Charge calculations in molecular mechanics 6: the calculation of partial atomic charges in nucleic acid bases and the electrostatic contribution to DNA base pairing.

A previously described scheme for the direct calculation of the partial atomic charges in molecules (CHARGE2) is applied to the nucleic acid bases. It is shown that inclusion of the omega-technique for the calculation of HMO derived pi charges is of particular importance for these highly polar systems. The molecular dipole moments obtained for the resulting charges are in very good agreement with the observed values for a variety of substituted purine and pyrimidine bases. The partial atomic charges for cytosine, thymine, guanine and adenine (as the 1-methyl and 9-methyl forms) are given and compared with values calculated by a variety of molecular orbital and empirical schemes. All the schemes reproduce the same general trends, with the possible exception of those calculated by the Del Re method, though the charges given by Kollman are in general somewhat larger than the others. The electrostatic contribution to the Watson-Crick base pair interaction energies are calculated using these partial atomic charges. The electrostatic contributions obtained from the M.O. derived atomic charges are less than half the observed values, as are those obtained by the Gasteiger method. The electrostatic contributions calculated from the CHARGE2 atomic charges and those of Kollman are in reasonable agreement with the observed values. The influence of a distant-dependent dielectric constant is examined, but no clear pattern emerges.     

The Influence of Charge Calculation on Molecular Dynamics Simulation of Adenine in Water

Abstract

Molecular dynamics simulations of an aqueous solution of adenine have been performed using different methods of charge calculation to evaluate the influence of the values of the atomic charges on the dynamical results and to incorporate new information about the interaction between adenine and water. Four sets of partial charges where computed using ab-initio methods. In all cases the hydration properties of adenine were similar. These results support the view that the simulations by molecular dynamics, at least for the regime of infinite dilution, are not sensitive with respect to the different sets of partial charges used. A net hydrophobic behavior of the adenine molecule, on the water was observed.     

Theoretical analysis of deoxycytidine-5'-phosphate protonation

The electron density distribution in deoxycytidine-5'-monophosphate (5'-dCMP) molecule and dianion has been studied by the method of CNDO/2. The comparison between the results of calculation for the neutral molecule and the data obtained by Pearlman and Kim shows that there is a linear correlation between the atomic charges calculated using quantum chemistry and those derived from X-ray results. However, partial charges for the deoxyribose fragment are correlated in a nonlinear manner. The influence of the protons added to the cytosine and phosphate residues on the atomic charges and bond orders of deoxy-cytidine-5'-monophosphate has been analyzed here. The conclusion has been drawn that the semiempirical quantum-chemical CNDO/2 technique is applicable to the mononucleotide studies.     

Incorporation of lone pairs into the electrostatic term in the empirical intra- and intermolecular energy calculations

The method hitherto used for estimating the electrostatic term in empirical intramolecular calculations of stable conformations of biologically important molecules and macromolecules and intermolecular calculations of molecular associations or packing energy in molecular crystals had been analyzed. It has been shown that the contribution of atomic hybridization moments is omitted in the calculation of electrostatic interactions from net atomic charges localized on nuclei which have been determined by standard quantum-chemical methods. This contribution plays an important part in determining electrostatic interactions, mainly in molecules containing atoms with lone pairs. Simultaneously, a modified method for calculating the electrostatic term comprising the interaction of the lone pairs, which are represented by atomic hybridization moments, has been proposed. The relationship between the atomic hybridization moment and the bond angle has been expressed for some typical configurations occurring in biologically important molecules. Finally, this new approach is illustrated by results of the conformational analysis of some model compounds for biomolecules and compared with the approach used so far for the estimation of the electrostatic interaction in empirical methods of calculation of the intra- and intermolecular energy.     

Average orientation of aromatic residues in proteins determined from linear dichroism spectroscopy. A comparison of results on bovine gamma-crystallins with X-ray data

The structures of the two very closely related proteins, bovine gamma II- and gamma IVa-crystallin have been studied by means of near-ultra-violet linear dichroism spectroscopy on squeezed polyacrylamide gel systems. The crystallin spectra are discussed in terms of the spectra of the aromatic chromophores present in these proteins and provide detailed information on the average orientation of these residues in the proteins. A comparison of our results with information based on crystallographic X-ray experiments shows excellent agreement, reflecting even some of the minor differences between the two proteins studied. Since linear dichroism measurements as performed here take a few days only, and can be done on most aqueous protein solutions, linear dichroism spectroscopy may give a valuable contribution to structural studies on proteins.     

A Detailed Study of VESPA Electrostatic Potential-Derived Atomic Charges

VESPA, an improved semiempirical method for the calculation of electrostatic potential-derived atomic charges has been tested. It is shown that this approach is even less dependent upon molecular orientation than "high density" CHELPG ab initio ESP-derived charges. The conformational dependence of VESPA charges has been investigated for rotation around the C-N bond in formamide and 11 different conformers of glycerolphosphorylcholine. The results obtained are also compared to the corresponding ab initio values. Finally, VESPA is used to calculate electrostatic potential-derived charges for bioorganic molecules. We discuss the abilities and the limitations of ESP charges in this area.     

Large variation in electrostatic contours upon addition of steric parameters and the effect of charge calculation schemes in CoMFA on mutagenicity of MX analogues

Partial atomic charge is a useful concept to describe physico-chemical properties of a molecule. For this, various schemes have been devised to get reasonable values. Mutagen X is an ideal set to test the effect of partial atomic charge variation. Therefore, we collected data from previous reports and studied various charge schemes. Our systematic study covers 26 charge calculation schemes along with a broad range of levels of theory. Charge calculation schemes include charges from charge equalisation, electrostatic potential fitting, molecular orbital and atomic polar tensor. Calculation levels span from empirical, semi-empirical, Hartree–Fock, density functional and Møller–Plesset 2. We also used two validation statistics for internal prediction. To observe the electrostatic effect accurately during comparative molecular field analysis (CoMFA) modelling, we first studied isolated electrostatic parameters to avoid interaction effect with steric parameters. The results clearly show that adding steric parameters does change statistical conclusions as well as CoMFA maps. Although there was a weak trend that quantum mechanical (QM)-derived charges gave better statistical values, it is not apparent statistically (alpha = 0.05). Particularly, Mülliken population analysis (MPA) did not produce better results. Therefore, when we excluded MPA schemes from QM calculation, the QM-derived charges were found to be significant, i.e. sophisticated charge schemes other than MPA with QM methods were found to be superior to simple empirical charge schemes. In addition, we demonstrated that in order to test charge schemes properly, excluding steric parameter is more important. This work exemplifies Occam's theorem of parsimony. A simpler model is a better model.     

Libraries of atomic multipole moments for precise modeling of electrostatic properties of amino acids

Summary Contemporary theoretical models used in describing electrostatic properties of amino acids in polypeptides rely usually on atomic point charges. Recently noted defects of such models in reproducing protein folding originate from the inadequate representation of the electrostatic term, in particular inability of atomic charges to account for local anisotropy of molecular charge distribution. Such defects could be corrected by multicenter multipole moments derived directly from any high quality quantum chemical wavefunctions. This is illustrated by comparison of monopole and multipole electrostatic interactions between some amino acids within glutathione S-transferase.High quality Point Charge Models (PCM) can be derived analytically from multipole moment databases. Preliminary results suggest that torsional potentials are controlled by electrostatic interactions of atomic multipoles.Examples illustrating various uses of multicenter multipole moment databases of protein building blocks in modeling various properties of amino acids and polypeptides have been described, including calculation of molecular electrostatic potentials, electric fields, interactions between amino acid residues, estimates of pK_a shifts and changes in catalytic activity induced by amino acid substitutions in mutated enzymes.     

Optical spectroscopic elucidation of beta-turns in disulfide bridged cyclic tetrapeptides

Vibrational circular dichroism (VCD) spectroscopic features of type II beta-turns were characterized previously, but, criteria for differentiation between beta-turn types had not been established yet. Model tetrapeptides, cyclized through a disulfide bridge, were designed on the basis of previous experimental results and the observed incidence of amino acid residues in the i + 1 and i + 2 positions in beta-turns, to determine the features of VCD spectra of type I and II beta-turns. The results were correlated with electronic circular dichroism (ECD) spectra and VCD spectra calculated from conformational data obtained by molecular dynamics (MD) simulations. All cyclic tetrapeptides yielded VCD signals with a higher frequency negative and a lower frequency positive couplet with negative lobes overlapping. MD simulations confirmed the conformational homogeneity of these peptides in solution. Comparison with ECD spectroscopy, MD, and quantum chemical calculation results suggested that the low frequency component of VCD spectra originating from the tertiary amide vibrations could be used to distinguish between types of beta-turn structures. On the basis of this observation, VCD spectroscopic features of type II and VIII beta-turns and ECD spectroscopic properties of a type VIII beta-turn were suggested. The need for independent experimental as well as theoretical investigations to obtain decisive conformational information was recognized.     

Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase

By using a combined quantum-mechanical and molecular-mechanical potential in molecular dynamics simulations, we have investigated the effects of the enzyme electric field of dihydrofolate reductase on the electronic polarization of its 5-protonated dihydrofolate substrate at various stages of the catalyzed hydride transfer reaction. Energy decomposition of the total electrostatic interaction energy between the ligands and the enzyme shows that the polarization effect is 4% of the total electrostatic interaction energy, and, significantly, it accounts for 9kcal/mol of transition state stabilization relative to the reactant state. Therefore it is essential to take account of substrate polarization for quantitative interpretation of enzymatic function and for calculation of binding free energies of inhibitors to a protein. Atomic polarizations are calculated as the differences in the average atomic charges on the atoms in gas phase and in molecular simulations of the enzyme; this analysis shows that the glutamate tail and the pterin ring are the highly polarized regions of the substrate. Electron density difference plots of the reactant and product complexes at instantaneous configurations in the enzyme active center confirm the inferences made on the basis of partial atomic charges.     

Calculation and display of electrostatic potentials

A general methodology is developed for incorporating accurate electrostatic information from ab initio molecular orbital calculations into molecular mechanics calculations. Examples are given of the method applied to simple aromatic organic molecules. A program has been developed for displaying the results of the ab initio calculations on a Silicon Graphics workstation. The technique developed here provides an alternative method for including electrostatic interactions in molecular mechanics calculations and is compared with other methods for determining atomic charges.     

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.     

Quantum chemical studies on the conformational structure of bacterial peptidoglycan. III. CNDO and INDO calculations on the N-acetyl-giucosamine

CNDO and INDO semi-empirical all valence M.O. methods have been applied to predict the side group dihedral angles of N-acetyl glucosamine in order to compare the results of empirical, MNDO and PCILO studies already reported.The net atomic charges and dipole moments have also been computed. The present calculation suggests that the net atomic charges remain almost constant for the different conformers considered.The CNDO, INDO and PCILO methods predict nearly the same orientations for the side groups. Moreover, the quantum chemical methods suggest significant improvements over the empirical results although, in general, similar conformational features are observed. However, the MNDO results for some of the side groups are different from the ones obtained by all the above methods.     

The intrinsic molecular potential of glyceryl monooleate layers and its effect on the conformation and orientation of an inserted molecule: example of gramicidin A.

It is shown by explicit calculation that the distribution of the atomic charges in the constituent molecules of a lipid monolayer or bilayer of glyceryl monooleate creates an intrinsic potential difference between the head region and the hydrocarbon region which tends to repel positive charges towards the exterior and attract negative charges to the interior. The analogies and differences between a bilayer and a monolayer are analyzed. The possible consequences of the intrinsic potential gradient in a lipid layer on the preferred orientation and conformation of a polar neutral molecule are illustrated on the case of a gramicidin A monomer.     

Linear dichroism of the complex between the gene 32 protein of bacteriophage T4 and poly(1,N6-ethenoadenylic acid)

We performed linear dichroism measurements in compressed polyacrylamide gels on the complex between the helix-destabilizing protein of bacteriophage T4, GP32 and poly(1,N6-ethenoadenylic acid), which is used as a model system for single-stranded DNA. A strong hyperchromism for poly(1,N6-ethenoadenylic acid) in the complex indicates a strongly altered conformation. The positive linear dichroism in the wavelength region where the bases absorb must be explained by a strong tilting of the bases in the complex. This finding is in accordance with results from earlier studies, using electric birefringence and circular dichroism measurements. Our measurements show that the angle between the bases and the local helix axis is 42(+/- 6)degrees. In addition, a pronounced contribution from the tryptophan residues of GP32 can be recognized, indicating that several of these residues have a specific orientation in the complex. The sign of the dichroism due to the tryptophan residues is the same as that due to the DNA bases. However, it is not sufficient to assume that all the observed dichroism is due to one or more intercalated tryptophan residues and there must be one or more additional tryptophan residues that make an angle of less than 40 degrees with the local helix axis. Some possible structures of the DNA-protein complex are discussed.     

Structural basis of human erythrocyte glucose transporter function in reconstituted vesicles

The transmembrane orientation of the human erythrocyte glucose transporter was assessed based on polarized Fourier transform infrared and ultraviolet circular dichroism spectroscopic data obtained from oriented multilamellar films of the reconstituted transporter vesicles. Infrared spectra revealed that there are distinct vibrations for alpha-helical structure while the vibrational frequencies specific to beta-structure are characteristically absent. Analysis of linear dichroism of the infrared spectra further indicated that these alpha-helices in the transporter are preferentially oriented perpendicular to the lipid bilayer plane forming an effective tilt of less than 38 degrees from the membrane normal. Such a preferential orientation was further supported by ultraviolet circular dichroism spectra which reveal that the 208 nm Moffit band found in the detergent-solubilized preparation is absent in the film preparation. Linear dichroism data further indicated that D-glucose, a typical substrate, further reduces this effective tilt angle slightly.     

A molecular view on the interaction of the trojan peptide penetratin with the polar interface of lipid bilayers

Penetratin belongs to the family of Trojan peptides that effectively enter cells and therefore can be used as cargoes for agents that are unable to penetrate the cell membrane. We applied polarized infrared spectroscopy in combination with the attenuated total reflection technique to extract information before penetratin binding to lipid membranes with molecular resolution. The amide I band of penetratin in the presence of zwitterionic dimyristoylphosphatidylcholine and of anionic lipid membranes composed of dioleoylphosphatidylcholine and dioleoylphosphatidylglycerol shows the characteristics of an antiparallel beta-sheet with a small fraction of turns. Both signatures have been interpreted in terms of a hairpin conformation. The infrared linear dichroism of the amide I band indicates that the peptide chain orients in an oblique fashion whereas the plane of the sheet aligns virtually parallel with respect to the membrane surface. The weak effect of the peptide on dimyristoylphosphatidylcholine gives indication of its superficial binding where the charged lysine and arginine side chains form H-bonds to the phosphate oxygens of the surrounding lipids. The determinants for internalization of penetratin appear to be a peptide sequence with a distribution of positively charged residues along a beta-sheet conformation, which enables the anchoring of the peptide in the polar part of the membranes and the effective compensation of anionic lipid charges.     

Complementary DNA base interactions: application of recently refined electrostatic interaction theory

Electrostatic interactions between the DNA bases in the Watson-Crick hydrogen bonding configuration are examined in both the molecular and the atomic multipole representation using three different methods of calculation: (a) CNDO wave functions and definitions of moments, (b) IEHT wave functions and division of two-center densities and (c) IHET wave functions with equally divided overlap densities. It is shown that the inclusion in the interaction series of terms at least as high as the quadrupole-quadrupole is required to quantitatively characterize the interactions. Convergence is more rapid with the atomic multipole representation and is unaffected by the type of assignment of formal charges. A quantitative approach to the problem of the role of electrostatic interactions in hydrogen bonding in DNA is thus provided, with obvious impact on the investigation of molecular recognition processes.     

Beyond CHELP: improved potential derived charges for sugars

The partitioning of the overall molecular charge distribution into atom centered monopole charges, while quantum mechanically ill-defined, is nevertheless a technique which finds applications in several broad classes of chemical problems. Charges derived from fits to electrostatic potentials have an intuitive appeal since, in principle, these could be derived from either theoretical or experimental data. It has been noted, however, that such potential derived charges can be conformationally dependent in ways that do not appear to reflect the changes in the molecular wavefunction. Both the algorithm used for selecting points at which the molecular electrostatic potential will be fit and the density of points used in the fit have been suggested to influence the resultant charges. Recently [Stouch TR, Williams DE (1992) J Comp Chem 13: 622–32; Stouch TR, Williams DE (1993) J Comp Chem 14: 858–66] it has been noted that numerical difficulties may make it impossible to fit all the atomic charges in a molecule. Singular value decomposition (SVD) of the linear least squares matrices used in fitting atom based monopoles to molecular electrostatic potentials provides a tool for evaluating the integrity of the calculated charges. Based on the SVD analysis for a selected group of molecules we have noted particularly that increasing the molecular size reduces the fraction of charges which can be validly assigned. Users of PD derived charges, especially those who are using those charges for tasks other than reproduction of the MEP, should be aware that there is a high probability that a significant portion of those charges are statistically unreliable. Therefore, charges in many biological molecules, such as sugars, prove to be difficult to obtain by potential derived (PD) methods such as CHELP or CHELPG. Results from the SVD can be used to both assess PD charges and to generate an improved, albeit incomplete, set. Improved PD fits are presented for a series of simple saccharides. Abbreviations: HF, Hartree-Fock; LLS, linear least squares; MEP, molecular electrostatic potential; PD, potential derived; SVD, singular value decomposition This revised version was published online in November 2006 with corrections to the Cover Date.