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Computer-Aided Structure-Based Drug Discovery
New advances in methods for structure-based drug discovery are described. Advances in the fundamental theory of ligand-receptor binding are described first, followed by advances in computer simulation methods based on simplified or more detailed models of molecular structure.
pKa Shift Effects on Backbone Amide Base-Catalyzed Hydrogen Exchange Rates in Peptides
F. Fogolari, G. Esposito, P. Viglino, J.M. Briggs and J.A. McCammon
Amide proton exchange (HX) rates are known to depend on protein primary structure as well as local and global protein structure and dynamics. Measurement of HX rates gives information on the local exposure of amide protons to solvent and on local rates of structural openings. It has long been recognized that the amide pKa directly influences the HX rate. Using the finite- difference solution of the Poisson-Boltzmann equation, we investigated the electrostatic effects on HX rates, via calculated shifts in the amide pKa for model compounds (N-methylacetamide, dipeptides entailing almost all amino acid sidechains, and a tripeptide). Rather than shifts in the same compound with varying environmental conditions, we address shifts in the HX rates of different compounds relative to each other. The results for selected model compounds which resemble Ala and Gly residues, with a standard choice of parameters, agree to a high degree of accuracy with experimentally determined rates. Application of the same methodology to naturally occurring amino acids is promising but requires refinement to take into account flexibility and inductive effects.
Correlation Between Rate of Enzyme-Substrate Diffusional Encounter and Average Boltzmann Factor Around Active Site
Huan-Xiang Zhou, James M. Briggs, Sylvia Tara and J. Andrew McCammon
The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., <5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate.
Solvation Studies of DMP323 and A76928 Bound to HIV Protease: Analysis of Water Sites Using Grand Canonical Monte Carlo Simulations
Tami J. Marrone, Haluk Resat, C. Nicholas Hodge, Chong-Hwan Chang and J. Andrew McCammon
We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV-I protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters which may not be resolved in the crystal structures. It can also be used to identify water positions around a putative drug candidate docked into a binding pocket. Knowledge of these water positions may be useful in designing drugs to utilize them as bridging groups or displace them in the binding pocket. In addition, the method should be useful in finding water sites in homology models of enzymes for which crystal structures are unavailable.
Quantum Dynamics of Proton Transfer Processes in Enzymatic Reactions. Simulations of Phospholipase A2
P. Bała, P. Grochowski, B. Lesyng and J.A. McCammon
Berichte der Bunsen-Gesellschaft für Physikalische Chemie, Vol. 120, No. 3, pp. 580-586 (1998)
For the past few years we have been developing a theoretical model capable of describing quantum dynamical processes which occur in molecular systems and in enzymatic active sites. This, in particular, includes proton transfer processes. Our most advanced studies have been performed for phospholipase A2, an enzyme which hydrolyzes phospholipids. The potential energy function for the active site is computed using an Approximate Valence Bond (AVB) method. The dynamics of the key proton in the enzyme's active site is described either by the classical molecular dynamics (MD/AVB model) or by the time-dependent Schroedinger equation. The dynamics of the remaining atoms of the enzyme are described using classical MD. The coupling between the quantum proton and the classical atoms is accomplished via Hellmann-Feynman forces, as well as the time-dependence of the potential energy function in the Schroedinger equation (QCMD/AVB model). The quantum proton transfer from the water molecule to histidine is followed by a nucleophilic attack of the created OH- group. The processes are simulated using the parallelized QCMD code.
Theory of Biomolecular Recognition
Specific, noncovalent binding of biomolecules can only be understood by consideration of structural, thermodynamic and kinetic issues. The theoretical foundations for such analyses have been clarified in the past year. Computational techniques for both particle-based models and continuum models continue to improve, and yield useful insights to an ever-wider range of biomolecular systems.
Correcting for Electrostatic Cutoffs in Free Energy Simulations: Toward Consistency Between Simulations with Different Cutoffs
H. Resat and J.A. McCammon
The use of electrostatic cutoffs in calculations of free energy differences by molecular simulations introduces errors. Even though both solute-solvent and solvent-solvent cutoffs are known to create discrepancies, past efforts have mostly been directed toward correcting for the solute-solvent cutoffs. In this work, an approach based on the generalized reaction field formalism is developed to correct for the solvent-solvent cutoff errors as well. It is shown using a series of simulation that when the cutoff lengths are significantly smaller than the half unit cell size, and the solute-solvent cutoff is not much larger than the solvent-solvent cutoff, the new algorithm is able to yield better agreement among simulations employing different truncation lengths.
Electrostatic Contributions to the Stability of Halophilic Proteins
A.H. Elcock and J.A. McCammon
Solution of the first crystal structures of proteins from a halophilic organism suggest that an abundance of acidic residues distributed over the protein surface is a key determinant of adaptation to high salt conditions. Although one extant theory suggests that acidic residues are favoured because of their superior water binding capacity, it is clear that extensive repulsive electrostatic interactions will also be present in such proteins at physiological pH. To investigate the magnitude and importance of such electrostatic interactions, we conducted a theoretical analysis of their contributions to the salt and pH dependence of stability of two halophilic proteins. Our approach centers around use of the Poisson-Boltzmann equation of classical electrostatics, applied at an atomic level of detail to crystal structures of the proteins. We first show that in using the method, it is important to account for the fact that the dielectric constant of water decreases at high salt concentrations, in order to reproduce experimental changes in pKas of small acids and bases. We then conduct a comparison of salt and pH effects on the stability of 2Fe-2S ferredoxins from the halophile Haloarcula marismortui and the non-halophile anabaena. In both proteins, substantial upward shifts in pKas accompany protein folding, though shifts are considerably larger on average in the halophile. Upward shifts for basic residues occur because of unfavourable electrostatic interactions with other acidic groups. Our calculations suggest that at pH 7 the stability of the halophilic protein is decreased by 18.2 kcal/mol on lowering the salt concentration from 5M to 100mM, a result which is in line with the fact that halophilic proteins generally unfold at low salt concentrations. For comparison, the non-halophilic ferredoxin is calculated to be destabilized by only 5.lkcal/mol over the same range. Analysis of the pH stability curve suggests that lowering the pH should increase the intrinsic stability of the halophilic protein at low salt concentrations, although in practice this is not observed because of aggregation effects. We also report the results of a similar analysis carried out on the tetrameric malate dehydrogenase from Haloarcula marismortui. In this case we investigate the salt and pH dependence of the various monomer-monomer interactions present in the tetramer. All monomermonomer interactions are found to make substantial contributions to the salt dependence of stability of the tetramer. Excellent agreement is obtained between our calculated results for the stability of the tetramer and experimental results. In particular, the finding that at 4M NaCl, the tetramer is stable only between pH 4.8 and 10 is accurately reproduced. Taken together, our results suggest that repulsive electrostatic interactions between acidic residues are a major factor in the destabilization of halophilic proteins in low salt conditions, and that these interactions remain destabilizing even at high salt concentrations. As a consequence, the role of acidic residues in halophilic proteins appears to be more one of preventing aggregation than making a positive contribution to intrinsic protein stability.
Analysis of Synaptic Transmission in the Neuromuscular Junction Using a Continuum Finite Element Model
Jason L. Smart and J. Andrew McCammon
There is a steadily-growing body of experimental data describing the diffusion of acetylcholine in the neuromuscular junction, and the subsequent miniature end plate currents produced at the post-synaptic membrane. In order to gain further insights into the structural features governing synaptic transmission, we have performed calculations using a simplified finite element model of the neuromuscular junction. The diffusing acetylcholine molecules are modeled as a continuum, whose spatial and temporal distribution is governed by the force-free diffusion equation. The finite element method was adopted because of its flexibility in modeling irregular geometries and complex boundary conditions. The resulting simulations are shown to be in accord with experiment, and with other simulations.
Conformation Gating as a Mechanism for Enzyme Specificity
Huan-Xiang Zhou, Stanislaw T. Wlodek and J. Andrew McCammon
Acetylcholinesterasae (AChE), with an active site located at the bottom of a narrow and deep gorge, provides a striking example of enzymes with buried active sites. Recent molecular dynamics (MD) simulations showed that reorientation of five aromatic rings leads to rapid opening and closing of the gate to the active site. In the present study the MD trajectory is used to quantitatively analyze the effect of the gate on the substrate binding rate constant. For a 2.4 A probe modeling acetylcholine, the gate is open only 2.4% of the time, but the quantitative analysis reveals that the substrate binding rate is slowed by merely a factor of 2. We rationalize this result by noting that the substrate, by virtue of Brownian motion, will make repeated attempts to enter the gate each time it is near the gate. If the gate is rapidly switching between the open and closed states, one of these attempts will coincide with an open state and then the substrate succeeds in entering the gate. However, there is a limit on the extent to which rapid gating dynamics can compensate for the small equilibrium probability of the open state. Thus the gate is effective in reducing the binding rate for a ligand 0.4 A bulkier by three orders of magnitude. This suggests a mechanism for achieving enzyme specificity without sacrificing efficiency.
Rapid Binding of a Cationic Active Site Inhibitor to Wild Type and Mutant Mouse Acetylcholinesterase: Brownian Dynamics Simulation Including Diffusion in the Active Site Gorge
Sylvia Tara, Adrian H. Elcock, Paul D. Kirchhoff, James M. Briggs, Zoran Radić, Palmer Taylor and J. Andrew McCammon
It is known that anionic surface residues play a role in the long range electrostatic attraction between acetylcholinesterase and cationic ligands. In our current investigation, we show that anionic residues also play an important role in the behavior of the ligand within the active site gorge of acetylcholinesterase. Negatively charged residues near the gorge opening not only attract positively charged ligands from solution to the enzyme, but can also restrict the motion of the ligand once it is inside of the gorge. We use Brownian dynamics techniques to calculate the rate constant for wild type and mutant acetylcholinesterase with a positively charged ligand. These calculations are performed by allowing the ligand to diffuse within the active site gorge. This is an extension of previously reported work in which a ligand was allowed to diffuse only to the enzyme surface. By setting the reaction criteria for the ligand closer to the active site, better agreement with experimental data is obtained. Although a number of residues influence the movement of the ligand within the gorge, Asp74 is shown to play a particularly important role in this function. Asp74 traps the ligand within the gorge, and in this way helps to ensure a reaction.
Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics Code
P. Bała, T. Clark, P. Grochowski, B. Lesyng, K. Nowinski and J.A. McCammon
In "Recent Advances in Applied Parallel Computing," B. Kagstrom, J. Dongarra, E. Elmroth, J. Wasniewski, Eds., (Lecture Notes in Computer Science 1541), Springer-Verlag Berlin-Heidelberg, pp. 20-27 (1998)
The parallel version of the Quantum Classical Molecular Dynamics code is presented. The execution time scales almost linearly with the number of processors. The measured overhead of the parallelization paradigm is extremely small which ensures the high efficiency of the presented method. Tools based on the Advanced Visualization System (AVS) framework were developed for visualization and analysis of the QCMD simulations.
Self-Organizing Neural Networks Bridge the Biomolecular Resolution Gap
W. Wriggers, R.A. Milligan, K. Schulten and J.A. McCammon
Topology representing neural networks are employed to generate pseudo-atomic structures of large-scale protein assemblies by combining high-resolution data with volumetric data at lower resolution. As an application example, actin monomers and structural subdomains are located in a 3D image reconstruction from electron micro-graphs. To test the reliability of the method, the resolution of the atomic model of an actin polymer is lowered to a level typically encountered in electron microscopic reconstructions. The atomic model is restored with a precision nine times the nominal resolution of the corresponding low-resolution density. The presented self-organizing computing method may be used as an information processing tool for the synthesis of structural data from a variety of biophysical sources.
Exciting Green Fluorescent Protein
V. Helms, E.F.Y. Hom, T.P. Straatsma, J.A. McCammon and P. Langhoff
Dynamical and luminescent properties of the Green Fluorescent Protein (GFP) are being explored via molecular dynamics (MD) simulations and quantum chemistry calculations with the aim of facilitating the rational development of GFP as a probe for cellular functions. Results from an MD simultion of wild type GFP demonstrate the rigidity of the structural framework of GFP, and a very stable hydrogen bond network around the chromophore. Furthermore, excited state calculations have been performed on the chromophore in vacuum, and we report about our work in progress here.
Brownian and Essential Dynamics Studies of the HIV-1 Integrase Catalytic Domain
Wolfgang Weber, Hagop Demirdjian, Roberto D. Lins, James M. Briggs, Ricardo Ferreira and J. Andrew McCammon
The three-dimensional structure of the active site region of the enzyme HIV-1 integrase is not unambiguously known. This region includes a flexible peptide loop that cannot be well resolved in crystallographic determinations. Here, we present two different computational approaches with different levels of resolution and on different timescales to understand this flexibility and to analyze the dynamics of this part of the protein.
Computer Simulation Studies of Acetylcholinesterase Dynamics and Activity
J.A. McCammon, S. Wlodek, T. Clark, P. Kirchhoff, L.R. Scott and S. Tara
Computer simulations of the activity of acetylcholinesterase (AChE) are shedding light on the origins of the selectivity, mechanism, and efficiency of the enzyme. In the following, a brief discussion is presented on two aspects of the the enzymatic activity: the role of the electrostatic field of the enzyme in speeding its binding of cationic substrates and inhibitors, and the role of fluctuations in the structure of the enzyme in facilitating this binding.