101
|
Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SCE. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 2016; 45:D219-D227. [PMID: 27899601 PMCID: PMC5210544 DOI: 10.1093/nar/gkw1056] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 01/16/2023] Open
Abstract
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.
Collapse
Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Biosciences and Medical Technology, University of Tampere, Finland
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | | | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Radoslav Davidović
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, 1/c Pázmány Péter sétány, 1117 Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Alessandra Gasparini
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - András Hatos
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France.,University ITMO, Institute of Bioengineering, St. Petersburg 197101, Russia
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary.,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Mauricio Macossay-Castillo
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Attila Meszaros
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Jordi Pujols
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France
| | | | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | | | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Fiorella Tonello
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,CNR Institute of Neurosceince, I-35121 Padova, Italy
| | - Konstantinos D Tsirigos
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Nevena Veljković
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium
| | - Per Warholm
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia.,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, AFMB, UMR 7257, Marseille, France
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy .,CNR Institute of Neurosceince, I-35121 Padova, Italy
| |
Collapse
|
102
|
Kathiriya JJ, Pathak RR, Bezginov A, Xue B, Uversky VN, Tillier ERM, Davé V. Structural pliability adjacent to the kinase domain highlights contribution of FAK1 IDRs to cytoskeletal remodeling. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:43-54. [PMID: 27718363 DOI: 10.1016/j.bbapap.2016.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 12/24/2022]
Abstract
Therapeutic protein kinase inhibitors are designed on the basis of kinase structures. Here, we define intrinsically disordered regions (IDRs) in structurally hybrid kinases. We reveal that 65% of kinases have an IDR adjacent to their kinase domain (KD). These IDRs are evolutionarily more conserved than IDRs distant to KDs. Strikingly, 36 kinases have adjacent IDRs extending into their KDs, defining a unique structural and functional subset of the kinome. Functional network analysis of this subset of the kinome uncovered FAK1 as topologically the most connected hub kinase. We identify that KD-flanking IDR of FAK1 is more conserved and undergoes more post-translational modifications than other IDRs. It preferentially interacts with proteins regulating scaffolding and kinase activity, which contribute to cytoskeletal remodeling. In summary, spatially and evolutionarily conserved IDRs in kinases may influence their functions, which can be exploited for targeted therapies in diseases including those that involve aberrant cytoskeletal remodeling.
Collapse
Affiliation(s)
- Jaymin J Kathiriya
- Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, United States
| | - Ravi Ramesh Pathak
- Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, United States
| | - Alexandr Bezginov
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, University of South Florida, Tampa, FL 33612, United States; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | | | - Vrushank Davé
- Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, United States; Department of Cancer Biology and Evolution, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States.
| |
Collapse
|
103
|
Szénási T, Oláh J, Szabó A, Szunyogh S, Láng A, Perczel A, Lehotzky A, Uversky VN, Ovádi J. Challenging drug target for Parkinson's disease: Pathological complex of the chameleon TPPP/p25 and alpha-synuclein proteins. Biochim Biophys Acta Mol Basis Dis 2016; 1863:310-323. [PMID: 27671864 DOI: 10.1016/j.bbadis.2016.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/02/2016] [Accepted: 09/20/2016] [Indexed: 12/27/2022]
Abstract
The hallmarks of Parkinson's disease and other synucleinopathies, Tubulin Polymerization Promoting Protein (TPPP/p25) and α-synuclein (SYN) have two key features: they are disordered and co-enriched/co-localized in brain inclusions. These Neomorphic Moonlighting Proteins display both physiological and pathological functions due to their interactions with distinct partners. To achieve the selective targeting of the pathological TPPP/p25-SYN but not the physiological TPPP/p25-tubulin complex, their interfaces were identified as a specific innovative strategy for the development of anti-Parkinson drugs. Therefore, the interactions of TPPP/p25 with tubulin and SYN were characterized which suggested the involvements of the 178-187 aa and 147-156 aa segments in the complexation of TPPP/p25 with tubulin and SYN, respectively. However, various truncated and deletion mutants reduced but did not abolish the interactions except one mutant; in addition synthetized fragments corresponding to the potential binding segments of TPPP/p25 failed to interact with SYN. In fact, the studies of the multiple interactions at molecular and cellular levels revealed the high conformational plasticity, chameleon feature, of TPPP/p25 that ensures exceptional functional resilience; the lack of previously identified binding segments could be replaced by other segments. The experimental results are underlined by distinct bioinformatics tools. All these data revealed that although targeting chameleon proteins is a challenging task, nevertheless, the validation of a drug target can be achieved by identifying the interface of complexes of the partner proteins existing at the given pathological conditions.
Collapse
Affiliation(s)
- Tibor Szénási
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Judit Oláh
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Adél Szabó
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Sándor Szunyogh
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - András Láng
- MTA-ELTE, Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Budapest 1117, Hungary.
| | - András Perczel
- MTA-ELTE, Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Budapest 1117, Hungary; Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest 1117, Hungary.
| | - Attila Lehotzky
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 33612 Tampa, FL, USA; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
| | - Judit Ovádi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| |
Collapse
|
104
|
De Mol E, Fenwick RB, Phang CTW, Buzón V, Szulc E, de la Fuente A, Escobedo A, García J, Bertoncini CW, Estébanez-Perpiñá E, McEwan IJ, Riera A, Salvatella X. EPI-001, A Compound Active against Castration-Resistant Prostate Cancer, Targets Transactivation Unit 5 of the Androgen Receptor. ACS Chem Biol 2016; 11:2499-505. [PMID: 27356095 DOI: 10.1021/acschembio.6b00182] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Castration-resistant prostate cancer is the lethal condition suffered by prostate cancer patients that become refractory to androgen deprivation therapy. EPI-001 is a recently identified compound active against this condition that modulates the activity of the androgen receptor, a nuclear receptor that is essential for disease progression. The mechanism by which this compound exerts its inhibitory activity is however not yet fully understood. Here we show, by using high resolution solution nuclear magnetic resonance spectroscopy, that EPI-001 selectively interacts with a partially folded region of the transactivation domain of the androgen receptor, known as transactivation unit 5, that is key for the ability of prostate cells to proliferate in the absence of androgens, a distinctive feature of castration-resistant prostate cancer. Our results can contribute to the development of more potent and less toxic novel androgen receptor antagonists for treating this disease.
Collapse
Affiliation(s)
- Eva De Mol
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - R. Bryn Fenwick
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Christopher T. W. Phang
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Victor Buzón
- Departament
de Bioquímica i Biología Molecular, and Institute of
Biomedicine, University of Barcelona (IBUB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elzbieta Szulc
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Alex de la Fuente
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Albert Escobedo
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jesús García
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carlos W. Bertoncini
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Eva Estébanez-Perpiñá
- Departament
de Bioquímica i Biología Molecular, and Institute of
Biomedicine, University of Barcelona (IBUB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Iain J. McEwan
- Institute
of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, IMS Building, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - Antoni Riera
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament
de Química Orgànica, Universitat de Barcelona, Martí
i Franqués 1-11, 08028 Barcelona, Spain
| | - Xavier Salvatella
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
105
|
Direct inhibition of c-Myc-Max heterodimers by celastrol and celastrol-inspired triterpenoids. Oncotarget 2016; 6:32380-95. [PMID: 26474287 PMCID: PMC4741700 DOI: 10.18632/oncotarget.6116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 09/26/2015] [Indexed: 01/22/2023] Open
Abstract
Many oncogenic signals originate from abnormal protein-protein interactions that are potential targets for small molecule inhibitors. However, the therapeutic disruption of these interactions has proved elusive. We report here that the naturally-occurring triterpenoid celastrol is an inhibitor of the c-Myc (Myc) oncoprotein, which is over-expressed in many human cancers. Most Myc inhibitors prevent the association between Myc and its obligate heterodimerization partner Max via their respective bHLH-ZIP domains. In contrast, we show that celastrol binds to and alters the quaternary structure of the pre-formed dimer and abrogates its DNA binding. Celastrol contains a reactive quinone methide group that promiscuously forms Michael adducts with numerous target proteins and other free sulfhydryl-containing molecules. Interestingly, triterpenoid derivatives lacking the quinone methide showed enhanced specificity and potency against Myc. As with other Myc inhibitors, these analogs rapidly reduced the abundance of Myc protein and provoked a global energy crisis marked by ATP depletion, neutral lipid accumulation, AMP-activated protein kinase activation, cell cycle arrest and apoptosis. They also inhibited the proliferation of numerous established human cancer cell lines as well as primary myeloma explants that were otherwise resistant to JQ1, a potent indirect Myc inhibitor. N-Myc amplified neuroblastoma cells showed similar responses and, in additional, underwent neuronal differentiation. These studies indicate that certain pharmacologically undesirable properties of celastrol such as Michael adduct formation can be eliminated while increasing selectivity and potency toward Myc and N-Myc. This, together with their low in vivo toxicity, provides a strong rationale for pursuing the development of additional Myc-specific triterpenoid derivatives.
Collapse
|
106
|
Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2. Virology 2016; 496:116-126. [PMID: 27289560 DOI: 10.1016/j.virol.2016.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
To be incorporated into progeny virions, the viral genome must be transported to the inner leaflet of the plasma membrane (PM) and accumulate there. Some viruses utilize lipid components to assemble at the PM. For example, simian virus 40 (SV40) targets the ganglioside GM1 and human immunodeficiency virus type 1 (HIV-1) utilizes phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2]. Recent studies clearly indicate that Rab11-mediated recycling endosomes are required for influenza A virus (IAV) trafficking of vRNPs to the PM but it remains unclear how IAV vRNP localized or accumulate underneath the PM for viral genome incorporation into progeny virions. In this study, we found that the second intrinsically disordered region (IDR2) of NP regulates two binding steps involved in viral genome packaging. First, IDR2 facilitates NP oligomer binding to viral RNA to form vRNP. Secondly, vRNP assemble by interacting with PI(4,5)P2 at the PM via IDR2. These findings suggest that PI(4,5)P2 functions as the determinant of vRNP accumulation at the PM.
Collapse
|
107
|
Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
Collapse
Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| |
Collapse
|
108
|
Lassalle MW, Kondou S. Uncovering the role of the flexible C-terminal tail: A model study with Strep-tagged GFP. BIOCHIMIE OPEN 2016; 2:1-8. [PMID: 29632832 PMCID: PMC5889473 DOI: 10.1016/j.biopen.2015.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/18/2015] [Indexed: 11/28/2022]
Abstract
Recently, it has been recognized that, much like an electric current in an electric circuit, dynamic disruptions from flexible, unstructured regions distal to the active region are transferred through the contact network to the active site and influence protein stability and/or function. As transmembrane proteins frequently possess the β-barrel structure, studies of proteins with this topology are required. The unstructured lid segments of the β-barrel GFP protein are conserved and could play a role in the backbone stabilization required for chromophore function. A study of the disordered C-terminus and the function within the lid is necessary. In this study, we entirely truncated the flexible C-terminal tail and investigated the N-terminal Strep-tagged GFP by fluorescence spectroscopy, and the temperature- and GdnHCl-induced unfolding by circular dichroism. The introduction of the unstructured Strep-tag itself changed the unfolding pathway. Truncating the entire flexible tail did not decrease the fluorescence intensity to a large extent; however, the protein stability changed dramatically. The temperature for half-denaturation T1/2 changed significantly from 79 °C for the wild-type to 72.8 °C for the mutant. Unfolding kinetics at different temperatures have been induced by 4 M GdnHCl, and the apparent Arrhenius activation energy decreased by 40% as compared to the wild-type.
Collapse
Affiliation(s)
- Michael W. Lassalle
- iCLA (International College of Liberal Arts), Yamanashi Gakuin University, 2-4-5 Sakaori, Kofu-city, Yamanashi-ken, 400-8575 Japan
| | - Shinobu Kondou
- Ehime Prefectural Police HQ, Forensic Science Laboratory, Japan
| |
Collapse
|
109
|
Kumar S, Birol M, Schlamadinger DE, Wojcik SP, Rhoades E, Miranker AD. Foldamer-mediated manipulation of a pre-amyloid toxin. Nat Commun 2016; 7:11412. [PMID: 27108700 PMCID: PMC4848510 DOI: 10.1038/ncomms11412] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/22/2016] [Indexed: 01/15/2023] Open
Abstract
Disordered proteins, such as those central to Alzheimer's and Parkinson's, are particularly intractable for structure-targeted therapeutic design. Here we demonstrate the capacity of a synthetic foldamer to capture structure in a disease relevant peptide. Oligoquinoline amides have a defined fold with a solvent-excluded core that is independent of its outwardly projected, derivatizable moieties. Islet amyloid polypeptide (IAPP) is a peptide central to β-cell pathology in type II diabetes. A tetraquinoline is presented that stabilizes a pre-amyloid, α-helical conformation of IAPP. This charged, dianionic compound is readily soluble in aqueous buffer, yet crosses biological membranes without cellular assistance: an unexpected capability that is a consequence of its ability to reversibly fold. The tetraquinoline docks specifically with intracellular IAPP and rescues β-cells from toxicity. Taken together, our work here supports the thesis that stabilizing non-toxic conformers of a plastic protein is a viable strategy for cytotoxic rescue addressable using oligoquinoline amides.
Collapse
Affiliation(s)
- Sunil Kumar
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Melissa Birol
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Diana E. Schlamadinger
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Slawomir P. Wojcik
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Elizabeth Rhoades
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Andrew D. Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
- Department of Chemical and Environmental Engineering, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| |
Collapse
|
110
|
Chou CC, Wang AHJ. Structural D/E-rich repeats play multiple roles especially in gene regulation through DNA/RNA mimicry. MOLECULAR BIOSYSTEMS 2016; 11:2144-51. [PMID: 26088262 DOI: 10.1039/c5mb00206k] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aspartic acid and glutamic acid repeats in proteins exhibit strong negative charge distribution and they may play special biological roles. From 39,684 unique structural data in the RCSB Protein Data Bank (PDB), 173 structures were found to contain ordered D/E-rich repeat structures, and 57 of them were related to DNA/RNA functions. The frequency of occurrence of glutamic acid (36.90%) was higher than that of aspartic acid (27.02%). Glycine (2.38%), alanine (2.68%), valine (3.54%), leucine (5.57%), and isoleucine (3.34%), but not methionine (0.91%), were the most abundant hydrophobic residues. The available complex structures suggested that D/E-rich proteins might be involved in DNA mimicry, mRNA processing and regulation of the transcription complex. The region surrounding the D/E-rich repeat sequences plays important roles in the binding specificity toward the target proteins. The numbers and composition of aspartic acid and glutamic acid might also affect binding properties. Aspartic acid and glutamic acid are disorder-promoting residues in the intrinsically disorder proteins. Our findings suggest that the D/E-rich repeats are unique components of intrinsically disordered proteins, which are involved in the gene regulation and could serve as potential druggable fragments or drug targets.
Collapse
Affiliation(s)
- Chia-Cheng Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
| | | |
Collapse
|
111
|
Prediction of intrinsically disordered regions in proteins using signal processing methods: application to heat-shock proteins. Med Biol Eng Comput 2016; 54:1831-1844. [DOI: 10.1007/s11517-016-1477-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
|
112
|
Kannan S, Lane DP, Verma CS. Long range recognition and selection in IDPs: the interactions of the C-terminus of p53. Sci Rep 2016; 6:23750. [PMID: 27030593 PMCID: PMC4814905 DOI: 10.1038/srep23750] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 11/09/2022] Open
Abstract
The C-terminal domain of p53 is an extensively studied IDP, interacting with different partners through multiple distinct conformations. To explore the interplay between preformed structural elements and intrinsic fluctuations in its folding and binding we combine extensive atomistic equilibrium and non-equilibrium simulations. We find that the free peptide segment rapidly interconverts between ordered and disordered states with significant populations of the conformations that are seen in the complexed states. The underlying global folding-binding landscape points to a synergistic mechanism in which recognition is dictated via long range electrostatic recognition which results in the formation of reactive structures as far away as 10 Å, and binding proceeds with the steering of selected conformations followed by induced folding at the target surface or within a close range.
Collapse
Affiliation(s)
| | - David P Lane
- p53 Laboratory (A*STAR), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| |
Collapse
|
113
|
Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries. Biochimie 2016; 125:112-8. [PMID: 27004461 DOI: 10.1016/j.biochi.2016.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 01/30/2023]
Abstract
The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine.
Collapse
|
114
|
Joshi P, Chia S, Habchi J, Knowles TPJ, Dobson CM, Vendruscolo M. A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins. ACS COMBINATORIAL SCIENCE 2016; 18:144-53. [PMID: 26923286 DOI: 10.1021/acscombsci.5b00129] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.
Collapse
Affiliation(s)
- Priyanka Joshi
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Sean Chia
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Johnny Habchi
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
115
|
Manigrasso MB, Pan J, Rai V, Zhang J, Reverdatto S, Quadri N, DeVita RJ, Ramasamy R, Shekhtman A, Schmidt AM. Small Molecule Inhibition of Ligand-Stimulated RAGE-DIAPH1 Signal Transduction. Sci Rep 2016; 6:22450. [PMID: 26936329 PMCID: PMC4776135 DOI: 10.1038/srep22450] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/15/2016] [Indexed: 12/21/2022] Open
Abstract
The receptor for advanced glycation endproducts (RAGE) binds diverse ligands linked to chronic inflammation and disease. NMR spectroscopy and x-ray crystallization studies of the extracellular domains of RAGE indicate that RAGE ligands bind by distinct charge- and hydrophobicity-dependent mechanisms. The cytoplasmic tail (ct) of RAGE is essential for RAGE ligand-mediated signal transduction and consequent modulation of gene expression and cellular properties. RAGE signaling requires interaction of ctRAGE with the intracellular effector, mammalian diaphanous 1 or DIAPH1. We screened a library of 58,000 small molecules and identified 13 small molecule competitive inhibitors of ctRAGE interaction with DIAPH1. These compounds, which exhibit in vitro and in vivo inhibition of RAGE-dependent molecular processes, present attractive molecular scaffolds for the development of therapeutics against RAGE-mediated diseases, such as those linked to diabetic complications, Alzheimer’s disease, and chronic inflammation, and provide support for the feasibility of inhibition of protein-protein interaction (PPI).
Collapse
Affiliation(s)
- Michaele B Manigrasso
- Diabetes Research Program, Department of Medicine, New York University Langone Medical Center, 550 First Avenue, New York, 10016 New York, USA
| | - Jinhong Pan
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, 12222 New York, USA
| | - Vivek Rai
- Diabetes Research Program, Department of Medicine, New York University Langone Medical Center, 550 First Avenue, New York, 10016 New York, USA
| | - Jinghua Zhang
- Diabetes Research Program, Department of Medicine, New York University Langone Medical Center, 550 First Avenue, New York, 10016 New York, USA
| | - Sergey Reverdatto
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, 12222 New York, USA
| | - Nosirudeen Quadri
- Diabetes Research Program, Department of Medicine, New York University Langone Medical Center, 550 First Avenue, New York, 10016 New York, USA
| | - Robert J DeVita
- RJD Medicinal Chemistry and Drug Discovery Consulting LLC, 332 W. Dudley Avenue, Westfield, New Jersey 07090, USA
| | - Ravichandran Ramasamy
- Diabetes Research Program, Department of Medicine, New York University Langone Medical Center, 550 First Avenue, New York, 10016 New York, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, 12222 New York, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Department of Medicine, New York University Langone Medical Center, 550 First Avenue, New York, 10016 New York, USA
| |
Collapse
|
116
|
Structure-based Inhibitor Design for the Intrinsically Disordered Protein c-Myc. Sci Rep 2016; 6:22298. [PMID: 26931396 PMCID: PMC4773988 DOI: 10.1038/srep22298] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/11/2016] [Indexed: 12/19/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are associated with various diseases and have been proposed as promising drug targets. However, conventional structure-based approaches cannot be applied directly to IDPs, due to their lack of ordered structures. Here, we describe a novel computational approach to virtually screen for compounds that can simultaneously bind to different IDP conformations. The test system used c-Myc, an oncoprotein containing a disordered basic helix-loop-helix-leucine zipper (bHLH-LZ) domain that adopts a helical conformation upon binding to Myc-associated factor X (Max). For the virtual screen, we used three binding pockets in representative conformations of c-Myc370–409, which is part of the disordered bHLH-LZ domain. Seven compounds were found to directly bind c-Myc370–409in vitro, and four inhibited the growth of the c-Myc-overexpressing cells by affecting cell cycle progression. Our approach of IDP conformation sampling, binding site identification, and virtual screening for compounds that can bind to multiple conformations provides a useful strategy for structure-based drug discovery targeting IDPs.
Collapse
|
117
|
Conformational transition of Aβ 42 inhibited by a mimetic peptide. A molecular modeling study using QM/MM calculations and QTAIM analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
118
|
Csizmok V, Follis AV, Kriwacki RW, Forman-Kay JD. Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling. Chem Rev 2016; 116:6424-62. [PMID: 26922996 DOI: 10.1021/acs.chemrev.5b00548] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent ∼30% of the proteome and enable unique regulatory mechanisms. In this review, we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of conformational ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultrasensitivity" and "regulated folding and unfolding". We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information.
Collapse
Affiliation(s)
- Veronika Csizmok
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center , Memphis, Tennessee 38163, United States
| | - Julie D Forman-Kay
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto , Toronto, ON M5S 1A8, Canada
| |
Collapse
|
119
|
Cino EA, Choy WY, Karttunen M. Characterization of the Free State Ensemble of the CoRNR Box Motif by Molecular Dynamics Simulations. J Phys Chem B 2016; 120:1060-8. [DOI: 10.1021/acs.jpcb.5b11565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Elio A. Cino
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Wing-Yiu Choy
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & the Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, Eindhoven 5600 MB, The Netherlands
| |
Collapse
|
120
|
Tantos A, Kalmar L, Tompa P. The role of structural disorder in cell cycle regulation, related clinical proteomics, disease development and drug targeting. Expert Rev Proteomics 2016; 12:221-33. [PMID: 25976105 DOI: 10.1586/14789450.2015.1042866] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding the molecular mechanisms of the regulation of cell cycle is a central issue in molecular cell biology, due to its fundamental role in the existence of cells. The regulatory circuits that make decisions on when a cell should divide are very complex and particularly subtly balanced in eukaryotes, in which the harmony of many different cells in an organism is essential for life. Several hundred proteins are involved in these processes, and a great deal of studies attests that most of them have functionally relevant intrinsic structural disorder. Structural disorder imparts many functional advantages on these proteins, and we discuss it in detail that it is involved in all key steps from signaling through the cell membrane to regulating transcription of proteins that execute timely responses to an ever-changing environment.
Collapse
Affiliation(s)
- Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | | | | |
Collapse
|
121
|
(Intrinsically disordered) splice variants in the proteome: implications for novel drug discovery. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0384-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
122
|
Yan J, Dunker AK, Uversky VN, Kurgan L. Molecular recognition features (MoRFs) in three domains of life. MOLECULAR BIOSYSTEMS 2016; 12:697-710. [DOI: 10.1039/c5mb00640f] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MoRFs are widespread intrinsically disordered protein-binding regions that have similar abundance and amino acid composition across the three domains of life.
Collapse
Affiliation(s)
- Jing Yan
- Department of Electrical and Computer Engineering
- University of Alberta
- Edmonton
- Canada
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics
- Indiana University School of Medicine
- Indianapolis
- USA
- Indiana University School of Informatics
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering
- University of Alberta
- Edmonton
- Canada
- Department of Computer Science
| |
Collapse
|
123
|
Ambadipudi S, Zweckstetter M. Targeting intrinsically disordered proteins in rational drug discovery. Expert Opin Drug Discov 2015; 11:65-77. [DOI: 10.1517/17460441.2016.1107041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Susmitha Ambadipudi
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, 37073 Göttingen, Germany
| |
Collapse
|
124
|
Progress in studying intrinsically disordered proteins with atomistic simulations. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:47-52. [DOI: 10.1016/j.pbiomolbio.2015.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/04/2015] [Accepted: 03/16/2015] [Indexed: 01/09/2023]
|
125
|
Targeting disordered proteins with small molecules using entropy. Trends Biochem Sci 2015; 40:491-6. [DOI: 10.1016/j.tibs.2015.07.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 12/31/2022]
|
126
|
Zhang Z, Boskovic Z, Hussain MM, Hu W, Inouye C, Kim HJ, Abole AK, Doud MK, Lewis TA, Koehler AN, Schreiber SL, Tjian R. Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation. eLife 2015; 4. [PMID: 26314865 PMCID: PMC4582147 DOI: 10.7554/elife.07777] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/27/2015] [Indexed: 12/13/2022] Open
Abstract
Intrinsically disordered proteins/regions (IDPs/IDRs) are proteins or peptide segments that fail to form stable 3-dimensional structures in the absence of partner proteins. They are abundant in eukaryotic proteomes and are often associated with human diseases, but their biological functions have been elusive to study. In this study, we report the identification of a tin(IV) oxochloride-derived cluster that binds an evolutionarily conserved IDR within the metazoan TFIID transcription complex. Binding arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II during the first (de novo) round of transcription initiation. However, the specific chemical probe does not affect reinitiation, which requires the re-entry of Pol II, thus, mechanistically distinguishing these two modes of transcription initiation. This work also suggests a new avenue for targeting the elusive IDRs by harnessing certain features of metal-based complexes for mechanistic studies, and for the development of novel pharmaceutical interventions. DOI:http://dx.doi.org/10.7554/eLife.07777.001 DNA contains instructions to make all the proteins and other molecules that drive essential processes in cells. To issue such specific sets of instructions, a section of DNA—called a gene—is first copied to make molecules of messenger ribonucleic acid (or mRNA for short) in a process called transcription. This process is tightly regulated in all living organisms so that only a subset of genes are actively transcribed at any time in a given cell. A group or ‘complex’ of proteins called TFIID plays an essential role in starting the transcription of genes that encode proteins in humans and other eukaryotic organisms. However, it is tricky to study how TFIID works because mutant cells that are missing individual components of the complex are unable to properly transcribe the required genes and soon die. Consequently, many studies of TFIID have used purified proteins in artificial systems where it is possible to examine particular aspects of TFIID activity in depth. Here, Zhang et al. used a combination of chemistry, biochemistry, and molecular biology techniques to identify a new molecule that can selectively bind to the TFIID complex. In an artificial system containing purified proteins and other molecules, this molecule ‘locks’ TFIID onto DNA and prevents a change in shape that is required for transcription to start. The experiments show that this rearrangement is only required to make the first mRNA copy of a gene because the molecule had no effect on initiating further rounds of transcription on the same DNA. Zhang et al.'s findings reveal that TFIID is very dynamic in controlling transcription, and that subsequent rounds of transcription follow a different path to make mRNAs. The next steps are to use new techniques such as single-molecule imaging to directly visualize the molecules involved in transcription, and to use the new molecule to block the start of transcription in living cells. DOI:http://dx.doi.org/10.7554/eLife.07777.002
Collapse
Affiliation(s)
- Zhengjian Zhang
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Zarko Boskovic
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Mahmud M Hussain
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Wenxin Hu
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Carla Inouye
- Li Ka Shing Center for Biomedical and Health Sciences, Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Han-Je Kim
- Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
| | - A Katherine Abole
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Mary K Doud
- Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
| | - Timothy A Lewis
- Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
| | - Angela N Koehler
- Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Robert Tjian
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| |
Collapse
|
127
|
Terakawa T, Higo J, Takada S. Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53. Biophys J 2015; 107:721-729. [PMID: 25099811 DOI: 10.1016/j.bpj.2014.06.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/28/2014] [Accepted: 06/18/2014] [Indexed: 10/24/2022] Open
Abstract
In eukaryotic proteins, intrinsically disordered regions (IDRs) are ubiquitous and often exist in linker regions that flank the functional domains of modular proteins, regulating their functions. For detailed structural ensemble modeling of IDRs, we propose a multiscale method for IDRs that possess significant long-range order in modular proteins and apply it to the eukaryotic transcription factor p53 as an example. First, we performed all-atom (AA) molecular dynamics (MD) simulations of the explicitly solvated p53 linker region, without experimental restraint terms, finding fractional long-range contacts within the linker. Second, we fed this AA MD ensemble into a coarse-grained (CG) model, finding an optimal set of contact potentials. The optimized CG MD simulations reproduced the contact probability map from the AA MD simulations. Finally, we performed the CG MD simulation of the tetrameric p53 fragments including the core domains, the linker, and the tetramerization domain. Using the obtained ensemble, we theoretically calculated the small angle x-ray scattering (SAXS) profile of this fragment. The obtained SAXS profile agrees well with the experiment. We also found that the long-range contacts in the p53 linker region are required to reproduce the experimental SAXS profile. The developed framework in which we calculate the long-range contact probability map from the AA MD simulation and incorporate it to the CG model can be applied to broad range of IDRs.
Collapse
Affiliation(s)
- Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.
| |
Collapse
|
128
|
Varadi M, Vranken W, Guharoy M, Tompa P. Computational approaches for inferring the functions of intrinsically disordered proteins. Front Mol Biosci 2015; 2:45. [PMID: 26301226 PMCID: PMC4525029 DOI: 10.3389/fmolb.2015.00045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/21/2015] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are ubiquitously involved in cellular processes and often implicated in human pathological conditions. The critical biological roles of these proteins, despite not adopting a well-defined fold, encouraged structural biologists to revisit their views on the protein structure-function paradigm. Unfortunately, investigating the characteristics and describing the structural behavior of IDPs is far from trivial, and inferring the function(s) of a disordered protein region remains a major challenge. Computational methods have proven particularly relevant for studying IDPs: on the sequence level their dependence on distinct characteristics determined by the local amino acid context makes sequence-based prediction algorithms viable and reliable tools for large scale analyses, while on the structure level the in silico integration of fundamentally different experimental data types is essential to describe the behavior of a flexible protein chain. Here, we offer an overview of the latest developments and computational techniques that aim to uncover how protein function is connected to intrinsic disorder.
Collapse
Affiliation(s)
- Mihaly Varadi
- Flemish Institute of Biotechnology Brussels, Belgium ; Department of Structural Biology, VIB, Vrije Universiteit Brussels Brussels, Belgium
| | - Wim Vranken
- Flemish Institute of Biotechnology Brussels, Belgium ; Department of Structural Biology, VIB, Vrije Universiteit Brussels Brussels, Belgium ; ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2 Brussels, Belgium
| | - Mainak Guharoy
- Flemish Institute of Biotechnology Brussels, Belgium ; Department of Structural Biology, VIB, Vrije Universiteit Brussels Brussels, Belgium
| | - Peter Tompa
- Flemish Institute of Biotechnology Brussels, Belgium ; Department of Structural Biology, VIB, Vrije Universiteit Brussels Brussels, Belgium
| |
Collapse
|
129
|
Cidre-Aranaz F, Alonso J. EWS/FLI1 Target Genes and Therapeutic Opportunities in Ewing Sarcoma. Front Oncol 2015; 5:162. [PMID: 26258070 PMCID: PMC4507460 DOI: 10.3389/fonc.2015.00162] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/06/2015] [Indexed: 12/31/2022] Open
Abstract
Ewing sarcoma is an aggressive bone malignancy that affect children and young adults. Ewing sarcoma is the second most common primary bone malignancy in pediatric patients. Although significant progress has been made in the treatment of Ewing sarcoma since it was first described in the 1920s, in the last decade survival rates have remained unacceptably invariable, thus pointing to the need for new approaches centered in the molecular basis of the disease. Ewing sarcoma driving mutation, EWS–FLI1, which results from a chromosomal translocation, encodes an aberrant transcription factor. Since its first characterization in 1990s, many molecular targets have been described to be regulated by this chimeric transcription factor. Their contribution to orchestrate Ewing sarcoma phenotype has been reported over the last decades. In this work, we will focus on the description of a selection of EWS/FLI1 targets, their functional role, and their potential clinical relevance. We will also discuss their role in other types of cancer as well as the need for further studies to be performed in order to achieve a broader understanding of their particular contribution to Ewing sarcoma development.
Collapse
Affiliation(s)
- Florencia Cidre-Aranaz
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III , Madrid , Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III , Madrid , Spain
| |
Collapse
|
130
|
Sammak S, Zinzalla G. Targeting protein-protein interactions (PPIs) of transcription factors: Challenges of intrinsically disordered proteins (IDPs) and regions (IDRs). PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:41-6. [PMID: 26126425 DOI: 10.1016/j.pbiomolbio.2015.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 12/26/2022]
Abstract
In this review we discuss recent progress in targeting the protein-protein interactions made by oncogenic transcription factors. We particularly focus on the challenges posed by the prevalence of intrinsically disordered regions in this class of protein and the strategies being used to overcome them.
Collapse
Affiliation(s)
- Susan Sammak
- Department of Microbiology, Cell and Tumour Biology, and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23A, Stockholm 171 65, Sweden
| | - Giovanna Zinzalla
- Department of Microbiology, Cell and Tumour Biology, and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23A, Stockholm 171 65, Sweden.
| |
Collapse
|
131
|
Nath A, Schlamadinger DE, Rhoades E, Miranker AD. Structure-Based Small Molecule Modulation of a Pre-Amyloid State: Pharmacological Enhancement of IAPP Membrane-Binding and Toxicity. Biochemistry 2015; 54:3555-64. [PMID: 25966003 DOI: 10.1021/acs.biochem.5b00052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Islet amyloid polypeptide (IAPP) is a peptide hormone whose pathological self-assembly is a hallmark of the progression of type II diabetes. IAPP-membrane interactions catalyze its higher-order self-assembly and also underlie its toxic effects toward cells. While there is great interest in developing small molecule reagents capable of altering the structure and behavior of oligomeric, membrane-bound IAPP, the dynamic and heterogeneous nature of this ensemble makes it recalcitrant to traditional approaches. Here, we build on recent insights into the nature of membrane-bound states and develop a combined computational and experimental strategy to address this problem. The generalized structural approach efficiently identified diverse compounds from large commercial libraries with previously unrecognized activities toward the gain-of-function behaviors of IAPP. The use of appropriate computational prescreening reduced the experimental burden by orders of magnitude relative to unbiased high-throughput screening. We found that rationally targeting experimentally derived models of membrane-bound dimers identified several compounds that demonstrate the remarkable ability to enhance IAPP-membrane binding and one compound that enhances IAPP-mediated cytotoxicity. Taken together, these findings imply that membrane binding per se is insufficient to generate cytotoxicity; instead, enhanced sampling of rare states within the membrane-bound ensemble may potentiate IAPP's toxic effects.
Collapse
Affiliation(s)
- Abhinav Nath
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, United States
| | - Diana E Schlamadinger
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, United States
| | - Elizabeth Rhoades
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, United States
| | - Andrew D Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, United States
| |
Collapse
|
132
|
Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015; 16:153. [PMID: 25968230 PMCID: PMC4427981 DOI: 10.1186/s12859-015-0592-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/23/2015] [Indexed: 12/03/2022] Open
Abstract
Background Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of the protein. Results Here we present DisCons (Disorder Conservation), a novel pipelined tool that combines the quantification of sequence- and disorder conservation to classify disordered residue positions. According to this scheme, the most interesting categories (for functional purposes) are constrained disordered residues and flexible disordered residues. The former residues show conservation of both the sequence and the property of disorder and are associated mainly with specific binding functionalities (e.g., short, linear motifs, SLiMs), whereas the latter class correspond to segments where disorder as a feature is important for function as opposed to the identity of the underlying sequence (e.g., entropic chains and linkers). DisCons therefore helps with elucidating the function(s) arising from the disordered state by analyzing individual proteins as well as large-scale proteomics datasets. Conclusions DisCons is an openly accessible sequence analysis tool that identifies and highlights structurally disordered segments of proteins where the conformational flexibility is conserved across homologs, and therefore potentially functional. The tool is freely available both as a web application and as stand-alone source code hosted at http://pedb.vib.be/discons.
Collapse
Affiliation(s)
- Mihaly Varadi
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | - Mainak Guharoy
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | | | - Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
| |
Collapse
|
133
|
Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015. [PMID: 25968230 DOI: 10.1186/s12859‐015‐0592‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of the protein. RESULTS Here we present DisCons (Disorder Conservation), a novel pipelined tool that combines the quantification of sequence- and disorder conservation to classify disordered residue positions. According to this scheme, the most interesting categories (for functional purposes) are constrained disordered residues and flexible disordered residues. The former residues show conservation of both the sequence and the property of disorder and are associated mainly with specific binding functionalities (e.g., short, linear motifs, SLiMs), whereas the latter class correspond to segments where disorder as a feature is important for function as opposed to the identity of the underlying sequence (e.g., entropic chains and linkers). DisCons therefore helps with elucidating the function(s) arising from the disordered state by analyzing individual proteins as well as large-scale proteomics datasets. CONCLUSIONS DisCons is an openly accessible sequence analysis tool that identifies and highlights structurally disordered segments of proteins where the conformational flexibility is conserved across homologs, and therefore potentially functional. The tool is freely available both as a web application and as stand-alone source code hosted at http://pedb.vib.be/discons .
Collapse
Affiliation(s)
- Mihaly Varadi
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | - Mainak Guharoy
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | | | - Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
| |
Collapse
|
134
|
Yu DJ, Li Y, Hu J, Yang X, Yang JY, Shen HB. Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:611-621. [PMID: 26357272 DOI: 10.1109/tcbb.2014.2359451] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Disulfide connectivity is an important protein structural characteristic. Accurately predicting disulfide connectivity solely from protein sequence helps to improve the intrinsic understanding of protein structure and function, especially in the post-genome era where large volume of sequenced proteins without being functional annotated is quickly accumulated. In this study, a new feature extracted from the predicted protein 3D structural information is proposed and integrated with traditional features to form discriminative features. Based on the extracted features, a random forest regression model is performed to predict protein disulfide connectivity. We compare the proposed method with popular existing predictors by performing both cross-validation and independent validation tests on benchmark datasets. The experimental results demonstrate the superiority of the proposed method over existing predictors. We believe the superiority of the proposed method benefits from both the good discriminative capability of the newly developed features and the powerful modelling capability of the random forest. The web server implementation, called TargetDisulfide, and the benchmark datasets are freely available at: http://csbio.njust.edu.cn/bioinf/TargetDisulfide for academic use.
Collapse
|
135
|
Marasco D, Scognamiglio PL. Identification of inhibitors of biological interactions involving intrinsically disordered proteins. Int J Mol Sci 2015; 16:7394-412. [PMID: 25849651 PMCID: PMC4425024 DOI: 10.3390/ijms16047394] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 03/01/2015] [Accepted: 03/06/2015] [Indexed: 11/16/2022] Open
Abstract
Protein-protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs) are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few "hot spots", thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs.
Collapse
Affiliation(s)
- Daniela Marasco
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy.
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy.
| |
Collapse
|
136
|
Fu Y, Guo Y, Wang Y, Luo J, Pu X, Li M, Zhang Z. Exploring the relationship between hub proteins and drug targets based on GO and intrinsic disorder. Comput Biol Chem 2015; 56:41-8. [PMID: 25854804 DOI: 10.1016/j.compbiolchem.2015.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 03/13/2015] [Accepted: 03/21/2015] [Indexed: 11/25/2022]
Abstract
Protein-protein interactions (PPIs) play essential roles in many biological processes. In protein-protein interaction networks, hubs involve in numbers of PPIs and may constitute an important source of drug targets. The intrinsic disorder proteins (IDPs) with unstable structures can promote the promiscuity of hubs and also involve in many disease pathways, so they also could serve as potential drug targets. Moreover, proteins with similar functions measured by semantic similarity of gene ontology (GO) terms tend to interact with each other. Here, the relationship between hub proteins and drug targets based on GO terms and intrinsic disorder was explored. The semantic similarities of GO terms and genes between two proteins, and the rate of intrinsic disorder residues of each protein were extracted as features to characterize the functional similarity between two interacting proteins. Only using 8 feature variables, prediction models by support vector machine (SVM) were constructed to predict PPIs. The accuracy of the model on the PPI data from human hub proteins is as high as 83.72%, which is very promising compared with other PPI prediction models with hundreds or even thousands of features. Then, 118 of 142 PPIs between hubs are correctly predicted that the two interacting proteins are targets of the same drugs. The results indicate that only 8 functional features are fully efficient for representing PPIs. In order to identify new targets from IDP dataset, the PPIs between hubs and IDPs are predicted by the SVM model and the model yields a prediction accuracy of 75.84%. Further research proves that 3 of 5 PPIs between hubs and IDPs are correctly predicted that the two interacting proteins are targets of the same drugs. All results demonstrate that the model with only 8-dimensional features from GO terms and intrinsic disorder still gives a good performance in predicting PPIs and further identifying drug targets.
Collapse
Affiliation(s)
- Yuanyuan Fu
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu 610064, PR China.
| | - Yuelong Wang
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Jiesi Luo
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu 610064, PR China.
| | - Zhihang Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| |
Collapse
|
137
|
Zhang Y, Cao H, Liu Z. Binding cavities and druggability of intrinsically disordered proteins. Protein Sci 2015; 24:688-705. [PMID: 25611056 DOI: 10.1002/pro.2641] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 01/20/2023]
Abstract
To assess the potential of intrinsically disordered proteins (IDPs) as drug design targets, we have analyzed the ligand-binding cavities of two datasets of IDPs (containing 37 and 16 entries, respectively) and compared their properties with those of conventional ordered (folded) proteins. IDPs were predicted to possess more binding cavity than ordered proteins at similar length, supporting the proposed advantage of IDPs economizing genome and protein resources. The cavity number has a wide distribution within each conformation ensemble for IDPs. The geometries of the cavities of IDPs differ from the cavities of ordered proteins, for example, the cavities of IDPs have larger surface areas and volumes, and are more likely to be composed of a single segment. The druggability of the cavities was examined, and the average druggable probability is estimated to be 9% for IDPs, which is almost twice that for ordered proteins (5%). Some IDPs with druggable cavities that are associated with diseases are listed. The optimism versus obstacles for drug design for IDPs is also briefly discussed.
Collapse
Affiliation(s)
- Yugang Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | | | | |
Collapse
|
138
|
Hong SH, Youbi SE, Hong SP, Kallakury B, Monroe P, Erkizan HV, Barber-Rotenberg JS, Houghton P, Üren A, Toretsky JA. Pharmacokinetic modeling optimizes inhibition of the 'undruggable' EWS-FLI1 transcription factor in Ewing Sarcoma. Oncotarget 2015; 5:338-50. [PMID: 24481407 PMCID: PMC3964211 DOI: 10.18632/oncotarget.1495] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Transcription factors have long been deemed ‘undruggable’ targets for therapeutics. Enhanced recognition of protein biochemistry as well as the need to have more targeted approaches to treat cancer has rendered transcription factors approachable for therapeutic development. Since transcription factors lack enzymatic domains, the specific targeting of these proteins has unique challenges. One challenge is the hydrophobic microenvironment that affects small molecules gaining access to block protein interactions. The most attractive transcription factors to target are those formed from tumor specific chromosomal translocations that are validated oncogenic driver proteins. EWS-FLI1 is a fusion protein that results from the pathognomonic translocation of Ewing sarcoma (ES). Our past work created the small molecule YK-4-279 that blocks EWS-FLI1 from interacting with RNA Helicase A (RHA). To fulfill long-standing promise in the field by creating a clinically useful drug, steps are required to allow for in vivo administration. These investigations identify the need for continuous presence of the small molecule protein-protein inhibitor for a period of days. We describe the pharmacokinetics of YK-4-279 and its individual enantiomers. In vivo studies confirm prior in vitro experiments showing (S)-YK-4-279 as the EWS-FLI1 specific enantiomer demonstrating both induction of apoptosis and reduction of EWS-FLI1 regulated caveolin-1 protein. We have created the first rat xenograft model of ES, treated with (S)-YK-4-279 dosing based upon PK modeling leading to a sustained complete response in 2 of 6 ES tumors. Combining laboratory studies, pharmacokinetic measurements, and modeling has allowed us to create a paradigm that can be optimized for in vivo systems using both in vitro data and pharmacokinetic simulations. Thus, (S)-YK-4-279 as a small molecule drug is ready for continued development towards a first-in-human, first-in-class, clinical trial.
Collapse
Affiliation(s)
- Sung-Hyeok Hong
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
139
|
Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 827:111-21. [DOI: 10.1007/978-94-017-9245-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
140
|
Joshi P, Vendruscolo M. Druggability of Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:383-400. [DOI: 10.1007/978-3-319-20164-1_13] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
141
|
Pickhardt M, Neumann T, Schwizer D, Callaway K, Vendruscolo M, Schenk D, St George-Hyslop P, Mandelkow EM, Dobson CM, McConlogue L, Mandelkow E, Tóth G. Identification of Small Molecule Inhibitors of Tau Aggregation by Targeting Monomeric Tau As a Potential Therapeutic Approach for Tauopathies. Curr Alzheimer Res 2015; 12:814-28. [PMID: 26510979 PMCID: PMC4976804 DOI: 10.2174/156720501209151019104951] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/13/2015] [Accepted: 06/26/2015] [Indexed: 12/15/2022]
Abstract
A potential strategy to alleviate the aggregation of intrinsically disordered proteins (IDPs) is to maintain the native functional state of the protein by small molecule binding. However, the targeting of the native state of IDPs by small molecules has been challenging due to their heterogeneous conformational ensembles. To tackle this challenge, we applied a high-throughput chemical microarray surface plasmon resonance imaging screen to detect the binding between small molecules and monomeric full-length Tau, a protein linked with the onset of a range of Tauopathies. The screen identified a novel set of drug-like fragment and lead-like compounds that bound to Tau. We verified that the majority of these hit compounds reduced the aggregation of different Tau constructs in vitro and in N2a cells. These results demonstrate that Tau is a viable receptor of drug-like small molecules. The drug discovery approach that we present can be applied to other IDPs linked to other misfolding diseases such as Alzheimer's and Parkinson's diseases.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
| | - Gergely Tóth
- Department of Clinical Neuroscienes, Wolfson Brain Imaging Center, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom.
| |
Collapse
|
142
|
Hackl EV. Effect of Temperature on the Conformation of Natively Unfolded Protein 4E-BP1 in Aqueous and Mixed Solutions Containing Trifluoroethanol and Hexafluoroisopropanol. Protein J 2014; 34:18-28. [DOI: 10.1007/s10930-014-9595-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
143
|
Parigi G, Rezaei-Ghaleh N, Giachetti A, Becker S, Fernandez C, Blackledge M, Griesinger C, Zweckstetter M, Luchinat C. Long-range correlated dynamics in intrinsically disordered proteins. J Am Chem Soc 2014; 136:16201-9. [PMID: 25331250 DOI: 10.1021/ja506820r] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Intrinsically disordered proteins (IDPs) are involved in a wide variety of physiological and pathological processes and are best described by ensembles of rapidly interconverting conformers. Using fast field cycling relaxation measurements we here show that the IDP α-synuclein as well as a variety of other IDPs undergoes slow reorientations at time scales comparable to folded proteins. The slow motions are not perturbed by mutations in α-synuclein, which are related to genetic forms of Parkinson's disease, and do not depend on secondary and tertiary structural propensities. Ensemble-based hydrodynamic calculations suggest that the time scale of the underlying correlated motion is largely determined by hydrodynamic coupling between locally rigid segments. Our study indicates that long-range correlated dynamics are an intrinsic property of IDPs and offers a general physical mechanism of correlated motions in highly flexible biomolecular systems.
Collapse
Affiliation(s)
- Giacomo Parigi
- Department of Chemistry "Ugo Schiff" and CERM, University of Florence , via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
144
|
Abstract
The partitioning of intracellular space beyond membrane-bound organelles can be achieved with collections of proteins that are multivalent or contain low-complexity, intrinsically disordered regions. These proteins can undergo a physical phase change to form functional granules or other entities within the cytoplasm or nucleoplasm that collectively we term “assemblage.” Intrinsically disordered proteins (IDPs) play an important role in forming a subset of cellular assemblages by promoting phase separation. Recent work points to an involvement of assemblages in disease states, indicating that intrinsic disorder and phase transitions should be considered in the development of therapeutics.
Collapse
Affiliation(s)
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037 Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| |
Collapse
|
145
|
Sigalov AB. Unusual biophysics of immune signaling-related intrinsically disordered proteins. SELF NONSELF 2014; 1:271-281. [PMID: 21487502 DOI: 10.4161/self.1.4.13641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered (ID) regions, the regions that lack a well-defined three-dimensional structure under physiological conditions, are preferentially located in the cytoplasmic segments of plasma membrane proteins, many of which are known to be involved in cell signaling. This is in line with our studies that demonstrated that cytoplasmic domains of signaling subunits of immune receptors, including those of ζ, CD3ε, CD3δ and CD3γ chains of T cell receptor, Igα and Igβ chains of B cell receptor as well as the Fc receptor γ chain represent a novel class of ID proteins (IDPs). The domains all have one or more copies of an immunoreceptor tyrosine-based activation motif, tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Our studies of these IDPs revealed several unusual biophysical phenomena, including (1) the specific dimerization of disordered protein molecules, (2) the fast and slow dimerization equilibrium, depending on the protein, (3) no disorder-to-order transition and the lack of significant chemical shift and peak intensity changes upon dimerization or interaction with a well-folded partner protein and (4) the dual mode of binding to model membranes (with and without folding), depending on the lipid bilayer stability. Here, I highlight several of these studies that not only facilitate a rethinking process of the fundamental paradigms in protein biophysics but also open new perspectives on the molecular mechanisms involved in receptor signaling.
Collapse
|
146
|
Abstract
MYC is a master regulator of stem cell state, embryogenesis, tissue homeostasis, and aging. As in health, in disease MYC figures prominently. Decades of biological research have identified a central role for MYC in the pathophysiology of cancer, inflammation, and heart disease. The centrality of MYC to such a vast breadth of disease biology has attracted significant attention to the historic challenge of developing inhibitors of MYC. This review will discuss therapeutic strategies toward the development of inhibitors of MYC-dependent transcriptional signaling, efforts to modulate MYC stability, and the elusive goal of developing potent, direct-acting inhibitors of MYC.
Collapse
Affiliation(s)
- Michael R McKeown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02141 Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
| |
Collapse
|
147
|
Arya S, Mukhopadhyay S. Ordered Water within the Collapsed Globules of an Amyloidogenic Intrinsically Disordered Protein. J Phys Chem B 2014; 118:9191-8. [DOI: 10.1021/jp504076a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Shruti Arya
- Department of Chemical Sciences and ‡Department of
Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector
81, S.A.S. Nagar, Mohali 140306, Punjab, India
| | - Samrat Mukhopadhyay
- Department of Chemical Sciences and ‡Department of
Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector
81, S.A.S. Nagar, Mohali 140306, Punjab, India
| |
Collapse
|
148
|
Uversky VN, Davé V, Iakoucheva LM, Malaney P, Metallo SJ, Pathak RR, Joerger AC. Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases. Chem Rev 2014; 114:6844-79. [PMID: 24830552 PMCID: PMC4100540 DOI: 10.1021/cr400713r] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Vrushank Davé
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, United States
| | - Prerna Malaney
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Steven J. Metallo
- Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, United States
| | - Ravi Ramesh Pathak
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
149
|
Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université , Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
| | | | | | | |
Collapse
|
150
|
van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones D, Kim PM, Kriwacki R, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright P, Babu MM. Classification of intrinsically disordered regions and proteins. Chem Rev 2014; 114:6589-631. [PMID: 24773235 PMCID: PMC4095912 DOI: 10.1021/cr400525m] [Citation(s) in RCA: 1410] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Robin van der Lee
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Centre
for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The
Netherlands
| | - Marija Buljan
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Benjamin Lang
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Gary W. Daughdrill
- Department
of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 3720 Spectrum Boulevard, Suite 321, Tampa, Florida 33612, United States
| | - A. Keith Dunker
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, H-4032 Debrecen, Nagyerdei krt 98, Hungary
| | - Julian Gough
- Department
of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, United Kingdom
| | - Joerg Gsponer
- Department
of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David
T. Jones
- Bioinformatics
Group, Department of Computer Science, University
College London, London, WC1E 6BT, United Kingdom
| | - Philip M. Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular
Genetics, and Department of Computer Science, University
of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Richard
W. Kriwacki
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
| | - Christopher J. Oldfield
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Rohit V. Pappu
- Department
of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Peter Tompa
- VIB Department
of Structural Biology, Vrije Universiteit
Brussel, Brussels, Belgium
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vladimir N. Uversky
- Department
of Molecular Medicine and USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation,
Russian Academy of Sciences, Pushchino,
Moscow Region, Russia
| | - Peter
E. Wright
- Department
of Integrative Structural and Computational Biology and Skaggs Institute
of Chemical Biology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - M. Madan Babu
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|