Ab initio force field for simulations of proteins and nucleic acids

We present a new self-consistent set of ab initio analytical pair potential to predict specific nonbonded interactions of protein with nucleic acid, of protein with protein, and of nucleic acid with nucleic acid. The purpose of this study is to represent the interaction between biological molecules with an accuracy equivalent to the ab initio molecular orbital calculations, which are used as reference data to obtain the pair potentials. Atoms in nucleic acids and proteins are classified according to their chemical environments. An “effective charge,” a modification of a charge obtained from the Mulliken population analysis, is introduced and used to represent the electrostatic energy. More than 30,000 SCF interaction energies have been calculated to provide the reference data for the fitting procedure that we have adopted in the parameterization of the potentials. The standard deviation is 1.61 kcal/mol for interaction energies spanning the range from about ?220 kcal/mol to +20 kcal/mol. Molecular dynamics simulations, using the above new set of force field, have been performed successfully for the systems where adequate treatments of specific interactions are required: The stability of α-helix of C-peptide and the interaction of spermine with oligonucleotide are examined as preliminary examples.     

An improved nucleic acid parameter set for the GROMOS force field

Over the past decades, the GROMOS force field for biomolecular simulation has primarily been developed for performing molecular dynamics (MD) simulations of polypeptides and, to a lesser extent, sugars. When applied to DNA, the 43A1 and 45A3 parameter sets of the years 1996 and 2001 produced rather flexible double-helical structures, in which the Watson-Crick hydrogen-bonding content was more limited than expected. To improve on the currently available parameter sets, the nucleotide backbone torsional-angle parameters and the charge distribution of the nucleotide bases are reconsidered based on quantum-chemical data. The new 45A4 parameter set resulting from this refinement appears to perform well in terms of reproducing solution NMR data and canonical hydrogen bonding. The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves.     

Fast force field expressions for computer simulations

It is the aim of this work to develop analytical force field expressions that can be rapidly evaluated by computers. The new expressions approximate the energy hypersurfaces as described by the usual force fields. The energies and the derivatives of the energy expressions, i. e. the forces acting on the atoms, in most cases can be very quickly calculated as functions of one squared distance of two atoms per interaction, avoiding slow operations like cosine, square root etc. Formulae and algorithms are given to calculate the parameters needed from those of the AMBER force field.     

Pulse-polarographic analysis of nucleic acids and proteins

Nucleic acids and proteins were studied by means of derivative and normal pulse polarography, and d.c. and a.c. polarography in connection with the dropping mercury electrode. It was shown that natural ribonucleic acids, as transfer, ribosomal and viral RNAs yield derivative pulse-polarographic peaks; from their heights and potentials conclusions can be made about their content of ordered structure in solution, similarly as in the case of deoxyribonucleic acids studied earlier. Synthetic single-stranded polyribo-cytidylic acid yields a well developed peak, whereas in the double-helical complex with polyriboguanylie acid it is inactive when using either derivative pulse polarography or d.c. polarography. Well developed peaks were obtained also with albumin (a protein containing reducible?S?S? groups), while only an inflex was observed on the d.c. polarogram. Proteins were also studied in media containing cobalt (Brdi?ka's solution) or nickel and it was shown that derivative pulse polarography due to its high sensitivity and accuracy enables us to carry out the measurements even in less common media than Brdi?ka's solution. This fact could be exploited in clinical chemistry as well as in the investigation of the nature of catalytic currents of proteins. The currents of double-helical polynucleotides obtained by means of normal pulse polarography exhibit a marked dependence on the initial potential and cannot represent a reliable indicator of structural changes of biopolymers in solution. They can however, be used in studies of the influence of the polynucleotide adsorption at different potentials on the subsequent reduction.     

Polymeric fluorescent dyes for labeling of proteins and nucleic acids

In order to increase the sensitivity of fluorescence labeling in biochemical reactions and diagnostic procedures a labeling technique with polymeric fluorescence dyes was established and tested for its applicability. The fluorescence dye is based on the fluorophor coumarine and was covalently linked to the model proteins strepavidine and IgG. The dye was synthesized by radical polymerization of three different types of functional monomers to ensure water solubility, covalent coupling to proteins, and fluorescence. The molecular weight range was between 20 and 200 kDa. Fractions of narrow molecular weight distribution were prepared by gel filtration on Superdex 200. The relationship between size and charge of the different fractions was analyzed by gel electrophoresis. Covalent conjugation to proteins was carried out by formation of a peptide bond between a carboxylic group of the functional monomers and an amino group of the protein mediated by 1-ethyl-3-(3-dimethylamino-propyl)-carbodiimide (EDC). A novel type of gel electrophoresis was developed in order to analyze and optimize the conjugation reaction; the results were in agreement with those from analytical ultracentrifugation with fluorescence detection. Hydrodynamic studies of the uncoupled dye and the protein-dye conjugates exhibited a drastic decrease of Stokes radius of the dye due to the coupling to the protein. Under optimum conditions the fluorescence intensity of a protein-polymeric dye conjugate was enhanced 40-fold compared to a monomeric dye. Biotin binding to the protein streptavidin was not affected significantly by the conjugation with the polymeric dye. At present, the applicability of the polymeric dye in biochemical and diagnostic reactions seems to be limited due to strong but unspecific hydrophobic interactions which might be overcome by using fluoresceine as monomeric dye.     

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.     

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.     

Thermo-biolithography: a technique for patterning nucleic acids and proteins

We describe a "biolithographic" technique in which the unique properties of biopolymeric materials and the selective catalytic activities of enzymes are exploited for patterning surfaces under simple and bio-friendly conditions. We begin by coating a reactive film of the polysaccharide chitosan onto an inorganic surface (glass or silicon wafer). Chitosan's pH-responsive solubility facilitates film deposition, while the nucleophilic properties of this polysaccharide allow simple chemistries or biochemistries to be used to covalently attach species to the film. The thermally responsive protein gelatin is then cast on top of the chitosan film, and the gelatin gel serves as a sacrificial "thermoresist". Pattern transfer is accomplished by applying a heated stamp to melt specific regions of the gelatin thermoresist and selectively expose the underlying chitosan. Finally, molecules are conjugated to the exposed chitosan sublayer and the sacrificial gelatin layer is removed (either by treating with warm water or protease). To demonstrate the concept, we patterned a reactive dye (NHS-fluorescein), a model 20-base oligonucleotide (using standard glutaraldehyde coupling chemistries), and a model green fluorescent protein (using tyrosinase-initiated conjugation). Because gelatin can be applied and removed under mild conditions, sequential thermo-biolithographic steps can be performed without destroying previously patterned biomacromolecules. These studies represent the first step toward exploiting nature's exquisite specificity for lithographic patterning.     

Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins

The implementation of molecular dynamics with the united-residue (UNRES) force field is extended to treat multichain proteins. Constant temperature was maintained in the simulations with Berendsen or Langevin thermostats. The method was tested on three alpha-helical proteins (1G6U and GCN4-p1, each with two chains, and 1C94, with four chains). Simulations were carried out for both the isolated single chains and the multichain complexes. The proteins were folded by starting from the extended conformation with random initial velocities and with the chains parallel to each other. No symmetry constraints or structure information were included for the single chains or the multichain complexes. In the case of single-chain simulations, a high percentage of the trajectories (100% for 1G6U, 90% for GCN4-p1, and 80% for 1C94) converged to nativelike structures (assumed as the experimental structure of a monomer in the multichain complex), showing that, for the proteins studied in this work with the UNRES force field, the interactions between chains are not critical for stabilization of the individual chains. In the case of multichain simulations, the native structures of the 1G6U and GCN4-p1 complexes, but not that of 1C94, are predicted successfully. The association of the subunits does not follow a unique mechanism; the monomers were observed to fold both before and simultaneously with their association.     

A convenient tool for studying the stability of proteins and nucleic acids

The aim of this work is to discuss the thermodynamic properties, obtained by differential scanning calorimetry (DSC), of the thermal transition of proteins and nucleic acids and to analyze these data using statistical thermodynamic relations. The denaturation of the ordered, specific structures of biological macromolecules is a cooperative process and in many cases the macromolecules undergo a two-state transition. Differential scanning calorimetry, giving direct thermodynamic information, has proved to be very useful in clarifying the energetics of macromolecule transitions and in characterizing their thermal stability. Here, various examples are discussed: i) the equilibrium thermal denaturation of ribonuclease A, a model for the use of DSC by following the temperature-unfolding of the proteins, a monomolecular transition; ii) the equilibrium thermal dissociation of a DNA double helix in two strands, an example of how DSC is used to follow a bimolecular process; iii) an example of the use of DSC for studying the melting of unimolecular and tetramolecular DNA quadruple-helices.     

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

Based on the AMBER polarizable model (ff02), we have re-optimized the parameters related to the main-chain (Phi, Psi) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., beta, P(II), alpha(R), and alpha(L) regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the beta, P(II) and alpha(R) regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)(7)-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization.     

ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various hydrocarbon/O2 systems. From simulations on methane/O2, o-xylene/O2, propene/O2, and benzene/O2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO2/H2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models.     

An all-atom force field for metallocenes

A new all-atom force field, for the molecular modeling of metallocenes was constructed. Quantum chemical calculations were performed to obtain several force field terms not yet defined in the literature. The remainder were transferred from the OPLS-AA/AMBER framework. The parametrization work included the obtention of geometrical parameters, torsion energy profiles, and distributions of atomic charges that blend smoothly with the OPLS-AA specification for a variety of organic molecular fragments. Validation was carried out by comparing simulated and experimental data for five different ferrocene derivatives in the crystalline phase. The present model can be regarded as a step toward a general force field for metallocenes, built in a systematic way, easily integrated with OPLS-AA, and transferable between different metal-ligand combinations.     

CHARMM force field and molecular dynamics simulations of protonated polyethylenimine

As a gene delivery vector, polyethylenimine (PEI) shows one of the highest transfection efficiencies, while effectively protecting DNA from enzyme degradation. The distinctive charge pattern of protonated PEI is widely considered responsible for fundamental process such as DNA condensation into PEI/DNA polyplexes (which are able to enter cells via endocytosis), proton sponge effect (which triggers the release of polyplexes from endosome), and release of DNA from polyplexes (to be further processed inside the nucleus). Our investigations are largely motivated by the crucial need for a realistic molecular mechanics force field (FF) for PEI, and, accordingly, we focus on two major issues: (1) development of a new atomistic (CHARMM) FF for PEI in different protonation states, rigorously derived from high‐quality ab initio calculations performed on model polymers, and (2) molecular dynamics investigations of solvated PEI, providing a detailed picture of the dynamic structuring thereof in dependence on their size and protonation state. The modeled PEI chains are essentially described in terms of gyration radius, end‐to‐end distance, persistence length, radial distribution functions, coordination numbers, and diffusion coefficients. They turn out to be more rigid than in other computational studies and we find diffusion coefficients in fair agreement with experimental data. The developed atomistic FF proves adequate for the realistic modeling of the size and protonation behavior of linear PEI, either as individual chains or composing polyplexes. © 2017 Wiley Periodicals, Inc.