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Bruley A, Mornon JP, Duprat E, Callebaut I. Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond. Biomolecules 2022; 12:1467. [PMID: 36291675 PMCID: PMC9599455 DOI: 10.3390/biom12101467] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 01/12/2023] Open
Abstract
AlphaFold2 (AF2) has created a breakthrough in biology by providing three-dimensional structure models for whole-proteome sequences, with unprecedented levels of accuracy. In addition, the AF2 pLDDT score, related to the model confidence, has been shown to provide a good measure of residue-wise disorder. Here, we combined AF2 predictions with pyHCA, a tool we previously developed to identify foldable segments and estimate their order/disorder ratio, from a single protein sequence. We focused our analysis on the AF2 predictions available for 21 reference proteomes (AFDB v1), in particular on their long foldable segments (>30 amino acids) that exhibit characteristics of soluble domains, as estimated by pyHCA. Among these segments, we provided a global analysis of those with very low pLDDT values along their entire length and compared their characteristics to those of segments with very high pLDDT values. We highlighted cases containing conditional order, as well as cases that could form well-folded structures but escape the AF2 prediction due to a shallow multiple sequence alignment and/or undocumented structure or fold. AF2 and pyHCA can therefore be advantageously combined to unravel cryptic structural features in whole proteomes and to refine predictions for different flavors of disorder.
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2
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Yamada Y, Obuchi K, Kikuchi N, Almarasy AA, Fujimori A. Immobilization of Trypsin from the Subphase to the Langmuir Monolayer of Fluorocarbon-Modified Single-Walled Carbon Nanotube and Its Activity Maintenance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5692-5701. [PMID: 35465664 DOI: 10.1021/acs.langmuir.2c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) synthesized by the improved arc discharge method were modified with a fluorocarbon chain, and the maintenance of trypsin activity upon adsorption from the subphase to the interfacial monolayer of SWCNTs was evaluated. The adsorption of trypsin on the fluorocarbon-modified SWCNT monolayer was confirmed by morphological and spectroscopic evaluations. Fiber morphology studies revealed that the fluorocarbon-modified SWCNT monolayer was covered by trypsin, and a trypsin-derived amide band was detected in the infrared spectra of the multilayers. After adsorption onto the fluorocarbon-modified SWCNT film, the ability of trypsin to cleave the fluorescent casein chain was maintained even at 160 °C. Furthermore, circular dichroism (CD) spectra showed that the second-order structure of the activity of trypsin adsorbed on the fluorocarbon-modified SWCNT was maintained up to nearly 200 °C. At 200 °C, the enhancement of emission intensity by casein chain cleavage was negligible, and the CD signal resulting from the negative Cotton effect was completely altered at 250 °C.
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Affiliation(s)
- Yuna Yamada
- Faculty of Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kei Obuchi
- Faculty of Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Nanata Kikuchi
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Ahmed A Almarasy
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Atsuhiro Fujimori
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
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3
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Bokor M, Tantos Á, Mészáros A, Jenei B, Haminda R, Tompa P, Tompa K. Molecular Motions and Interactions in Aqueous Solutions of Thymosin-β 4 , Stabilin CTD and Their 1 : 1 Complex, Studied by 1 H-NMR Spectroscopy. Chemphyschem 2020; 21:1420-1428. [PMID: 32469123 DOI: 10.1002/cphc.202000264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/20/2020] [Indexed: 12/23/2022]
Abstract
Wide-line 1 H NMR measurements were extended and all results were interpreted in a thermodynamics-based new approach on aqueous solutions of thymosin-β4 (Tβ4 ), stabilin cytoplasmic domain (CTD), and their 1 : 1 complex. Energy distributions of potential barriers controlling the motion of protein-bound water molecules were determined. Heterogeneous and homogeneous regions were found in the protein-water interface. The measure of heterogeneity of this interface gives quantitative value for the portion of disordered parts in the protein. Ordered structural elements were found extending up to ∼20 % of the individual whole proteins. About 40 % of the binding sites of free Tβ4 get involved in bonds holding the complex together. The complex has the most heterogeneous solvent accessible surface (SAS) in terms of protein-water interactions. The complex is more disordered than Tβ4 or stabilin CTD. The greater SAS area of the complex is interpreted as a clear sign of its open structure.
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Affiliation(s)
- M Bokor
- Department of Experimental Solid State Physics Wigner Research Centre, Konkoly-Thege út 29-33., 1121, Budapest, Hungary
| | - Á Tantos
- Research Group of Intrinsically Disordered Proteins, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - A Mészáros
- Research Group of Intrinsically Disordered Proteins, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - B Jenei
- Research Group of Intrinsically Disordered Proteins, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - R Haminda
- Chemical Institute, Eötvös Lóránd University, Pázmány P. sétány 1 A, 1117, Budapest
| | - P Tompa
- Research Group of Intrinsically Disordered Proteins, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary.,Peter Tompa Lab, VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
| | - K Tompa
- Department of Experimental Solid State Physics Wigner Research Centre, Konkoly-Thege út 29-33., 1121, Budapest, Hungary
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Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:1-78. [PMID: 32828463 PMCID: PMC7129803 DOI: 10.1016/bs.pmbts.2020.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.
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5
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Intrinsic Disorder-Based Emergence in Cellular Biology: Physiological and Pathological Liquid-Liquid Phase Transitions in Cells. Polymers (Basel) 2019; 11:polym11060990. [PMID: 31167414 PMCID: PMC6631845 DOI: 10.3390/polym11060990] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
The visible outcome of liquid-liquid phase transitions (LLPTs) in cells is the formation and disintegration of various proteinaceous membrane-less organelles (PMLOs). Although LLPTs and related PMLOs have been observed in living cells for over 200 years, the physiological functions of these transitions (also known as liquid-liquid phase separation, LLPS) are just starting to be understood. While unveiling the functionality of these transitions is important, they have come into light more recently due to the association of abnormal LLPTs with various pathological conditions. In fact, several maladies, such as various cancers, different neurodegenerative diseases, and cardiovascular diseases, are known to be associated with either aberrant LLPTs or some pathological transformations within the resultant PMLOs. Here, we will highlight both the physiological functions of cellular liquid-liquid phase transitions as well as the pathological consequences produced through both dysregulated biogenesis of PMLOs and the loss of their dynamics. We will also discuss the potential downstream toxic effects of proteins that are involved in pathological formations.
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6
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Tompa K, Bokor M, Tompa P. The Melting Diagram of Protein Solutions and Its Thermodynamic Interpretation. Int J Mol Sci 2018; 19:E3571. [PMID: 30424574 PMCID: PMC6274677 DOI: 10.3390/ijms19113571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/19/2018] [Accepted: 10/30/2018] [Indexed: 12/04/2022] Open
Abstract
Here we present a novel method for the characterization of the hydration of protein solutions based on measuring and evaluating two-component wide-line ¹H NMR signals. We also provide a description of key elements of the procedure conceived for the thermodynamic interpretation of such results. These interdependent experimental and theoretical treatments provide direct experimental insight into the potential energy surface of proteins. The utility of our approach is demonstrated through the examples of two proteins of distinct structural classes: the globular, structured ubiquitin; and the intrinsically disordered ERD10 (early response to dehydration 10). We provide a detailed analysis and interpretation of data recorded earlier by cooling and slowly warming the protein solutions through thermal equilibrium states. We introduce and use order parameters that can be thus derived to characterize the distribution of potential energy barriers inhibiting the movement of water molecules bound to the surface of the protein. Our results enable a quantitative description of the ratio of ordered and disordered parts of proteins, and of the energy relations of protein⁻water bonds in aqueous solutions of the proteins.
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Affiliation(s)
- Kálmán Tompa
- Institute for Solid State Physics and Optics, Wigner RCP of the HAS, Konkoly-Thege út 29-33, H-1121 Budapest, Hungary.
| | - Mónika Bokor
- Institute for Solid State Physics and Optics, Wigner RCP of the HAS, Konkoly-Thege út 29-33, H-1121 Budapest, Hungary.
| | - Péter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences of the HAS, Magyar Tudósok körút. 27, H-1117 Budapest, Hungary.
- VIB Center for Structural Biology, Vrije Universiteit Brussel, Building E, Pleinlaan 2, 1050 Brussel, Belgium.
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7
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Bitard‐Feildel T, Lamiable A, Mornon J, Callebaut I. Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences. Proteomics 2018; 18:e1800054. [PMID: 30299594 PMCID: PMC7168002 DOI: 10.1002/pmic.201800054] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/29/2018] [Indexed: 12/17/2022]
Abstract
Hydrophobic cluster analysis (HCA) is an original approach for protein sequence analysis, which provides access to the foldable repertoire of the protein universe, including yet unannotated protein segments ("dark proteome"). Foldable segments correspond to ordered regions, as well as to intrinsically disordered regions (IDRs) undergoing disorder to order transitions. In this review, how HCA can be used to give insight into this last category of foldable segments is illustrated, with examples matching known 3D structures. After reviewing the HCA principles, examples of short foldable segments are given, which often contain short linear motifs, typically matching hydrophobic clusters. These segments become ordered upon contact with partners, with secondary structure preferences generally corresponding to those observed in the 3D structures within the complexes. Such small foldable segments are sometimes larger than the segments of known 3D structures, including flanking hydrophobic clusters that may be critical for interaction specificity or regulation, as well as intervening sequences allowing fuzziness. Cases of larger conditionally disordered domains are also presented, with lower density in hydrophobic clusters than well-folded globular domains or with exposed hydrophobic patches, which are stabilized by interaction with partners.
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Affiliation(s)
- Tristan Bitard‐Feildel
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
- Laboratoire de Biologie Computationnelle et Quantitative (LCQB)Institute of Biology Paris‐Seine (IBPS)Centre national de la recherche scientifique (CNRS)Sorbonne Université75005ParisFrance
| | - Alexis Lamiable
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
| | - Jean‐Paul Mornon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
| | - Isabelle Callebaut
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC)Institut de recherche pour le développement (IRD)UMR CNRS 7590Muséum National d'Histoire NaturelleSorbonne Université75005ParisFrance
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8
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McCluskey K, Carlos Penedo J. An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters. Phys Chem Chem Phys 2018; 19:6921-6932. [PMID: 28225108 DOI: 10.1039/c6cp08798a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Riboswitches are short RNA motifs that sensitively and selectively bind cognate ligands to modulate gene expression. Like protein receptor-ligand pairs, their binding dynamics are traditionally categorized as following one of two paradigmatic mechanisms: conformational selection and induced fit. In conformational selection, ligand binding stabilizes a particular state already present in the receptor's dynamic ensemble. In induced fit, ligand-receptor interactions enable the system to overcome the energetic barrier into a previously inaccessible state. In this article, we question whether a polarized division of RNA binding mechanisms truly meets the conceptual needs of the field. We will review the history behind this classification of RNA-ligand interactions, and the way induced fit in particular has been rehabilitated by single-molecule studies of RNA aptamers. We will highlight several recent results from single-molecule experimental studies of riboswitches that reveal gaps or even contradictions between common definitions of the two terms, and we will conclude by proposing a more robust framework that considers the range of RNA behaviors unveiled in recent years as a reality to be described, rather than an increasingly unwieldy set of exceptions to the traditional models.
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Affiliation(s)
- K McCluskey
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK.
| | - J Carlos Penedo
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK. and Biomolecular Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9SS, UK.
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9
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Bokor M, Tantos Á, Mészáros A, Jenei B, Haminda R, Tompa P, Tompa K. Molecular Motions and Interactions in Aqueous Solutions of Thymosin-β 4 , Stabilin C-Terminal Domain (CTD) and Their 1:1 Complex Studied by 1 H NMR Spectroscopy. Chemphyschem 2018; 19:848-856. [PMID: 29274195 DOI: 10.1002/cphc.201701187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 01/08/2023]
Abstract
Wide-line 1 H NMR measurements were extended and all results were reinterpreted in a new thermodynamics-based approach to study aqueous solutions of thymosin-β4 (Tβ4 ), stabilin C-terminal domain (CTD) and their 1:1 complex. The energy distributions of the potential barriers, which control motion of protein-bound water molecules, were determined. Heterogeneous and homogeneous regions were found at the protein-water interface. The measure of heterogeneity gives a quantitative value for the portion of disordered parts in the protein. Ordered structural elements were found extending up to 20 % of the whole proteins. About 40 % of the binding sites of free Tβ4 become involved in bonds holding the complex together. The complex has the most heterogeneous solvent accessible surface (SAS) in terms of protein-water interactions. The complex is more disordered than Tβ4 or stabilin CTD. The greater SAS area of the complex is interpreted as a clear sign of its open structure.
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Affiliation(s)
- Mónika Bokor
- Experimental Solid State Research, Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Konkoly-Thege út 29-33. 1121, Budapest, Hungary
| | - Ágnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Attila Mészáros
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Bence Jenei
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Réka Haminda
- Chemical Institute, Eötvös Lóránd University, Pázmány P. sétány 1A, 1117, Budapest, Hungary
| | - Péter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary.,VIB Structural Biology Research Center (SBRC), Pleinlaan 2, 1050, Brussels, Belgium
| | - Kálmán Tompa
- Experimental Solid State Research, Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Konkoly-Thege út 29-33. 1121, Budapest, Hungary
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10
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Martin-Garcia JM, Conrad CE, Nelson G, Stander N, Zatsepin NA, Zook J, Zhu L, Geiger J, Chun E, Kissick D, Hilgart MC, Ogata C, Ishchenko A, Nagaratnam N, Roy-Chowdhury S, Coe J, Subramanian G, Schaffer A, James D, Ketwala G, Venugopalan N, Xu S, Corcoran S, Ferguson D, Weierstall U, Spence JCH, Cherezov V, Fromme P, Fischetti RF, Liu W. Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. IUCRJ 2017; 4:439-454. [PMID: 28875031 PMCID: PMC5571807 DOI: 10.1107/s205225251700570x] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/13/2017] [Indexed: 05/17/2023]
Abstract
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
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Affiliation(s)
- Jose M. Martin-Garcia
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie E. Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Garrett Nelson
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Natasha Stander
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - James Zook
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Lan Zhu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - James Geiger
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eugene Chun
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Mark C. Hilgart
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Alexander Schaffer
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Gihan Ketwala
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nagarajan Venugopalan
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Shenglan Xu
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Stephen Corcoran
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Dale Ferguson
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Uwe Weierstall
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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11
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Oláh J, Szénási T, Szabó A, Kovács K, Lőw P, Štifanić M, Orosz F. Tubulin Binding and Polymerization Promoting Properties of Tubulin Polymerization Promoting Proteins Are Evolutionarily Conserved. Biochemistry 2017; 56:1017-1024. [PMID: 28106390 DOI: 10.1021/acs.biochem.6b00902] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tubulin polymerization promoting proteins (TPPPs) constitute a eukaryotic protein family. There are three TPPP paralogs in the human genome, denoted as TPPP1-TPPP3. TPPP1 and TPPP3 are intrinsically unstructured proteins (IUPs) that bind and polymerize tubulin and stabilize microtubules, but TPPP2 does not. Vertebrate TPPPs originated from the ancient invertebrate TPPP by two-round whole-genome duplication; thus, whether the tubulin/microtubule binding function of TPPP1 and TPPP3 is a newly acquired property or was present in the invertebrate orthologs (generally one TPPP per species) has been an open question. To answer this question, we investigated a TPPP from a simple and early branching animal, the sponge Suberites domuncula. Bioinformatics, biochemical, immunochemical, spectroscopic, and electron microscopic data showed that the properties of the sponge protein correspond to those of TPPP1; namely, it is an IUP that strongly binds tubulin and induces its polymerization, proving that these features of animal TPPPs have been evolutionarily conserved.
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Affiliation(s)
- Judit Oláh
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest H-1117, Hungary
| | - Tibor Szénási
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest H-1117, Hungary
| | - Adél Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest H-1117, Hungary
| | - Kinga Kovács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest H-1117, Hungary
| | - Péter Lőw
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University , Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - Mauro Štifanić
- Department of Natural and Health Studies, Juraj Dobrila University of Pula , Zagrebačka 30, HR-52100 Pula, Croatia
| | - Ferenc Orosz
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest H-1117, Hungary
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12
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Ilizaliturri-Flores I, Correa-Basurto J, Bello M, Rosas-Trigueros JL, Zamora-López B, Benítez-Cardoza CG, Zamorano-Carrillo A. Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study. J Mol Model 2016; 22:98. [PMID: 27037822 DOI: 10.1007/s00894-016-2940-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/22/2016] [Indexed: 02/07/2023]
Abstract
Most of the B-cell lymphoma-2 (Bcl-2) protein structure has been elucidated; however, the conformation of its flexible loop domain (FLD) has not yet been experimentally predicted. Its high flexibility under physiological conditions is the reason. FLD behaves as an intrinsically disordered region (IDR) and can adopt regular structures in particular conditions associated with the control of Bcl-2's anti-apoptotic functions. In a previous contribution, we analyzed an engineered Bcl-2 construct (Bcl-2-Δ22Σ3) submitted to 25-ns MD and reported a disordered-to-helix transitions in a region of FLD (rFLD, residues 60-77). However, the conformational preferences in solution of rFLD in the nanosecond to microsecond scale were not analyzed. Herein, an average model was obtained for the native Bcl-2 protein by homology modeling and MD simulation techniques. From this, only the atomic coordinates corresponding to the rFLD were simulated for 1 μs by MD at 310 K. In concordance with previous studies, a disordered-to-helix transitions were exhibited, implying that this "interconversion of folding" in the rFLD suggest a possible set of conformations encoded in its sequence. Principal component analysis (PCA) showed that most of the conformational fluctuation of Bcl-2 is provided by rFLD. Dihedral PCA (dPCA) offered information about all the conformations of rFLD in the μs of the simulation, characterizing a dPCA-based free energy landscape of rFLD, and a conformational ensemble of fast interconverting conformations as other IDRs. Furthermore, despite the conformational heterogeneity of rFLD, the analysis of the dihedral angles (Φ, Ψ) showed that this region does not randomly explore the conformational space in solution.
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Affiliation(s)
| | - José Correa-Basurto
- Lab de Modelado Molecular y Diseño de Fármacos. ESM-IPN, Ciudad de México, Mexico
| | - Martiniano Bello
- Lab de Modelado Molecular y Diseño de Fármacos. ESM-IPN, Ciudad de México, Mexico
| | - Jorge L Rosas-Trigueros
- Lab Transdisciplinario de Investigación en Sistemas Evolutivos, ESCOM-IPN, Ciudad de México, Mexico
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13
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Espinoza-Fonseca LM, Kelekar A. High-resolution structural characterization of Noxa, an intrinsically disordered protein, by microsecond molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2016; 11:1850-6. [PMID: 25855872 DOI: 10.1039/c5mb00170f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
High-resolution characterization of the structure and dynamics of intrinsically disordered proteins (IDPs) remains a challenging task. Consequently, a detailed understanding of the structural and functional features of IDPs remains limited, as very few full-length disordered proteins have been structurally characterized. We have performed microsecond-long molecular dynamics (MD) simulations of Noxa, the smallest member of the large Bcl-2 family of apoptosis regulating proteins, to characterize in atomic-level detail the structural features of a disordered protein. A 2.5 μs MD simulation starting from an unfolded state of the protein revealed the formation of a central antiparallel β-sheet structure flanked by two disordered segments at the N- and C-terminal ends. This topology is in reasonable agreement with protein disorder predictions and available experimental data. We show that this fold plays an essential role in the intracellular function and regulation of Noxa. We demonstrate that unbiased MD simulations in combination with a modern force field reveal structural and functional features of disordered proteins at atomic-level resolution.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology and Biophysics University of Minnesota, Minneapolis, MN 55455, USA.
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14
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Banerjee S, De RK. Structural disorder: a tool for housekeeping proteins performing tissue-specific interactions. J Biomol Struct Dyn 2016; 34:1930-45. [DOI: 10.1080/07391102.2015.1095115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Sanghita Banerjee
- Machine Intelligence Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata 700108, India
| | - Rajat K. De
- Machine Intelligence Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata 700108, India
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15
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16
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Castillo P, Cetina AF, Méndez-Tenorio A, Espinoza-Fonseca LM, Barrón BL. Papillomavirus binding factor (PBF) is an intrinsically disordered protein with potential participation in osteosarcoma genesis, in silico evidence. Theor Biol Med Model 2014; 11:51. [PMID: 25471943 PMCID: PMC4265421 DOI: 10.1186/1742-4682-11-51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/21/2014] [Indexed: 11/17/2022] Open
Abstract
Background Papillomavirus binding factor (PBF) or zinc finger protein 395 is a transcription factor associated to a poor prognosis in patients with osteosarcoma, an aggressive bone cancer that predominantly affects adolescents. To investigate the role of the PBF protein in the osteosarcoma genesis, in this paper we present the bioinformatics analysis of physicochemical properties of PBF and its probable interactions with several key cellular targets. Results The physicochemical characteristics determined to PBF, disorder-promoting amino acids, flexibility, hydrophobicity, prediction of secondary and tertiary structures and probability to be crystallized, supported that this protein can be considered as an intrinsically disordered protein (IDP), with a zinc finger-like domain. The in silico analysis to find out PBF interactions with cellular factors, confirmed the experimentally demonstrated interaction of PBF with two key cellular proteins involved in regulation of cellular apoptosis, 14-3-3β and Scythe/BAT3 proteins. Furthermore, other interactions were found with proteins like HDAC1 and TPR which are known to be deregulated in several cancers. Experimental confirmation of specific interactions will contribute to understand the osteosarcoma process and might lead to the identification of new targets for diagnosis and treatments. Conclusions According to the in silico PBF analyses, this protein can be considered as an IDP capable to bind several key cellular factors, and these interactions might play an important role in the osteosarcoma process.
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Affiliation(s)
| | | | | | | | - Blanca L Barrón
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Casco de Santo Tomás, México, DF 11340, México.
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17
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Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université , Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
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18
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Marín M, Ott T. Intrinsic disorder in plant proteins and phytopathogenic bacterial effectors. Chem Rev 2014; 114:6912-32. [PMID: 24697726 DOI: 10.1021/cr400488d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Macarena Marín
- Genetics Institute, Faculty of Biology, Ludwig-Maximilians-University of Munich , Grosshaderner Strasse 2-4, 82152 Martinsried, Germany
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19
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Martin-Garcia JM, Hansen DT, Zook J, Loskutov AV, Robida MD, Craciunescu FM, Sykes KF, Wachter RM, Fromme P, Allen JP. Purification and biophysical characterization of the CapA membrane protein FTT0807 from Francisella tularensis. Biochemistry 2014; 53:1958-70. [PMID: 24593131 PMCID: PMC3985703 DOI: 10.1021/bi401644s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
The capA gene (FTT0807)
from Francisella
tularensis subsp. tularensis SCHU S4 encodes a 44.4
kDa integral membrane protein composed of 403 amino acid residues
that is part of an apparent operon that encodes at least two other
membrane proteins, CapB, and CapC, which together play a critical
role in the virulence and pathogenesis of this bacterium. The capA gene was overexpressed in Escherichia
coli as a C-terminal His6-tagged fusion
with a folding reporter green fluorescent protein (frGFP). Purification
procedures using several detergents were developed for the fluorescing
and membrane-bound product, yielding approximately 30 mg of pure protein
per liter of bacterial culture. Dynamic light scattering indicated
that CapA-frGFP was highly monodisperse, with a size that was dependent
upon both the concentration and choice of detergent. Circular dichroism
showed that CapA-frGFP was stable over the range of 3–9 for
the pH, with approximately half of the protein having well-defined
α-helical and β-sheet secondary structure. The addition
of either sodium chloride or calcium chloride at concentrations producing
ionic strengths above 0.1 M resulted in a small increase of the α-helical
content and a corresponding decrease in the random-coil content. Secondary-structure
predictions on the basis of the analysis of the sequence indicate
that the CapA membrane protein has two transmembrane helices with
a substantial hydrophilic domain. The hydrophilic domain is predicted
to contain a long disordered region of 50–60 residues, suggesting
that the increase of α-helical content at high ionic strength
could arise because of electrostatic interactions involving the disordered
region. CapA is shown to be an inner-membrane protein and is predicted
to play a key cellular role in the assembly of polysaccharides.
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Affiliation(s)
- Jose M Martin-Garcia
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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20
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Yin Z, Kelso MJ, Beck JL, Oakley AJ. Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp. J Med Chem 2013; 56:8665-73. [DOI: 10.1021/jm401118f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zhou Yin
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Michael J. Kelso
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Jennifer L. Beck
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Aaron J. Oakley
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
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21
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Breydo L, Mikheeva LM, Madeira PP, Zaslavsky BY, Uversky VN. Solvent interaction analysis of intrinsically disordered proteins in aqueous two-phase systems. MOLECULAR BIOSYSTEMS 2013; 9:3068-79. [PMID: 24072065 DOI: 10.1039/c3mb70329k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In an aqueous two-phase system (ATPS), the partitioning of a protein is defined by the differential interactions of the protein with aqueous media in the two phases. Our study shows that partitioning of proteins in a set of ATPSs of different ionic compositions can be used to quantify structural differences between α-synuclein, its variants and several globular proteins. Since application of ATPSs implies the use of high concentrations of two polymers in water when a certain threshold concentration of the polymers is exceeded, and since these levels of polymer concentrations are similar to those commonly used to mimic the effects of macromolecular crowding on proteins, we used circular dichroism spectroscopy to evaluate the structural consequences of placing proteins in solutions with high polymer concentrations and various ionic compositions.
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Affiliation(s)
- Leonid Breydo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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22
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Abstract
Inteins are intervening protein sequences that undergo self-excision from a precursor protein with the concomitant ligation of the flanking polypeptides. Split inteins are expressed in two separated halves, and the recognition and association of two halves are the first crucial step for initiating trans-splicing. In the present study, we carried out the structural and thermodynamic analysis on the interaction of two halves of DnaE split intein from Synechocystis sp. PCC6803. Both isolated halves (IN and IC) are disordered and undergo conformational transition from disorder to order upon association. ITC (isothermal titration calorimetry) reveals that the highly favourable enthalpy change drives the association of the two halves, overcoming the unfavourable entropy change. The high flexibility of two fragments and the marked thermodynamic preference provide a robust association for the formation of the well-folded IN/IC complex, which is the basis for reconstituting the trans-splicing activity of DnaE split intein.
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23
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Testa L, Brocca S, Santambrogio C, D'Urzo A, Habchi J, Longhi S, Uversky VN, Grandori R. Extracting structural information from charge-state distributions of intrinsically disordered proteins by non-denaturing electrospray-ionization mass spectrometry. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25068. [PMID: 28516012 PMCID: PMC5424789 DOI: 10.4161/idp.25068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/02/2013] [Accepted: 05/16/2013] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.
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Affiliation(s)
- Lorenzo Testa
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Annalisa D'Urzo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Johnny Habchi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Sonia Longhi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Vladimir N Uversky
- Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| | - Rita Grandori
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
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24
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Abstract
PP1 (protein phosphatase 1) is an essential serine/threonine phosphatase that plays a critical role in a broad range of biological processes, from muscle contraction to memory formation. PP1 achieves its biological specificity by forming holoenzymes with more than 200 known regulatory proteins. Interestingly, most of these regulatory proteins (≥ 70%) belong to the class of IDPs (intrinsically disordered proteins). Thus structural studies highlighting the interaction of these IDP regulatory proteins with PP1 are an attractive model system because it allows general parameters for a group of diverse IDPs that interact with the same binding partner to be identified, while also providing fundamental insights into PP1 biology. The present review provides a brief overview of our current understanding of IDP-PP1 interactions, including the importance of pre-formed secondary and tertiary structures for PP1 binding, as well as changes of IDP dynamics upon interacting with PP1.
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25
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Unusual biophysics of intrinsically disordered proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:932-51. [PMID: 23269364 DOI: 10.1016/j.bbapap.2012.12.008] [Citation(s) in RCA: 413] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/21/2012] [Accepted: 12/12/2012] [Indexed: 02/08/2023]
Abstract
Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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26
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Tantos A, Szrnka K, Szabo B, Bokor M, Kamasa P, Matus P, Bekesi A, Tompa K, Han KH, Tompa P. Structural disorder and local order of hNopp140. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:342-50. [PMID: 22906532 DOI: 10.1016/j.bbapap.2012.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 08/02/2012] [Accepted: 08/04/2012] [Indexed: 11/20/2022]
Abstract
Human nucleolar phosphoprotein p140 (hNopp 140) is a highly phosphorylated protein inhibitor of casein kinase 2 (CK2). As in the case of many kinase-inhibitor systems, the inhibitor has been described to belong to the family of intrinsically disordered proteins (IDPs), which often utilize transient structural elements to bind their cognate enzyme. Here we investigated the structural status of this protein both to provide distinct lines of evidence for its disorder and to point out its transient structure potentially involved in interactions and also its tendency to aggregate. Structural disorder of hNopp140 is apparent by its anomalous electrophoretic mobility, protease sensitivity, heat stability, hydrodynamic behavior on size-exclusion chromatography, (1)H NMR spectrum and differential scanning calorimetry scan. hNopp140 has a significant tendency to aggregate and the change of its circular dichroism spectrum in the presence of 0-80% TFE suggests a tendency to form local helical structures. Wide-line NMR measurements suggest the overall disordered character of the protein. In all, our data suggest that this protein falls into the pre-molten globule state of IDPs, with a significant tendency to become ordered in the presence of its partner as demonstrated in the presence of transcription factor IIB (TFIIB).
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Affiliation(s)
- Agnes Tantos
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
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27
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Pancsa R, Fuxreiter M. Interactions via intrinsically disordered regions: what kind of motifs? IUBMB Life 2012; 64:513-20. [PMID: 22535488 DOI: 10.1002/iub.1034] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/06/2012] [Indexed: 12/22/2022]
Abstract
Proteins containing intrinsically disordered (ID) regions are widespread in eukaryotic organisms and are mostly utilized in regulatory processes. ID regions can mediate binary interactions of proteins or promote organization of large assemblies. Post-translational modifications of ID regions often serve as decision points in signaling pathways. Why Nature distinguished ID proteins in molecular recognition functions? In a simple view, binding of ID regions is accompanied by a large entropic penalty as compared to folded proteins. Even in complexes however, ID regions can preserve their conformational freedom, thereby recruit further partners and perform various functions. What sort of benefits ID regions offer for molecular interactions and which properties are exploited in the corresponding complexes? Here, we review models explaining the recognition mechanisms of ID proteins. Motif-based interactions are central to all proposed scenarios, including prestructured elements, anchoring sites and linear motifs. We aim to extract consensus features of the models, which could be used to predict ID-binding sites for a variety of partners.
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Affiliation(s)
- Rita Pancsa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
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28
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Espinoza-Fonseca LM, Ilizaliturri-Flores I, Correa-Basurto J. Backbone conformational preferences of an intrinsically disordered protein in solution. MOLECULAR BIOSYSTEMS 2012; 8:1798-805. [PMID: 22506277 DOI: 10.1039/c2mb00004k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We have performed a 4-μs molecular dynamics simulation to investigate the native conformational preferences of the intrinsically disordered kinase-inducible domain (KID) of the transcription factor CREB in solution. There is solid experimental evidence showing that KID does not possess a bound-like structure in solution; however, it has been proposed that coil-to-helix transitions upon binding to its binding partner (CBP) are template-driven. While these studies indicate that IDPs possess a bias towards the bound structure, they do not provide direct evidence on the time-dependent conformational preferences of IDPs in atomic detail. Our simulation captured intrinsic conformational characteristics of KID that are in good agreement with experimental data such as a very small percentage of helical structure in its segment α(B) and structural disorder in solution. We used dihedral principal component analysis dPCA to map the conformations of KID in the microsecond timescale. By using principal components as reaction coordinates, we further constructed dPCA-based free energy landscapes of KID. Analysis of the free energy landscapes showed that KID is best characterized as a conformational ensemble of rapidly interconverting conformations. Interestingly, we found that despite the conformational heterogeneity of the backbone and the absence of substantial secondary structure, KID does not randomly sample the conformational space in solution: analysis of the (Φ, Ψ) dihedral angles showed that several individual residues of KID possess a strong bias toward the helical region of the Ramachandran plot. We suggest that the intrinsic conformational preferences of KID provide a bias toward the folded state without having to populate bound-like conformations before binding. Furthermore, we argue that these conformational preferences do not represent actual structural constraints which drive binding through a single pathway, which allows for specific interactions with multiple binding partners. Based on this evidence, we propose that the backbone conformational preferences of KID provide a thermodynamic advantage for folding and binding without negatively affecting the kinetics of binding. We further discuss the relation of our results to previous studies to rationalize the functional implications of the conformational preferences of IDPs, such as the optimization of structural disorder in protein-protein interactions. This study illustrates the importance in obtaining atomistic information of intrinsically disordered proteins in real time to reveal functional features arising from their complex conformational space.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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29
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Abstract
Based on early bioinformatic studies on a handful of species, the frequency of structural disorder of proteins is generally thought to be much higher in eukaryotes than in prokaryotes. To refine this view, we present here a comparative prediction study and analysis of 194 fully described eukaryotic proteomes and 87 reference prokaryotes for structural disorder. We found that structural disorder does distinguish eukaryotes from prokaryotes, but its frequency spans a very wide range in the two superkingdoms that largely overlap. The number of disordered binding regions and different Pfam domain types also contribute to distinguish eukaryotes from prokaryotes. Unexpectedly, the highest levels--and highest variability--of predicted disorder is found in protists, i.e. single-celled eukaryotes, often surpassing more complex eukaryote organisms, plants and animals. This trend contrasts with that of the number of domain types, which increases rather monotonously toward more complex organisms. The level of structural disorder appears to be strongly correlated with lifestyle, because some obligate intracellular parasites and endosymbionts have the lowest levels, whereas host-changing parasites have the highest level of predicted disorder. We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established.
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Affiliation(s)
- Rita Pancsa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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30
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Wald T, Bednárová L, Osička R, Pachl P, Šulc M, Lyngstadaas SP, Slaby I, Vondrášek J. Biophysical characterization of recombinant human ameloblastin. Eur J Oral Sci 2012; 119 Suppl 1:261-9. [DOI: 10.1111/j.1600-0722.2011.00913.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Affiliation(s)
- Monika Fuxreiter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
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32
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Lee KAW. Molecular recognition by the EWS transcriptional activation domain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:106-25. [PMID: 22399321 DOI: 10.1007/978-1-4614-0659-4_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Interactions between Intrinsically Disordered Protein Regions (IDRs) and their targets commonly exhibit localised contacts via target-induced disorder to order transitions. Other more complex IDR target interactions have been termed "fuzzy" because the IDR does not form a well-defined induced structure. In some remarkable cases of fuzziness IDR function is apparently sequence independent and conferred by amino acid composition. Such cases have been referred to as "random fuzziness" but the molecular features involved are poorly characterised. The transcriptional activation domain (EAD) of oncogenic Ewing's Sarcoma Fusion Proteins (EFPs) is an ≈280 residue IDR with a biased composition restricted to Ala, Gly, Gln, Pro, Ser, Thr and Tyr. Multiple aromatic side chains (exclusively from Try residues) and the particular EAD composition are crucial for molecular recognition but there appears to be no other major geometrically constrained requirement. Computational analysis of the EAD using PONDR (Molecular Kinetics, Inc. http://www.pondr. com) complements the functional data and shows, accordingly, that propensity for structural order within the EAD is conferred by Tyr residues. To conclude, molecular recognition by the EAD is extraordinarily malleable and involves multiple aromatic contacts facilitated by a flexible peptide backbone and, most likely, a limited number of weaker contributions from amenable side chains. I propose to refer to this mode of fuzzy recognition as "polyaromatic", noting that it shares some fundamental features with the "polyelectrostatic" (phosphorylation-dependent) interaction of the Sic1 Cdk inhibitor and Cdc4._I will also speculate on more detailed models for molecular recognition by the EAD and their relationship to native (non-oncogenic) EAD function.
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Affiliation(s)
- Kevin A W Lee
- Department of Biology, Hong Kong University of Science and Technology, Hong Kong, China.
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33
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Vuzman D, Levy Y. Intrinsically disordered regions as affinity tuners in protein–DNA interactions. ACTA ACUST UNITED AC 2012; 8:47-57. [DOI: 10.1039/c1mb05273j] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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34
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Espinoza-Fonseca LM. Aromatic residues link binding and function of intrinsically disordered proteins. ACTA ACUST UNITED AC 2012; 8:237-46. [DOI: 10.1039/c1mb05239j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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35
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Intrinsically disordered proteins may escape unwanted interactions via functional misfolding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:693-712. [DOI: 10.1016/j.bbapap.2011.03.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/16/2011] [Accepted: 03/16/2011] [Indexed: 12/30/2022]
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36
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Uversky VN. Intrinsically disordered proteins from A to Z. Int J Biochem Cell Biol 2011; 43:1090-103. [PMID: 21501695 DOI: 10.1016/j.biocel.2011.04.001] [Citation(s) in RCA: 327] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/31/2011] [Accepted: 04/01/2011] [Indexed: 01/13/2023]
Abstract
The ideas that proteins might possess specific functions without being uniquely folded into rigid 3D-structures and that these floppy polypeptides might constitute a noticeable part of any given proteome would have been considered as a preposterous fiction 15 or even 10 years ago. The situation has changed recently, and the existence of functional yet intrinsically disordered proteins and regions has become accepted by a significant number of protein scientists. These fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting and attractive targets for modern protein research. This review summarizes some of the major discoveries and breakthroughs in the field of intrinsic disorder by representing related concepts and definitions.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, FL 33612, USA.
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37
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Polverini E, Coll EP, Tieleman DP, Harauz G. Conformational choreography of a molecular switch region in myelin basic protein—Molecular dynamics shows induced folding and secondary structure type conversion upon threonyl phosphorylation in both aqueous and membrane-associated environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:674-83. [DOI: 10.1016/j.bbamem.2010.11.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Revised: 11/10/2010] [Accepted: 11/23/2010] [Indexed: 12/12/2022]
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38
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Huang Y, Liu Z. Anchoring intrinsically disordered proteins to multiple targets: lessons from N-terminus of the p53 protein. Int J Mol Sci 2011; 12:1410-30. [PMID: 21541066 PMCID: PMC3083713 DOI: 10.3390/ijms12021410] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/10/2011] [Accepted: 02/16/2011] [Indexed: 02/03/2023] Open
Abstract
Anchor residues, which are deeply buried upon binding, play an important role in protein–protein interactions by providing recognition specificity and facilitating the binding kinetics. Up to now, studies on anchor residues have been focused mainly on ordered proteins. In this study, we investigated anchor residues in intrinsically disordered proteins (IDPs) which are flexible in the free state. We identified the anchor residues of the N-terminus of the p53 protein (Glu17–Asn29, abbreviated as p53N) which are involved in binding with two different targets (MDM2 and Taz2), and analyzed their side chain conformations in the unbound states. The anchor residues in the unbound p53N were found to frequently sample conformations similar to those observed in the bound complexes (i.e., Phe19, Trp23, and Leu26 in the p53N-MDM2 complex, and Leu22 in the p53N-Taz2 complex). We argue that the bound-like conformations of the anchor residues in the unbound state are important for controlling the specific interactions between IDPs and their targets. Further, we propose a mechanism to account for the binding promiscuity of IDPs in terms of anchor residues and molecular recognition features (MoRFs).
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Affiliation(s)
- Yongqi Huang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Theoretical Biology, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Zhirong Liu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Theoretical Biology, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-10-62753422; Fax: +86-10-62751708
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39
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Marsh JA, Dancheck B, Ragusa MJ, Allaire M, Forman-Kay JD, Peti W. Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators. Structure 2010; 18:1094-103. [PMID: 20826336 PMCID: PMC2936704 DOI: 10.1016/j.str.2010.05.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/07/2010] [Accepted: 05/19/2010] [Indexed: 10/19/2022]
Abstract
Complete folding is not a prerequisite for protein function, as disordered and partially folded states of proteins frequently perform essential biological functions. In order to understand their functions at the molecular level, we utilized diverse experimental measurements to calculate ensemble models of three nonhomologous, intrinsically disordered proteins: I-2, spinophilin, and DARPP-32, which bind to and regulate protein phosphatase 1 (PP1). The models demonstrate that these proteins have dissimilar propensities for secondary and tertiary structure in their unbound forms. Direct comparison of these ensemble models with recently determined PP1 complex structures suggests a significant role for transient, preformed structure in the interactions of these proteins with PP1. Finally, we generated an ensemble model of partially disordered I-2 bound to PP1 that provides insight into the relationship between flexibility and biological function in this dynamic complex.
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Affiliation(s)
- Joseph A. Marsh
- Molecular Structure & Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada & Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Barbara Dancheck
- Department of Molecular Pharmacology, Physiology and Biotechnology & Department of Chemistry, Brown University, Providence, RI, 02912, USA
| | - Michael J. Ragusa
- Department of Molecular Pharmacology, Physiology and Biotechnology & Department of Chemistry, Brown University, Providence, RI, 02912, USA
| | - Marc Allaire
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Julie D. Forman-Kay
- Molecular Structure & Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada & Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology & Department of Chemistry, Brown University, Providence, RI, 02912, USA
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40
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Hydration water/interfacial water in crystalline lens. Exp Eye Res 2010; 91:76-84. [PMID: 20412792 DOI: 10.1016/j.exer.2010.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 03/19/2010] [Accepted: 04/13/2010] [Indexed: 11/23/2022]
Abstract
Wide-line (1)H NMR signal intensity, spin-lattice and spin-spin relaxation rates and differential scanning calorimetry (DSC) measurements were done on avian (chicken and turkey) crystalline lenses between -70 degrees C and +45 degrees C to provide quantitative measures of protein hydration characteristic of the protein-water interfacial region. These measures are of paramount importance in understanding both the physiology of crystalline lens and its transitions to the cataractous pathological state characterized by the formation of opaque protein aggregates. Water mobility shows a characteristic transition at about -60 degrees C, which is identified as the melting of the interfacial/hydrate water. The amount of water in the low-temperature mobile fraction is about h = 0.4 g water/g protein, which equals the hydration required for protein activity. The amount of mobile water is temperature-independent up to about -10 degrees C, with a significant increase at higher temperatures below 0 degrees C. Above 0 degrees C, the relaxation processes can be described by a single (for spin-lattice) and by a triple (for spin-spin relaxation) exponential function. The spin-spin relaxation rate component of R(2) = 10-20 s(-1) and its dynamical parameters characterize the interfacial water at ambient or physiological temperatures. When considered an independent phase, the specific heat of the hydrate water obtained by a combination of DSC and NMR data in the temperature range -43 degrees C to -28 degrees C is higher than that of pure/bulk water. This discrepancy can only be resolved by assuming that the hydrate water is in strong thermodynamic coupling with the protein matrix. The specific heat for the system composed of the protein molecule and its hydration water is 4.6 +/- 0.3 J g(-1) K(-1). Thus, in a thermodynamic sense, crystalline protein and its hydrate layer behave as a highly-interconnected single phase.
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41
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Miller M. The importance of being flexible: the case of basic region leucine zipper transcriptional regulators. Curr Protein Pept Sci 2009; 10:244-69. [PMID: 19519454 DOI: 10.2174/138920309788452164] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Large volumes of protein sequence and structure data acquired by proteomic studies led to the development of computational bioinformatic techniques that made possible the functional annotation and structural characterization of proteins based on their primary structure. It has become evident from genome-wide analyses that many proteins in eukaryotic cells are either completely disordered or contain long unstructured regions that are crucial for their biological functions. The content of disorder increases with evolution indicating a possibly important role of disorder in the regulation of cellular systems. Transcription factors are no exception and several proteins of this class have recently been characterized as premolten/molten globules. Yet, mammalian cells rely on these proteins to control expression of their 30,000 or so genes. Basic region:leucine zipper (bZIP) DNA-binding proteins constitute a major class of eukaryotic transcriptional regulators. This review discusses how conformational flexibility "built" into the amino acid sequence allows bZIP proteins to interact with a large number of diverse molecular partners and to accomplish their manifold cellular tasks in a strictly regulated and coordinated manner.
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Affiliation(s)
- Maria Miller
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.
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42
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Bae SH, Dyson HJ, Wright PE. Prediction of the rotational tumbling time for proteins with disordered segments. J Am Chem Soc 2009; 131:6814-21. [PMID: 19391622 DOI: 10.1021/ja809687r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For well-structured, rigid proteins, the prediction of rotational tumbling time (tau(c)) using atomic coordinates is reasonably accurate, but is inaccurate for proteins with long unstructured sequences. Under physiological conditions, many proteins contain long disordered segments that play important regulatory roles in fundamental biological events including signal transduction and molecular recognition. Here we describe an ensemble approach to the boundary element method that accurately predicts tau(c) for such proteins by introducing two layers of molecular surfaces whose correlated velocities decay exponentially with distance. Reliable prediction of tau(c) will help to detect intra- and intermolecular interactions and conformational switches between more ordered and less ordered states of the disordered segments. The method has been extensively validated using 12 reference proteins with 14 to 103 disordered residues at the N- and/or C-terminus and has been successfully employed to explain a set of published results on a system that incorporates a conformational switch.
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Affiliation(s)
- Sung-Hun Bae
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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43
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Teilum K, Olsen JG, Kragelund BB. Functional aspects of protein flexibility. Cell Mol Life Sci 2009; 66:2231-47. [PMID: 19308324 PMCID: PMC11115794 DOI: 10.1007/s00018-009-0014-6] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 02/24/2009] [Accepted: 03/04/2009] [Indexed: 12/29/2022]
Abstract
Proteins are dynamic entities, and they possess an inherent flexibility that allows them to function through molecular interactions within the cell, among cells and even between organisms. Appreciation of the non-static nature of proteins is emerging, but to describe and incorporate this into an intuitive perception of protein function is challenging. Flexibility is of overwhelming importance for protein function, and the changes in protein structure during interactions with binding partners can be dramatic. The present review addresses protein flexibility, focusing on protein-ligand interactions. The thermodynamics involved are reviewed, and examples of structure-function studies involving experimentally determined flexibility descriptions are presented. While much remains to be understood about protein flexibility, it is clear that it is encoded within their amino acid sequence and should be viewed as an integral part of their structure.
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Johan G. Olsen
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
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44
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Tompa K, Bánki P, Bokor M, Kamasa P, Lasanda G, Tompa P. Interfacial water at protein surfaces: wide-line NMR and DSC characterization of hydration in ubiquitin solutions. Biophys J 2009; 96:2789-98. [PMID: 19348762 DOI: 10.1016/j.bpj.2008.11.038] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 11/10/2008] [Indexed: 11/15/2022] Open
Abstract
Wide-line 1H-NMR and differential scanning calorimetry measurements were done in aqueous solutions and on lyophilized samples of human ubiquitin between -70 degrees C and +45 degrees C. The measured properties (size, thermal evolution, and wide-line NMR spectra) of the protein-water interfacial region are substantially different in the double-distilled and buffered-water solutions of ubiquitin. The characteristic transition in water mobility is identified as the melting of the nonfreezing/hydrate water. The amount of water in the low-temperature mobile fraction is 0.4 g/g protein for the pure water solution. The amount of mobile water is higher and its temperature dependence more pronounced for the buffered solution. The specific heat of the nonfreezing/hydrate water was evaluated using combined differential scanning calorimetry and NMR data. Considering the interfacial region as an independent phase, the values obtained are 5.0-5.8 J x g(-1) x K(-1), and the magnitudes are higher than that of pure/bulk water (4.2 J x g(-1) x K(-1)). This unexpected discrepancy can only be resolved in principle by assuming that hydrate water is in tight H-bond coupling with the protein matrix. The specific heat for the system composed of the protein molecule and its hydration water is 2.3 J x g(-1) x K(-1). It could be concluded that the protein ubiquitin and its hydrate layer behave as a highly interconnected single phase in a thermodynamic sense.
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Affiliation(s)
- Kálmán Tompa
- Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, Budapest, Hungary
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45
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Balázs A, Csizmok V, Buday L, Rakács M, Kiss R, Bokor M, Udupa R, Tompa K, Tompa P. High levels of structural disorder in scaffold proteins as exemplified by a novel neuronal protein, CASK-interactive protein1. FEBS J 2009; 276:3744-56. [PMID: 19523119 DOI: 10.1111/j.1742-4658.2009.07090.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
CASK-interactive protein1 is a newly recognized post-synaptic density protein in mammalian neurons. Although its N-terminal region contains several well-known functional domains, its entire C-terminal proline-rich region of 800 amino acids lacks detectable sequence homology to any previously characterized protein. We used multiple techniques for the structural characterization of this region and its three fragments. By bioinformatics predictions, CD spectroscopy, wide-line and 1H-NMR spectroscopy, limited proteolysis and gel filtration chromatography, we provided evidence that the entire proline-rich region of CASK-interactive protein1 is intrinsically disordered. We also showed that the proline-rich region is biochemically functional, as it interacts with the adaptor protein Abl-interactor-2. To extend the finding of a high level of disorder in this scaffold protein, we collected 74 scaffold proteins (also including proteins denoted as anchor and docking), and predicted their disorder by three different algorithms. We found that a very high fraction (53.6; on average) of the residues fall into local disorder and their ordered domains are connected by linker regions which are mostly disordered (64.5 on average). Because of this high frequency of disorder, the usual design of scaffold proteins of short globular domains (86 amino acids on average) connected by longer linker regions (140 amino acids on average) and the noted binding functions of these regions in both CASK-interactive protein1 and the other proteins studied, we suggest that structurally disordered regions prevail and play key recognition roles in scaffold proteins.
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Affiliation(s)
- Annamária Balázs
- Department of Medical Chemistry, Semmelweis University Medical School, Budapest, Hungary
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46
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Espinoza-Fonseca LM. Reconciling binding mechanisms of intrinsically disordered proteins. Biochem Biophys Res Commun 2009; 382:479-82. [DOI: 10.1016/j.bbrc.2009.02.151] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 02/26/2009] [Indexed: 11/15/2022]
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47
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Plasmodium falciparum merozoite surface protein 2 is unstructured and forms amyloid-like fibrils. Mol Biochem Parasitol 2009; 166:159-71. [PMID: 19450733 DOI: 10.1016/j.molbiopara.2009.03.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 03/30/2009] [Accepted: 03/30/2009] [Indexed: 12/30/2022]
Abstract
Several merozoite surface proteins are being assessed as potential components of a vaccine against Plasmodium falciparum, the cause of the most serious form of human malaria. One of these proteins, merozoite surface protein 2 (MSP2), is unusually hydrophilic and contains tandem sequence repeats, characteristics of intrinsically unstructured proteins. A range of physicochemical studies has confirmed that recombinant forms of MSP2 are largely unstructured. Both dimorphic types of MSP2 (3D7 and FC27) are equivalently extended in solution and form amyloid-like fibrils although with different kinetics and structural characteristics. These fibrils have a regular underlying beta-sheet structure and both fibril types stain with Congo Red, but only the FC27 fibrils stain with Thioflavin T. 3D7 MSP2 fibrils seeded the growth of fibrils from 3D7 or FC27 MSP2 monomer indicating the involvement of a conserved region of MSP2 in fibril formation. Consistent with this, digestion of fibrils with proteinase K generated resistant peptides, which included the N-terminal conserved region of MSP2. A monoclonal antibody that reacted preferentially with monomeric recombinant MSP2 did not react with the antigen in situ on the merozoite surface. Glutaraldehyde cross-linking of infected erythrocytes generated MSP2 oligomers similar to those formed by polymeric recombinant MSP2. We conclude that MSP2 oligomers containing intermolecular beta-strand interactions similar to those in amyloid fibrils may be a component of the fibrillar surface coat on P. falciparum merozoites.
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48
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Takahashi M, Mizuguchi M, Shinoda H, Aizawa T, Demura M, Okazawa H, Kawano K. Polyglutamine tract binding protein-1 is an intrinsically unstructured protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:936-43. [PMID: 19303059 DOI: 10.1016/j.bbapap.2009.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 02/27/2009] [Accepted: 03/03/2009] [Indexed: 12/24/2022]
Abstract
Polyglutamine tract binding protein-1 (PQBP-1) is a nuclear protein that interacts with disease proteins containing expanded polyglutamine repeats. PQBP-1 also interacts with RNA polymerase II and a spliceosomal protein U5-15kD. In the present study, we demonstrate that PQBP-1 is composed of a large unstructured region and a small folded core. Intriguingly, the large unstructured region encompasses two functional domains: a polar amino acid rich domain and a C-terminal domain. These findings suggest that PQBP-1 belongs to the family of intrinsically unstructured/disordered proteins. Furthermore, the binding of the target molecule U5-15kD induces only minor conformational changes into PQBP-1. Our results suggest that PQBP-1 includes high content of unstructured regions in the C-terminal domain, in spite of the binding of U5-15kD.
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Affiliation(s)
- Masaki Takahashi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630, Sugitani, Toyama 930-0194, Japan
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49
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Cold stability of intrinsically disordered proteins. FEBS Lett 2008; 583:465-9. [PMID: 19121309 DOI: 10.1016/j.febslet.2008.12.054] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 01/27/2023]
Abstract
Contrary to globular proteins, intrinsically disordered proteins (IDPs) lack a folded structure and they do not lose solubility at elevated temperatures. Although this should also be true at low temperatures, cold stability of IDPs has not been addressed in any scientific work so far. As direct characterization of cold-denaturation is difficult, we approached the problem through a freezing-induced loss-of-function model of globular-disordered functional protein pairs (m-calpain-calpastatin, tubulin-Map2c, Hsp90-ERD14). Our results affirm that in contrast with globular proteins IDPs are resistant to cold treatment. The theoretical and functional aspects of this observation are discussed.
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50
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Fuxreiter M, Tompa P, Simon I, Uversky VN, Hansen JC, Asturias FJ. Malleable machines take shape in eukaryotic transcriptional regulation. Nat Chem Biol 2008; 4:728-37. [PMID: 19008886 DOI: 10.1038/nchembio.127] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Transcriptional control requires the spatially and temporally coordinated action of many macromolecular complexes. Chromosomal proteins, transcription factors, co-activators and components of the general transcription machinery, including RNA polymerases, often use structurally or stoichiometrically ill-defined regions for interactions that convey regulatory information in processes ranging from chromatin remodeling to mRNA processing. Determining the functional significance of intrinsically disordered protein regions and developing conceptual models of their action will help to illuminate their key role in transcription regulation. Complexes comprising disordered regions often display short recognition elements embedded in flexible and sequentially variable environments that can lead to structural and functional malleability. This provides versatility to recognize multiple targets having different structures, facilitate conformational rearrangements and physically communicate with many partners in response to environmental changes. All these features expand the capacities of ordered complexes and give rise to efficient regulatory mechanisms.
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Affiliation(s)
- Monika Fuxreiter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29, H-1113, H-1518 Budapest, Hungary.
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