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Pal S, Chattopadhyay A. Extramembranous Regions in G Protein-Coupled Receptors: Cinderella in Receptor Biology? J Membr Biol 2019; 252:483-497. [DOI: 10.1007/s00232-019-00092-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
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52
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Mitra G. Application of native mass spectrometry in studying intrinsically disordered proteins: A special focus on neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140260. [PMID: 31382021 DOI: 10.1016/j.bbapap.2019.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022]
Abstract
Intrinsically disordered proteins (IDPs) are integral part of the proteome, regulating vital biological processes. Such proteins gained further visibility due to their key role in neurodegenerative diseases and cancer. IDPs however, escape structural characterization by traditional biophysical tools owing to their extreme flexibility and heterogeneity. In this review, we discuss the advantages of native mass spectrometry (MS) in analysing the atypical conformational dynamics of IDPs and recent advances made in the field. Especially, MS studies unravelling the conformational facets of IDPs involved in neurodegenerative diseases are highlighted. The limitations and the future promises of native MS while studying IDPs have been discussed.
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Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore 560034, Karnataka, India.
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53
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Entropy and Information within Intrinsically Disordered Protein Regions. ENTROPY 2019; 21:e21070662. [PMID: 33267376 PMCID: PMC7515160 DOI: 10.3390/e21070662] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs) note the high entropy at individual sequence positions and in conformations sampled in solution. This prevents application of the canonical sequence-structure-function paradigm to IDRs and motivates the development of new methods to extract information from IDR sequences. We argue that the information in IDR sequences cannot be fully revealed through positional conservation, which largely measures stable structural contacts and interaction motifs. Instead, considerations of evolutionary conservation of molecular features can reveal the full extent of information in IDRs. Experimental quantification of the large conformational entropy of IDRs is challenging but can be approximated through the extent of conformational sampling measured by a combination of NMR spectroscopy and lower-resolution structural biology techniques, which can be further interpreted with simulations. Conformational entropy and other biophysical features can be modulated by post-translational modifications that provide functional advantages to IDRs by tuning their energy landscapes and enabling a variety of functional interactions and modes of regulation. The diverse mosaic of functional states of IDRs and their conformational features within complexes demands novel metrics of information, which will reflect the complicated sequence-conformational ensemble-function relationship of IDRs.
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54
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He H, Zhao J, Sun G. Prediction of MoRFs in Protein Sequences with MLPs Based on Sequence Properties and Evolution Information. ENTROPY 2019; 21:e21070635. [PMID: 33267349 PMCID: PMC7515128 DOI: 10.3390/e21070635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/26/2019] [Accepted: 06/26/2019] [Indexed: 02/03/2023]
Abstract
Molecular recognition features (MoRFs) are one important type of intrinsically disordered proteins functional regions that can undergo a disorder-to-order transition through binding to their interaction partners. Prediction of MoRFs is crucial, as the functions of MoRFs are associated with many diseases and can therefore become the potential drug targets. In this paper, a method of predicting MoRFs is developed based on the sequence properties and evolutionary information. To this end, we design two distinct multi-layer perceptron (MLP) neural networks and present a procedure to train them. We develop a preprocessing process which exploits different sizes of sliding windows to capture various properties related to MoRFs. We then use the Bayes rule together with the outputs of two trained MLP neural networks to predict MoRFs. In comparison to several state-of-the-art methods, the simulation results show that our method is competitive.
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55
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Munshi S, Subramanian S, Ramesh S, Golla H, Kalivarathan D, Kulkarni M, Campos LA, Sekhar A, Naganathan AN. Engineering Order and Cooperativity in a Disordered Protein. Biochemistry 2019; 58:2389-2397. [PMID: 31002232 DOI: 10.1021/acs.biochem.9b00182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Structural disorder in proteins arises from a complex interplay between weak hydrophobicity and unfavorable electrostatic interactions. The extent to which the hydrophobic effect contributes to the unique and compact native state of proteins is, however, confounded by large compensation between multiple entropic and energetic terms. Here we show that protein structural order and cooperativity arise as emergent properties upon hydrophobic substitutions in a disordered system with non-intuitive effects on folding and function. Aided by sequence-structure analysis, equilibrium, and kinetic spectroscopic studies, we engineer two hydrophobic mutations in the disordered DNA-binding domain of CytR that act synergistically, but not in isolation, to promote structure, compactness, and stability. The double mutant, with properties of a fully ordered domain, exhibits weak cooperativity with a complex and rugged conformational landscape. The mutant, however, binds cognate DNA with an affinity only marginally higher than that of the wild type, though nontrivial differences are observed in the binding to noncognate DNA. Our work provides direct experimental evidence of the dominant role of non-additive hydrophobic effects in shaping the molecular evolution of order in disordered proteins and vice versa, which could be generalized to even folded proteins with implications for protein design and functional manipulation.
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Affiliation(s)
- Sneha Munshi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Sandhyaa Subramanian
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Samyuktha Ramesh
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Hemashree Golla
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Divakar Kalivarathan
- Department of Biotechnology , National Institute of Technology Warangal , Warangal 506004 , India
| | - Madhurima Kulkarni
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - Luis A Campos
- National Biotechnology Center , Consejo Superior de Investigaciones Científicas , Darwin 3, Campus de Cantoblanco , 28049 Madrid , Spain
| | - Ashok Sekhar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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56
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Charon J, Barra A, Walter J, Millot P, Hébrard E, Moury B, Michon T. First Experimental Assessment of Protein Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process. Mol Biol Evol 2019; 35:38-49. [PMID: 29029259 PMCID: PMC5850501 DOI: 10.1093/molbev/msx249] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Intrinsic disorder (ID) in proteins is defined as a lack of stable structure in physiological conditions. Intrinsically disordered regions (IDRs) are highly abundant in some RNA virus proteomes. Low topological constraints exerted on IDRs are expected to buffer the effect of numerous deleterious mutations and could be related to the remarkable adaptive potential of RNA viruses to overcome resistance of their host. To experimentally test this hypothesis in a natural pathosystem, a set of four variants of Potato virus Y (PVY; Potyvirus genus) containing various ID degrees in the Viral genome-linked (VPg) protein, a key determinant of potyvirus adaptation, was designed. To estimate the ID contribution to the VPg-based PVY adaptation, the adaptive ability of the four PVY variants was monitored in the pepper host (Capsicum annuum) carrying a recessive resistance gene. Intriguingly, the two mutants with the highest ID content displayed a significantly higher ability to restore infection in the resistant host, whereas the less intrinsically disordered mutant was unable to restore infection. The role of ID on virus adaptation may be due either to a larger exploration of evolutionary pathways or the minimization of fitness penalty caused by resistance-breaking mutations. This pioneering study strongly suggests the positive impact of ID in an RNA virus adaptive capacity.
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Affiliation(s)
- Justine Charon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France.,CNRS 5320, INSERM U1212, Pessac, France
| | - Amandine Barra
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France
| | - Jocelyne Walter
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France
| | | | - Eugénie Hébrard
- UMR Interactions Plantes-Microorganismes-Environnement, IRD, CIRAD, Université de Montpellier, Montpellier, France
| | | | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France
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57
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Dean S, Moreira-Leite F, Gull K. Basalin is an evolutionarily unconstrained protein revealed via a conserved role in flagellum basal plate function. eLife 2019; 8:42282. [PMID: 30810527 PMCID: PMC6392502 DOI: 10.7554/elife.42282] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/11/2019] [Indexed: 01/15/2023] Open
Abstract
Most motile flagella have an axoneme that contains nine outer microtubule doublets and a central pair (CP) of microtubules. The CP coordinates the flagellar beat and defects in CP projections are associated with motility defects and human disease. The CP nucleate near a ‘basal plate’ at the distal end of the transition zone (TZ). Here, we show that the trypanosome TZ protein ‘basalin’ is essential for building the basal plate, and its loss is associated with CP nucleation defects, inefficient recruitment of CP assembly factors to the TZ, and flagellum paralysis. Guided by synteny, we identified a highly divergent basalin ortholog in the related Leishmania species. Basalins are predicted to be highly unstructured, suggesting they may act as ‘hubs’ facilitating many protein-protein interactions. This raises the general concept that proteins involved in cytoskeletal functions and appearing organism-specific, may have highly divergent and cryptic orthologs in other species.
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Affiliation(s)
- Samuel Dean
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Flavia Moreira-Leite
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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58
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Walter J, Charon J, Hu Y, Lachat J, Leger T, Lafforgue G, Barra A, Michon T. Comparative analysis of mutational robustness of the intrinsically disordered viral protein VPg and of its interactor eIF4E. PLoS One 2019; 14:e0211725. [PMID: 30763345 PMCID: PMC6375565 DOI: 10.1371/journal.pone.0211725] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/20/2019] [Indexed: 01/02/2023] Open
Abstract
Conformational intrinsic disorder is a feature present in many virus proteins. Intrinsically disordered regions (IDRs) have weaker structural requirement than ordered regions and mutations in IDRs could have a lower impact on the virus fitness. This could favor its exploration of adaptive solutions. The potyviral protein VPg contains IDRs with determinants for adaptation to its host plant. To experimentally assess whether IDRs are more resistant to mutations than ordered regions, the biologically relevant interaction between mutant libraries of both VPg and the eukaryotic translation initiation factor 4E (eIF4E) and their respective wild type partner was examined using yeast two hybrid assay. Our data shows that VPg is significantly more robust to mutations than eIF4E and as such belongs to a particular class of intrinsically disordered proteins. This result is discussed from the standpoint of IDRs involvement in the virus adaptive processes.
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Affiliation(s)
- Jocelyne Walter
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
- * E-mail: (JW); (TM)
| | - Justine Charon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yihua Hu
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Joy Lachat
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Thomas Leger
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Guillaume Lafforgue
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Amandine Barra
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
- * E-mail: (JW); (TM)
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59
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Myers N, Olender T, Savidor A, Levin Y, Reuven N, Shaul Y. The Disordered Landscape of the 20S Proteasome Substrates Reveals Tight Association with Phase Separated Granules. Proteomics 2018; 18:e1800076. [PMID: 30039638 DOI: 10.1002/pmic.201800076] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/28/2018] [Indexed: 12/11/2022]
Abstract
Proteasomal degradation is the main route of regulated proteostasis. The 20S proteasome is the core particle (CP) responsible for the catalytic activity of all proteasome complexes. Structural constraints mean that only unfolded, extended polypeptide chains may enter the catalytic core of the 20S proteasome. It has been previously shown that the 20S CP is active in degradation of certain intrinsically disordered proteins (IDP) lacking structural constrains. Here, a comprehensive analysis of the 20S CP substrates in vitro is conducted. It is revealed that the 20S CP substrates are highly disordered. However, not all the IDPs are 20S CP substrates. The group of the IDPs that are 20S CP substrates, termed 20S-IDPome are characterized by having significantly more protein binding partners, more posttranslational modification sites, and are highly enriched for RNA binding proteins. The vast majority of them are involved in splicing, mRNA processing, and translation. Remarkably, it is found that low complexity proteins with prion-like domain (PrLD), which interact with GR or PR di-peptide repeats, are the most preferential 20S CP substrates. The finding suggests roles of the 20S CP in gene transcription and formation of phase-separated granules.
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Affiliation(s)
- Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
| | - Alon Savidor
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
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60
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Hosp F, Gutiérrez-Ángel S, Schaefer MH, Cox J, Meissner F, Hipp MS, Hartl FU, Klein R, Dudanova I, Mann M. Spatiotemporal Proteomic Profiling of Huntington's Disease Inclusions Reveals Widespread Loss of Protein Function. Cell Rep 2018; 21:2291-2303. [PMID: 29166617 PMCID: PMC5714591 DOI: 10.1016/j.celrep.2017.10.097] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/13/2017] [Accepted: 10/24/2017] [Indexed: 01/08/2023] Open
Abstract
Aggregation of polyglutamine-expanded huntingtin exon 1 (HttEx1) in Huntington’s disease (HD) proceeds from soluble oligomers to late-stage inclusions. The nature of the aggregates and how they lead to neuronal dysfunction is not well understood. We employed mass spectrometry (MS)-based quantitative proteomics to dissect spatiotemporal mechanisms of neurodegeneration using the R6/2 mouse model of HD. Extensive remodeling of the soluble brain proteome correlated with insoluble aggregate formation during disease progression. In-depth and quantitative characterization of the aggregates uncovered an unprecedented complexity of several hundred proteins. Sequestration to aggregates depended on protein expression levels and sequence features such as low-complexity regions or coiled-coil domains. In a cell-based HD model, overexpression of a subset of the sequestered proteins in most cases rescued viability and reduced aggregate size. Our spatiotemporally resolved proteome resource of HD progression indicates that widespread loss of cellular protein function contributes to aggregate-mediated toxicity. Spatiotemporally resolved brain proteome of wild-type and HD mice Quantitative characterization of huntingtin inclusion bodies in vivo Sequestration correlates with protein expression levels and specific sequence features Resupplying sequestered proteins ameliorates HTT-induced toxicity and inclusion size
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Affiliation(s)
- Fabian Hosp
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Sara Gutiérrez-Ángel
- Department Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin H Schaefer
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Jürgen Cox
- Computational Systems Biochemistry Laboratory, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Felix Meissner
- Experimental Systems Immunology Laboratory, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Mark S Hipp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - F-Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Rüdiger Klein
- Department Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Irina Dudanova
- Department Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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61
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Jamsheer K M, Shukla BN, Jindal S, Gopan N, Mannully CT, Laxmi A. The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions. J Biol Chem 2018; 293:13134-13150. [PMID: 29945970 DOI: 10.1074/jbc.ra118.002073] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/05/2018] [Indexed: 11/06/2022] Open
Abstract
The SNF1-related protein kinase 1 (SnRK1) is a heterotrimeric eukaryotic kinase that interacts with diverse proteins and regulates their activity in response to starvation and stress signals. Recently, the FCS-like zinc finger (FLZ) proteins were identified as a potential scaffold for SnRK1 in plants. However, the evolutionary and mechanistic aspect of this complex formation is currently unknown. Here, in silico analyses predicted that FLZ proteins possess conserved intrinsically disordered regions (IDRs) with a propensity for protein binding in the N and C termini across the plant lineage. We observed that the Arabidopsis FLZ proteins promiscuously interact with SnRK1 subunits, which formed different isoenzyme complexes. The FLZ domain was essential for mediating the interaction with SnRK1α subunits, whereas the IDRs in the N termini facilitated interactions with the β and βγ subunits of SnRK1. Furthermore, the IDRs in the N termini were important for mediating dimerization of different FLZ proteins. Of note, the interaction of FLZ with SnRK1 was confined to cytoplasmic foci, which colocalized with the endoplasmic reticulum. An evolutionary analysis revealed that in general, the IDR-rich regions are under more relaxed selection than the FLZ domain. In summary, the findings in our study reveal the structural details, origin, and evolution of a land plant-specific scaffold of SnRK1 formed by the coordinated actions of IDRs and structured regions in the FLZ proteins. We propose that the FLZ protein complex might be involved in providing flexibility, thus enhancing the binding repertoire of the SnRK1 hub in land plants.
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Affiliation(s)
- Muhammed Jamsheer K
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
| | - Brihaspati N Shukla
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
| | - Sunita Jindal
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
| | - Nandu Gopan
- the Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru-560064, India
| | | | - Ashverya Laxmi
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
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62
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Roy D, Rajyaguru PI. Suppressor of clathrin deficiency (Scd6)-An emerging RGG-motif translation repressor. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1479. [DOI: 10.1002/wrna.1479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Debadrita Roy
- Department of Biochemistry; Indian Institute of Science; Bangalore India
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63
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Banerjee S, Chakraborty S. Protein intrinsic disorder negatively associates with gene age in different eukaryotic lineages. MOLECULAR BIOSYSTEMS 2018; 13:2044-2055. [PMID: 28783193 DOI: 10.1039/c7mb00230k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of new protein-coding genes in a specific lineage or species provides raw materials for evolutionary adaptations. Until recently, the biology of new genes emerging particularly from non-genic sequences remained unexplored. Although the new genes are subjected to variable selection pressure and face rapid deletion, some of them become functional and are retained in the gene pool. To acquire functional novelties, new genes often get integrated into the pre-existing ancestral networks. However, the mechanism by which young proteins acquire novel interactions remains unanswered till date. Since structural orientation contributes hugely to the mode of proteins' physical interactions, in this regard, we put forward an interesting question - Do new genes encode proteins with stable folds? Addressing the question, we demonstrated that the intrinsic disorder inversely correlates with the evolutionary gene ages - i.e. young proteins are richer in intrinsic disorder than the ancient ones. We further noted that young proteins, which are initially poorly connected hubs, prefer to be structurally more disordered than well-connected ancient proteins. The phenomenon strikingly defies the usual trend of well-connected proteins being highly disordered in structure. We justified that structural disorder might help poorly connected young proteins to undergo promiscuous interactions, which provides the foundation for novel protein interactions. The study focuses on the evolutionary perspectives of young proteins in the light of structural adaptations.
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Affiliation(s)
- Sanghita Banerjee
- Machine Intelligence Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata 700108, India.
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64
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Pujols J, Santos J, Pallarès I, Ventura S. The Disordered C-Terminus of Yeast Hsf1 Contains a Cryptic Low-Complexity Amyloidogenic Region. Int J Mol Sci 2018; 19:ijms19051384. [PMID: 29734798 PMCID: PMC5983738 DOI: 10.3390/ijms19051384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 02/08/2023] Open
Abstract
Response mechanisms to external stress rely on networks of proteins able to activate specific signaling pathways to ensure the maintenance of cell proteostasis. Many of the proteins mediating this kind of response contain intrinsically disordered regions, which lack a defined structure, but still are able to interact with a wide range of clients that modulate the protein function. Some of these interactions are mediated by specific short sequences embedded in the longer disordered regions. Because the physicochemical properties that promote functional and abnormal interactions are similar, it has been shown that, in globular proteins, aggregation-prone and binding regions tend to overlap. It could be that the same principle applies for disordered protein regions. In this context, we show here that a predicted low-complexity interacting region in the disordered C-terminus of the stress response master regulator heat shock factor 1 (Hsf1) protein corresponds to a cryptic amyloid region able to self-assemble into fibrillary structures resembling those found in neurodegenerative disorders.
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Affiliation(s)
- Jordi Pujols
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
| | - Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
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65
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Abstract
Intracellular environments are heterogeneous milieus comprised of macromolecules, osmolytes, and a range of assemblies that include membrane-bound organelles and membraneless biomolecular condensates. The latter are nonstoichiometric assemblies of protein and RNA molecules. They represent distinct phases and form via intracellular phase transitions. Here, we present insights from recent studies and provide a perspective on how phase transitions that lead to biomolecular condensates might contribute to cellular functions.
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Affiliation(s)
- Alex S. Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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66
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Li XH, Chavali PL, Pancsa R, Chavali S, Babu MM. Function and Regulation of Phase-Separated Biological Condensates. Biochemistry 2018; 57:2452-2461. [PMID: 29392932 DOI: 10.1021/acs.biochem.7b01228] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Achieving functional specificity while minimizing cost to fitness is a key constraint during evolution. Formation of biological condensates by liquid-liquid phase separation (LLPS) appears to serve as an important regulatory mechanism to generate moderate specificity in molecular recognition while maintaining a reasonable cost for fitness in terms of design complexity. Formation of biological condensates serves as a unique mechanism of molecular recognition achieving some level of specificity without a huge cost to fitness. Rapid formation of biological condensates in vivo induced by specific cellular or environmental triggers has been shown to be an important mechanism for increasing cellular fitness. Here we discuss the functions and regulation of biological condensates, especially those formed by LLPS, involving interactions between proteins and nucleic acids. These condensates are spatially isolated within the cytosol or nucleus and can facilitate specific biochemical functions under conditions such as stress. The misregulation of biological condensates resulting in nondynamic aggregates has been implicated in a number of diseases. Understanding the functional importance of biological condensates and their regulation opens doors for development of therapies targeting dysfunctional biological condensates, as well as spatiotemporal engineering of functions in cells.
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Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Pavithra L Chavali
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Rita Pancsa
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - M Madan Babu
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
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67
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Arbesú M, Iruela G, Fuentes H, Teixeira JMC, Pons M. Intramolecular Fuzzy Interactions Involving Intrinsically Disordered Domains. Front Mol Biosci 2018; 5:39. [PMID: 29761107 PMCID: PMC5936776 DOI: 10.3389/fmolb.2018.00039] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
Structural disorder is an essential ingredient for function in many proteins and protein complexes. Fuzzy complexes describe the many instances where disorder is maintained as a critical element of protein interactions. In this minireview we discuss how intramolecular fuzzy interactions function in signaling complexes. Focussing on the Src family of kinases, we argue that the intrinsically disordered domains that are unique for each of the family members and display a clear fingerprint of long range interactions in Src, might have critical roles as functional sensor or effectors and mediate allosteric communication via fuzzy interactions.
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Affiliation(s)
- Miguel Arbesú
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Guillermo Iruela
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Héctor Fuentes
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - João M C Teixeira
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Miquel Pons
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
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68
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Davies HM, Nofal SD, McLaughlin EJ, Osborne AR. Repetitive sequences in malaria parasite proteins. FEMS Microbiol Rev 2018; 41:923-940. [PMID: 29077880 DOI: 10.1093/femsre/fux046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
Five species of parasite cause malaria in humans with the most severe disease caused by Plasmodium falciparum. Many of the proteins encoded in the P. falciparum genome are unusually enriched in repetitive low-complexity sequences containing a limited repertoire of amino acids. These repetitive sequences expand and contract dynamically and are among the most rapidly changing sequences in the genome. The simplest repetitive sequences consist of single amino acid repeats such as poly-asparagine tracts that are found in approximately 25% of P. falciparum proteins. More complex repeats of two or more amino acids are also common in diverse parasite protein families. There is no universal explanation for the occurrence of repetitive sequences and it is possible that many confer no function to the encoded protein and no selective advantage or disadvantage to the parasite. However, there are increasing numbers of examples where repetitive sequences are important for parasite protein function. We discuss the diverse roles of low-complexity repetitive sequences throughout the parasite life cycle, from mediating protein-protein interactions to enabling the parasite to evade the host immune system.
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Affiliation(s)
- Heledd M Davies
- The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Stephanie D Nofal
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Emilia J McLaughlin
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Andrew R Osborne
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, Malet Street, London, WC1E 7HX, United Kingdom
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69
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Khare H, Dey D, Madhu C, Senapati D, Raghothama S, Govindaraju T, Ramakumar S. Conformational heterogeneity in tails of DNA-binding proteins is augmented by proline containing repeats. MOLECULAR BIOSYSTEMS 2017; 13:2531-2544. [PMID: 29104984 DOI: 10.1039/c7mb00412e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A cationic terminal extension or tail is a common feature of many DNA-binding proteins. We show that a particular type of tail rich in proline, alanine and lysine belongs to the class of 'flexible disorder' and consists of characteristic pentapeptide repeats. Our designed peptides, (AAKKA)1-4 and (PAKKA)1-4, represent the tails of several bacterial DNA-binding proteins. Enhanced conformational sampling of these representative peptides using accelerated molecular dynamic simulations supported by circular dichroism spectroscopy and nuclear magnetic resonance studies demonstrates the role of frequent and interspersed prolines in augmenting conformational heterogeneity of the peptide backbone. Analysis of circular variance of backbone dihedral angles indicates alternating regions of relative rigidity and flexibility along the peptide sequence due to prolines. Preferred placement of lysines in the regions of higher backbone flexibility might improve DNA-binding by conformational selection. Our results could be relevant for rational de novo design of disordered peptides.
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Affiliation(s)
- Harshavardhan Khare
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India.
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70
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Klinger M. A role for macromolecular crowding in off-target binding of therapeutic antibodies. Protein Eng Des Sel 2017; 30:489-494. [PMID: 28873984 DOI: 10.1093/protein/gzx035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/21/2017] [Indexed: 01/09/2023] Open
Abstract
The nonspecific binding of certain therapeutic antibodies to tissues or to soluble biomolecules can accelerate their clearance from the circulation and undermine their benefit to patients. This article proposes that tandem amino acid repeat sequences in antibody hypervariable segments, particularly the complementarity determining regions (CDRs), can enhance this off-target binding. This hypothesis is based on two sets of observations. First, in a limited number of cases, antibodies with clusters of amino acid repeats in their CDRs have significantly higher clearance rates in experimental animals than otherwise identical antibodies without the repeats. Second, tandem amino acid repeats are abundant in intracellular hub proteins where they appear to promote the promiscuous binding of these proteins to a wide variety of other molecules. These nonspecific hub protein interactions are highly favored by the intense macromolecular crowding that permeates the cytoplasm. A survey of the variable region sequences of 137 antibodies in various stages of development revealed that 26 have at least one CDR containing a cluster of three closely spaced amino acid repeats. If the overall hypothesis is valid, then it suggests strategies for site-directed mutagenesis to improve pharmacokinetic behavior and for the design of more reliable in vitro binding assays to predict off-target binding in vivo.
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Affiliation(s)
- Martin Klinger
- Hawk BioDiscovery, 7465 Highway 51, Sterrett, AL 35147, USA
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71
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Dabas P, Sweta K, Ekka M, Sharma N. Structure function characterization of the ELL Associated Factor (EAF) from Schizosaccharomyces pombe. Gene 2017; 641:117-128. [PMID: 29032152 DOI: 10.1016/j.gene.2017.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 10/07/2017] [Accepted: 10/11/2017] [Indexed: 01/03/2023]
Abstract
EAF (ELL Associated Factor) proteins interact with the transcription elongation factor, ELL (Eleven nineteen Lysine rich Leukemia) and enhance its ability to stimulate RNA polymerase II-mediated transcriptional elongation in vitro. Schizosaccharomyces pombe contains a single homolog of EAF (SpEAF), which is not essential for survival of S. pombe in contrast to its essential higher eukaryotic homologs. The physiological role of SpEAF is not well understood. In this study, we show that S. pombe EAF is important in regulating growth of S. pombe cells during normal growth conditions. Moreover, SpEAF is also essential for survival under conditions of DNA damage, while its deletion does not affect growth under environmental stress conditions. Our in vivo structure-function studies further demonstrate that while both the amino and carboxyl terminal domains of SpEAF possess the potential to activate transcription, only the amino terminal domain of SpEAF is involved in interaction with the S. pombe ELL protein. The carboxyl-terminus of SpEAF is required for rescue of the growth defect under normal and DNA damaging conditions that is associated with the absence of SpEAF. Using bioinformatics and circular dichroism spectroscopy, we show that the carboxyl-terminus of SpEAF has a disordered conformation. Furthermore, addition of trifluoroethanol triggered its transition from a disordered to α-helical conformation. Taken together, the results presented here identify novel structural and functional features of SpEAF protein, providing insights into how EAF proteins may enforce transcriptional control of gene expression.
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Affiliation(s)
- Preeti Dabas
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi 110078, India
| | - Kumari Sweta
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi 110078, India
| | - Mary Ekka
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Opp. Sukhdev Vihar Bus Depot, New Delhi, Delhi 110025, India
| | - Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi 110078, India.
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72
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Poissonnier A, Sanséau D, Le Gallo M, Malleter M, Levoin N, Viel R, Morere L, Penna A, Blanco P, Dupuy A, Poizeau F, Fautrel A, Seneschal J, Jouan F, Ritz J, Forcade E, Rioux N, Contin-Bordes C, Ducret T, Vacher AM, Barrow PA, Flynn RJ, Vacher P, Legembre P. CD95-Mediated Calcium Signaling Promotes T Helper 17 Trafficking to Inflamed Organs in Lupus-Prone Mice. Immunity 2017; 45:209-23. [PMID: 27438772 PMCID: PMC4961226 DOI: 10.1016/j.immuni.2016.06.028] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/10/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022]
Abstract
CD95 ligand (CD95L) is expressed by immune cells and triggers apoptotic death. Metalloprotease-cleaved CD95L (cl-CD95L) is released into the bloodstream but does not trigger apoptotic signaling. Hence, the pathophysiological role of cl-CD95L remains unclear. We observed that skin-derived endothelial cells from systemic lupus erythematosus (SLE) patients expressed CD95L and that after cleavage, cl-CD95L promoted T helper 17 (Th17) lymphocyte transmigration across the endothelial barrier at the expense of T regulatory cells. T cell migration relied on a direct interaction between the CD95 domain called calcium-inducing domain (CID) and the Src homology 3 domain of phospholipase Cγ1. Th17 cells stimulated with cl-CD95L produced sphingosine-1-phosphate (S1P), which promoted endothelial transmigration by activating the S1P receptor 3. We generated a cell-penetrating CID peptide that prevented Th17 cell transmigration and alleviated clinical symptoms in lupus mice. Therefore, neutralizing the CD95 non-apoptotic signaling pathway could be an attractive therapeutic approach for SLE treatment. CD95-mediated Ca2+ response promotes endothelial transmigration of Th17 cells CD95 interacts with PLCγ1 to induce Ca2+ response and Th17 cell migration Ca2+ response stems from a CD95 region different from death domain Inhibition of the CD95-mediated Ca2+ response alleviates disease in lupus-prone mice
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Affiliation(s)
- Amanda Poissonnier
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Doriane Sanséau
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Matthieu Le Gallo
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Marine Malleter
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; Biosit, Plateforme H2P2, Biogenouest, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Nicolas Levoin
- Bioprojet Biotech, Rue du Chesnay Beauregard, 35760 Saint-Grégoire, France
| | - Roselyne Viel
- Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; Biosit, Plateforme H2P2, Biogenouest, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Lucie Morere
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Aubin Penna
- Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; INSERM U1085, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Patrick Blanco
- Université de Bordeaux, CHU Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; CNRS UMR 5164, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Alain Dupuy
- Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; Centre Hospitalier Universitaire Rennes, 2 Rue Henri Le Guilloux, 35022 Rennes, France
| | - Florence Poizeau
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Centre Hospitalier Universitaire Rennes, 2 Rue Henri Le Guilloux, 35022 Rennes, France
| | - Alain Fautrel
- Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; Biosit, Plateforme H2P2, Biogenouest, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Julien Seneschal
- Université de Bordeaux, CHU Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; INSERM U1035, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Florence Jouan
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France
| | - Jerome Ritz
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Edouard Forcade
- Université de Bordeaux, CHU Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; CNRS UMR 5164, 146 Rue Léo Saignat, 33076 Bordeaux, France; Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Nathalie Rioux
- Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; INSERM U1085, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; INSERM U1035, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Cécile Contin-Bordes
- Université de Bordeaux, CHU Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; CNRS UMR 5164, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Thomas Ducret
- Université de Bordeaux, CHU Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; INSERM U1045, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Anne-Marie Vacher
- Université de Bordeaux, CHU Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; INSERM U1218, Institut Bergonié, 33076 Bordeaux, France
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire LE12 5RD, United Kingdom
| | - Robin J Flynn
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire LE12 5RD, United Kingdom
| | - Pierre Vacher
- Université de Bordeaux, CHU Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; INSERM U1218, Institut Bergonié, 33076 Bordeaux, France
| | - Patrick Legembre
- Centre Eugène Marquis, Rue Bataille Flandres Dunkerque, 35042 Rennes, France; INSERM ERL440-OSS, Equipe Labellisée, Ligue Contre Le Cancer, 35042 Rennes, France; Université de Rennes 1, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France; Biosit, Plateforme H2P2, Biogenouest, 2 Ave. du Prof. Léon Bernard, 35043 Rennes, France.
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73
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Ahrens JB, Nunez-Castilla J, Siltberg-Liberles J. Evolution of intrinsic disorder in eukaryotic proteins. Cell Mol Life Sci 2017; 74:3163-3174. [PMID: 28597295 PMCID: PMC11107722 DOI: 10.1007/s00018-017-2559-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/23/2022]
Abstract
Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.
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Affiliation(s)
- Joseph B Ahrens
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Janelle Nunez-Castilla
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA.
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74
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Hausrath AC, Kingston RL. Conditionally disordered proteins: bringing the environment back into the fold. Cell Mol Life Sci 2017; 74:3149-3162. [PMID: 28597298 PMCID: PMC11107710 DOI: 10.1007/s00018-017-2558-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
For many proteins, biological function requires the folding of the polypeptide chain into a unique and persistent tertiary structure. This review concerns proteins that adopt a specific tertiary structure to function, but are otherwise partially or completely disordered. The biological cue for protein folding is environmental perturbation or minor post-translational modification. Hence, we term these proteins conditionally disordered. Many of these proteins recognize and bind other molecules, and conditional disorder has been hypothesized to allow for more nuanced control and regulation of binding processes. However, this remains largely unproven. The sequences of conditionally disordered proteins suggest their propensity to fold; yet, under the standard laboratory conditions, they do not do so, which may appear surprising. We argue that the surprise results from the failure to consider the role of the environment in protein structure formation and that conditional disorder arises as a natural consequence of the marginal stability of the folded state.
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Affiliation(s)
- Andrew C Hausrath
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand.
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75
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Kosciolek T, Buchan DWA, Jones DT. Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions. Sci Rep 2017; 7:6999. [PMID: 28765603 PMCID: PMC5539115 DOI: 10.1038/s41598-017-07156-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/23/2017] [Indexed: 11/08/2022] Open
Abstract
Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human proteins estimated to have long disordered regions. Computational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fashion, not accounting for the structural heterogeneity present in disordered regions. Here, we present a new de novo method, FRAGFOLD-IDP, which addresses this problem. Using 200 protein structural ensembles derived from NMR, we show that FRAGFOLD-IDP achieves superior results compared to methods which can predict related data (NMR order parameter, or crystallographic B-factor). FRAGFOLD-IDP produces very good predictions for 33.5% of cases and helps to get a better insight into the dynamics of the disordered ensembles. The results also show it is not necessary to predict the correct fold of the protein to reliably predict per-residue fluctuations. It implies that disorder is a local property and it does not depend on the fold. Our results are orthogonal to DynaMine, the only other method significantly better than the naïve prediction. We therefore combine these two using a neural network. FRAGFOLD-IDP enables better insight into backbone dynamics in IDPs and opens exciting possibilities for the design of disordered ensembles, disorder-to-order transitions, or design for protein dynamics.
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Affiliation(s)
- Tomasz Kosciolek
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel W A Buchan
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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76
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The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease. Biochem Soc Trans 2017; 44:1185-1200. [PMID: 27911701 PMCID: PMC5095923 DOI: 10.1042/bst20160172] [Citation(s) in RCA: 259] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/23/2022]
Abstract
In the 1960s, Christian Anfinsen postulated that the unique three-dimensional structure of a protein is determined by its amino acid sequence. This work laid the foundation for the sequence–structure–function paradigm, which states that the sequence of a protein determines its structure, and structure determines function. However, a class of polypeptide segments called intrinsically disordered regions does not conform to this postulate. In this review, I will first describe established and emerging ideas about how disordered regions contribute to protein function. I will then discuss molecular principles by which regulatory mechanisms, such as alternative splicing and asymmetric localization of transcripts that encode disordered regions, can increase the functional versatility of proteins. Finally, I will discuss how disordered regions contribute to human disease and the emergence of cellular complexity during organismal evolution.
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77
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Nikolic J, Le Bars R, Lama Z, Scrima N, Lagaudrière-Gesbert C, Gaudin Y, Blondel D. Negri bodies are viral factories with properties of liquid organelles. Nat Commun 2017; 8:58. [PMID: 28680096 PMCID: PMC5498545 DOI: 10.1038/s41467-017-00102-9] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/31/2017] [Indexed: 11/23/2022] Open
Abstract
Replication of Mononegavirales occurs in viral factories which form inclusions in the host-cell cytoplasm. For rabies virus, those inclusions are called Negri bodies (NBs). We report that NBs have characteristics similar to those of liquid organelles: they are spherical, they fuse to form larger structures, and they disappear upon hypotonic shock. Their liquid phase is confirmed by FRAP experiments. Live-cell imaging indicates that viral nucleocapsids are ejected from NBs and transported along microtubules to form either new virions or secondary viral factories. Coexpression of rabies virus N and P proteins results in cytoplasmic inclusions recapitulating NBs properties. This minimal system reveals that an intrinsically disordered domain and the dimerization domain of P are essential for Negri bodies-like structures formation. We suggest that formation of liquid viral factories by phase separation is common among Mononegavirales and allows specific recruitment and concentration of viral proteins but also the escape to cellular antiviral response. Negative strand RNA viruses, such as rabies virus, induce formation of cytoplasmic inclusions for genome replication. Here, Nikolic et al. show that these so-called Negri bodies (NBs) have characteristics of liquid organelles and they identify the minimal protein domains required for NB formation.
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Affiliation(s)
- Jovan Nikolic
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Romain Le Bars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Zoé Lama
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Scrima
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Yves Gaudin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Danielle Blondel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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78
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Neme R, Amador C, Yildirim B, McConnell E, Tautz D. Random sequences are an abundant source of bioactive RNAs or peptides. Nat Ecol Evol 2017; 1:0217. [PMID: 28580432 PMCID: PMC5447804 DOI: 10.1038/s41559-017-0127] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is generally assumed that new genes arise through duplication and/or recombination of existing genes. The probability that a new functional gene could arise out of random non-coding DNA is so far considered to be negligible, since it seems unlikely that such a RNA or protein sequence could have an initial function that influences the fitness of an organism. We have here tested this question systematically, by expressing clones with random sequences in E . coli and subjecting them to competitive growth. Contrary to expectations, we find that random sequences with bioactivity are not rare. In our experiments we find that up to 25% of the evaluated clones enhance the growth rate of their cells and up to 52% inhibit growth. Testing of individual clones in competition assays confirms their activity and provides an indication that their activity could be exerted either by the transcribed RNA or the translated peptide. This suggests that transcribed and translated random parts of the genome could indeed have a high potential to become functional. The results also suggest that random sequences may become an effective new source of molecules for studying cellular functions, as well as for pharmacological activity screening.
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Affiliation(s)
- Rafik Neme
- Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Cristina Amador
- Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Burcin Yildirim
- Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Ellen McConnell
- Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
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79
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Wang Y, Guo Y, Pu X, Li M. A sequence-based computational method for prediction of MoRFs. RSC Adv 2017. [DOI: 10.1039/c6ra27161h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular recognition features (MoRFs) are relatively short segments (10–70 residues) within intrinsically disordered regions (IDRs) that can undergo disorder-to-order transitions during binding to partner proteins.
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Affiliation(s)
- Yu Wang
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Xuemei Pu
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Menglong Li
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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80
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Fuchs JE, Schilling O, Liedl KR. Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. Curr Protein Pept Sci 2017; 18:905-913. [PMID: 27455965 PMCID: PMC5898033 DOI: 10.2174/1389203717666160724211231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/30/2017] [Accepted: 04/15/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in proteomics methodologies allow for high throughput profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights in the underlying macromolecular recognition events, as determinants of biomolecular specificity identified by proteomics approaches may be compared to structure-based analysis of corresponding protein-protein interfaces. METHOD Here, we present an overview of experimental and computational methodologies and tools applied in the area and provide an outlook beyond the protein class of proteases. RESULTS AND CONCLUSION We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.
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Affiliation(s)
- Julian E. Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Str. 17, D-79104 Freiburg, Germany and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104Freiburg, Germany
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020Innsbruck, Austria
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81
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Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) are involved in a wide range of cellular functions and they often facilitate interactions with RNAs, DNAs, and proteins. Although many computational methods can predict IDPs and IDRs in protein sequences, only a few methods predict their functions and these functions primarily concern protein binding. We describe how to use the first computational method DisoRDPbind for high-throughput prediction of multiple functions of disordered regions. Our method predicts the RNA-, DNA-, and protein-binding residues located in IDRs in the input protein sequences. DisoRDPbind provides accurate predictions and is sufficiently fast to make predictions for full genomes. Our method is implemented as a user-friendly webserver that is freely available at http://biomine.ece.ualberta.ca/DisoRDPbind/ . We overview our predictor, discuss how to run the webserver, and show how to interpret the corresponding results. We also demonstrate the utility of our method based on two case studies, human BRCA1 protein that binds various proteins and DNA, and yeast 60S ribosomal protein L4 that interacts with proteins and RNA.
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82
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Bahramali G, Goliaei B, Minuchehr Z, Marashi SA. A network biology approach to understanding the importance of chameleon proteins in human physiology and pathology. Amino Acids 2016; 49:303-315. [DOI: 10.1007/s00726-016-2361-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/05/2016] [Indexed: 12/20/2022]
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83
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Basu S, Bahadur RP. A structural perspective of RNA recognition by intrinsically disordered proteins. Cell Mol Life Sci 2016; 73:4075-84. [PMID: 27229125 PMCID: PMC7079799 DOI: 10.1007/s00018-016-2283-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/13/2016] [Accepted: 05/20/2016] [Indexed: 11/24/2022]
Abstract
Protein-RNA recognition is essential for gene expression and its regulation, which is indispensable for the survival of the living organism at one hand, on the other hand, misregulation of this recognition may lead to their extinction. Polymorphic conformation of both the interacting partners is a characteristic feature of such molecular recognition that promotes the assembly. Many RNA binding proteins (RBP) or regions in them are found to be intrinsically disordered, and this property helps them to play a central role in the regulatory processes. Sequence composition and the length of the flexible linkers between RNA binding domains in RBPs are crucial in making significant contacts with its partner RNA. Polymorphic conformations of RBPs can provide thermodynamic advantage to its binding partner while acting as a chaperone. Prolonged extensions of the disordered regions in RBPs also contribute to the stability of the large cellular machines including ribosome and viral assemblies. The involvement of these disordered regions in most of the significant cellular processes makes RBPs highly associated with various human diseases that arise due to their misregulation.
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Affiliation(s)
- Sushmita Basu
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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84
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Tutuncuoglu B, Jakovljevic J, Wu S, Gao N, Woolford JL. The N-terminal extension of yeast ribosomal protein L8 is involved in two major remodeling events during late nuclear stages of 60S ribosomal subunit assembly. RNA (NEW YORK, N.Y.) 2016; 22:1386-1399. [PMID: 27390266 PMCID: PMC4986894 DOI: 10.1261/rna.055798.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/24/2016] [Indexed: 06/01/2023]
Abstract
Assaying effects on pre-rRNA processing and ribosome assembly upon depleting individual ribosomal proteins (r-proteins) provided an initial paradigm for assembly of eukaryotic ribosomes in vivo-that each structural domain of ribosomal subunits assembles in a hierarchical fashion. However, two features suggest that a more complex pathway may exist: (i) Some r-proteins contain extensions that reach long distances across ribosomes to interact with multiple rRNA domains as well as with other r-proteins. (ii) Individual r-proteins may assemble in a stepwise fashion. For example, the globular domain of an r-protein might assemble separately from its extensions. Thus, these extensions might play roles in assembly that could not be revealed by depleting the entire protein. Here, we show that deleting or mutating extensions of r-proteins L7 (uL30) and L35 (uL29) from yeast reveal important roles in early and middle steps during 60S ribosomal subunit biogenesis. Detailed analysis of the N-terminal terminal extension of L8 (eL8) showed that it is necessary for late nuclear stages of 60S subunit assembly involving two major remodeling events: removal of the ITS2 spacer; and reorganization of the central protuberance (CP) containing 5S rRNA and r-proteins L5 (uL18) and L11 (uL5). Mutations in the L8 extension block processing of 7S pre-rRNA, prevent release of assembly factors Rpf2 and Rrs1 from pre-ribosomes, which is required for rotation of the CP, and block association of Sda1, the Rix1 complex, and the Rea1 ATPase involved in late steps of remodeling.
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Affiliation(s)
- Beril Tutuncuoglu
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jelena Jakovljevic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Shan Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ning Gao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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85
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Basu S, Bahadur RP. A structural perspective of RNA recognition by intrinsically disordered proteins. CELLULAR AND MOLECULAR LIFE SCIENCES : CMLS 2016. [PMID: 27229125 DOI: 10.1007/s00018‐016‐2283‐1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Protein-RNA recognition is essential for gene expression and its regulation, which is indispensable for the survival of the living organism at one hand, on the other hand, misregulation of this recognition may lead to their extinction. Polymorphic conformation of both the interacting partners is a characteristic feature of such molecular recognition that promotes the assembly. Many RNA binding proteins (RBP) or regions in them are found to be intrinsically disordered, and this property helps them to play a central role in the regulatory processes. Sequence composition and the length of the flexible linkers between RNA binding domains in RBPs are crucial in making significant contacts with its partner RNA. Polymorphic conformations of RBPs can provide thermodynamic advantage to its binding partner while acting as a chaperone. Prolonged extensions of the disordered regions in RBPs also contribute to the stability of the large cellular machines including ribosome and viral assemblies. The involvement of these disordered regions in most of the significant cellular processes makes RBPs highly associated with various human diseases that arise due to their misregulation.
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Affiliation(s)
- Sushmita Basu
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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86
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Malhis N, Jacobson M, Gsponer J. MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences. Nucleic Acids Res 2016; 44:W488-93. [PMID: 27174932 PMCID: PMC4987941 DOI: 10.1093/nar/gkw409] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/03/2016] [Indexed: 11/13/2022] Open
Abstract
Molecular recognition features, MoRFs, are short segments within longer disordered protein regions that bind to globular protein domains in a process known as disorder-to-order transition. MoRFs have been found to play a significant role in signaling and regulatory processes in cells. High-confidence computational identification of MoRFs remains an important challenge. In this work, we introduce MoRFchibi SYSTEM that contains three MoRF predictors: MoRFCHiBi, a basic predictor best suited as a component in other applications, MoRFCHiBi_ Light, ideal for high-throughput predictions and MoRFCHiBi_ Web, slower than the other two but best for high accuracy predictions. Results show that MoRFchibi SYSTEM provides more than double the precision of other predictors. MoRFchibi SYSTEM is available in three different forms: as HTML web server, RESTful web server and downloadable software at: http://www.chibi.ubc.ca/faculty/joerg-gsponer/gsponer-lab/software/morf_chibi/.
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Affiliation(s)
- Nawar Malhis
- Michael Smith Laboratories-Centre for High-Throughput Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Matthew Jacobson
- Michael Smith Laboratories-Centre for High-Throughput Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories-Centre for High-Throughput Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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87
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Abstract
How to design a ligand to bind multiple targets, rather than to a single target, is the focus of this review. Rational polypharmacology draws on knowledge that is both broad ranging and hierarchical. Computer-aided multitarget ligand design methods are described according to their nested knowledge level. Ligand-only and then receptor-ligand strategies are first described; followed by the metabolic network viewpoint. Subsequently strategies that view infectious diseases as multigenomic targets are discussed, and finally the disease level interpretation of medicinal therapy is considered. As yet there is no consensus on how best to proceed in designing a multitarget ligand. The current methodologies are bought together in an attempt to give a practical overview of how polypharmacology design might be best initiated.
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88
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Jacobs WM, Knowles TPJ, Frenkel D. Oligomers of Heat-Shock Proteins: Structures That Don't Imply Function. PLoS Comput Biol 2016; 12:e1004756. [PMID: 26928170 PMCID: PMC4771702 DOI: 10.1371/journal.pcbi.1004756] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/14/2016] [Indexed: 11/18/2022] Open
Abstract
Most proteins must remain soluble in the cytosol in order to perform their biological functions. To protect against undesired protein aggregation, living cells maintain a population of molecular chaperones that ensure the solubility of the proteome. Here we report simulations of a lattice model of interacting proteins to understand how low concentrations of passive molecular chaperones, such as small heat-shock proteins, suppress thermodynamic instabilities in protein solutions. Given fixed concentrations of chaperones and client proteins, the solubility of the proteome can be increased by tuning the chaperone-client binding strength. Surprisingly, we find that the binding strength that optimizes solubility while preventing irreversible chaperone binding also promotes the formation of weakly bound chaperone oligomers, although the presence of these oligomers does not significantly affect the thermodynamic stability of the solution. Such oligomers are commonly observed in experiments on small heat-shock proteins, but their connection to the biological function of these chaperones has remained unclear. Our simulations suggest that this clustering may not have any essential biological function, but rather emerges as a natural side-effect of optimizing the thermodynamic stability of the proteome.
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Affiliation(s)
- William M Jacobs
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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89
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Boomsma W, Nielsen SV, Lindorff-Larsen K, Hartmann-Petersen R, Ellgaard L. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases. PeerJ 2016; 4:e1725. [PMID: 26966660 PMCID: PMC4782732 DOI: 10.7717/peerj.1725] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/02/2016] [Indexed: 12/28/2022] Open
Abstract
The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work indicates that San1 is not a unique case, and that several other yeast and human E3 ligases have sequence properties that may allow them to recognize substrates by a similar mechanism as San1.
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Affiliation(s)
- Wouter Boomsma
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Sofie V Nielsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Lars Ellgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark
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90
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Redefining the BH3 Death Domain as a 'Short Linear Motif'. Trends Biochem Sci 2015; 40:736-748. [PMID: 26541461 PMCID: PMC5056427 DOI: 10.1016/j.tibs.2015.09.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/18/2015] [Accepted: 09/24/2015] [Indexed: 01/06/2023]
Abstract
B cell lymphoma-2 (BCL-2)-related proteins control programmed cell death through a complex network of protein–protein interactions mediated by BCL-2 homology 3 (BH3) domains. Given their roles as dynamic linchpins, the discovery of novel BH3-containing proteins has attracted considerable attention. However, without a clearly defined BH3 signature sequence the BCL-2 family has expanded to include a nebulous group of nonhomologous BH3-only proteins, now justified by an intriguing twist. We present evidence that BH3s from both ordered and disordered proteins represent a new class of short linear motifs (SLiMs) or molecular recognition features (MoRFs) and are diverse in their evolutionary histories. The implied corollaries are that BH3s have a broad phylogenetic distribution and could potentially bind to non-BCL-2-like structural domains with distinct functions. BCL-2 family interactions are mediated by evolutionarily diverse BH3 motifs to regulate apoptosis. Given their key roles, BH3 mimetics are in clinical trials as cancer therapies. The discovery of novel BH3-only proteins represents a major endeavor in the cell death field. As a result, BH3 motifs are reportedly present in a nebulous conglomerate of different proteins, both structured and intrinsically disordered. There is no rigorous definition of a BH3 motif. Currently available BH3 signatures are diverse and elusive for predicting new functional BH3-containing proteins. Redefining the BH3 motif as a new type of short linear motif (SLiM) or molecular recognition feature (MoRF) reconciles many puzzling features of this motif and opens up new avenues for research.
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91
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Emerging Roles of Disordered Sequences in RNA-Binding Proteins. Trends Biochem Sci 2015; 40:662-672. [DOI: 10.1016/j.tibs.2015.08.012] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/21/2015] [Accepted: 08/31/2015] [Indexed: 12/12/2022]
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92
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MyelStones: the executive roles of myelin basic protein in myelin assembly and destabilization in multiple sclerosis. Biochem J 2015; 472:17-32. [DOI: 10.1042/bj20150710] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The classic isoforms of myelin basic protein (MBP, 14–21.5 kDa) are essential to formation of the multilamellar myelin sheath of the mammalian central nervous system (CNS). The predominant 18.5-kDa isoform links together the cytosolic surfaces of oligodendrocytes, but additionally participates in cytoskeletal turnover and membrane extension, Fyn-mediated signalling pathways, sequestration of phosphoinositides and maintenance of calcium homoeostasis. All MBP isoforms are intrinsically disordered proteins (IDPs) that interact via molecular recognition fragments (MoRFs), which thereby undergo local disorder-to-order transitions. Their conformations and associations are modulated by environment and by a dynamic barcode of post-translational modifications, particularly phosphorylation by mitogen-activated and other protein kinases and deimination [a hallmark of demyelination in multiple sclerosis (MS)]. The MBPs are thus to myelin what basic histones are to chromatin. Originally thought to be merely structural proteins forming an inert spool, histones are now known to be dynamic entities involved in epigenetic regulation and diseases such as cancer. Analogously, the MBPs are not mere adhesives of compact myelin, but active participants in oligodendrocyte proliferation and in membrane process extension and stabilization during myelinogenesis. A central segment of these proteins is pivotal in membrane-anchoring and SH3 domain (Src homology 3) interaction. We discuss in the present review advances in our understanding of conformational conversions of this classic basic protein upon membrane association, including new thermodynamic analyses of transitions into different structural ensembles and how a shift in the pattern of its post-translational modifications is associated with the pathogenesis and potentially onset of demyelination in MS.
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93
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Malhis N, Wong ETC, Nassar R, Gsponer J. Computational Identification of MoRFs in Protein Sequences Using Hierarchical Application of Bayes Rule. PLoS One 2015; 10:e0141603. [PMID: 26517836 PMCID: PMC4627796 DOI: 10.1371/journal.pone.0141603] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/09/2015] [Indexed: 01/24/2023] Open
Abstract
Motivation Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is often the binding to globular protein domains via sequence elements known as molecular recognition features (MoRFs). Development of computational tools for the identification of candidate MoRF locations in amino acid sequences is an important task and an area of growing interest. Given the relative sparseness of MoRFs in protein sequences, the accuracy of the available MoRF predictors is often inadequate for practical usage, which leaves a significant need and room for improvement. In this work, we introduce MoRFCHiBi_Web, which predicts MoRF locations in protein sequences with higher accuracy compared to current MoRF predictors. Methods Three distinct and largely independent property scores are computed with component predictors and then combined to generate the final MoRF propensity scores. The first score reflects the likelihood of sequence windows to harbour MoRFs and is based on amino acid composition and sequence similarity information. It is generated by MoRFCHiBi using small windows of up to 40 residues in size. The second score identifies long stretches of protein disorder and is generated by ESpritz with the DisProt option. Lastly, the third score reflects residue conservation and is assembled from PSSM files generated by PSI-BLAST. These propensity scores are processed and then hierarchically combined using Bayes rule to generate the final MoRFCHiBi_Web predictions. Results MoRFCHiBi_Web was tested on three datasets. Results show that MoRFCHiBi_Web outperforms previously developed predictors by generating less than half the false positive rate for the same true positive rate at practical threshold values. This level of accuracy paired with its relatively high processing speed makes MoRFCHiBi_Web a practical tool for MoRF prediction. Availability http://morf.chibi.ubc.ca:8080/morf/.
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Affiliation(s)
- Nawar Malhis
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
- * E-mail: (NM); (JG)
| | - Eric T. C. Wong
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Roy Nassar
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Gsponer
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- * E-mail: (NM); (JG)
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94
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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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95
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Martins F, Gonçalves R, Oliveira J, Cruz-Monteagudo M, Nieto-Villar JM, Paz-y-Miño C, Rebelo I, Tejera E. Unravelling the relationship between protein sequence and low-complexity regions entropies: Interactome implications. J Theor Biol 2015; 382:320-7. [PMID: 26164061 DOI: 10.1016/j.jtbi.2015.06.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/12/2015] [Accepted: 06/28/2015] [Indexed: 10/23/2022]
Abstract
Low-complexity regions are sub-sequences of biased composition in a protein sequence. The influence of these regions over protein evolution, specific functions and highly interactive capacities is well known. Although protein sequence entropy has been largely studied, its relationship with low-complexity regions and the subsequent effects on protein function remains unclear. In this work we propose a theoretical and empirical model integrating the sequence entropy with local complexity parameters. Our results indicate that the protein sequence entropy is related with the protein length, the entropies inside and outside the low-complexity regions as well as their number and average size. We found a small but significant increment in the sequence entropy of hubs proteins. In agreement with our theoretical model, this increment is highly dependent of the balance between the increment of protein length and average size of the low-complexity regions. Finally, our models and proteins analysis provide evidence supporting that modifications in the average size is more relevant in hubs proteins than changes in the number of low-complexity regions.
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Affiliation(s)
- F Martins
- Department of Biochemistry, Faculty of Pharmacy, University of Porto, Portugal
| | - R Gonçalves
- Department of Biochemistry, Faculty of Pharmacy, University of Porto, Portugal
| | - J Oliveira
- Department of Biochemistry, Faculty of Pharmacy, University of Porto, Portugal
| | - M Cruz-Monteagudo
- Instituto de Investigaciones Biomédicas, Universidad de las Américas, Quito, Ecuador
| | - J M Nieto-Villar
- Dpto. de Química-Física, Fac. de Química, Universidad de La Habana, Cuba. Cátedra de Sistemas Complejos "H. Poincaré", Universidad de La Habana, Cuba
| | - C Paz-y-Miño
- Instituto de Investigaciones Biomédicas, Universidad de las Américas, Quito, Ecuador
| | - I Rebelo
- Department of Biochemistry, Faculty of Pharmacy, University of Porto, Portugal; UCIBIO@REQUIMTE, Portugal.
| | - E Tejera
- Instituto de Investigaciones Biomédicas, Universidad de las Américas, Quito, Ecuador
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96
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Tompa P, Schad E, Tantos A, Kalmar L. Intrinsically disordered proteins: emerging interaction specialists. Curr Opin Struct Biol 2015; 35:49-59. [PMID: 26402567 DOI: 10.1016/j.sbi.2015.08.009] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein-protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural-functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as 'interaction specialists'.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium; Vrije Universiteit Brussel, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
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97
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Chen L, Chuang M, Koorman T, Boxem M, Jin Y, Chisholm AD. Axon injury triggers EFA-6 mediated destabilization of axonal microtubules via TACC and doublecortin like kinase. eLife 2015; 4. [PMID: 26339988 PMCID: PMC4596636 DOI: 10.7554/elife.08695] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/03/2015] [Indexed: 01/09/2023] Open
Abstract
Axon injury triggers a series of changes in the axonal cytoskeleton that are prerequisites for effective axon regeneration. In Caenorhabditis elegans the signaling protein Exchange Factor for ARF-6 (EFA-6) is a potent intrinsic inhibitor of axon regrowth. Here we show that axon injury triggers rapid EFA-6-dependent inhibition of axonal microtubule (MT) dynamics, concomitant with relocalization of EFA-6. EFA-6 relocalization and axon regrowth inhibition require a conserved 18-aa motif in its otherwise intrinsically disordered N-terminal domain. The EFA-6 N-terminus binds the MT-associated proteins TAC-1/Transforming-Acidic-Coiled-Coil, and ZYG-8/Doublecortin-Like-Kinase, both of which are required for regenerative growth cone formation, and which act downstream of EFA-6. After injury TAC-1 and EFA-6 transiently relocalize to sites marked by the MT minus end binding protein PTRN-1/Patronin. We propose that EFA-6 acts as a bifunctional injury-responsive regulator of axonal MT dynamics, acting at the cell cortex in the steady state and at MT minus ends after injury. DOI:http://dx.doi.org/10.7554/eLife.08695.001 In the nervous system, cells called neurons carry information around the body. These cells have long thin projections called axons that allow the information to pass very quickly along the cell to junctions with other neurons. Neurons in adult mammals are limited in their ability to regenerate, so any damage to axons, for example, due to a stroke or a brain injury, tends to be permanent. Therefore, an important goal in neuroscience research is to discover the genes and proteins that are involved in regenerating axons as this may make it possible to develop new therapies. An internal scaffold called the cytoskeleton supports the three-dimensional shape of the axons. Changes in the cytoskeleton are required to allow neurons to regenerate axons after injury, and drugs that stabilize filaments called microtubules in the cytoskeleton can promote these changes. Chen et al. used a technique called laser microsurgery to sever individual axons in a roundworm known as C. elegans and then observed whether these axons could regenerate. The experiments reveal that a protein called EFA-6 blocks the regeneration of neurons by preventing rearrangements in the cytoskeleton. EFA-6 is normally found at the membrane that surrounds the neuron. However, Chen et al. show that when the axon is damaged, this protein rapidly moves to areas near the ends of microtubule filaments. EFA-6 interacts with two other proteins that are associated with microtubules and are required for axons to be able to regenerate. Chen et al.'s findings demonstrate that several proteins that regulate microtubule filaments play a key role in regenerating axons. All three of these proteins are found in humans and other animals so they have the potential to be targeted by drug therapies in future. The next challenge is to understand the details of how EFA-6 activity is affected by axon injury, and how this alters the cytoskeleton. DOI:http://dx.doi.org/10.7554/eLife.08695.002
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Affiliation(s)
- Lizhen Chen
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States.,University of California, San Diego, La Jolla, United States
| | - Marian Chuang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Thijs Koorman
- Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Mike Boxem
- Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Yishi Jin
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States.,University of California, San Diego, La Jolla, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, United States
| | - Andrew D Chisholm
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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98
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Iraci N, Stincardini C, Barreca ML, Biasini E. Decoding the function of the N-terminal tail of the cellular prion protein to inspire novel therapeutic avenues for neurodegenerative diseases. Virus Res 2015; 207:62-8. [DOI: 10.1016/j.virusres.2014.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/18/2014] [Accepted: 10/14/2014] [Indexed: 01/13/2023]
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99
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Sanchez de Groot N, Gomes RA, Villar-Pique A, Babu MM, Coelho AV, Ventura S. Proteome response at the edge of protein aggregation. Open Biol 2015; 5:140221. [PMID: 25673330 PMCID: PMC4345283 DOI: 10.1098/rsob.140221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proteins adopt defined structures and are crucial to most cellular functions. Their misfolding and aggregation is associated with numerous degenerative human disorders such as type II diabetes, Huntington's or Alzheimer's diseases. Here, we aim to understand why cells promote the formation of protein foci. Comparison of two amyloid-β-peptide variants, mostly insoluble but differently recruited by the cell (inclusion body versus diffused), reveals small differences in cell fitness and proteome response. We suggest that the levels of oxidative stress act as a sensor to trigger protein recruitment into foci. Our data support a common cytoplasmic response being able to discern and react to the specific properties of polypeptides.
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Affiliation(s)
- Natalia Sanchez de Groot
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ricardo A Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Anna Villar-Pique
- Department of Neurodegeneration and Restorative Research, University Medical Center Goettingen, Waldweg 33, Goettingen, Germany
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra (Barcelona), Spain
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100
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Teilum K, Olsen JG, Kragelund BB. Globular and disordered-the non-identical twins in protein-protein interactions. Front Mol Biosci 2015. [PMID: 26217672 PMCID: PMC4496568 DOI: 10.3389/fmolb.2015.00040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In biology proteins from different structural classes interact across and within classes in ways that are optimized to achieve balanced functional outputs. The interactions between intrinsically disordered proteins (IDPs) and other proteins rely on changes in flexibility and this is seen as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those of other protein-protein interactions. We find that ordered proteins and the disordered ones act as non-identical twins operating by similar principles but where the disordered proteins complexes are on average less stable by 2.5 kcal mol(-1).
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
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