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Volumn 8, Issue 11, 2012, Pages 4663-4671

The catalytic machinery of rhomboid proteases: Combined MD and QM simulations

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EID: 84869036564     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct3003767     Document Type: Article
Times cited : (11)

References (52)
  • 1
    • 58549108805 scopus 로고    scopus 로고
    • Rhomboid proteases and their biological functions
    • Freeman, M. Rhomboid proteases and their biological functions Annu. Rev. Genet. 2008, 42, 191-210
    • (2008) Annu. Rev. Genet. , vol.42 , pp. 191-210
    • Freeman, M.1
  • 2
    • 33751246749 scopus 로고    scopus 로고
    • Rhomboid proteins: Conserved membrane proteases with divergent biological functions
    • Urban, S. Rhomboid proteins: conserved membrane proteases with divergent biological functions Genes Dev. 2006, 20, 3054-3068
    • (2006) Genes Dev. , vol.20 , pp. 3054-3068
    • Urban, S.1
  • 3
    • 0035913908 scopus 로고    scopus 로고
    • Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases
    • Urban, S.; Lee, J.R.; Freeman, M. Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases Cell 2001, 107, 173-182
    • (2001) Cell , vol.107 , pp. 173-182
    • Urban, S.1    Lee . J, R.2    Freeman, M.3
  • 4
    • 80054893675 scopus 로고    scopus 로고
    • The rhomboid protease family: A decade of progress on function and mechanism
    • Urban, S.; Dickey, S. W. The rhomboid protease family: a decade of progress on function and mechanism Gen. Biol. 2011, 12, 231
    • (2011) Gen. Biol. , vol.12 , pp. 231
    • Urban, S.1    Dickey, S.W.2
  • 5
    • 14844300797 scopus 로고    scopus 로고
    • Mechanism of intramembrane proteolysis investigated with purified rhomboid proteases
    • Lemberg, M. K.; Menendez, J.; Misik, A.; Garcia, M.; Koth, C. M.; Freeman, M. Mechanism of intramembrane proteolysis investigated with purified rhomboid proteases EMBO J. 2005, 24, 464-472
    • (2005) EMBO J. , vol.24 , pp. 464-472
    • Lemberg, M.K.1    Menendez, J.2    Misik, A.3    Garcia, M.4    Koth, C.M.5    Freeman, M.6
  • 6
    • 13844306483 scopus 로고    scopus 로고
    • Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity
    • Urban, S.; Wolfe, M. S. Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 1883-1888
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 1883-1888
    • Urban, S.1    Wolfe, M.S.2
  • 7
    • 33846543356 scopus 로고    scopus 로고
    • The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis
    • Lemieux, M. J.; Fischer, S. J.; Cherney, M. M.; Bateman, K. S.; James, M. N. G. The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 750-754
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 750-754
    • Lemieux, M.J.1    Fischer, S.J.2    Cherney, M.M.3    Bateman, K.S.4    James, M.N.G.5
  • 9
    • 33750886311 scopus 로고    scopus 로고
    • Crystal structure of a rhomboid family intramembrane protease
    • Wang, Y.; Zhang, Y.; Ha, Y. Crystal structure of a rhomboid family intramembrane protease Nature 2006, 444, 179-183
    • (2006) Nature , vol.444 , pp. 179-183
    • Wang, Y.1    Zhang, Y.2    Ha, Y.3
  • 10
    • 33845365770 scopus 로고    scopus 로고
    • Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry
    • Wu, Z.; Yan, N.; Feng, L.; Yan, H.; Gu, L.; Shi, Y. Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry Nat. Struct. Mol. Biol. 2006, 13, 1084-1091
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 1084-1091
    • Wu, Z.1    Yan, N.2    Feng, L.3    Yan, H.4    Gu, L.5    Shi, Y.6
  • 11
    • 33846275257 scopus 로고    scopus 로고
    • Structural basis for intramembrane proteolysis by rhomboid serine proteases
    • Bibi, E.; Fass, D.; Ben-Shem, A. Structural basis for intramembrane proteolysis by rhomboid serine proteases Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 462-466
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 462-466
    • Bibi, E.1    Fass, D.2    Ben-Shem, A.3
  • 12
    • 33847793631 scopus 로고    scopus 로고
    • Open-cap conformation of intramembrane protease GlpG
    • Ha, Y. Open-cap conformation of intramembrane protease GlpG Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 2098-2102
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 2098-2102
    • Ha, Y.1
  • 13
    • 35748974498 scopus 로고    scopus 로고
    • The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG
    • Wang, Y.; Maegawa, S.; Akiyama, Y.; Ha, Y. The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG J. Mol. Biol. 2007, 374, 1104-1113
    • (2007) J. Mol. Biol. , vol.374 , pp. 1104-1113
    • Wang, Y.1    Maegawa, S.2    Akiyama, Y.3    Ha, Y.4
  • 15
    • 79952316125 scopus 로고    scopus 로고
    • Structure of rhomboid proteases in a lipid environment
    • Vinothkumar, K. R. Structure of rhomboid proteases in a lipid environment J. Mol. Biol. 2011, 407, 232-247
    • (2011) J. Mol. Biol. , vol.407 , pp. 232-247
    • Vinothkumar, K.R.1
  • 16
    • 84856292019 scopus 로고    scopus 로고
    • Catalytic mechanism of rhomboid protease GlpG probed by 3,4-dichloroisocoumarin and diisopropyl fluorophosphonate
    • Xue, Y.; Ha, Y. Catalytic mechanism of rhomboid protease GlpG probed by 3,4-dichloroisocoumarin and diisopropyl fluorophosphonate J. Biol. Chem. 2012, 287, 3099-3107
    • (2012) J. Biol. Chem. , vol.287 , pp. 3099-3107
    • Xue, Y.1    Ha, Y.2
  • 17
    • 84860711067 scopus 로고    scopus 로고
    • Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S subsites
    • Xue, Y.; Chowdhury, S.; Liu, X.; Akiyama, Y.; Ellman, J.; Ha, Y. Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S subsites Biochemistry 2012, 51, 3723-3731
    • (2012) Biochemistry , vol.51 , pp. 3723-3731
    • Xue, Y.1    Chowdhury, S.2    Liu, X.3    Akiyama, Y.4    Ellman, J.5    Ha, Y.6
  • 19
    • 74349127184 scopus 로고    scopus 로고
    • Taking the plunge: Integrating structural, enzymatic and computational insights into a unified model for membrane-immersed rhomboid proteolysis
    • Urban, S. Taking the plunge: integrating structural, enzymatic and computational insights into a unified model for membrane-immersed rhomboid proteolysis Biochem. J. 2010, 425, 501-512
    • (2010) Biochem. J. , vol.425 , pp. 501-512
    • Urban, S.1
  • 20
    • 66249133368 scopus 로고    scopus 로고
    • How intramembrane proteases bury reactions in membrane
    • Erez, E.; Fass, D.; Bibi, E. How intramembrane proteases bury reactions in membrane Nature 2009, 459, 371-378
    • (2009) Nature , vol.459 , pp. 371-378
    • Erez, E.1    Fass, D.2    Bibi, E.3
  • 21
    • 63649088506 scopus 로고    scopus 로고
    • Structure and mechanism of intramembrane protease
    • Ha, Y. Structure and mechanism of intramembrane protease Semin. Cell Dev. Biol. 2009, 20, 240-250
    • (2009) Semin. Cell Dev. Biol. , vol.20 , pp. 240-250
    • Ha, Y.1
  • 22
    • 65249188697 scopus 로고    scopus 로고
    • Intramembrane proteolysis
    • Wolfe, M. S. Intramembrane proteolysis Chem. Rev. 2009, 109, 1599-1612
    • (2009) Chem. Rev. , vol.109 , pp. 1599-1612
    • Wolfe, M.S.1
  • 23
    • 0036882394 scopus 로고    scopus 로고
    • Serine protease mechanism and specificity
    • Hedstrom, L. Serine protease mechanism and specificity Chem. Rev. 2002, 102, 4501-4524
    • (2002) Chem. Rev. , vol.102 , pp. 4501-4524
    • Hedstrom, L.1
  • 24
    • 61549125968 scopus 로고    scopus 로고
    • Rhomboid dynamics and lipid interactions
    • Bondar, A. N.; del Val, C.; White, S. H. Rhomboid dynamics and lipid interactions Structure 2009, 17, 395-405
    • (2009) Structure , vol.17 , pp. 395-405
    • Bondar, A.N.1    Del Val, C.2    White, S.H.3
  • 25
    • 84863534125 scopus 로고    scopus 로고
    • An Internal Water-Retention Site in the Rhomboid Intramembrane Protease GlpG Ensures Catalytic Efficiency
    • Zhou, Y.; Moin, S. M.; Urban, S.; Zhang, Y. An Internal Water-Retention Site in the Rhomboid Intramembrane Protease GlpG Ensures Catalytic Efficiency Structure 2012, 20, 1255-1263
    • (2012) Structure , vol.20 , pp. 1255-1263
    • Zhou, Y.1    Moin, S.M.2    Urban, S.3    Zhang, Y.4
  • 26
    • 84864751064 scopus 로고    scopus 로고
    • Multifaceted substrate capture scheme of a rhomboid protease
    • Reddy, T; Rainey, J. K. Multifaceted substrate capture scheme of a rhomboid protease J. Phys. Chem. B 2012, 116, 8942-8954
    • (2012) J. Phys. Chem. B , vol.116 , pp. 8942-8954
    • Reddy, T.1    Rainey, J.K.2
  • 28
    • 84869052837 scopus 로고    scopus 로고
    • YASARA Structure. (accessed Sept. 2012)
    • YASARA Structure. http://www.yasara.com (accessed Sept. 2012).
  • 29
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
    • Stewart, J. J. P. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements J. Mol. Model. 2007, 13, 1173-1213
    • (2007) J. Mol. Model. , vol.13 , pp. 1173-1213
    • Stewart, J.J.P.1
  • 30
    • 73349120806 scopus 로고    scopus 로고
    • Computational Chemistry: Colorado Springs, CO, (accessed Sept. 2012)
    • Stewart, J. J. P. MOPAC2009; Computational Chemistry: Colorado Springs, CO, 2008. http://OpenMOPAC.net (accessed Sept. 2012).
    • (2008) MOPAC2009
    • Stewart, J.J.P.1
  • 33
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto, S.; Kollman, P. A. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 35
    • 10344223464 scopus 로고    scopus 로고
    • Making optimal use of empirical energy functions: Force field parameterization in crystal space
    • Krieger, E.; Darden, T.; Nabuurs, S.; Finkelstein, A.; Vriend, G. Making optimal use of empirical energy functions: force field parameterization in crystal space Proteins 2004, 57, 678-683
    • (2004) Proteins , vol.57 , pp. 678-683
    • Krieger, E.1    Darden, T.2    Nabuurs, S.3    Finkelstein, A.4    Vriend, G.5
  • 36
    • 34548118300 scopus 로고    scopus 로고
    • The cooperative effect between active site ionized groups and water desolvation controls the alteration of acid/base catalysis in serine proteases
    • Shokhen, M.; Khazanov, N.; Albeck, A. The cooperative effect between active site ionized groups and water desolvation controls the alteration of acid/base catalysis in serine proteases ChemBioChem 2007, 8, 1416-1421
    • (2007) ChemBioChem , vol.8 , pp. 1416-1421
    • Shokhen, M.1    Khazanov, N.2    Albeck, A.3
  • 37
    • 39749176208 scopus 로고    scopus 로고
    • Screening of the active site from water by the incoming ligand triggers catalysis and inhibition in serine proteases
    • Shokhen, M.; Khazanov, N.; Albeck, A. Screening of the active site from water by the incoming ligand triggers catalysis and inhibition in serine proteases Proteins 2008, 70, 1578-1587
    • (2008) Proteins , vol.70 , pp. 1578-1587
    • Shokhen, M.1    Khazanov, N.2    Albeck, A.3
  • 38
    • 70450211370 scopus 로고    scopus 로고
    • Challenging a paradigm: Theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain
    • Shokhen, M.; Khazanov, N.; Albeck, A. Challenging a paradigm: Theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain Proteins 2009, 77, 916-926
    • (2009) Proteins , vol.77 , pp. 916-926
    • Shokhen, M.1    Khazanov, N.2    Albeck, A.3
  • 39
    • 79551493364 scopus 로고    scopus 로고
    • The mechanism of papain inhibition by peptidyl aldehydes
    • Shokhen, M.; Khazanov, N.; Albeck, A. The mechanism of papain inhibition by peptidyl aldehydes Proteins 2011, 79, 975-985
    • (2011) Proteins , vol.79 , pp. 975-985
    • Shokhen, M.1    Khazanov, N.2    Albeck, A.3
  • 40
    • 84961980743 scopus 로고
    • COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient
    • Klamt, A.; Schüümann, G. COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient J. Chem. Soc., Perkin Trans. 2 1993, 799-805
    • (1993) J. Chem. Soc., Perkin Trans. 2 , pp. 799-805
    • Klamt, A.1    Schüümann, G.2
  • 42
    • 0031358013 scopus 로고    scopus 로고
    • Calculation of absolute and relative acidities of substituted imidazoles in aqueous solvent
    • Topol, I. A.; Tawa, G. J.; Burt, S. K.; Rashin, A. A. Calculation of absolute and relative acidities of substituted imidazoles in aqueous solvent J. Phys. Chem. A 1997, 101, 10075-10081
    • (1997) J. Phys. Chem. A , vol.101 , pp. 10075-10081
    • Topol, I.A.1    Tawa, G.J.2    Burt, S.K.3    Rashin, A.A.4
  • 44
    • 34347250499 scopus 로고    scopus 로고
    • Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate
    • Baker, R. P.; Young, K.; Feng, L.; Shi, Y.; Urban, S. Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 8257-8262
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 8257-8262
    • Baker, R.P.1    Young, K.2    Feng, L.3    Shi, Y.4    Urban, S.5
  • 45
    • 0001650759 scopus 로고
    • Theoretical correlation of structure and energetic in the catalytic reaction of trypsin
    • Warshel, A.; Russel, S. Theoretical correlation of structure and energetic in the catalytic reaction of trypsin J. Am. Chem. Soc. 1986, 108, 6569-6579
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 6569-6579
    • Warshel, A.1    Russel, S.2
  • 47
    • 11644294259 scopus 로고    scopus 로고
    • Hybrid ab initio QM/ molecular mechanics calculations of free energy surfaces for enzymatic reactions: The nucleophilic attack in subtilisin
    • Bentzien, J.; Muller, R. P.; Florian, J.; Warshel, A. Hybrid ab initio QM/ molecular mechanics calculations of free energy surfaces for enzymatic reactions: the nucleophilic attack in subtilisin J. Phys. Chem. B. 1998, 102, 2293-2301
    • (1998) J. Phys. Chem. B. , vol.102 , pp. 2293-2301
    • Bentzien, J.1    Muller, R.P.2    Florian, J.3    Warshel, A.4
  • 48
    • 2242428041 scopus 로고    scopus 로고
    • Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: Insights into the active site hydrogen-bonding network
    • Topf, M.; Varnai, P.; Richards, W. G. Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: insights into the active site hydrogen-bonding network J. Am. Chem. Soc. 2002, 124, 14780-14788
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 14780-14788
    • Topf, M.1    Varnai, P.2    Richards, W.G.3
  • 49
    • 0141732211 scopus 로고    scopus 로고
    • Theoretical perspectives on the reaction mechanism of serine proteases: The reaction free energy profiles of the acylation process
    • Kato, S.; Ishida, T. Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process J. Am. Chem. Soc. 2003, 125, 12035-12048
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 12035-12048
    • Kato, S.1    Ishida, T.2
  • 50
    • 3042855462 scopus 로고    scopus 로고
    • Role of Asp102 in the catalytic relay system of serine proteases: A theoretical study
    • Ishida, T.; Kato, S. Role of Asp102 in the catalytic relay system of serine proteases: a theoretical study J. Am. Chem. Soc. 2004, 126, 7111-7118
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 7111-7118
    • Ishida, T.1    Kato, S.2
  • 51
    • 0026525805 scopus 로고
    • Histidine-aromatic interactions in barnase. Elevation of histidine pKa and contribution to protein stability
    • Loewnthal, R.; Sanco, J.; Fersht, A. Histidine-aromatic interactions in barnase. Elevation of histidine pKa and contribution to protein stability J. Mol. Biol. 1992, 224, 759-770
    • (1992) J. Mol. Biol. , vol.224 , pp. 759-770
    • Loewnthal, R.1    Sanco, J.2    Fersht, A.3
  • 52
    • 10644297502 scopus 로고    scopus 로고
    • Interplay between π-π Interactions and H-bonding ability of aromatic nitrogen bases
    • Mignon, P.; Loverix, S.; Greelings, P. Interplay between π-π interactions and H-bonding ability of aromatic nitrogen bases Chem. Phys. Lett. 2005, 401, 40-46
    • (2005) Chem. Phys. Lett. , vol.401 , pp. 40-46
    • Mignon, P.1    Loverix, S.2    Greelings, P.3


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