Dynamic interchange between two protonation states is characteristic of active sites of cholinesterases.
LBHB
QM/MM
biomolecular simulations
cholinesterase
enzymology
free energy profile
proton rearrangements
Journal
Protein science : a publication of the Protein Society
ISSN: 1469-896X
Titre abrégé: Protein Sci
Pays: United States
ID NLM: 9211750
Informations de publication
Date de publication:
Aug 2024
Aug 2024
Historique:
revised:
28
05
2024
received:
22
02
2024
accepted:
19
06
2024
medline:
18
7
2024
pubmed:
18
7
2024
entrez:
18
7
2024
Statut:
ppublish
Résumé
Cholinesterases are well-known and widely studied enzymes crucial to human health and involved in neurology, Alzheimer's, and lipid metabolism. The protonation pattern of active sites of cholinesterases influences all the chemical processes within, including reaction, covalent inhibition by nerve agents, and reactivation. Despite its significance, our comprehension of the fine structure of cholinesterases remains limited. In this study, we employed enhanced-sampling quantum-mechanical/molecular-mechanical calculations to show that cholinesterases predominantly operate as dynamic mixtures of two protonation states. The proton transfer between two non-catalytic glutamate residues follows the Grotthuss mechanism facilitated by a mediator water molecule. We show that this uncovered complexity of active sites presents a challenge for classical molecular dynamics simulations and calls for special treatment. The calculated proton transfer barrier of 1.65 kcal/mol initiates a discussion on the potential existence of two coupled low-barrier hydrogen bonds in the inhibited form of butyrylcholinesterase. These findings expand our understanding of structural features expressed by highly evolved enzymes and guide future advances in cholinesterase-related protein and drug design studies.
Substances chimiques
Protons
0
Butyrylcholinesterase
EC 3.1.1.8
Acetylcholinesterase
EC 3.1.1.7
Cholinesterases
EC 3.1.1.8
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e5100Subventions
Organisme : Russian Science Foundation
ID : 21-74-20113
Informations de copyright
© 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.
Références
Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, et al. GROMACS: high performance molecular simulations through multi‐level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2(September):19–25.
Aho N, Buslaev P, Jansen A, Bauer P, Groenhof G, Hess B. Scalable constant pH molecular dynamics in GROMACS. J Chem Theory Comput. 2022;18(10):6148–6160.
Amitay M, Shurki A. The structure of G117H mutant of butyrylcholinesterase: nerve agents scavenger. Proteins. 2009;77(2):370–377.
Amitay M, Shurki A. Hydrolysis of organophosphate compounds by mutant butyrylcholinesterase: a story of two histidines. Proteins. 2011;79(2):352–364.
Amrein BA, Bauer P, Duarte F, Carlsson ÅJ, Naworyta A, Mowbray SL, et al. Expanding the catalytic triad in epoxide hydrolases and related enzymes. ACS Catal. 2015;5(10):5702–5713.
Barducci A, Bussi G, Parrinello M. Well‐tempered metadynamics: a smoothly converging and tunable free‐energy method. Phys Rev Lett. 2008;100(2):020603.
Belyaeva J, Zlobin A, Maslova V, Golovin A. Modern non‐polarizable force fields diverge in modeling the enzyme‐substrate complex of a canonical serine protease. Phys Chem Chem Phys. 2023;25(8):6352–6361.
Bernetti M, Bussi G. Pressure control using stochastic cell rescaling. J Chem Phys. 2020;153(11):114107.
De Boer D, Nguyen N, Mao J, Moore J, Sorin EJ. A comprehensive review of cholinesterase modeling and simulation. Biomolecules. 2021;11(4):580. https://doi.org/10.3390/biom11040580
Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, et al. Ensemble‐based enzyme design can recapitulate the effects of laboratory directed evolution in silico. Nat Commun. 2020;11(1):4808.
Buslaev P, Aho N, Jansen A, Bauer P, Hess B, Groenhof G. Best practices in constant pH MD simulations: accuracy and sampling. J Chem Theory Comput. 2022;18(10):6134–6147.
Bussi G, Tribello GA. Analyzing and biasing simulations with PLUMED. Methods Mol Biol. 2019;2022:529–578.
Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. J Chem Phys. 2007;126(1):014101.
Caldeweyher E, Ehlert S, Hansen A, Neugebauer H, Spicher S, Bannwarth C, et al. A generally applicable atomic‐charge dependent London dispersion correction. J Chem Phys. 2019;150(15):154122.
Cassone G. Nuclear quantum effects largely influence molecular dissociation and proton transfer in liquid water under an electric field. J Phys Chem Lett. 2020;11(21):8983–8988.
Cheung J, Rudolph MJ, Burshteyn F, Cassidy MS, Gary EN, Love J, et al. Structures of human acetylcholinesterase in complex with pharmacologically important ligands. J Med Chem. 2012;55(22):10282–10286.
Correy GJ, Carr PD, Meirelles T, Mabbitt PD, Fraser NJ, Weik M, et al. Mapping the accessible conformational landscape of an insect carboxylesterase using conformational ensemble analysis and kinetic crystallography. Structure. 2016;24(6):977–987.
Crean RM, Gardner JM, Kamerlin SCL. Harnessing conformational plasticity to generate designer enzymes. J Am Chem Soc. 2020;142(26):11324–11342.
Drago VN, Dajnowicz S, Parks JM, Blakeley MP, Keen DA, Coquelle N, et al. An N⋯H⋯N low‐barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half‐reaction. Chem Sci. 2022;13(34):10057–10065.
Dvir H, Jiang HL, Wong DM, Harel M, Chetrit M, He XC, et al. X‐ray structures of Torpedo Californica acetylcholinesterase complexed with (+)‐huperzine A and (−)‐huperzine B: structural evidence for an active site rearrangement. Biochemistry. 2002;41(35):10810–10818.
Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, et al. OpenMM 7: rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol. 2017;13(7):e1005659.
Franklin MC, Rudolph MJ, Ginter C, Cassidy MS, Cheung J. Structures of paraoxon‐inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer Interface. Proteins. 2016;84(9):1246–1256.
Furtado‐Alle L, Tureck LV, de Oliveira CS, Hortega JVM, Souza RLR. Butyrylcholinesterase and lipid metabolism: possible dual role in metabolic disorders. Chem Biol Interact. 2023;383(September):110680.
Galvelis R, Doerr S, Damas JM, Harvey MJ, De Fabritiis G. A scalable molecular force field parameterization method based on density functional theory and quantum‐level machine learning. J Chem Inf Model. 2019;59(8):3485–3493.
García‐Meseguer R, Ortí E, Iñaki Tuñón J, Ruiz‐Pernía J, Aragó J. Insights into the enhancement of the poly(ethylene terephthalate) degradation by FAST‐PETase from computational modeling. J Am Chem Soc. 2023;145(35):19243–19255.
Gaus M, Cui Q, Elstner M. DFTB3: extension of the self‐consistent‐charge density‐functional tight‐binding method (SCC‐DFTB). J Chem Theory Comput. 2012;7(4):931–948.
Gaus M, Goez A, Elstner M. Parametrization and benchmark of DFTB3 for organic molecules. J Chem Theory Comput. 2013;9(1):338–354.
Gerlits O, Blakeley MP, Keen DA, Radić Z, Kovalevsky A. Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K‐TMA: towards a neutron structure. Curr Res Struct Biol. 2021;3(September):206–215.
Gerlits O, Fajer M, Cheng X, Blumenthal DK, Radić Z, Kovalevsky A. Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X‐ray crystallography and inelastic neutron scattering. Structure. 2022;30(11):1538–1549.e3.
Ghosh D, Wawrzak Z, Pletnev VZ, Li N, Kaiser R, Pangborn W, et al. Structure of uncomplexed and linoleate‐bound Candida cylindracea cholesterol esterase. Structure. 1995;3(3):279–288.
Gillet N, Elstner M, Kubař T. Coupled‐perturbed DFTB‐QM/MM metadynamics: application to proton‐coupled electron transfer. J Chem Phys. 2018;149(7):072328.
Grigorenko BL, Novichkova DA, Lushchekina SV, Zueva IV, Schopfer LM, Nemukhin AV, et al. Computer‐designed active human butyrylcholinesterase double mutant with a new catalytic triad. Chem Biol Interact. 2019;306(June):138–146.
Gutiérrez‐Fernández J, Vaquero ME, Prieto A, Barriuso J, Martínez MJ, Hermoso JA. Crystal structures of Ophiostoma piceae sterol esterase: structural insights into activation mechanism and product release. J Struct Biol. 2014;187(3):215–222.
Ha ZY, Mathew S, Yeong KY. Butyrylcholinesterase: a multifaceted pharmacological target and tool. Curr Protein Pept Sci. 2020;21(1):99–109.
Harel M, Kleywegt GJ, Ravelli RB, Silman I, Sussman JL. Crystal structure of an acetylcholinesterase‐Fasciculin complex: interaction of a three‐fingered toxin from snake venom with its target. Structure. 1995;3(12):1355–1366.
Henderson JA, Liu R, Harris JA, Huang Y, de Oliveira VM, Shen J. A guide to the continuous constant pH molecular dynamics methods in Amber and CHARMM [Article v1.0]. Living J Comput Mol Sci. 2022;4(1):1563. https://doi.org/10.33011/livecoms.4.1.1563
Hourahine B, Aradi B, Blum V, Bonafé F, Buccheri A, Camacho C, et al. DFTB+, a software package for efficient approximate density functional theory based atomistic simulations. J Chem Phys. 2020;152(12):124101.
Izadi S, Onufriev AV. Accuracy limit of rigid 3‐point water models. J Chem Phys. 2016;145(7):074501.
Jansen A, Aho N, Groenhof G, Buslaev P, Hess B. phbuilder: a tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS. J Chem Inf Model. 2024;64(3):567–574.
Jing L, Gaochan W, Kang D, Zhou Z, Song Y, Liu X, et al. Contemporary medicinal‐chemistry strategies for the discovery of selective butyrylcholinesterase inhibitors. Drug Discov Today. 2019;24(2):629–635.
Kagami L, Wilter A, Diaz A, Vranken W. The ACPYPE web server for small‐molecule MD topology generation. Bioinformatics. 2023;39(6):btad350. https://doi.org/10.1093/bioinformatics/btad350
Kemp MT, Lewandowski EM, Chen Y. Low barrier hydrogen bonds in protein structure and function. Biochim Biophys Acta Proteins Proteomics. 2021;1869(1):140557.
Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, et al. CP2K: an electronic structure and molecular dynamics software package – quickstep: efficient and accurate electronic structure calculations. J Chem Phys. 2020;152(19):194103.
Lai R, Cui Q. How to stabilize carbenes in enzyme active sites without metal ions. J Am Chem Soc. 2022;144(45):20739–20751.
Lindorff‐Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, et al. Improved side‐chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010;78(8):1950–1958.
Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal J‐P. Hybrid QM/MM molecular dynamics with AMOEBA polarizable embedding. J Chem Theory Comput. 2017;13(9):4025–4033.
Lushchekina S, Masson P. Catalytic bioscavengers against organophosphorus agents: mechanistic issues of self‐reactivating cholinesterases. Toxicology. 2018;409(November):91–102.
Lushchekina SV, Schopfer LM, Grigorenko BL, Nemukhin AV, Varfolomeev SD, Lockridge O, et al. Optimization of cholinesterase‐based catalytic bioscavengers against organophosphorus agents. Front Pharmacol. 2018;9(March):211.
Masson P, Fortier PL, Albaret C, Froment MT, Bartels CF, Lockridge O. Aging of di‐isopropyl‐phosphorylated human butyrylcholinesterase. Biochem J. 1997;327(Pt 2):601–607.
Meden A, Knez D, Jukič M, Brazzolotto X, Gršič M, Pišlar A, et al. Tryptophan‐derived butyrylcholinesterase inhibitors as promising leads against Alzheimer's disease. Chem Commun. 2019;55(26):3765–3768.
Millard CB, Lockridge O, Broomfield CA. Organophosphorus acid anhydride hydrolase activity in human butyrylcholinesterase: synergy results in a somanase. Biochemistry. 1998;37(1):237–247.
Mokrushina YA, Golovin AV, Smirnov IV, Chatziefthimiou SD, Stepanova AV, Bobik TV, et al. Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers. Proc Natl Acad Sci USA. 2020;117(37):22841–22848.
Nachon F, Asojo OA, Borgstahl GEO, Masson P, Lockridge O. Role of water in aging of human butyrylcholinesterase inhibited by echothiophate: the crystal structure suggests two alternative mechanisms of aging. Biochemistry. 2005;44(4):1154–1162.
Nichols DA, Hargis JC, Sanishvili R, Jaishankar P, Defrees K, Smith EW, et al. Ligand‐induced proton transfer and low‐barrier hydrogen bond revealed by X‐ray crystallography. J Am Chem Soc. 2015;137(25):8086–8095.
Nicolet Y, Lockridge O, Masson P, Fontecilla‐Camps JC, Nachon F. Crystal structure of human butyrylcholinesterase and of its complexes with substrate and products. J Biol Chem. 2003;278(42):41141–41147.
Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH. PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput. 2011;7(2):525–537.
Perz V, Hromic A, Baumschlager A, Steinkellner G, Pavkov‐Keller T, Gruber K, et al. An esterase from anaerobic Clostridium hathewayi can hydrolyze aliphatic‐aromatic polyesters. Environ Sci Technol. 2016;50(6):2899–2907.
Peters J, Martinez N, Trovaslet M, Scannapieco K, Koza MM, Masson P, et al. Dynamics of human acetylcholinesterase bound to non‐covalent and covalent inhibitors shedding light on changes to the water network structure. Phys Chem Chem Phys. 2016;18(18):12992–13001.
Poirier L, Jacquet P, Plener L, Masson P, Daudé D, Chabrière E. Organophosphorus poisoning in animals and enzymatic antidotes. Environ Sci Pollut Res Int. 2021;28(20):25081–25106.
Porter MA, Molina PA. The low‐barrier double‐well potential of the Oδ1‐H‐Oδ1 hydrogen bond in unbound HIV protease: a QM/MM characterization. J Chem Theory Comput. 2006;2(6):1675–1684.
Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL. Structure of acetylcholinesterase complexed with the nootropic alkaloid, (−)‐huperzine A. Nat Struct Biol. 1997;4(1):57–63.
Roston D, Demapan D, Cui Q. Extensive free‐energy simulations identify water as the base in nucleotide addition by DNA polymerase. Proc Natl Acad Sci USA. 2019;116(50):25048–25056.
Schnettler JD, Klein OJ, Kaminski TS, Colin P‐Y, Hollfelder F. Ultrahigh‐throughput directed evolution of a metal‐free α/β‐hydrolase with a Cys‐His‐Asp triad into an efficient phosphotriesterase. J Am Chem Soc. 2023;145(2):1083–1096.
Schrag JD, Cygler M. 1.8 Å refined structure of the lipase from Geotrichum candidum. J Mol Biol. 1993;230(2):575–591.
Shi Y, Xia Z, Zhang J, Best R, Chuanjie W, Ponder JW, et al. The polarizable atomic multipole‐based AMOEBA force field for proteins. J Chem Theory Comput. 2013;9(9):4046–4063.
Silman I. The multiple biological roles of the cholinesterases. Prog Biophys Mol Biol. 2021;162(July):41–56.
Sirin GS, Zhang Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J Phys Chem A. 2014;118(39):9132–9139.
Somarowthu S, Brodkin HR, Alejandro D'Aquino J, Ringe D, Ondrechen MJ, Beuning PJ. A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase. Biochemistry. 2011;50(43):9283–9295.
de Souza A, Victoria DJ, Scott JE, Nettleship NR, Charlton MH, Walsh MA, et al. Comparison of the structure and activity of glycosylated and aglycosylated human carboxylesterase 1. PLoS One. 2015;10(12):e0143919.
Sumida KH, Núñez‐Franco R, Kalvet I, Pellock SJ, Wicky BIM, Milles LF, et al. Improving protein expression, stability, and function with ProteinMPNN. J Am Chem Soc. 2024;146(3):2054–2061. https://doi.org/10.1021/jacs.3c10941
Terekhov SS, Mokrushina YA, Nazarov AS, Zlobin A, Zalevsky A, Bourenkov G, et al. A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding. Sci Adv. 2020;6(26):eaaz9861.
Terzyan S, Wang CS, Downs D, Hunter B, Zhang XC. Crystal structure of the catalytic domain of human bile salt activated lipase. Protein Sci. 2000;9(9):1783–1790.
Tiwary P, Parrinello M. A time‐independent free energy estimator for metadynamics. J Phys Chem B. 2015;119(3):736–742.
Vennelakanti V, Nazemi A, Mehmood R, Steeves AH, Kulik HJ. Harder, better, faster, stronger: large‐scale QM and QM/MM for predictive modeling in enzymes and proteins. Curr Opin Struct Biol. 2022;72(February):9–17.
Voevodin VV, Antonov AS, Nikitenko DA, Shvets PA, Sobolev SI, Sidorov IY, et al. Supercomputer Lomonosov‐2: large scale, deep monitoring and fine analytics for the user community. Supercomput Front Innov. 2019;6(2):4–11. https://doi.org/10.14529/jsfi190201
Wan X, Yao Y, Fang L, Liu J. Unexpected protonation state of Glu197 discovered from simulations of tacrine in butyrylcholinesterase. Phys Chem Chem Phys. 2018;20(21):14938–14946.
Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, et al. MolProbity: more and better reference data for improved all‐atom structure validation. Protein Sci. 2018;27(1):293–315.
Wilson CJ, de Groot BL, Gapsys V. Resolving coupled pH titrations using alchemical free energy calculations. J Comput Chem. 2024;45(17):1444–1455.
Yoo J, Aksimentiev A. New tricks for old dogs: improving the accuracy of biomolecular force fields by pair‐specific corrections to non‐bonded interactions. Phys Chem Chem Phys. 2018;20(13):8432–8449.
Zlobin A, Golovin A. Between protein fold and nucleophile identity: multiscale modeling of the TEV protease enzyme‐substrate complex. ACS Omega. 2022;7(44):40279–40292.
Zlobin A, Mokrushina Y, Terekhov S, Zalevsky A, Bobik T, Stepanova A, et al. QM/MM description of newly selected catalytic bioscavengers against organophosphorus compounds revealed reactivation stimulus mediated by histidine residue in the acyl‐binding loop. Front Pharmacol. 2018;9(August):834.
Zlobin AS, Zalevsky AO, Mokrushina YA, Kartseva OV, Golovin AV, Smirnov IV. The preferable binding pose of canonical butyrylcholinesterase substrates is unproductive for echothiophate. Acta Naturae. 2018;10(4):121–124.
Zlobin A, Diankin I, Pushkarev S, Golovin A. Probing the suitability of different Ca2+ parameters for long simulations of diisopropyl fluorophosphatase. Molecules. 2021;26(19):5839. https://doi.org/10.3390/molecules26195839
Zlobin A, Belyaeva J, Golovin A. Challenges in protein QM/MM simulations with intra‐backbone link atoms. J Chem Inf Model. 2023;63(2):546–560.