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Abstract:

Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of QM/MM methods for the study of reaction mechanisms is experiencing a continuous growth. Glycosyltransferases (GTs) catalyze the formation of glycosidic bonds, and are important for many biotechnological purposes, including drug targeting. Their reaction product may result with only one of the two possible stereochemical outcomes for the reacting anomeric center, and therefore, they are classified as either inverting or retaining GTs. While the inverting GT reaction mechanism has been widely studied, the retaining GT mechanism has always been controversial and several questions remain open to this day. In this work, we take advantage of our recent GPU implementation of a pure QM(DFT-PBE)/MM approach to explore the reaction and inhibition mechanism of MshA, a key retaining GT responsible for the first step of mycothiol biosynthesis, a low weight thiol compound found in pathogens like Mycobacterium tuberculosis that is essential for its survival under oxidative stress conditions. Our results show that the reaction proceeds via a front-side SNi-like concerted reaction mechanism (DNAN in IUPAC nomenclature) and has a 17.5 kcal/mol free energy barrier, which is in remarkable agreement with experimental data. Detailed analysis shows that the key reaction step is the diphosphate leaving group dissociation, leading to an oxocarbenium-ion-like transition state. In contrast, fluorinated substrate analogues increase the reaction barrier significantly, rendering the enzyme effectively inactive. Detailed analysis of the electronic structure along the reaction suggests that this particular inhibition mechanism is associated with fluorine's high electronegative nature, which hinders phosphate release and proper stabilization of the transition state. © 2016 American Chemical Society.

Registro:

Documento: Artículo
Título:Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis
Autor:Capurro, J.I.B.; Hopkins, C.W.; Sottile, G.P.; González Lebrero, M.C.; Roitberg, A.E.; Marti, M.A.
Filiación:Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, C1428EGA, Argentina
Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, C1428EGA, Argentina
Department of Physics, University of Florida, Gainesville, FL 32611, United States
Departamento de Ciencia y Tecnología, Universidad Nac+ional de Quilmes, Sáenz Peña 352, Bernal, B1876BXD, Argentina
Departamento de Quimica Inorgańica, Anlitica y Quiḿica Fiśica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, C1428EGA, Argentina
Insituto de Quimica Inorgańica, Materiales Ambiente y Energiá(INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, C1428EGA, Argentina
Department of Chemistry, University of Florida, Gainesville, FL 32611, United States
Palabras clave:Biosynthesis; Electronic structure; Enzymes; Free energy; Biochemical research; Concerted reactions; Enzymatic reaction; Glycosyl transferase; Glycosyltransferases; Inhibition mechanisms; Mycobacterium tuberculosis; Reaction mechanism; Biochemistry; amidase; bacterial protein; cysteine; glycopeptide; glycosyltransferase; inositol; metal; mycothiol; N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase; antagonists and inhibitors; biocatalysis; biosynthesis; chemistry; metabolism; Mycobacterium tuberculosis; quantum theory; Amidohydrolases; Bacterial Proteins; Biocatalysis; Cysteine; Glycopeptides; Glycosyltransferases; Inositol; Metals; Mycobacterium tuberculosis; Quantum Theory
Año:2017
Volumen:121
Número:3
Página de inicio:471
Página de fin:478
DOI: http://dx.doi.org/10.1021/acs.jpcb.6b10130
Título revista:Journal of Physical Chemistry B
Título revista abreviado:J Phys Chem B
ISSN:15206106
CODEN:JPCBF
CAS:amidase, 9012-56-0; cysteine, 4371-52-2, 52-89-1, 52-90-4; glycosyltransferase, 9033-07-2; inositol, 55608-27-0, 6917-35-7, 87-89-8; Amidohydrolases; Bacterial Proteins; Cysteine; Glycopeptides; Glycosyltransferases; Inositol; Metals; mycothiol; N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v121_n3_p471_Capurro

Referencias:

  • Lairson, L.L., Henrissat, B., Davies, G.J., Withers, S.G., Glycosyltransferases: Structures, functions, and mechanisms (2008) Annu. Rev. Biochem., 77, pp. 521-555
  • Tvaroška, I., Structural insights into the catalytic mechanism and transition state of glycosyltransferases using ab initio molecular modeling (2005) Trends Glycosci. Glycotechnol., 17, pp. 177-190
  • Kozmon, S., Tvaroška, I., Catalytic mechanism of glycosyltransferases: Hybrid quantum mechanical/molecular mechanical study of the Inverting N-Acetylglucosaminyltransferase i (2006) J. Am. Chem. Soc., 128, pp. 16921-16927
  • Krupicka, M., Tvaroška, I., Hybrid quantum mechanical/ molecular mechanical investigation of the β-1,4-galactosyltransferase-i mechanism (2009) J. Phys. Chem. B, 113, pp. 11314-11319
  • Tvaroška, I., Kozmon, S., Wimmerová, M., Koča, J., Substrate-assisted catalytic mechanism of o-glcnac transferase discovered by quantum mechanics/molecular mechanics investigation (2012) J. Am. Chem. Soc., 134, pp. 15563-15571
  • Tvaroška, I., Kozmon, S., Wimmerová, M., Koča, A., QM/MM investigation of the catalytic mechanism of metal-ion-independent core 2 β1,6-N-Acetylglucosaminyltransferase (2013) Chem. - Eur. J., 19, pp. 8153-8162
  • Kumari, M., Kozmon, S., Kulhánek, P., Štepán, J., Tvaroška, I., Koča, J., Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study (2015) J. Phys. Chem. B, 119, pp. 4371-4381
  • Cowdrey, W.A., Hughes, E.D., Ingold, C.K., Masterman, S., Scott, A.D., Reaction kinetics and the walden inversion. Part VI. Relation of steric orientation to mechanism in substitutions involving halogen atoms and simple or substituted hydroxyl groups (1937) J. Chem. Soc., pp. 1252-1271
  • Sinnott, M.L., Jencks, W.P., Solvolysis of D-glucopyranosyl derivatives in mixtures of ethanol and 2,2,2-trifluoroethanol (1980) J. Am. Chem. Soc., 102, pp. 2026-2032
  • Klein, H.W., Im, M.J., Palm, D., Mechanism of the phosphorylase reaction (1986) Eur. J. Biochem., 157, pp. 107-114
  • Persson, K., Ly, H.D., Dieckelmann, M., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C., Crystal structure of the retaining galactosyltransferase LgtC from neisseria meningitidis in complex with donor and acceptor sugar analogs (2001) Nat. Struct. Biol., 8, pp. 166-175
  • Errey, J.C., Lee, S.S., Gibson, R.P., Fleites, C.M., Barry, C.S., Jung, P.M.J., O'Sullivan, A.C., Davies, G.J., Mechanistic insight into enzymatic glycosyl transfer with retention of configuration through analysis of glycomimetic inhibitors (2010) Angew. Chem., 122, pp. 1256-1259
  • Raab, M., Kozmon, S., Tvaroška, I., Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior (2005) Carbohydr. Res., 340, pp. 1051-1057
  • Crespo, A., Scherlis, D.A., Martí, M.A., Ordejon, P., Roitberg, A.E., Estrin, D.A., A DFT-Based QM-MM approach designed for the treatment of large molecular systems: Application to chorismate mutase (2003) J. Phys. Chem. B, 107, pp. 13728-13736
  • Crespo, A., Martí, M.A., Roitberg, A.E., Amzel, L.M., Estrin, D.A., The catalytic mechanism of peptidylglycine α-hydroxylating monooxygenase investigated by computer simulation (2006) J. Am. Chem. Soc., 128, pp. 12817-12828
  • Capece, L., Lewis-Ballester, A., Yeh, S.R., Estrin, D.A., Martí, M.A., Complete reaction mechanism of indoleamine 2,3-dioxygenase as revealed by QM/MM simulations (2012) J. Phys. Chem. B, 116, pp. 1401-1413
  • Dumas, V.G., Defelipe, L.A., Petruk, A.A., Turjanski, A.G., Martí, M.A., QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential cytochrome P450 of Mycobacterium tuberculosis (2014) Proteins: Struct., Funct., Genet., 82, pp. 1004-1021
  • Ramírez, C.L., Zeida, A., Jara, G.E., Roitberg, A.E., Martí, M.A., Improving efficiency in SMD simulations through a hybrid differential relaxation algorithm (2014) J. Chem. Theory Comput., 10, pp. 4609-4617
  • Romero, J.M., Martin, M., Ramírez, C.L., Dumas, V.G., Martí, M.A., Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases (2015) Adv. Protein Chem. Struct. Biol., 100, pp. 33-65
  • Nitsche, M.A., Ferreira, M., Mocskos, E.E., González Lebrero, M.C., GPU accelerated implementation of density functional theory for hybrid QM/MM simulations (2014) J. Chem. Theory Comput., 10, pp. 959-967
  • Zeida, A., Babbush, R., Lebrero, M.C., Trujillo, M., Radi, R., Estrin, D.A., Molecular basis of the mechanism of thiol oxidation by hydrogen peroxide in aqueous solution: Challenging the SN2 paradigm (2012) Chem. Res. Toxicol., 25, pp. 741-746
  • Gómez, H., Mendoza, F., Lluch, J.M., Masgrau, L., QM/MM studies reveal how substrate-substrate and enzyme-substrate interactions modulate retaining glycosyltransferases catalysis and mechanism (2015) Adv. Protein Chem. Struct. Biol., 100, pp. 225-254
  • Tvaroška, I., Atomistic insight into the catalytic mechanism of glycosyltransferases by combined Quantum Mechanics/Molecular Mechanics (QM/MM) methods (2015) Carbohydr. Res., 403, pp. 38-47
  • Ardèvol, A., Iglesias-Fernández, J., Rojas-Cervellera, V., Rovira, C., The reaction mechanism of retaining glycosyltransferases (2016) Biochem. Soc. Trans., 44, pp. 51-60
  • Gómez, H., Polyak, I., Thiel, W., Lluch, J.M., Masgrau, L., Retaining glycosyltransferase mechanism studied by QM/MM methods: Lipopolysaccharyl-α-1,4-galactosyltransferase C Transfers α-galactose via an oxocarbenium ion-like transition state (2012) J. Am. Chem. Soc., 134, pp. 4743-4752
  • Ardèvol, A., Rovira, C., The molecular mechanism of enzymatic glycosyl transfer with retention of configuration: Evidence for a short-lived oxocarbenium-like species (2011) Angew. Chem., Int. Ed., 50, pp. 10897-10901
  • Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F., Pinto, B.M., Vocadlo, D.J., Substrate-guided front-face reaction revealed by combined structural snapshots and metadynamics for the polypeptide N-acetylgalactosaminyltransferase 2 (2014) Angew. Chem., Int. Ed., 53, pp. 8206-8210
  • Gómez, H., Rojas, R., Patel, D., Tabak, L.A., Lluch, J.M., Masgrau, L., A computational and experimental study of oglycosylation. Catalysis by human UDP-GalNAc polypeptide: GalNAc transferase-T2 (2014) Org. Biomol. Chem., 12, pp. 2645-2655
  • Trnka, T., Kozmon, S., Tvaroška, I., Koča, J., Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2 (2015) PLoS Comput. Biol., 11 (4), p. e1004061
  • Gómez, H., Lluch, J.M., Masgrau, L., Substrate-assisted and nucleophilically assisted catalysis in bovine α1,3-galactosyltransferase. Mechanistic implications for retaining glycosyltransferases (2013) J. Am. Chem. Soc., 135, pp. 7053-7063
  • Albesa-Jové, D., Mendoza, F., Rodrigo-Unzueta, A., Gomollón-Bel, F., Cifuente, J.O., Urresti, S., Comino, N., Lluch, J.M., A native ternary complex trapped in a crystal reveals the catalytic mechanism of a retaining glycosyltransferase (2015) Angew. Chem., Int. Ed., 54, pp. 9898-9902
  • Mendoza, F., Gómez, H., Lluch, J.M., Masgrau, L., α1,4-NAcetylhexosaminyltransferase EXTL2: The missing link for understanding glycosidic bond biosynthesis with retention of configuration (2016) ACS Catal., 6, pp. 2577-2589
  • Bobovská, A., Tvaroška, I., Kóňa, J., A theoretical study on the catalytic mechanism of the retaining α-1,2-mannosyltransferase Kre2p/Mnt1p: The impact of different metal ions on catalysis (2014) Org. Biomol. Chem., 12, pp. 4201-4210
  • Bobovská, A., Tvaroška, I., Kóňa, J., Theoretical study of enzymatic catalysis explains why the trapped covalent intermediate in the E303C mutant of glycosyltransferase GTB was not detected in the wild-type enzyme (2015) Glycobiology, 25, pp. 3-7
  • Vetting, M.W., Frantom, P.A., Blanchard, J.S., Structural and enzymatic analysis of MshA from corynebacterium glutamicum: Substrate-assisted catalysis (2008) J. Biol. Chem., 283, pp. 15834-15844
  • Newton, G.L., Buchmeier, N., Fahey, R.C., Biosynthesis and functions of mycothiol, the unique protective thiol of actinobacteria (2008) Microbiol. Mol. Biol. Rev., 72, pp. 471-494
  • Fan, F., Vetting, M.W., Frantom, P.A., Blanchard, J.S., Structures and mechanisms of the mycothiol biosynthetic enzymes (2009) Curr. Opin. Chem. Biol., 13, pp. 451-459
  • Newton, G.L., Unson, M.D., Anderberg, S.J., Aguilera, J.A., Oh, N.N., DelCardayre, S.B., Av-Gay, Y., Fahey, R.C., Characterization of mycobacterium smegmatis mutants defective in 1-d-myoinosityl-2-amino-2-deoxy-alpha-d-glucopyranoside and mycothiol biosynthesis (1999) Biochem. Biophys. Res. Commun., 255, pp. 239-244
  • Defelipe, L.A., Do Porto, D.F., Pereira Ramos, P.I., Nicolás, M.F., Sosa, E., Radusky, L., Lanzarotti, E., Marti, M.A., A whole genome bioinformatic approach to determine potential latent phase specific targets in mycobacterium tuberculosis (2016) Tuberculosis (Oxford, U. K.), 97, pp. 181-192
  • Frantom, P.A., Coward, J.K., Blanchard, J.S., UDP-(5F)-GlcNAc acts as a slow-binding inhibitor of MshA, a retaining glycosyltransferase (2010) J. Am. Chem. Soc., 132, pp. 6626-6627
  • Eswar, N., Eramian, D., Webb, B., Shen, M.Y., Sali, A., Protein structure modeling with modeller (2008) Methods Mol. Biol., 426, pp. 145-159
  • Gauto, D.F., Petruk, A.A., Modenutti, C.P., Blanco, J.I., Di Lella, S., Martí, M.A., Solvent structure improves docking prediction in lectin-carbohydrate complexes (2013) Glycobiology, 23, pp. 241-258
  • Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., Olson, A.J., AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility (2009) J. Comput. Chem., 30, pp. 2785-2791
  • Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., Simmerling, C., Ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB (2015) J. Chem. Theory Comput., 11, pp. 3696-3713
  • Kirschner, K.N., Yongye, A.B., Tschampel, S.M., Daniels, C.R., Foley, B.L., Woods, R.J., GLYCAM06: A generalizable biomolecular force field (2008) Carbohydrates. J. Comput. Chem., 29, pp. 622-655
  • Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Petersson, G.A., (2009) Gaussian 09, Revision A.1, , Gaussian, Inc.: Wallingford, CT
  • Götz, A.W., Clark, M.A., Walker, R.C., An extensible interface for QM/MM molecular dynamics simulations with amber (2014) J. Comput. Chem., 35, pp. 95-108
  • Valleau, J.P., Torrie, G.M., Modern theoretical chemistry (1977) Statistical Mechanics, Part A, 5. , Berne, B. J., Ed.; Plenum Press: New York
  • Kumar, S., Bouzida, D., Swendsen, R.H., Kollman, P.A., Rosenberg, J.M., The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method (1992) J. Comput. Chem., 13, pp. 1011-1021
  • Walker, R.C., Crowley, M.F., Case, D.A., The implementation of a fast and accurate QM/MM potential method in amber (2008) J. Comput. Chem., 29, pp. 1019-1031
  • De M Seabra, G., Walker, R.C., Elstner, M., Case, D.A., Roitberg, A.E., Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package (2007) J. Phys. Chem. A, 111, pp. 5655-5664
  • Yang, Y., Yu, H., York, D., Elstner, M., Cui, Q., Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization (2008) J. Chem. Theory Comput., 4, pp. 2067-2084
  • Gibson, R.P., Turkenburg, J.P., Charnock, S.J., Lloyd, R., Davies, G.J., Insights into trehalose synthesis provided by the structure of the retaining glucosyltransferase OtsA (2002) Chem. Biol., 9, pp. 1337-1346
  • Lee, S.S., Hong, S.Y., Errey, J.C., Izumi, A., Davies, G.J., Davis, B.G., Mechanistic evidence for a front-side, SNi-Type reaction in a retaining glycosyltransferase (2011) Nat. Chem. Biol., 7, pp. 631-637

Citas:

---------- APA ----------
Capurro, J.I.B., Hopkins, C.W., Sottile, G.P., González Lebrero, M.C., Roitberg, A.E. & Marti, M.A. (2017) . Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis. Journal of Physical Chemistry B, 121(3), 471-478.
http://dx.doi.org/10.1021/acs.jpcb.6b10130
---------- CHICAGO ----------
Capurro, J.I.B., Hopkins, C.W., Sottile, G.P., González Lebrero, M.C., Roitberg, A.E., Marti, M.A. "Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis" . Journal of Physical Chemistry B 121, no. 3 (2017) : 471-478.
http://dx.doi.org/10.1021/acs.jpcb.6b10130
---------- MLA ----------
Capurro, J.I.B., Hopkins, C.W., Sottile, G.P., González Lebrero, M.C., Roitberg, A.E., Marti, M.A. "Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis" . Journal of Physical Chemistry B, vol. 121, no. 3, 2017, pp. 471-478.
http://dx.doi.org/10.1021/acs.jpcb.6b10130
---------- VANCOUVER ----------
Capurro, J.I.B., Hopkins, C.W., Sottile, G.P., González Lebrero, M.C., Roitberg, A.E., Marti, M.A. Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis. J Phys Chem B. 2017;121(3):471-478.
http://dx.doi.org/10.1021/acs.jpcb.6b10130