The multifaceted roles of intrinsic disorder in protein complexes
暂无分享,去创建一个
[1] R. Kriwacki,et al. Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits. , 2008, Biochemistry.
[2] Vladimir N. Uversky,et al. The Mysterious Unfoldome: Structureless, Underappreciated, Yet Vital Part of Any Given Proteome , 2009, Journal of biomedicine & biotechnology.
[3] S. Teichmann,et al. Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways , 2013, Cell.
[4] V. Uversky. Natively unfolded proteins: A point where biology waits for physics , 2002, Protein science : a publication of the Protein Society.
[5] P. Tompa,et al. Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. , 2008, Trends in biochemical sciences.
[6] T. A. Graham,et al. Crystal structure of a beta-catenin/Tcf complex. , 2000, Cell.
[7] Lukasz Kurgan,et al. Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life , 2014, Cellular and Molecular Life Sciences.
[8] Jiahuai Han,et al. Casein Kinase I and Casein Kinase II Differentially Regulate Axin Function in Wnt and JNK Pathways* , 2002, The Journal of Biological Chemistry.
[9] David L. Spector,et al. Nuclear speckles: a model for nuclear organelles , 2003, Nature Reviews Molecular Cell Biology.
[10] T. Pederson,et al. Protein Mobility within the Nucleus—What Are the Right Moves? , 2001, Cell.
[11] Kenta Okamoto,et al. Dissecting β‐ring assembly pathway of the mammalian 20S proteasome , 2008, The EMBO journal.
[12] P. Wolynes,et al. The physics and bioinformatics of binding and folding—an energy landscape perspective , 2003, Biopolymers.
[13] R. Hartmann-Petersen,et al. Ubiquitin binding proteins protect ubiquitin conjugates from disassembly , 2003, FEBS letters.
[14] Vladimir N. Uversky,et al. Conditionally and transiently disordered proteins: awakening cryptic disorder to regulate protein function. , 2014, Chemical reviews.
[15] Lilia M. Iakoucheva,et al. Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes , 2006, PLoS Comput. Biol..
[16] Vladimir N Uversky,et al. Intrinsic disorder-based protein interactions and their modulators. , 2013, Current pharmaceutical design.
[17] J. Strahler,et al. Assembly of Saccharomyces cerevisiae 60S ribosomal subunits: role of factors required for 27S pre‐rRNA processing , 2011, The EMBO journal.
[18] R. Reeves,et al. Molecular biology of HMGA proteins: hubs of nuclear function. , 2001, Gene.
[19] Marc S. Cortese,et al. Structural Basis for Regulation of Protein Phosphatase 1 by Inhibitor-2* , 2007, Journal of Biological Chemistry.
[20] C. Brown,et al. Intrinsic protein disorder in complete genomes. , 2000, Genome informatics. Workshop on Genome Informatics.
[21] Zoran Obradovic,et al. The protein trinity—linking function and disorder , 2001, Nature Biotechnology.
[22] Axel T. Brunger,et al. Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[23] Paul Tempst,et al. SNAP receptors implicated in vesicle targeting and fusion , 1993, Nature.
[24] R. Kiss,et al. Calcium‐induced tripartite binding of intrinsically disordered calpastatin to its cognate enzyme, calpain , 2008, FEBS letters.
[25] A Keith Dunker,et al. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. , 2007, Biochemistry.
[26] S. Teichmann,et al. Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.
[27] E. Myers,et al. Limiting Amounts of Centrosome Material Set Centrosome Size in C. elegans Embryos , 2011, Current Biology.
[28] R. Parker,et al. Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae , 2007, The Journal of cell biology.
[29] V. Uversky. Unusual biophysics of intrinsically disordered proteins. , 2013, Biochimica et biophysica acta.
[30] C. Robinson,et al. Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry , 2007, Nature Protocols.
[31] Sergey Melnikov,et al. The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution , 2011, Science.
[32] A. Levine,et al. Induced α Helix in the VP16 Activation Domain upon Binding to a Human TAF , 1997 .
[33] E. Barbar,et al. Polybivalency and disordered proteins in ordering macromolecular assemblies. , 2015, Seminars in cell & developmental biology.
[34] Lukasz Kurgan,et al. More than just tails: intrinsic disorder in histone proteins. , 2012, Molecular bioSystems.
[35] László Buday,et al. Functional classification of scaffold proteins and related molecules , 2010, The FEBS journal.
[36] S. Vagner,et al. DNA damage: RNA-binding proteins protect from near and far. , 2014, Trends in biochemical sciences.
[37] T. Südhof,et al. Membrane Fusion: Grappling with SNARE and SM Proteins , 2009, Science.
[38] J. King,et al. Folding and assembly of oligomeric proteins in Escherichia coli. , 1992, Current opinion in biotechnology.
[39] R. Collier,et al. Use of phage display and polyvalency to design inhibitors of protein-protein interactions. , 2004, Methods in molecular biology.
[40] Peter Tompa,et al. The relationship between proteome size, structural disorder and organism complexity , 2011, Genome Biology.
[41] A. Dunker,et al. Disorder and sequence repeats in hub proteins and their implications for network evolution. , 2006, Journal of proteome research.
[42] V. Uversky,et al. Why are “natively unfolded” proteins unstructured under physiologic conditions? , 2000, Proteins.
[43] Vladimir N Uversky,et al. What does it mean to be natively unfolded? , 2002, European journal of biochemistry.
[44] Christopher J. Oldfield,et al. Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners , 2008, BMC Genomics.
[45] Christine D. Keating,et al. Aqueous Phase Separation as a Possible Route to Compartmentalization of Biological Molecules , 2012, Accounts of chemical research.
[46] Ruth Nussinov,et al. Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. , 2004, Journal of molecular biology.
[47] N. Sonenberg,et al. The translation initiation factor eIF-4E binds to a common motif shared by the translation factor eIF-4 gamma and the translational repressors 4E-binding proteins , 1995, Molecular and cellular biology.
[48] A. Gingras,et al. 4E binding proteins inhibit the translation factor eIF4E without folded structure. , 1998, Biochemistry.
[49] L. Pearl,et al. Structural basis for recruitment of glycogen synthase kinase 3β to the axin—APC scaffold complex , 2003, The EMBO journal.
[50] M. Kikuchi,et al. Structural flexibility of intrinsically disordered proteins induces stepwise target recognition. , 2013, The Journal of chemical physics.
[51] P. Tompa,et al. Limitations of induced folding in molecular recognition by intrinsically disordered proteins. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.
[52] V. Uversky,et al. Natively unfolded C‐terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin , 2003, Proteins.
[53] A. Levine,et al. Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain , 1996, Science.
[54] Jie J. Zheng,et al. Crystal structure of a full-length beta-catenin. , 2008, Structure.
[55] T. Misteli,et al. High mobility of proteins in the mammalian cell nucleus , 2000, Nature.
[56] Yongli Zhang,et al. High-Resolution Optical Tweezers for Single-Molecule Manipulation , 2013, The Yale journal of biology and medicine.
[57] P. Tompa. The interplay between structure and function in intrinsically unstructured proteins , 2005, FEBS letters.
[58] A. Keith Dunker,et al. Mining α-Helix-Forming Molecular Recognition Features with Cross Species Sequence Alignments† , 2007 .
[59] Peter E Wright,et al. Solution Structure of the KIX Domain of CBP Bound to the Transactivation Domain of CREB: A Model for Activator:Coactivator Interactions , 1997, Cell.
[60] P E Wright,et al. Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[61] G. V. Vande Woude,et al. Anthrax toxins , 1999, Cellular and Molecular Life Sciences CMLS.
[62] R. Perham,et al. Self-assembly of biological macromolecules. , 1975, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[63] Lukasz Kurgan,et al. A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome , 2013, Cellular and Molecular Life Sciences.
[64] Monika Fuxreiter,et al. Fuzzy complexes: a more stochastic view of protein function. , 2012, Advances in experimental medicine and biology.
[65] Christopher J. Oldfield,et al. The unfoldomics decade: an update on intrinsically disordered proteins , 2008, BMC Genomics.
[66] A Keith Dunker,et al. Signal transduction via unstructured protein conduits. , 2008, Nature chemical biology.
[67] T. A. Graham,et al. Crystal Structure of a β-Catenin/Tcf Complex , 2000, Cell.
[68] U. Jakob,et al. Conditional disorder in chaperone action. , 2012, Trends in biochemical sciences.
[69] P. Romero,et al. Stochastic machines as a colocalization mechanism for scaffold protein function , 2013, FEBS letters.
[70] M. Bolognesi,et al. Function and Structure of Inherently Disordered Proteins This Review Comes from a Themed Issue on Proteins Edited Prediction of Non-folding Proteins and Regions Frequency of Disordered Regions Protein Evolution Partitioning Unstructured Proteins and Regions into Groups Involvement of Inherently Diso , 2022 .
[71] William T Heller,et al. Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27 Kip1. , 2008, Journal of molecular biology.
[72] R. Lührmann,et al. Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis , 2010, Nature Structural &Molecular Biology.
[73] Christopher J. Oldfield,et al. Intrinsically disordered protein. , 2001, Journal of molecular graphics & modelling.
[74] A. Mohan. MoRFs A Dataset of Molecular Recognition Features , 2006 .
[75] Vladimir N Uversky,et al. Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates , 2015, FEBS letters.
[76] T. Creamer,et al. Transient disorder , 2013, Intrinsically disordered proteins.
[77] Haruki Nakamura,et al. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks , 2006, FEBS letters.
[78] Peter Tompa,et al. Structure and Function of Intrinsically Disordered Proteins , 2009 .
[79] S. Teichmann,et al. Assembly reflects evolution of protein complexes , 2008, Nature.
[80] A. Dunker,et al. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life , 2012, Journal of biomolecular structure & dynamics.
[81] A Keith Dunker,et al. Intrinsic disorder in scaffold proteins: getting more from less. , 2008, Progress in biophysics and molecular biology.
[82] N. Nakatsuji,et al. Ultrastructural characterization of spermatogenesis and its evolutionary conservation in the germline: Germinal granules in mammals , 2009, Molecular and Cellular Endocrinology.
[83] Anja Thalhammer,et al. Disordered Cold Regulated15 Proteins Protect Chloroplast Membranes during Freezing through Binding and Folding, But Do Not Stabilize Chloroplast Enzymes in Vivo1[W][OPEN] , 2014, Plant Physiology.
[84] C. Brangwynne. Phase transitions and size scaling of membrane-less organelles , 2013, The Journal of cell biology.
[85] Jeffrey R. Huth,et al. The solution structure of an HMG-I(Y)–DNA complex defines a new architectural minor groove binding motif , 1997, Nature Structural Biology.
[86] A. Dunker,et al. Understanding protein non-folding. , 2010, Biochimica et biophysica acta.
[87] M. Nissen,et al. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. , 1990, The Journal of biological chemistry.
[88] Reinhard Jahn,et al. Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution , 1998, Nature.
[89] George M. Whitesides,et al. Designing a polyvalent inhibitor of anthrax toxin , 2001, Nature Biotechnology.
[90] Debasis Dash,et al. Intrinsic unstructuredness and abundance of PEST motifs in eukaryotic proteomes , 2005, Proteins.
[91] C. Vonrhein,et al. Structure of the 30S ribosomal subunit , 2000, Nature.
[92] Kojima. Structure and function , 2005 .
[93] Marc S. Cortese,et al. Coupled folding and binding with α-helix-forming molecular recognition elements , 2005 .
[94] A Keith Dunker,et al. Intrinsic disorder and protein function. , 2002, Biochemistry.
[95] Vladislav Yu Orekhov,et al. Binding of intrinsically disordered proteins is not necessarily accompanied by a structural transition to a folded form. , 2007, Biochimie.
[96] L. Kay,et al. Protein dynamics and conformational disorder in molecular recognition , 2009, Journal of molecular recognition : JMR.
[97] Fei Huang,et al. Intrinsic Protein Disorder and Protein-Protein Interactions , 2012, Pacific Symposium on Biocomputing.
[98] Mike Tyers,et al. Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor , 2008, Proceedings of the National Academy of Sciences.
[99] H. Chan,et al. Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity , 2007, Proceedings of the National Academy of Sciences.
[100] Benedikt Westermann,et al. SNAREpins: Minimal Machinery for Membrane Fusion , 1998, Cell.
[101] Reinhard Jahn,et al. Structure and Conformational Changes in NSF and Its Membrane Receptor Complexes Visualized by Quick-Freeze/Deep-Etch Electron Microscopy , 1997, Cell.
[102] J. Scholey. Faculty Opinions recommendation of Characterization of the intraflagellar transport complex B core: direct interaction of the IFT81 and IFT74/72 subunits. , 2005 .
[103] Z. Obradovic,et al. Identification and functions of usefully disordered proteins. , 2002, Advances in protein chemistry.
[104] J. G. Patton,et al. Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. , 2005, Molecular biology of the cell.
[105] H. Dyson,et al. Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.
[106] Timothy D. Craggs,et al. Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles , 2015, Molecular cell.
[107] K. Tomoo,et al. Binding preference of eIF4E for 4E-binding protein isoform and function of eIF4E N-terminal flexible region for interaction, studied by SPR analysis. , 2007, Biochemical and biophysical research communications.
[108] G. Maul,et al. Review: properties and assembly mechanisms of ND10, PML bodies, or PODs. , 2000, Journal of structural biology.
[109] A. Levine,et al. Induced alpha helix in the VP16 activation domain upon binding to a human TAF. , 1997, Science.
[110] L. Hengst,et al. p27 binds cyclin–CDK complexes through a sequential mechanism involving binding-induced protein folding , 2004, Nature Structural &Molecular Biology.
[111] A. Sigalov,et al. Homooligomerization of the cytoplasmic domain of the T cell receptor zeta chain and of other proteins containing the immunoreceptor tyrosine-based activation motif. , 2004, Biochemistry.
[112] G. Siuzdak,et al. Molecular basis for the specificity of p27 toward cyclin-dependent kinases that regulate cell division. , 2005, Journal of molecular biology.
[113] V. Uversky. Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes. , 2011, Chemical Society reviews.
[114] V. Ramakrishnan,et al. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics , 2000, Nature.
[115] Matthias Mann,et al. Paraspeckles A Novel Nuclear Domain , 2002, Current Biology.
[116] R. Nussinov,et al. Mechanism and evolution of protein dimerization , 1998, Protein science : a publication of the Protein Society.
[117] K D Paull,et al. Proteolytic inactivation of MAP-kinase-kinase by anthrax lethal factor. , 1998, Science.
[118] H. Dyson,et al. Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.
[119] H. Dyson,et al. Mechanism of coupled folding and binding of an intrinsically disordered protein , 2007, Nature.
[120] S. Huang. Review: perinucleolar structures. , 2000, Journal of structural biology.
[121] M. Tyers,et al. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. , 2010, Structure.
[122] Robert Kiss,et al. High levels of structural disorder in scaffold proteins as exemplified by a novel neuronal protein, CASK‐interactive protein1 , 2009, The FEBS journal.
[123] Hideki Yamamoto,et al. Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain. , 2007, Acta Crystallographica. Section F : Structural Biology and Crystallization Communications.
[124] Ruedi Aebersold,et al. Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling , 2013, Cell.
[125] Marc S. Cortese,et al. Coupled folding and binding with alpha-helix-forming molecular recognition elements. , 2005, Biochemistry.
[126] A Keith Dunker,et al. Characterization of molecular recognition features, MoRFs, and their binding partners. , 2007, Journal of proteome research.
[127] J. Thornton,et al. An overview of the structures of protein-DNA complexes , 2000, Genome Biology.
[128] J. S. Sodhi,et al. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.
[129] S. Teichmann,et al. The Role of Salt Bridges, Charge Density, and Subunit Flexibility in Determining Disassembly Routes of Protein Complexes , 2013, Structure.
[130] V. Sheffield,et al. Intrinsic Protein-Protein Interaction-mediated and Chaperonin-assisted Sequential Assembly of Stable Bardet-Biedl Syndrome Protein Complex, the BBSome* , 2012, The Journal of Biological Chemistry.
[131] Lukasz Kurgan,et al. Disordered Proteinaceous Machines , 2014, Chemical reviews.
[132] V. Uversky. Intrinsically Disordered Proteins , 2000 .
[133] Sergey V. Melnikov,et al. The structure of the eukaryotic ribosome at 3.0 angstrom resolution. , 2011 .
[134] A. Hyman,et al. Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation , 2009, Science.
[135] N. Sonenberg,et al. Interaction of the eukaryotic initiation factor 4E with 4E-BP2 at a dynamic bipartite interface. , 2013, Structure.
[136] H. Dyson,et al. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. , 1999, Journal of molecular biology.
[137] V. Ramakrishnan,et al. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA. , 2002, Journal of molecular biology.
[138] A. Elofsson,et al. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? , 2006, Genome Biology.
[139] Christopher J. Oldfield,et al. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling , 2005, Journal of molecular recognition : JMR.
[140] Tony Pawson,et al. Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication , 2001, Nature.