Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization

Structural and clinical implications of amino acid substitutions in N-acetylgalactosamine-4-sulfatase: insight into mucopolysaccharidosis type VI

To elucidate the basis of mucopolysaccharidosis type VI (MPS VI) from the point of view of enzyme structure, we built structural models of mutant N-acetylgalactosamine-4-sulfatase (4S) resulting from 34 missense mutations (17 severe and 17 attenuated), and analyzed the influence of each amino acid replacement on the structure by calculating the number of atoms affected. Then, we calculated the average of solvent-accessible surface area value of the residues for which a substitution was identified in the severe MPS VI group and compared it with that in the attenuated MPS VI group. In the severe MPS VI group, the number of atoms influenced by a mutation was generally larger than that in the attenuated MPS VI group in both the main chain and the side chain, and residues associated with the mutations found in the severe MPS VI group tended to be less solvent-accessible than those in the attenuated MPS VI group. Furthermore, we analyzed the structural changes in 4S caused by six amino acid substitutions, for which the expressed proteins have been characterized, by means of color imaging. The results revealed that R95Q, G144R, H393P, and C521Y cause large structural changes, and that they are associated with the severe phenotype. On the other hand, G137V and Y210C are thought to cause small structural changes in a limited region resulting in the attenuated phenotype. Structural study is useful for elucidating the basis of MPS VI and predicting the influence of amino acid substitutions on clinical outcome, although there are a couple of exceptional cases.

Structural study on mutant alpha-L-iduronidases: insight into mucopolysaccharidosis type I

To elucidate the basis of mucopolysaccharidosis type I (MPS I), we constructed structural models of mutant alpha-L: -iduronidases (IDUAs) resulting from 33 amino acid substitutions that lead to MPS I (17 severe, eight intermediate, and eight attenuated). Then, we examined the structural changes in the enzyme protein by calculating the number of atoms affected and determined the root-mean-square distance (RMSD) and the solvent-accessible surface area (ASA). In the severe MPS I group, the number of atoms influenced by a mutation and the average RMSD value were larger than those in the attenuated group, and the residues associated with the mutations identified in the severe group tended to be less solvent accessible than those in the attenuated group. The clinically intermediate phenotype group exhibited intermediate values for the numbers of atoms affected, RMSD, and ASA between those in the severe group and those in the attenuated group. The results indicated that large structural changes had occurred in the core region in the severe MPS I group and small ones on the molecular surface in the attenuated MPS I group. Color imaging revealed the distributions and degrees of the structural changes caused by representative mutations for MPS I. Thus, structural analysis is useful for elucidating the basis of MPS I. As there was a difference in IDUA structural change between the severe MPS I group and the attenuated one, except for a couple of mutations, structural analysis can help predict the clinical outcome of the disease.

Simulations of structure and vibrational spectra of deoxyoctanucleotides

Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragments and subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared. Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum for (CG)(2) nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained for the dependence on the basis sequence.

Refined models for the preferential interactions of tryptophan with phosphocholines

A series of molecular models of the adducts formed between N-acetyl-l-tryptophan ethylamide and diacetyl-sn-glycero-3-phosphocholine have been generated. Using rOesy data that enabled us to place restrictions on the proximity of a number of key protons in the amino acid/phosphocholine pairs, a series of structures were generated following molecular dynamics and mechanics experiments using the CHARMM27 force field. These structures were then subjected to a series of clustering algorithms in order to classify the tight binding interactions between a single tryptophan and a phosphocholine. From these analyses, it is evident that: (i) binding is characterised by hydrogen bonding between the indole NH as donor and phosphate oxygen as acceptor, cation-carbonyl interactions between the choline ammonium and amide carbonyl groups and cation-pi interactions; (ii) cation-pi interactions are not always observed, particularly when their formation is at the expense of cation-carbonyl and hydrogen bonding interactions; (iii) on the basis of amino acid torsional parameters, it is possible to predict whether the phosphocholine headgroup will bind in a compact or elongated conformation. Extension of the procedures to characterise 2 : 1 Trp-PC binding revealed that the same intermolecular interactions are predominant; however, combinations of all three intermolecular interactions within the same adduct occur much more frequently due to the availability of donor/acceptor groups from both tryptophans in the 2 : 1 system.

Developing a coarse-grained force field for the diblock copolymer poly(styrene-b-butadiene) from atomistic simulation

We have developed a coarse-grained force field for the poly(styrene-b-butadiene) diblock copolymer. We describe the computational methods and discuss how they were applied to develop a coarse-grained force field for this diblock copolymer from the atomistic simulation. The new force field contains three different bonds, four angles, five dihedral angles, and three nonbonded terms. We successfully tested this coarse-grained model against the chain properties, including static and dynamic properties, derived from the atomistic simulation; the results suggest that the coarse-grained force field is an effective model.

Modeling of molecular packing and conformation in oligofluorenes

We describe the application of molecular modeling to study problems related to the packing and conformation of oligofluorene molecules in the solid state. First of all, we describe an improved force field for oligofluorenes. The model is based on the MM3 force field for the intramolecular degrees of freedom, but it relies on ab initio calculations for the torsion potential between two monomers and the electrostatic interactions. We also report ab initio calculations of the interaction potentials between fluorene and fluorenone units. The force field has been tested on the crystal structures of a fluorene monomer, a dimer, and a pentamer containing a fluorenone at the center. It has then been employed to study conformational defects of the chains, both in vacuo and in the bulk. We find that certain modes of inversion from right-handed to left-handed helices are also possible within the constraining environment of the crystals. The effect of the presence of two different types of side chains has been also addressed. Finally, the possibility of having two fluorene units parallel and close to each other has been investigated as a model of a ground-state precursor of an excimer. Our simulations show that this configuration is sterically and energetically unfavorable so that formation of an excimer following optical excitation appears to be unlikely.

A Force Field for Molecular Simulation of Tetrabutylphosphonium Amino Acid Ionic Liquids

An all-atom force field was set up for a new class of ionic liquids (ILs), tetrabutylphosphonium amino acid, on the basis of the AMBER force field with determining parameters related to the phosphorus atom and modifying several parameters. Ab initio quantum chemical calculations were employed to obtain molecular geometries, infrared frequencies, and torsion energy profiles. Atom partial charges were obtained by using the one-conformation, two-step restraint electrostatic potential approach. Molecular dynamics simulation was carried out in the isothermal-isobaric ensemble for 14 tetrabutylphosphonium amino acid ILs at two temperatures to validate the force field against the experimental densities and heat capacities at constant pressure. Computed thermodynamic properties are in good agreement with available experimental values. Moreover, radial distribution functions were investigated to depict the microscopic structures of these ILs.

Reverse-micelle formation in the partitioning of trivalent F-element cations by biphasic systems containing a tetraalkyldiglycolamide

The conditions for reverse-micelle formation were studied for solutions of tetra-n-octyldiglycolamide (TODGA) in alkane diluents equilibrated with aqueous solutions of nitric or hydrochloric acids in the presence and absence of Nd3+. Small-angle neutron scattering, vapor-pressure osmometry, and tensiometry are all consistent with the partial formation of TODGA dimers at the lowest acidities, transitioning to a polydisperse mixture containing TODGA monomers, dimers, and small reverse-micelles of TODGA tetramers at aqueous nitric acid acidities of 0.7 M or higher in the absence of Nd. Application of the Baxter model to the samples containing 0.005-0.015 M Nd reveals the persistence of tetrameric TODGA reverse-micelles with significant interparticle attraction between the polar cores of the micelles that increases with increasing organic phase concentrations of acid or Nd. Our experimental findings suggest that the peculiar behavior of TODGA with respect to the extraction of trivalent lanthanide and actinide cations arises from the affinity of these metal cations for the preformed TODGA reverse-micelle tetramers.

Statistical potential for assessment and prediction of protein structures

Protein structures in the Protein Data Bank provide a wealth of data about the interactions that determine the native states of proteins. Using the probability theory, we derive an atomic distance-dependent statistical potential from a sample of native structures that does not depend on any adjustable parameters (Discrete Optimized Protein Energy, or DOPE). DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. The DOPE potential was extracted from a nonredundant set of 1472 crystallographic structures. We tested DOPE and five other scoring functions by the detection of the native state among six multiple target decoy sets, the correlation between the score and model error, and the identification of the most accurate non-native structure in the decoy set. For all decoy sets, DOPE is the best performing function in terms of all criteria, except for a tie in one criterion for one decoy set. To facilitate its use in various applications, such as model assessment, loop modeling, and fitting into cryo-electron microscopy mass density maps combined with comparative protein structure modeling, DOPE was incorporated into the modeling package MODELLER-8.

Characterization of isomeric cationic porphyrins with beta-pyrrolic substituents by electrospray mass spectrometry: the singular behavior of a potential virus photoinactivator

Electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS/MS) have been used to differentiate the 2- and 4-methylpyridyl isomers of free-base and metallated cationic beta-vinylpyridylporphyrins. The analysis by ESI-MS/MS of the deuterated analogs and semiempirical calculations of structural and electronic parameters were also undertaken. The two free-base isomers are easily differentiated by ESI-MS/MS but the presence of a metallic center renders differentiation of the metallated isomers less effective. The data acquired show that of all the studied compounds, the free-base 2-methylpyridyl isomer, which was operative in the in vitro photoinactivation of Herpes simples virus, has a different gas-phase behavior. Local distortion of the macrocycle due to the presence of the beta-vinylpyridyl substituent occurs for all the compounds, but a different electron density distribution can account for the observed gas-phase behavior of this potential virus photoinactivator.

What determines the spectrum of protein native state structures?

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focuses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu.

Quantum correction to the pair distribution function

We report a numerical technique that allows the quantum effects of zero-point motion to be incorporated into Pair Distribution Functions calculated classically for molecules using Monte Carlo or Molecular Dynamics simulations. We establish the basis for this approximation using a diatomic molecule described by a Morse potential. The correction should significantly improve the agreement between modeled and experimental data, and facilitate conclusions about inter- and intra-molecular motion and flexibility. We describe a similar approach to obtain the energy and the specific heat.

An ant algorithm for the conformational analysis of flexible molecules

Originally, the ant system was developed for optimization in discrete search spaces such as the traveling salesman problem. We detail our adaptation of the algorithm to optimization in the continuous search space of conformational analysis. The parameters of the algorithm were tuned using a simple test molecule, undecane, and a drug molecule, imatinib. The algorithm is further tested on four more drug or drug-like molecules, on vitamin A and on alanine tetrapeptide.

Similarity measures based on Gaussian-type promolecular electron density models: Alignment of small rigid molecules

Various molecular similarity measures (overlap, Coulomb, kinetic, electrostatic energy) and similarity indices (Carbó, Hodgkin-Richards, Kulczynski, Shape Tanimoto) are applied to the superposition of 3D promolecular electron density (PED) distributions. The original aspect of the paper lies in the consideration of smoothed PEDs, which allow to decrease the number of local solutions to a superposition problem, together with the use of the less common kinetic and electrostatic energy similarity measures. Results are obtained for a family of five rigid endothiapepsin ligands that were already considered in previous applications, based on graph representations of their PED. In the present work, it is observed that the use of smoothed PED and the kinetic similarity measure, together with the Kulczynski or Shape Tanimoto index, performed the best to align molecules of different sizes.

Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.

Conformational Analysis of Nine-Membered Cyclic Acetals. Stereoelectronic Effect in 2,4- and 3,5-Benzodioxonine Derivatives

Conformations of the title compounds were examined using DFT calculations and NBO analysis in order to find the origins of their conformational preferences. The most stable conformations were TBC and TCBtype-1 for the 2,4- and 3,5-benzodioxonine derivatives, respectively. In both of these conformations the acetal moiety adopts the g+/-g+/- geometry. The NBO analysis yielded values of the stabilization energy associated with the stereoelectronic nO --> sigmaC-O* interactions that were highest for conformations other than the global minima. Conformers displaying the strongest interactions followed different patterns of atom arrangement within the acetal moiety, namely g+g-, and those in which one or both of the torsion angles within the C-O-C-O-C segment were close to 90 degrees . Steric repulsion caused by alkyl substituents at the anomeric carbon was found to influence the strength of the nO --> sigmaC-O* stabilization through modification of bond lengths and torsion angles. The adopted ground-state conformations result from accommodation of steric repulsions and stabilizing stereoelectronic interactions. It was shown that DFT calculations of conformational preferences of acetals together with GIAO prediction of 13C chemical shifts should be a useful methodology for studies on conformation and conformational equilibria of acetals in solution.

New Force Field for Molecular Simulation of Guanidinium-Based Ionic Liquids

An all-atom force field was proposed for a new class of room temperature ionic liquids (RTILs), N,N,N',N'-tetramethylguanidinium (TMG) RTILs. The model is based on the AMBER force field with modifications on several parameters. The refinements include (1) fitting the vibration frequencies for obtaining force coefficients of bonds and angles against the data obtained by ab initio calculations and/or by experiments and (2) fitting the torsion energy profiles of dihedral angles for obtaining torsion parameters against the data obtained by ab initio calculations. To validate the force field, molecular dynamics (MD) simulations at different temperatures were performed for five kinds of RTILs, where TMG acts as a cation and formate, lactate, perchlorate, trifluoroacetate, and trifluoromethylsulfonate act as anions. The predicted densities were in good agreement with the experimental data. Radial distribution functions (RDFs) and spatial distribution functions (SDFs) were investigated to depict the microscopic structures of the RTILs.

Molecular Dynamics Study of the Active Site of Methylamine Dehydrogenase

We have obtained AMBER94 force-field parameters for the TTQ cofactor of the enzyme methylamine dehydrogenase (MADH). This enzyme catalyzes the oxidation of methylamine to produce formaldehyde and ammonia. In the rate-determining step of the catalyzed reaction, a proton is transferred from the methyl group of the substrate to residue Asp76. We used the new parameters to perform molecular dynamics simulations of MADH in order to characterize the dynamics of the active site prior to the proton-transfer step. We found that only one of the oxygen atoms of Asp76 can act as an acceptor of the proton. The other oxygen interacts with Thr122 via a strong hydrogen bond. In contrast, because of the rotation the methyl group of the substrate, the three methyl hydrogen atoms are alternately in position to be transferred. The distance that the proton has to travel presents a broad distribution with a peak between 1.0 and 1.1 A and reaches values as short as 0.8 A. The fluctuation of the distance between the donor and the acceptor has the largest frequency component at 50 cm(-1), but the spectrum presents a rich structure between 10 and 400 cm(-1). The more important peaks appear below 250 cm(-1).

Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance

Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/pi interactions. Ab initio interaction energies for 20 carbohydrate-aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from -2.8 to -12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/pi interactions and classical H-bonds. The failure of Hartree-Fock method (interaction energies from +1.0 to -6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.

In Search of Excited-State Proton Transfer in the Lumichrome Dimer in the Solid State: Theoretical and Experimental Approach

Quantum chemical density functional theory (DFT) calculations and spectral data were employed to investigate the possibility of the excited-state double proton transfer (ESDPT) in lumichrome crystals. The calculations in a lumichrome dimer predict a transfer of a proton in the first excited state, leading to a cation-anion pair. The presently reported X-ray structure of 1,3-dimethyllumichrome and its complex solid-state luminescence indicate that also in this molecule intermolecular hydrogen bonds might be involved in the photophysics. The long-wavelength emission in lumichrome crystals peaked at 530 nm is attributed to excited-state proton transfer, whereas a wider emission band in methylated lumichrome derivatives peaked at 560 nm is attributed to ions formed upon photoexcitation of the crystals.

Theoretical Characterization of the (H2O)21 Cluster: Application of an n-body Decomposition Procedure

Two low-energy minima of (H2O)21 with very different H-bonding arrangements have been investigated with the B3LYP density functional and RIMP2 methods, as well as with the TIP4P, Dang-Chang, AMOEBA, and TTM2-F force fields. The AMOEBA and TTM2-F model potentials give an energy ordering that agrees with the results of the electronic structure calculations, while the TIP4P and Dang-Chang models give the opposite ordering. Insight into the role of many-body polarization for establishing the relative stability of the two isomers is provided by an n-body decomposition of the energies calculated using the various theoretical methods.

Engineering cyclic tetrapeptides containing chimeric amino acids as preferred reverse-turn scaffolds

Four residues making almost a complete 180 degrees turn in the direction of the peptide chain define a reverse turn, a common motif and recognition site in proteins. Cyclization between residues i and i + 3 and incorporation of heterochiral dipeptides (such as d-Pro-l-Pro) in the i + 1 and i + 2 positions are used to constrain a peptide to a reverse-turn conformation. A combined approach, cyclic tetrapeptides (CTPs) based on heterochiral dipeptides of chimeric amino acids, is evaluated as minimalist scaffolds for reverse-turn conformations. Cyclo-(d-Pro-l-Pro-d-Pro-l-Pro) has been studied with density functional theory (DFT) calculations and molecular dynamics simulations. The all-trans amide conformer was the most stable in vacuo, while the cis-trans-cis-trans (ctct) or trans-cis-trans-cis (tctc) amide conformer was more favored in water due to its large dipole moment. Different conformations could be selectively stabilized by different substitutions on the proline rings. Due to the small 12-membered ring and exocyclic constraints, conformational interconversions could only occur at high temperature. The presence of seven hydrogens on each ring that could be functionalized offers an overwhelming diversity to design molecules to probe receptors. The spatial relationships of C(alpha)-C(beta) vectors of reverse turns in proteins were subjected to principal component analysis for determination of the relative orientation of the C(alpha)-C(beta) vectors. Most reverse-turn structures could be mimicked effectively with a subset of CTP scaffolds with an root-mean-square displacement (RMSD) of approximately 0.5 A. Structural diversity of CTP scaffolds could be enhanced by the incorporation of proline analogues, such as azaproline (azPro) or pipecolic (Pip), azapipecolic (azPip), nipecotic (Nip), and isonipecotic (Inp) acids.

Evaluation of a neural networks QSAR method based on ligand representation using substituent descriptors. Application to HIV-1 protease inhibitors

We present here a neural networks method designed to predict biological activity based on a local representation of the ligand. The compounds of the series are represented by a vector mapping for each of four substituent properties: volume, log P, dipole moment and a simple 'steric' parameter relating to its shape. This ligand representation was tested using neural networks on a set of 42 cyclic-urea derivatives, inhibiting HIV-1 protease. The leave-one-out cross-validation using all descriptors in the input gave a correlation factor between prediction and experiment of 0.76 for the overall set and 0.88 when three outliers were left out. To rank the significance of the four descriptors, we further tested all combinations of two and three parameters for each substituent, using two disjunctive testing sets of five inhibitors. In these sets, vectors with extreme descriptor values were used either in the training or the testing set (sets A and B, respectively). The method is a very good interpolator (set A, 95+/-2% accuracy) but a less effective extrapolator (set B, 85+/-2% accuracy). Generally, the combinations including the 'steric' parameter predict better than average, while those containing the volume are less effective. The best prediction, 98.8+/-1.2%, was obtained when log P, the dipole and the steric parameter were used on set A. At the opposite end, the lowest ranked descriptor set was obtained when replacing log P with the volume, giving 92.3+/-6.7% accuracy over the set A.

Structural basis for the presence of a monoglucosylated oligosaccharide in mature glycoproteins

Arylphorin is an insect hexameric storage protein. The structures of the oligosaccharides attached to this protein have recently been determined. However, their precise functions remain to be established. Proteolysis and MALDI MS studies disclose that the amino acid residues Asn196 and Asn344 are N-glycosylated with Glc(1)Man(9)GlcNAc(2) and Man(5-6)GlcNAc(2) oligosaccharides, respectively. Interestingly, significant variations in the amounts of glycans involving Glc(1)Man(9)GlcNAc(2) are evident in arylphorins purified from larvae reared at different seasons. The data suggest that the metabolism of larvae and local protein structure contribute to glycan development. Three-dimensional model of the protein speculated that N-glycosidic linkage to Asn196 in the Glc(1)Man(9)GlcNAc(2) structure was buried inside the twofold axis of the hexamer, whereas oligosaccharide linkages to Asn344 were completely exposed to solvent. This finding is in agreement with previous biochemical data showing that limited Glc(1)Man(9)GlcNAc(2) was released by protein-N-glycosidase F under non-denaturing conditions, in contrast to Man(5-6)GlcNAc(2) oligosaccharides.

Empirical solvent correction for multiple amide group vibrational modes

Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.

Tubulin dipole moment, dielectric constant and quantum behavior: computer simulations, experimental results and suggestions

We used computer simulation to calculate the electric dipole moments of the alpha- and beta-tubulin monomers and dimer and found those to be |p(alpha)| = 552D, |p(beta)| = 1193D and |p(alphabeta)| = 1740D, respectively. Independent surface plasmon resonance (SPR) and refractometry measurements of the high-frequency dielectric constant and polarizability strongly corroborated our previous SPR-derived results, giving Deltan/Deltac approximately 1.800 x 10(-3)ml/mg. The refractive index of tubulin was measured to be n(tub) approximately 2.90 and the high-frequency tubulin dielectric constant k(tub) approximately 8.41, while the high-frequency polarizability was found to be alpha(tub) approximately 2.1 x 10(-33)C m(2)/V. Methods for the experimental determination of the low-frequency p are explored, as well as ways to test the often conjectured quantum coherence and entanglement properties of tubulin. Biobits, bioqubits and other applications to bioelectronics are discussed.

A simple method for faster nonbonded force evaluations

Accurate approximations are introduced for the evaluation of inverse interparticle distances such that square root or division operations are not required in the computation of interparticle interactions and forces. These generally applicable approximations are illustrated by incorporation into the protein simulation package TINKER along with several other speed enhancement strategies. With these modifications, implicit solvent Langevin dynamics simulations of proteins are performed factors of 4.6 times faster than the modified open source distributed program. Programming speedups are obtained by extensive vectorization, simplification of the inner loop to avoid IF statements, and by using lookup tables for the distance dependent "dielectric constant" in implicit solvent models. Benchmarks are provided for the all-atom, implicit solvent dynamics of Met-enkephalin, the villin headpiece, the B1 domain of protein-G, and barnase. We also discuss the more general applicability of the approximation methods to explicit solvent simulations and of look-up tables for other implicit solvent models such as the generalized Born models.

Towards protein folding with evolutionary techniques

We present design details and first tests of a new evolutionary algorithm approach to ab initio protein folding. It does not focus on dihedral angles exclusively, but mainly operates on introduction, extension, break-up, and destruction of secondary structure elements, given as correlated dihedral angle values. In first test applications to polyalanines (up to 60 residues) and random primary sequences (up to 40 residues), we demonstrate that this use of prior knowledge is well balanced: On the one hand, it ensures quick introduction of secondary structure elements if they are favorable for a given primary sequence, but still allows for efficient location of pure random coil solutions without enforcing any secondary structure elements, if folds of this type are preferred by the given primary sequence. Furthermore, the algorithm is clearly able to pack several secondary structure elements into favorable tertiary structure arrangements, although no part of the algorithm is explicitly designed to do this. In first test examples on real-life peptides between 21 and 44 residues from the Protein Data Bank, the quality of the results depends on the force field used (as expected); nevertheless, we can show that the algorithm is able to find structures in good agreement with the targets easily and consistently, if the force field allows for that.

Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF4] and acetonitrile by a refined force field

1-Butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) is one of the promising room-temperature ionic liquids. To test the refined force field for [bmim][BF4] proposed in our previously work (J. Phys. Chem. B, 2004, 108, 12978-12989), thermodynamic properties of mixtures of [bmim][BF4](1)+ acetonitrile (2) are presented by using molecular dynamics over the whole concentration range. The calculated densities are in good agreement with the experimental data with deviations less than 2%, indicating the force field is applicable to the mixtures. In addition, the diffusion constants, viscosities, heats of vaporization, cohesive energy densities and excess properties of the mixtures are reported. The microscopic structures are discussed in detail, corresponding to the thermodynamic properties.

The parameterization and validation of generalized born models using the pairwise descreening approximation

Generalized Born Surface Area (GBSA) models for water using the Pairwise Descreening Approximation (PDA) have been parameterized by two different methods. The first method, similar to that used in previously reported parameterizations, optimizes all parameters against the experimental free energies of hydration of organic molecules. The second method optimizes the PDA parameters to compensate only for systematic errors of the PDA. The best models are compared to Poisson-Boltzmann calculations and applied to the computation of potentials of mean force (PMFs) for the association of various molecules. PMFs present a more rigorous test of the ability of a solvation model to correctly reproduce the screening of intermolecular interactions by the solvent, than its accuracy at predicting free energies of hydration of small molecules. Models derived with the first method are sometimes shown to fail to compute accurate potentials of mean force because of large errors in the computation of Born radii, while no such difficulties are observed with the second method. Furthermore, accurate computation of the Born radii appears to be more important than good agreement with experimental free energies of solvation. We discuss the source of errors in the potentials of mean force and suggest means to reduce them. Our findings suggest that Generalized Born models that use the Pairwise Descreening Approximation and that are derived solely by unconstrained optimization of parameters against free energies of hydration should be applied to the modeling of intermolecular interactions with caution.