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Urea titration of a lipase from Pseudomonas sp. reveals four different conformational states, with a stable partially folded state explaining its high aggregation propensity. Int J Biol Macromol 2021; 174:32-41. [PMID: 33508357 DOI: 10.1016/j.ijbiomac.2021.01.153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
The conversion of soluble proteins into amyloid fibrils has importance in protein chemistry, biology, biotechnology and medicine. A novel lipase from Pseudomonas sp. was previously shown to have an extremely high aggregation propensity. It was therefore herein studied to elucidate the physicochemical and structural determinants of this extreme behaviour. Amyloid-like structures were found to form in samples up to 2.5-3.0 M using Thioflavin T fluorescence and Congo red binding assays. However, dynamic light scattering (DLS), static light scattering and turbidimetry revealed the existence of aggregates up to 4.0 M urea, without amyloid-like structure. Two monomeric conformational states were detected with intrinsic fluorescence, 8-anilinonaphthalene-1-sulfonate (ANS) binding and circular dichroism. These were further characterized in 7.5 M and 4.5 M urea using enzymatic activity measurements, tryptophan fluorescence quenching, DLS and nuclear magnetic resonance (NMR) and were found to consist of a largely disordered and a partially folded state, respectively, with the latter appearing stable, cooperative, fairly compact, non-active, α-helical, with largely buried hydrophobic residues. The persistence of a stable structure up to high concentrations of urea, in the absence of sequence characteristics typical of a high intrinsic aggregation propensity, explains the high tendency of this enzyme to form amyloid-like structures.
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Majumdar A, Mukhopadhyay S. Fluorescence Depolarization Kinetics to Study the Conformational Preference, Structural Plasticity, Binding, and Assembly of Intrinsically Disordered Proteins. Methods Enzymol 2018; 611:347-381. [DOI: 10.1016/bs.mie.2018.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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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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Malaga F, Mayberry O, Park DJ, Rodgers ME, Toptygin D, Schleif RF. A genetic and physical study of the interdomain linker of E. Coli
AraC protein-a trans
-subunit communication pathway. Proteins 2016; 84:448-60. [DOI: 10.1002/prot.24990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/23/2015] [Accepted: 01/12/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Fabiana Malaga
- Biology Department; UPCH; Lima San Martín De Porres Peru
| | - Ory Mayberry
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - David J. Park
- Tufts University Medical School; Boston Massachusetts
| | - Michael E. Rodgers
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - Dmitri Toptygin
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - Robert F. Schleif
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
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DeForte S, Reddy KD, Uversky VN. Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013). INTRINSICALLY DISORDERED PROTEINS 2015; 3:e984569. [PMID: 28293487 DOI: 10.4161/21690707.2014.984569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/19/2022]
Abstract
This is the 4th issue of the Digested Disorder series that represents reader's digest of the scientific literature on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the fourth quarter of 2013; i.e. during the period of October, November, and December of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability, and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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Bradford MK, Whitworth K, Wendland B. Pan1 regulates transitions between stages of clathrin-mediated endocytosis. Mol Biol Cell 2015; 26:1371-85. [PMID: 25631817 PMCID: PMC4454182 DOI: 10.1091/mbc.e14-11-1510] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Saccharomyces cerevisiae endocytic protein Pan1 is critical for coat interactions during three transitions of the endocytic pathway. Pan1 depletion arrests endocytosis and causes actin misregulation, leading to actin flares that are connected to the coat but not the membrane. The Pan1 central region is critical for endocytic and essential functions. Endocytosis is a well-conserved process by which cells invaginate small portions of the plasma membrane to create vesicles containing extracellular and transmembrane cargo proteins. Dozens of proteins and hundreds of specific binding interactions are needed to coordinate and regulate these events. Saccharomyces cerevisiae is a powerful model system with which to study clathrin-mediated endocytosis (CME). Pan1 is believed to be a scaffolding protein due to its interactions with numerous proteins that act throughout the endocytic process. Previous research characterized many Pan1 binding interactions, but due to Pan1's essential nature, the exact mechanisms of Pan1's function in endocytosis have been difficult to define. We created a novel Pan1-degron allele, Pan1-AID, in which Pan1 can be specifically and efficiently degraded in <1 h upon addition of the plant hormone auxin. The loss of Pan1 caused a delay in endocytic progression and weakened connections between the coat/actin machinery and the membrane, leading to arrest in CME. In addition, we determined a critical role for the central region of Pan1 in endocytosis and viability. The regions important for endocytosis and viability can be separated, suggesting that Pan1 may have a distinct role in the cell that is essential for viability.
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Affiliation(s)
| | - Karen Whitworth
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Beverly Wendland
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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DeForte S, Reddy KD, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013). INTRINSICALLY DISORDERED PROTEINS 2013; 1:e27454. [PMID: 28516028 PMCID: PMC5424790 DOI: 10.4161/idp.27454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 01/18/2023]
Abstract
The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a series of reader's digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA.,USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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