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Mathematics and Molecular Neurobiology
Nathan A. Baker, Kaihsu Tai, Richard Henchman, David Sept, Adrian Elcock, Michael Holst and J. Andrew McCammon
Advances in mathematics and computer technology, together with advances in structural biology, are opening the way to detailed modeling of biology at the molecular and cellular levels. One objective of such studies is the development of a more complete understanding of biological systems, including the emergence of behavior at the cellular level from that at the molecular level. Another objective is the development of more sophisticated models for structure-aided discovery of new pharmaceuticals.
Binding of Aminoglycoside Antibiotics to the Small Ribosomal Subunit: A Continuum Electrostatics Investigation
Chiansan Ma, Nathan A. Baker, Simpson Joseph and J. Andrew McCammon
The binding of paromomycin and similar antibiotics to the small (30S) ribosomal subunit has been studied using continuum electrostatics methods. Crystallographic information from a complex of paromomycin with the 30S subunit was used as a framework to develop structures of similar antibiotics in the same ribosomal binding site. Total binding energies were calculated from electrostatic properties obtained by by solution of the Poisson-Boltzmann equation combined with a surface area-dependent apolar term. These computed results showed good correlation with experimental data. Additionally, calculation of the ribosomal electrostatic potential in the paromomycin binding site provided insight into the electrostatic mechanisms for aminoglycoside binding and clues for the rational design of more effective antibiotics.
Molecular Dynamics of Acetylcholinesterase
Tongye Shen, Kaihsu Tai, Richard H. Henchman and J. Andrew McCammon
Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions, and suggests possible modes of regulation of the activity of the enzyme.
Extracting Hydration Sites around Proteins from Explicit Water Simulations
Richard H. Henchman and J. Andrew McCammon
Two new methods are assessed for determining the location of hydration sites around proteins from computer simulation. Current methods extract hydration sites from peaks in the water density constructed in the protein frame. However, the dynamic nature of the water molecules, the nearby protein residues and the protein reference frame as a whole tend to smear out the water density, making it more difficult to resolve sites. Two techniques are introduced to better resolve the water density. The first is to construct the water density from the time averaged position of each water molecule in the protein frame while the water remains within a given distance of this averaged position. The second technique is to construct the water density from the time averaged position of each water in the reference frame only of the nearby residues. Criteria for determining hydration sites from the water density are examined. Both techniques are found to significantly improve the detail in the water density and the number of hydration sites detected.
Enlarging the Landscape: Editorial Overview
J. Andrew McCammon and Peter G. Wolynes
Molecular theory and simulation are vibrant and essential elements of modern biology. Indeed, theory and simulation contribute to our understanding of structure-activity correlations with ever-increasing detail and scope. The detail is illustrated by recent work on the evolution of the excited electronic states in the green fluorescent protein and other macromolecules endowed with chromophores. And the range is illustrated by simulations of the activity of such supramolecular structures as ribosomes and the cytoskeleton.
Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A
Gergely Gidofalvi, Chung F. Wong and J. Andrew McCammon
This article describes a short project for an undergraduate to learn several techniques for computer-aided drug design. The project involves estimating the loss of the rotational entropy of the hydroxyl groups of balanol upon its binding to the enzyme protein kinase A (PKA), as the entropy loss can significantly influence PKA-balanol binding affinity. This work employs semi-empirical quantum mechanical techniques for estimating the potential energy curves for the rotation of the hydroxyl groups of balanol in vacuum and in PKA, and solves the Poisson equation to correct the potential energy curves for hydration effects. Statistical mechanical principles were then applied to estimate the desired entropy loss from the potential energy curves. The analysis focuses on examining the importance of hydration effects on influencing the rotational preference of the hydroxyl groups and the significance of the rotational entropy in determining binding affinity.
Properties of Water Molecules in the Active Site Gorge of Acetylcholinesterase from Computer Simulation
Richard H. Henchman, Kaihsu Tai, Tongye Shen and J. Andrew McCammon
A 10-ns trajectory from a molecular dynamics simulation is used to examine the structure and dynamics of water in the active site gorge of acetylcholinesterase to determine what influence water may have on its function. While the confining nature of the deep active site gorge slows down and structures water significantly compared to bulk water, water in the gorge is found to display a number of properties that may aid ligand entry and binding. These properties include fluctuations in the population of gorge waters, moderate disorder and mobility of water in the middle and entrance to the gorge, reduced water hydrogen-bonding ability, and transient cavities in the gorge.
Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5-ns Molecular Dynamics Simulation
Kaihsu Tai, Tongye Shen, Richard H. Henchman, Yves Bourne, Pascale Marchot and J. Andrew McCammon
Our previous molecular dynamics simulation (10 ns) of mouse acetylcholinesterase (EC 126.96.36.199) revealed complex fluctuations of the enzyme active site gorge. Now we report a 5 ns simulation of acetylcholinesterase complexed with fasciculin 2. Fasciculin 2 binds to the gorge entrance of acetylcholinesterase with excellent complementarity and many polar and hydrophobic interactions. In this simulation of the protein-protein complex, where fasciculin 2 appears to sterically block access of ligands to the gorge, again we observe a two-peaked probability distribution of the gorge width. When fasciculin is present, the gorge width distribution is altered such that the gorge is more likely to be narrow. Moreover, there are large increases in the opening of the alternative passages, namely the side door (near Thr 75) and the back door (near Tyr 449). Finally, the catalytic triad arrangement in the acetylcholinesterase active site is disrupted with fasciculin bound. These data support that, in addition to the steric obstruction seen in the crystal structure, fasciculin may inhibit acetylcholinesterase by combined allosteric and dynamical means. Additional data from these simulations can be found at http://mccammon.ucsd.edu/.
Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
Jung-Hsin Lin, Alexander L. Perryman, Julie R. Schames and J. Andrew McCammon
A novel computational methodology for drug design that accommodates receptor flexibility is described. This "relaxed-complex" method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor. We have shown that the ligand-enzyme binding modes are very sensitive to the enzyme conformations, and our approach is capable of finding the best ligand-enzyme complexes. This new method serves as the computational analog of the experimental "SAR by NMR" and "tether" methods, which permit a building block approach for constructing a very potent drug.
Bridging the Implicit and Explicit Solvent Approaches for Membrane Electrostatics
Jung-Hsin Lin, Nathan A. Baker and J. Andrew McCammon
Conformations of a zwitterionic bilayer were sampled from a molecular dynamics (MD) simulation and their electrostatic properties analyzed by solution of the Poisson equation. These traditionally implicit electrostatic calculations were performed in the presence of varying amounts of explicit solvent to assess the magnitude of error introduced by a uniform dielectric description of water surrounding the bilayer. It was observed that, while membrane dipole potential calculations in the presence of explicit water were significantly different than wholly implicit solvent calculations, the calculated dipole potential converged to a reasonable value when four or more hydration layers were included explicitly.
Molecular Dynamics Simulations of Macromolecules: A Perspective
Martin Karplus and J. Andrew McCammon
It is now twenty-five years since the first molecular dynamics simulation of a macromolecule of biological interest was published. The simulation concerned the bovine pancreatic trypsin inhibitor (BPTI), which has served as the "hydrogen molecule" of protein dynamics because of its small size, high stability and relatively accurate x-ray structure, available in 1975; interestingly, its physiological functions remain unknown. Although this simulation was done in vacuum with a crude molecular mechanism potential and lasted for only 9.2 ps, the results were instrumental in replacing our view of proteins as relatively rigid structures (In 1981, Sir D.L. Phillips commented: "Brass models of DNA and a variety of proteins dominated the scene and much of the thinking".) with the realization that they were dynamic systems, whose internal motions play a functional role. Of course, there were already experimental data, such as the hydrogen exchange experiments of Linderstrom-Lang and his coworkers pointing in this direction and the Feynman Lectures on Physics, published 14 years earlier contained the prescient sentence, "Certainly no subject or field is making more progress on so many fronts at the present moment than biology, and if we were to name the most powerful assumption of all, which leads one on and on in an attempt to understand life, it is that all things are made of atoms [italics in original], and that everything that living things do can be understood in terms of the jigglings and wigglings of atoms. [italics added]".
Unfolding Proteins under External Forces: A Solvable Model under the Self-consistent Pair Contact Probability Approximation
Tongye Shen, Lawrence S. Canino and J. Andrew McCammon
We extend a model of Micheletti, et. al. [Phys. Rev. Lett, 87, 088102] used to study protein conformations in equilibrium to the case in which there is an external force field. Under the self-consistent pair contact probability approximation, we show that this residue-level resolution model can still be solved when a constant, external force is used to pull at the termini of the protein. We implement the algorithm using heterogeneous contact parameters and study the force-induced unfolding of a helical segment from the protein GART and of the beta-stranded Ig and Fn-3 domains from the protein titin. The results are qualitatively consistent with the results from more expensive, atomistic dynamics simulation. Despite the mean-field-like approach, we observed a sharp and cooperative unfolding transition within this model.
Studying Enzyme Binding Specificity in Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach
Jeremy Kua, Yingkai Zhang and J. Andrew McCammon
A combined molecular dynamics simulation and multiple ligand docking approach is applied to study the binding specificity of acetylcholinesterase (AChE) with its natural substrate acetylcholine (ACh), a family of substrate analogs and choline. Calculated docking energies are well correlated to experimental kcat/KM values, as well as to experimental binding affinities of a related series of TMTFA inhibitors. The "esteratic" and "anionic" subsites are found to act together to achieve substrate binding specificity. We find that the presence of ACh in the active site of AChE not only stabilizes the setup of the catalytic triad, but also tightens both subsites to achieve better binding. The docking energy gained from this induced fit is 0.7 kcal/mol for ACh. For the binding of the substrate tail group to the anionic subsite, both the size and the positive charge of the tail group are important. The removal of the positive charge leads to a weaker binding of 1.1 kcal/mol loss in docking energy. Substituting each tail methyl group with hydrogen results in both an incremental loss in docking energy, and also a decrease in the percentage of structures docked in the active site correctly set up for catalysis.
Thalassiolins A-C: New Marine-derived Inhibitors of HIV cDNA Integrase
David C. Rowley, Mark S.T. Hansen, Denise Rhodes, Christoph A. Sotriffer, Haihong Ni, J. Andrew McCammon, Frederic D. Bushman and William Fenical
Replication of human immunodeficiency virus (HIV) requires the integration of viral cDNA into the host genome, a process mediated by the viral enzyme integrase. We describe a new series of HIV integrase inhibitors named thalassiolins A-C (1-3) isolated from the Caribbean sea grass Thalassia testudinum. The thalassiolins are distinguished from other flavones previously studied by the substitution of a sulfated beta-D-glucose at the 7-position, a substituent that imparts increased potency against integrase in biochemical assays as well as antiviral activity against HIV in cell culture. Thalassiolin A(1), the most active of these molecules, displays in vitro inhibition of the integrase catalyzed strand transfer reaction at 0.4 mu-M and an antiviral IC50 of 30 mu-M. Molecular modeling studies indicate a favorable binding mode is possible at the catalytic core domain of HIV-1 integrase.
Structural and Dynamical Properties of Water Around Acetylcholinesterase
Richard H. Henchman and J. Andrew McCammon
Structural and dynamic properties of water molecules around acetylcholinesterase are examined from a 10 ns molecular dynamics simulation to help understand how the protein alters water properties. Water structure is broken down into hydration sites constructed from the water density less than 3.6 Å from the protein surface. These sites are characterized according to occupancy, number of water neighbors, hydrogen bonds, dipole moment and residence time. The site description provides a convenient means to describe the extend and localization of these properties. Determining the network of paths that waters follow from site to site and measuring the rate of flow of waters from the sites to the bulk make it possible to quantitatively study the time scales and paths that water molecules follow as they move around the protein.
Role of the Catalytic Triad and Oxyanion Hole in Acetylcholinesterase Catalysis: An ab inito QM/MM Study
Yingkai Zhang, J. Kua and J.A. McCammon
The initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE) has been studied by a combined ab inito quantum mechanical/molecular mechanical (QM/MM) approach. The reaction proceeds through the nucleophilic addition of the Ser203 O to the carbonyl C of acetylcholine, and the reaction is facilitated by simultaneous proton transfer from Ser203 to His447. The calculated potential energy barrier at the MP2(6-31+G*) QM/MM level is 10.5 kcal/mol, consistent with the experimental reaction rate. The third residue of the catalytic triad, Glu334, is found to be essential in stabilizing the transition state through electrostatic interactions. The oxyanion hole, formed by peptidic NH groups from Gly121, Gly122, and Ala204, is also found to play an important role in catalysis. Our calculations indicate that, in the AChE-ACh Michaelis complex, only two hydrogen bonds are formed between the carbonyl oxygen of ACh and the peptidic NH groups of Gly121 and Gly122. As the reaction proceeds, the distance between the carbonyl oxygen of ACh and NH group of Ala204 becomes smaller, and the third hydrogen bond is formed both in the transition state and in the tetrahedral intermediate.
AutoDocking Dinucleotides to the HIV-1 Integrase Core Domain: Exploring Possible Binding Sites for Viral and Genomic DNA
Alexander L. Perryman and J. Andrew McCammon
To understand the binding of both viral and human DNA to HIV-1 Integrase, fully flexible dinucleotides were docked onto the core domain of Integrase. AutoDocking did identify sites on Integrase where favorable interactions with nucleotides can occur, and those sites were in agreement with recently published protein fingerprinting data. By analyzing the phosphates of the docked dinucleotides, we developed a model indicating where the viral cDNA and human DNA bind to the Integrase core domain.
Changes in Flexibility Upon Binding: Application of the Self-Consistent Pair Contact Probability Method to Protein-Protein Interactions
Lawrence S. Canino, Tongye Shen and J. Andrew McCammon
We extend the self-consistent pair contact probability (SCPCP) method to the evaluation of the partition function for a protein complex at thermodynamic equilibrium. Specifically, we adapt the method for multi-chain models and introduce a parameterization for amino acid-specific pairwise interactions. This method is simular to the Gaussian network model (GNM) but allows for the adjusting of the strengths of native state contacts. The method is first validated on a high resolution x-ray crystal structure of bovine Pancreatic Phospholipase A2 comparing calculated B-factors with reported values. We then examine binding-induced changes in flexibility in protein-protein complexes, comparing computed results with those obtained from x-ray crystal structures and molecular dynamics simulations. In particular, we focus on the mouse acetylcholinesterase:fasciculin II and the human α-thrombin:thrombomodulin complexes.