Lee S-J, Schlesinger PH, Wickline SA, Lanza GM, Baker NA. Simulation of fusion-mediated nanoemulsion interactions with model lipid bilayers. Soft Matter, in press.
Perfluorocarbon-based nanoemulsion particles have become promising platforms for the delivery of therapeutic and diagnostic agents to specific target cells in a non-invasive manner. A “contact-facilitated” delivery mechanism has been proposed wherein the emulsifying phospholipid monolayer on the nanoemulsion surface contacts and forms a lipid complex with the outer monolayer of target cell plasma membrane, allowing cargo to diffuse to the surface of target cell. While this mechanism is supported by experimental evidence, its molecular details are unknown.The present study develops a coarse-grained model of nanoemulsion particles that are compatible with the MARTINI force field. Simulations using this coarse-grained model have demonstrated multiple fusion events between the particles and a model vesicular lipid bilayer. The fusion proceeds in the following sequence: dehydration at the interface, close apposition of the particles, protrusion of hydrophobic molecules to the particle surface, transient lipid complex formation, absorption of nanoemulsion into the liposome. The initial monolayer disruption acts as a rate-limiting step and is strongly influenced by particle size as well as by the presence of phospholipids supporting negative spontaneous curvature. The core-forming perfluorocarbons play critical roles in initiating the fusion process by facilitating protrusion of hydrophobic moieties into the interface between the two particles. This study directly supports the hypothesized nanoemulsion delivery mechanism and provides the underlying molecular details that enable engineering of nanoemulsions for a variety of medical applications.
Tozammel Hossain KSM, Bailey-Kellogg C, Friedman AM, Bradley MJ, Baker N, Ramakrishnan N. Using physicochemical properties of amino acids to induce graphical models of residue couplings. BIOKDD ’11, 2011.
Residue coupling in protein families is an important indicator for structural and functional conservation. Two residues are coupled if changes of amino acid at one residue location are correlated with changes in the other. Many algorithmic techniques have been proposed to discover couplings in protein families. These approaches discover couplings over amino acid combinations but do not yield mechanistic or other explanations for such couplings. We propose to study couplings in terms of amino acid classes such as polarity, hydrophobicity, size, and reactivity, and present two algorithms for learning probabilistic graphical models of amino acid class-based residue couplings. Our probabilistic graphical models provide a sound basis for predictive, diagnostic, and abductive reasoning. Further, our methods can take optional structural priors into account for building graphical models. The resulting models are useful in assessing the likelihood of a new protein to be a member of a family and for designing new protein sequences by sampling from the graphical model. We apply our approaches to understand couplings in two protein families: Nickel-responsive transription factors (NikR) and G-protein coupled receptors (GPCRs). The results demonstrate that our graphcial models based on sequences, physicochemical properties, and protein structure are capable of detecting amino acid class-based couplings between important residues that play roles in activities of these two families.
Bradley MJ, Chivers PT, Baker NA. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal inter-domain allosteric communication pathways. J Mol Biol, 378, 1155-73, 2008.
E. coli NikR is a homotetrameric Ni2+- and DNA-binding protein that functions as a transcriptional repressor of the NikABCDE nickel permease. The protein is composed of 2 distinct domains. The N-terminal fifty amino acids of each chain forms part of the dimeric ribbon-helix-helix (RHH) domains, a well-studied DNA-binding fold. The eighty-three residue C-terminal nickel-binding domain forms an ACT-fold and contains the tetrameric interface. In this study, we have utilized an equilibrium molecular dynamics (MD) simulation in order to explore the conformational dynamics of the NikR tetramer and determine important residue interactions within and between the RHH and ACT domains to gain insight into the effects of Ni on DNA-binding activity. The molecular simulation data was analyzed using two different correlation measures based on fluctuations in atomic position and non-covalent contacts, together with a clustering algorithm to define groups of residues with similar correlation patterns for both types of correlation measure. Based on these analyses, we have defined a series of residue interrelationships that describe an allosteric communication pathway between the Ni2+ and DNA binding sites, which are separated by 40 A. Several of the residues identified by our analyses have been previously shown experimentally to be important for NikR function. An additional subset of the identified residues structurally connects the experimentally implicated residues and may help coordinate the allosteric communication between the ACT and RHH domains.
Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, 92, 3397-406, 2007.
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 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 the- oretical 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.
Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J, 88, 1659-1666, 2005.
The tetramer is the most important form for acetylcholinesterase in physiological conditions, i.e., in the neuromuscular junction and the nervous system. It is important to study the diffusion of acetylcholine to the active sites of the tetrameric enzyme to understand the overall signal transduction process in these cellular components. Crystallographic studies revealed two different forms of tetramers, suggesting a flexible tetramer model for acetylcholinesterase. Using a recently developed finite element solver for the steady-state Smoluchowski equation, we have calculated the reaction rate for three mouse acetylcholinesterase tetramers using these two crystal structures and an intermediate structure as templates. Our results show that the reaction rates differ for different individual active sites in the compact tetramer crystal structure, and the rates are similar for different individual active sites in the other crystal structure and the intermediate structure. In the limit of zero salt, the reaction rates per active site for the tetramers are the same as that for the monomer, whereas at higher ionic strength, the rates per active site for the tetramers are ~67%-75% of the rate for the monomer. By analyzing the effect of electrostatic forces on ACh diffusion, we find that electrostatic forces play an even more important role for the tetramers than for the monomer. This study also shows that the finite element solver is well suited for solving the diffusion problem within complicated geometries.
Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in CCMV simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers, 75, 325-337, 2004.
Although many viruses have been crystallized and the protein capsid structures have been determined by x-ray crystallography, the nucleic acids often cannot be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of cowpea chlorotic mottle virus. Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations.
Song Y, Zhang Y, Bajaj C, Baker NA. Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis. Biophys J, 87, 1558-66, 2004.
As described previously, continuum models, such as the Smoluchowski equation, offer a scalable framework for studying diffusion in biomolecular systems. This work presents new developments in the efficient solution of the continuum diffusion equation. Specifically, we present methods for adaptively refining finite element solutions of the Smoluchowski equation based on a posteriori error estimates. We also describe new, molecular-surface-based models, for diffusional reaction boundary criteria and compare results obtained from these models with the traditional spherical criteria. The new methods are validated by comparison of the calculated reaction rates with experimental values for wild-type and mutant forms of mouse acetylcholinesterase. The results show good agreement with experiment and help to define optimal reactive boundary conditions.
Vitalis A, Baker NA, McCammon JA. ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules. Mol Sim, 30, 45-61, 2004.
In this work we present a new software package (ISIM), which represents a flexible, computational tool for simulations of electrolyte solutions via a grand canonical Monte Carlo procedure (GCMC) with a specific capability of treating biomolecules in solution. The GCMC method provides a powerful tool for studying the ionic environments of highly charged macromolecules with attention to the atomic detail of both the solute and the mobile counterions. The ISIM software differs from previous schemes mainly by treating different ion types independently and offering a new parameterization procedure for calibrating excess chemical potentials and bulk ion concentrations. Additionally, ISIM leverages the APBS software package to provide accurate descriptions of the biomolecular electrostatic potential through the efficient solution of Poisson’s equation. ISIM has been validated on a variety of test systems; we successfully reproduce elementary properties of electrolyte solutions as well as theoretical and experimental results for challenging test systems like Calmodulin and DNA.
Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J Am Chem Soc, 124, 1438-42, 2002.
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 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.
Baker N, Tai K, Henchman R, Sept D, Elcock A, Holst M, McCammon JA. Mathematics and molecular neurobiology. Computational Methods for Macromolecules: Challenges and Applications. Gan HH, Schlick T, eds., 2002.
