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Prignano LA, Stevens MJ, Vanegas JM, Rempe SB, Dempski RE. Metadynamics simulations reveal mechanisms of Na+ and Ca2+ transport in two open states of the channelrhodopsin chimera, C1C2. PLoS One 2024; 19:e0309553. [PMID: 39241014 PMCID: PMC11379304 DOI: 10.1371/journal.pone.0309553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/30/2024] [Indexed: 09/08/2024] Open
Abstract
Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca2+ permeability vs. Na+ by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na+ and Ca2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.
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Affiliation(s)
- Lindsey A Prignano
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Mark J Stevens
- Sandia National Laboratories, Albuquerque, New Mexico, United States of America
| | - Juan M Vanegas
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Susan B Rempe
- Sandia National Laboratories, Albuquerque, New Mexico, United States of America
| | - Robert E Dempski
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
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2
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Liu H, Xiao Q, Wu X, Ma H, Li J, Guo X, Liu Z, Zhang Y, Luo Y. Mechanistic investigation of a D to N mutation in DAHP synthase that dictates carbon flux into the shikimate pathway in yeast. Commun Chem 2023; 6:152. [PMID: 37454208 DOI: 10.1038/s42004-023-00946-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023] Open
Abstract
3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key enzyme in the shikimate pathway for the biosynthesis of aromatic compounds. L-Phe and L-Tyr bind to the two main DAHPS isoforms and inhibit their enzyme activities, respectively. Synthetic biologists aim to relieve such inhibitions in order to improve the productivity of aromatic compounds. In this work, we reported a point mutant of yeast DHAPS, Aro3D154N, which retains the wild type enzyme activity but converts it highly inert to the inhibition by L-Phe. The Aro3 crystal structure along with the molecular dynamics simulations analysis suggests that the D154N mutation distant from the inhibitor binding cavity may reduce the binding affinity of L-Phe. Growth assays demonstrated that substitution of the conserved D154 with asparagine suffices to relieve the inhibition of L-Phe on Aro3, L-Tyr on Aro4, and the inhibitions on their corresponding homologues from diverse yeasts. The importance of our discovery is highlighted by the observation of 29.1% and 43.6% increase of yield for the production of tyrosol and salidroside respectively upon substituting ARO3 with ARO3D154N. We anticipate that this allele would be used broadly to increase the yield of various aromatic products in metabolically diverse microorganisms.
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Affiliation(s)
- Huayi Liu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen, 518071, China
| | - Qingjie Xiao
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), Chinese Academy of Sciences, Shanghai, 201210, China
| | - Xinxin Wu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - He Ma
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jian Li
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xufan Guo
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhenyu Liu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yunzi Luo
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen, 518071, China.
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3
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Liu B, Ding J, Liu Y, Wu J, Wu X, Chen Q, Li W. Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis. J Comput Aided Mol Des 2023; 37:325-338. [PMID: 37269435 DOI: 10.1007/s10822-023-00510-8] [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: 01/31/2023] [Accepted: 05/23/2023] [Indexed: 06/05/2023]
Abstract
FGFR3 kinase mutations are associated with a variety of malignancies, but FGFR3 mutant inhibitors have rarely been studied. Furthermore, the mechanism of pan-FGFR inhibitors resistance caused by kinase domain mutations is still unclear. In this study, we try to explain the mechanism of drug resistance to FGFR3 mutation through global analysis and local analysis based on molecular dynamics simulation, binding free energy analysis, umbrella sampling and community network analysis. The results showed that FGFR3 mutations caused a decrease in the affinity between drugs and FGFR3 kinase, which was consistent with the reported experimental results. Possible mechanisms are that mutations affect drug-protein affinity by altering the environment of residues near the hinge region where the protein binds to the drug, or by affecting the A-loop and interfering with the allosteric communication networks. In conclusion, we systematically elucidated the underlying mechanism of pan-FGFR inhibitor resistance caused by FGFR3 mutation based on molecular dynamics simulation strategy, which provided theoretical guidance for the development of FGFR3 mutant kinase inhibitors.
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Affiliation(s)
- Bo Liu
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Juntao Ding
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yugang Liu
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jianzhang Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiaoping Wu
- Institute of Tissue Transplantation and Immunology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, 510632, China
| | - Qian Chen
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314102, China.
| | - Wulan Li
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China.
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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4
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Liu Y, Liu J, He X. Different p Ka Shifts of Internal GLU8 in Human β-Endorphin Amyloid Revealing a Coupling of Internal Ionization and Stepwise Fibril Disassembly. J Phys Chem B 2023; 127:1089-1096. [PMID: 36696655 DOI: 10.1021/acs.jpcb.2c06706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
As a functional amyloid, human β-endorphin amyloid fibril features a β-solenoid conformation and store peptide hormones within acidic secretory granules, which would be released into the blood through fibril disassembly when the cellular milieu pH increases from acidic to neutral level on exocytosis. To gain detailed atomic mechanism of β-endorphin amyloid fibrils' pH-responsive disassembly, we conduct constant pH molecular dynamics simulations to investigate the structural and dynamical properties of β-endorphin amyloid fibrils in experiencing the environmental pH changes. Our results demonstrate a clear pKa shift of the internal ionizable residue of GLU8, and this shift becomes even more pronounced when it is buried more deeply in the amyloid fibrils. The unusual pKa of GLU8 reveals that its protonation state changes from the protonated state in the acidic secretory granule to the deprotonated state in the neutral pH conditions in the blood, where the deprotonation of GLU8 leads to unfavorable interactions within the hydrophobic core of the amyloid and subsequent fibril disassembly. The different pKa shifts of GLU8 relative to its positions in the amyloid fibril indicate that the β-endorphin amyloid fibril disassembly is a stepwise process, accounting for the experimental observation that the disassembly always initiates from the outermost layer. This study reveals the critical role of the protonation state of GLU8 in amyloid fibrils' pH-responsive disassembly, and provides clear insights for understanding the structural transitions of amyloids in hormone secretion. This study also provides theoretical basis for designing pH-sensitive biological tools for specific use with precise positioning of ionizable residues into the hydrophobic interior of proteins.
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Affiliation(s)
- Yiwei Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China
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5
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Balachandran N, Grainger RA, Rob T, Liuni P, Wilson DJ, Junop MS, Berti PJ. Role of Half-of-Sites Reactivity and Inter-Subunit Communications in DAHP Synthase Catalysis and Regulation. Biochemistry 2022; 61:2229-2240. [PMID: 36197914 DOI: 10.1021/acs.biochem.2c00465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
α-Carboxyketose synthases, including 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase (DAHPS), are long-standing targets for inhibition. They are challenging targets to create tight-binding inhibitors against, and inhibitors often display half-of-sites binding and partial inhibition. Half-of-sites inhibition demonstrates the existence of inter-subunit communication in DAHPS. We used X-ray crystallography and spatially resolved hydrogen-deuterium exchange (HDX) to reveal the structural and dynamic bases for inter-subunit communication in Escherichia coli DAHPS(Phe), the isozyme that is feedback-inhibited by phenylalanine. Crystal structures of this homotetrameric (dimer-of-dimers) enzyme are invariant over 91% of its sequence. Three variable loops make up 8% of the sequence and are all involved in inter-subunit contacts across the tight-dimer interface. The structures have pseudo-twofold symmetry indicative of inter-subunit communication across the loose-dimer interface, with the diagonal subunits B and C always having the same conformation as each other, while subunits A and D are variable. Spatially resolved HDX reveals contrasting responses to ligand binding, which, in turn, affect binding of the second substrate, erythrose-4-phosphate (E4P). The N-terminal peptide, M1-E12, and the active site loop that binds E4P, F95-K105, are key parts of the communication network. Inter-subunit communication appears to have a catalytic role in all α-carboxyketose synthase families and a regulatory role in some members.
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Affiliation(s)
| | - Ryan A Grainger
- Department of Biochemistry, Molecular Biology Lab, Western University, London, Ontario N6A 5C1, Canada
| | - Tamanna Rob
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Peter Liuni
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Murray S Junop
- Department of Biochemistry, Molecular Biology Lab, Western University, London, Ontario N6A 5C1, Canada
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6
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Li T, Yu L, Sun J, Liu J, He X. Ionization of D571 Is Coupled with SARS-CoV-2 Spike Up/Down Equilibrium Revealing the pH-Dependent Allosteric Mechanism of Receptor-Binding Domains. J Phys Chem B 2022; 126:4828-4839. [PMID: 35736566 PMCID: PMC9236204 DOI: 10.1021/acs.jpcb.2c02365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/05/2022] [Indexed: 11/30/2022]
Abstract
As a type I viral fusion protein, SARS-CoV-2 spike undergoes a pH-dependent switch to mediate the endosomal positioning of the receptor-binding domain to facilitate viral entry into cells and immune evasion. Gaps in our knowledge concerning the conformational transitions and key intramolecular motivations have hampered the development of effective therapeutics against the virus. To clarify the pH-sensitive elements on spike-gating the receptor-binding domain (RBD) opening and understand the details of the RBD opening transition, we performed microsecond-time scale constant pH molecular dynamics simulations in this study. We identified the deeply buried D571 with a clear pKa shift, suggesting a potential pH sensor, and showed the coupling of ionization of D571 with spike RBD-up/down equilibrium. We also computed the free-energy landscape for RBD opening and identified the crucial interactions that influence RBD dynamics. The atomic-level characterization of the pH-dependent spike activation mechanism provided herein offers new insights for a better understanding of the fundamental mechanisms of SARS-CoV-2 viral entry and infection and hence supports the discovery of novel therapeutics for COVID-19.
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Affiliation(s)
- Tong Li
- School of Traditional Chinese Pharmacy,
China Pharmaceutical University, Nanjing 210009,
China
| | - Lan Yu
- School of Science, China Pharmaceutical
University, Nanjing 210009, China
| | - Jingfang Sun
- School of Basic Medicine and Clinical Pharmacy,
China Pharmaceutical University, Nanjing 210009,
China
| | - Jinfeng Liu
- School of Basic Medicine and Clinical Pharmacy,
China Pharmaceutical University, Nanjing 210009,
China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular
Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule
Intelligent Syntheses, School of Chemistry and Molecular Engineering, East
China Normal University, Shanghai 200062, China
- New York University-East China Normal University
Center for Computational Chemistry, New York University
Shanghai, Shanghai 200062, China
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7
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Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021; 49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Allostery, in which binding of ligands to remote sites causes a functional change in the active sites, is a fascinating phenomenon observed in enzymes. Allostery can occur either with or without significant conformational changes in the enzymes, and the molecular basis of its mechanism can be difficult to decipher using only experimental techniques. Computational tools for analyzing enzyme sequences, structures, and dynamics can provide insights into the allosteric mechanism at the atomic level. Combining computational and experimental methods offers a powerful strategy for the study of enzyme allostery. The aromatic amino acid biosynthesis pathway is essential in microorganisms and plants. Multiple enzymes involved in this pathway are sensitive to feedback regulation by pathway end products and are known to use allostery to control their activities. To date, four enzymes in the aromatic amino acid biosynthesis pathway have been computationally investigated for their allosteric mechanisms, including 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, anthranilate synthase, chorismate mutase, and tryptophan synthase. Here we review the computational studies and findings on the allosteric mechanisms of these four enzymes. Results from these studies demonstrate the capability of computational tools and encourage future computational investigations of allostery in other enzymes of this pathway.
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8
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Diverse allosteric componentry and mechanisms control entry into aromatic metabolite biosynthesis. Curr Opin Struct Biol 2020; 65:159-167. [DOI: 10.1016/j.sbi.2020.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 02/01/2023]
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9
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Harjes E, Jameson GB, Tu YH, Burr N, Loo TS, Goroncy AK, Edwards PJB, Harjes S, Munro B, Göbl C, Sattlegger E, Norris GE. Experimentally based structural model of Yih1 provides insight into its function in controlling the key translational regulator Gcn2. FEBS Lett 2020; 595:324-340. [PMID: 33156522 DOI: 10.1002/1873-3468.13990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Yeast impact homolog 1 (Yih1), or IMPACT in mammals, is part of a conserved regulatory module controlling the activity of General Control Nonderepressible 2 (Gcn2), a protein kinase that regulates protein synthesis. Yih1/IMPACT is implicated not only in many essential cellular processes, such as neuronal development, immune system regulation and the cell cycle, but also in cancer. Gcn2 must bind to Gcn1 in order to impair the initiation of protein translation. Yih1 hinders this key Gcn1-Gcn2 interaction by binding to Gcn1, thus preventing Gcn2-mediated inhibition of protein synthesis. Here, we solved the structures of the two domains of Saccharomyces cerevisiae Yih1 separately using Nuclear Magnetic Resonance and determined the relative positions of the two domains using a range of biophysical methods. Our findings support a compact structural model of Yih1 in which the residues required for Gcn1 binding are buried in the interface. This model strongly implies that Yih1 undergoes a large conformational rearrangement from a latent closed state to a primed open state to bind Gcn1. Our study provides structural insight into the interactions of Yih1 with partner molecules.
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Affiliation(s)
- Elena Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
| | - Yi-Hsuan Tu
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Natalie Burr
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Trevor S Loo
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alexander K Goroncy
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Stefan Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Ben Munro
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Christoph Göbl
- Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Evelyn Sattlegger
- Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand.,School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Gillian E Norris
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
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10
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Jiao W, Fan Y, Blackmore NJ, Parker EJ. A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis. J Biol Chem 2020; 295:6252-6262. [PMID: 32217694 DOI: 10.1074/jbc.ra120.012605] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/20/2020] [Indexed: 01/08/2023] Open
Abstract
Allostery exploits the conformational dynamics of enzymes by triggering a shift in population ensembles toward functionally distinct conformational or dynamic states. Allostery extensively regulates the activities of key enzymes within biosynthetic pathways to meet metabolic demand for their end products. Here, we have examined a critical enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS), at the gateway to aromatic amino acid biosynthesis in Mycobacterium tuberculosis, which shows extremely complex dynamic allostery: three distinct aromatic amino acids jointly communicate occupancy to the active site via subtle changes in dynamics, enabling exquisite fine-tuning of delivery of these essential metabolites. Furthermore, this allosteric mechanism is co-opted by pathway branchpoint enzyme chorismate mutase upon complex formation. In this study, using statistical coupling analysis, site-directed mutagenesis, isothermal calorimetry, small-angle X-ray scattering, and X-ray crystallography analyses, we have pinpointed a critical node within the complex dynamic communication network responsible for this sophisticated allosteric machinery. Through a facile Gly to Pro substitution, we have altered backbone dynamics, completely severing the allosteric signal yet remarkably, generating a nonallosteric enzyme that retains full catalytic activity. We also identified a second residue of prime importance to the inter-enzyme communication with chorismate mutase. Our results reveal that highly complex dynamic allostery is surprisingly vulnerable and provide further insights into the intimate link between catalysis and allostery.
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Affiliation(s)
- Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Yifei Fan
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Nicola J Blackmore
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand .,Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
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11
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Hernández González JE, Hernández Alvarez L, Pascutti PG, Leite VBP. Prediction of Noncompetitive Inhibitor Binding Mode Reveals Promising Site for Allosteric Modulation of Falcipain-2. J Phys Chem B 2019; 123:7327-7342. [DOI: 10.1021/acs.jpcb.9b05021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jorge Enrique Hernández González
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Lilian Hernández Alvarez
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Pedro Geraldo Pascutti
- Laboratório de Dinâmica e Modelagem Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ave. Carlos
Chagas Filho, 373, CCS-Bloco D sala 30, Cidade Universitária
Ilha de Fundão, Rio de Janeiro, CEP 21941-902, Brazil
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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12
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Jiao W, Mittelstädt G, Moggré GJ, Parker EJ. Hinge Twists and Population Shifts Deliver Regulated Catalysis for ATP-PRT in Histidine Biosynthesis. Biophys J 2019; 116:1887-1897. [PMID: 31053263 DOI: 10.1016/j.bpj.2019.03.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/13/2019] [Accepted: 03/28/2019] [Indexed: 11/30/2022] Open
Abstract
Allosteric regulation plays an important role in the control of metabolic flux in biosynthetic pathways. In microorganisms, many enzymes in these pathways adopt different strategies of allostery to allow the tuning of their activities in response to metabolic demand. Thus, it is important to uncover the mechanism of allosteric signal transmission to fully comprehend the complex control of enzyme function and its evolution. ATP-phosphoribosyltransferase (ATP-PRT), as the first enzyme in the histidine biosynthetic pathway, is allosterically regulated by histidine and offers a good platform for the study of allostery. Two forms of ATP-PRT, namely long and short forms, were discovered that show different arrangements of their regulatory machinery. Crystal structures of the long-form ATP-PRT have revealed overall conformational changes in the inhibited state, but the observed changes in the active state are quite subtle, making the elucidation of its allosteric mechanism difficult. Here, we combine computational methods (ligand docking, quantum mechanics/molecular mechanics optimization, and molecular dynamic simulations) with experimental studies to probe the signal transmission between remote allosteric and active sites. Our results reveal that distinct conformational ensembles of the catalytic domain with different dynamic properties exist in the ligand-free and histidine-bound enzymes. These ensembles display different capabilities in supporting the catalytic and allosteric function of ATP-PRT. The findings give insight into the underlying mechanism of allostery and allow us to propose that the hinge twisting within the catalytic domain is the key for both enhancement of catalysis and provision of regulation in ATP-PRT enzymes.
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Affiliation(s)
- Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; School of Physical and Chemical Sciences, University of Canterbury, Christschurch, New Zealand.
| | - Gerd Mittelstädt
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Gert-Jan Moggré
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; School of Physical and Chemical Sciences, University of Canterbury, Christschurch, New Zealand
| | - Emily J Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; School of Physical and Chemical Sciences, University of Canterbury, Christschurch, New Zealand.
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13
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Long S, Wang J, Tian P. Significance of triple torsional correlations in proteins. RSC Adv 2019; 9:13949-13958. [PMID: 35519605 PMCID: PMC9064167 DOI: 10.1039/c9ra02191d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/21/2019] [Indexed: 11/21/2022] Open
Abstract
The free energy landscape (FEL) of a given complex molecular system is fundamentally the joint probability density of its many comprising degrees of freedom (DOFs). Computation of a complete FEL at atomistic scale is unfortunately intractable for a typical biomolecular system. The challenge of entropy calculation comes from various correlations among different DOFs. The common strategy to treat such complexity is expansion of the full correlation into various orders of local correlations. In reality, expansion is usually cut off at the second order (i.e. pairwise interactions) for protein torsional correlations without reliable estimation of the resulting error. Here, we estimated the mutual information of different torsion sets and found that triple correlations were significant for both local/distant residue pairs and consecutive backbone torsional segments. As expected, the third order approximations were found to be consistently better than the second order approximations. These findings were true for all analyzed proteins with different folds, were independent of the two different force fields utilized to generate trajectory sets, and were therefore likely to be of general importance for proteins. Additionally, binning strategies are of universal importance for numerical computation of correlations, we here provided a detailed comparison between equal-width and equal-sample binning for different bin numbers and demonstrated the impact of binning strategies on variances and biases of calculated mutual information. Our observation suggested that caution should be taken when quantitative comparison of correlations were intended between different studies with different binning strategies. Torsional mutual information for 10 typical residue pairs calculated with full joint distributions (MI), second order expansion (MI2), third order expansions (MI3), and their linear recombinations (MILR).![]()
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Affiliation(s)
| | | | - Pu Tian
- School of Life Science
- School Artificial Intelligence
- Jilin University
- Changchun
- China 130012
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14
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Liu J, Swails J, Zhang JZH, He X, Roitberg AE. A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. J Am Chem Soc 2018; 140:1639-1648. [PMID: 29308643 DOI: 10.1021/jacs.7b08569] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ionizable residues in the interior of proteins play essential roles, especially in biological energy transduction, but are relatively rare and seem incompatible with the complex and polar environment. We perform a comprehensive study of the internal ionizable residues on 21 variants of staphylococcal nuclease with internal Lys, Glu, or Asp residues. Using pH replica exchange molecular dynamics simulations, we find that, in most cases, the pKa values of these internal ionizable residues are shifted significantly from their values in solution. Our calculated results are in excellent agreement with the experimental observations of the Garcia-Moreno group. We show that the interpretation of the experimental pKa values requires the study of not only protonation changes but also conformational changes. The coupling between the protonation and conformational equilibria suggests a mechanism for efficient pH-sensing and regulation in proteins. This study provides new physical insights into how internal ionizable residues behave in the hydrophobic interior of proteins.
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Affiliation(s)
- Jinfeng Liu
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University , Shanghai, 200062, China.,Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States.,Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University , Nanjing, 210009, China
| | - Jason Swails
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - John Z H Zhang
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University , Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai, 200062, China
| | - Xiao He
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University , Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai, 200062, China
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
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15
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Remote electrochemical modulation of pK a in a rotaxane by co-conformational allostery. Proc Natl Acad Sci U S A 2017; 115:9385-9390. [PMID: 29255033 DOI: 10.1073/pnas.1712783115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allosteric control, one of Nature's most effective ways to regulate functions in biomolecular machinery, involves the transfer of information between distant sites. The mechanistic details of such a transfer are still an object of intensive investigation and debate, and the idea that intramolecular communication could be enabled by dynamic processes is gaining attention as a complement to traditional explanations. Mechanically interlocked molecules, owing to the particular kind of connection between their components and the resulting dynamic behavior, are attractive systems to investigate allosteric mechanisms and exploit them to develop functionalities with artificial species. We show that the pKa of an ammonium site located on the axle component of a [2]rotaxane can be reversibly modulated by changing the affinity of a remote recognition site for the interlocked crown ether ring through electrochemical stimulation. The use of a reversible ternary redox switch enables us to set the pKa to three different values, encompassing more than seven units. Our results demonstrate that in the axle the two sites do not communicate, and that in the rotaxane the transfer of information between them is made possible by the shuttling of the ring, that is, by a dynamic intramolecular process. The investigated coupling of electron- and proton-transfer reactions is reminiscent of the operation of the protein complex I of the respiratory chain.
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16
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Jiao W, Blackmore NJ, Nazmi AR, Parker EJ. Quaternary structure is an essential component that contributes to the sophisticated allosteric regulation mechanism in a key enzyme from Mycobacterium tuberculosis. PLoS One 2017; 12:e0180052. [PMID: 28665948 PMCID: PMC5493349 DOI: 10.1371/journal.pone.0180052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/08/2017] [Indexed: 01/26/2023] Open
Abstract
The first enzyme of the shikimate pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), adopts a range of distinct allosteric regulation mechanisms in different organisms, related to different quaternary assemblies. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) is a homotetramer, with the allosteric sites in close proximity to the interfaces. Here we examine the importance of the quaternary structure on catalysis and regulation, by amino acid substitution targeting the tetramer interface of MtuDAH7PS. Using only single amino acid substitutions either in, or remote from the interface, two dimeric variants of MtuDAH7PS (MtuDAH7PSF227D and MtuDAH7PSG232P) were successfully generated. Both dimeric variants maintained activity due to the distance between the sites of amino acid substitution and the active sites, but attenuated catalytic efficiency was observed. Both dimeric variants showed significantly disrupted allosteric regulation with greatly impaired binding affinity for one of the allosteric ligands. Molecular dynamics simulations revealed changes in protein dynamics and average conformations in the dimeric variant caused by amino acid substitution remote to the tetramer interface (MtuDAH7PSG232P), which are consistent with the observed reduction in catalytic efficiency and loss of allosteric response.
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Affiliation(s)
- Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Nicola J. Blackmore
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Ali Reza Nazmi
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
- * E-mail:
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17
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Ji M, Zheng G, Li X, Zhang Z, Jv G, Wang X, Wang J. Computational dissection of allosteric inhibition of the SH2 domain of Bcr-Abl kinase by the monobody inhibitor AS25. J Mol Model 2017; 23:183. [DOI: 10.1007/s00894-017-3353-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/19/2017] [Indexed: 11/30/2022]
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18
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Nazmi AR, Lang EJM, Bai Y, Allison TM, Othman MH, Panjikar S, Arcus VL, Parker EJ. Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate. J Biol Chem 2016; 291:21836-21847. [PMID: 27502275 DOI: 10.1074/jbc.m116.741637] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multifunctional proteins play a variety of roles in metabolism. Here, we examine the catalytic function of the combined 3-deoxy-d-arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM) from Geobacillus sp. DAH7PS operates at the start of the biosynthetic pathway for aromatic metabolites, whereas CM operates in a dedicated branch of the pathway for the biosynthesis of amino acids tyrosine and phenylalanine. In line with sequence predictions, the two catalytic functions are located in distinct domains, and these two activities can be separated and retain functionality. For the full-length protein, prephenate, the product of the CM reaction, acts as an allosteric inhibitor for the DAH7PS. The crystal structure of the full-length protein with prephenate bound and the accompanying small angle x-ray scattering data reveal the molecular mechanism of the allostery. Prephenate binding results in the tighter association between the dimeric CM domains and the tetrameric DAH7PS, occluding the active site and therefore disrupting DAH7PS function. Acquisition of a physical gating mechanism to control catalytic function through gene fusion appears to be a general mechanism for providing allostery for this enzyme.
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Affiliation(s)
- Ali Reza Nazmi
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Eric J M Lang
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Yu Bai
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Timothy M Allison
- the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 5QY, United Kingdom
| | - Mohamad H Othman
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Santosh Panjikar
- the Australian Synchrotron, Clayton, Melbourne, Victoria 3168, Australia.,the Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Vickery L Arcus
- the School of Science, University of Waikato, Hamilton 3240, New Zealand, and
| | - Emily J Parker
- the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
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19
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Clark AK, Wilder JH, Grayson AW, Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor. J Phys Chem B 2016; 120:8338-45. [PMID: 27110634 DOI: 10.1021/acs.jpcb.6b02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The promiscuous protein retinoid X receptor (RXR) displays essential allosteric regulation of several members in the nuclear hormone receptor superfamily via heterodimerization and (anti)cooperative binding of cognate ligands. Here, the structural basis of the positive allostery of RXR and constitutive androstane receptor (CAR) is revealed. In contrast, a similar computational approach had previously revealed the mechanism for negative allostery in the complex of RXR and thyroid receptor (TR). By comparing the positive and negative allostery of RXR complexed with CAR and TR respectively, we reported the promiscuous allosteric control involving RXR. We characterize the allosteric mechanism by expressing the correlated dynamics of selected residue-residue contacts which was extracted from atomistic molecular dynamics simulation and statistical analysis. While the same set of residues in the binding pocket of RXR may initiate the residue-residue interaction network, RXR uses largely different sets of contacts (only about one-third identical) and allosteric modes to regulate TR and CAR. The promiscuity of RXR control may originate from multiple factors, including (1) the frustrated fit of cognate ligand 9c to the RXR binding pocket and (2) the different ligand-binding features of TR (loose) versus CAR (tight) to their corresponding cognate ligands.
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Affiliation(s)
| | | | | | - Quentin R Johnson
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Richard J Lindsay
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Ricky B Nellas
- Institute of Chemistry, University of the Philippines Diliman , Quezon City, Philippines
| | | | - Tongye Shen
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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