1
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Jiao X, Di Sante G, Casimiro MC, Tantos A, Ashton AW, Li Z, Quach Y, Bhargava D, Di Rocco A, Pupo C, Crosariol M, Lazar T, Tompa P, Wang C, Yu Z, Zhang Z, Aldaaysi K, Vadlamudi R, Mann M, Skordalakes E, Kossenkov A, Du Y, Pestell RG. A cyclin D1 intrinsically disordered domain accesses modified histone motifs to govern gene transcription. Oncogenesis 2024; 13:4. [PMID: 38191593 PMCID: PMC10774418 DOI: 10.1038/s41389-023-00502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
The essential G1-cyclin, CCND1, is frequently overexpressed in cancer, contributing to tumorigenesis by driving cell-cycle progression. D-type cyclins are rate-limiting regulators of G1-S progression in mammalian cells via their ability to bind and activate CDK4 and CDK6. In addition, cyclin D1 conveys kinase-independent transcriptional functions of cyclin D1. Here we report that cyclin D1 associates with H2BS14 via an intrinsically disordered domain (IDD). The same region of cyclin D1 was necessary for the induction of aneuploidy, induction of the DNA damage response, cyclin D1-mediated recruitment into chromatin, and CIN gene transcription. In response to DNA damage H2BS14 phosphorylation occurs, resulting in co-localization with γH2AX in DNA damage foci. Cyclin D1 ChIP seq and γH2AX ChIP seq revealed ~14% overlap. As the cyclin D1 IDD functioned independently of the CDK activity to drive CIN, the IDD domain may provide a rationale new target to complement CDK-extinction strategies.
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Affiliation(s)
- Xuanmao Jiao
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | - Mathew C Casimiro
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Department of Science and Mathematics, Abraham Baldwin Agricultural College, Tifton, GA, 31794, USA
| | - Agnes Tantos
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
| | - Anthony W Ashton
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Division of Cardiovascular Medicine, Lankenau Institute for Medical Research, Wynnewood, PA, 19003, USA
| | - Zhiping Li
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Yen Quach
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | | | - Claudia Pupo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Marco Crosariol
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Peter Tompa
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Zhao Zhang
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Kawthar Aldaaysi
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Ratna Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | - Monica Mann
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | | | | | - Yanming Du
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Richard G Pestell
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba.
- The Wistar Institute, Philadelphia, PA, 19107, USA.
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2
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Chowdhury A, Borgia A, Ghosh S, Sottini A, Mitra S, Eapen RS, Borgia MB, Yang T, Galvanetto N, Ivanović MT, Łukijańczuk P, Zhu R, Nettels D, Kundagrami A, Schuler B. Driving forces of the complex formation between highly charged disordered proteins. Proc Natl Acad Sci U S A 2023; 120:e2304036120. [PMID: 37796987 PMCID: PMC10576128 DOI: 10.1073/pnas.2304036120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/22/2023] [Indexed: 10/07/2023] Open
Abstract
Highly disordered complexes between oppositely charged intrinsically disordered proteins present a new paradigm of biomolecular interactions. Here, we investigate the driving forces of such interactions for the example of the highly positively charged linker histone H1 and its highly negatively charged chaperone, prothymosin α (ProTα). Temperature-dependent single-molecule Förster resonance energy transfer (FRET) experiments and isothermal titration calorimetry reveal ProTα-H1 binding to be enthalpically unfavorable, and salt-dependent affinity measurements suggest counterion release entropy to be an important thermodynamic driving force. Using single-molecule FRET, we also identify ternary complexes between ProTα and H1 in addition to the heterodimer at equilibrium and show how they contribute to the thermodynamics observed in ensemble experiments. Finally, we explain the observed thermodynamics quantitatively with a mean-field polyelectrolyte theory that treats counterion release explicitly. ProTα-H1 complex formation resembles the interactions between synthetic polyelectrolytes, and the underlying principles are likely to be of broad relevance for interactions between charged biomolecules in general.
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Affiliation(s)
- Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Souradeep Ghosh
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Soumik Mitra
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Rohan S. Eapen
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | | | - Tianjin Yang
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Nicola Galvanetto
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
| | - Miloš T. Ivanović
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Paweł Łukijańczuk
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Ruijing Zhu
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Arindam Kundagrami
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
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3
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Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
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Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
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4
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Lázár T, Tantos A, Tompa P, Schad E. Intrinsic protein disorder uncouples affinity from binding specificity. Protein Sci 2022; 31:e4455. [PMID: 36305763 PMCID: PMC9601785 DOI: 10.1002/pro.4455] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins often function by molecular recognition, in which they undergo induced folding. Based on prior generalizations, the idea prevails in the IDP field that due to the entropic penalty of induced folding, the major functional advantage associated with this binding mode is "uncoupling" specificity from binding strength. Nevertheless, both weaker binding and high specificity of IDPs/IDRs rest on limited experimental observations, making these assumptions more speculations than evidence-supported facts. The issue is also complicated by the rather vague concept of specificity that lacks an exact measure, such as the Kd for binding strength. We addressed these issues by creating and analyzing a comprehensive dataset of well-characterized ID/globular protein complexes, for which both the atomic structure of the complex and free energy (ΔG, Kd ) of interaction is known. Through this analysis, we provide evidence that the affinity distributions of IDP/globular and globular/globular complexes show different trends, whereas specificity does not connote to weaker binding strength of IDPs/IDRs. Furthermore, protein disorder extends the spectrum in the direction of very weak interactions, which may have important regulatory consequences and suggest that, in a biological sense, strict correlation of specificity and binding strength are uncoupled by structural disorder.
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Affiliation(s)
- Tamas Lázár
- VIB‐VUB Center for Structural BiologyFlanders Institute for Biotechnology (VIB)BrusselsBelgium,Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Agnes Tantos
- Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
| | - Peter Tompa
- VIB‐VUB Center for Structural BiologyFlanders Institute for Biotechnology (VIB)BrusselsBelgium,Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium,Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
| | - Eva Schad
- Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
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5
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Musacchio A. On the role of phase separation in the biogenesis of membraneless compartments. EMBO J 2022; 41:e109952. [PMID: 35107832 PMCID: PMC8886532 DOI: 10.15252/embj.2021109952] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Molecular mechanistic biology has ushered us into the world of life’s building blocks, revealing their interactions in macromolecular complexes and inspiring strategies for detailed functional interrogations. The biogenesis of membraneless cellular compartments, functional mesoscale subcellular locales devoid of strong internal order and delimiting membranes, is among mechanistic biology’s most demanding current challenges. A developing paradigm, biomolecular phase separation, emphasizes solvation of the building blocks through low‐affinity, weakly adhesive unspecific interactions as the driver of biogenesis of membraneless compartments. Here, I discuss the molecular underpinnings of the phase separation paradigm and demonstrate that validating its assumptions is much more challenging than hitherto appreciated. I also discuss that highly specific interactions, rather than unspecific ones, appear to be the main driver of biogenesis of subcellular compartments, while phase separation may be harnessed locally in selected instances to generate material properties tailored for specific functions, as exemplified by nucleocytoplasmic transport.
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Affiliation(s)
- Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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6
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Jankovic B, Bozovic O, Hamm P. Intrinsic Dynamics of Protein-Peptide Unbinding. Biochemistry 2021; 60:1755-1763. [PMID: 33999611 DOI: 10.1021/acs.biochem.1c00262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The dynamics of peptide-protein binding and unbinding of a variant of the RNase S system has been investigated. To initiate the process, a photoswitchable azobenzene moiety has been covalently linked to the S-peptide, thereby switching its binding affinity to the S-protein. Transient fluorescence quenching was measured with the help of a time-resolved fluorometer, which has been specifically designed for these experiments and is based on inexpensive light-emitting diodes and laser diodes only. One mutant shows on-off behavior with no specific binding detectable in one of the states of the photoswitch. Unbinding is faster by at least 2 orders of magnitude, compared to that of other variants of the RNase S system. We conclude that unbinding is essentially barrier-less in that case, revealing the intrinsic dynamics of the unbinding event, which occurs on a time scale of a few hundred microseconds in a strongly stretched-exponential manner.
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Affiliation(s)
- Brankica Jankovic
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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7
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Shrestha UR, Smith JC, Petridis L. Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations. Commun Biol 2021; 4:243. [PMID: 33623120 PMCID: PMC7902620 DOI: 10.1038/s42003-021-01759-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
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Affiliation(s)
- Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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8
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Tan PS, Aramburu IV, Mercadante D, Tyagi S, Chowdhury A, Spitz D, Shammas SL, Gräter F, Lemke EA. Two Differential Binding Mechanisms of FG-Nucleoporins and Nuclear Transport Receptors. Cell Rep 2019; 22:3660-3671. [PMID: 29590630 PMCID: PMC5898484 DOI: 10.1016/j.celrep.2018.03.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/30/2018] [Accepted: 03/06/2018] [Indexed: 01/12/2023] Open
Abstract
Phenylalanine-glycine-rich nucleoporins (FG-Nups) are intrinsically disordered proteins, constituting the selective barrier of the nuclear pore complex (NPC). Previous studies showed that nuclear transport receptors (NTRs) were found to interact with FG-Nups by forming an “archetypal-fuzzy” complex through the rapid formation and breakage of interactions with many individual FG motifs. Here, we use single-molecule studies combined with atomistic simulations to show that, in sharp contrast, FG-Nup214 undergoes a coupled reconfiguration-binding mechanism when interacting with the export receptor CRM1. Association and dissociation rate constants are more than an order of magnitude lower than in the archetypal-fuzzy complex between FG-Nup153 and NTRs. Unexpectedly, this behavior appears not to be encoded selectively into CRM1 but rather into the FG-Nup214 sequence. The same distinct binding mechanisms are unperturbed in O-linked β-N-acetylglucosamine-modified FG-Nups. Our results have implications for differential roles of distinctly spatially distributed FG-Nup⋅NTR interactions in the cell. Identification of two differential binding mechanisms in the nuclear transport pathway FG-Nup214 does not bind CRM1 via an archetypal-fuzzy complex Glycosylated FG-Nups maintain their NTR-binding mechanisms Linker regions of FG-Nups may have functional relevance to the binding mechanism
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Affiliation(s)
- Piau Siong Tan
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Iker Valle Aramburu
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Davide Mercadante
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Mathematikon, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Swati Tyagi
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aritra Chowdhury
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel Spitz
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sarah L Shammas
- Department of New Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Mathematikon, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany.
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Johannes-von-Mullerweg 6, 55128 Mainz, Germany; Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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9
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Bose D, Chakrabarti A. Localizing the chaperone activity of erythroid spectrin. Cytoskeleton (Hoboken) 2019; 76:383-397. [DOI: 10.1002/cm.21556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Dipayan Bose
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
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10
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Crabtree MD, Shammas SL. Stopped-Flow Kinetic Techniques for Studying Binding Reactions of Intrinsically Disordered Proteins. Methods Enzymol 2018; 611:423-457. [PMID: 30471695 DOI: 10.1016/bs.mie.2018.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Intrinsically disordered proteins are abundant in signaling processes such as transcription. Suitable binding and unbinding rates of proteins with their partners are critical for allowing them to perform their biological roles. Understanding how these are achieved, and indeed designing strategies for intervening or modulating related biological processes, therefore requires kinetic studies. In this chapter, we describe stopped-flow-based methods for determining association and dissociation rate constants for pairs of macromolecular binding partners. We describe how to select the simplest appropriate model to describe the interaction, and highlight cases where it is possible to distinguish between induced fit and conformational selection binding mechanisms. Finally, we go on to describe methods for examining the role of electrostatic forces in binding processes, and for describing the transition state for binding processes that have folding associated with them.
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Affiliation(s)
- Michael D Crabtree
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sarah L Shammas
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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11
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Lindström I, Dogan J. Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain. ACS Chem Biol 2018; 13:1218-1227. [PMID: 29614221 DOI: 10.1021/acschembio.7b01105] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.
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Affiliation(s)
- Ida Lindström
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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12
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Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure. Proc Natl Acad Sci U S A 2017; 114:9882-9887. [PMID: 28847960 DOI: 10.1073/pnas.1705105114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of defined structure. Instead, they populate ensembles of rapidly interconverting conformations with marginal structural stabilities. Changes in solution conditions such as temperature and crowding agents consequently affect IDPs more than their folded counterparts. Here we reveal that the residual structure content of IDPs is modulated both by ionic strength and by the type of ions present in solution. We show that these ion-specific structural changes result in binding affinity shifts of up to sixfold, which happen through alteration of both association and dissociation rates. These effects follow the Hofmeister series, but unlike the well-established effects on the stability of folded proteins, they already occur at low, hypotonic concentrations of salt. We attribute this sensitivity to the marginal stability of IDPs, which could have physiological implications given the role of IDPs in signaling, the asymmetric ion profiles of different cellular compartments, and the role of ions in biology.
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13
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Lindström I, Dogan J. Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement. Biochemistry 2017; 56:4145-4153. [PMID: 28707474 DOI: 10.1021/acs.biochem.7b00428] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.
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Affiliation(s)
- Ida Lindström
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
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14
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Bose D, Patra M, Chakrabarti A. Effect of pH on stability, conformation, and chaperone activity of erythroid & non-erythroid spectrin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:694-702. [PMID: 28373029 DOI: 10.1016/j.bbapap.2017.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 11/29/2022]
Abstract
Spectrin, a major component of the eukaryotic membrane skeleton, has been shown to have chaperone like activity. Here we investigate the pH induced changes in the structure and stability of erythroid and brain spectrin by spectroscopic methods. We also correlate these changes with modulations of chaperone potential at different pH. We have followed the pH induced structural changes by circular dichroism spectroscopy and intrinsic tryptophan fluorescence. It is seen that lowering the pH from 9 has little effect on structure of the proteins till about pH6. At pH4, there is significant change of the secondary structure of the proteins, along with a 5nm hypsochromic shift of the emission maxima. Below pH4 the proteins undergo acid denaturation. Probing exposed hydrophobic patches on the proteins using protein-bound 8-anilinonaphthalene-1-sulfonate fluorescence demonstrates that there is higher solvent accessibility of hydrophobic surfaces in both forms of spectrin at around pH4. Dynamic light scattering and 90° light scattering studies show that the both forms of spectrin forms oligomers at pH~4. Chemical unfolding data shows that these oligomers are less stable than the tetrameric form. Aggregation studies with BSA show that at pH4, both spectrins exhibit better chaperone activity. This enhancement of chaperone like activity appears to result from an increase in regions of solvent-exposed hydrophobicity and oligomeric state of the spectrins which in turn are induced by moderately acid pH. This may have in-vivo implications in cells facing stress conditions where cytoplasmic pH is lowered.
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Affiliation(s)
- Dipayan Bose
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Malay Patra
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India.
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15
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Shammas SL. Mechanistic roles of protein disorder within transcription. Curr Opin Struct Biol 2017; 42:155-161. [PMID: 28262589 DOI: 10.1016/j.sbi.2017.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 12/28/2022]
Abstract
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.
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Affiliation(s)
- Sarah L Shammas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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16
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Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles. Proc Natl Acad Sci U S A 2016; 113:12490-12495. [PMID: 27791060 DOI: 10.1073/pnas.1602380113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their relative simplicity, bacteria have complex anatomy at the subcellular level. At the cell poles of Caulobacter crescentus, a 177-amino acid (aa) protein called PopZ self-assembles into 3D polymeric superstructures. Remarkably, we find that this assemblage interacts directly with at least eight different proteins, which are involved in cell cycle regulation and chromosome segregation. The binding determinants within PopZ include 24 aa at the N terminus, a 32-aa region near the C-terminal homo-oligomeric assembly domain, and portions of an intervening linker region. Together, the N-terminal 133 aa of PopZ are sufficient for interacting with all binding partners, even in the absence of homo-oligomeric assembly. Structural analysis of this region revealed that it is intrinsically disordered, similar to p53 and other hub proteins that organize complex signaling networks in eukaryotic cells. Through live-cell photobleaching, we find rapid binding kinetics between PopZ and its partners, suggesting many pole-localized proteins become concentrated at cell poles through rapid cycles of binding and unbinding within the PopZ scaffold. We conclude that some bacteria, similar to their eukaryotic counterparts, use intrinsically disordered hub proteins for network assembly and subcellular organization.
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17
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Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Finding Our Way in the Dark Proteome. J Am Chem Soc 2016; 138:9730-42. [PMID: 27387657 PMCID: PMC5051545 DOI: 10.1021/jacs.6b06543] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. We envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.
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Affiliation(s)
- Asmit Bhowmick
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - David H. Brookes
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037
| | - Julie D. Forman-Kay
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Daniel Gunter
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | | | - Gregory L. Hura
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - David E. Wemmer
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Peter E. Wright
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
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18
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Pantoja-Uceda D, Neira JL, Saelices L, Robles-Rengel R, Florencio FJ, Muro-Pastor MI, Santoro J. Dissecting the Binding between Glutamine Synthetase and Its Two Natively Unfolded Protein Inhibitors. Biochemistry 2016; 55:3370-82. [DOI: 10.1021/acs.biochem.6b00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - José L. Neira
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto
de Biocomputación y Física de Sistemas Complejos (BIFI),
Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Lorena Saelices
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Rocío Robles-Rengel
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Francisco J. Florencio
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - M. Isabel Muro-Pastor
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Jorge Santoro
- Instituto
de Química Física Rocasolano (IQFR), CSIC, 28006 Madrid, Spain
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19
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Umezawa K, Ohnuki J, Higo J, Takano M. Intrinsic disorder accelerates dissociation rather than association. Proteins 2016; 84:1124-33. [DOI: 10.1002/prot.25057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/16/2016] [Accepted: 04/24/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Umezawa
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Jun Ohnuki
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University; Suita Osaka 565-0871 Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
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20
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Shammas SL, Crabtree MD, Dahal L, Wicky BIM, Clarke J. Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies. J Biol Chem 2016; 291:6689-95. [PMID: 26851275 PMCID: PMC4807256 DOI: 10.1074/jbc.r115.692715] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of persistent structure. Since their identification more than a decade ago, many questions regarding their functional relevance and interaction mechanisms remain unanswered. Although most experiments have taken equilibrium and structural perspectives, fewer studies have investigated the kinetics of their interactions. Here we review and highlight the type of information that can be gained from kinetic studies. In particular, we show how kinetic studies of coupled folding and binding reactions, an important class of signaling event, are needed to determine mechanisms.
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Affiliation(s)
- Sarah L Shammas
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael D Crabtree
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Liza Dahal
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Basile I M Wicky
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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21
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Sherry KP, Johnson SE, Hatem CL, Majumdar A, Barrick D. Effects of Linker Length and Transient Secondary Structure Elements in the Intrinsically Disordered Notch RAM Region on Notch Signaling. J Mol Biol 2015; 427:3587-3597. [PMID: 26344835 DOI: 10.1016/j.jmb.2015.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/26/2015] [Accepted: 09/02/2015] [Indexed: 12/14/2022]
Abstract
Formation of the bivalent interaction between the Notch intracellular domain (NICD) and the transcription factor CBF-1/RBP-j, Su(H), Lag-1 (CSL) is a key event in Notch signaling because it switches Notch-responsive genes from a repressed state to an activated state. Interaction of the intrinsically disordered RBP-j-associated molecule (RAM) region of NICD with CSL is thought to both disrupt binding of corepressor proteins to CSL and anchor NICD to CSL, promoting interaction of the ankyrin domain of NICD with CSL through an effective concentration mechanism. To quantify the role of disorder in the RAM linker region on the effective concentration enhancement of Notch transcriptional activation, we measured the effects of linker length variation on activation. The resulting activation profile has general features of a worm-like chain model for effective concentration. However, deviations from the model for short sequence deletions suggest that RAM contains sequence-specific structural elements that may be important for activation. Structural characterization of the RAM linker with sedimentation velocity analytical ultracentrifugation and NMR spectroscopy reveals that the linker is compact and contains three transient helices and two extended and dynamic regions. To test if these secondary structure elements are important for activation, we made sequence substitutions to change the secondary structure propensities of these elements and measured transcriptional activation of the resulting variants. Substitutions to two of these nonrandom elements (helix 2, extended region 1) have effects on activation, but these effects do not depend on the nature of the substituting residues. Thus, the primary sequences of these elements, but not their secondary structures, are influencing signaling.
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Affiliation(s)
- Kathryn P Sherry
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Scott E Johnson
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Christine L Hatem
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Ananya Majumdar
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Doug Barrick
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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22
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Rogers JM, Suga H. Discovering functional, non-proteinogenic amino acid containing, peptides using genetic code reprogramming. Org Biomol Chem 2015; 13:9353-63. [PMID: 26280393 DOI: 10.1039/c5ob01336d] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The protein synthesis machinery of the cell, the ribosome and associated factors, is able to accurately follow the canonical genetic code, that which maps RNA sequence to protein sequence, to assemble functional proteins from the twenty or so proteinogenic amino acids. A number of innovative methods have arisen to take advantage of this accurate, and efficient, machinery to direct the assembly of non-proteinogenic amino acids. We review and compare these routes to 'reprogram the genetic code' including in vitro translation, engineered aminoacyl tRNA synthetases, and RNA 'flexizymes'. These studies show that the ribosome is highly tolerant of unnatural amino acids, with hundreds of unusual substrates of varying structure and chemistries being incorporated into protein chains. We also discuss how these methods have been coupled to selection techniques, such as phage display and mRNA display, opening up an exciting new avenue for the production of proteins and peptides with properties and functions beyond that which is possible using proteins composed entirely of the proteinogenic amino acids.
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Affiliation(s)
- J M Rogers
- Department of Chemistry, The University of Tokyo, Graduate School of Science, Tokyo, Japan.
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23
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Dogan J, Jonasson J, Andersson E, Jemth P. Binding Rate Constants Reveal Distinct Features of Disordered Protein Domains. Biochemistry 2015; 54:4741-50. [DOI: 10.1021/acs.biochem.5b00520] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jakob Dogan
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Josefin Jonasson
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Eva Andersson
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Per Jemth
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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24
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Teilum K, Olsen JG, Kragelund BB. Globular and disordered-the non-identical twins in protein-protein interactions. Front Mol Biosci 2015. [PMID: 26217672 PMCID: PMC4496568 DOI: 10.3389/fmolb.2015.00040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In biology proteins from different structural classes interact across and within classes in ways that are optimized to achieve balanced functional outputs. The interactions between intrinsically disordered proteins (IDPs) and other proteins rely on changes in flexibility and this is seen as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those of other protein-protein interactions. We find that ordered proteins and the disordered ones act as non-identical twins operating by similar principles but where the disordered proteins complexes are on average less stable by 2.5 kcal mol(-1).
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
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25
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Rogers JM, Oleinikovas V, Shammas SL, Wong CT, De Sancho D, Baker CM, Clarke J. Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. Proc Natl Acad Sci U S A 2014; 111:15420-5. [PMID: 25313042 PMCID: PMC4217413 DOI: 10.1073/pnas.1409122111] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here we examine a typical system, where a small disordered protein (PUMA, p53 upregulated modulator of apoptosis) folds to an α-helix when bound to a groove on the surface of a folded protein (MCL-1, induced myeloid leukemia cell differentiation protein). We follow the association of these proteins using rapid-mixing stopped flow, and examine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations. We demonstrate the utility of methods developed for the study of monomeric protein folding, including β-Tanford values, Leffler α, Φ-value analysis, and coarse-grained simulations, and propose a self-consistent mechanism for binding. Folding of the disordered protein before binding does not appear to be required and few, if any, specific interactions are required to commit to association. The majority of PUMA folding occurs after the transition state, in the presence of MCL-1. We also examine the role of the side chains of folded MCL-1 that make up the binding groove and find that many favor equilibrium binding but, surprisingly, inhibit the association process.
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Affiliation(s)
- Joseph M Rogers
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | | | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Chi T Wong
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M Baker
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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26
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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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27
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Knott M, Best RB. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model. J Chem Phys 2014; 140:175102. [PMID: 24811666 PMCID: PMC4032430 DOI: 10.1063/1.4873710] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/17/2014] [Indexed: 12/31/2022] Open
Abstract
Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.
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Affiliation(s)
- Michael Knott
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Robert B Best
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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28
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Abstract
Intrinsically disordered proteins (IDPs) and IDP regions fail to form a stable structure, yet they exhibit biological activities. Their mobile flexibility and structural instability are encoded by their amino acid sequences. They recognize proteins, nucleic acids, and other types of partners; they accelerate interactions and chemical reactions between bound partners; and they help accommodate posttranslational modifications, alternative splicing, protein fusions, and insertions or deletions. Overall, IDP-associated biological activities complement those of structured proteins. Recently, there has been an explosion of studies on IDP regions and their functions, yet the discovery and investigation of these proteins have a long, mostly ignored history. Along with recent discoveries, we present several early examples and the mechanisms by which IDPs contribute to function, which we hope will encourage comprehensive discussion of IDPs and IDP regions in biochemistry textbooks. Finally, we propose future directions for IDP research.
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Affiliation(s)
- Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202; ,
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29
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Iešmantavičius V, Dogan J, Jemth P, Teilum K, Kjaergaard M. Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307712] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Iešmantavičius V, Dogan J, Jemth P, Teilum K, Kjaergaard M. Helical propensity in an intrinsically disordered protein accelerates ligand binding. Angew Chem Int Ed Engl 2014; 53:1548-51. [PMID: 24449148 DOI: 10.1002/anie.201307712] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/28/2013] [Indexed: 11/11/2022]
Abstract
Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well-ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activation domain of the activator for thyroid hormone and retinoid receptors (ACTR) is intrinsically disordered and folds upon binding to the nuclear coactivator binding domain (NCBD) of the CREB binding protein. A number of mutants was designed that selectively perturbs the amount of secondary structure in unbound ACTR without interfering with the intermolecular interactions between ACTR and NCBD. Using NMR spectroscopy and fluorescence-monitored stopped-flow kinetic measurements we show that the secondary structure content in helix 1 of ACTR indeed influences the binding kinetics. The results thus support the notion of preformed secondary structure as an important determinant for molecular recognition in intrinsically disordered proteins.
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Affiliation(s)
- Vytautas Iešmantavičius
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N (Denmark)
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31
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Jemth P, Mu X, Engström Å, Dogan J. A frustrated binding interface for intrinsically disordered proteins. J Biol Chem 2014; 289:5528-33. [PMID: 24421312 DOI: 10.1074/jbc.m113.537068] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intrinsically disordered proteins are very common in the eukaryotic proteome, and many of them are associated with diseases. Disordered proteins usually undergo a coupled binding and folding reaction and often interact with many different binding partners. Using double mutant cycles, we mapped the energy landscape of the binding interface for two interacting disordered domains and found it to be largely suboptimal in terms of interaction free energies, despite relatively high affinity. These data depict a frustrated energy landscape for interactions involving intrinsically disordered proteins, which is likely a result of their functional promiscuity.
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Affiliation(s)
- Per Jemth
- From the Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
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32
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Hill SA, Kwa LG, Shammas SL, Lee JC, Clarke J. Mechanism of Assembly of the Non-Covalent Spectrin Tetramerization Domain from Intrinsically Disordered Partners. J Mol Biol 2014; 426:21-35. [PMID: 24055379 PMCID: PMC9082959 DOI: 10.1016/j.jmb.2013.08.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/24/2013] [Accepted: 08/20/2013] [Indexed: 01/29/2023]
Abstract
Interdomain interactions of spectrin are critical for maintenance of the erythrocyte cytoskeleton. In particular, “head-to-head” dimerization occurs when the intrinsically disordered C-terminal tail of β-spectrin binds the N-terminal tail of α-spectrin, folding to form the “spectrin tetramer domain”. This non-covalent three-helix bundle domain is homologous in structure and sequence to previously studied spectrin domains. We find that this tetramer domain is surprisingly kinetically stable. Using a protein engineering Φ-value analysis to probe the mechanism of formation of this tetramer domain, we infer that the domain folds by the docking of the intrinsically disordered β-spectrin tail onto the more structured α-spectrin tail.
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Affiliation(s)
- Stephanie A Hill
- University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK; Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lee Gyan Kwa
- University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK
| | - Sarah L Shammas
- University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jennifer C Lee
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jane Clarke
- University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK.
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Baines AJ. Link Up and Fold Up—Templating the Formation of Spectrin Tetramers. J Mol Biol 2014; 426:7-10. [DOI: 10.1016/j.jmb.2013.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dogan J, Gianni S, Jemth P. The binding mechanisms of intrinsically disordered proteins. Phys Chem Chem Phys 2013; 16:6323-31. [PMID: 24317797 DOI: 10.1039/c3cp54226b] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins are very common and instrumental for cellular signaling. Recently, a number of studies have investigated the kinetic binding mechanisms of IDPs and IDRs. These results allow us to draw conclusions about the energy landscape for the coupled binding and folding of disordered proteins. The association rate constants of IDPs cover a wide range (10(5)-10(9) M(-1) s(-1)) and are largely governed by long-range charge-charge interactions, similarly to interactions between well-folded proteins. Off-rate constants also differ significantly among IDPs (with half-lives of up to several minutes) but are usually around 0.1-1000 s(-1), allowing for rapid dissociation of complexes. Likewise, affinities span from pM to μM suggesting that the low-affinity high-specificity concept for IDPs is not straightforward. Overall, it appears that binding precedes global folding although secondary structure elements such as helices may form before the protein-protein interaction. Short IDPs bind in apparent two-state reactions whereas larger IDPs often display complex multi-step binding reactions. While the two extreme cases of two-step binding (conformational selection and induced fit) or their combination into a square mechanism is an attractive model in theory, it is too simplistic in practice. Experiment and simulation suggest a more complex energy landscape in which IDPs bind targets through a combination of conformational selection before binding (e.g., secondary structure formation) and induced fit after binding (global folding and formation of short-range intermolecular interactions).
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Affiliation(s)
- Jakob Dogan
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden.
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Shammas S, Travis AJ, Clarke J. Remarkably fast coupled folding and binding of the intrinsically disordered transactivation domain of cMyb to CBP KIX. J Phys Chem B 2013; 117:13346-56. [PMID: 23875714 PMCID: PMC3807845 DOI: 10.1021/jp404267e] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/22/2013] [Indexed: 01/25/2023]
Abstract
Association rates for interactions between folded proteins have been investigated extensively, allowing the development of computational and theoretical prediction methods. Less is known about association rates for complexes where one or more partner is initially disordered, despite much speculation about how they may compare to those for folded proteins. We have attached a fluorophore to the N-terminus of the 25 amino acid cMyb peptide used previously in NMR and equilibrium studies (termed FITC-cMyb), and used this to monitor the kinetics of its interaction with the KIX protein. We have investigated the ionic strength and temperature dependence of the kinetics, and conclude that the association process is extremely fast, apparently exceeding the rates predicted by formulations applicable to interactions between pairs of folded proteins. This is despite the fact that not all collisions result in complex formation (there is an observable activation energy for the association process). We propose that this is partially a result of the disordered nature of the FITC-cMyb peptide itself.
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Affiliation(s)
- Sarah
L. Shammas
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Alexandra J. Travis
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Jane Clarke
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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Rogers J, Steward A, Clarke J. Folding and binding of an intrinsically disordered protein: fast, but not 'diffusion-limited'. J Am Chem Soc 2013; 135:1415-22. [PMID: 23301700 PMCID: PMC3776562 DOI: 10.1021/ja309527h] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Indexed: 12/13/2022]
Abstract
Coupled folding and binding of intrinsically disordered proteins (IDPs) is prevalent in biology. As the first step toward understanding the mechanism of binding, it is important to know if a reaction is 'diffusion-limited' as, if this speed limit is reached, the association must proceed through an induced fit mechanism. Here, we use a model system where the 'BH3 region' of PUMA, an IDP, forms a single, contiguous α-helix upon binding the folded protein Mcl-1. Using stopped-flow techniques, we systematically compare the rate constant for association (k(+)) under a number of solvent conditions and temperatures. We show that our system is not 'diffusion-limited', despite having a k(+) in the often-quoted 'diffusion-limited' regime (10(5)-10(6) M(-1) s(-1) at high ionic strength) and displaying an inverse dependence on solvent viscosity. These standard tests, developed for folded protein-protein interactions, are not appropriate for reactions where one protein is disordered.
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Affiliation(s)
- Joseph
M. Rogers
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Annette Steward
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Jane Clarke
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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