101
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Meltzer RH, Thompson E, Soman KV, Song XZ, Ebalunode JO, Wensel TG, Briggs JM, Pedersen SE. Electrostatic steering at acetylcholine binding sites. Biophys J 2006; 91:1302-14. [PMID: 16751247 PMCID: PMC1518644 DOI: 10.1529/biophysj.106.081463] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The electrostatic environments near the acetylcholine binding sites on the nicotinic acetylcholine receptor (nAChR) and acetylcholinesterase were measured by diffusion-enhanced fluorescence energy transfer (DEFET) to determine the influence of long-range electrostatic interactions on ligand binding kinetics and net binding energy. Changes in DEFET from variously charged Tb3+ -chelates revealed net potentials of -20 mV at the nAChR agonist sites and -14 mV at the entrance to the AChE active site, in physiological ionic strength conditions. The potential at the alphadelta-binding site of the nAChR was determined independently in the presence of d-tubocurarine to be -14 mV; the calculated potential at the alphagamma-site was approximately threefold stronger than at the alphadelta-site. By determining the local potential in increasing ionic strength, Debye-Hückel theory predicted that the potentials near the nAChR agonist binding sites are constituted by one to three charges in close proximity to the binding site. Examination of the binding kinetics of the fluorescent acetylcholine analog dansyl-C6-choline at ionic strengths from 12.5 to 400 mM revealed a twofold decrease in association rate. Debye-Hückel analysis of the kinetics revealed a similar charge distribution as seen by changes in the potentials. To determine whether the experimentally determined potentials are reflected by continuum electrostatics calculations, solutions to the nonlinear Poisson-Boltzmann equation were used to compute the potentials expected from DEFET measurements from high-resolution models of the nAChR and AChE. These calculations are in good agreement with the DEFET measurements for AChE and for the alphagamma-site of the nAChR. We conclude that long-range electrostatic interactions contribute -0.3 and -1 kcal/mol to the binding energy at the nAChR alphadelta- and alphagamma-sites due to an increase in association rates.
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Affiliation(s)
- Robert H Meltzer
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
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102
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Thomas AS, Elcock AH. Direct Observation of Salt Effects on Molecular Interactions through Explicit-Solvent Molecular Dynamics Simulations: Differential Effects on Electrostatic and Hydrophobic Interactions and Comparisons to Poisson−Boltzmann Theory. J Am Chem Soc 2006; 128:7796-806. [PMID: 16771493 DOI: 10.1021/ja058637b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins and other biomolecules function in cellular environments that contain significant concentrations of dissolved salts and even simple salts such as NaCl can significantly affect both the kinetics and thermodynamics of macromolecular interactions. As one approach to directly observing the effects of salt on molecular associations, explicit-solvent molecular dynamics (MD) simulations have been used here to model the association of pairs of the amino acid analogues acetate and methylammonium in aqueous NaCl solutions of concentrations 0, 0.1, 0.3, 0.5, 1, and 2 M. By performing simulations of 500 ns duration for each salt concentration properly converged estimates of the free energy of interaction of the two molecules have been obtained for all intermolecular separation distances and geometries. The resulting free energy surfaces are shown to give significant new insights into the way salt modulates interactions between molecules containing both charged and hydrophobic groups and are shown to provide valuable new benchmarks for testing the description of salt effects provided by the simpler but faster Poisson-Boltzmann method. In addition, the complex many-dimensional free energy surfaces are shown to be decomposable into a number of one-dimensional effective energy functions. This decomposition (a) allows an unambiguous view of the qualitative differences between the salt dependence of electrostatic and hydrophobic interactions, (b) gives a clear rationalization for why salt exerts different effects on protein-protein association and dissociation rates, and (c) produces simplified energy functions that can be readily used in much faster Brownian dynamics simulations.
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Affiliation(s)
- Andrew S Thomas
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA
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103
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Bui JM, Radic Z, Taylor P, McCammon JA. Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase. Biophys J 2006; 90:3280-7. [PMID: 16473897 PMCID: PMC1432132 DOI: 10.1529/biophysj.105.075564] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The neurotoxin fasciculin-2 (FAS2) is a picomolar inhibitor of synaptic acetylcholinesterase (AChE). The dynamics of binding between FAS2 and AChE is influenced by conformational fluctuations both before and after protein encounter. Submicrosecond molecular dynamics trajectories of apo forms of fasciculin, corresponding to different conformational substates, are reported here with reference to the conformational changes of loop I of this three-fingered toxin. This highly flexible loop exhibits an ensemble of conformations within each substate corresponding to its functions. The high energy barrier found between the two major substates leads to transitions that are slow on the timescale of the diffusional encounter of noninteracting FAS2 and AChE. The more stable of the two apo substates may not be the one observed in the complex with AChE. It seems likely that the more stable apo form binds rapidly to AChE and conformational readjustments then occur in the resulting encounter complex.
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Affiliation(s)
- Jennifer M Bui
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA.
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104
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Parent KN, Doyle SM, Anderson E, Teschke CM. Electrostatic interactions govern both nucleation and elongation during phage P22 procapsid assembly. Virology 2005; 340:33-45. [PMID: 16045955 DOI: 10.1016/j.virol.2005.06.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 06/01/2005] [Accepted: 06/04/2005] [Indexed: 11/21/2022]
Abstract
Icosahedral capsid assembly is an example of a reaction controlled solely by the interactions of the proteins involved. Bacteriophage P22 procapsids can be assembled in vitro by mixing coat and scaffolding proteins in a nucleation-limited reaction, where scaffolding protein directs the proper assembly of coat protein. Here, we investigated the effect of the buffer composition on the interactions necessary for capsid assembly. Different concentrations of various salts, chosen to follow the electroselectivity series for anions, were added to the assembly reaction. The concentration and type of salt was found to be crucial for proper nucleation of procapsids. Nucleation in low salt concentrations readily occurred but led to bowl-like partial procapsids, as visualized by negative stain electron microscopy. The edge of the partial capsids remained assembly-competent since coat protein addition triggered procapsid completion. The addition of salt to the partial capsids also caused procapsid completion. In addition, each salt affected both assembly rates and the extent of procapsid formation. We hypothesize that low salt conditions increase the coat protein:scaffolding protein affinity, causing excessive nuclei to form, which decreases coat protein levels leading to incomplete assembly.
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Affiliation(s)
- Kristin N Parent
- Department of Molecular and Cell Biology, Unit 3125, University of Connecticut, Storrs, CT 06269-3125, USA
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105
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Branduardi D, Gervasio FL, Cavalli A, Recanatini M, Parrinello M. The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge. J Am Chem Soc 2005; 127:9147-55. [PMID: 15969593 DOI: 10.1021/ja0512780] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the ligand (tetramethylammonium) recognition by the peripheral anionic site and its penetration of the human AChE gorge by using atomistic molecular dynamics simulations and our recently developed metadynamics method. The role of both the peripheral anionic site and the formation of cation-pi interactions in the ligand entrance are clearly shown. In particular, a simulation with the W286A mutant shows the fundamental role of this residue in anchoring the ligand at the peripheral anionic site of the enzyme and in positioning it prior to the gorge entrance. Once the ligand is properly oriented, the formation of specific and synchronized cation-pi interactions with W86, F295, and Y341 enables the gorge penetration. Eventually, the ligand is stabilized in a free energy basin by means of cation-pi interactions with W86.
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Affiliation(s)
- Davide Branduardi
- Computational Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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106
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Choudhary MI, Nawaz SA, ul-Haq Z, Lodhi MA, Ghayur MN, Jalil S, Riaz N, Yousuf S, Malik A, Gilani AH, ur-Rahman A. Withanolides, a new class of natural cholinesterase inhibitors with calcium antagonistic properties. Biochem Biophys Res Commun 2005; 334:276-87. [PMID: 16108094 DOI: 10.1016/j.bbrc.2005.06.086] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The withanolides 1-3 and 4-5 isolated from Ajuga bracteosa and Withania somnifera, respectively, inhibited acetylcholinesterase (AChE, EC 3.1.1.7) and butyrylcholinesterase (BChE, EC 3.1.1.8) enzymes in a concentration-dependent fashion with IC50 values ranging between 20.5 and 49,2 microm and 29.0 and 85.2 microm for AChE and BChE, respectively. Lineweaver-Burk as well as Dixon plots and their secondary replots indicated that compounds 1, 3, and 5 are the linear mixed-type inhibitors of AChE, while 2 and 4 are non-competitive inhibitors of AChE with K(i) values ranging between 20.0 and 45.0 microm. All compounds were found to be non-competitive inhibitors of BChE with K(i) values ranging between 27.7 and 90.6 microm. Molecular docking study revealed that all the ligands are completely buried inside the aromatic gorge of AChE, while compounds 1, 3, and 5 extend up to the catalytic triad. A comparison of the docking results showed that all ligands generally adopt the same binding mode and lie parallel to the surface of the gorge. The superposition of the docked structures demonstrated that the non-flexible skeleton of the ligands always penetrates the aromatic gorge through the six-membered ring A, allowing their simultaneous interaction with more than one subsite of the active center. The affinity of ligands with AChE was found to be the cumulative effects of number of hydrophobic contacts and hydrogen bonding. Furthermore, all compounds also displayed dose-dependent (0.005-1.0 mg/mL) spasmolytic and Ca2+ antagonistic potentials in isolated rabbit jejunum preparations, compound 4 being the most active with an ED50 value of 0.09 +/- 0.001 mg/mL and 0.22 +/- 0.01 microg/mL on spontaneous and K+ -induced contractions, respectively. The cholinesterase inhibitory potential along with calcium antagonistic ability and safe profile in human neutrophil viability assay could make compounds 1-5 possible drug candidates for further study to treat Alzheimer's disease and associated problems.
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Affiliation(s)
- M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi-75270, Pakistan.
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107
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Martinez-Pena y Valenzuela I, Hume RI, Krejci E, Akaaboune M. In vivo regulation of acetylcholinesterase insertion at the neuromuscular junction. J Biol Chem 2005; 280:31801-8. [PMID: 15998641 DOI: 10.1074/jbc.m502874200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The efficiency of synaptic transmission between nerve and muscle depends on the number and density of acetylcholinesterase molecules (AChE) at the neuromuscular junction. However, little is known about the way this density is maintained and regulated in vivo. By using time lapse and quantitative fluorescence imaging assays in living mice, we demonstrated that insertion of new AChEs occurs within hours of saturating pre-existing AChEs with fasciculin2, a snake toxin that selectively labels AChE. In the absence of muscle postsynaptic activity or evoked nerve presynaptic neurotransmitter release, AChE insertion was decreased significantly, whereas direct stimulation of the muscle completely restored AChE insertion to control levels. This activity-dependent AChE insertion is mediated by intracellular calcium. In muscle stimulated in the presence of a Ca2+ channel blocker or calcium-permeable Ca2+ chelator, AChE insertion into synapses was significantly decreased, whereas ryanodine or ionophore A12387 treatment of blocked and unstimulated synapses significantly increased AChE insertion. These results demonstrated that synaptic activity is critical for AChE insertion and indicated that a rise in intracellular calcium either through voltage-gated calcium channels or from intracellular stores is critical for proper AChE insertion into the adult synapse.
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108
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Abstract
We have studied the catalytic efficiency of acetylcholinesterase (AChE) in various solutions with ion-disturbed water structure to explore the role that the water structure plays in the substrate-enzyme encounter. The extent of water structuring in the different aqueous solutions was determined by near-infrared spectroscopy. The influence of water structure on the degree of solvation and on the intramolecular mobility of AChE was investigated for different aqueous ionic solutions by small-angle x-ray scattering technique and depolarization fluorescence spectroscopy. It was found that the encounter process between AChE and acetylthiocholine was promoted in solutions with less structured water. In these solutions it was also found that AChE is less solvated coinciding with higher intramolecular mobility. The found experimental results suggest that the water structure may influence the substrate-enzyme encounter process by diminishing the AChE solvation shell and may help diffusion of the substrate through the gorge by enhancing the intramolecular mobility of AChE.
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Affiliation(s)
- Angela S F Ramos
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Spektroskopie und Photochemische Kinetik-Strukturdynamik (bio)chemischer Systeme, 37077 Göttingen, Germany
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109
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Li G, Sheng Z, Huang Z, Niu L. Kinetic mechanism of channel opening of the GluRDflip AMPA receptor. Biochemistry 2005; 44:5835-41. [PMID: 15823042 DOI: 10.1021/bi047413n] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AMPA-type ionotropic glutamate receptors mediate the majority of fast excitatory neurotransmission in the mammalian central nervous system and are essential for brain functions, such as memory and learning. Dysfunction of these receptors has been implicated in a variety of neurological diseases. Using a laser-pulse photolysis technique, we investigated the channel opening mechanism for GluRD(flip) or GluR4(flip) (i.e., the flip isoform of GluRD), an AMPA receptor subunit. The minimal kinetic mechanism for channel opening is consistent with binding of two glutamate molecules per receptor complex. The GluRD(flip) channel opens with a rate constant of (6.83 +/- 0.74) x 10(4) s(-1) and closes with a rate constant of (3.35 +/- 0.17) x 10(3) s(-1). On the basis of these rate constants, the channel opening probability is calculated to be 0.95 +/- 0.12. Furthermore, the shortest rise time (20-80% of the receptor current response to glutamate) is predicted to be 20 micros, which is approximately 8 times shorter than the previous estimate. These findings suggest that the kinetic property of GluRD(flip) is similar to that of GluR2Q(flip), another fast-activating AMPA receptor subunit.
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Affiliation(s)
- Gang Li
- Department of Chemistry, Center of Biochemistry and Biophysics, State University of New York, Albany, New York 12222, USA
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110
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Rocchia W. Poisson-boltzmann equation boundary conditions for biological applications. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.mcm.2005.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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111
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Huang X, Dong F, Zhou HX. Electrostatic Recognition and Induced Fit in the κ-PVIIA Toxin Binding to Shaker Potassium Channel. J Am Chem Soc 2005; 127:6836-49. [PMID: 15869307 DOI: 10.1021/ja042641q] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Brownian dynamics (BD) and molecular dynamics (MD) simulations and electrostatic calculations were performed to study the binding process of kappa-PVIIA to the Shaker potassium channel and the structure of the resulting complex. BD simulations, guided by electrostatic interactions, led to an initial alignment between the toxin and the channel protein. MD simulations were then carried out to allow for rearrangements from this initial structure. After approximately 4 ns, a critical "induced fit" process was observed to last for approximately 2 ns. In this process, the interface was reorganized, and side chains were moved so that favorable atomic contacts were formed or strengthened, while unfavorable contacts were eliminated. The final complex structure was stabilized through electrostatic interactions with the positively charged side chain of Lys7 of kappa-PVIIA deeply inserted into the channel pore and other hydrogen bonds and by hydrophobic interactions involving Phe9 and Phe23 of the toxin. The validity of the predicted structure for the complex was assessed by calculating the effects of mutating charged and polar residues of both the toxin and the channel protein, with the calculated effects correlating reasonably well with experimental data. The present study suggests a general binding mechanism, whereby proteins are pre-aligned in their diffusional encounter by long-range electrostatic attraction, and nanosecond-scale rearrangements within the initial complex then lead to a specifically bound complex.
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Affiliation(s)
- Xiaoqin Huang
- Institute of Molecular Biophysics and School of Computational Science, Department of Physics, Florida State University, Tallahassee, FL 32306, USA
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112
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Song Y, Zhang Y, Bajaj CL, Baker NA. Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis. Biophys J 2005; 87:1558-66. [PMID: 15345536 PMCID: PMC1304562 DOI: 10.1529/biophysj.104.041517] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As described previously, continuum models, such as the Smoluchowski equation, offer a scalable framework for studying diffusion in biomolecular systems. This work presents new developments in the efficient solution of the continuum diffusion equation. Specifically, we present methods for adaptively refining finite element solutions of the Smoluchowski equation based on a posteriori error estimates. We also describe new, molecular-surface-based models, for diffusional reaction boundary criteria and compare results obtained from these models with the traditional spherical criteria. The new methods are validated by comparison of the calculated reaction rates with experimental values for wild-type and mutant forms of mouse acetylcholinesterase. The results show good agreement with experiment and help to define optimal reactive boundary conditions.
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Affiliation(s)
- Yuhua Song
- Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
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113
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Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J 2005; 88:1659-65. [PMID: 15626705 PMCID: PMC1305222 DOI: 10.1529/biophysj.104.053850] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Accepted: 12/15/2004] [Indexed: 11/18/2022] Open
Abstract
The tetramer is the most important form for acetylcholinesterase in physiological conditions, i.e., in the neuromuscular junction and the nervous system. It is important to study the diffusion of acetylcholine to the active sites of the tetrameric enzyme to understand the overall signal transduction process in these cellular components. Crystallographic studies revealed two different forms of tetramers, suggesting a flexible tetramer model for acetylcholinesterase. Using a recently developed finite element solver for the steady-state Smoluchowski equation, we have calculated the reaction rate for three mouse acetylcholinesterase tetramers using these two crystal structures and an intermediate structure as templates. Our results show that the reaction rates differ for different individual active sites in the compact tetramer crystal structure, and the rates are similar for different individual active sites in the other crystal structure and the intermediate structure. In the limit of zero salt, the reaction rates per active site for the tetramers are the same as that for the monomer, whereas at higher ionic strength, the rates per active site for the tetramers are approximately 67%-75% of the rate for the monomer. By analyzing the effect of electrostatic forces on ACh diffusion, we find that electrostatic forces play an even more important role for the tetramers than for the monomer. This study also shows that the finite element solver is well suited for solving the diffusion problem within complicated geometries.
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Affiliation(s)
- Deqiang Zhang
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093, USA.
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114
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Dong H, Xiang YY, Farchi N, Ju W, Wu Y, Chen L, Wang Y, Hochner B, Yang B, Soreq H, Lu WY. Excessive expression of acetylcholinesterase impairs glutamatergic synaptogenesis in hippocampal neurons. J Neurosci 2005; 24:8950-60. [PMID: 15483114 PMCID: PMC6730061 DOI: 10.1523/jneurosci.2106-04.2004] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Acetylcholinesterase (AChE) exerts noncatalytic activities on neural cell differentiation, adhesion, and neuritogenesis independently of its catalytic function. The noncatalytic functions of AChE have been attributed to its peripheral anionic site (PAS)-mediated protein-protein interactions. Structurally, AChE is highly homologous to the extracellular domain of neuroligin, a postsynaptic transmembrane molecule that interacts with presynaptic beta-neurexins, thus facilitating synaptic formation and maturation. Potential effects of AChE expression on synaptic transmission, however, remain unknown. Using electrophysiology, immunocytochemistry, and molecular biological approaches, this study investigated the role of AChE in the regulation of synaptic formation and functions. We found that AChE was highly expressed in cultured embryonic hippocampal neurons at early culture days, particularly in dendritic compartments including the growth cone. Subsequently, the expression level of AChE declined, whereas synaptic activity and synaptic proteins progressively increased. Chronic blockade of the PAS of AChE with specific inhibitors selectively impaired glutamatergic functions and excitatory synaptic structures independently of cholinergic activation, while inducing AChE overexpression. Moreover, the PAS blockade-induced glutamatergic impairments were associated with a depressed expression of beta-neurexins and an accumulation of other synaptic proteins, including neuroligins, and were mostly preventable by antisense suppression of AChE expression. Our findings demonstrate that interference with the nonenzymatic features of AChE alters AChE expression, which impairs excitatory synaptic structure and functions.
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Affiliation(s)
- Haiheng Dong
- Sunnybrook and Women's College Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada M4N 3M5
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115
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Manojkumar TK, Cui C, Kim KS. Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine. J Comput Chem 2005; 26:606-11. [PMID: 15739192 DOI: 10.1002/jcc.20199] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Acylation of acetylcholine (ACh) catalyzed by acetylcholinesterase (AChE) has been studied using high-level theoretical calculations on a model system that mimics the reaction center of the enzyme, and compared with uncatalyzed acylation reaction. The geometries of all the intermediates and transition states, activation energies, and solvent effects have been calculated. The calculations predict simultaneous formation of two short-strong hydrogen bonds (SSHB) in the rate-determining transition state structures [the first SSHB involves the hydrogen atom of Ser-200 (H(s)) and another involves the hydrogen atom of His-440 (H(h))]. In the intermediate states, the H-bond corresponding to H(h) involves SSHB, whereas the one corresponding to H(s) does not.
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Affiliation(s)
- T K Manojkumar
- Creative Research Initiative Center for Superfunctional Materials, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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116
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Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J 2004; 86:2017-29. [PMID: 15041644 PMCID: PMC1304055 DOI: 10.1016/s0006-3495(04)74263-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been developed to solve the steady-state Smoluchowski equation to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to mouse acetylcholinesterase. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different reaction criteria. The calculated rates were compared with experimental data and show very good agreement when the correct reaction criterion is used. Additionally, these finite element methods require significantly less computational resources than existing particle-based Brownian dynamics methods.
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Affiliation(s)
- Yuhua Song
- Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
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117
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Bui JM, Henchman RH, McCammon JA. The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge. Biophys J 2004; 85:2267-72. [PMID: 14507691 PMCID: PMC1303452 DOI: 10.1016/s0006-3495(03)74651-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The dynamics of ligand movement through the constricted region of the acetylcholinesterase gorge is important in understanding how the ligand gains access to and is released from the active site of the enzyme. Molecular dynamics simulations of the simple ligand, tetramethylammonium, crossing this bottleneck region are conducted using umbrella potential sampling and activated flux techniques. The low potential of mean force obtained is consistent with the fast reaction rate of acetylcholinesterase observed experimentally. From the results of the activated dynamics simulations, local conformational fluctuations of the gorge residues and larger scale collective motions of the protein are found to correlate highly with the ligand crossing.
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Affiliation(s)
- Jennifer M Bui
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, USA.
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118
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Boyd AE, Dunlop CS, Wong L, Radic Z, Taylor P, Johnson DA. Nanosecond Dynamics of Acetylcholinesterase Near the Active Center Gorge. J Biol Chem 2004; 279:26612-8. [PMID: 15078872 DOI: 10.1074/jbc.m401482200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To delineate the role of peptide backbone flexibility and rapid molecular motion in acetylcholinesterase catalysis and inhibitor association, we investigated the decay of fluorescence anisotropy at three sites of fluorescein conjugation to cysteine-substitution mutants of the enzyme. One cysteine was placed in a loop at the peripheral site near the rim of the active center gorge (H287C); a second was in a helical region outside of the active center gorge (T249C); a third was at the tip of a small, flexible omega loop well separated from the gorge (A262C). Mutation and fluorophore conjugation did not appreciably alter catalytic or inhibitor binding parameters of the enzyme. The results show that each site examined was associated with a high degree of segmental motion; however, the A262C and H287C sites were significantly more flexible than the T249C site. Association of the active center inhibitor, tacrine, and the peripheral site peptide inhibitor, fasciculin, had no effect on the anisotropy decay of fluorophores at positions 249 and 262. Fasciculin, but not tacrine, on the other hand, dramatically altered the decay profile of the fluorophore at the 287 position, in a manner consistent with fasciculin reducing the segmental motion of the peptide chain in this local region. The results suggest that the motions of residues near the active center gorge and across from the Cys(69)-Cys(96) omega loop are uncoupled and that ligand binding at the active center or the peripheral site does not influence acetylcholinesterase conformational dynamics globally, but induces primarily domain localized decreases in flexibility proximal to the bound ligand.
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Affiliation(s)
- Aileen E Boyd
- Department of Pharmacology, University of California, La Jolla, California 92093-0636, USA
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119
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Bui JM, Tai K, McCammon JA. Acetylcholinesterase: Enhanced Fluctuations and Alternative Routes to the Active Site in the Complex with Fasciculin-2. J Am Chem Soc 2004; 126:7198-205. [PMID: 15186156 DOI: 10.1021/ja0485715] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 15 ns molecular dynamics simulation is reported for the complex of mouse acetylcholinesterase (mAChE) and the protein neurotoxin fasciculin-2. As compared to a 15 ns simulation of apo-mAChE, the structural fluctuations of the enzyme are substantially increased in magnitude for the enzyme in the complex. Fluctuations of part of the long omega loop (residues 69-96) are particularly enhanced. This loop forms one wall of the active site, and the enhanced fluctuations lead to additional routes of access to the active site.
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Affiliation(s)
- Jennifer M Bui
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, USA.
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120
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Zhou HX. Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment. Protein Sci 2004; 12:2379-82. [PMID: 14500897 PMCID: PMC2366933 DOI: 10.1110/ps.03216203] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The rapid binding of cytotoxic colicin E3 by its cognate immunity protein Im3 is essential in safeguarding the producing cell. The X-ray structure of the E3/Im3 complex shows that the Im3 molecule interfaces with both the C-terminal ribonuclease (RNase) domain and the N-terminal translocation domain of E3. The association and dissociation rates of the RNase domain and Im3 show drastically different sensitivities to ionic strength, as previously rationalized for electrostatically enhanced diffusion-limited protein-protein associations. Relative to binding to the RNase domain, binding to full-length E3 shows a comparable association rate but a significantly lower dissociation rate. This outcome is just what was anticipated by a theory for the binding of two linked domains to a protein. The E3/Im3 system thus provides a powerful paradigm for the interplay of theory and experiment.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
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121
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Stewart RC, Van Bruggen R. Association and dissociation kinetics for CheY interacting with the P2 domain of CheA. J Mol Biol 2004; 336:287-301. [PMID: 14741223 DOI: 10.1016/j.jmb.2003.11.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The chemotaxis system of Escherichia coli makes use of an extended two-component sensory response pathway in which CheA, an autophosphorylating protein histidine kinase (PHK) rapidly passes its phosphoryl group to CheY, a phospho-accepting response regulator protein (RR). The CheA-->CheY phospho-transfer reaction is 100-1000 times faster than the His-->Asp phospho-relays that operate in other (non-chemotaxis) two-component regulatory systems, suggesting that CheA and CheY have unique features that enhance His-->Asp phospho-transfer kinetics. One such feature could be the P2 domain of CheA. P2 encompasses a binding site for CheY, but an analogous RR-binding domain is not found in other PHKs. In previous work, we removed P2 from CheA, and this decreased the catalytic efficiency of CheA-->CheY phospho-transfer by a factor of 50-100. Here we examined the kinetics of the binding interactions between CheY and P2. The rapid association reaction (k(assn) approximately 10(8)M(-1)s(-1) at 25 degrees C and micro=0.03 M) exhibited a simple first-order dependence on P2 concentration and appeared to be largely diffusion-limited. Ionic strength (micro) had a moderate effect on k(assn) in a manner predictable based on the calculated electrostatic interaction energy of the protein binding surfaces and the expected Debye-Hückel shielding. The speed of binding reflects, in part, electrostatic interactions, but there is also an important contribution from the inherent plasticity of the complex and the resulting flexibility that this allows during the process of complex formation. Our results support the idea that the P2 domain of CheA contributes to the overall speed of phospho-transfer by promoting rapid association between CheY and CheA. However, this alone does not account for the ability of the chemotaxis system to operate much more rapidly than other two-component systems: k(cat) differences indicate that CheA and CheY also achieve the chemical events of phospho-transfer more rapidly than do PHK-RR pairs of slower systems.
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Affiliation(s)
- Richard C Stewart
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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122
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123
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Hicks SN, Smiley RD, Hamilton JB, Howell EE. Role of ionic interactions in ligand binding and catalysis of R67 dihydrofolate reductase. Biochemistry 2003; 42:10569-78. [PMID: 12962480 DOI: 10.1021/bi034643d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
R67 dihydrofolate reductase (DHFR), which catalyzes the NADPH dependent reduction of dihydrofolate to tetrahydrofolate, belongs to a type II family of R-plasmid encoded DHFRs that confer resistance to the antibacterial drug trimethoprim. Crystal structure data reveals this enzyme is a homotetramer that possesses a single active site pore. Only two charged residues in each monomer are located near the pore, K32 and K33. Site-directed mutants were constructed to probe the role of these residues in ligand binding and/or catalysis. As a result of the 222 symmetry of this enzyme, mutagenesis of one residue results in modification at four related sites. All mutants at K32 affected the quaternary structure, producing an inactive dimer. The K33M mutant shows only a 2-4-fold effect on K(m) values. Salt effects on ligand binding and catalysis for K33M and wildtype R67 DHFRs were investigated to determine if these lysines are involved in forming ionic interactions with the negatively charged substrates, dihydrofolate (overall charge of -2) and NADPH (overall charge of -3). Binding studies indicate that two ionic interactions occur between NADPH and R67 DHFR. In contrast, the binding of folate, a poor substrate, to R67 DHFR.NADPH appears weak as a titration in enthalpy is lost at low ionic strength. Steady-state kinetic studies for both wild type (wt) and K33M R67 DHFRs also support a strong electrostatic interaction between NADPH and the enzyme. Interestingly, quantitation of the observed salt effects by measuring the slopes of the log of ionic strength versus the log of k(cat)/K(m) plots indicates that only one ionic interaction is involved in forming the transition state. These data support a model where two ionic interactions are formed between NADPH and symmetry related K32 residues in the ground state. To reach the transition state, an ionic interaction between K32 and the pyrophosphate bridge is broken. This unusual scenario likely arises from the constraints imposed by the 222 symmetry of the enzyme.
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Affiliation(s)
- Stephanie N Hicks
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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124
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Xu Y, Shen J, Luo X, Silman I, Sussman JL, Chen K, Jiang H. How Does Huperzine A Enter and Leave the Binding Gorge of Acetylcholinesterase? Steered Molecular Dynamics Simulations. J Am Chem Soc 2003; 125:11340-9. [PMID: 16220957 DOI: 10.1021/ja029775t] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.
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Affiliation(s)
- Yechun Xu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Meteria Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China
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125
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Marvin JS, Lowman HB. Redesigning an antibody fragment for faster association with its antigen. Biochemistry 2003; 42:7077-83. [PMID: 12795603 DOI: 10.1021/bi026947q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Traditional approaches for increasing the affinity of protein-protein complexes focus on constructing highly complementary binding surfaces. Recent theoretical simulations and experimental results suggest that electrostatic steering forces can also be manipulated to increase association rates while leaving dissociation rates unchanged, thus increasing affinity. Here we demonstrate that electrostatic attraction can be enhanced between an antibody fragment and its cognate antigen through application of a few simple rules to identify potential on-rate amplification sites that lie at the periphery of the antigen-antibody interface.
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Affiliation(s)
- Jonathan S Marvin
- Genentech, Inc., Department of Protein Engineering, South San Francisco, California 94080, USA
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126
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Affiliation(s)
- Shoshana J Wodak
- Unite de Conformation de Macromolécules Biologique, Université Libre de Bruxelles CP 160/16, 1050 Brussels, Belgium
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127
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Kier LB, Cheng CK, Testa B. Studies of ligand diffusion pathways over a protein surface. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2003; 43:255-8. [PMID: 12546560 DOI: 10.1021/ci020383f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies were conducted on the behavior of simulated molecules diffusing within organized water, postulated to form from the hydropathic states of protein surface amino acid side chains. This organization is postulated to facilitate the diffusion of ligands across the protein surface to their effector. These studies reveal that the organized water can be disrupted in their diffusion facilitating function by the presence of some other solute in high concentration. It was also found from cellular automata simulations that chiral isomers behaved in a slightly different manner when in an asymmetric enclosure simulating a fragment of the organized water pathway. These findings have relevance to observations about the mechanism of action of nonspecific anesthetic agents.
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Affiliation(s)
- Lemont B Kier
- Institute of Medicinal Chemistry, University of Lausanne, CH-1015 Lausanne, Switzerland.
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128
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Darling RJ, Kuchibhotla U, Glaesner W, Micanovic R, Witcher DR, Beals JM. Glycosylation of erythropoietin affects receptor binding kinetics: role of electrostatic interactions. Biochemistry 2002; 41:14524-31. [PMID: 12463751 DOI: 10.1021/bi0265022] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Erythropoietin (EPO) is a cytokine produced by the kidney whose function is to stimulate red blood cell production in the bone marrow. Previously, it was shown that the affinity of EPO for its receptor, EPOR, is inversely related to the sialylation of EPO carbohydrate. To better understand the properties of EPO that modulate its receptor affinity, various glycoforms were analyzed using surface plasmon resonance. The system used has been well characterized and is based on previous reports employing an EPOR-Fc chimera captured on a Protein A surface. Using three variants of EPO containing different levels of sialylation, we determined that sialic acid decreased the association rate constant (k(on)) about 3-fold. Furthermore, glycosylated EPO had a 20-fold slower k(on) than nonglycosylated EPO, indicating that the core carbohydrate also negatively impacted k(on). The effect of electrostatic forces on EPO binding was studied by measuring binding kinetics in varying NaCl concentrations. Increasing NaCl concentration resulted in a slower k(on) while having little impact on k(off), suggesting that long-range electrostatic interactions are primarily important in determining the rate of association between EPO and EPOR. Furthermore, the glycosylation content (i.e., nonglycosylated vs glycosylated, sialylated vs desialylated) affected the overall sensitivities of k(on) to [NaCl], indicating that sialic acid and the glycan itself each impact the overall effect of these electrostatic forces.
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Affiliation(s)
- Ryan J Darling
- BioResearch Technologies and Proteins, Lilly Research Laboratories, Eli Lilly and Co., Indianapolis, Indiana 46285, USA
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129
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Zhang Y, Kua J, McCammon JA. Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc 2002; 124:10572-7. [PMID: 12197759 DOI: 10.1021/ja020243m] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE) has been studied by a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach. The reaction proceeds through the nucleophilic addition of the Ser203 O to the carbonyl C of acetylcholine, and the reaction is facilitated by simultaneous proton transfer from Ser203 to His447. The calculated potential energy barrier at the MP2(6-31+G) QM/MM level is 10.5 kcal/mol, consistent with the experimental reaction rate. The third residue of the catalytic triad, Glu334, is found to be essential in stabilizing the transition state through electrostatic interactions. The oxyanion hole, formed by peptidic NH groups from Gly121, Gly122, and Ala204, is also found to play an important role in catalysis. Our calculations indicate that, in the AChE-ACh Michaelis complex, only two hydrogen bonds are formed between the carbonyl oxygen of ACh and the peptidic NH groups of Gly121 and Gly122. As the reaction proceeds, the distance between the carbonyl oxygen of ACh and NH group of Ala204 becomes smaller, and the third hydrogen bond is formed both in the transition state and in the tetrahedral intermediate.
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Affiliation(s)
- Yingkai Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0365, USA.
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130
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Abstract
Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.
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Affiliation(s)
- Tongye Shen
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, and Department of Physics, University of California-San Diego, La Jolla, California 92093-0365, USA
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131
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Golicnik M, Stojan J. Multi-step analysis as a tool for kinetic parameter estimation and mechanism discrimination in the reaction between tight-binding fasciculin 2 and electric eel acetylcholinesterase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1597:164-72. [PMID: 12009416 DOI: 10.1016/s0167-4838(02)00285-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The mechanism of action of a potent peptidic inhibitor fasciculin 2 (Fas2) on electric eel acetylcholinesterase (eleelAChE) has been examined in a three-level analysis. Classical steps included equilibration experiments for the evaluation of high affinity binding constant and the existence of residual hydrolytic activity in a solution of completely Fas2 saturated enzyme. The two rate constants for the association (k(on)) and the dissociation (k(off)) of Fas2 with free enzyme were determined by the time course of residual enzyme activity measurements. In the third step, with a nonclassical progress curve analysis, we found that the Fas2-enzyme complex exhibited hydrolytic activity in a butyrylcholinesterase-like kinetics. The switch appears to be a consequence of steric obstruction, but also the consequence of subtle rapid conformational changes around catalytic site, upon slow single-step binding of large Fas2 molecule at the peripheral site. An unusual unilateral effect of bound Fas2 is reflected by acylation-independent association and dissociation rates and might indeed be due to inability of small acylation agent to influence the binding of a large opponent.
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Affiliation(s)
- Marko Golicnik
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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132
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Abstract
Although the idea that electrostatic potentials generated by enzymes can guide substrates to active sites is well established, it is not always appreciated that the same potentials can also promote the binding of molecules other than the intended substrate, with the result that such enzymes might be sensitive to the presence of competing molecules. To provide a novel means of studying such "electrostatic competition" effects, computer simulation methodology has been developed to allow the diffusion and association of many solute molecules around a single enzyme to be simulated. To demonstrate the power of the methodology, simulations have been conducted on an artificial fusion protein of citrate synthase (CS) and malate dehydrogenase (MDH) to assess the chances of oxaloacetate being channeled between the MDH and CS active sites. The simulations demonstrate that the probability of channeling is strongly dependent on the concentration of the initial substrate (malate) in the solution. In fact, the high concentrations of malate used in experiments appear high enough to abolish any channeling of oxaloacetate. The simulations provide a resolution of a serious discrepancy between previous simulations and experiments and raise important questions relating to the observability of electrostatically mediated substrate channeling in vitro and in vivo.
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Affiliation(s)
- Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 55242, USA.
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133
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Henchman RH, Tai K, Shen T, McCammon JA. Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation. Biophys J 2002; 82:2671-82. [PMID: 11964254 PMCID: PMC1302056 DOI: 10.1016/s0006-3495(02)75609-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A 10-ns trajectory from a molecular dynamics simulation is used to examine the structure and dynamics of water in the active site gorge of acetylcholinesterase to determine what influence water may have on its function. While the confining nature of the deep active site gorge slows down and structures water significantly compared to bulk water, water in the gorge is found to display a number of properties that may aid ligand entry and binding. These properties include fluctuations in the population of gorge waters, moderate disorder and mobility of water in the middle and entrance to the gorge, reduced water hydrogen-bonding ability, and transient cavities in the gorge.
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Affiliation(s)
- Richard H Henchman
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0365 USA.
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134
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Kier LB, Cheng CK, Testa B. A cellular automata model of ligand passage over a protein hydrodynamic landscape. J Theor Biol 2002; 215:415-26. [PMID: 12069486 DOI: 10.1006/jtbi.2001.2525] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The subject of ligand passage to an active site on a protein is addressed. Current views on the mechanism and the possible role of surface water are discussed. A theory is presented in which the pattern of hydropathic states of protein surface amino acid side chains is invoked as the influence on the relative hydrophobic effects of nearby water. The theory describes a ligand passage through the hydrodynamic near-surface water which exhibits temporary organized cavities resembling the chreodes introduced by Waddington. The passage of the ligand to the active site is facilitated by this dynamic mechanism. Cellular automata models of preferential directional diffusion through these chreodes support the theory. The theory may be invoked to explain a number of ligand-active site observations and serves as an idea for further studies.
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Affiliation(s)
- Lemont B Kier
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298, USA
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135
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Lewis WG, Green LG, Grynszpan F, Radić Z, Carlier PR, Taylor P, Finn MG, Sharpless KB. Click Chemistry In Situ: Acetylcholinesterase as a Reaction Vessel for the Selective Assembly of a Femtomolar Inhibitor from an Array of Building Blocks. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3757(20020315)114:6<1095::aid-ange1095>3.0.co;2-3] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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136
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Click Chemistry In Situ: Acetylcholinesterase as a Reaction Vessel for the Selective Assembly of a Femtomolar Inhibitor from an Array of Building Blocks. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3773(20020315)41:6%3c1053::aid-anie1053%3e3.0.co;2-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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137
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Lewis WG, Green LG, Grynszpan F, Radić Z, Carlier PR, Taylor P, Finn MG, Sharpless KB. Click chemistry in situ: acetylcholinesterase as a reaction vessel for the selective assembly of a femtomolar inhibitor from an array of building blocks. Angew Chem Int Ed Engl 2002; 41:1053-7. [PMID: 12491310 DOI: 10.1002/1521-3773(20020315)41:6<1053::aid-anie1053>3.0.co;2-4] [Citation(s) in RCA: 570] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Warren G Lewis
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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138
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Boschitsch AH, Fenley MO, Zhou HX. Fast Boundary Element Method for the Linear Poisson−Boltzmann Equation. J Phys Chem B 2002. [DOI: 10.1021/jp013607q] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander H. Boschitsch
- Continuum Dynamics, Inc., 34 Lexington Avenue, Ewing, New Jersey 08618-2302, Department of Physics, Washington University, St. Louis, Missouri 63130-4899, and Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104
| | - Marcia O. Fenley
- Continuum Dynamics, Inc., 34 Lexington Avenue, Ewing, New Jersey 08618-2302, Department of Physics, Washington University, St. Louis, Missouri 63130-4899, and Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104
| | - Huan-Xiang Zhou
- Continuum Dynamics, Inc., 34 Lexington Avenue, Ewing, New Jersey 08618-2302, Department of Physics, Washington University, St. Louis, Missouri 63130-4899, and Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104
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139
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Abstract
The structure of a protein-protein interaction, its affinity and thermodynamic characteristics depict a 'frozen' state of a complex. This picture ignores the kinetic nature of complex formation and dissociation, which are of major biological and biophysical interest. This review highlights recent advances in deciphering the kinetic pathway of protein-protein complexation, the nature of the encounter complex, transition state and intermediate along the reaction, and the effects of mutation, viscosity, pH and salt on association.
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Affiliation(s)
- Gideon Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel.
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140
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Shi J, Boyd AE, Radic Z, Taylor P. Reversibly bound and covalently attached ligands induce conformational changes in the omega loop, Cys69-Cys96, of mouse acetylcholinesterase. J Biol Chem 2001; 276:42196-204. [PMID: 11517229 DOI: 10.1074/jbc.m106896200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have used a combination of cysteine substitution mutagenesis and site-specific labeling to characterize the structural dynamics of mouse acetylcholinesterase (mAChE). Six cysteine-substituted sites of mAChE (Leu(76), Glu(81), Glu(84), Tyr(124), Ala(262), and His(287)) were labeled with the environmentally sensitive fluorophore, acrylodan, and the kinetics of substrate hydrolysis and inhibitor association were examined along with spectroscopic characteristics of the acrylodan-conjugated, cysteine-substituted enzymes. Residue 262, being well removed from the active center, appears unaffected by inhibitor binding. Following the binding of ligand, hypsochromic shifts in emission of acrylodan at residues 124 and 287, located near the perimeter of the gorge, reflect the exclusion of solvent and a hydrophobic environment created by the associated ligand. By contrast, the bathochromic shifts upon inhibitor binding seen for acrylodan conjugated to three omega loop (Omega loop) residues 76, 81, and 84 reveal that the acrylodan side chains at these positions are displaced from a hydrophobic environment and become exposed to solvent. The magnitude of fluorescence emission shift is largest at position 84 and smallest at position 76, indicating that a concerted movement of residues on the Omega loop accompanies gorge closure upon ligand binding. Acrylodan modification of substituted cysteine at position 84 reduces ligand binding and steady-state kinetic parameters between 1 and 2 orders of magnitude, but a similar substitution at position 81 only minimally alters the kinetics. Thus, combined kinetic and spectroscopic analyses provide strong evidence that conformational changes of the Omega loop accompany ligand binding.
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Affiliation(s)
- J Shi
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA
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141
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Abstract
Electrostatic interactions have been observed to play important roles in the kinetics of protein-protein association. Ionic strength, by its ability to modulate the magnitude of electrostatic interactions, has often been conveniently used to test their presence. From experiments on a wide range of associating proteins, a common feature has emerged: the on rates show strong dependence on ionic strength whereas the off rates are relatively insensitive. Here this feature is explained by an explicit description of a transition state for the association process and the suggestion that this transition is near the final bound state of two proteins. The molecular basis of the transition state in the bimolecular process lies in the fact that the bound state is characterized by local specific (e.g., van der Waals, hydrophobic, and electrostatic) interactions, whereas the unbound state is characterized by translational and rotational freedom. In the transition state the protein-protein pair encounters a free-energy maximum since its translational-rotational entropy is reduced while the specific interactions are not yet attained. In this formalism of the protein-protein association process, the enhancement of on rates by long-range electrostatic interactions can be written (analogous to an ordinary transition-state theory) in the form k(on) = k(0)(on)exp(-G(el)/k(B)T), where G(el) is the electrostatic free energy of the transition state.
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Affiliation(s)
- H X Zhou
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA.
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142
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Lenigk R, Lam E, Lai A, Wang H, Han Y, Carlier P, Renneberg R. Enzyme biosensor for studying therapeutics of Alzheimer's disease. Biosens Bioelectron 2001; 15:541-7. [PMID: 11419651 DOI: 10.1016/s0956-5663(00)00078-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An electrochemical method for the investigation and comparison of anti-Alzheimer medications that is based on the inhibition of the acetylcholinesterase is presented. The developed amperometric biosensor determines the in-vitro inhibition of the acetylcholinesterase that is co-immobilized with choline oxidase on the working electrode surface of a three-electrode system using gel entrapment. The sensor has been applied to determine the IC50 values of two known and one newly developed Alzheimer remedy. A simultaneous measurement with the photometric standard method shows the applicability of our method for fast drug screening.
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Affiliation(s)
- R Lenigk
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, PR China.
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143
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Kaplan D, Ordentlich A, Barak D, Ariel N, Kronman C, Velan B, Shafferman A. Does "butyrylization" of acetylcholinesterase through substitution of the six divergent aromatic amino acids in the active center gorge generate an enzyme mimic of butyrylcholinesterase? Biochemistry 2001; 40:7433-45. [PMID: 11412096 DOI: 10.1021/bi010181x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The active center gorge of human acetylcholinesterase (HuAChE) is lined by 14 aromatic residues, whereas in the closely related human butyrylcholinesterase (HuBChE) 3 of the aromatic active center residues (Phe295, Phe297, Tyr337) as well as 3 of the residues at the gorge entrance (Tyr72, Tyr124, Trp286) are replaced by aliphatic amino acids. To investigate whether this structural variability can account for the reactivity differences between the two enzymes, gradual replacement of up to all of the 6 aromatic residues in HuAChE by the corresponding residues in HuBChE was carried out. The affinities of the hexamutant (Y72N/Y124Q/W286A/F295L/F297V/Y337A) toward tacrine, decamethonium, edrophonium, huperzine A, or BW284C51 differed by about 5-, 80-, 170-, 25000-, and 17000-fold, respectively, from those of the wild-type HuAChE. For most of these prototypical noncovalent active center and peripheral site ligands, the hexamutant HuAChE displayed a reactivity phenotype closely resembling that of HuBChE. These results support the accepted view that the active center architectures of AChE and BChE differ mainly by the presence of a larger void space in BChE. Nevertheless, reactivity of the hexamutant HuAChE toward the substrates acetylthiocholine and butyrylthiocholine, or covalent ligands such as phosphonates and the transition state analogue m-(N,N,N-trimethylammonio)trifluoroacetophenone (TMTFA), is about 45-170-fold lower than that of HuBChE. Most of this reduction in reactivity can be related to the combined replacements of the three aromatic residues at the active center, Phe295, Phe297, and Tyr337. We propose that the hexamutant HuAChE, unlike BChE, is impaired in its capacity to accommodate certain tetrahedral species in the active center. This impairment may be related to the enhanced mobility of the catalytic histidine His447, which is observed in molecular dynamics simulations of the hexamutant and the F295L/F297V/Y337A HuAChE enzymes but not in the wild-type HuAChE.
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MESH Headings
- Acetylcholinesterase/chemistry
- Acetylcholinesterase/genetics
- Acetylcholinesterase/metabolism
- Amino Acid Substitution/genetics
- Benzenaminium, 4,4'-(3-oxo-1,5-pentanediyl)bis(N,N-dimethyl-N-2-propenyl-), Dibromide/chemistry
- Benzenaminium, 4,4'-(3-oxo-1,5-pentanediyl)bis(N,N-dimethyl-N-2-propenyl-), Dibromide/metabolism
- Binding Sites/genetics
- Butyrates/metabolism
- Butyrylcholinesterase/chemistry
- Butyrylcholinesterase/metabolism
- Cholinesterase Inhibitors/chemistry
- Cholinesterase Inhibitors/metabolism
- Decamethonium Compounds/chemistry
- Decamethonium Compounds/metabolism
- Edrophonium/chemistry
- Edrophonium/metabolism
- Humans
- Hydrolysis
- Kinetics
- Ligands
- Molecular Mimicry/genetics
- Mutagenesis, Site-Directed
- Organophosphorus Compounds/chemistry
- Organophosphorus Compounds/metabolism
- Substrate Specificity/genetics
- Tacrine/chemistry
- Tacrine/metabolism
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Affiliation(s)
- D Kaplan
- Departments of Biochemistry & Molecular Genetics and Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
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144
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Abstract
The discovery of the first neurotransmitter--acetylcholine--was soon followed by the discovery of its hydrolysing enzyme, acetylcholinesterase. The role of acetylcholinesterase in terminating acetylcholine-mediated neurotransmission made it the focus of intense research for much of the past century. But the complexity of acetylcholinesterase gene regulation and recent evidence for some of the long-suspected 'non-classical' actions of this enzyme have more recently driven a profound revolution in acetylcholinesterase research. Although our understanding of the additional roles of acetylcholinesterase is incomplete, the time is ripe to summarize the evidence on a remarkable diversity of acetylcholinesterase functions.
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145
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Gabdoulline RR, Wade RC. Protein-protein association: investigation of factors influencing association rates by brownian dynamics simulations. J Mol Biol 2001; 306:1139-55. [PMID: 11237623 DOI: 10.1006/jmbi.2000.4404] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rate of protein-protein association limits the response time due to protein-protein interactions. The bimolecular association rate may be diffusion-controlled or influenced, and in such cases, Brownian dynamics simulations of protein-protein diffusional association may be used to compute association rates. Here, we report Brownian dynamics simulations of the diffusional association of five different protein-protein pairs: barnase and barstar, acetylcholinesterase and fasciculin-2, cytochrome c peroxidase and cytochrome c, the HyHEL-5 antibody and hen egg lysozyme (HEL), and the HyHEL-10 antibody and HEL. The same protocol was used to compute the diffusional association rates for all the protein pairs in order to assess, by comparison to experimentally measured rates, whether the association of these proteins can be explained solely on the basis of diffusional encounter. The simulation protocol is similar to those previously derived for simulation of the association of barnase and barstar, and of acetylcholinesterase and fasciculin-2; these produced results in excellent agreement with experimental data for these protein pairs, with changes in association rate due to mutations reproduced within the limits of expected computational and modeling errors. Here, we find that for all protein pairs, the effects of mutations can be well reproduced by the simulations, even though the degree of the electrostatic translational and orientational steering varies widely between the cases. However, the absolute values of association rates for the acetylcholinesterase: fasciculin-2 and HyHEL-10 antibody: HEL pairs are overestimated. Comparison of bound and unbound protein structures shows that this may be due to gating resulting from protein flexibility in some of the proteins. This may lower the association rates compared to their bimolecular diffusional encounter rates.
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146
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Radić Z, Taylor P. Interaction kinetics of reversible inhibitors and substrates with acetylcholinesterase and its fasciculin 2 complex. J Biol Chem 2001; 276:4622-33. [PMID: 11036076 DOI: 10.1074/jbc.m006855200] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fasciculin 2 (Fas2), a three-fingered peptide of 61 amino acids, binds tightly to the peripheral site of acetylcholinesterases (AChE; EC ), occluding the entry portal into the active center gorge of the enzyme and inhibiting its catalytic activity. We investigated the mechanism of Fas2 inhibition by studying hydrolysis of cationic and neutral substrates and by determining the kinetics of interaction for fast equilibrating cationic and neutral reversible inhibitors with the AChE.Fas2 complex and free AChE. Catalytic parameters, derived by eliminating residual Fas2-resistant activity, reveal that Fas2 reduces k(cat)/K(m) up to 10(6)-fold for cationic substrates and less than 10(3)-fold for neutral substrates. Rate constants for association of reversible inhibitors with the active center of the AChE.Fas2 complex were reduced about 10(4)-fold for both cationic and neutral inhibitors, while dissociation rate constants were reduced 10(2)-to 10(3)-fold, compared with AChE alone. Rates of ligand association with both AChE and AChE.Fas2 complex were dependent on the protonation state of ionizable ligands but were also markedly reduced by protonation of enzyme residue(s) with pK(a) of 6.1-6.2. Linear free energy relationships between the equilibrium constant and the kinetic constants show that Fas2, presumably through an allosteric influence, markedly alters the position of the transition state in the reaction pathway. Since Fas2 complexation introduces an energetic barrier for hydrolysis of substrates that exceeds that found for association of reversible ligands, Fas2 influences catalytic parameters by a more complex mechanism than simple restriction of diffusional entry and exit from the active center. Conformational flexibility appears critical for facilitating ligand passage in the narrow active center gorge for both AChE and the AChE.Fas2 complex.
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Affiliation(s)
- Z Radić
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093-0636, USA
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147
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Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF. Protein docking using continuum electrostatics and geometric fit. PROTEIN ENGINEERING 2001; 14:105-13. [PMID: 11297668 DOI: 10.1093/protein/14.2.105] [Citation(s) in RCA: 219] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The computer program DOT quickly finds low-energy docked structures for two proteins by performing a systematic search over six degrees of freedom. A novel feature of DOT is its energy function, which is the sum of both a Poisson-Boltzmann electrostatic energy and a van der Waals energy, each represented as a grid-based correlation function. DOT evaluates the energy of interaction for many orientations of the moving molecule and maintains separate lists scored by either the electrostatic energy, the van der Waals energy or the composite sum of both. The free energy is obtained by summing the Boltzmann factor over all rotations at each grid point. Three important findings are presented. First, for a wide variety of protein-protein interactions, the composite-energy function is shown to produce larger clusters of correct answers than found by scoring with either van der Waals energy (geometric fit) or electrostatic energy alone. Second, free-energy clusters are demonstrated to be indicators of binding sites. Third, the contributions of electrostatic and attractive van der Waals energies to the total energy term appropriately reflect the nature of the various types of protein-protein interactions studied.
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Affiliation(s)
- J G Mandell
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA
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148
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Elcock AH, Sept D, McCammon JA. Computer Simulation of Protein−Protein Interactions. J Phys Chem B 2001. [DOI: 10.1021/jp003602d] [Citation(s) in RCA: 177] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Adrian H. Elcock
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242-1109, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - David Sept
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242-1109, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - J. Andrew McCammon
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242-1109, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
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149
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Koch U, Biasiol G, Brunetti M, Fattori D, Pallaoro M, Steinkühler C. Role of charged residues in the catalytic mechanism of hepatitis C virus NS3 protease: electrostatic precollision guidance and transition-state stabilization. Biochemistry 2001; 40:631-40. [PMID: 11170379 DOI: 10.1021/bi002160t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Maturational cleavage of the hepatitis C virus polyprotein involves the viral chymotrypsin-like serine protease NS3. The substrate binding site of this enzyme is unusually flat and featureless. We here show that NS3 has a highly asymmetric charge distribution that is characterized by strong positive potentials in the vicinity of its active site and in the S5/S6 region. Using electrostatic potential calculations, we identified determinants of this positive potential, and the role of six different residues was explored by site-directed mutagenesis. Mutation of residues in the vicinity of the active site led to changes in k(cat) values of a peptide substrate indicating that basic amino acids play a role in the stabilization of the transition state. Charge neutralization in the S5/S6 region increased the K(m) values of peptide substrates in a manner that depended on the presence of negatively charged residues in the P5 and P6 positions. K(i) values of hexapeptide acids spanning P6-P1 (product inhibitors) were affected by charge neutralization in both the active site region and the S5/S6 region. Pre-steady-state kinetic data showed that the electrostatic surface potential is used by this enzyme to enhance collision rates between peptidic ligands and the active site. Calculations of the interaction energies of protease-substrate or protease-inhibitor complexes showed that electrostatic interaction energies oppose the formation of a tightly bound complex due to an unfavorable change in the desolvation energy. We propose that desolvation costs are minimized by avoiding the formation of individual ion pair interactions through the use of clusters of positively charged residues in the generation of local electrostatic potentials.
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Affiliation(s)
- U Koch
- Istituto di Ricerche di Biologia Molecolare (IRBM) "P. Angeletti", Via Pontina Km 30,600, 00040 Pomezia, Italy
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150
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Tõugu V, Kesvatera T. Comparison of salt effects on the reactions of acetylcholinesterase with cationic and anionic inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1544:189-95. [PMID: 11341928 DOI: 10.1016/s0167-4838(00)00218-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The influence of inorganic salts on the inhibition of acetylcholinesterase by charged organophosphorous inhibitors has been studied. It has been shown that the salt effect on the reaction of acetylcholinesterase with anionic bis(p-nitrophenyl) phosphate is determined by the influence of added salts on the activity coefficient of the inhibitor. In contrast to the salt effects on the reaction of acetylcholinesterase with cationic compounds, it does not include contribution from the enzyme charges. The smaller salt effect in the case of anionic inhibitor can be explained assuming that the anionic inhibitor does not form a non-covalent complex with the enzyme before the phosphorylation step of the reaction. Comparison of salt effects on the substrate turnover showed that in the case of cholinesterases from natural sources they are larger than in the case of enzymes expressed in recombinant cell clones. The enhanced salt effects may result from post-translational modification of the enzyme.
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Affiliation(s)
- V Tõugu
- Laboratory of Bioorganic Chemistry, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618, Tallinn, Estonia.
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