151
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Krishnan N, Koveal D, Miller DH, Xue B, Akshinthala SD, Kragelj J, Jensen MR, Gauss CM, Page R, Blackledge M, Muthuswamy SK, Peti W, Tonks NK. Targeting the disordered C terminus of PTP1B with an allosteric inhibitor. Nat Chem Biol 2014; 10:558-66. [PMID: 24845231 PMCID: PMC4062594 DOI: 10.1038/nchembio.1528] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 04/16/2014] [Indexed: 01/23/2023]
Abstract
PTP1B, a validated therapeutic target for diabetes and obesity, has a critical positive role in HER2 signaling in breast tumorigenesis. Efforts to develop therapeutic inhibitors of PTP1B have been frustrated by the chemical properties of the active site. We define a new mechanism of allosteric inhibition that targets the C-terminal, noncatalytic segment of PTP1B. We present what is to our knowledge the first ensemble structure of PTP1B containing this intrinsically disordered segment, within which we identified a binding site for the small-molecule inhibitor MSI-1436. We demonstrate binding to a second site close to the catalytic domain, with cooperative effects between the two sites locking PTP1B in an inactive state. MSI-1436 antagonized HER2 signaling, inhibited tumorigenesis in xenografts and abrogated metastasis in the NDL2 mouse model of breast cancer, validating inhibition of PTP1B as a therapeutic strategy in breast cancer. This new approach to inhibition of PTP1B emphasizes the potential of disordered segments of proteins as specific binding sites for therapeutic small molecules.
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MESH Headings
- Allosteric Regulation/drug effects
- Allosteric Site/drug effects
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/enzymology
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Catalytic Domain
- Cholestanes/chemistry
- Cholestanes/pharmacology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Kinetics
- Mammary Neoplasms, Experimental/drug therapy
- Mammary Neoplasms, Experimental/enzymology
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/pathology
- Mice
- Models, Molecular
- Molecular Targeted Therapy
- Protein Binding/drug effects
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/antagonists & inhibitors
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Signal Transduction
- Spermine/analogs & derivatives
- Spermine/chemistry
- Spermine/pharmacology
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Affiliation(s)
- Navasona Krishnan
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Dorothy Koveal
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Daniel H. Miller
- Department of Molecular Pharmacology, Physiology and Biotechnology, and Department of Chemistry, Brown University, Providence, RI 02903, USA
| | - Bin Xue
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | | | - Jaka Kragelj
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Malene Ringkjøbing Jensen
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Carla-Maria Gauss
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Martin Blackledge
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Senthil K. Muthuswamy
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
- Ontario Cancer Institute, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, and Department of Chemistry, Brown University, Providence, RI 02903, USA
| | - Nicholas K. Tonks
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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152
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Malaney P, Pathak RR, Xue B, Uversky VN, Davé V. Intrinsic disorder in PTEN and its interactome confers structural plasticity and functional versatility. Sci Rep 2014; 3:2035. [PMID: 23783762 PMCID: PMC3687229 DOI: 10.1038/srep02035] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/03/2013] [Indexed: 12/19/2022] Open
Abstract
IDPs, while structurally poor, are functionally rich by virtue of their flexibility and modularity. However, how mutations in IDPs elicit diseases, remain elusive. Herein, we have identified tumor suppressor PTEN as an intrinsically disordered protein (IDP) and elucidated the molecular principles by which its intrinsically disordered region (IDR) at the carboxyl-terminus (C-tail) executes its functions. Post-translational modifications, conserved eukaryotic linear motifs and molecular recognition features present in the C-tail IDR enhance PTEN's protein-protein interactions that are required for its myriad cellular functions. PTEN primary and secondary interactomes are also enriched in IDPs, most being cancer related, revealing that PTEN functions emanate from and are nucleated by the C-tail IDR, which form pliable network-hubs. Together, PTEN higher order functional networks operate via multiple IDP-IDP interactions facilitated by its C-tail IDR. Targeting PTEN IDR and its interaction hubs emerges as a new paradigm for treatment of PTEN related pathologies.
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Affiliation(s)
- Prerna Malaney
- Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, USA
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153
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Wang H, Chauhan J, Hu A, Pendleton K, Yap JL, Sabato PE, Jones JW, Perri M, Yu J, Cione E, Kane MA, Fletcher S, Prochownik EV. Disruption of Myc-Max heterodimerization with improved cell-penetrating analogs of the small molecule 10074-G5. Oncotarget 2014; 4:936-47. [PMID: 23801058 PMCID: PMC3757250 DOI: 10.18632/oncotarget.1108] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The c-Myc (Myc) oncoprotein is a high-value therapeutic target given that it is deregulated in multiple types of cancer. However, potent small molecule inhibitors of Myc have been difficult to identify, particularly those whose mechanism relies on blocking the association between Myc and its obligate heterodimerization partner, Max. We have recently reported a structure-activity relationship study of one such small molecule, 10074-G5, and generated an analog, JY-3-094, with significantly improved ability to prevent or disrupt the association between recombinant Myc and Max proteins. However, JY-3094 penetrates cells poorly. Here, we show that esterification of a critical para-carboxylic acid function of JY-3-094 by various blocking groups significantly improves cellular uptake although it impairs the ability to disrupt Myc-Max association in vitro. These pro-drugs are highly concentrated within cells where JY-3-094 is then generated by the action of esterases. However, the pro-drugs are also variably susceptible to extracellular esterases, which can deplete extracellular reservoirs. Furthermore, while JY-3-094 is retained by cells for long periods of time, much of it is compartmentalized within the cytoplasm in a form that appears to be less available to interact with Myc. Our results suggest that persistently high extracellular levels of pro-drug, without excessive susceptibility to extracellular esterases, are critical to establishing and maintaining intracellular levels of JY-3-094 that are sufficient to provide for long-term inhibition of Myc-Max association. Analogs of JY-3-094 appear to represent promising small molecule Myc inhibitors that warrant further optimization.
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Affiliation(s)
- Huabo Wang
- Section of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
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154
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Szöllősi D, Horváth T, Han KH, Dokholyan NV, Tompa P, Kalmár L, Hegedűs T. Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins. PLoS One 2014; 9:e95795. [PMID: 24763499 PMCID: PMC3998973 DOI: 10.1371/journal.pone.0095795] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 03/30/2014] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available.
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Affiliation(s)
- Dániel Szöllősi
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics, University of Science and Technology, Yuseong-gu, Daejeon, Korea
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Péter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lajos Kalmár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás Hegedűs
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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155
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Konrat R. NMR contributions to structural dynamics studies of intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:74-85. [PMID: 24656082 PMCID: PMC3985426 DOI: 10.1016/j.jmr.2013.11.011] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/13/2013] [Accepted: 11/18/2013] [Indexed: 05/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions.
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Affiliation(s)
- Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
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156
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Mei Y, Su M, Soni G, Salem S, Colbert CL, Sinha SC. Intrinsically disordered regions in autophagy proteins. Proteins 2014; 82:565-78. [PMID: 24115198 PMCID: PMC3949125 DOI: 10.1002/prot.24424] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/15/2013] [Accepted: 09/02/2013] [Indexed: 12/19/2022]
Abstract
Autophagy is an essential eukaryotic pathway required for cellular homeostasis. Numerous key autophagy effectors and regulators have been identified, but the mechanism by which they carry out their function in autophagy is not fully understood. Our rigorous bioinformatic analysis shows that the majority of key human autophagy proteins include intrinsically disordered regions (IDRs), which are sequences lacking stable secondary and tertiary structure; suggesting that IDRs play an important, yet hitherto uninvestigated, role in autophagy. Available crystal structures corroborate the absence of structure in some of these predicted IDRs. Regions of orthologs equivalent to the IDRs predicted in the human autophagy proteins are poorly conserved, indicating that these regions may have diverse functions in different homologs. We also show that IDRs predicted in human proteins contain several regions predicted to facilitate protein-protein interactions, and delineate the network of proteins that interact with each predicted IDR-containing autophagy protein, suggesting that many of these interactions may involve IDRs. Lastly, we experimentally show that a BCL2 homology 3 domain (BH3D), within the key autophagy effector BECN1 is an IDR. This BH3D undergoes a dramatic conformational change from coil to α-helix upon binding to BCL2s, with the C-terminal half of this BH3D constituting a binding motif, which serves to anchor the interaction of the BH3D to BCL2s. The information presented here will help inform future in-depth investigations of the biological role and mechanism of IDRs in autophagy proteins.
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Affiliation(s)
- Yang Mei
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
- Center for Protease Research, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Minfei Su
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
- Center for Protease Research, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Gaurav Soni
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
- Center for Protease Research, North Dakota State University, Fargo, ND 58108-6050, USA
- Department of Computer Science, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Saeed Salem
- Department of Computer Science, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Christopher L. Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
- Center for Protease Research, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Sangita C. Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
- Center for Protease Research, North Dakota State University, Fargo, ND 58108-6050, USA
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157
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Forman-Kay JD, Mittag T. From sequence and forces to structure, function, and evolution of intrinsically disordered proteins. Structure 2014; 21:1492-9. [PMID: 24010708 DOI: 10.1016/j.str.2013.08.001] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/02/2013] [Accepted: 08/06/2013] [Indexed: 01/27/2023]
Abstract
Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties.
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Affiliation(s)
- Julie D Forman-Kay
- Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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158
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Fletcher S, Prochownik EV. Small-molecule inhibitors of the Myc oncoprotein. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:525-43. [PMID: 24657798 DOI: 10.1016/j.bbagrm.2014.03.005] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 03/09/2014] [Accepted: 03/12/2014] [Indexed: 01/23/2023]
Abstract
The c-Myc (Myc) oncoprotein is among the most attractive of cancer targets given that it is de-regulated in the majority of tumors and that its inhibition profoundly affects their growth and/or survival. However, its role as a seldom-mutated transcription factor, its lack of enzymatic activity for which suitable pharmaceutical inhibitors could be crafted and its expression by normal cells have largely been responsible for its being viewed as "undruggable". Work over the past several years, however, has begun to reverse this idea by allowing us to view Myc within the larger context of global gene regulatory control. Thus, Myc and its obligate heterodimeric partner, Max, are integral to the coordinated recruitment and post-translational modification of components of the core transcriptional machinery. Moreover, Myc over-expression re-programs numerous critical cellular functions and alters the cell's susceptibility to their inhibition. This new knowledge has therefore served as a framework upon which to develop new pharmaceutical approaches. These include the continuing development of small molecules which act directly to inhibit the critical Myc-Max interaction, those which act indirectly to prevent Myc-directed post-translational modifications necessary to initiate productive transcription and those which inhibit vital pathways upon which the Myc-transformed cell is particularly reliant. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology.
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Affiliation(s)
- Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, USA; University of Maryland Greenebaum Cancer Center, Baltimore, USA
| | - Edward V Prochownik
- Section of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, USA; Department of Microbiology and Molecular Genetics, The University of Pittsburgh School of Medicine, USA; The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
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159
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Liu Z, Huang Y. Advantages of proteins being disordered. Protein Sci 2014; 23:539-50. [PMID: 24532081 DOI: 10.1002/pro.2443] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/09/2014] [Accepted: 02/10/2014] [Indexed: 12/28/2022]
Abstract
The past decade has witnessed great advances in our understanding of protein structure-function relationships in terms of the ubiquitous existence of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). The structural disorder of IDPs/IDRs enables them to play essential functions that are complementary to those of ordered proteins. In addition, IDPs/IDRs are persistent in evolution. Therefore, they are expected to possess some advantages over ordered proteins. In this review, we summarize and survey nine possible advantages of IDPs/IDRs: economizing genome/protein resources, overcoming steric restrictions in binding, achieving high specificity with low affinity, increasing binding rate, facilitating posttranslational modifications, enabling flexible linkers, preventing aggregation, providing resistance to non-native conditions, and allowing compatibility with more available sequences. Some potential advantages of IDPs/IDRs are not well understood and require both experimental and theoretical approaches to decipher. The connection with protein design is also briefly discussed.
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Affiliation(s)
- Zhirong Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China; State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking University, Beijing, 100871, China; Center for Quantitative Biology, Peking University, Beijing, 100871, China
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160
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Tóth G, Gardai SJ, Zago W, Bertoncini CW, Cremades N, Roy SL, Tambe MA, Rochet JC, Galvagnion C, Skibinski G, Finkbeiner S, Bova M, Regnstrom K, Chiou SS, Johnston J, Callaway K, Anderson JP, Jobling MF, Buell AK, Yednock TA, Knowles TPJ, Vendruscolo M, Christodoulou J, Dobson CM, Schenk D, McConlogue L. Targeting the intrinsically disordered structural ensemble of α-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease. PLoS One 2014; 9:e87133. [PMID: 24551051 PMCID: PMC3925190 DOI: 10.1371/journal.pone.0087133] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/19/2013] [Indexed: 12/22/2022] Open
Abstract
The misfolding of intrinsically disordered proteins such as α-synuclein, tau and the Aβ peptide has been associated with many highly debilitating neurodegenerative syndromes including Parkinson’s and Alzheimer’s diseases. Therapeutic targeting of the monomeric state of such intrinsically disordered proteins by small molecules has, however, been a major challenge because of their heterogeneous conformational properties. We show here that a combination of computational and experimental techniques has led to the identification of a drug-like phenyl-sulfonamide compound (ELN484228), that targets α-synuclein, a key protein in Parkinson’s disease. We found that this compound has substantial biological activity in cellular models of α-synuclein-mediated dysfunction, including rescue of α-synuclein-induced disruption of vesicle trafficking and dopaminergic neuronal loss and neurite retraction most likely by reducing the amount of α-synuclein targeted to sites of vesicle mobilization such as the synapse in neurons or the site of bead engulfment in microglial cells. These results indicate that targeting α-synuclein by small molecules represents a promising approach to the development of therapeutic treatments of Parkinson’s disease and related conditions.
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Affiliation(s)
- Gergely Tóth
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Elan Pharmaceuticals, South San Francisco, California, United States of America
- * E-mail: (LM); (GT); (MV); (DS); (CMD)
| | - Shyra J. Gardai
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - Wagner Zago
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - Carlos W. Bertoncini
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- SEDIPFAR (Servicio De Descubrimiento, Diseño Y Desarrollo Pre-Clínico De Fármacos De La Argentina) drug discovery platform, Universidad Nacional de Rosario, Rosario, Argentina
| | - Nunilo Cremades
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Susan L. Roy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Mitali A. Tambe
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Celine Galvagnion
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Gaia Skibinski
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
- Taube-Koret Center for Neurodegenerative Disease Research, The Consortium for Frontotemporal Dementia Research, and The Hellman Family Foundation Program for Alzheimer’s Disease Research, San Francisco, California, United States of America
| | - Steven Finkbeiner
- Gladstone Institute of Neurological Disease, San Francisco, California, United States of America
- Taube-Koret Center for Neurodegenerative Disease Research, The Consortium for Frontotemporal Dementia Research, and The Hellman Family Foundation Program for Alzheimer’s Disease Research, San Francisco, California, United States of America
- Departments of Neurology and Physiology, UCSF, San Francisco, California, United States of America
| | - Michael Bova
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - Karin Regnstrom
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - San-San Chiou
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - Jennifer Johnston
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - Kari Callaway
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - John P. Anderson
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - Michael F. Jobling
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | - Alexander K. Buell
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ted A. Yednock
- Elan Pharmaceuticals, South San Francisco, California, United States of America
| | | | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (LM); (GT); (MV); (DS); (CMD)
| | - John Christodoulou
- Department of Structural & Molecular Biology, University College London, London, United Kingdom
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (LM); (GT); (MV); (DS); (CMD)
| | - Dale Schenk
- Elan Pharmaceuticals, South San Francisco, California, United States of America
- * E-mail: (LM); (GT); (MV); (DS); (CMD)
| | - Lisa McConlogue
- Elan Pharmaceuticals, South San Francisco, California, United States of America
- * E-mail: (LM); (GT); (MV); (DS); (CMD)
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161
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Antoniali G, Lirussi L, Poletto M, Tell G. Emerging roles of the nucleolus in regulating the DNA damage response: the noncanonical DNA repair enzyme APE1/Ref-1 as a paradigmatical example. Antioxid Redox Signal 2014; 20:621-39. [PMID: 23879289 PMCID: PMC3901381 DOI: 10.1089/ars.2013.5491] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 07/22/2013] [Indexed: 12/25/2022]
Abstract
SIGNIFICANCE An emerging concept in DNA repair mechanisms is the evidence that some key enzymes, besides their role in the maintenance of genome stability, display also unexpected noncanonical functions associated with RNA metabolism in specific subcellular districts (e.g., nucleoli). During the evolution of these key enzymes, the acquisition of unfolded domains significantly amplified the possibility to interact with different partners and substrates, possibly explaining their phylogenetic gain of functions. RECENT ADVANCES After nucleolar stress or DNA damage, many DNA repair proteins can freely relocalize from nucleoli to the nucleoplasm. This process may represent a surveillance mechanism to monitor the synthesis and correct assembly of ribosomal units affecting cell cycle progression or inducing p53-mediated apoptosis or senescence. CRITICAL ISSUES A paradigm for this kind of regulation is represented by some enzymes of the DNA base excision repair (BER) pathway, such as apurinic/apyrimidinic endonuclease 1 (APE1). In this review, the role of the nucleolus and the noncanonical functions of the APE1 protein are discussed in light of their possible implications in human pathologies. FUTURE DIRECTIONS A productive cross-talk between DNA repair enzymes and proteins involved in RNA metabolism seems reasonable as the nucleolus is emerging as a dynamic functional hub that coordinates cell growth arrest and DNA repair mechanisms. These findings will drive further analyses on other BER proteins and might imply that nucleic acid processing enzymes are more versatile than originally thought having evolved DNA-targeted functions after a previous life in the early RNA world.
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Affiliation(s)
- Giulia Antoniali
- Department of Medical and Biological Sciences, University of Udine , Udine, Italy
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162
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Two potential therapeutic antibodies bind to a peptide segment of membrane-bound IgE in different conformations. Nat Commun 2014; 5:3139. [DOI: 10.1038/ncomms4139] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/17/2013] [Indexed: 11/09/2022] Open
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163
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Kathiriya JJ, Pathak RR, Clayman E, Xue B, Uversky VN, Davé V. Presence and utility of intrinsically disordered regions in kinases. ACTA ACUST UNITED AC 2014; 10:2876-88. [DOI: 10.1039/c4mb00224e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We reveal presence of intrinsically disordered regions in human kinome and build a kinase–kinase interaction network identifying a novel SRC–SMAD relationship.
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Affiliation(s)
- Jaymin J. Kathiriya
- Morsani College of Medicine
- Department of Pathology and Cell Biology
- University of South Florida
- Tampa, USA
| | - Ravi Ramesh Pathak
- Morsani College of Medicine
- Department of Pathology and Cell Biology
- University of South Florida
- Tampa, USA
| | - Eric Clayman
- Morsani College of Medicine
- Department of Pathology and Cell Biology
- University of South Florida
- Tampa, USA
| | - Bin Xue
- Department of Cell Biology
- Microbiology and Molecular Biology
- University of South Florida
- Tampa, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine
- University of South Florida
- Tampa, USA
- USF Health Byrd Alzheimer's Research Institute
- University of South Florida
| | - Vrushank Davé
- Morsani College of Medicine
- Department of Pathology and Cell Biology
- University of South Florida
- Tampa, USA
- Department of Molecular Oncology
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164
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Free-Energy Landscape of Intrinsically Disordered Proteins Investigated by All-Atom Multicanonical Molecular Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:331-51. [DOI: 10.1007/978-3-319-02970-2_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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165
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Sangsuriya P, Huang JY, Chu YF, Phiwsaiya K, Leekitcharoenphon P, Meemetta W, Senapin S, Huang WP, Withyachumnarnkul B, Flegel TW, Lo CF. Construction and application of a protein interaction map for white spot syndrome virus (WSSV). Mol Cell Proteomics 2014; 13:269-82. [PMID: 24217020 PMCID: PMC3879619 DOI: 10.1074/mcp.m113.029199] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 10/21/2013] [Indexed: 01/28/2023] Open
Abstract
White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ∼28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein-protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture.
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Affiliation(s)
- Pakkakul Sangsuriya
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- §Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Jiun-Yan Huang
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Yu-Fei Chu
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Kornsunee Phiwsaiya
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- ‖National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pimlapas Leekitcharoenphon
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Watcharachai Meemetta
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Saengchan Senapin
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- ‖National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wei-Pang Huang
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Boonsirm Withyachumnarnkul
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- **Shrimp Genetic Improvement Center, Surat Thani 84100, Thailand
- ‡‡Department of Anatomy, Faculty of Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Timothy W. Flegel
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- ‖National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chu-Fang Lo
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
- ¶¶Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, Republic of China
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166
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Bjerregaard-Andersen K, Perdreau-Dahl H, Guldsten H, Praetorius J, Jensen JK, Morth JP. The N-terminal cytoplasmic region of NCBE displays features of an intrinsic disordered structure and represents a novel target for specific drug screening. Front Physiol 2013; 4:320. [PMID: 24223558 PMCID: PMC3819638 DOI: 10.3389/fphys.2013.00320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/15/2013] [Indexed: 01/18/2023] Open
Abstract
The sodium dependent bicarbonate transporter NCBE/NBCn2 is predominantly expressed in the central nervous system (CNS). The highest protein concentrations are found in the choroid plexus. The primary function of this integral plasma membrane transport protein is to regulate intracellular neuronal pH and also probably to maintain the pH homeostasis across the blood-cerebrospinal fluid barrier. NCBE is predicted to contain at least 10 transmembrane helices. The N- and C- termini are both cytoplasmic, with a large N-terminal domain (Nt-NCBE) and a relatively small C-terminal domain (Ct-NCBE). The Nt-NCBE is likely to be involved in bicarbonate recognition and transport and contains key areas of regulation involving pH sensing and protein-protein interactions. Intrinsic disordered protein regions (IDPRs) are defined as protein regions having no rigid three-dimensional structure under physiological conditions. They are believed to be involved in signaling networks in which specific, low affinity, protein-protein interactions play an important role. We predict that NCBE and other SoLute Carrier 4 (SLC4) family members have a high level of intrinsic disorder in their cytoplasmic regions. To provide biophysical evidence for the IDPRs predicted in Nt-NCBE, we produced pure (>99%), recombinant Nt-NCBE using E. coli as the expression host. The protein was used to perform differential scanning fluorescence spectroscopy (DSF), in order to search for small molecules that would induce secondary or tertiary structure in the IDPRs. We expect this to assist the development of selective pharmaceutical compounds against individual SLC4 family members. We have also determined a low resolution (4 Å) X-ray crystal structure of the N-terminal core domain. The N-terminal cytoplasmic domain (cdb3) of anion exchanger 1 (AE1) shares a similar fold with the N-terminal core domain of NCBE. Crystallization conditions for the full-length N-terminal domain have been sought, but only the core domain yields diffracting crystals.
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Affiliation(s)
- Kaare Bjerregaard-Andersen
- Norwegian Centre for Molecular Medicine, University of Oslo Oslo, Norway ; Danish Chinese Centre for Cancer and Proteases, Department for Molecular Biology and Genetics, University of Aarhus Aarhus, Denmark
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167
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Varadi M, Kosol S, Lebrun P, Valentini E, Blackledge M, Dunker AK, Felli IC, Forman-Kay JD, Kriwacki RW, Pierattelli R, Sussman J, Svergun DI, Uversky VN, Vendruscolo M, Wishart D, Wright PE, Tompa P. pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic Acids Res 2013; 42:D326-35. [PMID: 24174539 PMCID: PMC3964940 DOI: 10.1093/nar/gkt960] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states.
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Affiliation(s)
- Mihaly Varadi
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, Germany, CEA, CNRS, UJF-Grenoble 1, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble 38027, France, Indiana University School of Medicine; Indianapolis, IN, USA, Department of Chemistry, Center of Magnetic Resonance (CERM), University of Florence, Sesto Fiorentino, Italy, Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA, Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, Department of Chemistry, University of Cambridge, Cambridge, UK, Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest
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168
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Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins. PLoS Comput Biol 2013; 9:e1003249. [PMID: 24098099 PMCID: PMC3789766 DOI: 10.1371/journal.pcbi.1003249] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 08/15/2013] [Indexed: 11/19/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) were found to be widely associated with human diseases and may serve as potential drug design targets. However, drug design targeting IDPs is still in the very early stages. Progress in drug design is usually achieved using experimental screening; however, the structural disorder of IDPs makes it difficult to characterize their interaction with ligands using experiments alone. To better understand the structure of IDPs and their interactions with small molecule ligands, we performed extensive simulations on the c-Myc₃₇₀₋₄₀₉ peptide and its binding to a reported small molecule inhibitor, ligand 10074-A4. We found that the conformational space of the apo c-Myc₃₇₀₋₄₀₉ peptide was rather dispersed and that the conformations of the peptide were stabilized mainly by charge interactions and hydrogen bonds. Under the binding of the ligand, c-Myc₃₇₀₋₄₀₉ remained disordered. The ligand was found to bind to c-Myc₃₇₀₋₄₀₉ at different sites along the chain and behaved like a 'ligand cloud'. In contrast to ligand binding to more rigid target proteins that usually results in a dominant bound structure, ligand binding to IDPs may better be described as ligand clouds around protein clouds. Nevertheless, the binding of the ligand and a non-ligand to the c-Myc₃₇₀₋₄₀₉ target could be clearly distinguished. The present study provides insights that will help improve rational drug design that targets IDPs.
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169
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How to design a drug for the disordered proteins? Drug Discov Today 2013; 18:910-5. [DOI: 10.1016/j.drudis.2013.04.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/25/2013] [Accepted: 04/22/2013] [Indexed: 11/20/2022]
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170
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Camilloni C, Vendruscolo M. A relationship between the aggregation rates of α-synuclein variants and the β-sheet populations in their monomeric forms. J Phys Chem B 2013; 117:10737-41. [PMID: 23941114 DOI: 10.1021/jp405614j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Intrinsically disordered proteins constitute a significant part of the human proteome and carry out a wide range of different functions, including in particular signaling and regulation. Several of these proteins are vulnerable to aggregation, and their aberrant assemblies have been associated with a variety of neurodegenerative and systemic diseases. It remains unclear, however, the extent to which the conformational properties of intrinsically disordered proteins in their monomeric states influence the aggregation behavior of these molecules. Here we report a relationship between aggregation rates and secondary structure populations in the soluble monomeric states of a series of mutational variants of α-synuclein. Overall, we found a correlation of over 90% between the changes in β-sheet populations calculated from NMR chemical shift data and the changes in aggregation rates for eight human-to-mouse chimeric mutants. These results provide support to the idea of investigating therapeutic strategies based on the stabilization of the monomeric form of intrinsically disordered proteins through the alteration of their conformational properties.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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171
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Jin F, Liu Z. Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins. Biophys J 2013; 104:488-95. [PMID: 23442871 DOI: 10.1016/j.bpj.2012.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 11/17/2022] Open
Abstract
Intrinsically disordered proteins do not have stable secondary and/or tertiary structures but still function. More than 50 prediction methods have been developed and inherent relationships may be expected to exist among them. To investigate this, we conducted molecular simulations and algorithmic analyses on a minimal coarse-grained polypeptide model and discovered a common basis for the charge-hydropathy plot and packing-density algorithms that was verified by correlation analysis. The correlation analysis approach was applied to realistic datasets, which revealed correlations among some physical-chemical properties (charge-hydropathy plot, packing density, pairwise energy). The correlations indicated that these biophysical methods find a projected direction to discriminate ordered and disordered proteins. The optimized projection was determined and the ultimate accuracy limit of the existing algorithms is discussed.
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Affiliation(s)
- Fan Jin
- College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
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172
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Zhu M, Simone AD, Schenk D, Toth G, Dobson CM, Vendruscolo M. Identification of small-molecule binding pockets in the soluble monomeric form of the Aβ42 peptide. J Chem Phys 2013; 139:035101. [PMID: 23883055 PMCID: PMC5011423 DOI: 10.1063/1.4811831] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The aggregation of intrinsically disordered peptides and proteins is associated with a wide range of highly debilitating neurological and systemic disorders. In this work we explored the potential of a structure-based drug discovery procedure to target one such system, the soluble monomeric form of the Aβ42 peptide. We utilised for this purpose a set of structures of the Aβ42 peptide selected from clusters of conformations within an ensemble generated by molecular dynamics simulations. Using these structures we carried out fragment mapping calculations to identify binding "hot spots" on the monomeric form of the Aβ42 peptide. This procedure provided a set of hot spots with ligand efficiencies comparable to those observed for structured proteins, and clustered into binding pockets. Such binding pockets exhibited a propensity to bind small molecules known to interact with the Aβ42 peptide. Taken together these results provide an initial indication that fragment-based drug discovery may represent a potential therapeutic strategy for diseases associated with the aggregation of intrinsically disordered proteins.
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Affiliation(s)
- Maximillian Zhu
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Alfonso De Simone
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Dale Schenk
- Elan Pharmaceuticals, South San Francisco, CA 94080, USA
| | - Gergely Toth
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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173
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Choi UB, Kazi R, Stenzoski N, Wollmuth LP, Uversky VN, Bowen ME. Modulating the intrinsic disorder in the cytoplasmic domain alters the biological activity of the N-methyl-D-aspartate-sensitive glutamate receptor. J Biol Chem 2013; 288:22506-15. [PMID: 23782697 DOI: 10.1074/jbc.m113.477810] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The NMDA-sensitive glutamate receptor is a ligand-gated ion channel that mediates excitatory synaptic transmission in the nervous system. Extracellular zinc allosterically regulates the NMDA receptor by binding to the extracellular N-terminal domain, which inhibits channel gating. Phosphorylation of the intrinsically disordered intracellular C-terminal domain alleviates inhibition by extracellular zinc. The mechanism for this functional effect is largely unknown. Proline is a hallmark of intrinsic disorder, so we used proline mutagenesis to modulate disorder in the cytoplasmic domain. Proline depletion selectively uncoupled zinc inhibition with little effect on receptor biogenesis, surface trafficking, or ligand-activated gating. Proline depletion also reduced the affinity for a PDZ domain involved in synaptic trafficking and affected small molecule binding. To understand the origin of these phenomena, we used single molecule fluorescence and ensemble biophysical methods to characterize the structural effects of proline mutagenesis. Proline depletion did not eliminate intrinsic disorder, but the underlying conformational dynamics were changed. Thus, we altered the form of intrinsic disorder, which appears sufficient to affect the biological activity. These findings suggest that conformational dynamics within the intrinsically disordered cytoplasmic domain are important for the allosteric regulation of NMDA receptor gating.
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Affiliation(s)
- Ucheor B Choi
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
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174
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Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM. Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr Opin Struct Biol 2013; 23:443-50. [DOI: 10.1016/j.sbi.2013.03.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/19/2013] [Accepted: 03/25/2013] [Indexed: 12/31/2022]
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175
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Nath A, Sammalkorpi M, DeWitt DC, Trexler AJ, Elbaum-Garfinkle S, O'Hern CS, Rhoades E. The conformational ensembles of α-synuclein and tau: combining single-molecule FRET and simulations. Biophys J 2013. [PMID: 23199922 DOI: 10.1016/j.bpj.2012.09.032] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are increasingly recognized for their important roles in a range of biological contexts, both in normal physiological function and in a variety of devastating human diseases. However, their structural characterization by traditional biophysical methods, for the purposes of understanding their function and dysfunction, has proved challenging. Here, we investigate the model IDPs α-Synuclein (αS) and tau, that are involved in major neurodegenerative conditions including Parkinson's and Alzheimer's diseases, using excluded volume Monte Carlo simulations constrained by pairwise distance distributions from single-molecule fluorescence measurements. Using this, to our knowledge, novel approach we find that a relatively small number of intermolecular distance constraints are sufficient to accurately determine the dimensions and polymer conformational statistics of αS and tau in solution. Moreover, this method can detect local changes in αS and tau conformations that correlate with enhanced aggregation. Constrained Monte Carlo simulations produce ensembles that are in excellent agreement both with experimental measurements on αS and tau and with all-atom, explicit solvent molecular dynamics simulations of αS, with much lower configurational sampling requirements and computational expense.
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Affiliation(s)
- Abhinav Nath
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
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176
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Herbert C, Schieborr U, Saxena K, Juraszek J, De Smet F, Alcouffe C, Bianciotto M, Saladino G, Sibrac D, Kudlinzki D, Sreeramulu S, Brown A, Rigon P, Herault JP, Lassalle G, Blundell TL, Rousseau F, Gils A, Schymkowitz J, Tompa P, Herbert JM, Carmeliet P, Gervasio FL, Schwalbe H, Bono F. Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling. Cancer Cell 2013; 23:489-501. [PMID: 23597563 DOI: 10.1016/j.ccr.2013.02.018] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 12/12/2012] [Accepted: 02/19/2013] [Indexed: 01/12/2023]
Abstract
The fibroblast growth factor (FGF)/fibroblast growth factor receptor (FGFR) signaling network plays an important role in cell growth, survival, differentiation, and angiogenesis. Deregulation of FGFR signaling can lead to cancer development. Here, we report an FGFR inhibitor, SSR128129E (SSR), that binds to the extracellular part of the receptor. SSR does not compete with FGF for binding to FGFR but inhibits FGF-induced signaling linked to FGFR internalization in an allosteric manner, as shown by crystallography studies, nuclear magnetic resonance, Fourier transform infrared spectroscopy, molecular dynamics simulations, free energy calculations, structure-activity relationship analysis, and FGFR mutagenesis. Overall, SSR is a small molecule allosteric inhibitor of FGF/FGFR signaling, acting via binding to the extracellular part of the FGFR.
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Affiliation(s)
- Corentin Herbert
- E2C and LGCR-SDI Department, Sanofi Research and Development, 31100 Toulouse, France
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177
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Takakusagi Y, Manita D, Kusayanagi T, Izaguirre-Carbonell J, Takakusagi K, Kuramochi K, Iwabata K, Kanai Y, Sakaguchi K, Sugawara F. Mapping a disordered portion of the Brz2001-binding site on a plant monooxygenase, DWARF4, using a quartz-crystal microbalance biosensor-based T7 phage display. Assay Drug Dev Technol 2013; 11:206-15. [PMID: 23514038 DOI: 10.1089/adt.2012.478] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In small-molecule/protein interaction studies, technical difficulties such as low solubility of small molecules or low abundance of protein samples often restrict the progress of research. Here, we describe a quartz-crystal microbalance (QCM) biosensor-based T7 phage display in combination use with a receptor-ligand contacts (RELIC) bioinformatics server for application in a plant Brz2001/DWARF4 system. Brz2001 is a brassinosteroid biosynthesis inhibitor in the less-soluble triazole series of compounds that targets DWARF4, a cytochrome P450 (Cyp450) monooxygenase containing heme and iron. Using a Brz2001 derivative that has higher solubility in 70% EtOH and forms a self-assembled monolayer on gold electrode, we selected 34 Brz2001-recognizing peptides from a 15-mer T7 phage-displayed random peptide library using a total of four sets of one-cycle biopanning. The RELIC/MOTIF program revealed continuous and discontinuous short motifs conserved within the 34 Brz2001-selected 15-mer peptide sequences, indicating the increase of information content for Brz2001 recognition. Furthermore, an analysis of similarity between the 34 peptides and the amino-acid sequence of DWARF4 using the RELIC/MATCH program generated a similarity plot and a cluster diagram of the amino-acid sequence. Both of these data highlighted an internally located disordered portion of a catalytic site on DWARF4, indicating that this portion is essential for Brz2001 recognition. A similar trend was also noted by an analysis using another 26 Brz2001-selected peptides, and not observed using the 27 gold electrode-recognizing control peptides, demonstrating the reproducibility and specificity of this method. Thus, this affinity-based strategy enables high-throughput detection of the small-molecule-recognizing portion on the target protein, which overcomes technical difficulties such as sample solubility or preparation that occur when conventional methods are used.
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Affiliation(s)
- Yoichi Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
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178
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Messori L, Camarri M, Ferraro T, Gabbiani C, Franceschini D. Promising in Vitro anti-Alzheimer Properties for a Ruthenium(III) Complex. ACS Med Chem Lett 2013; 4:329-32. [PMID: 24900669 DOI: 10.1021/ml3003567] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 02/13/2013] [Indexed: 11/28/2022] Open
Abstract
Metal complexes represent today an attractive class of experimental anti-Alzheimer agents with the potential of blocking β-amyloid 1-42 aggregation and scavenging its toxicity. Three representative ruthenium(III) complexes, namely NAMI A, KP1019, and PMRU20, were specifically evaluated to this end in an established in vitro model of AD relying on primary cortical neurons. Notably, PMRU20 turned out to be highly effective in protecting cortical neurons against Aβ 1-42 toxicity, while the other tested ruthenium compounds were poorly active or even inactive; we also found that PMRU20 is virtually devoid of any significant toxicity in vitro at the applied concentrations. Interestingly, PMRU20 was neuroprotective even against the toxicity induced by Aβ 25-35. The direct reaction of PMRU20 with Aβ 1-42 was explored through ESI MS analysis and some adduct formation evidenced. In addition, thioflavin T assays revealed that PMRU20 greatly reduces Aβ 1-42 aggregation. The implications of these findings are discussed in relation to emerging treatment strategies for the Alzheimer's disease.
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Affiliation(s)
- Luigi Messori
- Department of Chemistry “Ugo
Schiff”, University of Florence,
Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Michela Camarri
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, 53100, Siena, Italy
| | - Teresa Ferraro
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, 53100, Siena, Italy
| | - Chiara Gabbiani
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Davide Franceschini
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, 53100, Siena, Italy
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179
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Knapman TW, Valette NM, Warriner SL, Ashcroft AE. Ion Mobility Spectrometry-Mass Spectrometry of Intrinsically Unfolded Proteins: Trying to Put Order into Disorder. CURR ANAL CHEM 2013; 9:181-191. [PMID: 23885220 PMCID: PMC3706957 DOI: 10.2174/1573411011309020004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 12/15/2011] [Accepted: 05/09/2012] [Indexed: 12/17/2022]
Abstract
Intrinsically disordered proteins do not adopt well-defined native structures and therefore present an intriguing challenge in terms of structural elucidation as they are relatively inaccessible to traditional approaches such as NMR and X-ray crystallography. Many members of this important group of proteins have a distinct biological function and frequently undergo a conformational change on binding to their physiological targets which can in turn modulate their function. Furthermore, many intrinsically unstructured proteins are associated with a wide range of major diseases including cancer and amyloid-related disorders. Here, electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) has been used to probe the conformational characteristics of two intrinsically disordered proteins: apo-cytochrome c and apo-osteocalcin. Both proteins are structured in their holo-states when bound to their respective substrates, but disordered in their apo-states. Here, the conformational properties of the holo- and the apo-protein forms for both species have been analysed and their mass spectral data and ion mobility spectrometry-derived collision cross-sectional areas, indicative of their physical size, compared to study the relationship between substrate binding and tertiary structure. In both cases, the intrinsically unstructured apo-states populated multiple conformations with larger cross-sectional areas than their holo-analogues, suggesting that intrinsic disorder in proteins does not preclude the formation of preferred conformations. Additionally, analysis of truncated analogues of osteocalcin has located the region of the protein responsible for the conformational changes detected upon metal cation binding. Together, the data illustrate the scope and utility of ESI-IMS-MS for studying the characteristics and properties of intrinsically disordered proteins whose analysis by other techniques is limited.
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Affiliation(s)
- T W Knapman
- Astbury Centre for Structural Molecular Biology, Faculty of Mathematics and Physical Sciences, University of Leeds, Leeds, LS2 9JT, UK
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180
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Mao AH, Lyle N, Pappu RV. Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J 2013; 449:307-18. [PMID: 23240611 PMCID: PMC4074364 DOI: 10.1042/bj20121346] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Intrinsically disordered proteins participate in important protein-protein and protein-nucleic acid interactions and control cellular phenotypes through their prominence as dynamic organizers of transcriptional, post-transcriptional and signalling networks. These proteins challenge the tenets of the structure-function paradigm and their functional mechanisms remain a mystery given that they fail to fold autonomously into specific structures. Solving this mystery requires a first principles understanding of the quantitative relationships between information encoded in the sequences of disordered proteins and the ensemble of conformations they sample. Advances in quantifying sequence-ensemble relationships have been facilitated through a four-way synergy between bioinformatics, biophysical experiments, computer simulations and polymer physics theories. In the present review we evaluate these advances and the resultant insights that allow us to develop a concise quantitative framework for describing the sequence-ensemble relationships of intrinsically disordered proteins.
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Affiliation(s)
- Albert H. Mao
- Medical Scientist Training Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
- Computational & Molecular Biophysics Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
| | - Nicholas Lyle
- Computational & Systems Biology Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
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181
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Oldfield CJ, Xue B, Van YY, Ulrich EL, Markley JL, Dunker AK, Uversky VN. Utilization of protein intrinsic disorder knowledge in structural proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:487-98. [PMID: 23232152 DOI: 10.1016/j.bbapap.2012.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 12/02/2012] [Accepted: 12/03/2012] [Indexed: 12/01/2022]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed.
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Affiliation(s)
- Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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182
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Verzele D, Madder A. Synthetic Progress in cMyc-Max Oncoprotein Miniaturization: Semi-Online Monitoring Gives Solid-Phase Access to Hydrophobic b(-HLH-)ZIP Peptidosteroid Tweezers. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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183
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Harvey SR, Porrini M, Stachl C, MacMillan D, Zinzalla G, Barran PE. Small-molecule inhibition of c-MYC:MAX leucine zipper formation is revealed by ion mobility mass spectrometry. J Am Chem Soc 2012; 134:19384-92. [PMID: 23106332 DOI: 10.1021/ja306519h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The leucine zipper interaction between MAX and c-MYC has been studied using mass spectrometry and drift time ion mobility mass spectrometry (DT IM-MS) in addition to circular dichroism spectroscopy. Peptides comprising the leucine zipper sequence with (c-MYC-Zip residues 402-434) and without a postulated small-molecule binding region (c-MYC-ZipΔDT residues 406-434) have been synthesized, along with the corresponding MAX leucine zipper (MAX-Zip residues 74-102). c-MYC-Zip:MAX-Zip complexes are observed both in the absence and in the presence of the reported small-molecule inhibitor 10058-F4 for both forms of c-MYC-Zip. DT IM-MS, in combination with molecular dynamics (MD), shows that the c-MYC-Zip:MAX-Zip complex [M+5H](5+) exists in two conformations, one extended with a collision cross section (CCS) of 1164 ± 9.3 Å(2) and one compact with a CCS of 982 ± 6.6 Å(2); similar values are observed for the two forms of c-MYC-ZipΔDT:MAX-Zip. Candidate geometries for the complexes have been evaluated with MD simulations. The helical leucine zipper structure previously determined from NMR measurements (Lavigne, P.; et al. J. Mol. Biol. 1998, 281, 165), altered to include the DT region and subjected to a gas-phase minimization, yields a CCS of 1247 Å(2), which agrees with the extended conformation we observe experimentally. More extensive MD simulations provide compact complexes which are found to be highly disordered, with CCSs that correspond to the compact form from experiment. In the presence of the ligand, the leucine zipper conformation is completely inhibited and only the more disordered species is observed, providing a novel method to study the effect of interactions of disordered systems and subsequent inhibition of the formation of an ordered helical complex.
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Affiliation(s)
- Sophie R Harvey
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
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184
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Abstract
IDPs (intrinsically disordered proteins) play crucial roles in many important cellular processes such as signalling or transcription and are attractive therapeutic targets for several diseases. The considerable structural flexibility of IDPs poses a challenge for rational drug discovery approaches. Consequently, structure-based drug design efforts to date have mostly focused on inhibiting interactions of IDPs with other proteins whose structure can be solved by conventional biophysical methods. Yet, in recent years, several examples of small molecules that bind to monomeric IDPs in their disordered states have been reported, suggesting that this approach may offer new opportunities for therapeutic interventions. Further developments of this strategy will greatly benefit from an improved understanding of molecular recognition mechanisms between small molecules and IDPs. The present article summarizes findings from experimental and computational studies of the mechanisms of interaction between small molecules and three IDPs in their disordered states: c-Myc, Aβ (amyloid β-peptide) and α-synuclein.
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185
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Tompa P. Intrinsically disordered proteins: a 10-year recap. Trends Biochem Sci 2012; 37:509-16. [PMID: 22989858 DOI: 10.1016/j.tibs.2012.08.004] [Citation(s) in RCA: 469] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 08/12/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
Abstract
The suggestion that the native state of many proteins is intrinsically disordered (or, as originally termed, unstructured) is now integral to our general view of protein structure and function. A little more than 10 years ago, however, such challenge to the almost dogmatic 'structure-function paradigm' was pure heresy due to the overwhelming evidence that structure determines function. A decade of steady progress turned skepticism around: this 10-year recap review outlines the situation a decade ago and the major directions of the breathtaking advance achieved by experimental and computational approaches. I show that the evidence for the generality and importance of this phenomenon is now so insurmountable that it demands the inclusion of 'unstructural' biology into mainstream biology and biochemistry textbooks.
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Affiliation(s)
- Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium.
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186
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Kalmar L, Homola D, Varga G, Tompa P. Structural disorder in proteins brings order to crystal growth in biomineralization. Bone 2012; 51:528-34. [PMID: 22634174 DOI: 10.1016/j.bone.2012.05.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/17/2012] [Accepted: 05/16/2012] [Indexed: 11/21/2022]
Abstract
Biomineralization, the generation of hard tissues of living organisms, is a process strictly regulated by hormones, enzymes and a range of regulatory proteins of which several resisted structural characterization thus far. Without actual generalizations, there have been scattered observations in the literature for the structural disorder of these proteins. To address this issue in general, we have collected SwissProt proteins involved in the formation of bone and teeth in vertebrates, annotated for biomineralization. All these proteins show an extremely high level of predicted disorder (with a mean of 53%), making them the most disordered functional class of the protein world. Exactly the same feature was established for evolutionarily more distant proteins involved in the formation of the silica wall of marine diatoms and the shell of oysters and other mollusks. Because these proteins also show an extremely biased amino acid composition, such as high negative charge, high frequency of Ser and Asp or Pro residues and repetitiveness, we also carried out a database search with these sequence features for further proteins. This search uncovered several further disordered proteins with clearly related functions, although their annotations made no mention of biomineralization. This general and very strong correlation between biomineralization, structural disorder of proteins and particular sequence features indicates that regulated growth of mineral phase in biology can only be achieved by the assistance of highly disordered proteins.
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Affiliation(s)
- Lajos Kalmar
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
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187
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Receveur-Brechot V, Durand D. How random are intrinsically disordered proteins? A small angle scattering perspective. Curr Protein Pept Sci 2012; 13:55-75. [PMID: 22044150 PMCID: PMC3394175 DOI: 10.2174/138920312799277901] [Citation(s) in RCA: 267] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 01/08/2023]
Abstract
While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex, are then reviewed. Indeed, recent computational advances have made it possible to readily extract maximum information from the scattering curve with a special emphasis on highly flexible systems, such as multidomain proteins and IDPs. Furthermore, integrated computational approaches now enable the generation of ensembles of conformers to translate the unique flexible characteristics of IDPs by taking into consideration the constraints of more and more various complementary experiment. In particular, a combination of SAXS with high-resolution techniques, such as x-ray crystallography and NMR, allows us to provide reliable models and to gain unique structural insights about the protein over multiple structural scales. The latest neutron scattering experiments also promise new advances in the study of the conformational changes of macromolecules involving more complex systems.
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188
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Wang Y, Cesena TI, Ohnishi Y, Burger-Caplan R, Lam V, Kirchhoff PD, Larsen SD, Larsen MJ, Nestler EJ, Rudenko G. Small molecule screening identifies regulators of the transcription factor ΔFosB. ACS Chem Neurosci 2012; 3:546-56. [PMID: 22860224 DOI: 10.1021/cn3000235] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/29/2012] [Indexed: 11/28/2022] Open
Abstract
ΔFosB protein accumulates in the striatum in response to chronic administration of drugs of abuse, L-DOPA, or stress, triggering long lasting neural and behavioral changes that underlie aspects of drug addiction, abnormal involuntary movements (dyskinesia), and depression. ΔFosB binds AP-1 DNA consensus sequences found in promoters of many genes and can both repress or activate gene transcription. In the striatum, ΔFosB is thought to dimerize with JunD to form a functional transcription factor, though strikingly JunD does not accumulate in parallel. One explanation is that ΔFosB can recruit different partners, including itself, depending on the neuron type in which it is induced and the chronic stimulus, generating protein complexes with different effects on gene transcription. To develop chemical probes to study ΔFosB, a high-throughput screen was carried out to identify small molecules that modulate ΔFosB function. Two compounds with low micromolar activity, termed C2 and C6, disrupt the binding of ΔFosB to DNA via different mechanisms, and in in vitro assays stimulate ΔFosB-mediated transcription. In cocaine-treated mice, C2 significantly elevates mRNA levels of the AMPA glutamate receptor GluR2 subunit with specificity, a known target gene of ΔFosB that plays a role in drug addiction and endogenous resilience mechanisms. C2 and C6 show different activities against ΔFosB homodimers compared to ΔFosB/JunD heterodimers, suggesting that these compounds can be used as probes to study the contribution of different ΔFosB-containing complexes on the regulation of gene transcription in biological systems and to assess the utility of ΔFosB as a therapeutic target.
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Affiliation(s)
| | | | - Yoko Ohnishi
- Fishberg Department of Neuroscience
and Friedman Brain Institute, Mount Sinai School of Medicine, New
York, New York 10029, United States
| | - Rebecca Burger-Caplan
- Fishberg Department of Neuroscience
and Friedman Brain Institute, Mount Sinai School of Medicine, New
York, New York 10029, United States
| | | | | | | | | | - Eric J. Nestler
- Fishberg Department of Neuroscience
and Friedman Brain Institute, Mount Sinai School of Medicine, New
York, New York 10029, United States
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189
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Goyal S, Gupta G, Qin H, Upadya MH, Tan YJ, Chow VTK, Song J. VAPC, an human endogenous inhibitor for hepatitis C virus (HCV) infection, is intrinsically unstructured but forms a "fuzzy complex" with HCV NS5B. PLoS One 2012; 7:e40341. [PMID: 22815741 PMCID: PMC3398895 DOI: 10.1371/journal.pone.0040341] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 06/04/2012] [Indexed: 01/11/2023] Open
Abstract
Nearly 200 million people are infected by hepatitis C virus (HCV) worldwide. For replicating the HCV genome, the membrane-associated machinery needs to be formed by both HCV non-structural proteins (including NS5B) and human host factors such as VAPB. Recently, the 99-residue VAPC, a splicing variant of VAPB, was demonstrated to inhibit HCV replication via binding to NS5B, thus acting as an endogenous inhibitor of HCV infection. So far, the structure of VAPC remains unknown, and its interaction with NS5B has not been biophysically characterized. In this study, we conducted extensive CD and NMR investigations on VAPC which led to several striking findings: 1) although the N-terminal 70 residues are identical in VAPC and VAPB, they constitute the characteristic β-barrel MSP fold in VAPB, while VAPC is entirely unstructured in solution, only with helical-like conformations weakly populated. 2) VAPC is indeed capable of binding to NS5B, with an average dissociation constant (Kd) of ∼20 µM. Intriguingly, VAPC remains dynamic even in the complex, suggesting that the VAPC-NS5B is a “fuzzy complex”. 3) NMR mapping revealed that the major binding region for NS5B is located over the C-terminal half of VAPC, which is composed of three discrete clusters, of which only the first contains the region identical in VAPC and VAPB. The second region containing ∼12 residues appears to play a key role in binding since mutation of 4 residues within this region leads to almost complete loss of the binding activity. 4) A 14-residue mimetic, VAPC-14 containing the second region, only has a ∼3-fold reduction of the affinity. Our study not only provides critical insights into how a human factor mediates the formation of the HCV replication machinery, but also leads to design of VAPC-14 which may be further used to explore the function of VAPC and to develop anti-HCV molecules.
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Affiliation(s)
- Shaveta Goyal
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
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190
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Michel J, Cuchillo R. The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-myc. PLoS One 2012; 7:e41070. [PMID: 22815918 PMCID: PMC3397933 DOI: 10.1371/journal.pone.0041070] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins are attractive therapeutic targets owing to their prevalence in several diseases. Yet their lack of well-defined structure renders ligand discovery a challenging task. An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers. Transcriptional activity of c-Myc is dependent on heterodimerization with partner protein Max. This protein-protein interaction is disrupted by the small molecule 10058-F4 (1), that binds to monomeric and disordered c-Myc. To rationalize the mechanism of inhibition, structural ensembles for the segment of the c-Myc domain that binds to 1 were computed in the absence and presence of the ligand using classical force fields and explicit solvent metadynamics molecular simulations. The accuracy of the computed structural ensembles was assessed by comparison of predicted and measured NMR chemical shifts. The small molecule 1 was found to perturb the composition of the apo equilibrium ensemble and to bind weakly to multiple distinct c-Myc conformations. Comparison of the apo and holo equilibrium ensembles reveals that the c-Myc conformations binding 1 are already partially formed in the apo ensemble, suggesting that 1 binds to c-Myc through an extended conformational selection mechanism. The present results have important implications for rational ligand design efforts targeting intrinsically disordered proteins.
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Affiliation(s)
- Julien Michel
- EastCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom.
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191
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Nagulapalli M, Parigi G, Yuan J, Gsponer J, Deraos G, Bamm VV, Harauz G, Matsoukas J, de Planque MRR, Gerothanassis IP, Babu MM, Luchinat C, Tzakos AG. Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex. Structure 2012; 20:522-33. [PMID: 22405011 DOI: 10.1016/j.str.2012.01.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 12/01/2011] [Accepted: 01/03/2012] [Indexed: 11/18/2022]
Abstract
Protein interactions within regulatory networks should adapt in a spatiotemporal-dependent dynamic environment, in order to process and respond to diverse and versatile cellular signals. However, the principles governing recognition pliability in protein complexes are not well understood. We have investigated a region of the intrinsically disordered protein myelin basic protein (MBP(145-165)) that interacts with calmodulin, but that also promiscuously binds other biomolecules (membranes, modifying enzymes). To characterize this interaction, we implemented an NMR spectroscopic approach that calculates, for each conformation of the complex, the maximum occurrence based on recorded pseudocontact shifts and residual dipolar couplings. We found that the MBP(145-165)-calmodulin interaction is characterized by structural heterogeneity. Quantitative comparative analysis indicated that distinct conformational landscapes of structural heterogeneity are sampled for different calmodulin-target complexes. Such structural heterogeneity in protein complexes could potentially explain the way that transient and promiscuous protein interactions are optimized and tuned in complex regulatory networks.
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Affiliation(s)
- Malini Nagulapalli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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192
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Gupta G, Qin H, Song J. Intrinsically unstructured domain 3 of hepatitis C Virus NS5A forms a "fuzzy complex" with VAPB-MSP domain which carries ALS-causing mutations. PLoS One 2012; 7:e39261. [PMID: 22720086 PMCID: PMC3374797 DOI: 10.1371/journal.pone.0039261] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/22/2012] [Indexed: 01/26/2023] Open
Abstract
Hepatitis C virus (HCV) affects nearly 200 million people worldwide and is a leading factor for serious chronic liver diseases. For replicating HCV genome, the membrane-associated replication machinery needs to be formed by both HCV non-structural proteins including NS5A and human host factors. Recently NS5A has been identified to bind ER-anchored human VAP proteins and consequently this interaction may serve as a novel target for design of anti-HCV drugs. So far no biophysical characterization of this interaction has been reported. Here, we dissected the 243-residue VAPB into 4 and 447-residue NS5A into 10 fragments, followed by CD and NMR characterization of their structural properties. Subsequently, binding interactions between these fragments have been extensively assessed by NMR HSQC titration which is very powerful in detecting even very weak binding. The studies lead to three important findings: 1). a "fuzzy complex" is formed between the intrinsically-unstructured third domain (D3) of NS5A and the well-structured MSP domain of VAPB, with an average dissociation constant (Kd) of ~5 µM. 2). The binding-important residues on both NS5A-D3 and VAPB-MSP have been successfully mapped out, which provided experimental constraints for constructing the complex structure. In the complex, unstructured D3 binds to three surface pockets on one side of the MSP structure. Interestingly, two ALS-causing mutations T46I and P56S are also located on the D3-MSP interface. Moreover, NS5A-D3, FFAT-containing proteins and EphA4 appear to have overlapped binding interfaces on the MSP domain. 3). NS5A-D3 has been experimentally confirmed to competes with EphA4 in binding to the MSP domain, and T46I mutation of MSP dramatically abolishes its binding ability to D3. Our study not only provides essential foundation for further deciphering structure and function of the HCV replication machinery, but may also shed light on rationalizing a recent observation that a chronic HCV patient surprisingly developed ALS-like syndrome.
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Affiliation(s)
- Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- * E-mail:
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193
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Chen J. Towards the physical basis of how intrinsic disorder mediates protein function. Arch Biochem Biophys 2012; 524:123-31. [PMID: 22579883 DOI: 10.1016/j.abb.2012.04.024] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 04/28/2012] [Accepted: 04/30/2012] [Indexed: 02/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an important class of functional proteins that is highly prevalent in biology and has broad association with human diseases. In contrast to structured proteins, free IDPs exist as heterogeneous and dynamical conformational ensembles under physiological conditions. Many concepts have been discussed on how such intrinsic disorder may provide crucial functional advantages, particularly in cellular signaling and regulation. Establishing the physical basis of these proposed phenomena requires not only detailed characterization of the disordered conformational ensembles, but also mechanistic understanding of the roles of various ensemble properties in IDP interaction and regulation. Here, we review the experimental and computational approaches that may be integrated to address many important challenges of establishing a "structural" basis of IDP function, and discuss some of the key emerging ideas on how the conformational ensembles of IDPs may mediate function, especially in coupled binding and folding interactions.
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Affiliation(s)
- Jianhan Chen
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA.
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Uversky VN. Intrinsically disordered proteins and novel strategies for drug discovery. Expert Opin Drug Discov 2012; 7:475-88. [PMID: 22559227 DOI: 10.1517/17460441.2012.686489] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION There is a natural abundance of intrinsically disordered proteins or intrinsically disordered protein regions (IDPs or IDPRs), that is, biologically active proteins/regions without stable structure. Their wide functional repertoire; the ability to participate in multiple interactions; the capability to fold at binding in a template-dependent manner and their common involvement in the pathogenesis of numerous human diseases suggest that these proteins should be seriously considered as novel drug targets. AREAS COVERED This article describes the major classes of ordered proteins traditionally used as drug targets and introduces the molecular mechanisms of drugs targeting ordered proteins. Furthermore, it illustrates basic ways of rational drug design for these proteins, and shows why these approaches cannot be directly used for intrinsic disorder-based drug design. Some of the new approaches utilized for finding drugs targeting IDPs/IDPRs are introduced. EXPERT OPINION There is a continuing progress in the design of small molecules for IDPs/IDPRs and several small molecules are found that specifically inhibit the disorder-based interaction of IDPs with their numerous partners. It is expected that the initial studies will be extended and novel intrinsic disorder-based drug design approaches will be developed. Furthermore, putative new targets will be identified, and a better understanding of the molecular mechanisms underlying modulation of promiscuous IDP binding will be achieved.
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Affiliation(s)
- Vladimir N Uversky
- University of South Florida, Byrd Alzheimer's Research Institute, College of Medicine, Department of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612, USA.
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195
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Rezaei-Ghaleh N, Blackledge M, Zweckstetter M. Intrinsically Disordered Proteins: From Sequence and Conformational Properties toward Drug Discovery. Chembiochem 2012; 13:930-50. [DOI: 10.1002/cbic.201200093] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Indexed: 01/31/2023]
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196
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Williams JJ, Hergenrother PJ. Artificial activation of toxin-antitoxin systems as an antibacterial strategy. Trends Microbiol 2012; 20:291-8. [PMID: 22445361 DOI: 10.1016/j.tim.2012.02.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/31/2012] [Accepted: 02/13/2012] [Indexed: 11/18/2022]
Abstract
Toxin-antitoxin (TA) systems are unique modules that effect plasmid stabilization via post-segregational killing of the bacterial host. The genes encoding TA systems also exist on bacterial chromosomes, and it has been speculated that these are involved in a variety of cellular processes. Interest in TA systems has increased dramatically over the past 5 years as the ubiquitous nature of TA genes on bacterial genomes has been revealed. The exploitation of TA systems as an antibacterial strategy via artificial activation of the toxin has been proposed and has considerable potential; however, efforts in this area remain in the early stages and several major questions remain. This review investigates the tractability of targeting TA systems to kill bacteria, including fundamental requirements for success, recent advances, and challenges associated with artificial toxin activation.
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Affiliation(s)
- Julia J Williams
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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197
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Tetenbaum-Novatt J, Hough LE, Mironska R, McKenney AS, Rout MP. Nucleocytoplasmic transport: a role for nonspecific competition in karyopherin-nucleoporin interactions. Mol Cell Proteomics 2012; 11:31-46. [PMID: 22357553 DOI: 10.1074/mcp.m111.013656] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleocytoplasmic transport occurs through the nuclear pore complex (NPC), which in yeast is a ~50 MDa complex consisting of ~30 different proteins. Small molecules can freely exchange through the NPC, but macromolecules larger than ~40 kDa must be aided across by transport factors, most of which belong to a related family of proteins termed karyopherins (Kaps). These transport factors bind to the disordered phenylalanine-glycine (FG) repeat domains in a family of NPC proteins termed FG nups, and this specific binding allows the transport factors to cross the NPC. However, we still know little in terms of the molecular and kinetic details regarding how this binding translates to selective passage of transport factors across the NPC. Here we show that the specific interactions between Kaps and FG nups are strongly modulated by the presence of a cellular milieu whose proteins appear to act as very weak competitors that nevertheless collectively can reduce Kap/FG nup affinities by several orders of magnitude. Without such modulation, the avidities between Kaps and FG nups measured in vitro are too tight to be compatible with the rapid transport kinetics observed in vivo. We modeled the multivalent interactions between the disordered repeat binding sites in the FG nups and multiple cognate binding sites on Kap, showing that they should indeed be sensitive to even weakly binding competitors; the introduction of such competition reduces the availability of these binding sites, dramatically lowering the avidity of their specific interactions and allowing rapid nuclear transport.
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Affiliation(s)
- Jaclyn Tetenbaum-Novatt
- The Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
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198
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Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics. Biomolecules 2012; 2:104-21. [PMID: 24970129 PMCID: PMC4030872 DOI: 10.3390/biom2010104] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/11/2012] [Accepted: 02/12/2012] [Indexed: 12/13/2022] Open
Abstract
The phosphorylated kinase-inducible activation domain (pKID) adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity; the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.
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199
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Inhibition of human papillomavirus DNA replication by an E1-derived p80/UAF1-binding peptide. J Virol 2012; 86:3486-500. [PMID: 22278251 DOI: 10.1128/jvi.07003-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The papillomavirus E1 helicase is recruited by E2 to the viral origin, where it assembles into a double hexamer that orchestrates replication of the viral genome. We previously identified the cellular WD40 repeat-containing protein p80/UAF1 as a novel interaction partner of E1 from anogenital human papillomavirus (HPV) types. p80 was found to interact with the first 40 residues of HPV type 31 (HPV31) E1, and amino acid substitutions within this domain abrogated the maintenance of the viral episome in keratinocytes. In this study, we report that these p80-binding substitutions reduce by 70% the ability of E1 to support transient viral DNA replication without affecting its interaction with E2 and assembly at the origin in vivo. Microscopy studies revealed that p80 is relocalized from the cytoplasm to discrete subnuclear foci by E1 and E2. Chromatin immunoprecipitation assays further revealed that p80 is recruited to the viral origin in an E1- and E2-dependent manner. Interestingly, overexpression of a 40-amino-acid-long p80-binding peptide, derived from HPV31 E1, was found to inhibit viral DNA replication by preventing the recruitment of endogenous p80 to the origin. Mutant peptides defective for p80 interaction were not inhibitory, demonstrating the specificity of this effect. Characterization of this E1 peptide by nuclear magnetic resonance (NMR) showed that it is intrinsically disordered in solution, while mapping studies indicated that the WD repeats of p80 are required for E1 interaction. These results provide additional evidence for the requirement for p80 in anogenital HPV DNA replication and highlight the potential of E1-p80 interaction as a novel antiviral target.
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200
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Zhang W, Ganguly D, Chen J. Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins. PLoS Comput Biol 2012; 8:e1002353. [PMID: 22253588 PMCID: PMC3257294 DOI: 10.1371/journal.pcbi.1002353] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/30/2011] [Indexed: 01/08/2023] Open
Abstract
To understand the interplay of residual structures and conformational fluctuations in the interaction of intrinsically disordered proteins (IDPs), we first combined implicit solvent and replica exchange sampling to calculate atomistic disordered ensembles of the nuclear co-activator binding domain (NCBD) of transcription coactivator CBP and the activation domain of the p160 steroid receptor coactivator ACTR. The calculated ensembles are in quantitative agreement with NMR-derived residue helicity and recapitulate the experimental observation that, while free ACTR largely lacks residual secondary structures, free NCBD is a molten globule with a helical content similar to that in the folded complex. Detailed conformational analysis reveals that free NCBD has an inherent ability to substantially sample all the helix configurations that have been previously observed either unbound or in complexes. Intriguingly, further high-temperature unbinding and unfolding simulations in implicit and explicit solvents emphasize the importance of conformational fluctuations in synergistic folding of NCBD with ACTR. A balance between preformed elements and conformational fluctuations appears necessary to allow NCBD to interact with different targets and fold into alternative conformations. Together with previous topology-based modeling and existing experimental data, the current simulations strongly support an “extended conformational selection” synergistic folding mechanism that involves a key intermediate state stabilized by interaction between the C-terminal helices of NCBD and ACTR. In addition, the atomistic simulations reveal the role of long-range as well as short-range electrostatic interactions in cooperating with readily fluctuating residual structures, which might enhance the encounter rate and promote efficient folding upon encounter for facile binding and folding interactions of IDPs. Thus, the current study not only provides a consistent mechanistic understanding of the NCBD/ACTR interaction, but also helps establish a multi-scale molecular modeling framework for understanding the structure, interaction, and regulation of IDPs in general. Intrinsically disordered proteins (IDPs) are now widely recognized to play fundamental roles in biology and to be frequently associated with human diseases. Although the potential advantages of intrinsic disorder in cellular signaling and regulation have been widely discussed, the physical basis for these proposed phenomena remains sketchy at best. An integration of multi-scale molecular modeling and experimental characterization is necessary to uncover the molecular principles that govern the structure, interaction, and regulation of IDPs. In this work, we characterize the conformational properties of two IDPs involved in transcription regulation at the atomistic level and further examine the roles of these properties in their coupled binding and folding interactions. Our simulations suggest interplay among residual structures, conformational fluctuations, and electrostatic interactions that allows efficient synergistic folding of these two IDPs. In particular, we propose that electrostatic interactions might play an important role in facilitating rapid folding and binding recognition of IDPs, by enhancing the encounter rate and promoting efficient folding upon encounter.
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Affiliation(s)
- Weihong Zhang
- Department of Biochemistry, Kansas State University, Manhattan, Kansas, United States of America
| | - Debabani Ganguly
- Department of Biochemistry, Kansas State University, Manhattan, Kansas, United States of America
| | - Jianhan Chen
- Department of Biochemistry, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
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