Dynamics of the acetylcholinesterase tetramer

The kinetic and molecular docking analysis of interactions between three V-type nerve agents and four human cholinesterases

G and V-type nerve agents represent the most toxic chemical warfare agents. Their primary toxicity was the consequence of the covalent inhibition of the pivotal acetylcholinesterase (AChE), which induces overstimulation of cholinergic receptors and overaccumulation of cholines, eventually leading to death by respiratory arrest. The inhibitory and reactivation kinetics of cholinesterase (ChE) are essential for the toxicology and countermeasures of nerve agents. Medical defensive research on V-type nerve agents (V agents) has been mainly reported on VX and VR. Here we demonstrated the first systematical kinetic analysis between the type of ChE [native or recombinant human AChE and butyrylcholinesterase (BChE)] and three V agents, including VX, VR, and Vs, another isomer of VX, and highlighted the effects of native and recombinant ChE differences. The spontaneous reactivation and aging kinetics data of Vs-inhibited BChEs were firstly reported here. The results showed that AChE was more easily inhibited by three V agent compared to BChE, regardless of whether it is native or recombinant. The increased inhibitory potency order on AChE was VX, Vs, then VR, and on BChE was VX, then Vs and VR. The difference between native and recombinant ChE could influence the inhibition, aging, and spontaneous reactivation kinetics of three V agents, whether AChE or BChE, which was systematically revealed for the first time. For inhibition kinetics, the k_i of three V agents for recombinant AChE was significantly higher than native AChE, and the stronger the inhibitory potency of V agents, the more pronounced difference in k_i. In terms of aging and spontaneous reactivation kinetics, recombinant ChE was found to be more prone to spontaneous reactivation, but more resistant to aging compared to native ChE, particularly for AChE. The performed covalent molecular docking results partially explained the effects of differences between native and recombinant ChE on enzyme kinetics from the perspective of binding energy and conformation.

In silico analyses of acetylcholinesterase (AChE) and its genetic variants in interaction with the anti-Alzheimer drug Rivastigmine

Alzheimer's disease (AD) is the leading cause of dementia worldwide. Despite causing great social and economic impact, there is currently no cure for AD. The most effective therapy to manage AD symptoms is based on acetylcholinesterase inhibitors (AChEi), from which rivastigmine presented numerous benefits. However, mutations in AChE, which affect approximately 5% of the population, can modify protein structure and function, changing the individual response to Alzheimer's treatment. In this study, we performed computer simulations of AChE wild type and variants R34Q, P135A, V333E, and H353N, identified by one or more genome-wide association studies, to evaluate their effects on protein structure and interaction with rivastigmine. The functional effects of AChE variants were predicted using eight machine learning algorithms, while the evolutionary conservation of AChE residues was analyzed using the ConSurf server. Autodock4.2.6 was used to predict the binding modes for the hAChE-rivastigmine complex, which is still unknown. Molecular dynamics (MD) simulations were performed in triplicates for the AChE wild type and mutants using the GROMACS packages. Among the analyzed variants, P135A was classified as deleterious by all the functional prediction algorithms, in addition to occurring at highly conserved positions, which may have harmful consequences on protein function. The molecular docking results suggested that rivastigmine interacts with hAChE at the upper active-site gorge, which was further confirmed by MD simulations. Our MD findings also suggested that the complex hAChE-rivastigmine remains stable over time. The essential dynamics revealed flexibility alterations at the active-site gorge upon mutations P135A, V333E, and H353N, which may lead to strong and nonintuitive consequences to hAChE binding. Nonetheless, similar binding affinities were registered in the MMPBSA analysis for the hAChE wild type and variants when complexed to rivastigmine. Finally, our findings indicated that the rivastigmine binding to hAChE is an energetically favorable process mainly driven by negatively charged amino acids.

Caenorhabditis elegans as a possible model to screen anti-Alzheimer's therapeutics

Alzheimer's disease (AD) is regarded as one of the significant health burdens, as the prevalence is raising worldwide and gradually reaching to epidemic proportions. Consequently, a number of scientific investigations have been initiated to derive therapeutics to combat AD with a concurrent advancement in pharmacological methods and experimental models. Whilst, the available experimental pharmacological approaches both in vivo and in vitro led to the development of AD therapeutics, the precise manner by which experimental models mimic either one or more biomarkers of human pathology of AD is gaining scientific attentions. Caenorhabditis elegans (C. elegans) has been regarded as an emerging model for various reasons, including its high similarities with the biomarkers of human AD. Our review supports the versatile nature of C. elegans and collates that it is a well-suited model to elucidate various molecular mechanisms by which AD therapeutics elicit their pharmacological effects. It is apparent that C. elegans is capable of establishing the pathological processes that links the endoplasmic reticulum and mitochondria dysfunctions in AD, exploring novel molecular cascades of AD pathogenesis and underpinning causal and consequential changes in the associated proteins and genes. In summary, C. elegans is a unique and feasible model for the screening of anti-Alzheimer's therapeutics and has the potential for further scientific exploration.

Diagnoses of Pathological States Based on Acetylcholinesterase and Butyrylcholinesterase

Two cholinesterases exist: Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). While AChE plays a crucial role in neurotransmissions, BChE has no specific function apart from the detoxification of some drugs and secondary metabolites from plants. Thus, both AChE and BChE can serve as biochemical markers of various pathologies. Poisoning by nerve agents like sarin, soman, tabun, VX, novichok and overdosing by drugs used in some neurodegenerative disorders like Alzheimer´s disease and myasthenia gravis, as well as poisoning by organophosphorus pesticides are relevant to this issue. But it appears that changes in these enzymes take place in other processes including oxidative stress, inflammation, some types of cancer and genetically conditioned diseases. In this review, the cholinesterases are introduced, the mechanism of inhibitors action is explained and the relations between the cholinesterases and pathologies are explained.

Phenoxyethyl Piperidine/Morpholine Derivatives as PAS and CAS Inhibitors of Cholinesterases: Insights for Future Drug Design

Acetylcholinesterase (AChE) catalyzes the conversion of Aβ peptide to its aggregated form and the peripheral anionic site (PAS) of AChE is mainly involved in this phenomenon. Also catalytic active site (CAS) of donepezil stimulates the break-down of acetylcholine (ACh) and depletion of ACh in cholinergic synapses are well established in brains of patients with AD. In this study, a set of compounds bearing phenoxyethyl amines were synthesized and their inhibitory activity toward electric eel AChE (eeAChE) and equine butyrylcholinesterase (eqBuChE) were evaluated. Molecular dynamics (MD) was employed to record the binding interactions of best compounds against human cholinesterases (hAChE and hBuChE) as well as donepezil as reference drug. In vitro results revealed that compound 5c is capable of inhibiting eeAChE activity at IC₅₀ of 0.50 µM while no inhibitory activity was found for eqBuChE for up to 100 µM concentrations. Compound 5c, also due to its facile synthesis, small structure and high selectivity for eeAChE would be very interesting candidate in forthcoming studies. The main interacting parts of compound 5c and compound 7c (most potent eeAChE and eqBuChE inhibitors respectively) with receptors which confer selectivity for AChE and BuChE inhibition were identified, discussed, and compared with donepezil’s interactions. Also during MD simulation it was discovered for the first time that binding of substrates like donepezil to dual CAS and PAS or solely CAS region might have a suppressive impact on 4-α-helical bundles near the tryptophan amphiphilic tetramerization (WAT) domain of AChE and residues which are far away from AChE active site. The results proposed that residues involved in donepezil interactions (Trp86 and Phe295) which are located in CAS and mid-gorge are the mediator of conformational changes in whole protein structure.

Single-particle enumeration-based ultrasensitive enzyme activity quantification with fluorescent polymer nanoparticles

Acetylcholinesterase (AChE) plays a vital role in nerve conduction through rapidly hydrolyzing the neurotransmitter acetylcholine (ACh) and is correlated with Alzheimer's disease. In this work, a label-free single-particle enumeration (SPE) method for the quantitative detection of acetylcholinesterase (AChE) activity is developed. The design is based on the fluorescence resonance energy transfer (FRET) between fluorescent conjugated polymer nanoparticles (FCPNPs) and MnO2 nanosheets. The fluorescence of FCPNPs can be effectively quenched by MnO2 nanosheets via hydrogen bonding interaction. In the presence of acetylcholinesterase (AChE), acetylthiocholine (ATCh) could be hydrolyzed to thiocholine (TCh), which can reduce MnO2 to Mn2+ and trigger the decomposition of MnO2 nanosheets. As a result, the fluorescence of FCPNPs is restored. Taking advantage of the superior brightness and stable fluorescence emission from individual FCPNPs, the accurate quantification of AChE is achieved by statistically counting the fluorescent particles on the glass slide surface. A linear range from 5 to 1600 μU mL-1 is obtained for AChE assay and the limit-of-detection (LOD) is 1.02 μU mL-1, which is far below the spectroscopic measurements in bulk solution. In the human serum sample, satisfactory recovery efficiencies are determined in a range of 91.0%-103.0%. Furthermore, pesticide carbaryl as an inhibitor of AChE activity was detected. The LOD is 1.12 pg mL-1 with linear responses ranging from 5 to 300 pg mL-1, which demonstrates the feasibility of this approach for AChE inhibitor screening. As a consequence, the label-free SPE-based method affords a promising platform for the sensitive detection of target molecules in the future.

Hot Spots for Protein Partnerships at the Surface of Cholinesterases and Related α/β Hydrolase Fold Proteins or Domains-A Structural Perspective

The hydrolytic enzymes acetyl- and butyryl-cholinesterase, the cell adhesion molecules neuroligins, and the hormonogenic macromolecule thyroglobulin are a few of the many members of the α/β hydrolase fold superfamily of proteins. Despite their distinctive functions, their canonical subunits, with a molecular surface area of ~20,000 Ų, they share binding patches and determinants for forming homodimers and for accommodating structural subunits or protein partners. Several of these surface regions of high functional relevance have been mapped through structural or mutational studies, while others have been proposed based on biochemical data or molecular docking studies. Here, we review these binding interfaces and emphasize their specificity versus potentially multifunctional character.

Computational Studies on Acetylcholinesterases

Functions of biomolecules, in particular enzymes, are usually modulated by structural fluctuations. This is especially the case in a gated diffusion-controlled reaction catalyzed by an enzyme such as acetylcholinesterase. The catalytic triad of acetylcholinesterase is located at the bottom of a long and narrow gorge, but it catalyzes the extremely rapid hydrolysis of the neurotransmitter, acetylcholine, with a reaction rate close to the diffusion-controlled limit. Computational modeling and simulation have produced considerable advances in exploring the dynamical and conformational properties of biomolecules, not only aiding in interpreting the experimental data, but also providing insights into the internal motions of the biomolecule at the atomic level. Given the remarkably high catalytic efficiency and the importance of acetylcholinesterase in drug development, great efforts have been made to understand the dynamics associated with its functions by use of various computational methods. Here, we present a comprehensive overview of recent computational studies on acetylcholinesterase, expanding our views of the enzyme from a microstate of a single structure to conformational ensembles, strengthening our understanding of the integration of structure, dynamics and function associated with the enzyme, and promoting the structure-based and/or mechanism-based design of new inhibitors for it.

Rate Constants and Mechanisms of Protein-Ligand Binding

Whereas protein-ligand binding affinities have long-established prominence, binding rate constants and binding mechanisms have gained increasing attention in recent years. Both new computational methods and new experimental techniques have been developed to characterize the latter properties. It is now realized that binding mechanisms, like binding rate constants, can and should be quantitatively determined. In this review, we summarize studies and synthesize ideas on several topics in the hope of providing a coherent picture of and physical insight into binding kinetics. The topics include microscopic formulation of the kinetic problem and its reduction to simple rate equations; computation of binding rate constants; quantitative determination of binding mechanisms; and elucidation of physical factors that control binding rate constants and mechanisms.

Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations.

Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PolB from Polymerization to Editing

Replicative DNA polymerases (Pols) frequently possess two distinct DNA processing activities: DNA synthesis (polymerization) and proofreading (3'-5' exonuclease activity). The polymerase and exonuclease reactions are performed alternately and are spatially separated in different protein domains. Thus, the growing DNA primer terminus has to undergo dynamic conformational switching between two distinct functional sites on the polymerase. Furthermore, the transition from polymerization (pol) mode to exonuclease (exo) mode must occur in the context of a DNA Pol holoenzyme, wherein the polymerase is physically associated with processivity factor proliferating cell nuclear antigen (PCNA) and primer-template DNA. The mechanism of this conformational switching and the role that PCNA plays in it have remained obscure, largely due to the dynamic nature of ternary Pol/PCNA/DNA assemblies. Here, we present computational models of ternary assemblies for archaeal polymerase PolB. We have combined all available structural information for the binary complexes with electron microscopy data and have refined atomistic models for ternary PolB/PCNA/DNA assemblies in pol and exo modes using molecular dynamics simulations. In addition to the canonical PIP-box/interdomain connector loop (IDCL) interface of PolB with PCNA, contact analysis of the simulation trajectories revealed new secondary binding interfaces, distinct between the pol and exo states. Using targeted molecular dynamics, we explored the conformational transition from pol to exo mode. We identified a hinge region between the thumb and palm domains of PolB that is critical for conformational switching. With the thumb domain anchored onto the PCNA surface, the neighboring palm domain executed rotational motion around the hinge, bringing the core of PolB down toward PCNA to form a new interface with the clamp. A helix from PolB containing a patch of arginine residues was involved in the binding, locking the complex in the exo mode conformation. Together, these results provide a structural view of how the transition between the pol and exo states of PolB is coordinated through PCNA to achieve efficient proofreading.

Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics

Revealing the processes of ligand-protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H-bonds) play a crucial role in optimizing ligand-protein interactions and ligand specificity. In addition to the formation of stable H-bonds in the final bound state, the formation of transient H-bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H-bonds on the kinetic properties is little understood. Guided by results from coarse-grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H-bond donor or acceptor of a drug result in switching intermolecular and intramolecular H-bond pairs during ligand recognition processes. We studied two major types of HIV-1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H-bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H-bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics.

Research on the regulation of the spatial structure of acetylcholinesterase tetramer with high efficiency by AFM

Atomic force microscopy (AFM) was applied for obtaining structural information about acetylcholinesterase (AChE) tetramer (AChE G₄) before and after reaction with S-acetylcholine iodide (S-ACh), in the presence or absence of propidium iodide (PI), an inhibitor for peripheral anionic sites (PAS). An iced-bath ultrasound was used to prepare the phospholipid membrane. Ves-fusion technique was applied for incorporating AChE G₄ in a lipid layer on mica. Before reaction with substrates, the single AChE G₄ particle was ellipsoid in shape with a clear border. It had a smooth surface with a central projection. The four subunits of a single enzyme particle were arranged tightly (no separated subunits being found, with an average size of 89 ± 7 nm in length, 68 ± 9 nm in width, and 6 ± 3 nm in height). After reaction with S-ACh in the absence of PI, the loose arrangement of subunits of AChE G₄ was seen, with an average size of 104 ± 7 nm in length, 91 ± 5 nm in width, and 8 ± 2 nm in height. Also there was free-flowing space amongst the four subunits of the AChE G₄. This was consistent with the results of the ×-ray diffraction crystallography and molecular dynamics studies. The apparent free space was the central path of AChE G₄, changing from small to big, to small, to lateral door appearance, with an average size of 60 ± 5 nm in length and 51 ± 9 nm in width. The size of lateral door was 52 ± 5 nm in width and 32 ± 3 nm in depth on average. In the presence of PI, S-ACh could not cause topological structure changes of AChE G₄. AFM verified that the central path might govern the turnover of the enzyme morphologically, and the interactions between PI and S-ACh might gate the creation of a central path and the opening of ACG in monomer; and the combination of S-ACh with peripheral anionic sites is conducive to the opening of ACG while PI can inhibit this action. Resolution at the inframolecular level is favorable in providing substantial information on how the spatial structure is adapted to the high efficiency of AChE molecules.

Mechanistic insights into phosphopeptide--BRCT domain association: preorganization, flexibility, and phosphate recognition

Promiscuous proteins are commonly observed in biological systems, for example, in modular domains that recognize phosphopeptides during signal transduction. This promiscuous recognition is of fundamental interest in chemistry and biology but is challenging when designing phosphopeptides in silico for cell biology studies. To investigate promiscuous recognition and binding processes of phosphopeptides and the modular domain, we selected a domain essential in breast cancer-the breast-cancer-associated protein 1 (BRCA1) C-terminal (BRCT) repeats as our model system. We performed molecular dynamics simulations and detailed analyses of the dihedral space to study protein fluctuation and conformational changes with phosphopeptide binding. We also studied the association processes of phosphorylated and unphosphorylated peptides using Brownian dynamics with a coarse-grained model. We found that the BRCT domain is preorganized for phosphopeptide binding but has a moderate arrangement of side chains to form complexes with various types of phosphopeptides. Phosphopeptide binding restricts the system motion in general, while the nonpolar phosphopeptide becomes more flexible in the bound state. Our analysis found that the BRCT domain utilizes different mechanisms, usually termed lock and key, induced-fit, and population-shift/conformational-selection models, to recognize peptides with different features. Brownian dynamics simulations revealed that the charged phosphate group may not always accelerate peptide association processes, but it helps the phosphopeptide orient into binding pockets accurately and stabilizes the complex. This work provides insights into molecular recognition in the promiscuous protein system.

Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites

We consider the diffusion-influenced rate coefficient of ligand binding to a site located in a deep pocket on a protein; the binding pocket is flexible and can reorganize in response to ligand entrance. We extend to this flexible protein-ligand system a formalism developed previously [A. M. Berezhkovskii, A, Szabo, and H.-X. Zhou, J. Chem. Phys. 135, 075103 (2011)] for breaking the ligand-binding problem into an exterior problem and an interior problem. Conformational fluctuations of a bottleneck or a lid and the binding site are modeled as stochastic gating. We present analytical and Brownian dynamics simulation results for the case of a cylindrical pocket containing a binding site at the bottom. Induced switch, whereby the conformation of the protein adapts to the incoming ligand, leads to considerable rate enhancement.

Active site gating and substrate specificity of butyrylcholinesterase and acetylcholinesterase: insights from molecular dynamics simulations

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.

Evidence for impaired vagus nerve activity in heart failure

Parasympathetic control of the heart via the vagus nerve is the primary mechanism that regulates beat-to-beat control of heart rate. Additionally, the vagus nerve exerts significant effects at the AV node, as well as effects on both atrial and ventricular myocardium. Vagal control is abnormal in heart failure, occurring at early stages of left ventricular dysfunction, and this reduced vagal function is associated with worse outcomes in patients following myocardial infarction and with heart failure. While central control mechanisms are abnormal, one of the primary sites of attenuated vagal control is at the level of the parasympathetic ganglion. It remains to be seen whether or not preventing or treating abnormal vagal control of the heart improves prognosis.

Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change

Conformational change during protein-ligand binding may significantly affect both the binding mechanism and the rate constant. Most earlier theories and simulations treated conformational change as stochastic gating with transition rates between reactive and nonreactive conformations uncoupled to ligand binding. Recently, we introduced a dual-transition-rates model in which the transition rates between reactive and nonreactive conformations depend on the protein-ligand distance [H.-X. Zhou, Biophys. J. 98, L15 (2010)]. Analytical results of that model showed that the apparent binding mechanism switches from conformational selection to induced fit, when the rates of conformational transitions increase from being much slower than the diffusional approach of the protein-ligand pair to being much faster. The conformational-selection limit (k(CS)) and the induced-fit limit (k(IF)) provide lower and upper bounds, respectively, for the binding rate constant. Here we introduce a general model in which the energy surface of the protein in conformational space is coupled to ligand binding, and present a method for calculating the binding rate constant from Brownian dynamics simulations. Analytical and simulation results show that, for an energy surface that switches from favoring the nonreactive conformation while the ligand is away to favoring the reactive conformation while the ligand is near, k(CS) and k(IF) become close and, thus, provide tight bounds to the binding rate constant. This finding has significant mechanistic implications and presents routes for obtaining good estimates of the rate constant at low cost.

Gated Diffusion-controlled Reactions

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.

Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer

The function of many proteins, such as enzymes, is modulated by structural fluctuations. This is especially the case in gated diffusion-controlled reactions (where the rates of the initial diffusional encounter and of structural fluctuations determine the overall rate of the reaction) and in oligomeric proteins (where function often requires a coordinated movement of individual subunits). A classic example of a diffusion-controlled biological reaction catalyzed by an oligomeric enzyme is the hydrolysis of synaptic acetylcholine (ACh) by tetrameric acetylcholinesterase (AChEt). Despite decades of efforts, the extent to which enzymatic efficiency of AChEt (or any other enzyme) is modulated by flexibility is not fully determined. This article attempts to determine the correlation between the dynamics of AChEt and the rate of reaction between AChEt and ACh. We employed equilibrium and nonequilibrium electro-diffusion models to compute rate coefficients for an ensemble of structures generated by molecular dynamics simulation. We found that, for the static initial model, the average reaction rate per active site is approximately 22-30% slower in the tetramer than in the monomer. However, this effect of tetramerization is modulated by the intersubunit motions in the tetramer such that a complex interplay of steric and electrostatic effects either guides or blocks the substrate into or from each of the four active sites. As a result, the rate per active site calculated for some of the tetramer structures is only approximately 15% smaller than the rate in the monomer. We conclude that structural dynamics minimizes the adverse effect of tetramerization, allowing the enzyme to maintain similar enzymatic efficiency in different oligomerization states.

Model of human butyrylcholinesterase tetramer by homology modeling and dynamics simulation

A mutant of human butyrylcholinesterase (BChE) with high activity against cocaine would be highly promising as a drug for therapeutic treatment of cocaine abuse and overdose. It is desirable to design a recombinant BChE mutant with a long half-life in human circulation. Studies showed that BChE subunits can be assembled by a peptide containing the proline-rich attachment domain (PRAD) to form a stable tetramer. The models of BChE tetramer complexed with PRAD with various sequences have been constructed, in the present study, on the basis of homology modeling and molecular dynamics simulation of explicit water-solvated systems. The 3D models enable us to understand how the BChE subunits are arranged in the tetramer and how the tetramerization domain of BChE is associated with PRAD to form a stable tetramer of human BChE. It has been shown that the six conserved hydrophobic residues located on the C-terminal of BChE are responsible for the key electrostatic and hydrophobic interactions between the tetramerization domain of BChE and PRAD. The simulated tetramer structures suggest that mutation of three residues, i.e., Phe547, Met554, and Phe561, to other hydrophobic residues may be beneficial for increasing the binding between the tetramerization domain of BChE and PRAD. Thus, the detailed structural insights obtained from this study may be valuable for rational design of a recombinant BChE tetramer with a longer residence time in circulation.

Hydrolysis of acetylthiocoline, o-nitroacetanilide and o-nitrotrifluoroacetanilide by fetal bovine serum acetylcholinesterase

Besides esterase activity, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) hydrolyze o-nitroacetanilides through aryl acylamidase activity. We have reported that BuChE tetramers and monomers of human blood plasma differ in o-nitroacetanilide (ONA) hydrolysis. The homology in quaternary structure and folding of subunits in the prevalent BuChE species (G4(H)) of human plasma and AChE forms of fetal bovine serum prompted us to study the esterase and amidase activities of fetal bovine serum AChE. The k(cat)/K(m) values for acetylthiocholine (ATCh), ONA and its trifluoro derivative N-(2-nitrophenyl)-trifluoroacetamide (F-ONA) were 398 x 10(6) M(-1) min(-1), 0.8 x 10(6) M(-1) min(-1), and 17.5 x 10(6) M(-1) min(-1), respectively. The lack of inhibition of amidase activity at high F-ONA concentrations makes it unlikely that there is a role for the peripheral anionic site (PAS) in F-ONA degradation, but the inhibition of ATCh, ONA and F-ONA hydrolysis by the PAS ligand fasciculin-2 points to the transit of o-nitroacetalinides near the PAS on their way to the active site. Sedimentation analysis confirmed substrate hydrolysis by tetrameric 10.9S AChE. As compared with esterase activity, amidase activity was less sensitive to guanidine hydrochloride. This reagent led to the formation of 9.3S tetramers with partially unfolded subunits. Their capacity to hydrolyze ATCh and F-ONA revealed that, despite the conformational change, the active site architecture and functionality of AChE were partially retained.

Multiscale methods for macromolecular simulations

In this article we review the key modeling tools available for simulating biomolecular systems. We consider recent developments and representative applications of mixed quantum mechanics/molecular mechanics (QM/MM), elastic network models (ENMs), coarse-grained molecular dynamics, and grid-based tools for calculating interactions between essentially rigid protein assemblies. We consider how the different length scales can be coupled, both in a sequential fashion (e.g. a coarse-grained or grid model using parameterization from MD simulations), and via concurrent approaches, where the calculations are performed together and together control the progression of the simulation. We suggest how the concurrent coupling approach familiar in the context of QM/MM calculations can be generalized, and describe how this has been done in the CHARMM macromolecular simulation package.