51
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Orhan IE. Nature: a substantial source of auspicious substances with acetylcholinesterase inhibitory action. Curr Neuropharmacol 2013; 11:379-87. [PMID: 24381529 PMCID: PMC3744902 DOI: 10.2174/1570159x11311040003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/26/2022] Open
Abstract
Acetylcholinesterase (AChE) (EC 3.1.1.7) is an important enzyme that breaks down of acetylcholine in synaptic cleft in neuronal junctions. Inhibition of AChE is associated with treatment of several diseases such as Alzheimer's disease (AD), myasthenia gravis, and glaucoma as well as the mechanisms of insecticide and anthelmintic drugs. Several AChE inhibitors are available in clinical use currently for the treatment of AD; however, none of them has ability, yet, to seize progress of the disease. Consequently, an extensive research has been going on finding new AChE inhibitors. In this sense, natural inhibitors have gained great attention due to their encouraging effects toward AChE. In this review, promising candidate molecules with marked AChE inhibition from both plant and animal sources will be underlined.
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Affiliation(s)
- Ilkay Erdogan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330 Ankara, Turkey
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmacy, Eastern Mediterranean University, Gazimagosa, The Northern Cyprus via Turkey
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52
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Jackson CJ, Liu JW, Carr PD, Younus F, Coppin C, Meirelles T, Lethier M, Pandey G, Ollis DL, Russell RJ, Weik M, Oakeshott JG. Structure and function of an insect α-carboxylesterase (αEsterase7) associated with insecticide resistance. Proc Natl Acad Sci U S A 2013; 110:10177-82. [PMID: 23733941 PMCID: PMC3690851 DOI: 10.1073/pnas.1304097110] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Insect carboxylesterases from the αEsterase gene cluster, such as αE7 (also known as E3) from the Australian sheep blowfly Lucilia cuprina (LcαE7), play an important physiological role in lipid metabolism and are implicated in the detoxification of organophosphate (OP) insecticides. Despite the importance of OPs to agriculture and the spread of insect-borne diseases, the molecular basis for the ability of α-carboxylesterases to confer OP resistance to insects is poorly understood. In this work, we used laboratory evolution to increase the thermal stability of LcαE7, allowing its overexpression in Escherichia coli and structure determination. The crystal structure reveals a canonical α/β-hydrolase fold that is very similar to the primary target of OPs (acetylcholinesterase) and a unique N-terminal α-helix that serves as a membrane anchor. Soaking of LcαE7 crystals in OPs led to the capture of a crystallographic snapshot of LcαE7 in its phosphorylated state, which allowed comparison with acetylcholinesterase and rationalization of its ability to protect insects against the effects of OPs. Finally, inspection of the active site of LcαE7 reveals an asymmetric and hydrophobic substrate binding cavity that is well-suited to fatty acid methyl esters, which are hydrolyzed by the enzyme with specificity constants (∼10(6) M(-1) s(-1)) indicative of a natural substrate.
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Affiliation(s)
- Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
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53
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Wang Y, King JR, Wu P, Pelzman DL, Beratan DN, Toone EJ. Enthalpic Signature of Methonium Desolvation Revealed in a Synthetic Host–Guest System Based on Cucurbit[7]uril. J Am Chem Soc 2013; 135:6084-91. [DOI: 10.1021/ja311327v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Wang
- Department of
Biochemistry, Duke University Medical Center, Durham, North Carolina
27710, United States
| | | | | | - Daniel L. Pelzman
- Department of
Biochemistry, Duke University Medical Center, Durham, North Carolina
27710, United States
| | - David N. Beratan
- Department of
Biochemistry, Duke University Medical Center, Durham, North Carolina
27710, United States
| | - Eric J. Toone
- Department of
Biochemistry, Duke University Medical Center, Durham, North Carolina
27710, United States
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54
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Cholinesterase confabs and cousins: approaching forty years. Chem Biol Interact 2013; 203:10-3. [PMID: 23085121 DOI: 10.1016/j.cbi.2012.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/04/2012] [Accepted: 10/09/2012] [Indexed: 11/23/2022]
Abstract
In the past four decades of cholinesterase (ChE) research, we have seen substantive evolution of the field from one centered around substrate and inhibitor kinetic profiles and compound characterizations to the analysis of ChE structure, first through the gene families and then by X-ray crystallographic determinations of the free enzymes and their complexes and conjugates. Indeed, these endeavors have been facilitated by recombinant DNA technologies, structure determinations and parallel studies in related proteins in the α/β-hydrolase fold family. This approach has not only contributed to a fundamental understanding of structure and function of a large family of hydrolase-like proteins possessing functions other than catalysis, but also has been used to develop new practical strategies for scavenging and antidotal activity in cases of organophosphate insecticide or nerve agent exposure.
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55
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Trovaslet M, Trapp M, Weik M, Nachon F, Masson P, Tehei M, Peters J. Relation between dynamics, activity and thermal stability within the cholinesterase family. Chem Biol Interact 2013; 203:14-8. [DOI: 10.1016/j.cbi.2012.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/30/2012] [Accepted: 08/02/2012] [Indexed: 11/17/2022]
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56
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On quantum mechanical – molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase. Chem Biol Interact 2013; 203:51-6. [DOI: 10.1016/j.cbi.2012.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/29/2012] [Accepted: 08/31/2012] [Indexed: 11/20/2022]
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57
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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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58
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De Jaco A, Dubi N, Camp S, Taylor P. Congenital hypothyroidism mutations affect common folding and trafficking in the α/β-hydrolase fold proteins. FEBS J 2012; 279:4293-305. [PMID: 23035660 DOI: 10.1111/febs.12019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/27/2012] [Accepted: 09/28/2012] [Indexed: 12/19/2022]
Abstract
The α/β-hydrolase fold superfamily of proteins is composed of structurally related members that, despite great diversity in their catalytic, recognition, adhesion and chaperone functions, share a common fold governed by homologous residues and conserved disulfide bridges. Non-synonymous single nucleotide polymorphisms within the α/β-hydrolase fold domain in various family members have been found for congenital endocrine, metabolic and nervous system disorders. By examining the amino acid sequence from the various proteins, mutations were found to be prevalent in conserved residues within the α/β-hydrolase fold of the homologous proteins. This is the case for the thyroglobulin mutations linked to congenital hypothyroidism. To address whether correct folding of the common domain is required for protein export, we inserted the thyroglobulin mutations at homologous positions in two correlated but simpler α/β-hydrolase fold proteins known to be exported to the cell surface: neuroligin3 and acetylcholinesterase. Here we show that these mutations in the cholinesterase homologous region alter the folding properties of the α/β-hydrolase fold domain, which are reflected in defects in protein trafficking, folding and function, and ultimately result in retention of the partially processed proteins in the endoplasmic reticulum. Accordingly, mutations at conserved residues may be transferred amongst homologous proteins to produce common processing defects despite disparate functions, protein complexity and tissue-specific expression of the homologous proteins. More importantly, a similar assembly of the α/β-hydrolase fold domain tertiary structure among homologous members of the superfamily is required for correct trafficking of the proteins to their final destination.
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Affiliation(s)
- Antonella De Jaco
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
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59
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Beri V, Auletta JT, Maharvi GM, Wood JF, Fauq AH, Rosenberry TL. Hydrolysis of low concentrations of the acetylthiocholine analogs acetyl(homo)thiocholine and acetyl(nor)thiocholine by acetylcholinesterase may be limited by selective gating at the enzyme peripheral site. Chem Biol Interact 2012; 203:38-43. [PMID: 23047027 DOI: 10.1016/j.cbi.2012.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/30/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Abstract
Hydrolysis of acetylcholine by acetylcholinesterase (AChE) is extremely rapid, with a second-order hydrolysis rate constant k(E) (often denoted k(cat)/K(M)) that approaches 10(8) M(-1) s(-1). AChE contains a deep active site gorge with two sites of ligand binding, an acylation site (or A-site) containing the catalytic triad at the base of the gorge and a peripheral site (or P-site) near the gorge entrance. The P-site is known to contribute to catalytic efficiency with acetylthiocholine (AcSCh) by transiently trapping the substrate in a low affinity complex on its way to the A-site, where a short-lived acyl enzyme intermediate is produced. Here we ask whether the P-site does more than simply trap the substrate but in fact selectively gates entry to the A-site to provide specificity for AcSCh (and acetylcholine) relative to the close structural analogs acetyl(homo)thiocholine (Ac-hSCh, which adds one additional methylene group to thiocholine) and acetyl(nor)thiocholine (Ac-nSCh, which deletes one methylene group from thiocholine). We synthesized Ac-hSCh and Ac-nSCh and overcame technical difficulties associated with instability of the northiocholine hydrolysis product. We then compared the catalytic parameters of these substrates with AChE to those of AcSCh. Values of k(E) for Ac-hSCh and Ac-nSCh were about 2% of that for AcSCh. The k(E) for AcSCh is close to the theoretical diffusion-controlled limit for the substrate association rate constant, but kE values for Ac-hSCh or Ac-nSCh are too low to be limited by diffusion control. However, analyses of kinetic solvent isotope effects and inhibition patterns for P-site inhibitors indicate that these two analogs also do not equilibrate with the A-site prior to the initial acylation step of catalysis. We propose that kE for these substrates is partially rate-limited by a gating step that involves the movement of bound substrate from the P-site to the A-site.
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Affiliation(s)
- Veena Beri
- Mayo Clinic College of Medicine, Department of Neuroscience, Jacksonville, FL 32224, United States
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60
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Kannan M, Manivel P, Geetha K, Muthukumaran J, Rao HSP, Krishna R. Synthesis and in silico evaluation of 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives against Alzheimer disease: to understand their interacting mechanism with acetylcholinesterase. J Chem Biol 2012; 5:151-66. [PMID: 24052808 DOI: 10.1007/s12154-012-0084-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022] Open
Abstract
Anomalous action of human acetylcholinesterase (hAChE) in Alzheimer's disease (AD) was restrained by various AChE inhibitors, of which the specific and potent lead candidate Donepezil is used for treating the disease AD. Besides the specificity, the observed undesirable side effects caused by Donepezil invoked the quest for new lead molecules with the increased potency and specificity for AChE. The present study elucidates the potency of six 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives to form a specific interaction with the peripheral anionic site and catalytic anionic subsite residues of hAChE. The NMSMs were prepared in good yield from 1,1-di(methylsulfanyl)-2-nitroethylene and primary amine (or) amino acid esters. In silico interaction analysis reveals specific and potent interactions between hAChE and selected ligand molecules. The site-specific interactions formed between these molecules also results in a conformational change in the orientation of active site residues of hAChE, which prevents them from being accessed by beta-amyloid protein (Aβ), which is a causative agent for amyloid plaque formation and acetylcholine (ACh). In silico interaction analysis between the ligand-bounded hAChE with Aß and ACh confirms this observation. The variation in the conformation of hAChE associated with the decreased ability of Aβ and ACh to access the respective functional residues of hAChE induced by the novel NMSMs favors their selection for in vivo analysis to present themselves as new members of hAChE inhibitors.
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Affiliation(s)
- M Kannan
- Centre for Bioinformatics, Pondicherry University, Pondicherry, 605 014 India
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61
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Barcelos RP, de Lima Portella R, Lugokenski TH, da Rosa EJF, Amaral GP, Garcia LFM, Bresolin L, Carratu V, Soares FAA, de Vargas Barbosa NB. Isatin-3-N4-benzilthiosemicarbazone, a non-toxic thiosemicarbazone derivative, protects and reactivates rat and human cholinesterases inhibited by methamidophos in vitro and in silico. Toxicol In Vitro 2012; 26:1030-9. [DOI: 10.1016/j.tiv.2012.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 04/09/2012] [Accepted: 04/10/2012] [Indexed: 11/27/2022]
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62
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Paz A, Roth E, Ashani Y, Xu Y, Shnyrov VL, Sussman JL, Silman I, Weiner L. Structural and functional characterization of the interaction of the photosensitizing probe methylene blue with Torpedo californica acetylcholinesterase. Protein Sci 2012; 21:1138-52. [PMID: 22674800 PMCID: PMC3537235 DOI: 10.1002/pro.2101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 05/16/2012] [Accepted: 05/16/2012] [Indexed: 11/09/2022]
Abstract
The photosensitizer, methylene blue (MB), generates singlet oxygen that irreversibly inhibits Torpedo californica acetylcholinesterase (TcAChE). In the dark, it inhibits reversibly. Binding is accompanied by a bathochromic absorption shift, used to demonstrate displacement by other acetylcholinesterase inhibitors interacting with the catalytic "anionic" subsite (CAS), the peripheral "anionic" subsite (PAS), or bridging them. MB is a noncompetitive inhibitor of TcAChE, competing with reversible inhibitors directed at both "anionic" subsites, but a single site is involved in inhibition. MB also quenches TcAChE's intrinsic fluorescence. It binds to TcAChE covalently inhibited by a small organophosphate (OP), but not an OP containing a bulky pyrene. Differential scanning calorimetry shows an ~8° increase in the denaturation temperature of the MB/TcAChE complex relative to native TcAChE, and a less than twofold increase in cooperativity of the transition. The crystal structure reveals a single MB stacked against Trp279 in the PAS, oriented down the gorge toward the CAS; it is plausible that irreversible inhibition is associated with photooxidation of this residue and others within the active-site gorge. The kinetic and spectroscopic data showing that inhibitors binding at the CAS can impede binding of MB are reconciled by docking studies showing that the conformation adopted by Phe330, midway down the gorge, in the MB/TcAChE crystal structure, precludes simultaneous binding of a second MB at the CAS. Conversely, binding of ligands at the CAS dislodges MB from its preferred locus at the PAS. The data presented demonstrate that TcAChE is a valuable model for understanding the molecular basis of local photooxidative damage.
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Affiliation(s)
- Aviv Paz
- Department of Neurobiology, Weizmann Institute of ScienceRehovot 76100, Israel
- Department of Structural Biology, Weizmann Institute of ScienceRehovot 76100, Israel
| | - Esther Roth
- Department of Neurobiology, Weizmann Institute of ScienceRehovot 76100, Israel
| | - Yacov Ashani
- Department of Neurobiology, Weizmann Institute of ScienceRehovot 76100, Israel
| | - Yechun Xu
- Department of Neurobiology, Weizmann Institute of ScienceRehovot 76100, Israel
- Department of Structural Biology, Weizmann Institute of ScienceRehovot 76100, Israel
| | - Valery L Shnyrov
- Department of Biochemistry and Molecular Biology, Universidad de SalamancaSalamanca 37007, Spain
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of ScienceRehovot 76100, Israel
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of ScienceRehovot 76100, Israel
| | - Lev Weiner
- Department of Chemical Research Support, Weizmann Institute of ScienceRehovot 76100, Israel
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63
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Brazzolotto X, Wandhammer M, Ronco C, Trovaslet M, Jean L, Lockridge O, Renard PY, Nachon F. Human butyrylcholinesterase produced in insect cells: huprine-based affinity purification and crystal structure. FEBS J 2012; 279:2905-16. [DOI: 10.1111/j.1742-4658.2012.08672.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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64
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Coppin CW, Jackson CJ, Sutherland T, Hart PJ, Devonshire AL, Russell RJ, Oakeshott JG. Testing the evolvability of an insect carboxylesterase for the detoxification of synthetic pyrethroid insecticides. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:343-352. [PMID: 22300675 DOI: 10.1016/j.ibmb.2012.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/18/2012] [Accepted: 01/20/2012] [Indexed: 05/31/2023]
Abstract
Esterases have been implicated in metabolic resistance to synthetic pyrethroids in several insect species but little is yet known of the molecular basis for these effects. In this work modern directed evolution technology was used to test to what extent it is possible to genetically enhance the pyrethroid hydrolytic activity of the E3 carboxylesterase from the blowfly Lucilia cuprina. High throughput screening of a random mutant library with individual stereoisomers of fluorogenic analogues of two type II pyrethroids identified 17 promising variants that were then also tested with the commercial pyrethroid deltamethrin. Between them, these variants displayed significantly improved activities for all the substrates tested. Amino acid substitutions at ten different residues were clearly implicated in the improvements, although most only enhanced activity for a subset of the stereoisomers. Several new combinations of the most promising amino acid substitutions were then made, and negative epistatic effects were found in most of the combinations, but significant improvements were also found in a minority of them. The best mutant recovered contained three amino acid changes and hydrolysed deltamethrin at more than 100 times the rate of wild-type E3. Structural analysis shows that nine of the ten mutated residues improving pyrethroid or analogue activities cluster in putative substrate binding pockets in the active site, with the three mutations of largest effect all increasing the volume of the acyl pocket.
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Affiliation(s)
- Chris W Coppin
- CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia.
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65
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Zhang Y, Hei T, Cai Y, Gao Q, Zhang Q. Affinity Binding-Guided Fluorescent Nanobiosensor for Acetylcholinesterase Inhibitors via Distance Modulation between the Fluorophore and Metallic Nanoparticle. Anal Chem 2012; 84:2830-6. [DOI: 10.1021/ac300436m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Yaodong Zhang
- Key
Laboratory of Applied Surface and Colloid Chemistry of Ministry of
Education, ‡Key Laboratory of Analytical Chemistry
for Life Science of Shaanxi Province, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, Xi’an 710062, China
| | - Tingting Hei
- Key
Laboratory of Applied Surface and Colloid Chemistry of Ministry of
Education, ‡Key Laboratory of Analytical Chemistry
for Life Science of Shaanxi Province, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, Xi’an 710062, China
| | - Yanan Cai
- Key
Laboratory of Applied Surface and Colloid Chemistry of Ministry of
Education, ‡Key Laboratory of Analytical Chemistry
for Life Science of Shaanxi Province, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, Xi’an 710062, China
| | - Qunqun Gao
- Key
Laboratory of Applied Surface and Colloid Chemistry of Ministry of
Education, ‡Key Laboratory of Analytical Chemistry
for Life Science of Shaanxi Province, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, Xi’an 710062, China
| | - Qi Zhang
- Key
Laboratory of Applied Surface and Colloid Chemistry of Ministry of
Education, ‡Key Laboratory of Analytical Chemistry
for Life Science of Shaanxi Province, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, Xi’an 710062, China
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66
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Ronco C, Carletti E, Colletier JP, Weik M, Nachon F, Jean L, Renard PY. Huprine Derivatives as Sub-Nanomolar Human Acetylcholinesterase Inhibitors: From Rational Design to Validation by X-ray Crystallography. ChemMedChem 2011; 7:400-5. [DOI: 10.1002/cmdc.201100438] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Indexed: 11/06/2022]
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67
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Fang L, Pan Y, Muzyka JL, Zhan CG. Active site gating and substrate specificity of butyrylcholinesterase and acetylcholinesterase: insights from molecular dynamics simulations. J Phys Chem B 2011; 115:8797-805. [PMID: 21682268 PMCID: PMC3135420 DOI: 10.1021/jp112030p] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Butyrylcholinesterase (BChE) and acetylcholinesterase (AChE) are highly homologous proteins with distinct substrate preferences. In this study we compared the active sites of monomers and tetramers of human BChE and human AChE after performing molecular dynamics (MD) simulations in water-solvated systems. By comparing the conformational dynamics of gating residues of AChE and BChE, we found that the gating mechanisms of the main door of AChE and BChE are responsible for their different substrate specificities. Our simulation of the tetramers of AChE and BChE indicates that both enzymes could have two dysfunctional active sites due to their restricted accessibility to substrates. The further study on catalytic mechanisms of multiple forms of AChE and BChE would benefit from our comparison of the active sites of the monomers and tetramers of both enzymes.
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Affiliation(s)
- Lei Fang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Yongmei Pan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | | | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
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68
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Long JZ, Cravatt BF. The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem Rev 2011; 111:6022-63. [PMID: 21696217 DOI: 10.1021/cr200075y] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jonathan Z Long
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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69
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Sanson B, Colletier JP, Xu Y, Lang PT, Jiang H, Silman I, Sussman JL, Weik M. Backdoor opening mechanism in acetylcholinesterase based on X-ray crystallography and molecular dynamics simulations. Protein Sci 2011; 20:1114-8. [PMID: 21594947 DOI: 10.1002/pro.661] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 05/06/2011] [Accepted: 05/06/2011] [Indexed: 11/10/2022]
Abstract
The transient opening of a backdoor in the active-site wall of acetylcholinesterase, one of nature's most rapid enzymes, has been suggested to contribute to the efficient traffic of substrates and products. A crystal structure of Torpedo californica acetylcholinesterase in complex with the peripheral-site inhibitor aflatoxin is now presented, in which a tyrosine at the bottom of the active-site gorge rotates to create a 3.4-Å wide exit channel. Molecular dynamics simulations show that the opening can be further enlarged by movement of Trp84. The crystallographic and molecular dynamics simulation data thus point to the interface between Tyr442 and Trp84 as the key element of a backdoor, whose opening permits rapid clearance of catalysis products from the active site. Furthermore, the crystal structure presented provides a novel template for rational design of inhibitors and reactivators, including anti-Alzheimer drugs and antidotes against organophosphate poisoning.
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Affiliation(s)
- Benoît Sanson
- Comissariat à l'Energie Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
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70
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Kang TS, Georgieva D, Genov N, Murakami MT, Sinha M, Kumar RP, Kaur P, Kumar S, Dey S, Sharma S, Vrielink A, Betzel C, Takeda S, Arni RK, Singh TP, Kini RM. Enzymatic toxins from snake venom: structural characterization and mechanism of catalysis. FEBS J 2011; 278:4544-76. [PMID: 21470368 DOI: 10.1111/j.1742-4658.2011.08115.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Snake venoms are cocktails of enzymes and non-enzymatic proteins used for both the immobilization and digestion of prey. The most common snake venom enzymes include acetylcholinesterases, l-amino acid oxidases, serine proteinases, metalloproteinases and phospholipases A(2) . Higher catalytic efficiency, thermal stability and resistance to proteolysis make these enzymes attractive models for biochemists, enzymologists and structural biologists. Here, we review the structures of these enzymes and describe their structure-based mechanisms of catalysis and inhibition. Some of the enzymes exist as protein complexes in the venom. Thus we also discuss the functional role of non-enzymatic subunits and the pharmacological effects of such protein complexes. The structures of inhibitor-enzyme complexes provide ideal platforms for the design of potent inhibitors which are useful in the development of prototypes and lead compounds with potential therapeutic applications.
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Affiliation(s)
- Tse Siang Kang
- Department of Pharmacy, National University of Singapore, Singapore
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71
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McCammon JA. Gated Diffusion-controlled Reactions. BMC BIOPHYSICS 2011; 4:4. [PMID: 21595999 PMCID: PMC3093672 DOI: 10.1186/2046-1682-4-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 03/02/2011] [Indexed: 11/28/2022]
Abstract
The binding and active sites of proteins are often dynamically occluded by motion of the nearby polypeptide. A variety of theoretical and computational methods have been developed to predict rates of ligand binding and reactivity in such cases. Two general approaches exist, "protein centric" approaches that explicitly treat only the protein target, and more detailed dynamical simulation approaches in which target and ligand are both treated explicitly. This mini-review describes recent work in this area and some of the biological implications.
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Affiliation(s)
- J Andrew McCammon
- Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0365, USA.
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72
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Zhou Y, Wang S, Zhang Y. Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. J Phys Chem B 2010; 114:8817-25. [PMID: 20550161 DOI: 10.1021/jp104258d] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with a B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multistep free-energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack on the carbonyl carbon, with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of the His447 ring needs to be adjusted very slightly, and then, the proton transfers from His447 to the product, and the break of the scissile bond happens spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1-2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms.
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Affiliation(s)
- Yanzi Zhou
- Department of Chemistry, New York University, New York, New York 10003, USA
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73
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Structure–function relationships of the α/β-hydrolase fold domain of neuroligin: A comparison with acetylcholinesterase. Chem Biol Interact 2010; 187:49-55. [DOI: 10.1016/j.cbi.2010.01.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/15/2010] [Accepted: 01/18/2010] [Indexed: 11/18/2022]
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74
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Auletta JT, Johnson JL, Rosenberry TL. Molecular basis of inhibition of substrate hydrolysis by a ligand bound to the peripheral site of acetylcholinesterase. Chem Biol Interact 2010; 187:135-41. [PMID: 20493829 DOI: 10.1016/j.cbi.2010.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 05/11/2010] [Accepted: 05/13/2010] [Indexed: 10/19/2022]
Abstract
Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to the catalytic efficiency of substrate hydrolysis by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. Ligands that bind to the A-site invariably inhibit the hydrolysis of all AChE substrates, but ligands that bind to the P-site inhibit the hydrolysis of some substrates but not others. To clarify the basis of this difference, we focus here on second-order rate constants for substrate hydrolysis (k(E)), a parameter that reflects the binding of ligands only to the free form of the enzyme and not to enzyme-substrate intermediates. We first describe an inhibitor competition assay that distinguishes whether a ligand is inhibiting AChE by binding to the A-site or the P-site. We then show that the P-site-specific ligand thioflavin T inhibits the hydrolysis of the rapidly hydrolyzed substrate acetylthiocholine but fails to show any inhibition of the slowly hydrolyzed substrates ATMA (3-(acetamido)-N,N,N-trimethylanilinium) and carbachol. We derive an expression for k(E) that accounts for these observations by recognizing that the rate-limiting steps for these substrates differ. The rate-limiting step for the slow substrates is the general base-catalyzed acylation reaction k(2), a step that is unaffected by bound thioflavin T. In contrast, the rate-limiting step for acetylthiocholine is either substrate association or substrate migration to the A-site, and these steps are blocked by bound thioflavin T.
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Affiliation(s)
- Jeffrey T Auletta
- Mayo Clinic College of Medicine, Department of Neuroscience and Pharmacology, 4500 San Pablo Road, Jacksonville, FL 32224, USA
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75
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Rosenberry TL. Strategies to resolve the catalytic mechanism of acetylcholinesterase. J Mol Neurosci 2010; 40:32-9. [PMID: 19757206 DOI: 10.1007/s12031-009-9250-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 07/20/2009] [Indexed: 11/25/2022]
Abstract
Acetylcholinesterase (AChE) hydrolyzes its physiological substrate acetylcholine at one of the highest known catalytic rates. Two sites of ligand interaction have been identified: an acylation site or A-site at the base of the active-site gorge and a peripheral site or P-site at its mouth. Although much is known about AChE structure and the role of specific residues in catalysis, a detailed understanding of the catalytic mechanism and the role of the P-site has lagged far behind. In recent years, we have clarified how the P-site and A-site interact to promote catalysis. Our studies revealed that the P-site mediates substrate trapping and that ligand binding to the P-site can result in steric blockade of the A-site as well as allosteric activation of substrate hydrolysis. Because a general, nonequilibrium treatment of AChE catalysis results in complex enzyme kinetic formulations, three simpler, overlapping strategies are presented here that provide significant insights into the AChE catalytic mechanism. The strategies are (1) to choose substrates, preferably close analogs of acetylcholine, that render some intermediates in the general reaction scheme negligible; (2) obtain some of the thermodynamic parameters in this scheme with experiments that are independent of kinetic measurements.
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Affiliation(s)
- Terrone L Rosenberry
- Departments of Neuroscience and Pharmacology, College of Medicine, Mayo Clinic, Jacksonville, FL 32224, USA.
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76
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Matsuoka D, Nakasako M. Prediction of Hydration Structures around Hydrophilic Surfaces of Proteins by Using the Empirical Hydration Distribution Functions from a Database Analysis. J Phys Chem B 2010; 114:4652-63. [DOI: 10.1021/jp9100224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daisuke Matsuoka
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
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77
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Dvir H, Silman I, Harel M, Rosenberry TL, Sussman JL. Acetylcholinesterase: from 3D structure to function. Chem Biol Interact 2010; 187:10-22. [PMID: 20138030 DOI: 10.1016/j.cbi.2010.01.042] [Citation(s) in RCA: 460] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 01/26/2010] [Accepted: 01/28/2010] [Indexed: 11/28/2022]
Abstract
By rapid hydrolysis of the neurotransmitter, acetylcholine, acetylcholinesterase terminates neurotransmission at cholinergic synapses. Acetylcholinesterase is a very fast enzyme, functioning at a rate approaching that of a diffusion-controlled reaction. The powerful toxicity of organophosphate poisons is attributed primarily to their potent inhibition of acetylcholinesterase. Acetylcholinesterase inhibitors are utilized in the treatment of various neurological disorders, and are the principal drugs approved thus far by the FDA for management of Alzheimer's disease. Many organophosphates and carbamates serve as potent insecticides, by selectively inhibiting insect acetylcholinesterase. The determination of the crystal structure of Torpedo californica acetylcholinesterase permitted visualization, for the first time, at atomic resolution, of a binding pocket for acetylcholine. It also allowed identification of the active site of acetylcholinesterase, which, unexpectedly, is located at the bottom of a deep gorge lined largely by aromatic residues. The crystal structure of recombinant human acetylcholinesterase in its apo-state is similar in its overall features to that of the Torpedo enzyme; however, the unique crystal packing reveals a novel peptide sequence which blocks access to the active-site gorge.
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Affiliation(s)
- Hay Dvir
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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78
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Schuster D, Kern L, Hristozov DP, Terfloth L, Bienfait B, Laggner C, Kirchmair J, Grienke U, Wolber G, Langer T, Stuppner H, Gasteiger J, Rollinger JM. Applications of integrated data mining methods to exploring natural product space for acetylcholinesterase inhibitors. Comb Chem High Throughput Screen 2010; 13:54-66. [PMID: 20214575 PMCID: PMC3547168 DOI: 10.2174/138620710790218212] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nature, especially the plant kingdom, is a rich source for novel bioactive compounds that can be used as lead compounds for drug development. In order to exploit this resource, the two neural network-based virtual screening techniques novelty detection with self-organizing maps (SOMs) and counterpropagation neural network were evaluated as tools for efficient lead structure discovery. As application scenario, significant descriptors for acetylcholinesterase (AChE) inhibitors were determined and used for model building, theoretical model validation, and virtual screening. Top-ranked virtual hits from both approaches were docked into the AChE binding site to approve the initial hits. Finally, in vitro testing of selected compounds led to the identification of forsythoside A and (+)-sesamolin as novel AChE inhibitors.
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Affiliation(s)
- Daniela Schuster
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
- Inte:Ligand Softwareentwicklung und Consulting GmbH, Clemens-Maria-Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria
| | - Lisa Kern
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
| | | | - Lothar Terfloth
- Molecular Networks GmbH, Henkestr. 91, D-91052 Erlangen, Germany
| | - Bruno Bienfait
- Molecular Networks GmbH, Henkestr. 91, D-91052 Erlangen, Germany
| | - Christian Laggner
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
| | - Johannes Kirchmair
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
- Inte:Ligand Softwareentwicklung und Consulting GmbH, Clemens-Maria-Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria
| | - Ulrike Grienke
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
| | - Gerhard Wolber
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
- Inte:Ligand Softwareentwicklung und Consulting GmbH, Clemens-Maria-Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria
| | - Thierry Langer
- Prestwick Chemical Inc., Boulevard Gonthier d’Andernach, 67100 Illkirch, France
| | - Hermann Stuppner
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
| | - Johann Gasteiger
- Molecular Networks GmbH, Henkestr. 91, D-91052 Erlangen, Germany
| | - Judith M. Rollinger
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria and Center of Molecular Biosciences Innsbruck (CMBI)
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79
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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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80
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Guo L, Suarez AI, Braden MR, Gerdes JM, Thompson CM. Inhibition of acetylcholinesterase by chromophore-linked fluorophosphonates. Bioorg Med Chem Lett 2009; 20:1194-7. [PMID: 20034789 DOI: 10.1016/j.bmcl.2009.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 11/28/2009] [Accepted: 12/02/2009] [Indexed: 11/29/2022]
Abstract
Fluorophosphonate (FP) head groups were tethered to a variety of chromophores (C) via a triazole group and tested as FPC inhibitors of recombinant mouse (rMoAChE) and electric eel (EEAChE) acetylcholinesterase. The inhibitors showed bimolecular inhibition constants (k(i)) ranging from 0.3 x 10(5)M(-1)min(-1) to 10.4 x 10(5)M(-1)min(-1). When tested against rMoAChE, the dansyl FPC was 12.5-fold more potent than the corresponding inhibitor bearing a Texas Red as chromophore, whereas the Lissamine and dabsyl chromophores led to better anti-EEAChE inhibitors. Most inhibitors were equal or better inhibitors of rMoAChE than EEAChE. 3-Azidopropyl fluorophosphonate, which served as one of the FP head groups, showed excellent inhibitory potency against both AChE's ( congruent with 1 x 10(7)M(-1)min(-1)) indicating, in general, that addition of the chromophore reduced the overall anti-AChE activity. Covalent attachment of the dabsyl-FPC analog to rMoAChE was demonstrated using size exclusion chromatography and spectroscopic analysis, and visualized using molecular modeling.
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Affiliation(s)
- Lilu Guo
- Department of Chemistry, The University of Montana, Missoula, MT 59812, United States
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81
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Sharabi O, Peleg Y, Mashiach E, Vardy E, Ashani Y, Silman I, Sussman JL, Shifman JM. Design, expression and characterization of mutants of fasciculin optimized for interaction with its target, acetylcholinesterase. Protein Eng Des Sel 2009; 22:641-8. [PMID: 19643977 PMCID: PMC2742391 DOI: 10.1093/protein/gzp045] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Predicting mutations that enhance protein–protein affinity remains a challenging task, especially for high-affinity complexes. To test our capability to improve the affinity of such complexes, we studied interaction of acetylcholinesterase with the snake toxin, fasciculin. Using the program ORBIT, we redesigned fasciculin's sequence to enhance its interactions with Torpedo californica acetylcholinesterase. Mutations were predicted in 5 out of 13 interfacial residues on fasciculin, preserving most of the polar inter-molecular contacts seen in the wild-type toxin/enzyme complex. To experimentally characterize fasciculin mutants, we developed an efficient strategy to over-express the toxin in Escherichia coli, followed by refolding to the native conformation. Despite our predictions, a designed quintuple fasciculin mutant displayed reduced affinity for the enzyme. However, removal of a single mutation in the designed sequence produced a quadruple mutant with improved affinity. Moreover, one designed mutation produced 7-fold enhancement in affinity for acetylcholinesterase. This led us to reassess our criteria for enhancing affinity of the toxin for the enzyme. We observed that the change in the predicted inter-molecular energy, rather than in the total energy, correlates well with the change in the experimental free energy of binding, and hence may serve as a criterion for enhancement of affinity in protein–protein complexes.
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Affiliation(s)
- Oz Sharabi
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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82
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Khan MTH. Molecular interactions of cholinesterases inhibitors using in silico methods: current status and future prospects. N Biotechnol 2009; 25:331-46. [PMID: 19491049 DOI: 10.1016/j.nbt.2009.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by a low amount of acetylcholine (ACh) in hippocampus and cortex. Acetylcholinesterase (AChE) is one of the most important enzymes in many living organisms including human being and other vertebrates, insects like mosquitoes, among others. Several reports have been published where it has been clearly shown that the genesis of amyloid protein plaques associated with AD is connected to modifications of both AChE and butyrylcholinesterase (BChE), since the plaque is significantly decreased in AD patients using cholinesterase inhibitors (ChEIs). This review gives some examples of these inhibitors discovered during past couple of years that have shown very prominent interactions at the active site triad of the proteins as well as different other parts of the active site like, peripheral anionic site (PAS), oxyanionic hole, anionic subsite or acyl binding pocket (ABP). Most of the inhibition and their interactions have been visualized by X-ray crystallography, but some of the other inhibitors have been studied either by molecular docking or molecular dynamic (MD) simulations or by both the in silico methods. Some of these prominent studies have been crucially observed and reported here.
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Affiliation(s)
- Mahmud Tareq Hassan Khan
- Department of Pharmacology, Institute of Medical Biology, University of Tromsø, 9037 Tromsø, Norway(1)
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83
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Lee J, Wang X, Di Jeso B, Arvan P. The cholinesterase-like domain, essential in thyroglobulin trafficking for thyroid hormone synthesis, is required for protein dimerization. J Biol Chem 2009; 284:12752-61. [PMID: 19276074 DOI: 10.1074/jbc.m806898200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The carboxyl-terminal cholinesterase-like (ChEL) domain of thyroglobulin (Tg) has been identified as critically important in Tg export from the endoplasmic reticulum. In a number of human kindreds suffering from congenital hypothyroidism, and in the cog congenital goiter mouse and rdw rat dwarf models, thyroid hormone synthesis is inhibited because of mutations in the ChEL domain that block protein export from the endoplasmic reticulum. We hypothesize that Tg forms homodimers through noncovalent interactions involving two predicted alpha-helices in each ChEL domain that are homologous to the dimerization helices of acetylcholinesterase. This has been explored through selective epitope tagging of dimerization partners and by inserting an extra, unpaired Cys residue to create an opportunity for intermolecular disulfide pairing. We show that the ChEL domain is necessary and sufficient for Tg dimerization; specifically, the isolated ChEL domain can dimerize with full-length Tg or with itself. Insertion of an N-linked glycan into the putative upstream dimerization helix inhibits homodimerization of the isolated ChEL domain. However, interestingly, co-expression of upstream Tg domains, either in cis or in trans, overrides the dimerization defect of such a mutant. Thus, although the ChEL domain provides a nidus for Tg dimerization, interactions of upstream Tg regions with the ChEL domain actively stabilizes the Tg dimer complex for intracellular transport.
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Affiliation(s)
- Jaemin Lee
- Cell and Molecular Biology Program, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
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84
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Ahmed M, Batista J, Rocha T, Mazzanti CM, Hassan W, Morsch VM, Loro VL, Thomé G, Schetinger MRC. Comparative study of the inhibitory effect of antidepressants on cholinesterase activity in Bungarus sindanus (krait) venom, human serum and rat striatum. J Enzyme Inhib Med Chem 2009; 23:912-7. [PMID: 18608756 DOI: 10.1080/14756360701809977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Cholinesterases are divided into two classes based on differences in their substrate specificity and tissue distribution: acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). These enzymes may be inhibited by several compounds, such as antidepressants. The antidepressants paroxetine, imipramine, clomipramine and sertraline inhibited both venom AChE as well as human serum BChE in a concentration-dependent manner but had no effect on AChE in the rat brain striatum. The IC(50) of venom calculated for imipramine was 0.3 mM, paroxetine 0.38 mM, clomipramine 0.34 mM and sertraline 0.35 mM. Analysis of kinetic data indicated that the inhibition caused by sertraline and paroxetine was mixed, i.e. K(m) values increased and V(max) decreased in a concentration dependent manner. Imipramine and clomipramine exhibited competitive inhibition, i.e. K(m) values increased and V(max) remained constant. The present results suggest that these therapeutic agents used for depression can also be considered as inhibitors of snake venom and human serum cholinesterase.
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Affiliation(s)
- Mushtaq Ahmed
- Departamento de Quimica, Centro de Ciencias Naturais e Exatas, Universidade Federal de Santa Maria, Brazil
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85
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Rosenberry TL, Sonoda LK, Dekat SE, Cusack B, Johnson JL. Analysis of the reaction of carbachol with acetylcholinesterase using thioflavin T as a coupled fluorescence reporter. Biochemistry 2008; 47:13056-63. [PMID: 19006330 PMCID: PMC2655144 DOI: 10.1021/bi8015197] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acylated enzyme intermediate is produced. Carbamates are very poor substrates that, like other AChE substrates, form an initial enzyme-substrate complex with free AChE (E) and proceed to an acylated enzyme intermediate (EC), which is then hydrolyzed. However, the hydrolysis of EC is slow enough to resolve the acylation and deacylation steps on the catalytic pathway. Here, we focus on the reaction of carbachol (carbamoylcholine) with AChE. The kinetics and thermodynamics of this reaction are of special interest because carbachol is an isosteric analogue of the physiological substrate acetylcholine. We show that the reaction can be monitored with thioflavin T as a fluorescent reporter group. The fluorescence of thioflavin T is strongly enhanced when it binds to the P-site of AChE, and this fluorescence is partially quenched when a second ligand binds to the A-site to form a ternary complex. Analysis of the fluorescence reaction profiles was challenging because four thermodynamic parameters and two fluorescence coefficients were fitted from the combined data both for E and for EC. Respective equilibrium dissociation constants of 6 and 26 mM were obtained for carbachol binding to the A- and P-sites in E and of 2 and 32 mM for carbachol binding to the A- and P-sites in EC. These constants for the binding of carbachol to the P-site are about an order of magnitude larger (i.e., indicating lower affinity) than previous estimates for the binding of acetylthiocholine to the P-site.
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Affiliation(s)
- Terrone L Rosenberry
- Mayo Clinic College of Medicine, Department of Neuroscience, Jacksonville, Florida 32224, USA.
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86
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Piłat Z, Antosiewicz JM. Multiple Protonation Equilibria in Electrostatics of Protein−Protein Binding. J Phys Chem B 2008; 112:15074-85. [DOI: 10.1021/jp8029659] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zofia Piłat
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Zwirki i Wigury 93 St., Warsaw 02-089, Poland
| | - Jan M. Antosiewicz
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Zwirki i Wigury 93 St., Warsaw 02-089, Poland
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87
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Bui JM, Andrew McCammon J. Intrinsic conformational flexibility of acetylcholinesterase. Chem Biol Interact 2008; 175:303-4. [PMID: 18452905 DOI: 10.1016/j.cbi.2008.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2007] [Accepted: 03/04/2008] [Indexed: 11/17/2022]
Abstract
Proteins have been metaphorically described--due to the introduction and extraordinary advances in biomolecular dynamics and computational biophysics over the past decades--as "kicking and screaming" molecules [G. Weber, Adv. Protein Chem. 29 (1975) 1-83]. In fact, dynamic fluctuations in protein structural conformation have been known to play an important role in protein function. However, fundamental mechanisms by which protein fluctuations couple with catalytic function of particular enzymes remain poorly understood. To understand the dynamical properties of acetylcholinesterase (AChE) in rapid termination of cationic neurotransmitter, acetylcholine at neurosynaptic junctions, multiple molecular dynamics (MD) trajectories of AChE in the presence and absence of its inhibitors [J.M. Bui, J.A. McCammon, Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 15451-15456; J.M. Bui, Z. Radic, P. Taylor, J.A. McCammon, Biophys. J. 90 (2006) 3280-3287; J.M. Bui, K. Tai, J.A. McCammon, J. Am. Chem. Soc. 126 (2004) 7198-7205; J.M. Bui, R.H. Henchman, J.A. McCammon, Biophys. J. 85 (2003) 2267-2272] have been conducted and correlated with its inhibitory mechanisms. The intrinsic flexibilities of AChE, particularly of the long omega loop, are important in facilitating the ligand's inhibition of the enzyme.
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Affiliation(s)
- Jennifer M Bui
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
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88
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Comoletti D, Grishaev A, Whitten AE, Taylor P, Trewhella J. Characterization of the solution structure of a neuroligin/beta-neurexin complex. Chem Biol Interact 2008; 175:150-5. [PMID: 18550038 PMCID: PMC2587492 DOI: 10.1016/j.cbi.2008.04.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 04/09/2008] [Accepted: 04/09/2008] [Indexed: 11/20/2022]
Abstract
Neuroligins are post-synaptic cell adhesion molecules that promote synaptic maturation and stabilization upon binding with pre-synaptic partners, the alpha- and beta-neurexins. Using a combination of analytical ultracentrifugation, small angle X-ray, and neutron scattering, we have characterized the low-resolution three-dimensional structure of the extracellular domain of the neuroligins, free in solution, and in complex with beta-neurexin. The globular extracellular domain of the neuroligins forms stable homodimers through a four-helix bundle typical of the cholinesterases and other members of the alpha/beta-hydrolase fold family. The presence of the stalk region adds to the extracellular domain of neuroligin-1 an elongated structure, suggesting a rod-like nature of the stalk domain. Sedimentation equilibrium coupled with solution scattering data of the beta-neurexin/neuroligin-1 complex indicated a 2:2 stoichiometry where two beta-neurexin molecules bind to a neuroligin-1 dimer. Deuteration of neurexin allowed us to collect neutron scattering data that, in combination with other biochemical techniques, provide a basis for optimizing the positioning of each component in a detailed computational model of the neuroligin/neurexin complex. As several mutations of both neurexin and neuroligin genes have been linked to autism spectrum disorders and mental retardation, these new structures provide an important framework for the study of altered structure and function of these synaptic proteins.
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Affiliation(s)
- Davide Comoletti
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA 92093-0650, USA.
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89
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Fruchart-Gaillard C, Mourier G, Marquer C, Stura E, Birdsall NJM, Servent D. Different Interactions between MT7 Toxin and the Human Muscarinic M1 Receptor in Its Free and N-Methylscopolamine-Occupied States. Mol Pharmacol 2008; 74:1554-63. [DOI: 10.1124/mol.108.050773] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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90
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Rosenberry TL, Sonoda LK, Dekat SE, Cusack B, Johnson JL. Monitoring the reaction of carbachol with acetylcholinesterase by thioflavin T fluorescence and acetylthiocholine hydrolysis. Chem Biol Interact 2008; 175:235-41. [PMID: 18602908 DOI: 10.1016/j.cbi.2008.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 06/06/2008] [Indexed: 11/19/2022]
Abstract
Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. Carbamates are very poor substrates that, like other AChE substrates, form an initial enzyme-substrate complex and proceed to an acylated enzyme intermediate which is then hydrolyzed. However, the hydrolysis of the carbamoylated enzyme is slow enough to resolve the acylation and deacylation steps on the catalytic pathway. Here we show that the reaction of carbachol (carbamoylcholine) with AChE can be monitored both with acetylthiocholine as a reporter substrate and with thioflavin T as a fluorescent reporter group. The fluorescence of thioflavin T is strongly enhanced when it binds to the P-site of AChE, and this fluorescence is partially quenched when a second ligand binds to the A-site to form a ternary complex. These fluorescence changes allow not only the monitoring of the course of the carbamoylation reaction but also the determination of carbachol affinities for the A- and P-sites.
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Affiliation(s)
- Terrone L Rosenberry
- Mayo Clinic College of Medicine, Departments of Neuroscience and Pharmacology, 4500 San Pablo Road, Jacksonville, FL 32224, USA.
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91
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Silman I, Sussman JL. Acetylcholinesterase: how is structure related to function? Chem Biol Interact 2008; 175:3-10. [PMID: 18586019 DOI: 10.1016/j.cbi.2008.05.035] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 05/23/2008] [Accepted: 05/29/2008] [Indexed: 10/22/2022]
Abstract
In accordance with its biological role, termination of neurotransmission at cholinergic synapses by rapid hydrolysis of the neurotransmitter, acetylcholine, acetylcholinesterase is one of nature's most efficient enzymes. Solution of its three-dimensional structure revealed that its active site is located at the bottom of a deep and narrow gorge. Such an architecture was unanticipated in view of its high turnover number. The present review examines how the highly specialized structure of acetylcholinesterase, with its sequestered active site, contributes to its catalytic efficacy, and discusses how the traffic of substrate and products to and from the active site is controlled.
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Affiliation(s)
- Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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92
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Harel M, Sonoda LK, Silman I, Sussman JL, Rosenberry TL. Crystal structure of thioflavin T bound to the peripheral site of Torpedo californica acetylcholinesterase reveals how thioflavin T acts as a sensitive fluorescent reporter of ligand binding to the acylation site. J Am Chem Soc 2008; 130:7856-61. [PMID: 18512913 DOI: 10.1021/ja7109822] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acetylcholinesterase plays a key role in cholinergic synaptic transmission by hydrolyzing the neurotransmitter acetylcholine with one of the highest known catalytic rate constants. Hydrolysis occurs in a narrow and deep gorge that contains two sites of ligand binding: A peripheral site, or P-site, near the gorge entrance that contributes to catalytic efficiency both by transiently trapping substrate molecules as they enter the gorge and by allosterically accelerating the transfer of the substrate acyl group to a serine hydroxyl in an acylation site or A-site at the base of the gorge. Thioflavin T is a useful reporter of ligand interactions with the A-site. It binds specifically to the P-site with fluorescence that is enhanced approximately 1000-fold over that of unbound thioflavin T, and the enhanced fluorescence is quenched 1.5- to 4-fold when another ligand binds to the A-site in a ternary complex. To clarify the structural basis of this advantageous signal change, we here report the X-ray structure of the complex of thioflavin T with Torpedo californica acetylcholinesterase. The two aromatic rings in thioflavin T are coplanar and are packed snugly parallel to the aromatic side chains of Trp279, Tyr334, and Phe330. Overlays of this structure with the crystal structures of Torpedo californica acetylcholinesterase complexes with either edrophonium or m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, two small aromatic ligands that bind specifically to the A-site, indicate that the phenyl side chain of Phe330 must rotate to sterically accommodate both thioflavin T and the A-site ligand in the ternary complex. This rotation may allow some relaxation of the strict coplanarity of the aromatic rings in the bound thioflavin T and result in partial quenching of its fluorescence.
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Affiliation(s)
- Michal Harel
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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93
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Zaheer-ul H, Uddin R, Yuan H, Petukhov PA, Choudhary MI, Madura JD. Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. J Chem Inf Model 2008; 48:1092-103. [PMID: 18444627 DOI: 10.1021/ci8000056] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of structurally related steroidal alkaloids as butyrylcholinesterase (BuChE) inhibitors. Docking studies were employed to position the inhibitors into the BuChE active site to determine the most probable binding mode. The strategy was to explore multiple inhibitor conformations in producing a more reliable 3D-QSAR model. These multiple conformations were derived using the FlexS program. The conformation selection step for CoMFA was done by genetic algorithm. The genetic algorithm based CoMFA approach was found to be the best. Both CoMFA and CoMSIA yielded significant cross-validated q(2) values of 0.701 and 0.627 and the r(2) values of 0.979 and 0.982, respectively. These statistically significant models were validated by a test set of five compounds. Comparison of CoMFA and CoMSIA contour maps helped to identify structural requirements for the inhibitors and serves as a basis for the design of the next generation of the inhibitor analogues. The results demonstrate that the combination of ligand-based and receptor-based modeling with use of a genetic algorithm is a powerful approach to build 3D-QSAR models. These data can be used for the lead optimization process with respect to inhibition enhancement which is important for the drug discovery and development for Alzheimer's disease.
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Affiliation(s)
- Haq Zaheer-ul
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical & Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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94
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Alsallaq R, Zhou HX. Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 2008; 71:320-35. [PMID: 17932929 DOI: 10.1002/prot.21679] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to approximately 10(5)-10(6) M(-1) s(-1). Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys J 1997;73:2441-2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by $k_{\bf D}$ = $k_{D}0\ {exp} ( - \langle U_{el} \rangle;{\star}/k_{B} T),$ where k(D) and k(D0) are the rates in the presence and absence of electrostatic interactions, respectively, U(el) is the average electrostatic interaction energy in a "transient-complex" ensemble, and k(B)T is the thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with the experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007;15:215-224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations.
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Affiliation(s)
- Ramzi Alsallaq
- Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
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95
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Fabrichny IP, Leone P, Sulzenbacher G, Comoletti D, Miller MT, Taylor P, Bourne Y, Marchot P. Structural analysis of the synaptic protein neuroligin and its beta-neurexin complex: determinants for folding and cell adhesion. Neuron 2008; 56:979-91. [PMID: 18093521 DOI: 10.1016/j.neuron.2007.11.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 11/19/2007] [Accepted: 11/26/2007] [Indexed: 11/25/2022]
Abstract
The neuroligins are postsynaptic cell adhesion proteins whose associations with presynaptic neurexins participate in synaptogenesis. Mutations in the neuroligin and neurexin genes appear to be associated with autism and mental retardation. The crystal structure of a neuroligin reveals features not found in its catalytically active relatives, such as the fully hydrophobic interface forming the functional neuroligin dimer; the conformations of surface loops surrounding the vestigial active center; the location of determinants that are critical for folding and processing; and the absence of a macromolecular dipole and presence of an electronegative, hydrophilic surface for neurexin binding. The structure of a beta-neurexin-neuroligin complex reveals the precise orientation of the bound neurexin and, despite a limited resolution, provides substantial information on the Ca2+-dependent interactions network involved in trans-synaptic neurexin-neuroligin association. These structures exemplify how an alpha/beta-hydrolase fold varies in surface topography to confer adhesion properties and provide templates for analyzing abnormal processing or recognition events associated with autism.
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Affiliation(s)
- Igor P Fabrichny
- Biochimie des Interactions Moléculaires et Cellulaires, CNRS FRE-2738, Institut Fédératif de Recherche Jean Roche, Université de la Méditerranée, Faculté de Médecine Secteur Nord, F-13916 Marseille Cedex 20, France
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96
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Structural basis for synaptic adhesion mediated by neuroligin-neurexin interactions. Nat Struct Mol Biol 2007; 15:50-6. [PMID: 18084303 DOI: 10.1038/nsmb1350] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 11/16/2007] [Indexed: 12/31/2022]
Abstract
The heterophilic synaptic adhesion molecules neuroligins and neurexins are essential for establishing and maintaining neuronal circuits by modulating the formation and maturation of synapses. The neuroligin-neurexin adhesion is Ca2+-dependent and regulated by alternative splicing. We report a structure of the complex at a resolution of 2.4 A between the mouse neuroligin-1 (NL1) cholinesterase-like domain and the mouse neurexin-1beta (NX1beta) LNS (laminin, neurexin and sex hormone-binding globulin-like) domain. The structure revealed a delicate neuroligin-neurexin assembly mediated by a hydrophilic, Ca2+-mediated and solvent-supplemented interface, rendering it capable of being modulated by alternative splicing and other regulatory factors. Thermodynamic data supported a mechanism wherein splicing site B of NL1 acts by modulating a salt bridge at the edge of the NL1-NX1beta interface. Mapping neuroligin mutations implicated in autism indicated that most such mutations are structurally destabilizing, supporting deficient neuroligin biosynthesis and processing as a common cause for this brain disorder.
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97
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Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA. Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B 2007; 112:270-5. [PMID: 18052268 DOI: 10.1021/jp074900e] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Poisson-Nernst-Planck (PNP) equation provides a continuum description of electrostatic-driven diffusion and is used here to model the diffusion and reaction of acetylcholine (ACh) with acetylcholinesterase (AChE) enzymes. This study focuses on the effects of ion and substrate concentrations on the reaction rate and rate coefficient. To this end, the PNP equations are numerically solved with a hybrid finite element and boundary element method at a wide range of ion and substrate concentrations, and the results are compared with the partially coupled Smoluchowski-Poisson-Boltzmann model. The reaction rate is found to depend strongly on the concentrations of both the substrate and ions; this is explained by the competition between the intersubstrate repulsion and the ionic screening effects. The reaction rate coefficient is independent of the substrate concentration only at very high ion concentrations, whereas at low ion concentrations the behavior of the rate depends strongly on the substrate concentration. Moreover, at physiological ion concentrations, variations in substrate concentration significantly affect the transient behavior of the reaction. Our results offer a reliable estimate of reaction rates at various conditions and imply that the concentrations of charged substrates must be coupled with the electrostatic computation to provide a more realistic description of neurotransmission and other electrodiffusion and reaction processes.
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Affiliation(s)
- Y C Zhou
- Department of Mathematics, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365, USA
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98
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Affiliation(s)
- Y. C. Zhou
- Department of Mathematics, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - Benzhuo Lu
- Department of Mathematics, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - Gary A. Huber
- Department of Mathematics, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - Michael J. Holst
- Department of Mathematics, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - J. Andrew McCammon
- Department of Mathematics, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
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99
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Abstract
Acetylcholinesterase rapidly hydrolyzes the neurotransmitter acetylcholine in cholinergic synapses, including the neuromuscular junction. The tetramer is the most important functional form of the enzyme. Two low-resolution crystal structures have been solved. One is compact with two of its four peripheral anionic sites (PAS) sterically blocked by complementary subunits. The other is a loose tetramer with all four subunits accessible to solvent. These structures lacked the C-terminal amphipathic t-peptide (WAT domain) that interacts with the proline-rich attachment domain (PRAD). A complete tetramer model (AChEt) was built based on the structure of the PRAD/WAT complex and the compact tetramer. Normal mode analysis suggested that AChEt could exist in several conformations with subunits fluctuating relative to one another. Here, a multiscale simulation involving all-atom molecular dynamics and C alpha-based coarse-grained Brownian dynamics simulations was carried out to investigate the large-scale intersubunit dynamics in AChEt. We sampled the ns-mus timescale motions and found that the tetramer indeed constitutes a dynamic assembly of monomers. The intersubunit fluctuation is correlated with the occlusion of the PAS. Such motions of the subunits "gate" ligand-protein association. The gates are open more than 80% of the time on average, which suggests a small reduction in ligand-protein binding. Despite the limitations in the starting model and approximations inherent in coarse graining, these results are consistent with experiments which suggest that binding of a substrate to the PAS is only somewhat hindered by the association of the subunits.
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100
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Taylor P, Reiner E, Kovarik Z, Radić Z. Application of Recombinant DNA Methods for Production of Cholinesterases as Organophosphate Antidotes and Detectors. Arh Hig Rada Toksikol 2007; 58:339-45. [PMID: 17913689 DOI: 10.2478/v10004-007-0027-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Application of Recombinant DNA Methods for Production of Cholinesterases as Organophosphate Antidotes and DetectorsTo develop new avenues for synthesizing novel antidotes for organophosphate poisoning and for detection of the organophosphates, we have turned to recombinant DNA methods to synthesize cholinesterases with unusual properties. For antidotal therapy we describe mutations of the native mouse and human enzymes that allow for enhanced rates of oxime reactivation. Such enzymes, when localized in the circulation, would enable the circulating cholinesterase to become a catalytic rather than simply a stoichiometric scavenger. Hence, "oxime-assisted catalysis" provides a means for scavenging the organophosphates in the circulation thereby minimizing their tissue penetration and toxicity. Accordingly, the oxime antidote or prophylactic agent has a dual action within the circulation and at the tissue level. Second, through a novel chemistry, termed freeze-frame, click chemistry, we have used organophosphate conjugates of acetylcholinesterase as templates for the synthesis of novel nucleophilic reactivating agents. Finally, acetylcholinesterase can be modified through cysteine substitution mutagenesis and attachment of fluorophores at the substitution positions. When linked at certain locations in the molecule, the attached fluorophore is sensitive to organophosphate conjugation with acetylcholinesterase, and thus the very target of insecticide or nerve agent action becomes a detection molecule for organophosphate exposure.
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Affiliation(s)
- Palmer Taylor
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093-0657, USA.
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