1
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Fersht AR. From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding. Q Rev Biophys 2024; 57:e4. [PMID: 38597675 DOI: 10.1017/s0033583523000045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the β-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of β- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.
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Affiliation(s)
- Alan R Fersht
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Gonville and Caius College, University of Cambridge, Cambridge, UK
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2
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Diop A, Pietrangeli P, Pennacchietti V, Pagano L, Toto A, Di Felice M, Di Matteo S, Marcocci L, Malagrinò F, Gianni S. Addressing the Binding Mechanism of the Meprin and TRAF-C Homology Domain of the Speckle-Type POZ Protein Using Protein Engineering. Int J Mol Sci 2023; 24:17364. [PMID: 38139193 PMCID: PMC10743451 DOI: 10.3390/ijms242417364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Protein-protein interactions play crucial roles in a wide range of biological processes, including metabolic pathways, cell cycle progression, signal transduction, and the proteasomal system. For PPIs to fulfill their biological functions, they require the specific recognition of a multitude of interacting partners. In many cases, however, protein-protein interaction domains are capable of binding different partners in the intracellular environment, but they require precise regulation of the binding events in order to exert their function properly and avoid misregulation of important molecular pathways. In this work, we focused on the MATH domain of the E3 Ligase adaptor protein SPOP in order to decipher the molecular features underlying its interaction with two different peptides that mimic its physiological partners: Puc and MacroH2A. By employing stopped-flow kinetic binding experiments, together with extensive site-directed mutagenesis, we addressed the roles of specific residues, some of which, although far from the binding site, govern these transient interactions. Our findings are compatible with a scenario in which the binding of the MATH domain with its substrate is characterized by a fine energetic network that regulates its interactions with different ligands. Results are briefly discussed in the context of previously existing work regarding the MATH domain.
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Affiliation(s)
- Awa Diop
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Paola Pietrangeli
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Valeria Pennacchietti
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Livia Pagano
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Angelo Toto
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Mariana Di Felice
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Sara Di Matteo
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Lucia Marcocci
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Francesca Malagrinò
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 Coppito, Italy
| | - Stefano Gianni
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
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3
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Illumination of a progressive allosteric mechanism mediating the glycine receptor activation. Nat Commun 2023; 14:795. [PMID: 36781912 PMCID: PMC9925812 DOI: 10.1038/s41467-023-36471-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
Pentameric ligand-gated ion channel mediate signal transduction at chemical synapses by transiting between resting and open states upon neurotransmitter binding. Here, we investigate the gating mechanism of the glycine receptor fluorescently labeled at the extracellular-transmembrane interface by voltage-clamp fluorometry (VCF). Fluorescence reports a glycine-elicited conformational change that precedes pore opening. Low concentrations of glycine, partial agonists or specific mixtures of glycine and strychnine trigger the full fluorescence signal while weakly activating the channel. Molecular dynamic simulations of a partial agonist bound-closed Cryo-EM structure show a highly dynamic nature: a marked structural flexibility at both the extracellular-transmembrane interface and the orthosteric site, generating docking properties that recapitulate VCF data. This work illuminates a progressive propagating transition towards channel opening, highlighting structural plasticity within the mechanism of action of allosteric effectors.
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4
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Cummins MC, Jacobs TM, Teets FD, DiMaio F, Tripathy A, Kuhlman B. AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein. Protein Sci 2022; 31:e4368. [PMID: 35762713 PMCID: PMC9207892 DOI: 10.1002/pro.4368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/09/2022] [Accepted: 05/28/2022] [Indexed: 11/12/2022]
Abstract
Using the molecular modeling program Rosetta, we designed a de novo protein, called SEWN0.1, which binds the heterotrimeric G protein Gαq. The design is helical, well-folded, and primarily monomeric in solution at a concentration of 10 μM. However, when we solved the crystal structure of SEWN0.1 at 1.9 Å, we observed a dimer in a conformation incompatible with binding Gαq . Unintentionally, we had designed a protein that adopts alternate conformations depending on its oligomeric state. Recently, there has been tremendous progress in the field of protein structure prediction as new methods in artificial intelligence have been used to predict structures with high accuracy. We were curious if the structure prediction method AlphaFold could predict the structure of SEWN0.1 and if the prediction depended on oligomeric state. When AlphaFold was used to predict the structure of monomeric SEWN0.1, it produced a model that resembles the Rosetta design model and is compatible with binding Gαq , but when used to predict the structure of a dimer, it predicted a conformation that closely resembles the SEWN0.1 crystal structure. AlphaFold's ability to predict multiple conformations for a single protein sequence should be useful for engineering protein switches.
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Affiliation(s)
- Matthew C. Cummins
- Department of PharmacologyUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Tim M. Jacobs
- Department of Bioinformatics and Computational BiologyUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
- AbCellera Biologics Inc.VancouverBritish ColumbiaCanada
| | - Frank D. Teets
- Department of Bioinformatics and Computational BiologyUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
- Department of Computational BiologyAndoverMassachusettsUSA
| | - Frank DiMaio
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Ashutosh Tripathy
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Brian Kuhlman
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
- Lineburger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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5
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Changeux JP, Christopoulos A. Allosteric modulation as a unifying mechanism for receptor function and regulation. Diabetes Obes Metab 2017; 19 Suppl 1:4-21. [PMID: 28880476 DOI: 10.1111/dom.12959] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Four major receptor families enable cells to respond to chemical and physical signals from their proximal environment. The ligand- and voltage-gated ion channels, G-protein-coupled receptors, nuclear hormone receptors and receptor tyrosine kinases are all allosteric proteins that carry multiple, spatially distinct, yet conformationally linked ligand-binding sites. Recent studies point to common mechanisms governing the allosteric transitions of these receptors, including the impact of oligomerization, pre-existing and functionally distinct conformational ensembles, intrinsically disordered regions, and the occurrence of allosteric modulatory sites. Importantly, synthetic allosteric modulators are being discovered for these receptors, providing an enriched, yet challenging, landscape for novel therapeutics.
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MESH Headings
- Allosteric Regulation/drug effects
- Allosteric Site/drug effects
- Animals
- Binding Sites/drug effects
- Dimerization
- Drug Discovery/trends
- Drugs, Investigational/chemistry
- Drugs, Investigational/pharmacology
- Humans
- Ligand-Gated Ion Channels/agonists
- Ligand-Gated Ion Channels/antagonists & inhibitors
- Ligand-Gated Ion Channels/chemistry
- Ligand-Gated Ion Channels/metabolism
- Ligands
- Models, Molecular
- Protein Conformation/drug effects
- Protein Multimerization/drug effects
- Receptor Protein-Tyrosine Kinases/agonists
- Receptor Protein-Tyrosine Kinases/antagonists & inhibitors
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Voltage-Gated Sodium Channels/chemistry
- Voltage-Gated Sodium Channels/metabolism
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Affiliation(s)
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, VIC 3052 Parkville, Australia
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6
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Nemecz Á, Prevost MS, Menny A, Corringer PJ. Emerging Molecular Mechanisms of Signal Transduction in Pentameric Ligand-Gated Ion Channels. Neuron 2017; 90:452-70. [PMID: 27151638 DOI: 10.1016/j.neuron.2016.03.032] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 01/07/2016] [Accepted: 03/24/2016] [Indexed: 10/21/2022]
Abstract
Nicotinic acetylcholine, serotonin type 3, γ-amminobutyric acid type A, and glycine receptors are major players of human neuronal communication. They belong to the family of pentameric ligand-gated ion channels, sharing a highly conserved modular 3D structure. Recently, high-resolution structures of both open- and closed-pore conformations have been solved for a bacterial, an invertebrate, and a vertebrate receptor in this family. These data suggest that a common gating mechanism occurs, coupling neurotransmitter binding to pore opening, but they also pinpoint significant differences among subtypes. In this Review, we summarize the structural and functional data in light of these gating models and speculate about their mechanistic consequences on ion permeation, pathological mutations, as well as functional regulation by orthosteric and allosteric effectors.
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Affiliation(s)
- Ákos Nemecz
- Channel-Receptors Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR 3571, 75015 Paris, France
| | - Marie S Prevost
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Anaïs Menny
- Channel-Receptors Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR 3571, 75015 Paris, France; Université Pierre et Marie Curie (UPMC), Cellule Pasteur, 75005 Paris, France
| | - Pierre-Jean Corringer
- Channel-Receptors Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR 3571, 75015 Paris, France.
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7
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Allosteric Modulation as a Unifying Mechanism for Receptor Function and Regulation. Cell 2016; 166:1084-1102. [DOI: 10.1016/j.cell.2016.08.015] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/13/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
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8
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Suksuwan A, Lomlim L, Dickert FL, Suedee R. Tracking the chemical surface properties of racemic thalidomide and its enantiomers using a biomimetic functional surface on a quartz crystal microbalance. J Appl Polym Sci 2015. [DOI: 10.1002/app.42309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Acharee Suksuwan
- Department of Pharmaceutical Chemistry; Faculty of Pharmaceutical Sciences; Molecular Recognition Materials Research Unit, NANOTEC Center of Excellence at PSU/Drug Delivery System Research Center, Prince of Songkla University; Hat Yai Songkhla 90112 Thailand
| | - Luelak Lomlim
- Department of Pharmaceutical Chemistry; Faculty of Pharmaceutical Sciences; Molecular Recognition Materials Research Unit, NANOTEC Center of Excellence at PSU/Drug Delivery System Research Center, Prince of Songkla University; Hat Yai Songkhla 90112 Thailand
| | - Franz L. Dickert
- Department of Analytical Chemistry; University of Vienna; Währingerstrasse 38 A-1090 Vienna Austria
| | - Roongnapa Suedee
- Department of Pharmaceutical Chemistry; Faculty of Pharmaceutical Sciences; Molecular Recognition Materials Research Unit, NANOTEC Center of Excellence at PSU/Drug Delivery System Research Center, Prince of Songkla University; Hat Yai Songkhla 90112 Thailand
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9
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Abstract
Ion channels are membrane-bound enzymes whose catalytic sites are ion-conducting pores that open and close (gate) in response to specific environmental stimuli. Ion channels are important contributors to cell signaling and homeostasis. Our current understanding of gating is the product of 60 plus years of voltage-clamp recording augmented by intervention in the form of environmental, chemical, and mutational perturbations. The need for good phenomenological models of gating has evolved in parallel with the sophistication of experimental technique. The goal of modeling is to develop realistic schemes that not only describe data, but also accurately reflect mechanisms of action. This review covers three areas that have contributed to the understanding of ion channels: traditional Eyring kinetic theory, molecular dynamics analysis, and statistical thermodynamics. Although the primary emphasis is on voltage-dependent channels, the methods discussed here are easily generalized to other stimuli and could be applied to any ion channel and indeed any macromolecule.
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10
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Sahdeo S, Wallace T, Hirakawa R, Knoflach F, Bertrand D, Maag H, Misner D, Tombaugh GC, Santarelli L, Brameld K, Milla ME, Button DC. Characterization of RO5126946, a Novel α7 nicotinic acetylcholine receptor-positive allosteric modulator. J Pharmacol Exp Ther 2014; 350:455-68. [PMID: 24917542 DOI: 10.1124/jpet.113.210963] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Both preclinical evidence and clinical evidence suggest that α7 nicotinic acetylcholine receptor activation (α7nAChR) improves cognitive function, the decline of which is associated with conditions such as Alzheimer's disease and schizophrenia. Moreover, allosteric modulation of α7nAChR is an emerging therapeutic strategy in an attempt to avoid the rapid desensitization properties associated with the α7nAChR after orthosteric activation. We used a calcium assay to screen for positive allosteric modulators (PAMs) of α7nAChR and report on the pharmacologic characterization of the novel compound RO5126946 (5-chloro-N-[(1S,3R)-2,2-dimethyl-3-(4-sulfamoyl-phenyl)-cyclopropyl]-2-methoxy-benzamide), which allosterically modulates α7nAChR activity. RO5126946 increased acetylcholine-evoked peak current and delayed current decay but did not affect the recovery of α7nAChRs from desensitization. In addition, RO5126946's effects were absent when nicotine-evoked currents were completely blocked by coapplication of the α7nAChR-selective antagonist methyl-lycaconitine. RO5126946 enhanced α7nAChR synaptic transmission and positively modulated GABAergic responses. The absence of RO5126946 effects at human α4β2nAChR and 5-hydroxytryptamine 3 receptors, among others, indicated selectivity for α7nAChRs. In vivo, RO5126946 is orally bioavailable and brain-penetrant and improves associative learning in a scopolamine-induced deficit model of fear conditioning in rats. In addition, procognitive effects of RO5126946 were investigated in the presence of nicotine to address potential pharmacologic interactions on behavior. RO5126946 potentiated nicotine's effects on fear memory when both compounds were administered at subthreshold doses and did not interfere with procognitive effects observed when both compounds were administered at effective doses. Overall, RO5126946 is a novel α7nAChR PAM with cognitive-enhancing properties.
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Affiliation(s)
- Sunil Sahdeo
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Tanya Wallace
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Ryoko Hirakawa
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Frederic Knoflach
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Daniel Bertrand
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Hans Maag
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Dinah Misner
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Geoffrey C Tombaugh
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Luca Santarelli
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Ken Brameld
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Marcos E Milla
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
| | - Donald C Button
- Roche Palo Alto, Palo Alto, California (S.S., T.W., R.H., H.M., K.B., M.E.M., D.C.B.); F. Hoffmann-La Roche AG, pRED, Pharma Research and Early Development, Discovery Neuroscience, Grenzacherstrasse, Basel, Switzerland (F.K., L.S.); gRED South San Francisco, California (D.M.); HiQScreen Sarl, Geneva, Switzerland (D.B.); and Psychogenics Inc., Tarrytown, New York (G.C.T.)
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11
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Colquhoun D, Lape R. Perspectives on: conformational coupling in ion channels: allosteric coupling in ligand-gated ion channels. ACTA ACUST UNITED AC 2013. [PMID: 23183696 PMCID: PMC3514732 DOI: 10.1085/jgp.201210844] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- David Colquhoun
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London WC1E 6BT, England, UK.
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12
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Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system. Proc Natl Acad Sci U S A 2013; 110:14942-7. [PMID: 23980173 DOI: 10.1073/pnas.1307337110] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A classical dogma of molecular biology dictates that the 3D structure of a protein is necessary for its function. However, a considerable fraction of the human proteome, although functional, does not adopt a defined folded state under physiological conditions. These intrinsically disordered proteins tend to fold upon binding to their partners with a molecular mechanism that is elusive to experimental characterization. Indeed, although many hypotheses have been put forward, the functional role (if any) of disorder in these intrinsically denatured systems is still shrouded in mystery. Here, we characterize the structure of the transition state of the binding-induced folding in the reaction between the KIX domain of the CREB-binding protein and the transactivation domain of c-Myb. The analysis, based on the characterization of a series of conservative site-directed mutants, reveals a very high content of native-like structure in the transition state and indicates that the recognition between KIX and c-Myb is geometrically precise. The implications of our results in the light of previous work on intrinsically unstructured systems are discussed.
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Levantino M, Spilotros A, Cammarata M, Schirò G, Ardiccioni C, Vallone B, Brunori M, Cupane A. The Monod-Wyman-Changeux allosteric model accounts for the quaternary transition dynamics in wild type and a recombinant mutant human hemoglobin. Proc Natl Acad Sci U S A 2012; 109:14894-9. [PMID: 22927385 PMCID: PMC3443182 DOI: 10.1073/pnas.1205809109] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The acknowledged success of the Monod-Wyman-Changeux (MWC) allosteric model stems from its efficacy in accounting for the functional behavior of many complex proteins starting with hemoglobin (the paradigmatic case) and extending to channels and receptors. The kinetic aspects of the allosteric model, however, have been often neglected, with the exception of hemoglobin and a few other proteins where conformational relaxations can be triggered by a short and intense laser pulse, and monitored by time-resolved optical spectroscopy. Only recently the application of time-resolved wide-angle X-ray scattering (TR-WAXS), a direct structurally sensitive technique, unveiled the time scale of hemoglobin quaternary structural transition. In order to test the generality of the MWC kinetic model, we carried out a TR-WAXS investigation in parallel on adult human hemoglobin and on a recombinant protein (HbYQ) carrying two mutations at the active site [Leu(B10)Tyr and His(E7)Gln]. HbYQ seemed an ideal test because, although exhibiting allosteric properties, its kinetic and structural properties are different from adult human hemoglobin. The structural dynamics of HbYQ unveiled by TR-WAXS can be quantitatively accounted for by the MWC kinetic model. Interestingly, the main structural change associated with the R-T allosteric transition (i.e., the relative rotation and translation of the dimers) is approximately 10-fold slower in HbYQ, and the drop in the allosteric transition rate with ligand saturation is steeper. Our results extend the general validity of the MWC kinetic model and reveal peculiar thermodynamic properties of HbYQ. A possible structural interpretation of the characteristic kinetic behavior of HbYQ is also discussed.
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Affiliation(s)
- Matteo Levantino
- Department of Physics, University of Palermo, Via Archirafi 36, I-90123 Palermo, Italy
| | - Alessandro Spilotros
- Department of Physics, University of Palermo, Via Archirafi 36, I-90123 Palermo, Italy
| | - Marco Cammarata
- Institut de Physique de Rennes, Centre National de la Recherche Scientifique, 263 Avenue Général Leclerc, 35042 Rennes, France; and
| | - Giorgio Schirò
- Department of Physics, University of Palermo, Via Archirafi 36, I-90123 Palermo, Italy
| | - Chiara Ardiccioni
- Department of Biochemical Sciences, and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza—University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences, and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza—University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Maurizio Brunori
- Department of Biochemical Sciences, and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza—University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Antonio Cupane
- Department of Physics, University of Palermo, Via Archirafi 36, I-90123 Palermo, Italy
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Abstract
Membrane proteins (MPs) mediate important physiological processes for the cell via extracellular and intracellular interactions. To better understand the biochemical and structural bases of these interactions, well-characterized preparations of purified MPs are required. This introduction reviews common problems encountered in MP preparation.
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Affiliation(s)
- Mark L Chiu
- Biologics Research, Biotechnology Center of Excellence, Janssen Research & Development, Radnor, Pennsylvania, USA
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Abstract
The Monod-Wyman-Changeux (MWC) model was conceived in 1965 to account for the signal transduction and cooperative properties of bacterial regulatory enzymes and hemoglobin. It was soon extended to pharmacological receptors for neurotransmitters and other macromolecular entities involved in intracellular and intercellular communications. Five decades later, the two main hypotheses of the model are reexamined on the basis of a variety of regulatory proteins with known X-ray structures: (a) Regulatory proteins possess an oligomeric structure with symmetry properties, and (b) the allosteric interactions between topographically distinct sites are mediated by a conformational transition established between a few preestablished states with conservation of symmetry and ligand-directed conformational selection. Several well-documented examples are adequately represented by the MWC model, yet a few possible exceptions are noted. New questions are raised concerning the dynamics of the allosteric transitions and more complex supramolecular ensembles.
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Affiliation(s)
- Jean-Pierre Changeux
- Collège de France & Institut Pasteur, URA CNRS 2182, Paris Cedex 15 75724, France.
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Haq SR, Chi CN, Bach A, Dogan J, Engström Å, Hultqvist G, Karlsson OA, Lundström P, Montemiglio LC, Strømgaard K, Gianni S, Jemth P. Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains. J Am Chem Soc 2011; 134:599-605. [PMID: 22129097 DOI: 10.1021/ja209341w] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K(d) correlate with changes in k(off).
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Affiliation(s)
- S Raza Haq
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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Abstract
Rapid advances in our collective understanding of biomolecular structure and, in concert, of biochemical systems, coupled with developments in computational methods, have massively impacted the field of medicinal chemistry over the past two decades, with even greater changes appearing on the horizon. In this perspective, we endeavor to profile some of the most prominent determinants of change and speculate as to further evolution that may consequently occur during the next decade. The five main angles to be addressed are: protein-protein interactions; peptides and peptidomimetics; molecular diversity and pharmacological space; molecular pharmacodynamics (significance, potential and challenges); and early-stage clinical efficacy and safety. We then consider, in light of these, the future of medicinal chemistry and the educational preparation that will be required for future medicinal chemists.
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Affiliation(s)
- Seetharama D Satyanarayanajois
- Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe LA 71201, USA.
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Changeux JP, Edelstein S. Conformational selection or induced fit? 50 years of debate resolved. F1000 BIOLOGY REPORTS 2011; 3:19. [PMID: 21941598 PMCID: PMC3169905 DOI: 10.3410/b3-19] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Exactly 50 years ago, biochemists raised the question of the mechanism of the conformational change that mediates “allosteric” interactions between regulatory sites and biologically active sites in regulatory/receptor proteins. Do the different conformations involved already exist spontaneously in the absence of the regulatory ligands (Monod-Wyman-Changeux), such that the complementary protein conformation would be selected to mediate signal transduction, or do particular ligands induce the receptor to adopt the conformation best suited to them (Koshland-Nemethy-Filmer—induced fit)? This is not just a central question for biophysics, it also has enormous importance for drug design. Recent advances in techniques have allowed detailed experimental and theoretical comparisons with the formal models of both scenarios. Also, it has been shown that mutated receptors can adopt constitutively active confirmations in the absence of ligand. There have also been demonstrations that the atomic resolution structures of the same protein are essentially the same whether ligand is bound or not. These and other advances in past decades have produced a situation where the vast majority of the data using different categories of regulatory proteins (including regulatory enzymes, ligand-gated ion channels, G protein-coupled receptors, and nuclear receptors) support the conformational selection scheme of signal transduction.
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Affiliation(s)
- Jean-Pierre Changeux
- Collège de France and Institut PasteurCNRS URA 2182, 25 rue du Dr Roux, 75015 ParisFrance
| | - Stuart Edelstein
- European Bioinformatics Institute and University of GenevaWellcome Trust Genome Campus, Hinxton, CB10 1SDUK
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Ribrault C, Sekimoto K, Triller A. From the stochasticity of molecular processes to the variability of synaptic transmission. Nat Rev Neurosci 2011; 12:375-87. [PMID: 21685931 DOI: 10.1038/nrn3025] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The variability of the postsynaptic response following a single action potential arises from two sources: the neurotransmitter release is probabilistic, and the postsynaptic response to neurotransmitter release has variable timing and amplitude. At individual synapses, the number of molecules of a given type that are involved in these processes is small enough that the stochastic (random) properties of molecular events cannot be neglected. How the stochasticity of molecular processes contributes to the variability of synaptic transmission, its sensitivity and its robustness to molecular fluctuations has important implications for our understanding of the mechanistic basis of synaptic transmission and of synaptic plasticity.
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Affiliation(s)
- Claire Ribrault
- Laboratoire Matières et Systèmes Complexes, CNRS-UMR7057, Université Paris 7, F-75205 Paris cedex 13, France
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