메뉴 건너뛰기




Volumn 55, Issue 42, 2016, Pages 5907-5916

Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; AMMONIA; CATALYSIS; ENERGY BARRIERS; MOLECULAR DYNAMICS; MOLECULAR MODELING; QUANTUM THEORY; REACTION INTERMEDIATES; REACTION KINETICS; THERMODYNAMICS;

EID: 84993953607     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.6b00822     Document Type: Article
Times cited : (8)

References (52)
  • 1
    • 79953877213 scopus 로고    scopus 로고
    • Crystal structure of type III glutamine synthetase: Surprising reversal of the inter-ring interface
    • van Rooyen, J. M., Abratt, V. R., Belrhali, H., and Sewell, T. (2011) Crystal structure of type III glutamine synthetase: Surprising reversal of the inter-ring interface Structure 19, 471-483 10.1016/j.str.2011.02.001
    • (2011) Structure , vol.19 , pp. 471-483
    • Van Rooyen, J.M.1    Abratt, V.R.2    Belrhali, H.3    Sewell, T.4
  • 4
    • 65249121277 scopus 로고    scopus 로고
    • The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling
    • Bernard, S. M. and Habash, D. Z. (2009) The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling New Phytol. 182, 608-620 10.1111/j.1469-8137.2009.02823.x
    • (2009) New Phytol. , vol.182 , pp. 608-620
    • Bernard, S.M.1    Habash, D.Z.2
  • 5
    • 0033933445 scopus 로고    scopus 로고
    • The presence of GSI-like genes in higher plants: Support for the paralogous evolution of GSI and GSII genes
    • Mathis, R., Gamas, P., Meyer, Y., and Cullimore, J. V. (2000) The presence of GSI-like genes in higher plants: support for the paralogous evolution of GSI and GSII genes J. Mol. Evol. 50, 116-122 10.1007/s002399910013
    • (2000) J. Mol. Evol. , vol.50 , pp. 116-122
    • Mathis, R.1    Gamas, P.2    Meyer, Y.3    Cullimore, J.V.4
  • 6
    • 0347579854 scopus 로고    scopus 로고
    • Expressed sequence tag analysis of adult human lens for the NEIBank Project: Over 2000 non-redundant transcripts, novel genes and splice variants
    • Wistow, G., Bernstein, S. L., Wyatt, M. K., Behal, A., Touchman, J. W., Bouffard, G., Smith, D., and Peterson, K. (2002) Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants Mol. Vision 8, 171-184
    • (2002) Mol. Vision , vol.8 , pp. 171-184
    • Wistow, G.1    Bernstein, S.L.2    Wyatt, M.K.3    Behal, A.4    Touchman, J.W.5    Bouffard, G.6    Smith, D.7    Peterson, K.8
  • 7
    • 33845220269 scopus 로고    scopus 로고
    • Lengsin is a survivor of an ancient family of class i glutamine synthetases re-engineered by evolution for a role in the vertebrate lens
    • Wyatt, K., White, H. E., Wang, L., Bateman, O. A., Slingsby, C., Orlova, E. V., and Wistow, G. (2006) Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens Structure 14, 1823-1834 10.1016/j.str.2006.10.008
    • (2006) Structure , vol.14 , pp. 1823-1834
    • Wyatt, K.1    White, H.E.2    Wang, L.3    Bateman, O.A.4    Slingsby, C.5    Orlova, E.V.6    Wistow, G.7
  • 9
    • 36349018892 scopus 로고    scopus 로고
    • Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design
    • Krajewski, W. W., Collins, R., Holmberg-Schiavone, L., Jones, T. A., Karlberg, T., and Mowbray, S. L. (2008) Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design J. Mol. Biol. 375, 217-228 10.1016/j.jmb.2007.10.029
    • (2008) J. Mol. Biol. , vol.375 , pp. 217-228
    • Krajewski, W.W.1    Collins, R.2    Holmberg-Schiavone, L.3    Jones, T.A.4    Karlberg, T.5    Mowbray, S.L.6
  • 10
    • 0024417277 scopus 로고
    • Refined atomic model of glutamine synthetase at 3.5 A resolution
    • Yamashita, M., Almassy, R., Janson, C., Cascio, D., and Eisenberg, D. (1989) Refined atomic model of glutamine synthetase at 3.5 A resolution J. Biol. Chem. 264, 17681-17690
    • (1989) J. Biol. Chem. , vol.264 , pp. 17681-17690
    • Yamashita, M.1    Almassy, R.2    Janson, C.3    Cascio, D.4    Eisenberg, D.5
  • 12
    • 0002324178 scopus 로고
    • Glutamine synthetase of Escherichia coli: Some physical and chemical properties
    • Ginsburg, A. (1972) Glutamine synthetase of Escherichia coli: some physical and chemical properties Adv. Protein Chem. 26, 1-79 10.1016/S0065-3233(08)60139-4
    • (1972) Adv. Protein Chem. , vol.26 , pp. 1-79
    • Ginsburg, A.1
  • 13
    • 80455173502 scopus 로고    scopus 로고
    • Glutamine synthetase is a molecular target of nitric oxide in root nodules of Medicago truncatula and is regulated by tyrosine nitration
    • Melo, P. M., Silva, L. S., Ribeiro, I., Seabra, A. R., and Carvalho, H. G. (2011) Glutamine synthetase is a molecular target of nitric oxide in root nodules of Medicago truncatula and is regulated by tyrosine nitration Plant Physiol. 157, 1505-1517 10.1104/pp.111.186056
    • (2011) Plant Physiol. , vol.157 , pp. 1505-1517
    • Melo, P.M.1    Silva, L.S.2    Ribeiro, I.3    Seabra, A.R.4    Carvalho, H.G.5
  • 14
    • 0023476734 scopus 로고
    • Purification of the glutamine synthetase II isozyme of Drosophila melanogaster and structural and functional comparison of glutamine synthetases i and II
    • De Pinto, V., Caggese, C., Prezioso, G., and Ritossa, F. (1987) Purification of the glutamine synthetase II isozyme of Drosophila melanogaster and structural and functional comparison of glutamine synthetases I and II Biochem. Genet. 25, 821-836 10.1007/BF00502602
    • (1987) Biochem. Genet. , vol.25 , pp. 821-836
    • De Pinto, V.1    Caggese, C.2    Prezioso, G.3    Ritossa, F.4
  • 15
    • 26844488226 scopus 로고    scopus 로고
    • A single glutamine synthetase gene produces tissue-specific subcellular localization by alternative splicing
    • Matthews, G. D., Gould, R. M., and Vardimon, L. (2005) A single glutamine synthetase gene produces tissue-specific subcellular localization by alternative splicing FEBS Lett. 579, 5527-5534 10.1016/j.febslet.2005.08.082
    • (2005) FEBS Lett. , vol.579 , pp. 5527-5534
    • Matthews, G.D.1    Gould, R.M.2    Vardimon, L.3
  • 16
    • 84155160658 scopus 로고    scopus 로고
    • The stressed synapse: The impact of stress and glucocorticoids on glutamate transmission
    • Popoli, M., Yan, Z., McEwen, B. S., and Sanacora, G. (2012) The stressed synapse: the impact of stress and glucocorticoids on glutamate transmission Nat. Rev. Neurosci. 13, 22-37 10.1038/nrn3138
    • (2012) Nat. Rev. Neurosci. , vol.13 , pp. 22-37
    • Popoli, M.1    Yan, Z.2    McEwen, B.S.3    Sanacora, G.4
  • 18
    • 0036093019 scopus 로고    scopus 로고
    • Glutamine synthetase in brain: Effect of ammonia
    • Suarez, I., Bodega, G., and Fernandez, B. (2002) Glutamine synthetase in brain: effect of ammonia Neurochem. Int. 41, 123-142 10.1016/S0197-0186(02)00033-5
    • (2002) Neurochem. Int. , vol.41 , pp. 123-142
    • Suarez, I.1    Bodega, G.2    Fernandez, B.3
  • 19
    • 0033963901 scopus 로고    scopus 로고
    • Neuronal expression of glutamine synthetase in Alzheimer's disease indicates a profound impairment of metabolic interactions with astrocytes
    • Robinson, S. R. (2000) Neuronal expression of glutamine synthetase in Alzheimer's disease indicates a profound impairment of metabolic interactions with astrocytes Neurochem. Int. 36, 471-482 10.1016/S0197-0186(99)00150-3
    • (2000) Neurochem. Int. , vol.36 , pp. 471-482
    • Robinson, S.R.1
  • 20
    • 84886311261 scopus 로고    scopus 로고
    • Astrocytes and glutamate homoeostasis in Alzheimer's disease: A decrease in glutamine synthetase, but not in glutamate transporter-1, in the prefrontal cortex
    • Kulijewicz-Nawrot, M., Syková, E., Chvátal, A., Verkhratsky, A., and Rodríguez, J. J. (2013) Astrocytes and glutamate homoeostasis in Alzheimer's disease: a decrease in glutamine synthetase, but not in glutamate transporter-1, in the prefrontal cortex ASN Neuro 5, 273-282 10.1042/AN20130017
    • (2013) ASN Neuro , vol.5 , pp. 273-282
    • Kulijewicz-Nawrot, M.1    Syková, E.2    Chvátal, A.3    Verkhratsky, A.4    Rodríguez, J.J.5
  • 21
    • 0035576818 scopus 로고    scopus 로고
    • Changes in the cellular distribution of glutamine synthetase in Alzheimer's disease
    • Robinson, S. R. (2001) Changes in the cellular distribution of glutamine synthetase in Alzheimer's disease J. Neurosci. Res. 66, 972-980 10.1002/jnr.10057
    • (2001) J. Neurosci. Res. , vol.66 , pp. 972-980
    • Robinson, S.R.1
  • 22
    • 79960887452 scopus 로고    scopus 로고
    • Age-dependent decrease in glutamine synthetase expression in the hippocampal astroglia of the triple transgenic Alzheimer's disease mouse model: Mechanism for deficient glutamatergic transmission?
    • Olabarria, M., Noristani, H. N., Verkhratsky, A., and Rodríguez, J. J. (2011) Age-dependent decrease in glutamine synthetase expression in the hippocampal astroglia of the triple transgenic Alzheimer's disease mouse model: mechanism for deficient glutamatergic transmission? Mol. Neurodegener. 6, 55 10.1186/1750-1326-6-55
    • (2011) Mol. Neurodegener. , vol.6 , pp. 55
    • Olabarria, M.1    Noristani, H.N.2    Verkhratsky, A.3    Rodríguez, J.J.4
  • 23
    • 84947043914 scopus 로고    scopus 로고
    • Astrocytes from adult Wistar rats aged in vitro show changes in glial functions
    • Souza, D. G., Bellaver, B., Raupp, G. S., Souza, D. O., and Quincozes-Santos, A. (2015) Astrocytes from adult Wistar rats aged in vitro show changes in glial functions Neurochem. Int. 90, 93-97 10.1016/j.neuint.2015.07.016
    • (2015) Neurochem. Int. , vol.90 , pp. 93-97
    • Souza, D.G.1    Bellaver, B.2    Raupp, G.S.3    Souza, D.O.4    Quincozes-Santos, A.5
  • 26
    • 0342526461 scopus 로고
    • Activated glutamate intermediate in the enzymatic synthesis of glutamine
    • Krishnaswamy, P., Pamiljans, V., and Meister, A. (1960) Activated glutamate intermediate in the enzymatic synthesis of glutamine J. Biol. Chem. 235, PC39-PC40
    • (1960) J. Biol. Chem. , vol.235 , pp. PC39-PC40
    • Krishnaswamy, P.1    Pamiljans, V.2    Meister, A.3
  • 27
    • 0015522451 scopus 로고
    • Substrate binding and reaction intermediates of glutamine synthetase (Escherichia coli W) as studied by isotope exchanges
    • Wedler, F. and Boyer, P. (1972) Substrate binding and reaction intermediates of glutamine synthetase (Escherichia coli W) as studied by isotope exchanges J. Biol. Chem. 247, 984-992
    • (1972) J. Biol. Chem. , vol.247 , pp. 984-992
    • Wedler, F.1    Boyer, P.2
  • 28
    • 0017189048 scopus 로고
    • Catalytic mechanisms of glutamine synthetase enzymes. Studies with analogs of possible intermediates and transition states
    • Wedler, F. C. and Horn, B. R. (1976) Catalytic mechanisms of glutamine synthetase enzymes. Studies with analogs of possible intermediates and transition states J. Biol. Chem. 251, 7530-7538
    • (1976) J. Biol. Chem. , vol.251 , pp. 7530-7538
    • Wedler, F.C.1    Horn, B.R.2
  • 29
    • 0028082017 scopus 로고
    • Structural model for the reaction mechanism of glutamine synthetase, based on five crystal structures of enzyme-substrate complexes
    • Liaw, S. H. and Eisenberg, D. (1994) Structural model for the reaction mechanism of glutamine synthetase, based on five crystal structures of enzyme-substrate complexes Biochemistry 33, 675-681 10.1021/bi00169a007
    • (1994) Biochemistry , vol.33 , pp. 675-681
    • Liaw, S.H.1    Eisenberg, D.2
  • 30
    • 84959467438 scopus 로고    scopus 로고
    • Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies
    • Frieg, B., Görg, B., Homeyer, N., Keitel, V., Häussinger, D., and Gohlke, H. (2016) Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies PLoS Comput. Biol. 12, e1004693 10.1371/journal.pcbi.1004693
    • (2016) PLoS Comput. Biol. , vol.12 , pp. e1004693
    • Frieg, B.1    Görg, B.2    Homeyer, N.3    Keitel, V.4    Häussinger, D.5    Gohlke, H.6
  • 31
    • 84971254850 scopus 로고    scopus 로고
    • Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations
    • Moreira, C., Ramos, M. J., and Fernandes, P. A. (2016) Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations Chem.-Eur. J. 22, 9218-9225 10.1002/chem.201600305
    • (2016) Chem. - Eur. J. , vol.22 , pp. 9218-9225
    • Moreira, C.1    Ramos, M.J.2    Fernandes, P.A.3
  • 32
    • 34547559704 scopus 로고    scopus 로고
    • PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    • Dolinsky, T. J., Czodrowski, P., Li, H., Nielsen, J. E., Jensen, J. H., Klebe, G., and Baker, N. A. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Res. 35, W522-W525 10.1093/nar/gkm276
    • (2007) Nucleic Acids Res. , vol.35 , pp. W522-W525
    • Dolinsky, T.J.1    Czodrowski, P.2    Li, H.3    Nielsen, J.E.4    Jensen, J.H.5    Klebe, G.6    Baker, N.A.7
  • 33
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: visual molecular dynamics J. Mol. Graphics 14, 33-38 10.1016/0263-7855(96)00018-5
    • (1996) J. Mol. Graphics , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 34
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly, C. I., Cieplak, P., Cornell, W., and Kollman, P. A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model J. Phys. Chem. 97, 10269-10280 10.1021/j100142a004
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.3    Kollman, P.A.4
  • 35
    • 0037495965 scopus 로고    scopus 로고
    • Development of polyphosphate parameters for use with the AMBER force field
    • Meagher, K. L., Redman, L. T., and Carlson, H. A. (2003) Development of polyphosphate parameters for use with the AMBER force field J. Comput. Chem. 24, 1016-1025 10.1002/jcc.10262
    • (2003) J. Comput. Chem. , vol.24 , pp. 1016-1025
    • Meagher, K.L.1    Redman, L.T.2    Carlson, H.A.3
  • 37
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P., Ciccotti, G., and Berendsen, H. J. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23, 327-341 10.1016/0021-9991(77)90098-5
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.3
  • 38
    • 33748460871 scopus 로고    scopus 로고
    • Imaging the migration pathways for O 2, CO, NO, and Xe inside myoglobin
    • Cohen, J., Arkhipov, A., Braun, R., and Schulten, K. (2006) Imaging the migration pathways for O 2, CO, NO, and Xe inside myoglobin Biophys. J. 91, 1844-1857 10.1529/biophysj.106.085746
    • (2006) Biophys. J. , vol.91 , pp. 1844-1857
    • Cohen, J.1    Arkhipov, A.2    Braun, R.3    Schulten, K.4
  • 39
    • 47049083320 scopus 로고    scopus 로고
    • Finding gas migration pathways in proteins using implicit ligand sampling
    • Cohen, J., Olsen, K. W., and Schulten, K. (2008) Finding gas migration pathways in proteins using implicit ligand sampling Methods Enzymol. 437, 439-457 10.1016/S0076-6879(07)37022-5
    • (2008) Methods Enzymol. , vol.437 , pp. 439-457
    • Cohen, J.1    Olsen, K.W.2    Schulten, K.3
  • 42
  • 43
    • 79958242994 scopus 로고    scopus 로고
    • Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins
    • Forti, F., Boechi, L., Estrin, D. A., and Marti, M. A. (2011) Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins J. Comput. Chem. 32, 2219-2231 10.1002/jcc.21805
    • (2011) J. Comput. Chem. , vol.32 , pp. 2219-2231
    • Forti, F.1    Boechi, L.2    Estrin, D.A.3    Marti, M.A.4
  • 45
    • 18744400238 scopus 로고    scopus 로고
    • Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase
    • Crespo, A., Martí, M. A., Estrin, D. A., and Roitberg, A. E. (2005) Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase J. Am. Chem. Soc. 127, 6940-6941 10.1021/ja0452830
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 6940-6941
    • Crespo, A.1    Martí, M.A.2    Estrin, D.A.3    Roitberg, A.E.4
  • 46
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. (1997) Nonequilibrium equality for free energy differences Phys. Rev. Lett. 78, 2690 10.1103/PhysRevLett.78.2690
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690
    • Jarzynski, C.1
  • 47
    • 51649087455 scopus 로고    scopus 로고
    • Dynamical characterization of the heme NO oxygen binding (HNOX) domain. Insight into soluble guanylate cyclase allosteric transition†
    • Capece, L., Estrin, D. A., and Marti, M. A. (2008) Dynamical characterization of the heme NO oxygen binding (HNOX) domain. Insight into soluble guanylate cyclase allosteric transition† Biochemistry 47, 9416-9427 10.1021/bi800682k
    • (2008) Biochemistry , vol.47 , pp. 9416-9427
    • Capece, L.1    Estrin, D.A.2    Marti, M.A.3
  • 48
    • 84926371613 scopus 로고    scopus 로고
    • Protein topology determines cysteine oxidation fate: The case of sulfenyl amide formation among protein families
    • Defelipe, L. A., Lanzarotti, E., Gauto, D., Marti, M. A., and Turjanski, A. G. (2015) Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families PLoS Comput. Biol. 11, e1004051 10.1371/journal.pcbi.1004051
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004051
    • Defelipe, L.A.1    Lanzarotti, E.2    Gauto, D.3    Marti, M.A.4    Turjanski, A.G.5
  • 49
    • 33748269730 scopus 로고    scopus 로고
    • Free energy calculations with non-equilibrium methods: Applications of the Jarzynski relationship
    • Xiong, H., Crespo, A., Marti, M., Estrin, D., and Roitberg, A. E. (2006) Free energy calculations with non-equilibrium methods: applications of the Jarzynski relationship Theor. Chem. Acc. 116, 338-346 10.1007/s00214-005-0072-2
    • (2006) Theor. Chem. Acc. , vol.116 , pp. 338-346
    • Xiong, H.1    Crespo, A.2    Marti, M.3    Estrin, D.4    Roitberg, A.E.5
  • 50
    • 23044445202 scopus 로고    scopus 로고
    • Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights
    • Krajewski, W. W., Jones, T. A., and Mowbray, S. L. (2005) Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights Proc. Natl. Acad. Sci. U. S. A. 102, 10499-10504 10.1073/pnas.0502248102
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 10499-10504
    • Krajewski, W.W.1    Jones, T.A.2    Mowbray, S.L.3
  • 51
    • 0030671445 scopus 로고    scopus 로고
    • Expression, purification, and characterization of recombinant human glutamine synthetase
    • Listrom, D. C., Morizono, H., Rajagopal, S. B., McCann, T. M., Tuchman, M., and Allewell, M. N. (1997) Expression, purification, and characterization of recombinant human glutamine synthetase Biochem. J. 328, 159-163 10.1042/bj3280159
    • (1997) Biochem. J. , vol.328 , pp. 159-163
    • Listrom, D.C.1    Morizono, H.2    Rajagopal, S.B.3    McCann, T.M.4    Tuchman, M.5    Allewell, M.N.6
  • 52
    • 85012045784 scopus 로고    scopus 로고
    • Central Role of Glutamate Metabolism in the Maintenance of Nitrogen Homeostasis in Normal and Hyperammonemic Brain
    • Cooper, A. J. and Jeitner, T. M. (2016) Central Role of Glutamate Metabolism in the Maintenance of Nitrogen Homeostasis in Normal and Hyperammonemic Brain Biomolecules 6, 16 10.3390/biom6020016
    • (2016) Biomolecules , vol.6 , pp. 16
    • Cooper, A.J.1    Jeitner, T.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.