151
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Abstract
Inteins are intervening protein sequences that undergo self-excision from a precursor protein with the concomitant ligation of the flanking polypeptides. Split inteins are expressed in two separated halves, and the recognition and association of two halves are the first crucial step for initiating trans-splicing. In the present study, we carried out the structural and thermodynamic analysis on the interaction of two halves of DnaE split intein from Synechocystis sp. PCC6803. Both isolated halves (IN and IC) are disordered and undergo conformational transition from disorder to order upon association. ITC (isothermal titration calorimetry) reveals that the highly favourable enthalpy change drives the association of the two halves, overcoming the unfavourable entropy change. The high flexibility of two fragments and the marked thermodynamic preference provide a robust association for the formation of the well-folded IN/IC complex, which is the basis for reconstituting the trans-splicing activity of DnaE split intein.
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152
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Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (January/February/March, 2013). INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25496. [PMID: 28516015 PMCID: PMC5424799 DOI: 10.4161/idp.25496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 01/13/2023]
Abstract
The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for “intrinsically disordered protein OR natively unfolded protein” returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a “Digested Disorder” project, which will encompass a series of reader’s digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two 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 covers papers published during the period of January, February and March 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)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicince; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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153
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Testa L, Brocca S, Santambrogio C, D'Urzo A, Habchi J, Longhi S, Uversky VN, Grandori R. Extracting structural information from charge-state distributions of intrinsically disordered proteins by non-denaturing electrospray-ionization mass spectrometry. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25068. [PMID: 28516012 PMCID: PMC5424789 DOI: 10.4161/idp.25068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/02/2013] [Accepted: 05/16/2013] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.
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Affiliation(s)
- Lorenzo Testa
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Annalisa D'Urzo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Johnny Habchi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Sonia Longhi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Vladimir N Uversky
- Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| | - Rita Grandori
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
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154
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Bertini I, Felli IC, Gonnelli L, Vasantha Kumar MV, Pierattelli R. High-resolution characterization of intrinsic disorder in proteins: expanding the suite of (13)C-detected NMR spectroscopy experiments to determine key observables. Chembiochem 2013; 12:2347-52. [PMID: 23106082 DOI: 10.1002/cbic.201100406] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Order in disorder: The characterization of intrinsically disordered proteins by NMR spectroscopy is a necessity on the one hand and a continuous challenge on the other. We propose two experiments that provide diagnostic parameters to monitor the degree of unfolding of a polypeptide. The test was performed on the yeast Cox17 protein, known to gain its function through maturation from an intrinsically disordered state (see figure).
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Affiliation(s)
- Ivano Bertini
- CERM University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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155
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Mao AH, Lyle N, Pappu RV. Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J 2013; 449:307-18. [PMID: 23240611 PMCID: PMC4074364 DOI: 10.1042/bj20121346] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Intrinsically disordered proteins participate in important protein-protein and protein-nucleic acid interactions and control cellular phenotypes through their prominence as dynamic organizers of transcriptional, post-transcriptional and signalling networks. These proteins challenge the tenets of the structure-function paradigm and their functional mechanisms remain a mystery given that they fail to fold autonomously into specific structures. Solving this mystery requires a first principles understanding of the quantitative relationships between information encoded in the sequences of disordered proteins and the ensemble of conformations they sample. Advances in quantifying sequence-ensemble relationships have been facilitated through a four-way synergy between bioinformatics, biophysical experiments, computer simulations and polymer physics theories. In the present review we evaluate these advances and the resultant insights that allow us to develop a concise quantitative framework for describing the sequence-ensemble relationships of intrinsically disordered proteins.
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Affiliation(s)
- Albert H. Mao
- Medical Scientist Training Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
- Computational & Molecular Biophysics Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
| | - Nicholas Lyle
- Computational & Systems Biology Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
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156
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Deryusheva EI, Selivanova OM, Serdyuk IN. Loops and repeats in proteins as footprints of molecular evolution. BIOCHEMISTRY (MOSCOW) 2013; 77:1487-99. [DOI: 10.1134/s000629791213007x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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157
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Hobro AJ, Standley DM, Ahmad S, Smith NI. Deconstructing RNA: optical measurement of composition and structure. Phys Chem Chem Phys 2013; 15:13199-208. [DOI: 10.1039/c3cp52406j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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158
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Abstract
Though lacking a well-defined three-dimensional structure, intrinsically unstructured proteins are ubiquitous in nature. These molecules play crucial roles in many cellular processes, especially signaling and regulation. Surprisingly, even enzyme catalysis can tolerate substantial disorder. This observation contravenes conventional wisdom but is relevant to an understanding of how protein dynamics modulates enzyme function. This chapter reviews properties and characteristics of disordered proteins, emphasizing examples of enzymes that lack defined structures, and considers implications of structural disorder for catalytic efficiency and evolution.
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159
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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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160
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Mittal J, Yoo TH, Georgiou G, Truskett TM. Structural ensemble of an intrinsically disordered polypeptide. J Phys Chem B 2012. [PMID: 23205890 DOI: 10.1021/jp308984e] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins (IDPs), which play key roles in cell signaling and regulation, do not display specific tertiary structure when isolated in solution. Instead, they dynamically explore an ensemble of unfolded configurations, adopting more stable, ordered structures only after binding to their ligands. Whether ligands induce IDP structural changes upon binding or simply bind to pre-existing conformers that are populated within the IDP's structural ensemble is not well understood. Molecular simulations can provide information with the spatiotemporal resolution necessary to resolve these issues. Here, we report on the conformational ensemble of a 15-residue wild-type p53 fragment from the TAD domain and its mutant (TAD-P27L) obtained by replica exchange molecular dynamics simulation using an optimized (fully atomistic, explicit solvent) protein model and the experimental validation of the simulation results. We use a clustering method based on structural similarity to identify conformer states populated by the peptides in solution from the simulated ensemble. We show that p53 populates solution structures that strongly resemble the ligand (MDM2)-bound structure, but at the same time, the conformational free-energy landscape is relatively flat in the absence of the ligand.
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Affiliation(s)
- Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
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161
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Oldfield CJ, Xue B, Van YY, Ulrich EL, Markley JL, Dunker AK, Uversky VN. Utilization of protein intrinsic disorder knowledge in structural proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:487-98. [PMID: 23232152 DOI: 10.1016/j.bbapap.2012.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 12/02/2012] [Accepted: 12/03/2012] [Indexed: 12/01/2022]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed.
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Affiliation(s)
- Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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162
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The major mRNP protein YB-1: structural and association properties in solution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:559-67. [PMID: 23220387 DOI: 10.1016/j.bbapap.2012.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/07/2012] [Accepted: 11/27/2012] [Indexed: 02/04/2023]
Abstract
YB-1 is a major mRNP protein participating in the regulation of transcription and translation of a wide range of eukaryotic genes in many organisms probably due to its influence on mRNA packing into mRNPs. While the functional properties of YB-1 are extensively studied, little is known about its structural properties. In the present work we focused on studying its secondary structure, rigidity of its tertiary structure, compactness, and oligomerization in vitro by using far UV-CD, DSC, one-dimensional (1)H NMR, SAXS, sedimentation and FPLC. It was shown that only the cold shock domain within the entire YB-1 chain has a well-packed tertiary structure undergoing cooperative heat and cold denaturation transitions. In contrast, the rest of the YB-1 molecule is not rigidly packed and consists of PP II-like helical secondary structure elements and coil-like regions. At the same time, the overall dimension of the protein molecule is unexpectedly small. The polypeptide chains of YB-1 have a high tendency to form oligomers at neutral pH, while the extent and structural organization of the oligomers depend on protein concentration and ionic strength varying from compact monomeric units up to high molecular weight oligomers. These oligomers in solution are unstable and dissociate upon protein concentration decrease.
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163
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Alves C, Cunha C. Order and disorder in viral proteins: new insights into an old paradigm. Future Virol 2012. [DOI: 10.2217/fvl.12.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conventional dogma stating that proteins must fold into a well-defined structure in order to display biological function is being challenged everyday as new data emerge on the relevance of disordered regions and intrinsically disordered proteins. Viral proteins in particular can benefit greatly from the conformational flexibility granted by partially folded or unfolded protein segments. It enables them to adapt to hostile and changing environmental conditions, interact with the required host machinery while evading host defence mechanisms and tolerate the high mutation rates viral genomes are prone to. In this review, we will summarize and discuss the importance of the recent research field of protein disorder that is proving vital to gain better understanding of the roles and functions of viral proteins.
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Affiliation(s)
- Carolina Alves
- Medical Microbiology Unit, Center for Malaria & Tropical Diseases, Institute of Hygiene & Tropical Medicine, Nova University, Lisbon, Portugal
| | - Celso Cunha
- Medical Microbiology Unit, Center for Malaria & Tropical Diseases, Institute of Hygiene & Tropical Medicine, Nova University, Lisbon, Portugal
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164
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Lambrughi M, Papaleo E, Testa L, Brocca S, De Gioia L, Grandori R. Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation. Front Physiol 2012. [PMID: 23189058 PMCID: PMC3504315 DOI: 10.3389/fphys.2012.00435] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cyclin-dependent kinase inhibitors (CKIs) are key regulatory proteins of the eukaryotic cell cycle, which modulate cyclin-dependent kinase (Cdk) activity. CKIs perform their inhibitory effect by the formation of ternary complexes with a target kinase and its cognate cyclin. These regulators generally belong to the class of intrinsically disordered proteins (IDPs), which lack a well-defined and organized three-dimensional (3D) structure in their free state, undergoing folding upon binding to specific partners. Unbound IDPs are not merely random-coil structures, but can present intrinsically folded structural units (IFSUs) and collapsed conformations. These structural features can be relevant to protein function in vivo. The yeast CKI Sic1 is a 284-amino acid IDP that binds to Cdk1 in complex with the Clb5,6 cyclins, preventing phosphorylation of G1 substrates and, therefore, entrance to the S phase. Sic1 degradation, triggered by multiple phosphorylation events, promotes cell-cycle progression. Previous experimental studies pointed out a propensity of Sic1 and its isolated domains to populate both extended and compact conformations. The present contribution provides models for compact conformations of the Sic1 kinase-inhibitory domain (KID) by all-atom molecular dynamics (MD) simulations in explicit solvent and in the absence of interactors. The results are integrated by spectroscopic and spectrometric data. Helical IFSUs are identified, along with networks of intramolecular interactions. The results identify a group of putative hub residues and networks of electrostatic interactions, which are likely to be involved in the stabilization of the globular states.
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Affiliation(s)
- Matteo Lambrughi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milan, Italy
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165
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Velma V, Broome HJ, Hebert MD. Regulated specific proteolysis of the Cajal body marker protein coilin. Chromosoma 2012; 121:629-42. [PMID: 23064547 DOI: 10.1007/s00412-012-0387-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/25/2012] [Accepted: 10/03/2012] [Indexed: 12/27/2022]
Abstract
Cajal bodies (CB) are subnuclear domains that contain various proteins with diverse functions including the CB marker protein coilin. In this study, we investigate the proteolytic activity of calpain on coilin. Here, we report a 28-kDa cleaved coilin fragment detected by two coilin antibodies that is cell cycle regulated, with levels that are consistently reduced during mitosis. We further show that an in vitro calpain assay with full-length or C-terminal coilin recombinant protein releases the same size cleaved fragment. Furthermore, addition of exogenous RNA to purified coilin induces proteolysis by calpain. We also report that the relative levels of this cleaved coilin fragment are susceptible to changes induced by various cell stressors, and that coilin localization is affected by inhibition or knockdown of calpain both under normal and stressed conditions. Collectively, our data suggest that coilin is subjected to regulated specific proteolysis by calpain, and this processing may play a role in the regulation of coilin activity and CB formation.
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Affiliation(s)
- Venkatramreddy Velma
- Department of Biochemistry, The University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216-4505, USA
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166
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Song J, Gao F, Cui RZ, Shuang F, Liang W, Huang X, Zhuang W. Investigating the structural origin of trpzip2 temperature dependent unfolding fluorescence line shape based on a Markov state model simulation. J Phys Chem B 2012; 116:12669-76. [PMID: 22994891 DOI: 10.1021/jp304714q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vibrationally resolved fluorescence spectra of the β-hairpin trpzip2 peptide at two temperatures as well as during a T-jump unfolding process are simulated on the basis of a combination of Markov state models and quantum chemistry schemes. The broad asymmetric spectral line shape feature is reproduced by considering the exciton-phonon couplings. The temperature dependent red shift observed in the experiment has been attributed to the state population changes of specific chromophores. Through further theoretical study, it is found that both the environment's electric field and the chromophores' geometry distortions are responsible for tryptophan fluorescence shift.
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Affiliation(s)
- Jian Song
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, 116023, China
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167
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Bermel W, Bertini I, Chill J, Felli IC, Haba N, Kumar M. V. V, Pierattelli R. Exclusively Heteronuclear13C-Detected Amino-Acid-Selective NMR Experiments for the Study of Intrinsically Disordered Proteins (IDPs). Chembiochem 2012; 13:2425-32. [DOI: 10.1002/cbic.201200447] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Indexed: 12/20/2022]
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168
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Bardwell JCA, Jakob U. Conditional disorder in chaperone action. Trends Biochem Sci 2012; 37:517-25. [PMID: 23018052 DOI: 10.1016/j.tibs.2012.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/17/2012] [Accepted: 08/29/2012] [Indexed: 11/18/2022]
Abstract
Protein disorder remains an intrinsically fuzzy concept. Its role in protein function is difficult to conceptualize and its experimental study is challenging. Although a wide variety of roles for protein disorder have been proposed, establishing that disorder is functionally important, particularly in vivo, is not a trivial task. Several molecular chaperones have now been identified as conditionally disordered proteins; fully folded and chaperone-inactive under non-stress conditions, they adopt a partially disordered conformation upon exposure to distinct stress conditions. This disorder appears to be vital for their ability to bind multiple aggregation-sensitive client proteins and to protect cells against the stressors. The study of these conditionally disordered chaperones should prove useful in understanding the functional role for protein disorder in molecular recognition.
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Affiliation(s)
- James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
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169
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Santner AA, Croy CH, Vasanwala FH, Uversky VN, Van YYJ, Dunker AK. Sweeping away protein aggregation with entropic bristles: intrinsically disordered protein fusions enhance soluble expression. Biochemistry 2012; 51:7250-62. [PMID: 22924672 DOI: 10.1021/bi300653m] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intrinsically disordered, highly charged protein sequences act as entropic bristles (EBs), which, when translationally fused to partner proteins, serve as effective solubilizers by creating both a large favorable surface area for water interactions and large excluded volumes around the partner. By extending away from the partner and sweeping out large molecules, EBs can allow the target protein to fold free from interference. Using both naturally occurring and artificial polypeptides, we demonstrate the successful implementation of intrinsically disordered fusions as protein solubilizers. The artificial fusions discussed herein have a low level of sequence complexity and a high net charge but are diversified by means of distinctive amino acid compositions and lengths. Using 6xHis fusions as controls, soluble protein expression enhancements from 65% (EB60A) to 100% (EB250) were observed for a 20-protein portfolio. Additionally, these EBs were able to more effectively solubilize targets compared to frequently used fusions such as maltose-binding protein, glutathione S-transferase, thioredoxin, and N utilization substance A. Finally, although these EBs possess very distinct physiochemical properties, they did not perturb the structure, conformational stability, or function of the green fluorescent protein or the glutathione S-transferase protein. This work thus illustrates the successful de novo design of intrinsically disordered fusions and presents a promising technology and complementary resource for researchers attempting to solubilize recalcitrant proteins.
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Affiliation(s)
- Aaron A Santner
- Molecular Kinetics Inc., Indianapolis, Indiana 46268, United States
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170
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Durand E, Derrez E, Audoly G, Spinelli S, Ortiz-Lombardia M, Raoult D, Cascales E, Cambillau C. Crystal structure of the VgrG1 actin cross-linking domain of the Vibrio cholerae type VI secretion system. J Biol Chem 2012; 287:38190-9. [PMID: 22898822 DOI: 10.1074/jbc.m112.390153] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Vibrio cholerae is the cause of the diarrheal disease cholera. V. cholerae produces RtxA, a large toxin of the MARTX family, which is targeted to the host cell cytosol, where its actin cross-linking domain (ACD) cross-links G-actin, leading to F-actin depolymerization, cytoskeleton rearrangements, and cell rounding. These effects on the cytoskeleton prevent phagocytosis and bacterial engulfment by macrophages, thus preventing V. cholerae clearance from the gut. The V. cholerae Type VI secretion-associated VgrG1 protein also contains a C-terminal ACD, which shares 61% identity with MARTX ACD and has been shown to covalently cross-link G-actin. Here, we purified the VgrG1 C-terminal domain and determined its crystal structure. The VgrG1 ACD exhibits a V-shaped three-dimensional structure, formed of 12 β-strands and nine α-helices. Its active site comprises five residues that are conserved in MARTX ACD toxin, within a conserved area of ∼10 Å radius. We showed that less than 100 ACD molecules are sufficient to depolymerize the actin filaments of a fibroblast cell in vivo. Mutagenesis studies confirmed that Glu-16 is critical for the F-actin depolymerization function. Co-crystals with divalent cations and ATP reveal the molecular mechanism of the MARTX/VgrG toxins and offer perspectives for their possible inhibition.
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Affiliation(s)
- Eric Durand
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Marseille Cedex 09, France
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171
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Stauch K, Kieken F, Sorgen P. Characterization of the structure and intermolecular interactions between the connexin 32 carboxyl-terminal domain and the protein partners synapse-associated protein 97 and calmodulin. J Biol Chem 2012; 287:27771-88. [PMID: 22718765 PMCID: PMC3431650 DOI: 10.1074/jbc.m112.382572] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/20/2012] [Indexed: 12/20/2022] Open
Abstract
In Schwann cells, connexin 32 (Cx32) can oligomerize to form intracellular gap junction channels facilitating a shorter pathway for metabolite diffusion across the layers of the myelin sheath. The mechanisms of Cx32 intracellular channel regulation have not been clearly defined. However, Ca(2+), pH, and the phosphorylation state can regulate Cx32 gap junction channels, in addition to the direct interaction of protein partners with the carboxyl-terminal (CT) domain. In this study, we used different biophysical methods to determine the structure and characterize the interaction of the Cx32CT domain with the protein partners synapse-associated protein 97 (SAP97) and calmodulin (CaM). Our results revealed that the Cx32CT is an intrinsically disordered protein that becomes α-helical upon binding CaM. We identified the GUK domain as the minimal SAP97 region necessary for the Cx32CT interaction. The Cx32CT residues affected by the binding of CaM and the SAP97 GUK domain were determined as well as the dissociation constants for these interactions. We characterized three Cx32CT Charcot-Marie-Tooth disease mutants (R219H, R230C, and F235C) and identified that whereas they all formed functional channels, they all showed reduced binding affinity for SAP97 and CaM. Additionally, we report that in RT4-D6P2T rat schwannoma cells, Cx32 is differentially phosphorylated and exists in a complex with SAP97 and CaM. Our studies support the importance of protein-protein interactions in the regulation of Cx32 gap junction channels and myelin homeostasis.
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Affiliation(s)
- Kelly Stauch
- From the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Fabien Kieken
- From the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Paul Sorgen
- From the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198
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172
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Receveur-Brechot V, Durand D. How random are intrinsically disordered proteins? A small angle scattering perspective. Curr Protein Pept Sci 2012; 13:55-75. [PMID: 22044150 PMCID: PMC3394175 DOI: 10.2174/138920312799277901] [Citation(s) in RCA: 264] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 01/08/2023]
Abstract
While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex, are then reviewed. Indeed, recent computational advances have made it possible to readily extract maximum information from the scattering curve with a special emphasis on highly flexible systems, such as multidomain proteins and IDPs. Furthermore, integrated computational approaches now enable the generation of ensembles of conformers to translate the unique flexible characteristics of IDPs by taking into consideration the constraints of more and more various complementary experiment. In particular, a combination of SAXS with high-resolution techniques, such as x-ray crystallography and NMR, allows us to provide reliable models and to gain unique structural insights about the protein over multiple structural scales. The latest neutron scattering experiments also promise new advances in the study of the conformational changes of macromolecules involving more complex systems.
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173
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Nagulapalli M, Parigi G, Yuan J, Gsponer J, Deraos G, Bamm VV, Harauz G, Matsoukas J, de Planque MRR, Gerothanassis IP, Babu MM, Luchinat C, Tzakos AG. Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex. Structure 2012; 20:522-33. [PMID: 22405011 DOI: 10.1016/j.str.2012.01.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 12/01/2011] [Accepted: 01/03/2012] [Indexed: 11/18/2022]
Abstract
Protein interactions within regulatory networks should adapt in a spatiotemporal-dependent dynamic environment, in order to process and respond to diverse and versatile cellular signals. However, the principles governing recognition pliability in protein complexes are not well understood. We have investigated a region of the intrinsically disordered protein myelin basic protein (MBP(145-165)) that interacts with calmodulin, but that also promiscuously binds other biomolecules (membranes, modifying enzymes). To characterize this interaction, we implemented an NMR spectroscopic approach that calculates, for each conformation of the complex, the maximum occurrence based on recorded pseudocontact shifts and residual dipolar couplings. We found that the MBP(145-165)-calmodulin interaction is characterized by structural heterogeneity. Quantitative comparative analysis indicated that distinct conformational landscapes of structural heterogeneity are sampled for different calmodulin-target complexes. Such structural heterogeneity in protein complexes could potentially explain the way that transient and promiscuous protein interactions are optimized and tuned in complex regulatory networks.
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Affiliation(s)
- Malini Nagulapalli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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174
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Arrigoni A, Grillo B, Vitriolo A, De Gioia L, Papaleo E. C-terminal acidic domain of ubiquitin-conjugating enzymes: A multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes. J Struct Biol 2012; 178:245-59. [DOI: 10.1016/j.jsb.2012.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 04/01/2012] [Accepted: 04/03/2012] [Indexed: 11/30/2022]
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175
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Johnson DE, Xue B, Sickmeier MD, Meng J, Cortese MS, Oldfield CJ, Le Gall T, Dunker AK, Uversky VN. High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative. J Struct Biol 2012; 180:201-15. [PMID: 22651963 DOI: 10.1016/j.jsb.2012.05.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/11/2012] [Accepted: 05/18/2012] [Indexed: 10/28/2022]
Abstract
The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represents a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using predictors of natural disordered regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apomyoglobin, and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins.
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Affiliation(s)
- Derrick E Johnson
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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176
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Hervás R, Oroz J, Galera-Prat A, Goñi O, Valbuena A, Vera AM, Gómez-Sicilia À, Losada-Urzáiz F, Uversky VN, Menéndez M, Laurents DV, Bruix M, Carrión-Vázquez M. Common features at the start of the neurodegeneration cascade. PLoS Biol 2012; 10:e1001335. [PMID: 22666178 PMCID: PMC3362641 DOI: 10.1371/journal.pbio.1001335] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 04/06/2012] [Indexed: 12/30/2022] Open
Abstract
A single-molecule study reveals that neurotoxic proteins share common structural features that may trigger neurodegeneration, thus identifying new targets for therapy and diagnosis. Amyloidogenic neurodegenerative diseases are incurable conditions with high social impact that are typically caused by specific, largely disordered proteins. However, the underlying molecular mechanism remains elusive to established techniques. A favored hypothesis postulates that a critical conformational change in the monomer (an ideal therapeutic target) in these “neurotoxic proteins” triggers the pathogenic cascade. We use force spectroscopy and a novel methodology for unequivocal single-molecule identification to demonstrate a rich conformational polymorphism in the monomer of four representative neurotoxic proteins. This polymorphism strongly correlates with amyloidogenesis and neurotoxicity: it is absent in a fibrillization-incompetent mutant, favored by familial-disease mutations and diminished by a surprisingly promiscuous inhibitor of the critical monomeric β-conformational change, neurotoxicity, and neurodegeneration. Hence, we postulate that specific mechanostable conformers are the cause of these diseases, representing important new early-diagnostic and therapeutic targets. The demonstrated ability to inhibit the conformational heterogeneity of these proteins by a single pharmacological agent reveals common features in the monomer and suggests a common pathway to diagnose, prevent, halt, or reverse multiple neurodegenerative diseases. Neurodegenerative diseases like Alzheimer's or Parkinson's are currently incurable. They are caused by different proteins that, under certain circumstances, aggregate and become toxic as we grow older, but the molecular events underlying this process remain unclear. The lack of a well-defined structure, and the tendency of these “neurotoxic proteins” to aggregate make them difficult to study using conventional techniques. Here, we use an established single-molecule manipulation technique combined with a new protein-engineering strategy to show that all these proteins can adopt a rich collection of structures (conformers) that includes a high proportion of mechanostable conformers, which are associated with toxicity and disease. We also find that a known drug can block the formation of these mechanostable structures in different neurotoxic proteins. We suggest that the most mechanostable conformers, or their precursors, may trigger the pathogenic cascade that results in toxicity. We thus propose that these mechanostable structures are ideal targets for early diagnosis, prevention, and treatment of these fatal diseases.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Javier Oroz
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Albert Galera-Prat
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Oscar Goñi
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Alejandro Valbuena
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Andrés M. Vera
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Àngel Gómez-Sicilia
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Fernando Losada-Urzáiz
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Vladimir N. Uversky
- University of South Florida, College of Medicine and Byrd Alzheimer's Research Institute, Tampa, Florida, United States of America
- Institute for Biological Instrumentation. Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
- * E-mail:
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177
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MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics 2012; 13:111. [PMID: 22624656 PMCID: PMC3465245 DOI: 10.1186/1471-2105-13-111] [Citation(s) in RCA: 256] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 04/26/2012] [Indexed: 11/28/2022] Open
Abstract
Background Intrinsically unstructured proteins (IUPs) lack a well-defined three-dimensional structure. Some of them may assume a locally stable structure under specific conditions, e.g. upon interaction with another molecule, while others function in a permanently unstructured state. The discovery of IUPs challenged the traditional protein structure paradigm, which stated that a specific well-defined structure defines the function of the protein. As of December 2011, approximately 60 methods for computational prediction of protein disorder from sequence have been made publicly available. They are based on different approaches, such as utilizing evolutionary information, energy functions, and various statistical and machine learning methods. Results Given the diversity of existing intrinsic disorder prediction methods, we decided to test whether it is possible to combine them into a more accurate meta-prediction method. We developed a method based on arbitrarily chosen 13 disorder predictors, in which the final consensus was weighted by the accuracy of the methods. We have also developed a disorder predictor GSmetaDisorder3D that used no third-party disorder predictors, but alignments to known protein structures, reported by the protein fold-recognition methods, to infer the potentially structured and unstructured regions. Following the success of our disorder predictors in the CASP8 benchmark, we combined them into a meta-meta predictor called GSmetaDisorderMD, which was the top scoring method in the subsequent CASP9 benchmark. Conclusions A series of disorder predictors described in this article is available as a MetaDisorder web server at http://iimcb.genesilico.pl/metadisorder/. Results are presented both in an easily interpretable, interactive mode and in a simple text format suitable for machine processing.
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178
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Moreno-Córdoba I, Diago-Navarro E, Barendregt A, Heck AJR, Alfonso C, Díaz-Orejas R, Nieto C, Espinosa M. The toxin-antitoxin proteins relBE2Spn of Streptococcus pneumoniae: characterization and association to their DNA target. Proteins 2012; 80:1834-46. [PMID: 22488579 DOI: 10.1002/prot.24081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 03/21/2012] [Accepted: 03/23/2012] [Indexed: 01/07/2023]
Abstract
The chromosome of the pathogenic Gram-positive bacterium Streptococcus pneumoniae contains between six to 10 operons encoding toxin-antitoxin systems (TAS). TAS are widespread and redundant in bacteria and archaea and their role, albeit still obscure, may be related to important aspects of bacteria lifestyle like response to stress. One of the most abundant TAS is the relBE family, being present in the chromosome of many bacteria and archaea. Because of the high rates of morbility and mortality caused by S. pneumoniae, it has been interesting to gain knowledge on the pneumococcal TAS, among them the RelBE2Spn proteins. Here, we have analyzed the DNA binding capacity of the RelB2Spn antitoxin and the RelB2Spn-RelE2Spn proteins by band-shift assays. Thus, a DNA region encompassing the operator region of the proteins was identified. In addition, we have used analytical ultracentrifugation and native mass spectrometry to measure the oligomerization state of the antitoxin alone and the RelBE2Spn complex in solution bound or unbound to its DNA substrate. Using native mass spectrometry allowed us to unambiguously determine the stoichiometry of the RelB2Spn and of the RelBE2Spn complex alone or associated to its DNA target.
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Affiliation(s)
- Inma Moreno-Córdoba
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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179
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Felli IC, Pierattelli R. Recent progress in NMR spectroscopy: Toward the study of intrinsically disordered proteins of increasing size and complexity. IUBMB Life 2012; 64:473-81. [DOI: 10.1002/iub.1045] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/04/2012] [Indexed: 11/09/2022]
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180
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Sikirzhytski V, Topilina NI, Takor GA, Higashiya S, Welch JT, Uversky VN, Lednev IK. Fibrillation mechanism of a model intrinsically disordered protein revealed by 2D correlation deep UV resonance Raman spectroscopy. Biomacromolecules 2012; 13:1503-9. [PMID: 22515261 DOI: 10.1021/bm300193f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding of numerous biological functions of intrinsically disordered proteins (IDPs) is of significant interest to modern life science research. A large variety of serious debilitating diseases are associated with the malfunction of IDPs including neurodegenerative disorders and systemic amyloidosis. Here we report on the molecular mechanism of amyloid fibrillation of a model IDP (YE8) using 2D correlation deep UV resonance Raman spectroscopy. YE8 is a genetically engineered polypeptide, which is completely unordered at neutral pH yet exhibits all properties of a fibrillogenic protein at low pH. The very first step of the fibrillation process involves structural rearrangements of YE8 at the global structure level without the detectable appearance of secondary structural elements. The formation of β-sheet species follows the global structural changes and proceeds via the simultaneous formation of turns and β-strands. The kinetic mechanism revealed is an important new contribution to understanding of the general fibrillation mechanism proposed for IDP.
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Affiliation(s)
- Vitali Sikirzhytski
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, New York 12222, USA
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181
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Guo J, Yang XQ, He XT, Wu NN, Wang JM, Gu W, Zhang YY. Limited aggregation behavior of β-conglycinin and its terminating effect on glycinin aggregation during heating at pH 7.0. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:3782-3791. [PMID: 22429197 DOI: 10.1021/jf300409y] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this work, different thermal aggregation behaviors of soy β-conglycinin and glycinin at pH 7.0 were characterized with size exclusion chromatography and low-angle light scattering. Limited aggregation that grew via the consumption of "monomers" was detected in β-conglycinin, forming soluble aggregates. For glycinin, the association between the aggregates that led to the appearance of insoluble materials was observed. Heated with β-conglycinin, the assembly between the glycinin aggregates was terminated and its solubility was recovered. The structure of the soluble and insoluble aggregates was analyzed by small-angle X-ray scattering and dynamic light scattering. Unlike the β-conglycinin soluble aggregates that possessed limited size and less compact conformation, particles with a denser core and a less dense outer shell were found in the glycinin insoluble aggregates. Evidence is presented to reveal the transition between the soluble and insoluble aggregates and the role of β-conglycinin in the solubilization of the soy protein aggregates during heating.
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Affiliation(s)
- Jian Guo
- Protein Research and Development Center, Department of Food Science and Technology, South China University of Technology, Guangzhou, People's Republic of China
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182
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Chen L, Balabanidou V, Remeta DP, Minetti CASA, Portaliou AG, Economou A, Kalodimos CG. Structural instability tuning as a regulatory mechanism in protein-protein interactions. Mol Cell 2012; 44:734-44. [PMID: 22152477 DOI: 10.1016/j.molcel.2011.09.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/22/2011] [Accepted: 09/10/2011] [Indexed: 10/14/2022]
Abstract
Protein-protein interactions mediate a vast number of cellular processes. Here, we present a regulatory mechanism in protein-protein interactions mediated by finely tuned structural instability and coupled with molecular mimicry. We show that a set of type III secretion (TTS) autoinhibited homodimeric chaperones adopt a molten globule-like state that transiently exposes the substrate binding site as a means to become rapidly poised for binding to their cognate protein substrates. Packing defects at the homodimeric interface stimulate binding, whereas correction of these defects results in less labile chaperones that give rise to nonfunctional biological systems. The protein substrates use structural mimicry to offset the weak spots in the chaperones and to counteract their autoinhibitory conformation. This regulatory mechanism of protein activity is evolutionarily conserved among several TSS systems and presents a lucid example of functional advantage conferred upon a biological system by finely tuned structural instability.
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Affiliation(s)
- Li Chen
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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183
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Baker ES, Luckner SR, Krause KL, Lambden PR, Clarke IN, Ward VK. Inherent structural disorder and dimerisation of murine norovirus NS1-2 protein. PLoS One 2012; 7:e30534. [PMID: 22347381 PMCID: PMC3274520 DOI: 10.1371/journal.pone.0030534] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 12/23/2011] [Indexed: 11/28/2022] Open
Abstract
Human noroviruses are highly infectious viruses that cause the majority of acute, non-bacterial epidemic gastroenteritis cases worldwide. The first open reading frame of the norovirus RNA genome encodes for a polyprotein that is cleaved by the viral protease into six non-structural proteins. The first non-structural protein, NS1-2, lacks any significant sequence similarity to other viral or cellular proteins and limited information is available about the function and biophysical characteristics of this protein. Bioinformatic analyses identified an inherently disordered region (residues 1–142) in the highly divergent N-terminal region of the norovirus NS1-2 protein. Expression and purification of the NS1-2 protein of Murine norovirus confirmed these predictions by identifying several features typical of an inherently disordered protein. These were a biased amino acid composition with enrichment in the disorder promoting residues serine and proline, a lack of predicted secondary structure, a hydrophilic nature, an aberrant electrophoretic migration, an increased Stokes radius similar to that predicted for a protein from the pre-molten globule family, a high sensitivity to thermolysin proteolysis and a circular dichroism spectrum typical of an inherently disordered protein. The purification of the NS1-2 protein also identified the presence of an NS1-2 dimer in Escherichia coli and transfected HEK293T cells. Inherent disorder provides significant advantages including structural flexibility and the ability to bind to numerous targets allowing a single protein to have multiple functions. These advantages combined with the potential functional advantages of multimerisation suggest a multi-functional role for the NS1-2 protein.
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Affiliation(s)
- Estelle S. Baker
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sylvia R. Luckner
- Department of Biochemistry, School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Kurt L. Krause
- Department of Biochemistry, School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Paul R. Lambden
- Molecular Microbiology and Infection, School of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ian N. Clarke
- Molecular Microbiology and Infection, School of Medicine, University of Southampton, Southampton, United Kingdom
| | - Vernon K. Ward
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- * E-mail:
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184
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Uversky VN, Dunker AK. Multiparametric Analysis of Intrinsically Disordered Proteins: Looking at Intrinsic Disorder through Compound Eyes. Anal Chem 2012; 84:2096-104. [DOI: 10.1021/ac203096k] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vladimir N. Uversky
- Department
of Molecular Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow
Region, Russia
| | - A. Keith Dunker
- Center for
Computational Biology and Bioinformatics, Department of Biochemistry
and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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185
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Zhang W, Ganguly D, Chen J. Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins. PLoS Comput Biol 2012; 8:e1002353. [PMID: 22253588 PMCID: PMC3257294 DOI: 10.1371/journal.pcbi.1002353] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/30/2011] [Indexed: 01/08/2023] Open
Abstract
To understand the interplay of residual structures and conformational fluctuations in the interaction of intrinsically disordered proteins (IDPs), we first combined implicit solvent and replica exchange sampling to calculate atomistic disordered ensembles of the nuclear co-activator binding domain (NCBD) of transcription coactivator CBP and the activation domain of the p160 steroid receptor coactivator ACTR. The calculated ensembles are in quantitative agreement with NMR-derived residue helicity and recapitulate the experimental observation that, while free ACTR largely lacks residual secondary structures, free NCBD is a molten globule with a helical content similar to that in the folded complex. Detailed conformational analysis reveals that free NCBD has an inherent ability to substantially sample all the helix configurations that have been previously observed either unbound or in complexes. Intriguingly, further high-temperature unbinding and unfolding simulations in implicit and explicit solvents emphasize the importance of conformational fluctuations in synergistic folding of NCBD with ACTR. A balance between preformed elements and conformational fluctuations appears necessary to allow NCBD to interact with different targets and fold into alternative conformations. Together with previous topology-based modeling and existing experimental data, the current simulations strongly support an “extended conformational selection” synergistic folding mechanism that involves a key intermediate state stabilized by interaction between the C-terminal helices of NCBD and ACTR. In addition, the atomistic simulations reveal the role of long-range as well as short-range electrostatic interactions in cooperating with readily fluctuating residual structures, which might enhance the encounter rate and promote efficient folding upon encounter for facile binding and folding interactions of IDPs. Thus, the current study not only provides a consistent mechanistic understanding of the NCBD/ACTR interaction, but also helps establish a multi-scale molecular modeling framework for understanding the structure, interaction, and regulation of IDPs in general. Intrinsically disordered proteins (IDPs) are now widely recognized to play fundamental roles in biology and to be frequently associated with human diseases. Although the potential advantages of intrinsic disorder in cellular signaling and regulation have been widely discussed, the physical basis for these proposed phenomena remains sketchy at best. An integration of multi-scale molecular modeling and experimental characterization is necessary to uncover the molecular principles that govern the structure, interaction, and regulation of IDPs. In this work, we characterize the conformational properties of two IDPs involved in transcription regulation at the atomistic level and further examine the roles of these properties in their coupled binding and folding interactions. Our simulations suggest interplay among residual structures, conformational fluctuations, and electrostatic interactions that allows efficient synergistic folding of these two IDPs. In particular, we propose that electrostatic interactions might play an important role in facilitating rapid folding and binding recognition of IDPs, by enhancing the encounter rate and promoting efficient folding upon encounter.
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Affiliation(s)
- Weihong Zhang
- Department of Biochemistry, Kansas State University, Manhattan, Kansas, United States of America
| | - Debabani Ganguly
- Department of Biochemistry, Kansas State University, Manhattan, Kansas, United States of America
| | - Jianhan Chen
- Department of Biochemistry, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
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186
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Salvay AG, Communie G, Ebel C. Sedimentation velocity analytical ultracentrifugation for intrinsically disordered proteins. Methods Mol Biol 2012; 896:91-105. [PMID: 22821519 DOI: 10.1007/978-1-4614-3704-8_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The size of intrinsically disordered proteins (IDPs) is large compared to their molecular mass and the resulting mass-to-size ratio is unusual. The sedimentation coefficient, which can be obtained from sedimentation velocity (SV) analytical ultracentrifugation (AUC), is directly related to this ratio and can be easily interpreted in terms of frictional ratio. This chapter is a step-by-step protocol for setting up, executing and analyzing SV experiments in the context of the characterization of IDPs, based on a real case study of the partially folded C-terminal domain of Sendai virus nucleoprotein.
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Affiliation(s)
- Andrés G Salvay
- Institut de Biologie Structurale, CEA-CNRS-Université, Grenoble, France
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187
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Habchi J, Longhi S. Structural disorder within paramyxovirus nucleoproteins and phosphoproteins. ACTA ACUST UNITED AC 2012; 8:69-81. [DOI: 10.1039/c1mb05204g] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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188
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Follis AV, Galea CA, Kriwacki RW. Intrinsic Protein Flexibility in Regulation of Cell Proliferation: Advantages for Signaling and Opportunities for Novel Therapeutics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:27-49. [DOI: 10.1007/978-1-4614-0659-4_3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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189
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Lotti M, Longhi S. Mutual effects of disorder and order in fusion proteins between intrinsically disordered domains and fluorescent proteins. ACTA ACUST UNITED AC 2012; 8:105-13. [DOI: 10.1039/c1mb05244f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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190
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Oroz J, Hervás R, Valbuena A, Carrión-Vázquez M. Unequivocal single-molecule force spectroscopy of intrinsically disordered proteins. Methods Mol Biol 2012; 896:71-87. [PMID: 22821518 DOI: 10.1007/978-1-4614-3704-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Intrinsically disordered proteins (IDPs) are predicted to represent about one third of the eukaryotic proteome. The dynamic ensemble of conformations of this steadily growing class of proteins has remained hardly accessible for bulk biophysical techniques. However, single-molecule techniques provide a useful means of studying these proteins. Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is one of such techniques, which has certain peculiarities that make it an important methodology to analyze the biophysical properties of IDPs. However, several drawbacks inherent to this technique can complicate such analysis. We have developed a protein engineering strategy to overcome these drawbacks such that an unambiguous mechanical analysis of proteins, including IDPs, can be readily performed. Using this approach, we have recently characterized the rich conformational polymorphism of several IDPs. Here, we describe a simple protocol to perform the nanomechanical analysis of IDPs using this new strategy, a procedure that in principle can also be followed for the nanomechanical analysis of any protein.
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Affiliation(s)
- Javier Oroz
- Instituto Cajal, CSIC and Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
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191
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Natalello A, Ami D, Doglia SM. Fourier transform infrared spectroscopy of intrinsically disordered proteins: measurement procedures and data analyses. Methods Mol Biol 2012; 895:229-44. [PMID: 22760323 DOI: 10.1007/978-1-61779-927-3_16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A peculiar property of intrinsically disordered proteins (IDPs), or of intrinsically disordered domains, is the absence of a well-defined three dimensional structure under native conditions. Moreover, IDPs usually acquire a specific structure in the presence of different interactors. In this framework, Fourier transform infrared (FTIR) spectroscopy is a powerful tool to assess the disordered character of a protein and to study its induced folding. In this chapter, we will show the detailed experimental procedures to measure the FTIR spectra of protein samples and the spectral analyses required to obtain information on the protein secondary structures and aggregation.
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Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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192
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Size-exclusion chromatography in structural analysis of intrinsically disordered proteins. Methods Mol Biol 2012; 896:179-94. [PMID: 22821524 DOI: 10.1007/978-1-4614-3704-8_11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gel-filtration chromatography, also known as size-exclusion chromatography (SEC) or gel-permeation chromatography, is a useful tool for structural and conformational analyses of intrinsically disordered proteins (IDPs). SEC can be utilized for the estimation of the hydrodynamic dimensions of a given IDP, for evaluation of the association state, for the analysis of IDP interactions with binding partners, and for the induced folding studies. It also can be used to physically separate IDP conformers based on their hydrodynamic dimensions, thus providing a unique possibility for the independent analysis of their physicochemical properties.
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193
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Sigalov AB. Interplay Between Protein Order, Disorder and Oligomericity in Receptor Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:50-73. [DOI: 10.1007/978-1-4614-0659-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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194
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Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, Zhou Y. SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J Biomol Struct Dyn 2012; 29:799-813. [PMID: 22208280 PMCID: PMC3297974 DOI: 10.1080/073911012010525022] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Short and long disordered regions of proteins have different preference for different amino acid residues. Different methods often have to be trained to predict them separately. In this study, we developed a single neural-network-based technique called SPINE-D that makes a three-state prediction first (ordered residues and disordered residues in short and long disordered regions) and reduces it into a two-state prediction afterwards. SPINE-D was tested on various sets composed of different combinations of Disprot annotated proteins and proteins directly from the PDB annotated for disorder by missing coordinates in X-ray determined structures. While disorder annotations are different according to Disprot and X-ray approaches, SPINE-D's prediction accuracy and ability to predict disorder are relatively independent of how the method was trained and what type of annotation was employed but strongly depend on the balance in the relative populations of ordered and disordered residues in short and long disordered regions in the test set. With greater than 85% overall specificity for detecting residues in both short and long disordered regions, the residues in long disordered regions are easier to predict at 81% sensitivity in a balanced test dataset with 56.5% ordered residues but more challenging (at 65% sensitivity) in a test dataset with 90% ordered residues. Compared to eleven other methods, SPINE-D yields the highest area under the curve (AUC), the highest Mathews correlation coefficient for residue-based prediction, and the lowest mean square error in predicting disorder contents of proteins for an independent test set with 329 proteins. In particular, SPINE-D is comparable to a meta predictor in predicting disordered residues in long disordered regions and superior in short disordered regions. SPINE-D participated in CASP 9 blind prediction and is one of the top servers according to the official ranking. In addition, SPINE-D was examined for prediction of functional molecular recognition motifs in several case studies.
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Affiliation(s)
- Tuo Zhang
- School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eshel Faraggi
- School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Bin Xue
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Yaoqi Zhou
- School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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195
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Kiefhaber T, Bachmann A, Jensen KS. Dynamics and mechanisms of coupled protein folding and binding reactions. Curr Opin Struct Biol 2011; 22:21-9. [PMID: 22129832 DOI: 10.1016/j.sbi.2011.09.010] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 09/27/2011] [Indexed: 11/28/2022]
Abstract
Protein folding coupled to binding of a specific ligand is frequently observed in biological processes. In recent years numerous studies have addressed the structural properties of the unfolded proteins in the absence of their ligands. Surprisingly few time-resolved investigations on coupled folding and binding reactions have been published up to date and the dynamics and kinetic mechanisms of these processes are still only poorly understood. Especially, it is still unsolved for most systems which conformation of the protein is recognized by the ligand (conformational selection vs. folding-after-binding) and whether the ligand influences the folding kinetics. Here we review experimental methods, kinetic models and time-resolved experimental studies of coupled folding and binding reactions.
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Affiliation(s)
- Thomas Kiefhaber
- Munich Center for Integrated Protein Science at the Chemistry Department, TU München, Lichtenbergstrasse 4, D-85747 Garching, Germany.
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196
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Fukuchi S, Sakamoto S, Nobe Y, Murakami SD, Amemiya T, Hosoda K, Koike R, Hiroaki H, Ota M. IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. Nucleic Acids Res 2011; 40:D507-11. [PMID: 22067451 PMCID: PMC3245138 DOI: 10.1093/nar/gkr884] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
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Affiliation(s)
- Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan.
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197
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Shishkov A, Bogacheva E, Fedorova N, Ksenofontov A, Badun G, Radyukhin V, Lukashina E, Serebryakova M, Dolgov A, Chulichkov A, Dobrov E, Baratova L. Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium. FEBS J 2011; 278:4905-16. [PMID: 21985378 DOI: 10.1111/j.1742-4658.2011.08392.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The structure of the C-terminal domain of the influenza virus A matrix M1 protein, for which X-ray diffraction data were still missing, was studied in acidic solution. Matrix M1 protein was bombarded with thermally-activated tritium atoms, and the resulting intramolecular distribution of the tritium label was analyzed to assess the steric accessibility of the amino acid residues in this protein. This technique revealed that interdomain loops and the C-terminal domain of the protein are the most accessible to labeling with tritium atoms. A model of the spatial arrangement of the C-terminal domain of matrix M1 protein was generated using rosetta software adjusted to the data obtained by tritium planigraphy experiments. This model suggests that the C-terminal domain is an almost flat layer with a three-α-helical structure. To explain the high level of tritium label incorporation into the C-terminal domain of the M1 protein in an acidic solution, we also used independent experimental approaches (CD spectroscopy, limited proteolysis and MALDI-TOF MS analysis of the proteolysis products, dynamic light scattering and analytical ultracentrifugation), as well as multiple computational algorithms, to analyse the intrinsic protein disorder. Taken together, the results obtained in the present study indicate that the C-terminal domain is weakly structured. We hypothesize that the specific 3D structural peculiarities of the M1 protein revealed in acidic pH solution allow the protein greater structural flexibility and enable it to interact effectively with the components of the host cell.
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Affiliation(s)
- Alexander Shishkov
- N N Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
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198
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Saelices L, Galmozzi CV, Florencio FJ, Muro-Pastor MI, Neira JL. The Inactivating Factor of Glutamine Synthetase IF17 Is an Intrinsically Disordered Protein, Which Folds upon Binding to Its Target. Biochemistry 2011; 50:9767-78. [DOI: 10.1021/bi2009272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lorena Saelices
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - Carla V. Galmozzi
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - Francisco J. Florencio
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - M. Isabel Muro-Pastor
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - José L. Neira
- Instituto de Biologı́a
Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
- Instituto de Biocomputación y Fı́sica de Sistemas Complejos, Zaragoza,
Spain
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199
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Rahman LN, Smith GST, Bamm VV, Voyer-Grant JAM, Moffatt BA, Dutcher JR, Harauz G. Phosphorylation of Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2 facilitates cation-induced conformational changes and actin assembly. Biochemistry 2011; 50:9587-604. [PMID: 21970344 DOI: 10.1021/bi201205m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Group 2 late embryogenesis abundant (LEA) proteins, also known as dehydrins, are intrinsically disordered proteins that are expressed in plants experiencing extreme environmental conditions such as drought or low temperatures. These proteins are characterized by the presence of at least one conserved, lysine-rich K-segment and sometimes by one or more serine-rich S-segments that are phosphorylated. Dehydrins may stabilize proteins and membrane structures during environmental stress and can sequester and scavenge metal ions. Here, we investigate how the conformations of two dehydrins from Thellungiella salsuginea, denoted as TsDHN-1 (acidic) and TsDHN-2 (basic), are affected by pH, interactions with cations and membranes, and phosphorylation. Both TsDHN-1 and TsDHN-2 were expressed as SUMO fusion proteins for in vitro phosphorylation by casein kinase II (CKII), and structural analysis by circular dichroism and attenuated total reflection-Fourier transform infrared spectroscopy. We show that the polyproline II conformation can be induced in the dehydrins by their environmental conditions, including changes in the concentration of divalent cations such as Ca(2+). The assembly of actin by these dehydrins was assessed by sedimentation assays and viewed by transmission electron and atomic force microscopy. Phosphorylation allowed both dehydrins to polymerize actin filaments. These results support the hypothesis that dehydrins stabilize the cytoskeleton under stress conditions and further that phosphorylation may be an important feature of this stabilization.
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Affiliation(s)
- Luna N Rahman
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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200
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Keppel TR, Howard BA, Weis DD. Mapping Unstructured Regions and Synergistic Folding in Intrinsically Disordered Proteins with Amide H/D Exchange Mass Spectrometry. Biochemistry 2011; 50:8722-32. [DOI: 10.1021/bi200875p] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Theodore R. Keppel
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
| | - Brent A. Howard
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
| | - David D. Weis
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
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