1
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Gárate F, Dokas S, Lanfranco MF, Canavan C, Wang I, Correia JJ, Maillard RA. cAMP is an allosteric modulator of DNA-binding specificity in the cAMP receptor protein from Mycobacterium tuberculosis. J Biol Chem 2021; 296:100480. [PMID: 33640453 PMCID: PMC8026907 DOI: 10.1016/j.jbc.2021.100480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
Allosteric proteins with multiple subunits and ligand-binding sites are central in regulating biological signals. The cAMP receptor protein from Mycobacterium tuberculosis (CRPMTB) is a global regulator of transcription composed of two identical subunits, each one harboring structurally conserved cAMP- and DNA-binding sites. The mechanisms by which these four binding sites are allosterically coupled in CRPMTB remain unclear. Here, we investigate the binding mechanism between CRPMTB and cAMP, and the linkage between cAMP and DNA interactions. Using calorimetric and fluorescence-based assays, we find that cAMP binding is entropically driven and displays negative cooperativity. Fluorescence anisotropy experiments show that apo-CRPMTB forms high-order CRPMTB–DNA oligomers through interactions with nonspecific DNA sequences or preformed CRPMTB–DNA complexes. Moreover, we find that cAMP prevents and reverses the formation of CRPMTB–DNA oligomers, reduces the affinity of CRPMTB for nonspecific DNA sequences, and stabilizes a 1-to-1 CRPMTB–DNA complex, but does not increase the affinity for DNA like in the canonical CRP from Escherichia coli (CRPEcoli). DNA-binding assays as a function of cAMP concentration indicate that one cAMP molecule per homodimer dissociates high-order CRPMTB–DNA oligomers into 1-to-1 complexes. These cAMP-mediated allosteric effects are lost in the double-mutant L47P/E178K found in CRP from Mycobacterium bovis Bacille Calmette-Guérin (CRPBCG). The functional behavior, thermodynamic stability, and dimerization constant of CRPBCG are not due to additive effects of L47P and E178K, indicating long-range interactions between these two sites. Altogether, we provide a previously undescribed archetype of cAMP-mediated allosteric regulation that differs from CRPEcoli, illustrating that structural homology does not imply allosteric homology.
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Affiliation(s)
- Fernanda Gárate
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Stephen Dokas
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Maria Fe Lanfranco
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Clare Canavan
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Irina Wang
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - John J Correia
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Rodrigo A Maillard
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA.
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2
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Prabhakant A, Panigrahi A, Krishnan M. Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding. J Chem Inf Model 2020; 60:6366-6376. [PMID: 33108170 DOI: 10.1021/acs.jcim.0c00617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CAP, which entails repositioning of DNA recognition helices (F-helices) in the DBD to dock favorably to the target DNA. Despite considerable progress, much remains to be understood about the mechanistic details of DNA recognition by CAP and about the map of allosteric pathways involved in CAP-mediated gene transcription. The present study uses molecular dynamics and umbrella sampling simulations to investigate the mechanism of cAMP- and DNA-induced changes in the conformation and energetics of F-helices observed during the allosteric regulation of CAP by cAMP and the subsequent binding to the DNA promoter region. Using novel collective variables, the free energy profiles associated with the orientation and dynamics of F-helices in the unliganded, cAMP-bound, and cAMP-DNA-bound states of CAP are calculated and compared. The binding-induced alterations in the resultant free energy profiles reveal important flexibility constraints imposed on DBD upon cAMP and DNA binding. A comprehensive analysis of residue-wise interaction maps reveals potential allosteric pathways between CBD and DBD that facilitate the allosteric transduction of regulatory signals in CAP. The revelation that the predicted allosteric pathways crisscross the intersubunit interface offers important clues on the microscopic origin of the intersubunit cooperativity and dimer stability of CAP.
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Affiliation(s)
- Akshay Prabhakant
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhinandan Panigrahi
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
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3
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Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. Allostery in Its Many Disguises: From Theory to Applications. Structure 2019; 27:566-578. [PMID: 30744993 PMCID: PMC6688844 DOI: 10.1016/j.str.2019.01.003] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/29/2018] [Accepted: 01/02/2019] [Indexed: 12/19/2022]
Abstract
Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
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Affiliation(s)
| | | | - Nikolay V Dokholyan
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Departments of Pharmacology and Biochemistry & Molecular Biology, Penn State Medical Center, Hershey, PA, USA
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A(∗)STAR), and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jing Li
- Departments of Biology and T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, USA
| | - Vincent J Hilser
- Departments of Biology and T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, USA
| | - Ivet Bahar
- School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | | | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg, Germany
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Jerome Eberhardt
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177 CNRS & Université de Strasbourg, Strasbourg, France
| | | | - Peter G Bolhuis
- van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam, Netherlands
| | - Jocelyne Vreede
- van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam, Netherlands
| | - Pietro Faccioli
- Physics Department, Università di Trento and INFN-TIFPA, Trento, Italy
| | - Simone Orioli
- Physics Department, Università di Trento and INFN-TIFPA, Trento, Italy
| | - Riccardo Ravasio
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Le Yan
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Carolina Brito
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Matthieu Wyart
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Paraskevi Gkeka
- Structure Design and Informatics, Sanofi R&D, Chilly-Mazarin, France
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Giulia Palermo
- Department of Chemistry and Biochemistry, University of California, San Diego, USA; Department of Bioengineering, University of California Riverside, CA 92507, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, USA
| | - Joanna Panecka-Hofman
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS) and Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Munich, Germany
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, Robert H Smith Faculty of Agriculture Food and Environment, The Hebrew University, Jerusalem, Israel
| | - Ruth Nussinov
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA
| | - Hyunbum Jang
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tom McLeish
- Department of Physics, University of York, York, UK
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4
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Schaefer C, de Bruijn RAJ, McLeish TCB. Ligand-regulated oligomerisation of allosterically interacting proteins. SOFT MATTER 2018; 14:6961-6968. [PMID: 30009315 DOI: 10.1039/c8sm00943k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The binding of ligands to distinct sites at proteins or at protein clusters is often cooperative or anti-cooperative due to allosteric signalling between those sites. The allostery is usually attributed to a configurational change of the proteins from a relaxed to a configurationally different tense state. Alternatively, as originally proposed by Cooper and Dryden, a tense state may be achieved by merely restricting the thermal vibrations of the protein around its mean configuration. In this work, we provide theoretical tools to investigate fluctuation allostery using cooling and titration experiments in which ligands regulate dimerisation, or ring or chain formation. We discuss in detail how ligands may regulate the supramolecular (co)polymerisation of liganded and unliganded proteins.
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Affiliation(s)
- Charley Schaefer
- Department of Physics, Durham University, South Road, Durham, DH1 3LE, UK.
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5
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McLeish T, Schaefer C, von der Heydt AC. The 'allosteron' model for entropic allostery of self-assembly. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170186. [PMID: 29735739 PMCID: PMC5941180 DOI: 10.1098/rstb.2017.0186] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2018] [Indexed: 12/20/2022] Open
Abstract
Using the simple 'allosteron' model, we show that it is possible, in principle, to elicit pathways by which fluctuation allostery affects self-assembly of protein complexes. We treat the cases of (i) protein fibrils and nucleation, (ii) n-mer protein complexes, and (iii) weakly attractive allosteric interactions in protein-like soft nanoscale objects that can be tuned to define exclusive self-associating families.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Tom McLeish
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK
| | - C Schaefer
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK
| | - A C von der Heydt
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK
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6
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Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes? Biophys J 2015; 109:1240-50. [PMID: 26338443 DOI: 10.1016/j.bpj.2015.08.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/02/2015] [Accepted: 08/07/2015] [Indexed: 11/23/2022] Open
Abstract
We examine the contrast between mechanisms for allosteric signaling that involve structural change, and those that do not, from the perspective of allosteric pathways. In particular we treat in detail the case of fluctuation-allostery by which amplitude modulation of the thermal fluctuations of the elastic normal modes conveys the allosteric signal, and address the question of what an allosteric pathway means in this case. We find that a perturbation theory of thermal elastic solids and nonperturbative approach (by super-coarse-graining elasticity into internal bending modes) have opposite signatures in their structure of correlated pathways. We illustrate the effect from analysis of previous results from GlxR of Corynebacterium glutamicum, an example of the CRP/FNR transcription family of allosteric homodimers. We find that the visibility of both correlated pathways and disconnected sites of correlated motion in this protein suggests that mechanisms of local elastic stretch and bend are recruited for the purpose of creating and controlling allosteric cooperativity.
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7
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Townsend PD, Rodgers TL, Glover LC, Korhonen HJ, Richards SA, Colwell LJ, Pohl E, Wilson MR, Hodgson DRW, McLeish TCB, Cann MJ. The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein. J Biol Chem 2015; 290:22225-35. [PMID: 26187469 PMCID: PMC4571973 DOI: 10.1074/jbc.m115.669267] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 12/20/2022] Open
Abstract
Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The catabolite activator protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data are not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second site CAP mutations. As the degree of correlated motion between the cAMP-contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP toward noncooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a noncooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring.
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Affiliation(s)
- Philip D Townsend
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and
| | - Thomas L Rodgers
- the School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Laura C Glover
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - Heidi J Korhonen
- the Biophysical Sciences Institute, and the Departments of Chemistry and the Department of Chemistry, University of Turku, 20014 Turku, Finland, and
| | | | - Lucy J Colwell
- the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Ehmke Pohl
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - Mark R Wilson
- the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - David R W Hodgson
- the Biophysical Sciences Institute, and the Departments of Chemistry and
| | - Tom C B McLeish
- the Biophysical Sciences Institute, and the Departments of Chemistry and Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Martin J Cann
- From the School of Biological and Biomedical Sciences, the Biophysical Sciences Institute, and
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8
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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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9
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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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10
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Townsend PD, Jungwirth B, Pojer F, Bußmann M, Money VA, Cole ST, Pühler A, Tauch A, Bott M, Cann MJ, Pohl E. The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors. PLoS One 2014; 9:e113265. [PMID: 25469635 PMCID: PMC4254451 DOI: 10.1371/journal.pone.0113265] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/16/2014] [Indexed: 12/01/2022] Open
Abstract
The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in bacterial metabolic regulatory networks. In C. glutamicum, which is widely used for the industrial production of amino acids and serves as a non-pathogenic model organism for members of the Corynebacteriales including Mycobacterium tuberculosis, the GlxR homodimer controls the transcription of a large number of genes involved in carbon metabolism. GlxR therefore represents a key target for understanding the regulation and coordination of C. glutamicum metabolism. Here we investigate cylic AMP and DNA binding of GlxR from C. glutamicum and describe the crystal structures of apo GlxR determined at a resolution of 2.5 Å, and two crystal forms of holo GlxR at resolutions of 2.38 and 1.82 Å, respectively. The detailed structural analysis and comparison of GlxR with CRP reveals that the protein undergoes a distinctive conformational change upon cyclic AMP binding leading to a dimer structure more compatible to DNA-binding. As the two binding sites in the GlxR homodimer are structurally identical dynamic changes upon binding of the first ligand are responsible for the allosteric behavior. The results presented here show how dynamic and structural changes in GlxR lead to optimization of orientation and distance of its two DNA-binding helices for optimal DNA recognition.
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Affiliation(s)
- Philip D. Townsend
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Britta Jungwirth
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Florence Pojer
- Global Health Institute, Protein Crystallography Core Facility, Ecole Poytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Bußmann
- Institute of Bio- and Geosciences, IBG-1:Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Victoria A. Money
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Stewart T. Cole
- Global Health Institute, Protein Crystallography Core Facility, Ecole Poytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andreas Tauch
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1:Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin J. Cann
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Ehmke Pohl
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- * E-mail:
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11
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McLeish TCB, Rodgers TL, Wilson MR. Allostery without conformation change: modelling protein dynamics at multiple scales. Phys Biol 2013; 10:056004. [PMID: 24021665 DOI: 10.1088/1478-3975/10/5/056004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The original ideas of Cooper and Dryden, that allosteric signalling can be induced between distant binding sites on proteins without any change in mean structural conformation, has proved to be a remarkably prescient insight into the rich structure of protein dynamics. It represents an alternative to the celebrated Monod-Wyman-Changeux mechanism and proposes that modulation of the amplitude of thermal fluctuations around a mean structure, rather than shifts in the structure itself, give rise to allostery in ligand binding. In a complementary approach to experiments on real proteins, here we take a theoretical route to identify the necessary structural components of this mechanism. By reviewing and extending an approach that moves from very coarse-grained to more detailed models, we show that, a fundamental requirement for a body supporting fluctuation-induced allostery is a strongly inhomogeneous elastic modulus. This requirement is reflected in many real proteins, where a good approximation of the elastic structure maps strongly coherent domains onto rigid blocks connected by more flexible interface regions.
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Affiliation(s)
- T C B McLeish
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
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12
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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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13
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Liu YY, Shih CH, Hwang JK, Chen CC. Deriving correlated motions in proteins from X-ray structure refinement by using TLS parameters. Gene 2013; 518:52-8. [DOI: 10.1016/j.gene.2012.11.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/27/2012] [Indexed: 12/14/2022]
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14
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Berezovsky IN. Thermodynamics of allostery paves a way to allosteric drugs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:830-5. [PMID: 23376182 DOI: 10.1016/j.bbapap.2013.01.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/16/2013] [Accepted: 01/21/2013] [Indexed: 12/30/2022]
Abstract
We overview here our recent work on the thermodynamic view of allosteric regulation and communication. Starting from the geometry-based prediction of regulatory binding sites in a static structure, we move on to exploring a connection between ligand binding and the intrinsic dynamics of the protein molecule. We describe here two recently introduced measures, binding leverage and leverage coupling, which allow one to analyze the molecular basis of allosteric regulation. We discuss the advantages of these measures and show that they work universally in proteins of different sizes, oligomeric states, and functions. We also point the problems that have to be solved before completing an atomic level description of allostery, and briefly discuss ideas for computational design of allosteric drugs. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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Affiliation(s)
- Igor N Berezovsky
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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15
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Campanello GC, Ma Z, Grossoehme NE, Guerra AJ, Ward BP, Dimarchi RD, Ye Y, Dann CE, Giedroc DP. Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family. J Mol Biol 2013; 425:1143-57. [PMID: 23353829 DOI: 10.1016/j.jmb.2013.01.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/13/2013] [Accepted: 01/16/2013] [Indexed: 11/18/2022]
Abstract
The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97' NH(ε2)...O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A "cavity" introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, -T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression.
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16
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Riera TV, Zheng L, Josephine HR, Min D, Yang W, Hedstrom L. Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase. Biochemistry 2011; 50:8508-18. [PMID: 21870820 PMCID: PMC3186055 DOI: 10.1021/bi200785s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allosteric activators are generally believed to shift the equilibrium distribution of enzyme conformations to favor a catalytically productive structure; the kinetics of conformational exchange is seldom addressed. Several observations suggested that the usual allosteric mechanism might not apply to the activation of IMP dehydrogenase (IMPDH) by monovalent cations. Therefore, we investigated the mechanism of K(+) activation in IMPDH by delineating the kinetic mechanism in the absence of monovalent cations. Surprisingly, the K(+) dependence of k(cat) derives from the rate of flap closure, which increases by ≥65-fold in the presence of K(+). We performed both alchemical free energy simulations and potential of mean force calculations using the orthogonal space random walk strategy to computationally analyze how K(+) accelerates this conformational change. The simulations recapitulate the preference of IMPDH for K(+), validating the computational models. When K(+) is replaced with a dummy ion, the residues of the K(+) binding site relax into ordered secondary structure, creating a barrier to conformational exchange. K(+) mobilizes these residues by providing alternate interactions for the main chain carbonyls. Potential of mean force calculations indicate that K(+) changes the shape of the energy well, shrinking the reaction coordinate by shifting the closed conformation toward the open state. This work suggests that allosteric regulation can be under kinetic as well as thermodynamic control.
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Affiliation(s)
- Thomas V. Riera
- Graduate Program in Biochemistry, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
| | - Lianqing Zheng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 USA
| | - Helen R. Josephine
- Department of Biology, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
| | - Donghong Min
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 USA
| | - Wei Yang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306 USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
- Department of Chemistry, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
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17
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Mitternacht S, Berezovsky IN. Binding leverage as a molecular basis for allosteric regulation. PLoS Comput Biol 2011; 7:e1002148. [PMID: 21935347 PMCID: PMC3174156 DOI: 10.1371/journal.pcbi.1002148] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/21/2011] [Indexed: 12/21/2022] Open
Abstract
Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ability of a binding site to couple to the intrinsic motions of a protein. We use Monte Carlo simulations to generate potential binding sites and either normal modes or pairs of crystal structures to describe relevant motions. We analyze single catalytic domains and multimeric allosteric enzymes with complex regulation. For the majority of the analyzed proteins, we find that both catalytic and allosteric sites have high binding leverage. Furthermore, our analysis of the catabolite activator protein, which is allosteric without conformational change, shows that its regulation involves other types of motion than those modulated at sites with high binding leverage. Our results point to the importance of incorporating dynamic information when predicting functional sites. Because it is possible to calculate binding leverage from a single crystal structure it can be used for characterizing proteins of unknown function and predicting latent allosteric sites in any protein, with implications for drug design. Allosteric protein regulation is the mechanism by which binding of a molecule to one site in a protein affects the activity at another site. Although the two classical phenomenological models, Monod-Wyman-Changeux (MWC) and Koshland-Némethy-Filmer (KNF), span from the case of hemoglobin to membrane receptors, they do not describe the intramolecular interactions involved. The coupling between two allosterically connected sites commonly takes place through coherent collective motion involving the whole protein. We therefore introduce a quantity called binding leverage to measure the strength of the coupling between particular binding sites and such motions. We show that high binding leverage is a characteristic of both allosteric sites and catalytic sites, emphasizing that both enzymatic function and allosteric regulation require a coupling between ligand binding and protein dynamics. We also consider the first known case of purely entropic allostery, where ligand binding only affects the amplitudes of fluctuations. We find that the binding site in this protein does not primarily connect to collective motions – instead the modulation of fluctuations is controlled from a deeply buried and highly connected site. Finally, sites with high binding leverage but no known biological function could be latent allosteric sites, and thus drug targets.
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Affiliation(s)
- Simon Mitternacht
- Computational Biology Unit/UNI Research, University of Bergen, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Igor N. Berezovsky
- Computational Biology Unit/UNI Research, University of Bergen, Bergen, Norway
- * E-mail:
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18
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Zhu L, Frenkel D, Bolhuis PG. Role of fluctuations in ligand binding cooperativity of membrane receptors. PHYSICAL REVIEW LETTERS 2011; 106:168103. [PMID: 21599417 DOI: 10.1103/physrevlett.106.168103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Indexed: 05/30/2023]
Abstract
Signal transduction upon binding of a ligand to a membrane protein can occur not only via allosteric conformational changes but also through fluctuations. We report a numerical study on the influence of conformational fluctuations on the cooperativity of a binding reaction in a simple model of an integral membrane receptor consisting of transmembrane helices. We find that small fluctuations lateral as well as perpendicular to the membrane can increase the cooperativity, with the former more dominant. Moreover, too much fluctuation induces negative cooperativity. Proteins with fewer than four helices do not show positive cooperativity under any circumstances. This behavior is rather robust, and independent of the receptor topology or ligand size. Fluctuations measured in all-atom molecular dynamics simulations of a G-protein coupled receptor fall within the predicted region of maximum cooperativity.
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Affiliation(s)
- Lizhe Zhu
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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Zhan H, Camargo M, Matthews KS. Positions 94-98 of the lactose repressor N-subdomain monomer-monomer interface are critical for allosteric communication. Biochemistry 2010; 49:8636-45. [PMID: 20804152 DOI: 10.1021/bi101106x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The central region of the LacI N-subdomain monomer-monomer interface includes residues K84, V94, V95, V96, S97, and M98. The side chains of these residues line the β-strands at this interface and interact to create a network of hydrophobic, charged, and polar interactions that significantly rearranges in different functional states of LacI. Prior work showed that converting K84 to an apolar residue or converting V96 to an acidic residue impedes the allosteric response to inducer. Thus, we postulated that a disproportionate number of substitutions in this region of the monomer-monomer interface would alter the complex features of the LacI allosteric response. To explore this hypothesis, acidic, basic, polar, and apolar mutations were introduced at positions 94-98. Despite their varied locations along the β-strands that flank the interface, ∼70% of the mutations impact allosteric behavior, with the most significant effects found for charged substitutions. Of note, many of the LacI variants with minor functional impact exhibited altered stability to urea denaturation. The results confirm the critical role of amino acids 94-98 and indicate that this N-subdomain interface forms a primary pathway in LacI allosteric response.
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Affiliation(s)
- Hongli Zhan
- Department of Biochemistry and Cell Biology, Rice University, MS-140, 6100 South Main Street, Houston, Texas 77005, USA
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