyacheslav M Abramov
- Institute of Immunological Engineering, 142380 Lyubuchany, Moscow Region, Russia
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48
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Choi J, Terazima M. Denaturation of a Protein Monitored by Diffusion Coefficients: Myoglobin. J Phys Chem B 2002. [DOI: 10.1021/jp0256802] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jungkwon Choi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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49
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Buchner J, Rudolph R, Lilie H. Intradomain disulfide bonds impede formation of the alternatively folded state of antibody chains. J Mol Biol 2002; 318:829-36. [PMID: 12054826 DOI: 10.1016/s0022-2836(02)00171-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Antibodies undergo significant conformational changes upon acidification, leading to the formation of an alternatively folded state. Here, we analyzed the conformation of MAK 33 Fab and its light chain at acidic pH, both in the reduced and oxidized form. At acidic pH, the proteins exhibited a highly structured, but non-native conformation, corresponding to the alternatively folded state, previously described for the intact antibody. However, the requirements to form this alternative structure were different for the oxidized and reduced protein. Whereas in the oxidized form of the immunoglobulin light chain the alternatively folded state could only be detected at pH<1.4, the reduced light chain already adopted this structure at pH 2. Thermal denaturation measurements revealed that, surprisingly, the alternatively folded state of the reduced light chain was more stable than that of the oxidized protein at pH 1.4. This indicates that the intradomain disulfide bonds, which stabilize the native state of antibody domains, impede the formation of the alternatively folded state.
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Affiliation(s)
- Johannes Buchner
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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50
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Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang C, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic Z. Intrinsically disordered protein. J Mol Graph Model 2002; 19:26-59. [PMID: 11381529 DOI: 10.1016/s1093-3263(00)00138-8] [Citation(s) in RCA: 1738] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Proteins can exist in a trinity of structures: the ordered state, the molten globule, and the random coil. The five following examples suggest that native protein structure can correspond to any of the three states (not just the ordered state) and that protein function can arise from any of the three states and their transitions. (1) In a process that likely mimics infection, fd phage converts from the ordered into the disordered molten globular state. (2) Nucleosome hyperacetylation is crucial to DNA replication and transcription; this chemical modification greatly increases the net negative charge of the nucleosome core particle. We propose that the increased charge imbalance promotes its conversion to a much less rigid form. (3) Clusterin contains an ordered domain and also a native molten globular region. The molten globular domain likely functions as a proteinaceous detergent for cell remodeling and removal of apoptotic debris. (4) In a critical signaling event, a helix in calcineurin becomes bound and surrounded by calmodulin, thereby turning on calcineurin's serine/threonine phosphatase activity. Locating the calcineurin helix within a region of disorder is essential for enabling calmodulin to surround its target upon binding. (5) Calsequestrin regulates calcium levels in the sarcoplasmic reticulum by binding approximately 50 ions/molecule. Disordered polyanion tails at the carboxy terminus bind many of these calcium ions, perhaps without adopting a unique structure. In addition to these examples, we will discuss 16 more proteins with native disorder. These disordered regions include molecular recognition domains, protein folding inhibitors, flexible linkers, entropic springs, entropic clocks, and entropic bristles. Motivated by such examples of intrinsic disorder, we are studying the relationships between amino acid sequence and order/disorder, and from this information we are predicting intrinsic order/disorder from amino acid sequence. The sequence-structure relationships indicate that disorder is an encoded property, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those in the Protein Data Bank. Recent predictions on 29 genomes indicate that proteins from eucaryotes apparently have more intrinsic disorder than those from either bacteria or archaea, with typically > 30% of eucaryotic proteins having disordered regions of length > or = 50 consecutive residues.
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Affiliation(s)
- A K Dunker
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA.
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