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Castro NSS, Laia CAT, Maiti BK, Cerqueira NMFSA, Moura I, Carepo MSP. Small phospho-donors phosphorylate MorR without inducing protein conformational changes. Biophys Chem 2018; 240:25-33. [PMID: 29883882 DOI: 10.1016/j.bpc.2018.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/10/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Phosphorylation is an essential mechanism of protein control and plays an important role in biology. The two-component system (TCS) is a bacterial regulation mechanism mediated by a response regulator (RR) protein and a kinase protein, which synchronize the regulatory circuit according to the environment. Phosphorylation is a key element in TCS function as it controls RR activity. In the present study, we characterize the behavior of MorR, an RR associated with Mo homeostasis, upon acetylphosphate and phosphoramidate treatment in vitro. Our results show that MorR was phosphorylated by both phospho-donors. Fluorescence experiments showed that MorR tryptophan emission is quenched by phosphoramidate. Furthermore, theoretical and computational results demonstrate that phosphorylation by phosphoramidate is more favorable than that by acetylphosphate. In conclusion, phosphorylated MorR is a monomeric protein and phosphorylation does not appear to induce observable conformational changes in the protein structure.
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Affiliation(s)
- Nathália S S Castro
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - César A T Laia
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Biplab K Maiti
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Nuno M F S A Cerqueira
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Isabel Moura
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Marta S P Carepo
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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2
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A network of molecular switches controls the activation of the two-component response regulator NtrC. Nat Commun 2015; 6:7283. [DOI: 10.1038/ncomms8283] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 04/26/2015] [Indexed: 12/22/2022] Open
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3
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Liu MS, Wang D, Morimoto H, Yim HCH, Irving AT, Williams BRG, Sadler AJ. Molecular dynamics reveal a novel kinase-substrate interface that regulates protein translation. J Mol Cell Biol 2014; 6:473-85. [PMID: 25404612 DOI: 10.1093/jmcb/mju044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A key control point in gene expression is the initiation of protein translation, with a universal stress response being constituted by inhibitory phosphorylation of the eukaryotic initiation factor 2α (eIF2α). In humans, four kinases sense diverse physiological stresses to regulate eIF2α to control cell differentiation, adaptation, and survival. Here we develop a computational molecular model of eIF2α and one of its kinases, the protein kinase R, to simulate the dynamics of their interaction. Predictions generated by coarse-grained dynamics simulations suggest a novel mode of action. Experimentation substantiates these predictions, identifying a previously unrecognized interface in the protein complex, which is constituted by dynamic residues in both eIF2α and its kinases that are crucial to regulate protein translation. These findings call for a reinterpretation of the current mechanism of action of the eIF2α kinases and demonstrate the value of conducting computational analysis to evaluate protein function.
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Affiliation(s)
- Ming S Liu
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Melbourne, VIC 3168, Australia CSIRO - Computational Informatics and Digital Productivity Flagship, Private Bag 10, Clayton South, VIC 3169, Australia
| | - Die Wang
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Melbourne, VIC 3168, Australia
| | - Hiroyuki Morimoto
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Melbourne, VIC 3168, Australia Department of Anatomy, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka 807-8555, Japan
| | - Howard C H Yim
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Melbourne, VIC 3168, Australia
| | - Aaron T Irving
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Melbourne, VIC 3168, Australia
| | - Bryan R G Williams
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Melbourne, VIC 3168, Australia Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Anthony J Sadler
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Melbourne, VIC 3168, Australia Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3168, Australia
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4
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Villali J, Pontiggia F, Clarkson MW, Hagan MF, Kern D. Evidence against the "Y-T coupling" mechanism of activation in the response regulator NtrC. J Mol Biol 2014; 426:1554-67. [PMID: 24406745 DOI: 10.1016/j.jmb.2013.12.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/18/2013] [Accepted: 12/24/2013] [Indexed: 01/17/2023]
Abstract
The dominant theory on the mechanism of response regulators activation in two-component bacterial signaling systems is the "Y-T coupling" mechanism, wherein the χ1 rotameric state of a highly conserved aromatic residue correlates with the activation of the protein via structural rearrangements coupled to a conserved tyrosine. In this paper, we present evidence that, in the receiver domain of the response regulator nitrogen regulatory protein C (NtrC(R)), the interconversion of this tyrosine (Y101) between its rotameric states is actually faster than the rate of inactive/active conversion and is not correlated to the activation process. Data gathered from NMR relaxation dispersion experiments show that a subset of residues surrounding the conserved tyrosine sense a process that is occurring at a faster rate than the inactive/active conformational transition. We show that this process is related to χ1 rotamer exchange of Y101 and that mutation of this aromatic residue to a leucine eliminated this second faster process without affecting activation. Computational simulations of NtrC(R) in its active conformation further demonstrate that the rotameric state of Y101 is uncorrelated with the global conformational transition during activation. Moreover, the tyrosine does not appear to be involved in the stabilization of the active form upon phosphorylation and is not essential in propagating the signal downstream for ATPase activity of the central domain. Our data provide experimental evidence against the generally accepted "Y-T coupling" mechanism of activation in NtrC(R).
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Affiliation(s)
- Janice Villali
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Francesco Pontiggia
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Michael W Clarkson
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA 02452, USA
| | - Dorothee Kern
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA.
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5
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Tripathi S, Portman JJ. Allostery and Folding of the N-terminal Receiver Domain of Protein NtrC. J Phys Chem B 2013; 117:13182-93. [DOI: 10.1021/jp403181p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Swarnendu Tripathi
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
| | - John J. Portman
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
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6
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Fuchigami S, Fujisaki H, Matsunaga Y, Kidera A. Protein Functional Motions: Basic Concepts and Computational Methodologies. ADVANCING THEORY FOR KINETICS AND DYNAMICS OF COMPLEX, MANY-DIMENSIONAL SYSTEMS: CLUSTERS AND PROTEINS 2011. [DOI: 10.1002/9781118087817.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Farrell DW, Lei M, Thorpe MF. Comparison of pathways from the geometric targeting method and targeted molecular dynamics in nitrogen regulatory protein C. Phys Biol 2011; 8:026017. [DOI: 10.1088/1478-3975/8/2/026017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
A statistical mechanical model of allosteric transitions in proteins is developed by extending the structure-based model of protein folding to cases of multiple native conformations. The partition function is calculated exactly within the model and the free-energy surface reflecting allostery is derived. This approach is applied to an example protein, the receiver domain of the bacterial enhancer-binding protein NtrC. The model predicts the large entropy associated with a combinatorial number of preexisting transition routes. This large entropy lowers the free-energy barrier of the allosteric transition, which explains the large structural fluctuation observed in the NMR data of NtrC. The global allosteric transformation of NtrC is explained by the shift of preexisting distribution of conformations upon phosphorylation, but the local structural adjustment around the phosphorylation site is explained by the complementary induced-fit mechanism. Structural disordering accompanied by fluctuating interactions specific to two allosteric conformations underlies a large number of routes of allosteric transition.
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Bourret RB. Receiver domain structure and function in response regulator proteins. Curr Opin Microbiol 2010; 13:142-9. [PMID: 20211578 DOI: 10.1016/j.mib.2010.01.015] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
Abstract
During signal transduction by two-component regulatory systems, sensor kinases detect and encode input information while response regulators (RRs) control output. Most receiver domains function as phosphorylation-mediated switches within RRs, but some transfer phosphoryl groups in multistep phosphorelays. Conserved features of receiver domain amino acid sequence correlate with structure and hence function. Receiver domains catalyze their own phosphorylation and dephosphorylation in reactions requiring a divalent cation. Molecular dynamics simulations are supplementing structural investigation of the conformational changes that underlie receiver domain switch function. As understanding of features shared by all receiver domains matures, factors conferring differences (e.g. in reaction rate or specificity) are receiving increased attention. Numerous examples of atypical receiver or pseudo-receiver domains that function without phosphorylation have recently been characterized.
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Affiliation(s)
- Robert B Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
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10
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Liu MS, Todd BD, Sadus RJ. Allosteric Conformational Transition in Adenylate Kinase: Dynamic Correlations and Implication for Allostery. Aust J Chem 2010. [DOI: 10.1071/ch09449] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An essential aspect of protein science is to determine the deductive relationship between structure, dynamics, and various sets of functions. The role of dynamics is currently challenging our understanding of protein functions, both experimentally and theoretically. To verify the internal fluctuations and dynamics correlations in an enzyme protein undergoing conformational transitions, we have applied a coarse-grained dynamics algorithm using the elastic network model for adenylate kinase. Normal mode analysis reveals possible dynamical and allosteric pathways for the transition between the open and the closed states of adenylate kinase. As the ligands binding induces significant flexibility changes of the nucleotides monophosphate (NMP) domain and adenosine triphosphate (ATP) domain, the diagonalized correlation between different structural transition states shows that most correlated motions occur between the NMP domain and the helices surrounding the ATP domain. The simultaneous existence of positive and negative correlations indicates that the conformational changes of adenylate kinase take place in an allosteric manner. Analyses of the cumulated normal mode overlap coefficients and long-range correlated motion provide new insights of operating mechanisms and dynamics of adenylate kinase. They also suggest a quantitative dynamics criterion for determining the allosteric cooperativity, which may be applicable to other proteins.
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11
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Damjanović A, García-Moreno E B, Brooks BR. Self-guided Langevin dynamics study of regulatory interactions in NtrC. Proteins 2009; 76:1007-19. [PMID: 19384996 DOI: 10.1002/prot.22439] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiple self-guided Langevin dynamics (SGLD) simulations were performed to examine structural and dynamical properties of the receiver domain of nitrogen regulatory protein C (NtrC(r)). SGLD and MD simulations of the phosphorylated active form structure suggest a mostly stable but broad structural ensemble of this protein. The finite difference Poisson-Boltzmann calculations of the pK(a) values of the active site residues suggest an increase in the pK(a) of His-84 on phosphorylation of Asp-54. In SGLD simulations of the phosphorylated active form with charged His-84, the average position of the regulatory helix alpha4 is found closer to the starting structure than in simulations with the neutral His-84. To model the transition pathway, the phosphate group was removed from the simulations. After 7 ns of simulations, the regulatory helix alpha4 was found approximately halfway between positions in the NMR structures of the active and inactive forms. Removal of the phosphate group stimulated loss of helix alpha4, suggesting that the pathway of conformational transition may involve partial unfolding mechanism. The study illustrates the potential utility of the SGLD method in studies of the coupling between ligand binding and conformational transitions.
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Affiliation(s)
- Ana Damjanović
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
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