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Csizmok V, Follis AV, Kriwacki RW, Forman-Kay JD. Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling. Chem Rev 2016; 116:6424-62. [PMID: 26922996 DOI: 10.1021/acs.chemrev.5b00548] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent ∼30% of the proteome and enable unique regulatory mechanisms. In this review, we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of conformational ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultrasensitivity" and "regulated folding and unfolding". We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information.
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Affiliation(s)
- Veronika Csizmok
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center , Memphis, Tennessee 38163, United States
| | - Julie D Forman-Kay
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto , Toronto, ON M5S 1A8, Canada
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52
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Limited cooperativity in protein folding. Curr Opin Struct Biol 2016; 36:58-66. [DOI: 10.1016/j.sbi.2015.12.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/09/2015] [Indexed: 01/07/2023]
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53
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Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discov Today 2015; 21:562-72. [PMID: 26691874 PMCID: PMC7108309 DOI: 10.1016/j.drudis.2015.11.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 12/18/2022]
Abstract
Coronavirus nucleocapsid proteins are appealing drug targets against coronavirus-induced diseases. A variety of compounds targeting the coronavirus nucleocapsid protein have been developed. Many of these compounds show potential antiviral activity.
The advent of severe acute respiratory syndrome (SARS) in the 21st century and the recent outbreak of Middle-East respiratory syndrome (MERS) highlight the importance of coronaviruses (CoVs) as human pathogens, emphasizing the need for development of novel antiviral strategies to combat acute respiratory infections caused by CoVs. Recent studies suggest that nucleocapsid (N) proteins from coronaviruses and other viruses can be useful antiviral drug targets against viral infections. This review aims to provide readers with a concise survey of the structural features of coronavirus N proteins and how these features provide insights into structure-based development of therapeutics against coronaviruses. We will also present our latest results on MERS-CoV N protein and its potential as an antiviral drug target.
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54
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Peng Z, Kurgan L. High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder. Nucleic Acids Res 2015; 43:e121. [PMID: 26109352 PMCID: PMC4605291 DOI: 10.1093/nar/gkv585] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/24/2015] [Accepted: 05/24/2015] [Indexed: 01/05/2023] Open
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein-protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/.
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Affiliation(s)
- Zhenling Peng
- Center for Applied Mathematics, Tianjin University, Tianjin, 300072, P.R. China Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2V4, Canada
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2V4, Canada
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55
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Inaba S, Maeno A, Sakurai K, Narayanan SP, Ikegami T, Akasaka K, Oda M. Functional conformer of c-Myb DNA-binding domain revealed by variable temperature studies. FEBS J 2015; 282:4497-514. [DOI: 10.1111/febs.13508] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Satomi Inaba
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University; Kyoto Japan
| | - Akihiro Maeno
- High Pressure Protein Research Center; Institute of Advanced Technology; Kinki University; Wakayama Japan
| | - Kazumasa Sakurai
- High Pressure Protein Research Center; Institute of Advanced Technology; Kinki University; Wakayama Japan
| | | | | | - Kazuyuki Akasaka
- High Pressure Protein Research Center; Institute of Advanced Technology; Kinki University; Wakayama Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University; Kyoto Japan
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56
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Czerwoniec A, Kasprzak JM, Bytner P, Dobrychłop M, Bujnicki JM. Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome. FEBS Lett 2015; 589:2603-10. [PMID: 26226426 DOI: 10.1016/j.febslet.2015.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 01/02/2023]
Abstract
Mitochondrial pre-mRNAs in trypanosomatids undergo RNA editing to be converted into translatable mRNAs. The reaction is characterized by the insertion and deletion of uridine residues and is catalyzed by a macromolecular protein complex called the editosome. Despite intensive research, structural information for the majority of editosome proteins is still missing and no high resolution structure for the editosome exists. Here we present a comprehensive structural bioinformatics analysis of all proteins of the Trypanosoma brucei editosome. We specifically focus on the interplay between intrinsic order and disorder. According to computational predictions, editosome proteins involved in the basal reaction steps of the processing cycle are mostly ordered. By contrast, thirty percent of the amino acid content of the editosome is intrinsically disordered, which includes most prominently proteins with OB-fold domains. Based on the data we suggest a functional model, in which the structurally disordered domains of the complex are correlated with the RNA binding and RNA unfolding activity of the T. brucei editosome.
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Affiliation(s)
- Anna Czerwoniec
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.
| | - Joanna M Kasprzak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Patrycja Bytner
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Mateusz Dobrychłop
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.
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57
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Suarez IP, Burdisso P, Benoit MPMH, Boisbouvier J, Rasia RM. Induced folding in RNA recognition by Arabidopsis thaliana DCL1. Nucleic Acids Res 2015; 43:6607-19. [PMID: 26101256 PMCID: PMC4513881 DOI: 10.1093/nar/gkv627] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/07/2015] [Indexed: 11/25/2022] Open
Abstract
DCL1 is the ribonuclease that carries out miRNA biogenesis in plants. The enzyme has two tandem double stranded RNA binding domains (dsRBDs) in its C-terminus. Here we show that the first of these domains binds precursor RNA fragments when isolated and cooperates with the second domain in the recognition of substrate RNA. Remarkably, despite showing RNA binding activity, this domain is intrinsically disordered. We found that it acquires a folded conformation when bound to its substrate, being the first report of a complete dsRBD folding upon binding. The free unfolded form shows tendency to adopt folded conformations, and goes through an unfolded bound state prior to the folding event. The significance of these results is discussed by comparison with the behavior of other dsRBDs.
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Affiliation(s)
- Irina P Suarez
- Instituto de Biología Molecular y Celular de Rosario. 27 de Febrero 210 bis, predio CCT, 2000 Rosario, Argentina Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Suipacha 531, 2000 Rosario, Argentina
| | - Paula Burdisso
- Instituto de Biología Molecular y Celular de Rosario. 27 de Febrero 210 bis, predio CCT, 2000 Rosario, Argentina Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Suipacha 531, 2000 Rosario, Argentina
| | - Matthieu P M H Benoit
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France Université Joseph Fourier - Grenoble 1, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
| | - Jèrôme Boisbouvier
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France Université Joseph Fourier - Grenoble 1, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
| | - Rodolfo M Rasia
- Instituto de Biología Molecular y Celular de Rosario. 27 de Febrero 210 bis, predio CCT, 2000 Rosario, Argentina Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Suipacha 531, 2000 Rosario, Argentina
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58
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Latysheva NS, Flock T, Weatheritt RJ, Chavali S, Babu MM. How do disordered regions achieve comparable functions to structured domains? Protein Sci 2015; 24:909-22. [PMID: 25752799 PMCID: PMC4456105 DOI: 10.1002/pro.2674] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
The traditional structure to function paradigm conceives of a protein's function as emerging from its structure. In recent years, it has been established that unstructured, intrinsically disordered regions (IDRs) in proteins are equally crucial elements for protein function, regulation and homeostasis. In this review, we provide a brief overview of how IDRs can perform similar functions to structured proteins, focusing especially on the formation of protein complexes and assemblies and the mediation of regulated conformational changes. In addition to highlighting instances of such functional equivalence, we explain how differences in the biological and physicochemical properties of IDRs allow them to expand the functional and regulatory repertoire of proteins. We also discuss studies that provide insights into how mutations within functional regions of IDRs can lead to human diseases.
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Affiliation(s)
| | - Tilman Flock
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | | | - Sreenivas Chavali
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
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59
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Kong X, Liu J, Li L, Yue L, Zhang L, Jiang H, Xie X, Luo C. Functional interplay between the RK motif and linker segment dictates Oct4-DNA recognition. Nucleic Acids Res 2015; 43:4381-92. [PMID: 25870414 PMCID: PMC4482079 DOI: 10.1093/nar/gkv323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 03/30/2015] [Indexed: 01/20/2023] Open
Abstract
The POU family transcription factor Oct4 plays pivotal roles in regulating pluripotency and somatic cell reprogramming. Previous studies have indicated an important role for major groove contacts in Oct4–DNA recognition; however, the contributions of the RK motif in the POUh domain and the linker segment joining the two DNA-binding domains remain poorly understood. Here, by combining molecular modelling and functional assays, we find that the RK motif is essential for Oct4–DNA association by recognizing the narrowed DNA minor groove. Intriguingly, computational simulations reveal that the function of the RK motif may be finely tuned by H-bond interactions with the partially disordered linker segment and that breaking these interactions significantly enhances the DNA binding and reprogramming activities of Oct4. These findings uncover a self-regulatory mechanism for specific Oct4–DNA recognition and provide insights into the functional crosstalk at the molecular level that may illuminate mechanistic studies of the Oct protein family and possibly transcription factors in the POU family. Our gain-of-function Oct4 mutants might also be useful tools for use in reprogramming and regenerative medicine.
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Affiliation(s)
- Xiangqian Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Liu
- Chinese Academy of Sciences Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lianchun Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Liyan Yue
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lihong Zhang
- Chinese Academy of Sciences Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xin Xie
- Chinese Academy of Sciences Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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60
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A critical evaluation of in silico methods for detection of membrane protein intrinsic disorder. Biophys J 2014; 106:1638-49. [PMID: 24739163 DOI: 10.1016/j.bpj.2014.02.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/03/2014] [Accepted: 02/25/2014] [Indexed: 11/23/2022] Open
Abstract
Intrinsically disordered regions in proteins possess important biological roles including transcriptional regulation, molecular recognition, and provision of sites for posttranslational modification. In three-dimensional crystallization of both soluble and membrane proteins, identification and removal of disordered regions is often necessary for obtaining crystals possessing sufficient long-range order for structure determination. Disordered regions can be identified experimentally, with techniques such as limited proteolysis coupled with mass spectrometry, or computationally, by using disorder prediction programs, of which many are available. Although these programs use various methods to predict disorder from a protein's primary sequence, they all were developed using information derived from soluble protein structures. Therefore, their performance and accuracy when applied to integral membrane proteins remained an open question. We evaluated the performance of 13 disorder prediction programs on a dataset containing 343 membrane proteins, and upon subdatasets containing only α-helical or β-barrel proteins. These programs were ranked using multiple metrics, including metrics specifically created for membrane proteins. Analysis of these data shows a clear distinction between programs that accurately predict disordered regions in membrane proteins and programs which perform poorly, and allows for the robust integration of in silico disorder prediction into our PSI:Biology membrane protein structural genomics pipeline.
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61
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Preitner N, Quan J, Nowakowski DW, Hancock ML, Shi J, Tcherkezian J, Young-Pearse TL, Flanagan JG. APC is an RNA-binding protein, and its interactome provides a link to neural development and microtubule assembly. Cell 2014; 158:368-382. [PMID: 25036633 DOI: 10.1016/j.cell.2014.05.042] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/23/2014] [Accepted: 05/28/2014] [Indexed: 01/12/2023]
Abstract
Adenomatous polyposis coli (APC) is a microtubule plus-end scaffolding protein important in biology and disease. APC is implicated in RNA localization, although the mechanisms and functional significance remain unclear. We show APC is an RNA-binding protein and identify an RNA interactome by HITS-CLIP. Targets were highly enriched for APC-related functions, including microtubule organization, cell motility, cancer, and neurologic disease. Among the targets is β2B-tubulin, known to be required in human neuron and axon migration. We show β2B-tubulin is synthesized in axons and localizes preferentially to dynamic microtubules in the growth cone periphery. APC binds the β2B-tubulin 3' UTR; experiments interfering with this interaction reduced β2B-tubulin mRNA axonal localization and expression, depleted dynamic microtubules and the growth cone periphery, and impaired neuron migration. These results identify APC as a platform binding functionally related protein and RNA networks, and suggest a self-organizing model for the microtubule to localize synthesis of its own subunits.
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Affiliation(s)
- Nicolas Preitner
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Jie Quan
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Dan W Nowakowski
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Melissa L Hancock
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Jianhua Shi
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph Tcherkezian
- Laboratory for Therapeutic Development, Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Tracy L Young-Pearse
- Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John G Flanagan
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA.
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62
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Mallik S, Kundu S. Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation. J Biomol Struct Dyn 2014; 33:639-56. [PMID: 24697502 DOI: 10.1080/07391102.2014.900457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein-rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.
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Affiliation(s)
- Saurav Mallik
- a Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, APC Road, Kolkata 700009 , India
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63
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Tayal N, Choudhary P, Pandit SB, Sandhu KS. Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions. MOLECULAR BIOSYSTEMS 2014; 10:1469-80. [PMID: 24668165 DOI: 10.1039/c3mb70539k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite recent advances, it is yet not clear how intrinsically disordered regions in proteins recognize their targets without any defined structures. Short linear motifs had been proposed to mediate molecular recognition by disordered regions; however, the underlying structural prerequisite remains elusive. Moreover, the role of short linear motifs in DNA recognition has not been studied. We report a repertoire of short evolutionarily Conserved Recognition Elements (CoREs) in long intrinsically disordered regions, which have very distinct amino-acid propensities from those of known motifs, and exhibit a strong tendency to retain their three-dimensional conformations compared to adjacent regions. The majority of CoREs directly interact with the DNA in the available 3D structures, which is further supported by literature evidence, analyses of ΔΔG values of DNA-binding energies and threading-based prediction of DNA binding potential. CoREs were enriched in cancer-associated missense mutations, further strengthening their functional nature. Significant enrichment of glycines in CoREs and the preference of glycyl ϕ-Ψ values within the left-handed bridge range in the l-disallowed region of the Ramachandran plot suggest that Gly-to-nonGly mutations within CoREs might alter the backbone conformation and consequently the function, a hypothesis that we reconciled using available mutation data. We conclude that CoREs might serve as bait for DNA recognition by long disordered regions and that certain mutations in these peptides can disrupt their DNA binding potential and consequently the protein function. We further hypothesize that the preferred conformations of CoREs and of glycyl residues therein might play an important role in DNA binding. The highly ordered nature of CoREs hints at a therapeutic strategy to inhibit malicious molecular interactions using small molecules mimicking CoRE conformations.
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Affiliation(s)
- Nitish Tayal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) - Mohali, Knowledge City, Sector-81, SAS Nagar, Mohali 140306, India.
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64
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Chang CK, Hou MH, Chang CF, Hsiao CD, Huang TH. The SARS coronavirus nucleocapsid protein--forms and functions. Antiviral Res 2014; 103:39-50. [PMID: 24418573 PMCID: PMC7113676 DOI: 10.1016/j.antiviral.2013.12.009] [Citation(s) in RCA: 337] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/08/2013] [Accepted: 12/20/2013] [Indexed: 12/14/2022]
Abstract
Coronavirus N proteins share the same modular organization. Structures of SARS-CoV N protein provide insight into nucleocapsid formation. N protein binds to nucleic acid at multiple sites in a coupled-allostery manner. A RNP packaging model highlighting the importance of disorder and modularity is proposed.
The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. It is a protein with multifarious activities. In this article we will review our current understanding of the N protein structure and its interaction with nucleic acid. Highlights of the progresses include uncovering the modular organization, determining the structures of the structural domains, realizing the roles of protein disorder in protein–protein and protein–nucleic acid interactions, and visualizing the ribonucleoprotein (RNP) structure inside the virions. It was also demonstrated that N-protein binds to nucleic acid at multiple sites with a coupled-allostery manner. We propose a SARS-CoV RNP model that conforms to existing data and bears resemblance to the existing RNP structures of RNA viruses. The model highlights the critical role of modular organization and intrinsic disorder of the N protein in the formation and functions of the dynamic RNP capsid in RNA viruses. This paper forms part of a symposium in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Ming-Hon Hou
- Department of Life Science, National Chung Hsing University, Taichung 40254, Taiwan, ROC
| | - Chi-Fon Chang
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Tai-huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC; The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC; Department of Physics, National Taiwan Normal University, Taipei 11677, Taiwan, ROC.
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65
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Tan C, Li W, Wang W. Localized frustration and binding-induced conformational change in recognition of 5S RNA by TFIIIA zinc finger. J Phys Chem B 2013; 117:15917-25. [PMID: 24266699 DOI: 10.1021/jp4052165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein TFIIIA is composed of nine tandemly arranged Cys2His2 zinc fingers. It can bind either to the 5S RNA gene as a transcription factor or to the 5S RNA transcript as a chaperone. Although structural and biochemical data provided valuable information on the recognition between the TFIIIIA and the 5S DNA/RNA, the involved conformational motions and energetic factors contributing to the binding affinity and specificity remain unclear. In this work, we conducted MD simulations and MM/GBSA calculations to investigate the binding-induced conformational changes in the recognition of the 5S RNA by the central three zinc fingers of TFIIIA and the energetic factors that influence the binding affinity and specificity at an atomistic level. Our results revealed drastic interdomain conformational changes between these three zinc fingers, involving the exposure/burial of several crucial DNA/RNA binding residues, which can be related to the competition between DNA and RNA for the binding of TFIIIA. We also showed that the specific recognition between finger 4/finger 6 and the 5S RNA introduces frustrations to the nonspecific interactions between finger 5 and the 5S RNA, which may be important to achieve optimal binding affinity and specificity.
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Affiliation(s)
- Cheng Tan
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing, Jiangsu 210093, China
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Baker CM, Best RB. Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013; 4:182-198. [PMID: 34354764 DOI: 10.1002/wcms.1167] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well-defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, with approximately 20% of all eukaryotic proteins disordered, and found at the heart of many biochemical networks. To fulfil their biological roles, many IDPs need to bind to proteins and/or nucleic acids. And while unstructured in solution, IDPs typically fold into a well-defined three-dimensional structure upon interaction with a binding partner. The flexibility and structural diversity inherent to IDPs makes this coupled folding and binding difficult to study at atomic resolution by experiment alone, and computer simulation currently offers perhaps the best opportunity to understand this process. But simulation of coupled folding and binding is itself extremely challenging; these molecules are large and highly flexible, and their binding partners, such as DNA or cyclins, are also often large. Therefore, their study requires either or both simplified representations and advanced enhanced sampling schemes. It is not always clear that existing simulation techniques, optimized for studying folded proteins, are well-suited to IDPs. In this article, we examine the progress that has been made in the study of coupled folding and binding using molecular dynamics simulation. We summarise what has been learnt, and examine the state of the art in terms of both methodologies and models. We also consider the lessons to be learnt from advances in other areas of simulation and highlight the issues that remain of be addressed.
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Affiliation(s)
- Christopher M Baker
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM. Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr Opin Struct Biol 2013; 23:443-50. [DOI: 10.1016/j.sbi.2013.03.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/19/2013] [Accepted: 03/25/2013] [Indexed: 12/31/2022]
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Sunami T, Kono H. Local conformational changes in the DNA interfaces of proteins. PLoS One 2013; 8:e56080. [PMID: 23418514 PMCID: PMC3571985 DOI: 10.1371/journal.pone.0056080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/03/2013] [Indexed: 11/18/2022] Open
Abstract
When a protein binds to DNA, a conformational change is often induced so that the protein will fit into the DNA structure. Therefore, quantitative analyses were conducted to understand the conformational changes in proteins. The results showed that conformational changes in DNA interfaces are more frequent than in non-interfaces, and DNA interfaces have more conformational variations in the DNA-free form. As expected, the former indicates that interaction with DNA has some influence on protein structure. The latter suggests that the intrinsic conformational flexibility of DNA interfaces is important for adjusting their conformation for DNA. The amino acid propensities of the conformationally changed regions in DNA interfaces indicate that hydrophilic residues are preferred over the amino acids that appear in the conformationally unchanged regions. This trend is true for disordered regions, suggesting again that intrinsic flexibility is of importance not only for DNA binding but also for interactions with other molecules. These results demonstrate that fragments destined to be DNA interfaces have an intrinsic flexibility and are composed of amino acids with the capability of binding to DNA. This information suggests that the prediction of DNA binding sites may be improved by the integration of amino acid preference for DNA and one for disordered regions.
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Affiliation(s)
- Tomoko Sunami
- Molecular Modeling and Simulation Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kizugawa, Kyoto, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kizugawa, Kyoto, Japan
- * E-mail:
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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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Abstract
Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics.
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Affiliation(s)
| | - Jan Attig
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Abstract
Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics.
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Espinoza-Fonseca LM. Dynamic optimization of signal transduction via intrinsic disorder. MOLECULAR BIOSYSTEMS 2011; 8:194-7. [PMID: 22080214 DOI: 10.1039/c1mb05412k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
It is widely accepted that the inherent flexibility of intrinsically disordered proteins (IDPs) correlates with essential functions in the cell such as signaling. However, the mechanisms by which disorder dynamically facilitates and optimizes signal transduction remain unclear. In this study, we have used a computational protocol to evaluate the interplay between the intrinsic disorder of p27(kip1) and the collective motions of its binding partners, cyclin dependent kinase 2 (CDK2) and cyclin A (CA). We found that the synergy between intrinsic disorder of p27(kip1) and the essential collective motions of the CDK2-CA complex introduces a set of sequential steps to dynamically optimize signal transduction. Our observations indicate that optimized p27(kip1)-mediated signaling originates from a combination of adaptive folding, and the cooperativity between its residual disorder and the functional collective motions of the CDK2-CA complex.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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