A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field

The performance of the GROMOS96 parameter set 45A3 developed for aliphatic alkanes is tested on a bilayer of dipalmitoylphosphatidylcholine (DPPC) in water in the liquid-crystalline L(alpha) phase. Variants of the force-field parameter set as well as different sets of simulation conditions or simulation parameter sets are evaluated. In the case of the force-field parameters, the van der Waals constants for the non-bonded interaction of the ester carbonyl carbon and the partial charges and charge group definition of the phosphatidylcholine head group are examined. On the methodological side, different cut-off distances for the non-bonded interactions, use of a reaction-field force due to long-range electrostatic interactions, the frequency of removal of the centre of mass motion and the strength of the coupling of the pressure of the system to the pressure bath are tested. The area per lipid, as a measure of structure, the order parameters of the chain carbons, as a measure of membrane fluidity, and the translational diffusion of the lipids in the plane of the bilayer are calculated and compared with experimental values. An optimal set of simulation parameters for which the GROMOS96 parameter set 45A3 yields a head group area, chain order parameters and a lateral diffusion coefficient in accordance with the experimental data is listed.     

Validation of the 53A6 GROMOS force field

The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)₂, and a proteinogenic ³-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding–unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized.     

An improved generalized AMBER force field (GAFF) for urea

We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.     

Extraction of horseradish peroxidase and its conjugates formed by surface-active agent micelles

The author studied peculiarities of the extraction of horseradish peroxidase (HRP) and its conjugates with 3 and 7 molecules of progesterone (PROG) from the aqueous solution into heptane and chloroform containing reversed micelles of surfactants. Micelles of cetyltrimethylammonium bromide, Aerosol OT, and Triton X-45 protect the enzyme from denaturation in the biphasic system. The enzyme is readily extracted from the aqueous phase in the organic medium containing reversed micelles of surfactants at low values of pH. The addition of PEG-6000 (5%) to the aqueous phase enhances the enzyme solubilization at pH 8.6-9.0. The enzyme solubilization significantly increases, when surfactants with unlike charges are used. Inorganic salts decrease the specific solubilization of the enzyme. The HRP modification with progesterone has a weak effect on the enzyme solubilization with reversed micelles.     

Statistical analysis of unlabeled point sets: comparing molecules in chemoinformatics

We consider Bayesian methodology for comparing two or more unlabeled point sets. Application of the technique to a set of steroid molecules illustrates its potential utility involving the comparison of molecules in chemoinformatics and bioinformatics. We initially match a pair of molecules, where one molecule is regarded as random and the other fixed. A type of mixture model is proposed for the point set coordinates, and the parameters of the distribution are a labeling matrix (indicating which pairs of points match) and a concentration parameter. An important property of the likelihood is that it is invariant under rotations and translations of the data. Bayesian inference for the parameters is carried out using Markov chain Monte Carlo simulation, and it is demonstrated that the procedure works well on the steroid data. The posterior distribution is difficult to simulate from, due to multiple local modes, and we also use additional data (partial charges on atoms) to help with this task. An approximation is considered for speeding up the simulation algorithm, and the approximating fast algorithm leads to essentially identical inference to that under the exact method for our data. Extensions to multiple molecule alignment are also introduced, and an algorithm is described which also works well on the steroid data set. After all the steroid molecules have been matched, exploratory data analysis is carried out to examine which molecules are similar. Also, further Bayesian inference for the multiple alignment problem is considered.     

Temperature dependence of the binding of endotoxins to the polycationic peptides polymyxin B and its nonapeptide

The interaction between endotoxins-free lipid A and various lipopolysaccharide (LPS) chemotypes with different sugar chain lengths-and the polycationic peptides polymyxin B and polymyxin nonapeptide has been investigated by isothermal titration calorimetry between 20 and 50 degrees C. The results show a strong dependence of the titration curves on the phase state of the endotoxins. In the gel phase (<30 degrees C for LPS and <45 degrees C for lipid A), an endothermic reaction is observed, for which the driving force is an entropically driven endotoxin-polymyxin interaction, due to disruption of the ordered water structure and cation assembly in the lipid A backbone and adjacent molecules. In the liquid crystalline phase (>35 degrees C for LPS and >47 degrees C for lipid A) an exothermic reaction takes place, which is mainly due to the strong electrostatic interaction of the polymyxins with the negative charges of the endotoxins, i.e., the entropic change DeltaS is much lower than in the gel phase. For endotoxins with short sugar chains (lipid A, LPS Re, LPS Rc) the stoichiometry of the polymyxin binding corresponds to pure charge neutralization; for the compounds with longer sugar chains (LPS Ra, LPS S-form) this is no longer valid. This can be related to the lower susceptibility of the corresponding bacterial strains to antibiotics.     

Proton NMR bandshape studies of lamellar liquid crystals and gel phases containing lecithins and cholesterol.

Proton NMR spectra for gel and liquid crystalline samples, composed of dimyristoyl and/or dipalmitoyl lecithin, cholesterol and water, can be consistently interpreted in terms of mesophase symmetry and molecular diffusion according to a model proposed by Wennerstrom (Wennerstrom, H. (1973) Chem. Phys. Lett. 18, 41-44). It is shown by computer simulation that the characteristic "super-lorentzian" bandshape of the lamellar mesophase can be described by the superposition of three gaussian curves. The NMR signal of the gel phase can be simulated by the superposition of two gaussian curves with widths at half height of 2.5 kHz and 19 kHz. An upper limit of the lateral diffusion coefficient of the lecithin molecules in the gel phase is calculated to be about 5-10(-15) m-2/s. It is therefore concluded that the static intermolecular dipolar couplings average to zero in the lamellar mesophase. An estimation of the order parameter of the liquid crystalline phase is made from experimental data and a calculated "rigid lattice" linewidth. A two phase system is shown to exist in the temperature range 28-34 degrees C for a mesophase of a mixture of dimyristoyl and dipalmitoyl lecithin. The presence of cholesterol results in enhanced lateral diffusion of the lecithin molecules at temperatures below the Chapman transition point.     

Running WILD: the case for exploring mixed parameter sets in sensitivity analysis

The robustness of clades to parameter variation may be a desirable quality or even a goal in phylogenetic analyses. Sensitivity analyses used to assess clade stability have invoked the incongruence length difference (ILD or _WILD) metric, a measure of congruence among datasets, to compare a series of most‐parsimonious results from re‐running analyses under different analytical conditions. It is also common practice to select a single “optimal” parameter set that minimizes _WILD across all parameter sets. However, the divergent molecular evolution of ribosomal genes and protein‐encoding genes—specifically the bias against transversion events in coding genes of conserved function—suggests that deployment of multiple parameter sets could outperform the use of a single parameter set applied to all molecules. We explored congruence in five published datasets by including mixed parameter sets in our sensitivity analysis. In four cases, mixed parameter sets outperformed the previously reported, single optimal parameter set. Conversely, multiple parameter sets did not outperform a single optimal parameter set in a case in which actual strong topological conflict exists between data partitions. Exploration of mixed parameter sets may prove useful when combining ribosomal and protein‐encoding genes, due to the relatively higher frequency of single‐ and double‐base pair indel events in the former, and the relatively lower frequency of transversions in the latter.
© The Willi Hennig Society 2010.     

Interactions and compatibility of 11 S globulin from Vicia faba seeds and sodium salt of carboxymethylcellulose in an aqueous medium

This work studies specific interactions and compatibility between a legumin and a linear carboxylated polysaccharide using gel permeation chromatography, sedimentation analysis, SDS gel electrophoresis, viscometry and phase analysis measurements. It uses the system water/11 S globulin/CMC as a model. Carboxymethylcellulose (CMC) molecules are able to cause a partial dissociation of the protein, subsequent formation of soluble interbiopolymeric complexes and partial aggregation of the free non combined protein at room temperature and pH 6.0-6.5. The maximal binding of biopolymers is observed at their equimolar ratio. The decrease in temperature of the mixture from 293 to 277 K leads to formation of the complex coacervate. The increase in pH from 6.0 to 7.6 results in suppression of complex formation and manifestation of the phenomenon of thermodynamic incompatibility if the total concentration of biopolymers in the system exceeds the critical concentration of segregative phase separation.     

Molecular Dynamics Simulations of Zinc Ions in Water Using CHARMM

Molecular Dynamics simulations of a zinc ion with 123 and 525 TIP3P-water molecules were carried out with CHARMM using two different Lennard-Jones parameter sets for the Zn²⁺ ion. The results were compared to published experimental and simulation data. Good agreement was found for radial distribution functions, number of hydrogen bonds, and diffusion coefficients. Experimental radial distribution functions were better reproduced by the original CHARMM22 parameter set than by the parameter set modified by Stote and Karplus. Diffusion coefficients were found to depend on the system size rather than on the parameter set used and were better reproduced by the larger systems. The divalent zinc ion exerts a strong influence on its hydration shell as indicated by the high first peak of the radial distribution function. Water molecules in the vicinity of the zinc ion show a slight deformation of the O-H bond length and of the H-O-H bond angle as compared to pure water. No water molecules from the first hydration shell were exchanged during 1 ns of MD simulation.Electronic Supplementary Material available.     

Anion transport through the contraluminal cell membrane of renal proximal tubule. The influence of hydrophobicity and molecular charge distribution on the inhibitory activity of organic anions

Three different mechanisms of anion transport have been identified for the contraluminal membrane in the proximal tubule of the rat kidney. These mechanisms are specific for the transport of sulfate, dicarboxylate and p-aminohippurate anions. Sulfate transport is inhibited by bivalent organic anions with a distance between the charges of less than 7 A. The sulfate system acts in two modes: in a planar mode for anions with flat charged residues such as COO- and a charge separation of 3-4 A or in a bulky mode for groups such as SO3H- and a charge separation of 4-7 A. Monovalent anions can be accepted if there is a hydrophobic core next to the negative charges. Dicarboxylate transport is inhibited exclusively by anions with two charge centers located within 5 to 9 A, one of those possibly being a partial charge of -0.5 elementary charges. p-Aminohippurate transport is inhibited by monovalent anions, if these have a hydrophobic domain with a minimal length of about 4 A. Bivalent anions inhibit, if they have a charge distance of 6-10 A; both charges can be partial charges of about -0.5 elementary charges. Longer bivalent anions can be effective provided they have a sufficiently large hydrophobic domain. For the sulfate and p-aminohippurate systems it is found that anions with high acidity yield good inhibition. The overlapping specificities of the three systems with respect to charge distance and hydrophobicity allow them to accept a large variety of organic anions.     

The Search for the Spatial and Electronic Requirements of a Drug

A new program called GAMMA (genetic algorithm for multiple molecule alignment) has been developed for the superimposition of several three-dimensional chemical structures. Superimposition of molecules and evaluation of structural similarity is an important task in drug design and pharmaceutical research. Similarities of compounds are determined by this program either based on their structural or their physicochemical properties by defining different matching criteria. These matching criteria are atomic properties such as atomic number or partial atomic charges. The program is based on a combination of a genetic algorithm with a numerical optimization process. A major goal of this hybrid procedure is to address the conformational flexibility of ligand molecules adequately. Thus, only one conformation per structure is necessary and the program can work even when only one conformation of a compound is stored in a database. The genetic algorithm optimizes in a nondeterministic process the size and the geometric fit of the overlay. The geometric fit of the conformations is further improved by changing torsional angles combining the genetic algorithm and the directed tweak method. The determination of the fitness of a superimposition is based on the Pareto optimization. As an application the superimposition of a set of Cytochrome P450c17 enzyme inhibitors has been performed.Electronic Supplementary Material available.     

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement.     

An X-ray diffraction study of the effect of alpha-tocopherol on the structure and phase behaviour of bilayers of dimyristoylphosphatidylethanolamine.

The effect of alpha-tocopherol on the thermotropic phase transition behaviour of aqueous dispersions of dimyristoylphosphatidylethanolamine was examined using synchrotron X-ray diffraction methods. The temperature of gel to liquid-crystalline (Lbeta-->Lalpha) phase transition decreases from 49.5 to 44.5 degrees C and temperature range where gel and liquid-crystalline phases coexist increases from 4 to 8 degrees C with increasing concentration of alpha-tocopherol up to 20 mol%. Codispersion of dimyristoylphosphatidylethanolamine containing 2.5 mol% alpha-tocopherol gives similar lamellar diffraction patterns as those of the pure phospholipid both in heating and cooling scans. With 5 mol% alpha-tocopherol in the phospholipid, however, an inverted hexagonal phase is induced which coexists with the lamellar gel phase at temperatures just before transition to liquid-crystalline lamellar phase. The presence of 10 mol% alpha-tocopherol shows a more pronounced inverted hexagonal phase in the lamellar gel phase but, in addition, another non-lamellar phase appears with the lamellar liquid-crystalline phase at higher temperature. This non-lamellar phase coexists with the lamellar liquid-crystalline phase of the pure phospholipid and can be indexed by six diffraction orders to a cubic phase of Pn3m or Pn3 space groups and with a lattice constant of 12.52+/-0.01 nm at 84 degrees C. In mixed aqueous dispersions containing 20 mol% alpha-tocopherol, only inverted hexagonal phase and lamellar phase were observed. The only change seen in the wide-angle scattering region was a transition from sharp symmetrical diffraction peak at 0.43 nm, typical of gel phases, to broad peaks centred at 0.47 nm signifying disordered hydrocarbon chains in all the mixtures examined. Electron density calculations through the lamellar repeat of the gel phase using six orders of reflection indicated no difference in bilayer thickness due to the presence of 10 mol% alpha-tocopherol. The results were interpreted to indicate that alpha-tocopherol is not randomly distributed throughout the phospholipid molecules oriented in bilayer configuration, but it exists either as domains coexisting with gel phase bilayers of pure phospholipid at temperatures lower than Tm or, at higher temperatures, as inverted hexagonal phase consisting of a defined stoichiometry of phospholipid and alpha-tocopherol molecules.     

Calculations of the charge distribution in dodecyltrimethylammonium: a quantum chemical investigation

In this work we report the atomic partial charges evaluated on dodecyltrimethylammonium ion. The values obtained from 17 quantum methods [CHELP, CHELPG, MK, NPA at (HF, LDA, PBE, B3LYP)//6-31G++(d,p) level and APT at B3LYP//6-31G++(d,p)] on the molecule optimised at B3LYP/6-31G++(d,p) level were compared to two semiempirical methods (Gasteiger and Qeq) and the commercial force field PCFF. All methods based on quantum calculation gave a positive charge delocalised on at least the first four alkyl groups of the tail. However, those deriving partial charges from the electrostatic potential gave an unrealistic set of alternative positive and negative alkyl group charges along the tail. In comparison, the NPA and APT methods lead to a steady decrease in the partial charges from the third alkyl group, and agreed closely with the representation of the electrostatic potential mapped onto the 0.002 au isodensity surface. The choice of the exchange correlation treatment does not drastically influence the atomic partial charges.     

Partial atomic charges of amino acids in proteins

Using a semiempirical quantum mechanical procedure (FCPAC) we have calculated the partial atomic charges of amino acids from 494 high-resolution protein structures. To analyze the influence of the protein's environment, we considered each residue under two conditions: either as the center of a tripeptide with PDB structure geometry (free) or as the center of 13-16 amino acid clusters extracted from the PDB structure (buried). The partial atomic charges from residues in helices and in sheets were separated. The FCPAC partial atomic charges of the Cbeta and Calpha of most residues correlate with their helix propensity, positively for Cbeta and negatively for Calpha (r2 = 0.76 and 0.6, respectively). The main consequence of burying residues in proteins is the polarization of the backbone C=O bond, which is more pronounced in helices than in sheets. The average shift of the oxygen partial charges that results from burying is -0.120 in helix and -0.084 in sheet with the charge of the proton as unit. Linear correlations are found between the average NMR chemical shifts and the average FCPAC partial charges of Calpha (r2 = 0.8-0.85), N (r3 = 0.67-0.72), and Cbeta (r2 = 0.62) atoms. Correlations for helix and beta-sheet FCPAC partial charges show parallel regressions, suggesting that the charge variations due to burying in proteins differentiate between the dihedral angle effects and the polarization of backbone atoms.     

Basis set validation for polyatomic cation-water interactions

A study of the effects of counterpoise (CP) corrections in polyatomic cation-water interactions is added to the systematic analysis performed in the past of the basis set superposition error (BSSE) in neutral and anionic adducts. The interaction with water of the ammonium cation and its methyl and -CHO derivatives is considered due to the need to model accurately this functional group, which is common in biological molecules. The basis sets employed are the STO-3G and MINI-1 minimal basis sets and the 3-21G, 4-31G and 6-31G** extended ones. In addition, the 6-311++G (2d,p) and 6-311++G (3d, 2p) basis sets have been used for the smallest system, at the SCF and MP2 levels, both without and with CP correction. These basis sets give an equilibrium distance slightly larger and an interaction energy less favourable than the 6-31G** basis set at the corresponding level, while the inclusion of correlation corrections produces a stronger H-bond at a shorter distance. The results confirm the previous hint of a lower incidence of BSSEs in medium size cationic systems, at a different extent for the various basis sets. While the STO-3G basis set is sharply affected by BSSEs in both the equilibrium distance and the interaction energy, the MINI-1 basis set shows a small BSSE, though its trend is not completely satisfactory because the charge transfer component has an anomalous behaviour with respect to our reference basis set. The 4-31G basis set is the only one able to hold comparison with the 6-31G**, even though the interaction energy produced is slightly overestimated. The 3-21G basis set, when corrected, almost parallels the 4-31G one in this set of compounds. The reliability of the CPED correction is checked and discussed.     

Improved Parameters for Generating Partial Charges: Correlation with Observed Dipole Moments

The Universal Force Field was initially combined with the Charge Equilibrium Scheme in the molecular mechanics program AMMP in order to generate partial charges for protein atoms. A new parameter set with improved generation of partial charges has been derived in order to analyse a wider range of atoms and compounds. The electrostatic parameters were modified to achieve better correlation with experimental dipole moments for a training set of 160 compounds, which included alkali metal halogenides, saturated and unsaturated hydrocarbons, alcohols, ethers, amines, thiols, sulphides, oxo compounds, aromatic and heteroaromatic molecules. The correlation coefficient for the calculated and experimental dipole moments was improved from 0.57 to 0.98. The new parameters were tested for another 149 compounds and the correlation coefficient increased from 0.48 to 0.85. The newly generated Modified Parameter Set for AMMP (MOPSA) improves the predictive power of the program, especially in the area of the macromolecular modelling and drug design, where the nonbonded energies play a crucial role.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s008940050114     

Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.