51
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Choi JH, Laurent AH, Hilser VJ, Ostermeier M. Design of protein switches based on an ensemble model of allostery. Nat Commun 2015; 6:6968. [PMID: 25902417 PMCID: PMC4704092 DOI: 10.1038/ncomms7968] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 03/17/2015] [Indexed: 02/07/2023] Open
Abstract
Switchable proteins that can be regulated through exogenous or endogenous inputs have a broad range of biotechnological and biomedical applications. Here we describe the design of switchable enzymes based on an ensemble allosteric model. First, we insert an enzyme domain into an effector-binding domain such that both domains remained functionally intact. Second, we induce the fusion to behave as a switch through the introduction of conditional conformational flexibility designed to increase the conformational entropy of the enzyme domain in a temperature- or pH-dependent fashion. We confirm the switching behaviour in vitro and in vivo. Structural and thermodynamic studies support the hypothesis that switching result from an increase in conformational entropy of the enzyme domain in the absence of effector. These results support the ensemble model of allostery and embody a strategy for the design of protein switches.
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Affiliation(s)
- Jay H Choi
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400N Charles Street, Baltimore, Maryland 21218, USA
| | - Abigail H Laurent
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400N Charles Street, Baltimore, Maryland 21218, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, 3400N Charles Street, Baltimore, Maryland 21218, USA
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400N Charles Street, Baltimore, Maryland 21218, USA
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52
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Niessen KA, Xu M, Markelz AG. Terahertz optical measurements of correlated motions with possible allosteric function. Biophys Rev 2015; 7:201-216. [PMID: 28510171 DOI: 10.1007/s12551-015-0168-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/26/2015] [Indexed: 10/23/2022] Open
Abstract
A suggested mechanism for allosteric response is the distortion of the energy landscape with agonist binding changing the protein structure's access to functional configurations. Intramolecular vibrations are indicative of the energy landscape and may have trajectories that enable functional conformational change. Here, we discuss the development of an optical method to measure the intramolecular vibrations in proteins, namely, crystal anisotropy terahertz microscopy, and the various approaches which can be used to identify the spectral data with specific structural motions.
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Affiliation(s)
- Katherine A Niessen
- Department of Physics, University at Buffalo (SUNY), Buffalo, NY, 14260, USA
| | - Mengyang Xu
- Department of Physics, University at Buffalo (SUNY), Buffalo, NY, 14260, USA
| | - A G Markelz
- Department of Physics, University at Buffalo (SUNY), Buffalo, NY, 14260, USA.
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53
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Townsend PD, Rodgers TL, Pohl E, Wilson MR, McLeish TCB, Cann MJ. Global low-frequency motions in protein allostery: CAP as a model system. Biophys Rev 2015; 7:175-182. [PMID: 26000062 PMCID: PMC4432019 DOI: 10.1007/s12551-015-0163-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/12/2015] [Indexed: 11/28/2022] Open
Abstract
Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. There is considerable evidence that allosteric cooperativity can be communicated by the modulation of protein dynamics without conformational change. The Catabolite Activator Protein (CAP) of Escherichia coli is an important experimental exemplar for entropically driven allostery. Here we discuss recent experimentally supported theoretical analysis that highlights the role of global low-frequency dynamics in allostery in CAP and identify how allostery arises as a natural consequence of changes in global low-frequency protein fluctuations on ligand binding.
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Affiliation(s)
- Philip D Townsend
- Biophysical Sciences Institute, Durham University, Durham, UK ; School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - Thomas L Rodgers
- Biophysical Sciences Institute, Durham University, Durham, UK ; Department of Chemistry, Durham University, Durham, UK ; School of Chemical Engineering and Analytical Sciences, University of Manchester, Manchester, UK
| | - Ehmke Pohl
- Biophysical Sciences Institute, Durham University, Durham, UK ; School of Biological and Biomedical Sciences, Durham University, Durham, UK ; Department of Chemistry, Durham University, Durham, UK
| | - Mark R Wilson
- Biophysical Sciences Institute, Durham University, Durham, UK ; Department of Chemistry, Durham University, Durham, UK
| | - Tom C B McLeish
- Biophysical Sciences Institute, Durham University, Durham, UK ; Department of Chemistry, Durham University, Durham, UK ; Department of Physics, Durham University, Durham, UK
| | - Martin J Cann
- Biophysical Sciences Institute, Durham University, Durham, UK ; School of Biological and Biomedical Sciences, Durham University, Durham, UK
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54
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Zhao Q. A thermodynamic and theoretical view for enzyme regulation. BIOCHEMISTRY (MOSCOW) 2015; 80:1-7. [DOI: 10.1134/s0006297915010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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55
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Schneider R, Maurin D, Communie G, Kragelj J, Hansen DF, Ruigrok RWH, Jensen MR, Blackledge M. Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR. J Am Chem Soc 2015; 137:1220-9. [PMID: 25551399 DOI: 10.1021/ja511066q] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite playing important roles throughout biology, molecular recognition mechanisms in intrinsically disordered proteins remain poorly understood. We present a combination of (1)H(N), (13)C', and (15)N relaxation dispersion NMR, measured at multiple titration points, to map the interaction between the disordered domain of Sendai virus nucleoprotein (NT) and the C-terminal domain of the phosphoprotein (PX). Interaction with PX funnels the free-state equilibrium of NT by stabilizing one of the previously identified helical substates present in the prerecognition ensemble in a nonspecific and dynamic encounter complex on the surface of PX. This helix then locates into the binding site at a rate coincident with intrinsic breathing motions of the helical groove on the surface of PX. The binding kinetics of complex formation are thus regulated by the intrinsic free-state conformational dynamics of both proteins. This approach, providing high-resolution structural and kinetic information about a complex folding and binding interaction trajectory, can be applied to a number of experimental systems to provide a general framework for understanding conformational disorder in biomolecular function.
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56
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Perez RB, Tischer A, Auton M, Whitten ST. Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins. Proteins 2014; 82:3373-84. [PMID: 25244701 DOI: 10.1002/prot.24692] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/26/2014] [Accepted: 09/16/2014] [Indexed: 01/12/2023]
Abstract
Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (R(h)) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP(II)) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in R(h) were not associated with folding. The experiments showed that changes in local PP(II) structure cause changes in R(h) that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs.
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Affiliation(s)
- Romel B Perez
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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57
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Substrate-dependent switching of the allosteric binding mechanism of a dimeric enzyme. Nat Chem Biol 2014; 10:937-42. [PMID: 25218742 DOI: 10.1038/nchembio.1626] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/21/2014] [Indexed: 11/08/2022]
Abstract
Enzyme activity is commonly controlled by allostery, where ligand binding at one site alters the activities of distant sites. Classical explanations for multisubunit proteins involve conformational transitions that are fundamentally deterministic. For example, in the Monod-Wyman-Changeaux (MWC) paradigm, conformational transitions occur simultaneously in all subunits. In the Koshland-Nemethy-Filmer (KNF) paradigm, conformational transitions only occur in ligand-bound subunits. In contrast, recent models predict conformational changes that are governed by probabilities rather than absolute rules. To better understand allostery at the molecular level, we applied a recently developed spectroscopic and calorimetric method to the interactions of a dimeric enzyme with two different ligands. We found that conformational transitions appear MWC-like for a ligand that binds at the dimer interface and KNF-like for a distal ligand. These results provide strong experimental support for probabilistic allosteric theory predictions that an enzyme can exhibit a mixture of MWC and KNF character, with the balance partly governed by subunit interface energies.
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58
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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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59
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van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones D, Kim PM, Kriwacki R, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright P, Babu MM. Classification of intrinsically disordered regions and proteins. Chem Rev 2014; 114:6589-631. [PMID: 24773235 PMCID: PMC4095912 DOI: 10.1021/cr400525m] [Citation(s) in RCA: 1424] [Impact Index Per Article: 142.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Robin van der Lee
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Centre
for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The
Netherlands
| | - Marija Buljan
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Benjamin Lang
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Gary W. Daughdrill
- Department
of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 3720 Spectrum Boulevard, Suite 321, Tampa, Florida 33612, United States
| | - A. Keith Dunker
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, H-4032 Debrecen, Nagyerdei krt 98, Hungary
| | - Julian Gough
- Department
of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, United Kingdom
| | - Joerg Gsponer
- Department
of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David
T. Jones
- Bioinformatics
Group, Department of Computer Science, University
College London, London, WC1E 6BT, United Kingdom
| | - Philip M. Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular
Genetics, and Department of Computer Science, University
of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Richard
W. Kriwacki
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
| | - Christopher J. Oldfield
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Rohit V. Pappu
- Department
of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Peter Tompa
- VIB Department
of Structural Biology, Vrije Universiteit
Brussel, Brussels, Belgium
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vladimir N. Uversky
- Department
of Molecular Medicine and USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation,
Russian Academy of Sciences, Pushchino,
Moscow Region, Russia
| | - Peter
E. Wright
- Department
of Integrative Structural and Computational Biology and Skaggs Institute
of Chemical Biology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - M. Madan Babu
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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60
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The ensemble nature of allostery. Nature 2014; 508:331-9. [PMID: 24740064 DOI: 10.1038/nature13001] [Citation(s) in RCA: 874] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/03/2014] [Indexed: 02/07/2023]
Abstract
Allostery is the process by which biological macromolecules (mostly proteins) transmit the effect of binding at one site to another, often distal, functional site, allowing for regulation of activity. Recent experimental observations demonstrating that allostery can be facilitated by dynamic and intrinsically disordered proteins have resulted in a new paradigm for understanding allosteric mechanisms, which focuses on the conformational ensemble and the statistical nature of the interactions responsible for the transmission of information. Analysis of allosteric ensembles reveals a rich spectrum of regulatory strategies, as well as a framework to unify the description of allosteric mechanisms from different systems.
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61
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Bandi S, Singh SM, Mallela KMG. The C-terminal domain of the utrophin tandem calponin-homology domain appears to be thermodynamically and kinetically more stable than the full-length protein. Biochemistry 2014; 53:2209-11. [PMID: 24678640 DOI: 10.1021/bi500120e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Domains are in general less stable than the corresponding full-length proteins. Human utrophin tandem calponin-homology (CH) domain seems to be an exception. Reversible, equilibrium denaturant melts indicate that the isolated C-terminal domain (CH2) is thermodynamically more stable than the tandem CH domain. Thermal melts show that CH2 unfolds at a temperature higher than that at which the full-length protein unfolds. Stopped-flow kinetics indicates that CH2 unfolds slower than the full-length protein, indicating its higher kinetic stability. Thus, the utrophin tandem CH domain may be one of the few proteins in which an isolated domain is more stable than the corresponding full-length protein.
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Affiliation(s)
- Swati Bandi
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus , 12850 East Montview Boulevard, C238, Aurora, Colorado 80045, United States
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62
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Jensen MR, Zweckstetter M, Huang JR, Blackledge M. Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 2014; 114:6632-60. [PMID: 24725176 DOI: 10.1021/cr400688u] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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63
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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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64
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Abstract
The question of how allostery works was posed almost 50 years ago. Since then it has been the focus of much effort. This is for two reasons: first, the intellectual curiosity of basic science and the desire to understand fundamental phenomena, and second, its vast practical importance. Allostery is at play in all processes in the living cell, and increasingly in drug discovery. Many models have been successfully formulated, and are able to describe allostery even in the absence of a detailed structural mechanism. However, conceptual schemes designed to qualitatively explain allosteric mechanisms usually lack a quantitative mathematical model, and are unable to link its thermodynamic and structural foundations. This hampers insight into oncogenic mutations in cancer progression and biased agonists' actions. Here, we describe how allostery works from three different standpoints: thermodynamics, free energy landscape of population shift, and structure; all with exactly the same allosteric descriptors. This results in a unified view which not only clarifies the elusive allosteric mechanism but also provides structural grasp of agonist-mediated signaling pathways, and guides allosteric drug discovery. Of note, the unified view reasons that allosteric coupling (or communication) does not determine the allosteric efficacy; however, a communication channel is what makes potential binding sites allosteric.
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Affiliation(s)
- Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Center for Cancer Research, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Center for Cancer Research, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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65
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A disorder-induced domino-like destabilization mechanism governs the folding and functional dynamics of the repeat protein IκBα. PLoS Comput Biol 2013; 9:e1003403. [PMID: 24367251 PMCID: PMC3868533 DOI: 10.1371/journal.pcbi.1003403] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 11/07/2013] [Indexed: 11/19/2022] Open
Abstract
The stability of the repeat protein IκBα, a transcriptional inhibitor in mammalian cells, is critical in the functioning of the NF-κB signaling module implicated in an array of cellular processes, including cell growth, disease, immunity and apoptosis. Structurally, IκBα is complex, with both ordered and disordered regions, thus posing a challenge to the available computational protocols to model its conformational behavior. Here, we introduce a simple procedure to model disorder in systems that undergo binding-induced folding that involves modulation of the contact map guided by equilibrium experimental observables in combination with an Ising-like Wako-Saitô-Muñoz-Eaton model. This one-step procedure alone is able to reproduce a variety of experimental observables, including ensemble thermodynamics (scanning calorimetry, pre-transitions, m-values) and kinetics (roll-over in chevron plot, intermediates and their identity), and is consistent with hydrogen-deuterium exchange measurements. We further capture the intricate distance-dynamics between the domains as measured by single-molecule FRET by combining the model predictions with simple polymer physics arguments. Our results reveal a unique mechanism at work in IκBα folding, wherein disorder in one domain initiates a domino-like effect partially destabilizing neighboring domains, thus highlighting the effect of symmetry-breaking at the level of primary sequences. The offshoot is a multi-state and a dynamic conformational landscape that is populated by increasingly partially folded ensembles upon destabilization. Our results provide, in a straightforward fashion, a rationale to the promiscuous binding and short intracellular half-life of IκBα evolutionarily engineered into it through repeats with variable stabilities and expand the functional repertoire of disordered regions in proteins.
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66
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Tompa P. Multisteric Regulation by Structural Disorder in Modular Signaling Proteins: An Extension of the Concept of Allostery. Chem Rev 2013; 114:6715-32. [DOI: 10.1021/cr4005082] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Peter Tompa
- VIB Department of Structural
Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Institute of Enzymology, Biological Research Center, Hungarian Academy
of Sciences, Budapest H-1113, Hungary
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67
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Xia Y, DiPrimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weis DD, Anderson JC, Karanicolas J. The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation. J Am Chem Soc 2013; 135:18840-9. [PMID: 24313858 DOI: 10.1021/ja407644b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ability to selectively activate function of particular proteins via pharmacological agents is a longstanding goal in chemical biology. Recently, we reported an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. However, rationally identifying analogous de novo binding sites in other enzymes represents a key challenge for extending this approach to introduce allosteric control into other enzymes. Here we show that mutation sites leading to protein inactivation via tryptophan-to-glycine substitution and allowing (partial) reactivation by the subsequent addition of indole are remarkably frequent. Through a suite of methods including a cell-based reporter assay, computational structure prediction and energetic analysis, fluorescence studies, enzymology, pulse proteolysis, X-ray crystallography, and hydrogen-deuterium mass spectrometry, we find that these switchable proteins are most commonly modulated indirectly, through control of protein stability. Addition of indole in these cases rescues activity not by reverting a discrete conformational change, as we had observed in the sole previously reported example, but rather rescues activity by restoring protein stability. This important finding will dramatically impact the design of future switches and sensors built by this approach, since evaluating stability differences associated with cavity-forming mutations is a far more tractable task than predicting allosteric conformational changes. By analogy to natural signaling systems, the insights from this study further raise the exciting prospect of modulating stability to design optimal recognition properties into future de novo switches and sensors built through chemical rescue of structure.
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Affiliation(s)
- Yan Xia
- Department of Molecular Biosciences, ‡Department of Chemistry, §Protein Structure Laboratory, and ∥Center for Bioinformatics, University of Kansas , Lawrence, Kansas 66045, United States
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68
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Simons SS, Edwards DP, Kumar R. Minireview: dynamic structures of nuclear hormone receptors: new promises and challenges. Mol Endocrinol 2013; 28:173-82. [PMID: 24284822 DOI: 10.1210/me.2013-1334] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Therapeutic targeting of nuclear receptors (NRs) is presently restricted due to 2 constraints: 1) a limited knowledge of the structural dynamics of intact receptor when complexed to DNA and coregulatory proteins; and 2) the inability to more selectively modulate NR actions at specific organ/gene targets. A major obstacle has been the current lack of understanding about the function and structure of the intrinsically disordered N-terminal domain that contains a major regulatory transcriptional activation function (AF1). Current studies of both mechanism of action and small molecule-selective receptor modulators for clinical uses target the structured pocket of the ligand-binding domain to modulate coregulatory protein interactions with the other activation function AF2. However, these approaches overlook AF1 activity. Recent studies have shown that highly flexible intrinsically disordered regions of transcription factors, including that of the N-terminal domain AF1 of NRs, not only are critical for several aspects of NR action but also can be exploited as drug targets, thereby opening unique opportunities for endocrine-based therapies. In this review article, we discuss the role of structural flexibilities in the allosteric modulation of NR activity and future perspectives for therapeutic interventions.
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Affiliation(s)
- S Stoney Simons
- Steroid Hormones Section (S.S.S.), Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892; Departments of Molecular & Cellular Biology and Pathology & Immunology (D.P.E.), Baylor College of Medicine, Houston, Texas 77030; and Department of Basic Sciences (R.K.), The Commonwealth Medical College, Scranton, Pennsylvania 18510
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69
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Rodgers TL, Townsend PD, Burnell D, Jones ML, Richards SA, McLeish TCB, Pohl E, Wilson MR, Cann MJ. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors. PLoS Biol 2013; 11:e1001651. [PMID: 24058293 PMCID: PMC3769225 DOI: 10.1371/journal.pbio.1001651] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 07/31/2013] [Indexed: 12/11/2022] Open
Abstract
Allostery in bacterial transcription factors arises from changes in global low-frequency protein dynamics. Amino acids that regulate low-frequency dynamics are identified and seen to be evolutionarily conserved. Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein “design space” that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to occupy a dynamic space that fine-tunes biological activity and thus establishes the means to engineer allosteric mechanisms driven by low-frequency dynamics. Allostery is a process by which a molecule binding to one site of a protein alters the activity of the protein at another site. Allostery is typically thought to occur through a change in protein structure, but there is now clear evidence that the dynamic properties of a protein can also regulate allostery without a change in overall conformation. Here we examine two members of a large family of bacterial transcription factors and provide a mechanism to describe the allosteric binding of their activating ligands. We demonstrate, in these systems, that allostery arises as a natural consequence of changes in global low-frequency protein fluctuations on ligand binding. We further demonstrate that the higher dimensional parameter space that describes all potential variant transcription factors can be reduced to a two-dimensional free energy landscape that determines the key molecular parameters that predominantly regulate allostery. We additionally show that the amino acids we determine as contributing sensitively to allosteric control tend to be conserved in diverse bacteria; thus we identify a link between residues that contribute to low-frequency fluctuations and evolutionary selection pressures.
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Affiliation(s)
- Thomas L. Rodgers
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Philip D. Townsend
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - David Burnell
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Matthew L. Jones
- Department of Physics, Durham University, Durham, United Kingdom
| | - Shane A. Richards
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - Tom C. B. McLeish
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
- Department of Physics, Durham University, Durham, United Kingdom
| | - Ehmke Pohl
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - Mark R. Wilson
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Martin J. Cann
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
- * E-mail:
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70
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Weinkam P, Sali A. Mapping polymerization and allostery of hemoglobin S using point mutations. J Phys Chem B 2013; 117:13058-68. [PMID: 23957820 DOI: 10.1021/jp4025156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hemoglobin is a complex system that undergoes conformational changes in response to oxygen, allosteric effectors, mutations, and environmental changes. Here, we study allostery and polymerization of hemoglobin and its variants by application of two previously described methods: (i) AllosMod for simulating allostery dynamics given two allosterically related input structures and (ii) a machine-learning method for dynamics- and structure-based prediction of the mutation impact on allostery (Weinkam et al. J. Mol. Biol. 2013, 425, 647-661), now applicable to systems with multiple coupled binding sites, such as hemoglobin. First, we predict the relative stabilities of substates and microstates of hemoglobin, which are determined primarily by entropy within our model. Next, we predict the impact of 866 annotated mutations on hemoglobin's oxygen binding equilibrium. We then discuss a subset of 30 mutations that occur in the presence of the sickle cell mutation and whose effects on polymerization have been measured. Seven of these HbS mutations occur in three predicted druggable binding pockets that might be exploited to directly inhibit polymerization; one of these binding pockets is not apparent in the crystal structure, but only in structures generated by AllosMod. For the 30 mutations, we predict that mutation-induced conformational changes within a single tetramer tend not to significantly impact polymerization; instead, these mutations more likely impact polymerization by directly perturbing a polymerization interface. Finally, our analysis of allostery allows us to hypothesize why hemoglobin evolved to have multiple subunits and a persistent low frequency sickle cell mutation.
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Affiliation(s)
- Patrick Weinkam
- Department of Bioengineering and Therapeutic Sciences, ‡Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco , San Francisco, California 94158, United States
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71
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Simons SS, Kumar R. Variable steroid receptor responses: Intrinsically disordered AF1 is the key. Mol Cell Endocrinol 2013; 376:81-4. [PMID: 23792173 PMCID: PMC3781172 DOI: 10.1016/j.mce.2013.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/06/2013] [Accepted: 06/07/2013] [Indexed: 11/22/2022]
Abstract
Steroid hormones, acting through their cognate receptor proteins, see widespread clinical applications due to their ability to alter the induction or repression of numerous genes. However, steroid usage is limited by the current inability to control off-target, or non-specific, side-effects. Recent results from three separate areas of research with glucocorticoid and other steroid receptors (cofactor-induced changes in receptor structure, the ability of ligands to alter remote regions of receptor structure, and how cofactor concentration affects both ligand potency and efficacy) indicate that a key element of receptor activity is the intrinsically disordered amino-terminal domain. These results are combined to construct a novel framework within which to logically pursue various approaches that could afford increased selectivity in steroid-based therapies.
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Affiliation(s)
- S. Stoney Simons
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, MD, United States
- Corresponding authors. Address: Bldg. 10, Room 8N-307B, NIDDK/CEB, NIH, Bethesda, MD 20892-1772, United States. Tel.: +1 301 496 6796; fax: +1 301 402 3572 (S.S. Simons Jr.). Address: Department of Basic Sciences, The Commonwealth Medical College, 525 Pine Street, Scranton, PA 18509, United States. Tel.: +1 570 504 9675; fax: +1 570 504 9660 (R. Kumar). (S.S. Simons Jr.), (R. Kumar)
| | - Raj Kumar
- Department of Basic Sciences, The Commonwealth Medical College, Scranton, PA, United States
- Corresponding authors. Address: Bldg. 10, Room 8N-307B, NIDDK/CEB, NIH, Bethesda, MD 20892-1772, United States. Tel.: +1 301 496 6796; fax: +1 301 402 3572 (S.S. Simons Jr.). Address: Department of Basic Sciences, The Commonwealth Medical College, 525 Pine Street, Scranton, PA 18509, United States. Tel.: +1 570 504 9675; fax: +1 570 504 9660 (R. Kumar). (S.S. Simons Jr.), (R. Kumar)
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72
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Ferreon ACM, Ferreon JC, Wright PE, Deniz AA. Modulation of allostery by protein intrinsic disorder. Nature 2013; 498:390-4. [PMID: 23783631 PMCID: PMC3718496 DOI: 10.1038/nature12294] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 05/17/2013] [Indexed: 12/26/2022]
Abstract
Allostery is an intrinsic property of many globular proteins and enzymes that is indispensable for cellular regulatory and feedback mechanisms. Recent theoretical and empirical observations indicate that allostery is also manifest in intrinsically disordered proteins, which account for a substantial proportion of the proteome. Many intrinsically disordered proteins are promiscuous binders that interact with multiple partners and frequently function as molecular hubs in protein interaction networks. The adenovirus early region 1A (E1A) oncoprotein is a prime example of a molecular hub intrinsically disordered protein. E1A can induce marked epigenetic reprogramming of the cell within hours after infection, through interactions with a diverse set of partners that include key host regulators such as the general transcriptional coactivator CREB binding protein (CBP), its paralogue p300, and the retinoblastoma protein (pRb; also called RB1). Little is known about the allosteric effects at play in E1A-CBP-pRb interactions, or more generally in hub intrinsically disordered protein interaction networks. Here we used single-molecule fluorescence resonance energy transfer (smFRET) to study coupled binding and folding processes in the ternary E1A system. The low concentrations used in these high-sensitivity experiments proved to be essential for these studies, which are challenging owing to a combination of E1A aggregation propensity and high-affinity binding interactions. Our data revealed that E1A-CBP-pRb interactions have either positive or negative cooperativity, depending on the available E1A interaction sites. This striking cooperativity switch enables fine-tuning of the thermodynamic accessibility of the ternary versus binary E1A complexes, and may permit a context-specific tuning of associated downstream signalling outputs. Such a modulation of allosteric interactions is probably a common mechanism in molecular hub intrinsically disordered protein function.
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Affiliation(s)
- Allan Chris M Ferreon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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73
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Gruet A, Dosnon M, Vassena A, Lombard V, Gerlier D, Bignon C, Longhi S. Dissecting partner recognition by an intrinsically disordered protein using descriptive random mutagenesis. J Mol Biol 2013; 425:3495-509. [PMID: 23811056 DOI: 10.1016/j.jmb.2013.06.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 02/06/2023]
Abstract
In view of getting insights into the molecular determinants of the binding efficiency of intrinsically disordered proteins (IDPs), we used random mutagenesis. As a proof of concept, we chose the interaction between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein and assessed how amino acid substitutions introduced at random within NTAIL affect partner recognition. In contrast with directed evolution approaches, we did not apply any selection and used the gene library approach not for production purposes but for achieving a better understanding of the NTAIL/XD interaction. For that reason, and to differentiate our approach from similar approaches that make use of systematic (i.e., targeted) mutagenesis, we propose to call it "descriptive random mutagenesis" (DRM). NTAIL variants generated by error-prone PCR were picked at random in the absence of selection pressure and were characterized in terms of sequence and binding abilities toward XD. DRM not only identified determinants of NTAIL/XD interaction that were in good agreement with previous work but also provided new insights. In particular, we discovered that the primary interaction site is poorly evolvable in terms of binding abilities toward XD. We also identified a critical NTAIL residue whose role in stabilizing the NTAIL/XD complex had previously escaped detection, and we identified NTAIL regulatory sites that dampen the interaction while being located outside the primary interaction site. Results show that DRM is a valuable approach to study binding abilities of IDPs.
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Affiliation(s)
- Antoine Gruet
- CNRS and Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13288 Marseille, France
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74
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Protein mechanics: how force regulates molecular function. Biochim Biophys Acta Gen Subj 2013; 1830:4762-8. [PMID: 23791949 DOI: 10.1016/j.bbagen.2013.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 05/26/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Regulation of proteins is ubiquitous and vital for any organism. Protein activity can be altered chemically, by covalent modifications or non-covalent binding of co-factors. Mechanical forces are emerging as an additional way of regulating proteins, by inducing a conformational change or by partial unfolding. SCOPE We review some advances in experimental and theoretical techniques to study protein allostery driven by mechanical forces, as opposed to the more conventional ligand driven allostery. In this respect, we discuss recent single molecule pulling experiments as they have substantially augmented our view on the protein allostery by mechanical signals in recent years. Finally, we present a computational analysis technique, Force Distribution Analysis, that we developed to reveal allosteric pathways in proteins. MAJOR CONCLUSIONS Any kind of external perturbation, being it ligand binding or mechanical stretching, can be viewed as an external force acting on the macromolecule, rendering force-based experimental or computational techniques, a very general approach to the mechanics involved in protein allostery. GENERAL SIGNIFICANCE This unifying view might aid to decipher how complex allosteric protein machineries are regulated on the single molecular level.
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Abstract
Allostery is a biological phenomenon of fundamental importance in regulation and signaling, and efforts to understand this process have led to the development of numerous models. In spite of individual successes in understanding the structural determinants of allostery in well-documented systems, much less success has been achieved in identifying a set of quantitative and transferable ground rules that provide an understanding of how allostery works. Are there organizing principles that allow us to relate structurally different proteins, or are the determinants of allostery unique to each system? Using an ensemble-based model, we show that allosteric phenomena can be formulated in terms of conformational free energies of the cooperative elements in a protein and the coupling interactions between them. Interestingly, the resulting allosteric ground rules provide a framework to reconcile observations that challenge purely structural models of site-to-site coupling, including (a) allostery in the absence of pathways of structural distortions, (b) allostery in the absence of any structural change, and (c) the ability of allosteric ligands to act as agonists under some circumstances and antagonists under others. The ensemble view of allostery that emerges provides insights into the energetic prerequisites of site-to-site coupling and thus into how allostery works.
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Affiliation(s)
- Vincent J Hilser
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
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77
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Abstract
Allostery is a biological phenomenon of critical importance in metabolic regulation and cell signalling. The fundamental premise of classical models that describe allostery is that structure mediates 'action at a distance'. Recently, this paradigm has been challenged by the enrichment of IDPs (intrinsically disordered proteins) or ID (intrinsically disordered) segments in transcription factors and signalling pathways of higher organisms, where an allosteric response from external signals is requisite for regulated function. This observation strongly suggests that IDPs elicit the capacity for finely tunable allosteric regulation. Is there a set of transferable ground rules that reconcile these disparate allosteric phenomena? We focus on findings from the human GR (glucocorticoid receptor) which is a nuclear transcription factor in the SHR (steroid hormone receptor) family. GR contains an intrinsically disordered NTD (N-terminal domain) that is obligatory for transcription activity. Different GR translational isoforms have various lengths of NTD and by studying these isoforms we found that the full-length ID NTD consists of two thermodynamically distinct coupled regions. The data are interpreted in the context of an EAM (ensemble allosteric model) that considers only the intrinsic and measurable energetics of allosteric systems. Expansion of the EAM is able to reconcile the paradox that ligands for SHRs can be agonists and antagonists in a cell-context-dependent manner. These findings suggest a mechanism by which SHRs in particular, and IDPs in general, may have evolved to couple thermodynamically distinct ID segments. The ensemble view of allostery that is illuminated provides organizing principles to unify the description of all allosteric systems and insight into 'how' allostery works.
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78
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de Ronde W, Rein ten Wolde P, Mugler A. Protein logic: a statistical mechanical study of signal integration at the single-molecule level. Biophys J 2013; 103:1097-107. [PMID: 23009860 DOI: 10.1016/j.bpj.2012.07.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/19/2012] [Accepted: 07/23/2012] [Indexed: 10/27/2022] Open
Abstract
Information processing and decision-making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years, however, both experimentalists and theorists have begun to appreciate that cellular decision-making can also be performed at the level of a single protein, giving rise to the notion of protein logic. Here we systematically explore protein logic using a well-known statistical mechanical model. As an example system, we focus on receptors that bind either one or two ligands, and their associated dimers. Notably, we find that a single heterodimer can realize any of the 16 possible logic gates, including the XOR gate, by variation of biochemical parameters. We then introduce what to our knowledge is a novel idea: that a set of receptors with fixed parameters can encode functionally unique logic gates simply by forming different dimeric combinations. An exhaustive search reveals that the simplest set of receptors (two single-ligand receptors and one double-ligand receptor) can realize several different groups of three unique gates, a result for which the parametric analysis of single receptors and dimers provides a clear interpretation. Both results underscore the surprising functional freedom readily available to cells at the single-protein level.
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Affiliation(s)
- Wiet de Ronde
- Foundation for Fundamental Research on Matter (FOM) Institute AMOLF, Amsterdam, The Netherlands.
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79
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Matthews JM, Potts JR. The tandem β-zipper: Modular binding of tandem domains and linear motifs. FEBS Lett 2013; 587:1164-71. [DOI: 10.1016/j.febslet.2013.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/07/2013] [Accepted: 01/07/2013] [Indexed: 11/17/2022]
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Abstract
The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial.
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Affiliation(s)
- Judith P. Klinman
- Department of Chemistry, Department of Molecular and Cell Biology, and the California Institute for Quantitative Sciences, University of California, Berkeley, California 94720;
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294;
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81
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Schrank TP, Wrabl JO, Hilser VJ. Conformational heterogeneity within the LID domain mediates substrate binding to Escherichia coli adenylate kinase: function follows fluctuations. Top Curr Chem (Cham) 2013; 337:95-121. [PMID: 23543318 DOI: 10.1007/128_2012_410] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins exist as dynamic ensembles of molecules, implying that protein amino acid sequences evolved to code for both the ground state structure as well as the entire energy landscape of excited states. Accumulating theoretical and experimental evidence suggests that enzymes use such conformational fluctuations to facilitate allosteric processes important for substrate binding and possibly catalysis. This phenomenon can be clearly demonstrated in Escherichia coli adenylate kinase, where experimentally observed local unfolding of the LID subdomain, as opposed to a more commonly postulated rigid-body opening motion, is related to substrate binding. Because "entropy promoting" glycine mutations designed to increase specifically the local unfolding of the LID domain also affect substrate binding, changes in the excited energy landscape effectively tune the function of this enzyme without changing the ground state structure or the catalytic site. Thus, additional thermodynamic information, above and beyond the single folded structure of an enzyme-substrate complex, is likely required for a full and quantitative understanding of how enzymes work.
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Affiliation(s)
- Travis P Schrank
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555-1068, USA,
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Schaub LJ, Campbell JC, Whitten ST. Thermal unfolding of the N-terminal region of p53 monitored by circular dichroism spectroscopy. Protein Sci 2012; 21:1682-8. [PMID: 22915551 DOI: 10.1002/pro.2146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/14/2012] [Accepted: 08/20/2012] [Indexed: 12/29/2022]
Abstract
It has been estimated that 30% of eukaryotic protein and 70% of transcription factors are intrinsically disordered (ID). The biochemical significance of proteins that lack stable tertiary structure, however, is not clearly understood, largely owing to an inability to assign well-defined structures to specific biological tasks. In an attempt to investigate the structural character of ID protein, we have measured the circular dichroism spectrum of the N-terminal region of p53 over a range of temperatures and solution conditions. p53 is a well-studied transcription factor that has a proline-rich N-terminal ID region containing two activation domains. High proline content is a property commonly associated with ID, and thus p53 may be a good model system for investigating the biochemical importance of ID. The spectra presented here suggest that the N-terminal region of p53 may adopt an ordered structure under physiological conditions and that this structure can be thermally unfolded in an apparent two-state manner. The midpoint temperature for this thermal unfolding of the N-terminal region of p53 was at the near-physiological temperature of 39°C, suggesting the possibility of a physiological role for the observed structural equilibrium.
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Affiliation(s)
- Leasha J Schaub
- Department of Chemistry and Biochemistry, Texas State University-San Marcos, San Marcos, Texas 78666, USA
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83
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Abstract
IDPs (intrinsically disordered proteins) are common in eukaryotic genomes and have regulatory roles. In the cell, they are disordered, although not completely random. They bind weakly, but specifically, often remaining partially disordered even when bound. Whereas folded globular proteins have ‘executive’ roles in the cell, IDPs have an essential administrative function, making sure that the executive functions are properly co-ordinated. This makes them a good target for pharmaceutical intervention.
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84
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Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity. Expert Rev Mol Med 2012; 14:e16. [PMID: 22831787 DOI: 10.1017/erm.2012.10] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions (PPIs) control the assembly of multi-protein complexes and, thus, these contacts have enormous potential as drug targets. However, the field has produced a mix of both exciting success stories and frustrating challenges. Here, we review known examples and explore how the physical features of a PPI, such as its affinity, hotspots, off-rates, buried surface area and topology, might influence the chances of success in finding inhibitors. This analysis suggests that concise, tight binding PPIs are most amenable to inhibition. However, it is also clear that emerging technical methods are expanding the repertoire of 'druggable' protein contacts and increasing the odds against difficult targets. In particular, natural product-like compound libraries, high throughput screens specifically designed for PPIs and approaches that favour discovery of allosteric inhibitors appear to be attractive routes. The first group of PPI inhibitors has entered clinical trials, further motivating the need to understand the challenges and opportunities in pursuing these types of targets.
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85
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Li J, Motlagh HN, Chakuroff C, Thompson EB, Hilser VJ. Thermodynamic dissection of the intrinsically disordered N-terminal domain of human glucocorticoid receptor. J Biol Chem 2012; 287:26777-87. [PMID: 22669939 DOI: 10.1074/jbc.m112.355651] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Intrinsically disordered (ID) sequence segments are abundant in cell signaling proteins and transcription factors. Because ID regions commonly fold as part of their intracellular function, it is crucial to understand the folded states as well as the transitions between the unfolded and folded states. Specifically, it is important to determine 1) whether large ID segments contain different thermodynamically and/or functionally distinct regions, 2) whether any ID regions fold upon activation, 3) the degree of coupling between the different ID regions, and 4) whether the stability of ID domains is a determinant of function. In this study, we thermodynamically characterized the full-length ID N-terminal domain (NTD) of human glucocorticoid receptor (GR) and two of its naturally occurring translational isoforms. The protective osmolyte trimethylamine N-oxide (TMAO) was used to induce folding transitions. Each of the three NTD isoforms was found to undergo a cooperative folding transition that is thermodynamically indistinguishable (based on m-values) from that of a globular protein of similar size. The extrapolated stabilities for the NTD isoforms showed clear correlation with the known activities of their corresponding GR translational isoforms. The data reveal that the full-length NTD can be viewed as having at least two thermodynamically coupled regions, a functional region, which is indispensable for GR transcriptional activity, and a regulatory region, the length of which serves to regulate the stability of NTD and thus the activity of GR. These results suggest a new functional paradigm whereby steroid hormone receptors in particular and ID proteins in general can have multiple functionally distinct ID regions that interact and modulate the stability of important functional sites.
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Affiliation(s)
- Jing Li
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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