Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis

FEBS Journal

Volumn 280, Issue 1, 2013, Pages 115-126

  Novikov, Fedor N ^a   Stroganov, Oleg V ^a   Khaliullin, Ilyas G ^a   Panin, Nikolay V ^a   Shapovalova, Irina V ^a   Chilov, Ghermes G ^a   Švedas, Vytas K ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

catalytic mechanism; molecular docking; molecular dynamics; penicillin acylase; substrate binding

Indexed keywords

PENICILLIN AMIDASE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME DEGRADATION; ENZYME LOCALIZATION; ENZYME SUBSTRATE COMPLEX; ENZYME SYNTHESIS; HYDROGEN BOND; HYDROPHOBICITY; MICHAELIS CONSTANT; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; BIOCATALYSIS; CATALYTIC DOMAIN; ESCHERICHIA COLI PROTEINS; HYDROGEN BONDING; KINETICS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PENICILLIN AMIDASE; PROTEIN BINDING; THERMODYNAMICS;

EID: 84872008300     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.12054     Document Type: Article

References (30)

1. Svedas VK, Savchenko MV, Beltser AI, &, Guranda DF, (1996) Enantioselective penicillin acylase-catalyzed reactions. Factors governing substrate and stereospecificity of the enzyme. Ann N-Y Acad Sci 799, 659-669.
2. Duggleby HJ, Tolley SP, Hill CP, Dodson EJ, Dodson G, &, Moody PC, (1995) Penicillin acylase has a single-amino-acid catalytic centre. Nature 373, 264-268.
3. Brannigan JA, Dodson G, Duggleby HJ, Moody PC, Smith JL, Tomchick DR, &, Murzin AG, (1995) A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature 378, 416-419.
4. Alkema WBL, Hensgens CMH, Kroezinga EH, de Vries E, Floris R, van der Laan J-M, Dijkstra BW, &, Janssen DB, (2000) Characterization of the β-lactam binding site of penicillin acylase of Escherichia coli by structural and site-directed mutagenesis studies. Protein Eng 13, 857-863.
5. McVey CE, Walsh MA, Dodson GG, Wilson KS, &, Brannigan JA, (2001) Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism. J Mol Biol 313, 139-150.
6. Chilov GG, Stroganov OV, &, Svedas VK, (2008) Molecular modeling studies of substrate binding by penicillin acylase. Biochemistry (Moscow) 73, 56-64.
7. Alkema WBL, Prins AK, de Vries E, &, Janssen DB, (2002) Role of αArg145 and βArg263 in the active site of penicillin acylase of Escherichia coli. Biochem J 365, 303-309.
8. Done SH, Brannigan JA, Moody PC, &, Hubbard RE, (1998) Ligand induced conformational change in penicillin acylase. J Mol Biol 284, 463-475.
9. Hu H, Elstner M, &, Hermans J, (2003) Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins Struct Funct Genet 50, 451-463.
10. Simmerling C, Strockbine B, &, Roitberg AE, (2002) All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 124, 11258-11259.
11. Garcia AE, &, Sanbonmatsu KY, (2002) α-Helical stabilization by side chain shielding of backbone hydrogen bonds. PNAS 99, 2782-2787.
12. Berezin IV, Klyosov AA, Nys PS, Savitskaya EM, &, Svedas VK, (1974) Kinetics of penicillin amidase-catalyzed hydrolysis of benzylpenicillin. Antibiotiki (Rus.) 19, 880-887.
13. Svedas V, Guranda D, van Langen L, van Rantwijk F, &, Sheldon R, (1997) Kinetic study of penicillin acylase from Alcaligenes faecalis. FEBS Lett 417, 414-418.
14. 4-tetrahydrophthalate monophenyl esters. J Am Chem Soc 118, 2595-2605.
15. Chilov GG, Sidorova AV, &, Svedas VK, (2007) Quantum chemical studies of the catalytic mechanism of N-terminal nucleophile hydrolase. Biochemistry (Moscow) 72, 495-500.
16. Yasnaya AS, Yamskova OV, Guranda DT, Shcherbakova TA, Tishkov VI, &, Svedas VK, (2008) Cloning of penicillin acylase from Escherichia coli: catalytic properties of recombinant enzymes. Moscow Univ Chem Res Bull (Rus) 49, 127-133.
17. Svedas VK, Margolin AL, Sherstiuk SF, Klyosov AA, &, Berezin IV, (1977) Inactivation of soluble and immobilized penicillin acylase from E. coli by phenylmethylsulfonylfluoride: kinetic analysis and titration of enzyme active sites. Bioorg Khimiya (Rus) 3, 546-553.
18. Berendsen HJC, van der Spoel D, &, van Drunen R, (1995) GROMACS: A message-passing parallel molecular dynamics implementation. Comp Phys Comm 91, 43-56.
19. Lindahl E, Hess B, &, van der Spoel D, (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 8, 306-317.
20. http://www.gromacs.org.
21. Jorgensen WL, &, Tirado-Rives J, (1988) The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110, 1657-1666.
22. Jorgensen WL, Chandrasekhar JD, Madura R, Impey W, &, Klein ML, (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79, 926-935.
23. Feenstra KA, Hess B, &, Berendsen HJC, (1999) Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J Comp Chem 20, 786-798.
24. Hess B, Bekker H, Berendsen HJC, &, Fraaije JGEM, (1997) LINCS: A linear constraint solver for molecular simulations. J Comp Chem 18, 1463-1472.
25. Tironi IG, Sperb R, Smith PE, &, van Gunsteren WF, (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102, 5451-5459.
26. Shmidt MW, Baldringe KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, et al,. (1993) General atomic and molecular electronic structure system. J Comp Chem 14, 1347-1363.
27. Granovsky AA, http://classic.chem.msu.su/gran/gamess/index.html.
28. Bayly CL, Cieplak P, Cornell WD, &, Kollman PA, (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J Phys Chem 97, 10269-10280.
29. Stroganov OV, Chilov GG, &, Svedas VK, (2003) Force field parametrization for 6-aminopenicillanic acid. J Mol Struct (Theochem) 631, 117-125.
30. Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, &, Chilov GG, (2008) Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening. J Chem Inf Model 48, 2371-2385.