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Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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2
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Trapp M, Trovaslet M, Nachon F, Koza MM, van Eijck L, Hill F, Weik M, Masson P, Tehei M, Peters J. Energy Landscapes of Human Acetylcholinesterase and Its Huperzine A-Inhibited Counterpart. J Phys Chem B 2012. [DOI: 10.1021/jp304704h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcus Trapp
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
- Institut Laue Langevin, F-38042 Grenoble Cédex
9, France
| | - Marie Trovaslet
- Institut de Recherche Biomédicale des Armées, F-38700 La Tronche,
France
| | - Florian Nachon
- Institut de Recherche Biomédicale des Armées, F-38700 La Tronche,
France
| | - Marek M. Koza
- Institut Laue Langevin, F-38042 Grenoble Cédex
9, France
| | - Lambert van Eijck
- Delft University of Technology, Faculty of Applied Sciences, RST/NPM2
Mekelweg 15, 2629JB Delft Netherlands
| | - Flynn Hill
- School of Chemistry and
Centre for
Medical Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Martin Weik
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
| | - Patrick Masson
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
- Institut de Recherche Biomédicale des Armées, F-38700 La Tronche,
France
| | - Moeava Tehei
- School of Chemistry and
Centre for
Medical Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Australian Institute of Nuclear Science and Engineering (AINSE), Menai, NSW,
Australia
| | - Judith Peters
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
- Institut Laue Langevin, F-38042 Grenoble Cédex
9, France
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Sirin GS, Zhou Y, Lior-Hoffmann L, Wang S, Zhang Y. Aging mechanism of soman inhibited acetylcholinesterase. J Phys Chem B 2012; 116:12199-207. [PMID: 22984913 PMCID: PMC3475498 DOI: 10.1021/jp307790v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nervous system that hydrolyzes neurotransmitter acetylcholine (ACh) and terminates synaptic signals. The catalytic serine of AChE can be phosphonylated by soman, one of the most potent nerve agents, and subsequently undergo an aging reaction. This phosphonylation and aging process leads to irreversible AChE inhibition, results in accumulation of excess ACh at the synaptic clefts, and causes neuromuscular paralysis. By employing Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have characterized the aging mechanism of soman phosphonylated AChE and determined its free energy profile. This aging reaction starts with the scission of the O2-Cα bond, which is followed by methyl migration, and results in a tertiary carbenium intermediate. At the transition state, the scissile O2-Cα bond is already cleaved with an average O-C distance of 3.2 ± 0.3 Å and the migrating methyl group is shared between Cα and Cβ carbons with C-C distances of 1.9 ± 0.1 and 1.8 ± 0.1 Å, respectively. The negatively charged phosphonate group is stabilized by a salt bridge with the imidazole ring of the catalytic histidine. A major product of aging, 2,3-dimethyl-2-butanol can be formed swiftly by the reaction of a water molecule. Our characterized mechanism and simulation results provide new detailed insights into this important biochemical process.
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Affiliation(s)
- Gulseher Sarah Sirin
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, New York, 10016
- Department of Chemistry, New York University, New York, New York, 10003
| | - Yanzi Zhou
- Department of Chemistry, New York University, New York, New York, 10003
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Lee Lior-Hoffmann
- Department of Chemistry, New York University, New York, New York, 10003
| | - Shenglong Wang
- Department of Chemistry, New York University, New York, New York, 10003
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York, 10003
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Peters J, Trovaslet M, Trapp M, Nachon F, Hill F, Royer E, Gabel F, van Eijck L, Masson P, Tehei M. Activity and molecular dynamics relationship within the family of human cholinesterases. Phys Chem Chem Phys 2012; 14:6764-70. [DOI: 10.1039/c2cp23817a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Structural approach to the aging of phosphylated cholinesterases. Chem Biol Interact 2010; 187:157-62. [DOI: 10.1016/j.cbi.2010.03.027] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Revised: 03/08/2010] [Accepted: 03/12/2010] [Indexed: 12/18/2022]
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6
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Sanson B, Nachon F, Colletier JP, Froment MT, Toker L, Greenblatt HM, Sussman JL, Ashani Y, Masson P, Silman I, Weik M. Crystallographic snapshots of nonaged and aged conjugates of soman with acetylcholinesterase, and of a ternary complex of the aged conjugate with pralidoxime. J Med Chem 2009; 52:7593-603. [PMID: 19642642 DOI: 10.1021/jm900433t] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organophosphate compounds (OP) are potent inhibitors of acetylcholinesterases (AChEs) and can cause lethal poisoning in humans. Inhibition of AChEs by the OP soman involves phosphonylation of the catalytic serine, and subsequent dealkylation produces a form known as the "aged" enzyme. The nonaged form can be reactivated to a certain extent by nucleophiles, such as pralidoxime (2-PAM), whereas aged forms of OP-inhibited AChEs are totally resistant to reactivation. Here, we solved the X-ray crystal structures of AChE from Torpedo californica (TcAChE) conjugated with soman before and after aging. The absolute configuration of the soman stereoisomer adduct in the nonaged conjugate is P(S)C(R). A structural reorientation of the catalytic His440 side chain was observed during the aging process. Furthermore, the crystal structure of the ternary complex of the aged conjugate with 2-PAM revealed that the orientation of the oxime function does not permit nucleophilic attack on the phosphorus atom, thus providing a plausible explanation for its failure to reactivate the aged soman/AChE conjugate. Together, these three crystal structures provide an experimental basis for the design of new reactivators.
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Affiliation(s)
- Benoît Sanson
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Joseph Fourier, 41 Rue Jules Horowitz, 38027 Grenoble, France
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Butyrylcholinesterase for protection from organophosphorus poisons: catalytic complexities and hysteretic behavior. Arch Biochem Biophys 2009; 494:107-20. [PMID: 20004171 DOI: 10.1016/j.abb.2009.12.005] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/24/2009] [Accepted: 12/01/2009] [Indexed: 12/13/2022]
Abstract
Butyrylcholinesterase is a promiscuous enzyme that displays complex kinetic behavior. It is toxicologically important because it detoxifies organophosphorus poisons (OP) by making a covalent bond with the OP. The OP and the butyrylcholinesterase are both inactivated in the process. Inactivation of butyrylcholinesterase has no adverse effects. However, inactivation of acetylcholinesterase in nerve synapses can be lethal. OP-inhibited butyrylcholinesterase and acetylcholinesterase can be reactivated with oximes provided the OP has not aged. Strategies for preventing the toxicity of OP include (a) treatment with an OP scavenger, (b) reaction of non-aged enzyme with oximes, (c) reactivation of aged enzyme, (d) slowing down aging with peripheral site ligands, and (e) design of mutants that rapidly hydrolyze OP. Option (a) has progressed through phase I clinical trials with human butyrylcholinesterase. Option (b) is in routine clinical use. The others are at the basic research level. Butyrylcholinesterase displays complex kinetic behavior including activation by positively charged esters, ability to hydrolyze amides, and a lag time (hysteresis) preceding hydrolysis of benzoylcholine and N-methylindoxyl acetate. Mass spectrometry has identified new OP binding motifs on tyrosine and lysine in proteins that have no active site serine. It is proposed, but not yet proven, that low dose exposure involves OP modification of proteins that have no active site serine.
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