Acetylcholinesterase: electrostatic steering increases the rate of ligand binding

Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations

Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.

From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus

With an estimated 1 billion people affected across the globe, influenza is one of the most serious health concerns worldwide. Therapeutic treatments have encompassed a number of key functional viral proteins, mainly focused on the M2 proton channel and neuraminidase. This review highlights the efforts spent in targeting the M2 proton channel, which mediates the proton transport toward the interior of the viral particle as a preliminary step leading to the release of the fusion peptide in hemagglutinin and the fusion of the viral and endosomal membranes. Besides the structural and mechanistic aspects of the M2 proton channel, attention is paid to the challenges posed by the development of efficient small molecule inhibitors and the evolution toward novel ligands and scaffolds motivated by the emergence of resistant strains.

Searching for Hydrodynamic Orienting Effects in the Association of Tri-N-acetylglucosamine with Hen Egg-White Lysozyme

Using stopped-flow fluorometry, we determined rate constants for the formation of diffusional encounter complexes of tri-N-acetylglucosamine (NAG₃) with hen egg-white lysozyme (k_a^WT) and its double mutant Asp48Asn/Lys116Gln (k_a^MT). We defined binding anisotropy, κ ≡ (k_a^WT – k_a^MT)/(k_a^WT + k_a^MT), and determined its ionic strength dependence. Our goal was to check if this ionic strength dependence provides information about the orienting hydrodynamic effects in the ligand-binding process. We also computed ionic strength dependence of the binding anisotropy from Brownian dynamics simulations using simple models of the lysozyme–NAG₃ system. The results of our experiments indicate that in the case of lysozyme and NAG₃ such hydrodynamic orienting effects are rather negligible. On the other hand, the results of our Brownian dynamics simulations prove that there exist molecular systems for which such orienting effects are substantial. However, the ionic strength dependence of the rate constants for the wild-type and modified systems do not exhibit any qualitative features that would allow us to conclude the presence of hydrodynamic orienting effects from stopped-flow experiments alone. Nevertheless, the results of our simulations suggest the presence of hydrodynamic orienting effects in the receptor–ligand association when the anisotropy of binding depends on the solvent viscosity.

Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6)

Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6 We find that capsid hexamers and pentamers have differential binding modes for IP6 Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid.

Gene Silencing Mechanisms Revealed by Dynamics of Guide, Target, and Duplex Binding to Argonaute

Argonaute (Ago) protein plays a central role in silencing gene expression by binding a "guide" strand to the base-pair with a complementary mRNA and degrading the mRNA. The current understanding of how Ago-guide and Ago-guide-mRNA complexes assemble is based mainly on static crystal structures; the associated kinetic pathways remain unknown/unclear. By simulating the successive binding of guide/target strand to Thermus thermophilus Ago (TtAgo) and computing the respective free energy landscapes, we directly visualize how TtAgo silencing complexes form and function. We show that the guide binding rate depends on its initial loading position onto TtAgo. Subsequent target recognition beyond the scissile 10-11 nucleotides must overcome a substantial energy barrier for TtAgo's nucleotide-binding groove to expand widely. This work reveals novel roles for the core TtAgo domains and shows how the kinetic barriers that must be overcome for critical structural changes to occur lead to target repression/cleavage.

Diffusional Encounter Rate Constants for Xanthone and 2-Naphthoic Acid by Flash Photolysis Experiments and Brownian Dynamics Simulations: Substantial Effects of Polarizability of the Triplet State

Diffusional encounter rate constants, for xanthone and 2-naphthoic acid molecules in their triplet states with xanthone or 2-naphthoic acid molecules in their triplet or singlet states, were determined using nanosecond laser flash photolysis spectroscopy. Simultaneously, Brownian dynamics simulations were used to compute these rate constants for assumed models of encountering molecules. Altogether, a global fit to transient absorption progress curves, reporting populations of triplet state xanthone and triplet state 2-naphthoic acid molecules, allowed us to determine six diffusional encounter rate constants from our experiments. The most important result of this study is the detection of substantial effects of the electric polarizability of molecules in their triplet state, visible for xanthone triplet and 2-naphthoic acid ground states, a homo triplet-triplet annihilation of 2-naphthoic acid, and a hetero triplet-triplet annihilation for xanthone and 2-naphthoic acid.

Structural Consideration of the Working Mechanism of Fold Type I Transaminases From Eubacteria: Overt and Covert Movement

Transaminases (TAs) reversibly catalyze the transfer reaction of an amino group between an amino group donor and an amino group acceptor, using pyridoxal 5′-phosphate (PLP) as a cofactor. TAs are categorized according to the amino group position of the donor substrate and respective TAs recognize their own specific substrates. Over the past decade, a number of TA structures have been determined by X-ray crystallography. On the basis of the structural information, the detailed mechanism of substrate recognition by TAs has also been elucidated. In this review, fold type I TAs are addressed intensively. Comparative studies on structural differences between the apo and holo forms of fold type I TAs have demonstrated that regions containing the active site exhibit structural plasticity in the apo form, facilitating PLP insertion into the active site. In addition, given that TAs recognize two different kinds of substrates, they possess dual substrate specificity. It is known that spatial rearrangements of active site residues occur upon binding of the substrates. Intriguingly, positively charged residues are predominantly distributed at the active site cavity. The electric field generated by such charge distributions may attract negatively charged molecules, such as PLP and amino group acceptors, into the active site. Indeed, TAs show remarkable dynamics in diverse aspects. In this review, we describe the comprehensive working mechanism of fold type I TAs, with a focus on conformational changes.

Carboxypeptidase Y activity and maintenance is modulated by a large helical structure

Yeast carboxypeptidase Y (CPY) is a serine protease with broad substrate specificity. Structurally, CPY belongs to the α/β hydrolase fold family and contains characteristic large helices, termed the V‐shape helix, above the active site cavity. Four intramolecular disulfide bonds are located in and around the V‐shape helix. In this study, mutant CPYs were constructed in which one of these disulfide bonds was disrupted. Mutants lacking the C193–C207 bond located at the beginning of the V‐shape helix aggregated easily, while mutants lacking the C262–C268 bond located at the end of the V‐shape helix displayed decreased hydrolytic activity. The results indicate that the V‐shape helix is involved in CPY catalysis and in maintenance of its conformation.

Does Ionic Screening Lower Activation Barriers for Conformational Transitions in Proteins?

In this work, we investigated the kinetics of binding of hen egg-white lysozyme with tri- N-acetylglucosamine in aqueous solutions, at two values of pH, 3.2 and 11, as a function of ionic strength, by a stopped-flow method with tryptophyl fluorescence observation of the transients. We analyzed registered reaction progress curves by employing numerical integration of appropriate chemical master equations. We discriminated between several binding models and established that the process observed in experiments follows a two-step mechanism, composed of four elementary stages: diffusional formation of an encounter complex, dissociation of the encounter complex, conformational transition of the encounter complex to the final complex, and the reverse transformation, i.e., from the final complex to the encounter complex. We evaluated rate constants of these elementary stages and determined their dependencies on solution ionic strength. Regardless of solution pH, rate constants of both forward and reverse conformational transitions increase with an increasing ionic strength. This suggests that ionic screening of intramolecular electrostatic interactions may act to lower the activation barrier for conformational transition in proteins.

Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins

Human gut Bacteroides use surface-exposed lipoproteins to bind and metabolize complex polysaccharides. Although vitamins and other nutrients are also essential for commensal fitness, much less is known about how commensal bacteria compete with each other or the host for these critical resources. Unlike in Escherichia coli, transport loci for vitamin B₁₂ (cobalamin) and other corrinoids in human gut Bacteroides are replete with conserved genes encoding proteins whose functions are unknown. Here we report that one of these proteins, BtuG, is a surface-exposed lipoprotein that is essential for efficient B₁₂ transport in B. thetaiotaomicron. BtuG binds B₁₂ with femtomolar affinity and can remove B₁₂ from intrinsic factor, a critical B₁₂ transport protein in humans. Our studies suggest that Bacteroides use surface-exposed lipoproteins not only for capturing polysaccharides, but also to acquire key vitamins in the gut.

Eating is the first step in an hours-long process that extracts the nutrients we need to live. It not only nourishes us, but also a vast community of bacteria in our gut called the microbiota. The gut microbiota acts like an extension of our immune system and helps us stay healthy in many ways. For example, it blocks pathogens from making us sick. But too many gut bacteria in the wrong parts of our intestines can be harmful.

Some people are prone to developing a dangerous overgrowth of bacteria in their small intestine where most of our dietary nutrients get absorbed. This overgrowth can lead to many problems including vitamin B12 deficiency even when they eat plenty of it. To understand why, scientists must learn how microbes affect our ability to absorb nutrients from food and how the microbes themselves capture nutrients like vitamin B12 as they pass through our digestive tract.

Now, Wexler et al. show that some gut microbes may be able to pirate vitamin B12 from us as it passes through the digestive tract. Wexler et al. showed that a protein called BtuG on the surface of a type of gut bacteria called Bacteriodes grabs onto vitamin B12 with extraordinary strength. In fact, these bacterial proteins bind to vitamin B12 so strongly that they can even pry it away from our own vitamin B12 collecting protein.

When Bacteriodes with and without BtuG were placed in mice with no gut bacteria of their own, bacteria with BtuG rapidly outcompeted those lacking the protein. The experiments suggest that competition for vitamin B12 among microbes has favored bacteria that are better at capturing the nutrient. More studies are needed to learn whether BtuG contributes to vitamin B12 deficiencies in humans with gut bacteria overgrowth and determine the best ways to combat such deficiencies.

Hydrodynamic Steering in Protein Association Revisited: Surprisingly Minuscule Effects of Considerable Torques

We investigate the previously postulated hydrodynamic steering phenomenon, resulting from complication of molecular shapes, its magnitude and possible relevance for protein-ligand and protein-protein diffusional encounters, and the kinetics of diffusion-controlled association. We consider effects of hydrodynamic interactions in a prototypical model system consisting of a cleft enzyme and an elongated substrate, and real protein-protein complexes, that of barnase and barstar, and human growth hormone and its binding protein. The kinetics of diffusional encounters is evaluated on the basis of rigid-body Brownian dynamics simulations in which hydrodynamic interactions between molecules are modeled using the bead-shell method for detailed description of molecular surfaces, and the first-passage-time approach. We show that magnitudes of steering torques resulting from the hydrodynamic coupling of associating molecules, evaluated for the studied systems on the basis of the Stokes-Einstein type relations for arbitrarily shaped rigid bodies, are comparable with magnitudes of torques resulting from electrostatic interactions of binding partners. Surprisingly, however, unlike in the case of electrostatic torques that strongly affect the diffusional encounter, overall effects of hydrodynamic steering torques on the association kinetics, while clearly discernible in Brownian dynamics simulations, are rather minute. We explain this result as a consequence of the thermal agitation of the binding partners. Our finding is relevant for the general understanding of a wide spectrum of molecular processes in solution but there is also a more practical aspect to it if one considers the low level of shape detail of models that are usually employed to evaluate hydrodynamic interactions in particle-based Stokesian and Brownian dynamics simulations of multicomponent biomolecular systems. Results described in the current work justify, in part at least, such a low-resolution description.

Gorge Motions of Acetylcholinesterase Revealed by Microsecond Molecular Dynamics Simulations

Acetylcholinesterase, with a deep, narrow active-site gorge, attracts enormous interest due to its particularly high catalytic efficiency and its inhibitors used for treatment of Alzheimer’s disease. To facilitate the massive pass-through of the substrate and inhibitors, “breathing” motions to modulate the size of the gorge are an important prerequisite. However, the molecular mechanism that governs such motions is not well explored. Here, to systematically investigate intrinsic motions of the enzyme, we performed microsecond molecular dynamics simulations on the monomer and dimer of Torpedo californica acetylcholinesterase (TcAChE) as well as the complex of TcAChE bound with the drug E2020. It has been revealed that protein-ligand interactions and dimerization both keep the gorge in bulk, and opening events of the gorge increase dramatically compared to the monomer. Dynamics of three subdomains, S3, S4 and the Ω-loop, are tightly associated with variations of the gorge size while the dynamics can be changed by ligand binding or protein dimerization. Moreover, high correlations among these subdomains provide a basis for remote residues allosterically modulating the gorge motions. These observations are propitious to expand our understanding of protein structure and function as well as providing clues for performing structure-based drug design.

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.

Dynamics theory for molecular liquids based on an interaction site model

Dynamics theories for molecular liquids based on an interaction site model have been developed over the past few decades and proved to be powerful tools to investigate various dynamical phenomena.

Nonlocal Poisson-Fermi model for ionic solvent

We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as special cases, and its solution is the convolution of a solution of the corresponding nonlocal Poisson dielectric model with a Yukawa-like kernel function. The Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.

Electrostatic Steering Accelerates C3d:CR2 Association

Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts.

An Electrostatic Funnel in the GABA-Binding Pathway

The γ-aminobutyric acid type A receptor (GABA_A-R) is a major inhibitory neuroreceptor that is activated by the binding of GABA. The structure of the GABA_A-R is well characterized, and many of the binding site residues have been identified. However, most of these residues are obscured behind the C-loop that acts as a cover to the binding site. Thus, the mechanism by which the GABA molecule recognizes the binding site, and the pathway it takes to enter the binding site are both unclear. Through the completion and detailed analysis of 100 short, unbiased, independent molecular dynamics simulations, we have investigated this phenomenon of GABA entering the binding site. In each system, GABA was placed quasi-randomly near the binding site of a GABA_A-R homology model, and atomistic simulations were carried out to observe the behavior of the GABA molecules. GABA fully entered the binding site in 19 of the 100 simulations. The pathway taken by these molecules was consistent and non-random; the GABA molecules approach the binding site from below, before passing up behind the C-loop and into the binding site. This binding pathway is driven by long-range electrostatic interactions, whereby the electrostatic field acts as a ‘funnel’ that sweeps the GABA molecules towards the binding site, at which point more specific atomic interactions take over. These findings define a nuanced mechanism whereby the GABA_A-R uses the general zwitterionic features of the GABA molecule to identify a potential ligand some 2 nm away from the binding site.

Neurotransmitters convey signals from one neuron to the next and are indispensable to the functioning of the nervous system. These small molecules bind to receptors to exert their action. One of the most important neurotransmitters is γ-aminobutyric acid (GABA), which binds to its type A receptor to exert an inhibitory influence on the neuron. Many drugs, both medicinal and nefarious, bind to these neuroreceptors and alter the balance of neuronal signals in the brain. There is a fine balance between these drugs eliciting the desired effect, and causing unwanted and sometimes irreversible alterations in neural behavior. To study this critical binding event, we are using computational simulations to observe precisely how the GABA molecule binds to its type A receptor (GABA_A-receptor). One hundred individual simulations were carried out where GABA was placed near the binding site and then allowed to freely bind to the GABA_A-receptor. Binding occurred in 19 of these simulations. Statistical analysis of these binding simulations reveals the consistent pathway taken by GABA molecules to enter the binding site. This improved understanding of the binding event enables development of safer medicinal neuroactive drugs and countermeasures for effects of neuronal chemical trauma.

Steric and Dynamic Parameters Influencing In Situ Cycloadditions to Form Triazole Inhibitors with Crystalline Acetylcholinesterase

Ligand binding sites on acetylcholinesterase (AChE) comprise an active center, at the base of a deep and narrow gorge lined by aromatic residues, and a peripheral site at the gorge entry. These features launched AChE as a reaction vessel for in situ click-chemistry synthesis of high-affinity TZ2PA6 and TZ2PA5 inhibitors, forming a syn-triazole upon cycloaddition within the gorge from alkyne and azide reactants bound at the two sites, respectively. Subsequent crystallographic analyses of AChE complexes with the TZ2PA6 regioisomers demonstrated that syn product association is accompanied by side chain reorganization within the gorge, freezing-in-frame a conformation distinct from an unbound state or anti complex. To correlate inhibitor dimensions with reactivity and explore whether in situ cycloaddition could be accelerated in a concentrated, crystalline template, we developed crystal-soaking procedures and solved structures of AChE complexes with the TZ2PA5 regioisomers and their TZ2/PA5 precursors (2.1-2.7 Å resolution). The structures reveal motions of residue His447 in the active site and, unprecedentedly, residue Tyr341 at the gorge mouth, associated with TZ2 binding and coordinated with other side chain motions in the gorge that may guide AChE toward a transient state favoring syn-triazole formation. Despite precursor binding to crystalline AChE, coupling of rapid electric field fluctuations in the gorge with proper alignments of the azide and alkyne reactants to form the triazole remains a likely limiting step. These observations point to a prime requirement for AChE to interconvert dynamically between sequential conformations to promote favorable electrostatic factors enabling a productive apposition of the reactants for reactivity.

Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling

Signaling in cells often involves co-localization of the signaling molecules. Most experimental evidence has shown that intracellular compartmentalization restricts the range of action of the second messenger, 3'-5'-cyclic adenosine monophosphate (cAMP), which is degraded by phosphodiesterases (PDEs). The objective of this study is to understand the details of molecular encounter that may play a role in efficient operation of the cAMP signaling apparatus. The results from electrostatic potential calculations and Brownian dynamics simulations suggest that positive potential of the active site from PDE enhances capture of diffusing cAMP molecules. This electrostatic steering between cAMP and the active site of a PDE plays a major role in the enzyme-substrate encounter, an effect that may be of significance in sequestering cAMP released from a nearby binding site or in attracting more freely diffusing cAMP molecules.

High-Throughput Screening for Positive Allosteric Modulators Identified Potential Therapeutics against Acetylcholinesterase Inhibition

The current standard of care for treatment of organophosphate (OP) poisoning includes pretreatment with the weak reversible acetylcholinesterase (AChE) inhibitor pyridostigmine bromide. Because this drug is an AChE inhibitor, similar side effects exist as with OP poisoning. In an attempt to provide a therapeutic capable of mitigating AChE inhibition without such side effects, high-throughput screening was performed to identify a compound capable of increasing the catalytic activity of AChE. Herein, two such novel positive allosteric modulators (PAMs) of AChE are presented. These PAMs increase AChE activity threefold, but they fail to upshift the apparent IC50 of a variety of OPs. Further development and optimization of these compounds may lead to pre- and/or postexposure therapeutics with broad-spectrum efficacy against pesticide and nerve agent poisoning. In addition, they could be used to complement the current therapeutic standard of care to increase the activity of uninhibited AChE, potentially increasing the efficacy of current therapeutics in addition to altering the therapeutic window.

Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics

Background

The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors.

Methods

We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with “imperfect” reaction rates.

Results

The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates.

Conclusions

Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.

A simplified electrostatic model for hydrolase catalysis

Toward the development of an electrostatic model for enzyme catalysis, the active site of the enzyme is represented by a cavity whose surface (and beyond) is populated by electric charges as determined by pH and the enzyme's structure. The electric field in the cavity is obtained from electrostatics and a suitable computer program. The key chemical bond in the substrate, at its ends, has partial charges with opposite signs determined from published force-field parameters. The electric field attracts one end of the bond and repels the other, causing bond tension. If that tension exceeds the attractive force between the atoms, the bond breaks; the enzyme is then a successful catalyst. To illustrate this very simple model, based on numerous assumptions, some results are presented for three hydrolases: hen-egg white lysozyme, bovine trypsin and bovine ribonuclease. Attention is given to the effect of pH.

A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations

Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.

Layer-by-layer assembled carbon nanotube-acetylcholinesterase/biopolymer renewable interfaces: SPR and electrochemical characterization

Developing simple, reliable, and cost-effective methods of renewing an inhibited biocatalyst (e.g., enzymatic interfaces) on biosensors is needed to advance multiuse, reusable sensor applications. We report a method for the renewal of layer-by-layer (LbL) self-assembled inhibition-based enzymatic interfaces in multiwalled carbon nanotube (MWCNT) armored acetylcholinesterase (AChE) biosensors. The self-assembly process of MWCNT dispersed enzymes/biopolymers was investigated using surface plasmon resonance (SPR). The LbL fabrication consisted of alternating cushion layers of positively charged CNT-polyethylenimine (CNT-PEI) and negatively charged CNT-deoxyribonucleic acid (CNT-DNA) and a functional interface consisting of alternating layers of CNT-PEI and negatively charged CNT-acetylcholine esterase (CNT-AChE, pH 7.4). The observed SPR response signal increased while assembling the different layers, indicating the buildup of multiple layers on the Au surface. A partial desorption of the top enzymatic layer in the LbL structure was observed with a desorption strategy employing alkaline treatment. This indicates that the strong interaction of CNT-biopolymer conjugates with the Au surface was a result of both electrostatic interactions between biopolymers and the surface binding energy from CNTs: the closer the layers are to the Au surface, the stronger the interactions. In contrast, a similar LbL assembly of soluble enzyme/polyelectrolytes resulted in stronger desorption on the surface after the alkaline treatment; this led to the investigation of AChE layer removal, permanently inhibited after pesticide exposure on glassy carbon (GC) electrodes, while keeping the cushion layers intact. The desorption strategy permitted the SPR and electrochemical electrode surfaces to be regenerated multiple times by the subsequent self-assembly of fresh PEI/AChE layers. Flow-mode electrochemical amperometric analysis demonstrated good stability toward the determination of acetylcholine with 97.1 ± 2.7% renewability. Our simple, inexpensive approach shows the potential of renewable LbL self-assembled functional interfaces for multiple uses in a wide field of applications such as biosensing, various biotechnological processes, and the food and health industries.

First three-dimensional structure of Toxoplasma gondii thymidylate synthase-dihydrofolate reductase: insights for catalysis, interdomain interactions, and substrate channeling

Most species, such as humans, have monofunctional forms of thymidylate synthase (TS) and dihydrofolate reductase (DHFR) that are key folate metabolism enzymes making critical folate components required for DNA synthesis. In contrast, several parasitic protozoa, including Toxoplasma gondii , contain a unique bifunctional thymidylate synthase-dihydrofolate reductase (TS-DHFR) having the catalytic activities contained on a single polypeptide chain. The prevalence of T. gondii infections across the world, especially for those immunocompromised, underscores the need to understand TS-DHFR enzyme function and to find new avenues to exploit for the design of novel antiparasitic drugs. As a first step, we have solved the first three-dimensional structures of T. gondii TS-DHFR at 3.7 Å and of a loop truncated TS-DHFR, removing several flexible surface loops in the DHFR domain, improving resolution to 2.2 Å. Distinct structural features of the TS-DHFR homodimer include a junctional region containing a kinked crossover helix between the DHFR domains of the two adjacent monomers, a long linker connecting the TS and DHFR domains, and a DHFR domain that is positively charged. The roles of these unique structural features were probed by site-directed mutagenesis coupled with presteady state and steady state kinetics. Mutational analysis of the crossover helix region combined with kinetic characterization established the importance of this region not only in DHFR catalysis but also in modulating the distal TS activity, suggesting a role for TS-DHFR interdomain interactions. Additional kinetic studies revealed that substrate channeling occurs in which dihydrofolate is directly transferred from the TS to DHFR active site without entering bulk solution. The crystal structure suggests that the positively charged DHFR domain governs this electrostatically mediated movement of dihydrofolate, preventing release from the enzyme. Taken together, these structural and kinetic studies reveal unique, functional regions on the T. gondii TS-DHFR enzyme that may be targeted for inhibition, thus paving the way for designing species specific inhibitors.

Attractive hydration forces in DNA-dendrimer interactions on the nanometer scale

The energetic contribution of attractive hydration forces arising from water ordering is an interesting but often neglected aspect of macromolecular interactions. Ordering effects of water can bring about cooperativity in many intermolecular transactions, in both the short and long range. Given its high charge density, this is of particular importance for DNA. For instance, in nanotechnology, highly charged dendrimers are used for DNA compaction and transfection. Hypothesizing that water ordering and hydration forces should be maximal for DNA complexes that show charge complementarity (positive-negative), we present here an analysis of water ordering from molecular dynamics simulations and free energy calculations of the interaction between DNA and a nanoparticle with a high positive charge density. Our results indicate not only that complexation of the dendrimer with DNA affects the local water structure but also that ordered water molecules facilitate long-range interactions between the molecules. This contributes significantly to the free energy of binding of dendrimers to DNA and extends the interaction well beyond the electrostatic range of the DNA. Such water effects are of potentially substantial importance in cases when molecules appear to recognize each other across sizable distances, or for which kinetic rates are too fast to be due to pure diffusion. Our results are in good agreement with experiments on the role of solvent in DNA condensation by multivalent cations and exemplify a microscopic realization of mean-field phenomenological theories for hydration forces between mesoscopic surfaces.

Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein

Many receptors and ion channels are activated by ligands. One key question concerns the binding mechanism. Does the ligand induce conformational changes in the protein via the induced-fit mechanism? Or does the protein preexist as an ensemble of conformers and the ligand selects the most complementary one, via the conformational selection mechanism? Here, we study ligand binding of a tetrameric cyclic nucleotide-gated channel from Mesorhizobium loti and of its monomeric binding domain (CNBD) using rapid mixing, mutagenesis, and structure-based computational biology. Association rate constants of ∼10(7) M(-1) s(-1) are compatible with diffusion-limited binding. Ligand binding to the full-length CNG channel and the isolated CNBD differ, revealing allosteric control of the CNBD by the effector domain. Finally, mutagenesis of allosteric residues affects only the dissociation rate constant, suggesting that binding follows the induced-fit mechanism. This study illustrates the strength of combining mutational, kinetic, and computational approaches to unravel important mechanistic features of ligand binding.

Crystal structures of Acetobacter aceti succinyl-coenzyme A (CoA):acetate CoA-transferase reveal specificity determinants and illustrate the mechanism used by class I CoA-transferases

Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases suggested that acyl-CoA binding energy is used to accelerate rate-limiting acyl transfers by compressing the substrate thioester tightly against the catalytic glutamate [White, H., and Jencks, W. P. (1976) J. Biol. Chem. 251, 1688-1699]. The class I CoA-transferase succinyl-CoA:acetate CoA-transferase is an acetic acid resistance factor (AarC) with a role in a variant citric acid cycle in Acetobacter aceti. In an effort to identify residues involved in substrate recognition, X-ray crystal structures of a C-terminally His(6)-tagged form (AarCH6) were determined for several wild-type and mutant complexes, including freeze-trapped acetylglutamyl anhydride and glutamyl-CoA thioester adducts. The latter shows the acetate product bound to an auxiliary site that is required for efficient carboxylate substrate recognition. A mutant in which the catalytic glutamate was changed to an alanine crystallized in a closed complex containing dethiaacetyl-CoA, which adopts an unusual curled conformation. A model of the acetyl-CoA Michaelis complex demonstrates the compression anticipated four decades ago by Jencks and reveals that the nucleophilic glutamate is held at a near-ideal angle for attack as the thioester oxygen is forced into an oxyanion hole composed of Gly388 NH and CoA N2″. CoA is nearly immobile along its entire length during all stages of the enzyme reaction. Spatial and sequence conservation of key residues indicates that this mechanism is general among class I CoA-transferases.

Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine

Pancreatic adenocarcinoma is the most lethal of the solid tumors and the fourth-leading cause of cancer-related death in North America. Matrix metalloproteinases (MMPs) have long been targeted as a potential anticancer therapy because of their seminal role in angiogenesis and extracellular matrix (ECM) degradation of tumor survival and invasion. However, the inhibition specificity to MMPs and the molecular-level understanding of the inhibition mechanism remain largely unresolved. Here, we found that endohedral metallofullerenol Gd@C(82)(OH)(22) can successfully inhibit the neoplastic activity with experiments at animal, tissue, and cellular levels. Gd@C(82)(OH)(22) effectively blocks tumor growth in human pancreatic cancer xenografts in a nude mouse model. Enzyme activity assays also show Gd@C(82)(OH)(22) not only suppresses the expression of MMPs but also significantly reduces their activities. We then applied large-scale molecular-dynamics simulations to illustrate the molecular mechanism by studying the Gd@C(82)(OH)(22)-MMP-9 interactions in atomic detail. Our data demonstrated that Gd@C(82)(OH)(22) inhibits MMP-9 mainly via an exocite interaction, whereas the well-known zinc catalytic site only plays a minimal role. Steered by nonspecific electrostatic, hydrophobic, and specific hydrogen-bonding interactions, Gd@C(82)(OH)(22) exhibits specific binding modes near the ligand-specificity loop S1', thereby inhibiting MMP-9 activity. Both the suppression of MMP expression and specific binding mode make Gd@C(82)(OH)(22) a potentially more effective nanomedicine for pancreatic cancer than traditional medicines, which usually target the proteolytic sites directly but fail in selective inhibition. Our findings provide insights for de novo design of nanomedicines for fatal diseases such as pancreatic cancer.

Small-angle X-ray scattering analysis of the bifunctional antibiotic resistance enzyme aminoglycoside (6') acetyltransferase-ie/aminoglycoside (2'') phosphotransferase-ia reveals a rigid solution structure

Aminoglycoside (6') acetyltransferase-Ie/aminoglycoside (2″) phosphotransferase-Ia [AAC(6')-Ie/APH(2″)-Ia] is one of the most problematic aminoglycoside resistance factors in clinical pathogens, conferring resistance to almost every aminoglycoside antibiotic available to modern medicine. Despite 3 decades of research, our understanding of the structure of this bifunctional enzyme remains limited. We used small-angle X-ray scattering (SAXS) to model the structure of this bifunctional enzyme in solution and to study the impact of substrate binding on the enzyme. It was observed that the enzyme adopts a rigid conformation in solution, where the N-terminal AAC domain is fixed to the C-terminal APH domain and not loosely tethered. The addition of acetyl-coenzyme A, coenzyme A, GDP, guanosine 5'-[β,γ-imido]triphosphate (GMPPNP), and combinations thereof to the protein resulted in only modest changes to the radius of gyration (R(G)) of the enzyme, which were not consistent with any large changes in enzyme structure upon binding. These results imply some selective advantage to the bifunctional enzyme beyond coexpression as a single polypeptide, likely linked to an improvement in enzymatic properties. We propose that the rigid structure contributes to improved electrostatic steering of aminoglycoside substrates toward the two active sites, which may provide such an advantage.

Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics

Acetylcholinesterase is an enzyme with a very high turnover rate; it quenches the neurotransmitter, acetylcholine, at the synapse. We have investigated the kinetics of the enzyme reaction by calculating the diffusion rate of the substrate molecule along an active site channel inside the enzyme from atomic-level molecular dynamics simulations. In contrast to the previous works, we have found that the internal substrate diffusion is the determinant of the acetylcholinesterase kinetics in the low substrate concentration limit. Our estimate of the overall bimolecular reaction rate constant for the enzyme is in good agreement with the experimental data. In addition, the present calculation provides a reasonable explanation for the effects of the ionic strength of solution and the mutation of surface residues of the enzyme. The study suggests that internal diffusion of the substrate could be a key factor in understanding the kinetics of enzymes of similar characteristics.

The role of long-range intermolecular interactions in discovery of new drugs

INTRODUCTION

Long-range intermolecular interactions (interactions at distances between 100 and 1000 Å) play an important role in the interaction between drugs and therapeutic targets, and design techniques based on this concept could significantly improve and accelerate new drug discovery. Understanding these long-range intermolecular interactions will also help further our understanding of the molecular mechanisms and the underlying basic biological processes.

AREAS COVERED

This article looks at the physical bases of long-range intermolecular interactions in biological systems with a brief review of the literature data to support this concept. The article also gives some examples of techniques used in drug discovery that were based on the long-range intermolecular interaction concept.

EXPERT OPINION

The electron-ion interaction potential (EIIP) and average quasivalence number (AQVN) concepts shed new light on the role of long-range intermolecular interactions in biological systems. Further research of physicochemical mechanisms underlying long-range interactions between biological molecules is necessary for a better understanding of the basic biological processes. The addition of the computer-aided design techniques based on the EIIP/AQVN concept to the research and development will lead not only to a significant reduction in cost but also to an acceleration in the development of new drugs.

Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

Reliable predictions of relative binding free energies are essential in drug discovery, where chemists modify promising compounds with the aim of increasing binding affinity. Conventional Thermodynamic Integration (TI) approaches can estimate corresponding changes in binding free energies, but suffer from inadequate sampling due to ruggedness of the molecular energy surfaces. Here, we present an improved TI strategy for computing relative binding free energies of congeneric ligands. This strategy employs a specific, unphysical single-reference (SR) state and Hamiltonian replica exchange (HREX) to locally enhance sampling. We then apply this strategy to compute relative binding free energies of twelve ligands in the L99A mutant of T4 Lysozyme. Besides the ligands, our approach enhances hindered rotations of the important V111, as well as V87 and L118 sidechains. Concurrently, we devise practical strategies to monitor and improve HREX-SRTI efficiency. Overall, the HREX-SRTI results agree well (R(2) = 0.76, RMSE = 0.3 kcal/mol) with available experimental data. When optimized for efficiency, the HREX-SRTI precision matches that of experimental measurements.

Brownian dynamics study of the association between the 70S ribosome and elongation factor G

Protein synthesis on the ribosome involves a number of external protein factors that bind at its functional sites. One key factor is the elongation factor G (EF-G) that facilitates the translocation of transfer RNAs between their binding sites, as well as advancement of the messenger RNA by one codon. The details of the EF-G/ribosome diffusional encounter and EF-G association pathway still remain unanswered. Here, we applied Brownian dynamics methodology to study bimolecular association in the bacterial EF-G/70S ribosome system. We estimated the EF-G association rate constants at 150 and 300 mM monovalent ionic strengths and obtained reasonable agreement with kinetic experiments. We have also elucidated the details of EF-G/ribosome association paths and found that positioning of the L11 protein of the large ribosomal subunit is likely crucial for EF-G entry to its binding site.

Association and electrostatic steering of alpha-lactalbumin-lysozyme heterodimers

The salt and pH dependent association of hen egg white lysozyme with alpha-lactalbumin whey proteins has been studied using molecular level Monte Carlo simulations. A highly uneven charge distribution of alpha-lactalbumin leads to strongly ordered heterodimers that may facilitate the formation of structured, mesoscopic aggregates. This electrostatic steering gives rise to 80% alignment at 5 mM 1 : 1 salt which, due to screening, diminishes to 60% at 100 mM salt. The free energy of interaction minima, dominated by electrostatics, ranges between -9 kT at 1 mM salt to -2 kT at 100 mM (neutral pH). Calculated osmotic second virial cross coefficients indicate complexation in the pH interval 6-10. Multivalent ions are found to effectively destabilize the protein complex and, at constant ionic strength, the order is La(3+) > Ca(2+) > Mg(2+) > Na(+). Upon binding of calcium to alpha-lactalbumin both the interaction and orientational alignment with lysozyme are reduced due to induced changes in the whey protein charge distribution. This potentially explains the experimentally observed absence of supramolecular structuring for the calcium loaded holo alpha-lactalbumin. Where available, good agreement is found with experimental data.

Association of aminoglycosidic antibiotics with the ribosomal A-site studied with Brownian dynamics

Brownian dynamics methodology was applied to simulate the encounter of aminoglycosidic antibiotics with the ribosomal A-site RNA. Studied antibiotics included neamine, neomycin, ribostamycin and paromomycin which differ in chemical structure, the number of pseudo-sugar rings and the net charge. The influence of structural, electrostatic and hydrodynamic properties of antibiotics on the kinetics of their association with the ribosomal A-site was analyzed. The computed diffusion limited rates of association are of the order of 10(10)[Formula: see text] and they weakly depend on ionic strength. Prior to binding antibiotics often slide along the RNA groove with the time scale of approximately 10 ns per base pair in case of neamine. We observed that upon forming the encounter complex aminoglycosides displace from the binding pocket up to two Mg(2+) ions.

Molecular basis of prodrug activation by human valacyclovirase, an alpha-amino acid ester hydrolase

Chemical modification to improve biopharmaceutical properties, especially oral absorption and bioavailability, is a common strategy employed by pharmaceutical chemists. The approach often employs a simple structural modification and utilizes ubiquitous endogenous esterases as activation enzymes, although such enzymes are often unidentified. This report describes the crystal structure and specificity of a novel activating enzyme for valacyclovir and valganciclovir. Our structural insights show that human valacyclovirase has a unique binding mode and specificity for amino acid esters. Biochemical data demonstrate that the enzyme hydrolyzes esters of alpha-amino acids exclusively and displays a broad specificity spectrum for the aminoacyl moiety similar to tricorn-interacting aminopeptidase F1. Crystal structures of the enzyme, two mechanistic mutants, and a complex with a product analogue, when combined with biochemical analysis, reveal the key determinants for substrate recognition; that is, a flexible and mostly hydrophobic acyl pocket, a localized negative electrostatic potential, a large open leaving group-accommodating groove, and a pivotal acidic residue, Asp-123, after the nucleophile Ser-122. This is the first time that a residue immediately after the nucleophile has been found to have its side chain directed into the substrate binding pocket and play an essential role in substrate discrimination in serine hydrolases. These results as well as a phylogenetic analysis establish that the enzyme functions as a specific alpha-amino acid ester hydrolase. Valacyclovirase is a valuable target for amino acid ester prodrug-based oral drug delivery enhancement strategies.

Computational methods for biomolecular electrostatics

An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate, and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion, and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems, with a particular focus on how computational tools can be used to investigate these types of interactions.

Relating destabilizing regions to known functional sites in proteins

BACKGROUND

Most methods for predicting functional sites in protein 3D structures, rely on information on related proteins and cannot be applied to proteins with no known relatives. Another limitation of these methods is the lack of a well annotated set of functional sites to use as benchmark for validating their predictions. Experimental findings and theoretical considerations suggest that residues involved in function often contribute unfavorably to the native state stability. We examine the possibility of systematically exploiting this intrinsic property to identify functional sites using an original procedure that detects destabilizing regions in protein structures. In addition, to relate destabilizing regions to known functional sites, a novel benchmark consisting of a diverse set of hand-curated protein functional sites is derived.

RESULTS

A procedure for detecting clusters of destabilizing residues in protein structures is presented. Individual residue contributions to protein stability are evaluated using detailed atomic models and a force-field successfully applied in computational protein design. The most destabilizing residues, and some of their closest neighbours, are clustered into destabilizing regions following a rigorous protocol. Our procedure is applied to high quality apo-structures of 63 unrelated proteins. The biologically relevant binding sites of these proteins were annotated using all available information, including structural data and literature curation, resulting in the largest hand-curated dataset of binding sites in proteins available to date. Comparing the destabilizing regions with the annotated binding sites in these proteins, we find that the overlap is on average limited, but significantly better than random. Results depend on the type of bound ligand. Significant overlap is obtained for most polysaccharide- and small ligand-binding sites, whereas no overlap is observed for most nucleic acid binding sites. These differences are rationalised in terms of the geometry and energetics of the binding site.

CONCLUSION

We find that although destabilizing regions as detected here can in general not be used to predict binding sites in protein structures, they can provide useful information, particularly on the location of functional sites that bind polysaccharides and small ligands. This information can be exploited in methods for predicting function in protein structures with no known relatives. Our publicly available benchmark of hand-curated functional sites in proteins should help other workers derive and validate new prediction methods.

Photodynamic inhibition of acetylcholinesterase after two-photon excitation of copper tetrasulfophthalocyanine

Sequential two-photon (2-gamma) activated copper tetrasulfophthalocyanine (CuPcS(4)) was shown capable of inactivating acetylcholinesterase (ACE). ACE activity was measured photometrically by the Ellman method. Simultaneous irradiation of ACE in the presence of CuPcS(4) with 514 nm (183 mW/cm(2)) and 670 nm (86 mW/cm(2)) continuous wave (CW) light induced a 20-50% increase in enzyme inhibition as compared to one-photon (1-gamma) irradiation, using either 514- or 670-nm (CW) light at the same fluences. The enzyme activity was not affected by CuPcS(4) or light alone, decreased linearly with the irradiation time, and was shown to be oxygen-dependent. We conclude that the photoinactivation of ACE with sequential 2-gamma irradiation involves reactive oxygen species produced by the interaction of the upper excited T(n) state of CuPcS(4) with molecular oxygen. As CuPcS(4) shows little activity as a conventional 1-gamma photosensitizer, unwanted side effects such as prolonged skin sensitivity are eliminated rendering 2-gamma photodynamic therapy advantageous for the treatment of selected medical applications.

Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations

This article describes the numerical solution of the time-dependent Smoluchowski equation to study diffusion in biomolecular systems. Specifically, finite element methods have been developed to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to the mouse acetylcholinesterase (mAChE) monomer and several tetramers. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different time steps. Calculated rates show very good agreement with experimental and theoretical steady-state studies. Furthermore, these finite element methods require significantly fewer computational resources than existing particle-based Brownian dynamics methods and are robust for complicated geometries. The key finding of biological importance is that the rate accelerations of the monomeric and tetrameric mAChE that result from electrostatic steering are preserved under the non-steady-state conditions that are expected to occur in physiological circumstances.