메뉴 건너뛰기




Volumn 119, Issue 40, 2015, Pages 12838-12845

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; INTEGRAL EQUATIONS; KINETICS; PHOSPHATES; PROTEINS;

EID: 84944065256     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b07238     Document Type: Article
Times cited : (44)

References (46)
  • 1
    • 78649474147 scopus 로고    scopus 로고
    • Ras History: The Saga Continues
    • Cox, A. D.; Der, C. J. Ras History: The Saga Continues Small GTPases 2010, 1, 2-27 10.4161/sgtp.1.1.12178
    • (2010) Small GTPases , vol.1 , pp. 2-27
    • Cox, A.D.1    Der, C.J.2
  • 2
    • 0037805547 scopus 로고    scopus 로고
    • RAS Oncogenes: The First 30 Years
    • Malumbres, M.; Barbacid, M. RAS Oncogenes: The First 30 Years Nat. Rev. Cancer 2003, 3, 459-465 10.1038/nrc1097
    • (2003) Nat. Rev. Cancer , vol.3 , pp. 459-465
    • Malumbres, M.1    Barbacid, M.2
  • 3
    • 0030772378 scopus 로고    scopus 로고
    • The Ras-RasGAP Complex: Structural Basis for GTPase Activation and its Loss in Oncogenic Ras Mutants
    • Scheffzek, K.; Ahmadian, M. R.; Kabsch, W.; Wiesmuller, L.; Lautwein, A.; Schmitz, F.; Wittinghofer, A. The Ras-RasGAP Complex: Structural Basis for GTPase Activation and its Loss in Oncogenic Ras Mutants Science 1997, 277, 333-338 10.1126/science.277.5324.333
    • (1997) Science , vol.277 , pp. 333-338
    • Scheffzek, K.1    Ahmadian, M.R.2    Kabsch, W.3    Wiesmuller, L.4    Lautwein, A.5    Schmitz, F.6    Wittinghofer, A.7
  • 4
    • 33749014394 scopus 로고    scopus 로고
    • A Phosphoryl Transfer Intermediate in the GTPase Reaction of Ras in Complex with its GTPase-Activating Protein
    • Kötting, C.; Blessenohl, M.; Suveyzdis, Y.; Goody, R. S.; Wittinghofer, A.; Gerwert, K. A Phosphoryl Transfer Intermediate in the GTPase Reaction of Ras in Complex with its GTPase-Activating Protein Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 13911-13916 10.1073/pnas.0604128103
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 13911-13916
    • Kötting, C.1    Blessenohl, M.2    Suveyzdis, Y.3    Goody, R.S.4    Wittinghofer, A.5    Gerwert, K.6
  • 5
    • 44049093161 scopus 로고    scopus 로고
    • The GAP Arginine Finger Movement into the Catalytic Site of Ras Increases the Activation Entropy
    • Kötting, C.; Kallenbach, A.; Suveyzdis, Y.; Wittinghofer, A.; Gerwert, K. The GAP Arginine Finger Movement into the Catalytic Site of Ras Increases the Activation Entropy Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 6260-6265 10.1073/pnas.0712095105
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 6260-6265
    • Kötting, C.1    Kallenbach, A.2    Suveyzdis, Y.3    Wittinghofer, A.4    Gerwert, K.5
  • 6
    • 84866534653 scopus 로고    scopus 로고
    • Ras and GTPase-Activating Protein (GAP) Drive GTP into a Precatalytic State as Revealed by Combining FTIR and Biomolecular Simulations
    • Rudack, T.; Xia, F.; Schlitter, J.; Kötting, C.; Gerwert, K. Ras and GTPase-Activating Protein (GAP) Drive GTP into a Precatalytic State as Revealed by Combining FTIR and Biomolecular Simulations Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 15295-15300 10.1073/pnas.1204333109
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 15295-15300
    • Rudack, T.1    Xia, F.2    Schlitter, J.3    Kötting, C.4    Gerwert, K.5
  • 7
    • 84870903225 scopus 로고    scopus 로고
    • (-)-Guanosine Diphosphate Intermediate in Ras-GAP Decoded from FTIR Experiments by Biomolecular Simulations
    • (-)-Guanosine Diphosphate Intermediate in Ras-GAP Decoded from FTIR Experiments by Biomolecular Simulations J. Am. Chem. Soc. 2012, 134, 20041-20044 10.1021/ja310496e
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 20041-20044
    • Xia, F.1    Rudack, T.2    Cui, Q.3    Kötting, C.4    Gerwert, K.5
  • 8
    • 0026711081 scopus 로고
    • Mutational and Kinetic Analyses of the GTPase-Activating Protein (GAP)-p21 Interaction: The C-Terminal Domain of GAP is not Sufficient for Full Activity
    • Gideon, P.; John, J.; Frech, M.; Lautwein, A.; Clark, R.; Scheffler, J. E.; Wittinghofer, A. Mutational and Kinetic Analyses of the GTPase-Activating Protein (GAP)-p21 Interaction: The C-Terminal Domain of GAP is not Sufficient for Full Activity Mol. Cell. Biol. 1992, 12, 2050-2056
    • (1992) Mol. Cell. Biol. , vol.12 , pp. 2050-2056
    • Gideon, P.1    John, J.2    Frech, M.3    Lautwein, A.4    Clark, R.5    Scheffler, J.E.6    Wittinghofer, A.7
  • 9
    • 0028925947 scopus 로고
    • Substrate-Assisted Catalysis as a Mechanism for GTP Hydrolysis of p21ras and other GTP-Binding Proteins
    • Schweins, T.; Geyer, M.; Scheffzek, K.; Warshel, A.; Kalbitzer, H. R.; Wittinghofer, A. Substrate-Assisted Catalysis as a Mechanism for GTP Hydrolysis of p21ras and other GTP-Binding Proteins Nat. Struct. Biol. 1995, 2, 36-44 10.1038/nsb0195-36
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 36-44
    • Schweins, T.1    Geyer, M.2    Scheffzek, K.3    Warshel, A.4    Kalbitzer, H.R.5    Wittinghofer, A.6
  • 10
    • 0028789134 scopus 로고
    • Kinetics of Inorganic Phosphate Release during the Interaction of p21ras with the GTPases-Activating Proteins, p120-GAP and Neurofibromin
    • Nixon, A. E.; Brune, M.; Lowe, P. N.; Webb, M. R. Kinetics of Inorganic Phosphate Release during the Interaction of p21ras with the GTPases-Activating Proteins, p120-GAP and Neurofibromin Biochemistry 1995, 34, 15592-15598 10.1021/bi00047a026
    • (1995) Biochemistry , vol.34 , pp. 15592-15598
    • Nixon, A.E.1    Brune, M.2    Lowe, P.N.3    Webb, M.R.4
  • 11
    • 0037426364 scopus 로고    scopus 로고
    • The Mechanism of Ras GTPase Activation by Neurofibromin
    • Phillips, R. A.; Hunter, J. L.; Eccleston, J. F.; Webb, M. R. The Mechanism of Ras GTPase Activation by Neurofibromin Biochemistry 2003, 42, 3956-3965 10.1021/bi027316z
    • (2003) Biochemistry , vol.42 , pp. 3956-3965
    • Phillips, R.A.1    Hunter, J.L.2    Eccleston, J.F.3    Webb, M.R.4
  • 12
    • 84888586550 scopus 로고    scopus 로고
    • Kinetic Mechanisms of Mutation-Dependent Harvey Ras Activation and their Relevance for the Development of Costello Syndrome
    • Wey, M.; Lee, J.; Jeong, S. S.; Kim, J.; Heo, J. Kinetic Mechanisms of Mutation-Dependent Harvey Ras Activation and their Relevance for the Development of Costello Syndrome Biochemistry 2013, 52, 8465-8479 10.1021/bi400679q
    • (2013) Biochemistry , vol.52 , pp. 8465-8479
    • Wey, M.1    Lee, J.2    Jeong, S.S.3    Kim, J.4    Heo, J.5
  • 13
    • 0017100947 scopus 로고
    • Theoretical Studies of Enzymic Reactions: Dielectric Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme
    • Warshel, A.; Levitt, M. Theoretical Studies of Enzymic Reactions: Dielectric Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme J. Mol. Biol. 1976, 103, 227-249 10.1016/0022-2836(76)90311-9
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 14
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM Methods for Biomolecular Systems
    • Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems Angew. Chem., Int. Ed. 2009, 48, 1198-229 10.1002/anie.200802019
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 1198-1229
    • Senn, H.M.1    Thiel, W.2
  • 15
    • 84949115336 scopus 로고    scopus 로고
    • Using Quantum Mechanical Approaches to Study Biological Systems
    • Merz, K. M., Jr. Using Quantum Mechanical Approaches to Study Biological Systems Acc. Chem. Res. 2014, 47, 2804-2811 10.1021/ar5001023
    • (2014) Acc. Chem. Res. , vol.47 , pp. 2804-2811
    • Merz, Jr.K.M.1
  • 16
    • 84876719258 scopus 로고    scopus 로고
    • Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology
    • van der Kamp, M. V.; Mulholland, A. J. Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology Biochemistry 2013, 52, 2708-2728 10.1021/bi400215w
    • (2013) Biochemistry , vol.52 , pp. 2708-2728
    • Van Der Kamp, M.V.1    Mulholland, A.J.2
  • 17
    • 0034663856 scopus 로고    scopus 로고
    • How Does GAP Catalyze the GTP Reaction of Ras? A Computer Simulation Study
    • Glennon, T. M.; Villa, J.; Warshel, A. How Does GAP Catalyze the GTP Reaction of Ras? A Computer Simulation Study Biochemistry 2000, 39, 9641-9651 10.1021/bi000640e
    • (2000) Biochemistry , vol.39 , pp. 9641-9651
    • Glennon, T.M.1    Villa, J.2    Warshel, A.3
  • 18
    • 1442324695 scopus 로고    scopus 로고
    • Why Does the Ras Switch Break by Oncogenic Mutations?
    • Shurki, A.; Warshel, A. Why Does the Ras Switch Break by Oncogenic Mutations? Proteins: Struct., Funct., Genet. 2004, 55, 1-10 10.1002/prot.20004
    • (2004) Proteins: Struct., Funct., Genet. , vol.55 , pp. 1-10
    • Shurki, A.1    Warshel, A.2
  • 19
    • 84890841823 scopus 로고    scopus 로고
    • Quantitative Exploration of the Molecular Origin of the Activation of GTPase
    • Prasad, B. R.; Plotnikov, N. V.; Lameira, J.; Warshel, A. Quantitative Exploration of the Molecular Origin of the Activation of GTPase Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 20509-20514 10.1073/pnas.1319854110
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 20509-20514
    • Prasad, B.R.1    Plotnikov, N.V.2    Lameira, J.3    Warshel, A.4
  • 20
    • 36549014517 scopus 로고    scopus 로고
    • Role of the Arginine Finger in Ras.RasGAP Revealed by QM/MM Calculations
    • te Heesen, H.; Gerwert, K.; Schlitter, J. Role of the Arginine Finger in Ras.RasGAP Revealed by QM/MM Calculations FEBS Lett. 2007, 581, 5677-5684 10.1016/j.febslet.2007.11.026
    • (2007) FEBS Lett. , vol.581 , pp. 5677-5684
    • Te Heesen, H.1    Gerwert, K.2    Schlitter, J.3
  • 21
    • 82655179943 scopus 로고    scopus 로고
    • The Specific Vibrational Modes of GTP in Solution and Bound to Ras: A Detailed Theoretical Analysis by QM/MM Simulations
    • Xia, F.; Rudack, T.; Kötting, C.; Schlitter, J.; Gerwert, K. The Specific Vibrational Modes of GTP in Solution and Bound to Ras: A Detailed Theoretical Analysis by QM/MM Simulations Phys. Chem. Chem. Phys. 2011, 13, 21451-21460 10.1039/c1cp22741f
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 21451-21460
    • Xia, F.1    Rudack, T.2    Kötting, C.3    Schlitter, J.4    Gerwert, K.5
  • 22
    • 84864759029 scopus 로고    scopus 로고
    • The role of magnesium for Geometry and Charge in GTP Hydrolysis, Revealed by Quantum Mechanics/Molecular Mechanics Simulations
    • Rudack, T.; Xia, F.; Schlitter, J.; Kötting, C.; Gerwert, K. The role of magnesium for Geometry and Charge in GTP Hydrolysis, Revealed by Quantum Mechanics/Molecular Mechanics Simulations Biophys. J. 2012, 103, 293-302 10.1016/j.bpj.2012.06.015
    • (2012) Biophys. J. , vol.103 , pp. 293-302
    • Rudack, T.1    Xia, F.2    Schlitter, J.3    Kötting, C.4    Gerwert, K.5
  • 26
    • 33845985649 scopus 로고    scopus 로고
    • Mechanisms of Guanosine Triphosphate Hydrolysis by Ras and Ras-GAP Proteins as Rationalized by Ab Initio QM/MM Simulations
    • Grigorenko, B. L.; Nemukhin, A. V.; Shadrina, M. S.; Topol, I. A.; Burt, S. K. Mechanisms of Guanosine Triphosphate Hydrolysis by Ras and Ras-GAP Proteins as Rationalized by Ab Initio QM/MM Simulations Proteins: Struct., Funct., Genet. 2007, 66, 456-466 10.1002/prot.21228
    • (2007) Proteins: Struct., Funct., Genet. , vol.66 , pp. 456-466
    • Grigorenko, B.L.1    Nemukhin, A.V.2    Shadrina, M.S.3    Topol, I.A.4    Burt, S.K.5
  • 27
    • 84910635300 scopus 로고    scopus 로고
    • Modeling the Role of G12V and G13V Ras Mutations in the RasGAP Catalyzed Hydrolysis Reaction of Guanosine Triphosphate
    • Khrenova, M. G.; Mironov, V. A.; Grigorenko, B. L.; Nemukhin, A. V. Modeling the Role of G12V and G13V Ras Mutations in the RasGAP Catalyzed Hydrolysis Reaction of Guanosine Triphosphate Biochemistry 2014, 53, 7093-7099 10.1021/bi5011333
    • (2014) Biochemistry , vol.53 , pp. 7093-7099
    • Khrenova, M.G.1    Mironov, V.A.2    Grigorenko, B.L.3    Nemukhin, A.V.4
  • 28
    • 84929654989 scopus 로고    scopus 로고
    • Computational Characterization of the Chemical Step in the GTP Hydrolysis by Ras-GAP for the Wild-Type and G13V Mutated Ras
    • Mironov, V. A.; Khrenova, M. G.; Lychko, L. A.; Nemukhin, A. V. Computational Characterization of the Chemical Step in the GTP Hydrolysis by Ras-GAP for the Wild-Type and G13V Mutated Ras Proteins: Struct., Funct., Genet. 2015, 83, 1046-1053 10.1002/prot.24802
    • (2015) Proteins: Struct., Funct., Genet. , vol.83 , pp. 1046-1053
    • Mironov, V.A.1    Khrenova, M.G.2    Lychko, L.A.3    Nemukhin, A.V.4
  • 29
    • 84905822657 scopus 로고    scopus 로고
    • Overview of Simulation Studies on the Enzymatic Activity and Conformational Dynamics of the GTPase Ras
    • Prakash, P.; Gorfe, A. A. Overview of Simulation Studies on the Enzymatic Activity and Conformational Dynamics of the GTPase Ras Mol. Simul. 2014, 40, 839-847 10.1080/08927022.2014.895000
    • (2014) Mol. Simul. , vol.40 , pp. 839-847
    • Prakash, P.1    Gorfe, A.A.2
  • 31
    • 84921370433 scopus 로고    scopus 로고
    • What Vibrations Tell Us about GTPases
    • Kötting, C.; Gerwert, K. What Vibrations Tell Us about GTPases Biol. Chem. 2015, 396, 131-144 10.1515/hsz-2014-0219
    • (2015) Biol. Chem. , vol.396 , pp. 131-144
    • Kötting, C.1    Gerwert, K.2
  • 33
    • 0001475454 scopus 로고    scopus 로고
    • Toward Reliable Density Functionals without Adjustable Parameters: The PBE0Model
    • Adamo, C.; Barone, V. Toward Reliable Density Functionals without Adjustable Parameters: The PBE0Model J. Chem. Phys. 1999, 110, 6158-6170 10.1063/1.478522
    • (1999) J. Chem. Phys. , vol.110 , pp. 6158-6170
    • Adamo, C.1    Barone, V.2
  • 34
    • 77951680464 scopus 로고    scopus 로고
    • A Consistent and Accurate Ab Initio Parameterization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu
    • Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parameterization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu J. Chem. Phys. 2010, 132, 154104 10.1063/1.3382344
    • (2010) J. Chem. Phys. , vol.132 , pp. 154104
    • Grimme, S.1    Antony, J.2    Ehrlich, S.3    Krieg, H.4
  • 38
    • 0033571343 scopus 로고    scopus 로고
    • The Pre-Hydrolysis State of p21(Ras) in Complex with GTP: New Insights into the Role of Water Molecules in the GTP Hydrolysis Reaction of Ras-like Proteins
    • Scheidig, A. J.; Burmester, C.; Goody, R. S. The Pre-Hydrolysis State of p21(Ras) in Complex with GTP: New Insights into the Role of Water Molecules in the GTP Hydrolysis Reaction of Ras-like Proteins Structure 1999, 7, 1311-1324 10.1016/S0969-2126(00)80021-0
    • (1999) Structure , vol.7 , pp. 1311-1324
    • Scheidig, A.J.1    Burmester, C.2    Goody, R.S.3
  • 39
    • 65349110014 scopus 로고    scopus 로고
    • QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena?
    • Gleeson, M. P.; Gleeson, D. QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? J. Chem. Inf. Model. 2009, 49, 670-677 10.1021/ci800419j
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 670-677
    • Gleeson, M.P.1    Gleeson, D.2
  • 40
    • 67349218843 scopus 로고    scopus 로고
    • Application of the PM6Method to Modeling Proteins
    • Stewart, J. J. Application of the PM6Method to Modeling Proteins J. Mol. Model. 2009, 15, 765-808 10.1007/s00894-008-0420-y
    • (2009) J. Mol. Model. , vol.15 , pp. 765-808
    • Stewart, J.J.1
  • 41
    • 84940571544 scopus 로고    scopus 로고
    • Enhanced Semiempirical QM Methods for Biomolecular Interactions
    • Yilmazer, N. D.; Korth, M. Enhanced Semiempirical QM Methods for Biomolecular Interactions Comput. Struct. Biotechnol. J. 2015, 13, 169-175 10.1016/j.csbj.2015.02.004
    • (2015) Comput. Struct. Biotechnol. J. , vol.13 , pp. 169-175
    • Yilmazer, N.D.1    Korth, M.2
  • 42
    • 0028027596 scopus 로고
    • GTPase Mechanism of G Proteins from the 1.7-A Crystal Structure of Transducin Alpha-GDP-AIF-4
    • Sondek, J.; Lambright, D. G.; Noel, J. P.; Hamm, H. E.; Sigler, P. B. GTPase Mechanism of G Proteins from the 1.7-A Crystal Structure of Transducin Alpha-GDP-AIF-4 Nature 1994, 372, 276-279 10.1038/372276a0
    • (1994) Nature , vol.372 , pp. 276-279
    • Sondek, J.1    Lambright, D.G.2    Noel, J.P.3    Hamm, H.E.4    Sigler, P.B.5
  • 43
    • 41649087361 scopus 로고    scopus 로고
    • The Retinitis Pigmentosa 2 Gene Product Is a GTPase Activating Protein for Arf-like 3
    • Veltel, S.; Gasper, R.; Eisenacher, E.; Wittinghofer, A. The Retinitis Pigmentosa 2 Gene Product Is a GTPase Activating Protein for Arf-like 3 Nat. Struct. Mol. Biol. 2008, 15, 373-380 10.1038/nsmb.1396
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 373-380
    • Veltel, S.1    Gasper, R.2    Eisenacher, E.3    Wittinghofer, A.4
  • 44
    • 0027405662 scopus 로고
    • Probing the Structure and Mechanism of Ras Protein with an Expanded Genetic Code
    • Chung, H.-H.; Benson, D. R.; Schultz, P. G. Probing the Structure and Mechanism of Ras Protein with an Expanded Genetic Code Science 1993, 259, 806-809 10.1126/science.8430333
    • (1993) Science , vol.259 , pp. 806-809
    • Chung, H.-H.1    Benson, D.R.2    Schultz, P.G.3
  • 45
    • 84944449188 scopus 로고    scopus 로고
    • Why Does Mutation of Gln61 in Ras by the Nitro Analog NGln Maintain Activity of Ras-GAP in Hydrolysis of Guanosine Triphosphate?
    • in press. DOI
    • Khrenova, M. G.; Grigorenko, B. L.; Mironov, V. A.; Nemukhin, A. V. Why Does Mutation of Gln61 in Ras by the Nitro Analog NGln Maintain Activity of Ras-GAP in Hydrolysis of Guanosine Triphosphate? Proteins: Struct., Funct., Genet., in press. DOI: 10.1002/prot.24927
    • Proteins: Struct., Funct., Genet.
    • Khrenova, M.G.1    Grigorenko, B.L.2    Mironov, V.A.3    Nemukhin, A.V.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.