CFF91 Force Field Research Articles

Molecular Insight into the Synergism between the Minor Allele of Human Liver Peroxisomal Alanine:Glyoxylate Aminotransferase and the F152I Mutation

Human liver peroxisomal alanine:glyoxylate aminotransferase (AGT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that converts glyoxylate into glycine. AGT deficiency causes primary hyperoxaluria type 1 (PH1), a rare autosomal recessive disorder, due to a marked increase in hepatic oxalate production. Normal human AGT exists as two polymorphic variants: the major (AGT-Ma) and the minor (AGT-Mi) allele. AGT-Mi causes the PH1 disease only when combined with some mutations. In this study, the molecular basis of the synergism between AGT-Mi and F152I mutation has been investigated through a detailed biochemical characterization of AGT-Mi and the Phe(152) variants combined either with the major (F152I-Ma, F152A-Ma) or the minor allele (F152I-Mi). Although these species show spectral features, kinetic parameters, and PLP binding affinity similar to those of AGT-Ma, the Phe(152) variants exhibit the following differences with respect to AGT-Ma and AGT-Mi: (i) pyridoxamine 5'-phosphate (PMP) is released during the overall transamination leading to the conversion into apoenzymes, and (ii) the PMP binding affinity is at least 200-1400-fold lower. Thus, Phe(152) is not an essential residue for transaminase activity, but plays a role in selectively stabilizing the AGT-PMP complex, by a proper orientation of Trp(108), as suggested by bioinformatic analysis. These data, together with the finding that apoF152I-Mi is the only species that at physiological temperature undergoes a time-dependent inactivation and concomitant aggregation, shed light on the molecular defects resulting from the association of the F152I mutation with AGT-Mi, and allow to speculate on the responsiveness to pyridoxine therapy of PH1 patients carrying this mutation.

Structural properties and dynamics of C 12E 5 molecules adsorbed at water/air interfaces: A molecular dynamic study

We investigate structural and dynamical properties of a pentaethylene glycol monododecyl ether monolayer (C 12E 5) adsorbed at water/air interface for varying surface densities. The model we consider relies on an atomic description and consists of a water sample of few thousands of molecules on the top of which surfactant molecules are adsorbed with a molecular surface area A ranging between 0.64 nm 2 and 0.51 nm 2. The time evolution of this model is ruled by the CFF91 force field that includes intra- and inter-molecular degrees of freedom for both surfactant and water molecules. The interface model we consider herein is hence described in all atomic details. The variation of surface area A presents the interest to allow the description of the influence of the molar area on the mass density profile of the studied monolayers. The surfactant molecule tilt angles to the interface are also studied and show a weak A-dependence. The narrowness of the mass density distributions and the large values of the tilt angles observed in the simulations indicate a strongly entangled behaviour of the surfactant molecules in the monolayers. Transport properties are also studied and the diffusion coefficient of the surfactant molecules is estimated.

Specificity in Transmembrane Helix-Helix Interactions Mediated by Aromatic Residues

Aromatic residues have been previously shown to mediate the self-assembly of different soluble proteins through pi-pi interactions (McGaughey, G. B., Gagne, M., and Rappe, A. K. (1998) J. Biol. Chem. 273, 15458-15463). However, their role in transmembrane (TM) assembly is not yet clear. In this study, we performed statistical analysis of the frequency of occurrence of aromatic pairs in a bacterial TM data base that provided an initial indication that the appearance of a specific aromatic pattern, Aromatic-XX-Aromatic, is not coincidental, similar to the well characterized QXXS motif. The QXXS motif was previously shown to be both critical and sufficient for stabilizing TM self-assembly. Using the ToxR system, we monitored the dimerization propensities of TM domains that contain mutations of interacting residues to aromatic amino acids and demonstrated that aromatic residues can adequately stabilize self-association. Importantly, we have provided an example of a natural TM domain, the cholera toxin secretion protein EpsM, whose TM self-assembly is mediated by an aromatic motif (WXXW). This is, in fact, the first evidence that aromatic residues are involved in the dimerization of a wild type TM domain. The association mediated by aromatic residues was found to be sensitive to the TM sequence, suggesting that aromatic residue motifs can provide a general means for specificity in TM assembly. Molecular dynamics provided a structural explanation for this backbone sequence sensitivity.

Designing amino acid residues with single-conformations

Drug design can benefit from the use of non-coded amino acids, such as alpha-amino isobutyric acids (Aib) or sarcosine (N-methyl-glycine). Non-coded amino acids can confer resistance to enzymatic degradation and increase the conformational stability of the peptides. We have simulated the conformational effects of combining N-methylation, bulky groups on the Calpha atom and/or thioamides using the class II CFF91 force field and our thioamide force field parameters. Although single amino acid substitutions (e.g. Aib) can restrict the available conformations, they do not necessarily lead to unique conformers, however, we predict that some of the amino acids described in this report will fold to a single phi, psi conformation (e.g. N-methylated and thioamide penicillamine). Several other amino acid/thiopeptide combinations were designed, which are predicted to prefer only two conformations. Novel amino acids of this type should prove useful for designing peptides with defined conformations.

Converting a β-Glycosidase into a β-Transglycosidase by Directed Evolution

Directed evolution was applied to the beta-glycosidase of Thermus thermophilus in order to increase its ability to synthesize oligosaccharide by transglycosylation. Wild-type enzyme was able to transfer the glycosyl residue with a yield of 50% by self-condensation and of about 8% by transglycosylation on disaccharides without nitrophenyl at their reducing end. By using a simple screening procedure, we could produce mutant enzymes possessing a high transferase activity. In one step of random mutagenesis and in vitro recombination, the hydrolysis of substrates and of transglycosylation products was considerably reduced. For certain mutants, synthesis by self-condensation of nitrophenyl glycosides became nearly quantitative, whereas synthesis by transglycosylation on maltose and on cellobiose could reach 60 and 75%, respectively. Because the most efficient mutations, F401S and N282T, were located just in front of the subsite (-1), molecular modeling techniques were used to explain their effects on the synthesis reaction; we can suggest that repositioning of the glycone in the (-1) subsite together with a better fit of the acceptor in the (+1) subsite might favor the attack of a glycosyl acceptor in the mutant at the expense of water. Thus these new transglycosidases constitute an interesting alternative for the synthesis of oligosaccharides by using stable and accessible donor substrates.

Numerical Analysis of Nonionic Surfactant Monolayers at Water/Air Interfaces

The time evolution of a monododecyl pentaethylene glycol monolayer at the water−air interface is investigated using velocity rescaled NVT molecular dynamics. The model we consider consists of 40 surfactant molecules and 2350 water molecules enclosed in a periodic box. The time evolution of this system is ruled by the CFF91 force field that includes intra- and intermolecular degrees of freedom for both surfactant and water molecules. The interface we consider herein is hence described in all atomic detail. We discuss the initial condition problem and study the relaxation properties to stationarity. Transient regimes of self-assembly of the surfactant chains in entangled structures in both air and water are described. From the stationary configuration, we define the interface location, determine the mass distribution across the interface, and discuss the validity of the tilt angles notion when structural roughness is considered. Using pair distribution functions, we show that, besides typical tilt angles, monododecyl pentaethylene glycol molecules might also develop domains on the interface that suggest an in-plane orientational order.

Tetrathiophene on Graphite: Molecular Dynamics Simulations

AbstractSummary: We describe molecular dynamics simulations of α‐tetrathiophene molecules deposited on a flat graphite substrate, at two different temperatures (300 K and 400 K) and several degrees of coverage (from approximately one to three molecular layers). The simulations employ a modified version of the CFF91 force field, with the torsion parameters tailored on high‐level ab initio calculations on 2,2′‐bithiophene. We found that the molecules in the first layer were relatively planar and packed against the underlying surface, while those outside it were not arranged in well‐defined layers and were more conformationally disordered. On the time scale of the simulation, the molecules did not crystallize but rather achieved a liquid crystalline‐like state with their average director parallel to the surface.Side view of the final configuration in the simulation of 24 tetrathiophenes at 300 K. Molecules are depicted with different shades of gray according to their z coordinate (first, second or third layer).imageSide view of the final configuration in the simulation of 24 tetrathiophenes at 300 K. Molecules are depicted with different shades of gray according to their z coordinate (first, second or third layer).

Previtamin D3 with a trans-Fused Decalin CD-ring Has Pronounced Genomic Activity

Deletion of C19 in the structure of 1 alpha,25-dihydroxyvitamin D3 [1,25(OH)2D3] does not substantially alter the biological potency but prevents the conversion between the vitamin and the previtamin form. Hence, this modification allows the study of locked previtamin and vitamin forms. The locked 19-nor-1,25(OH)2-previtamin D3 analog (19-nor-previtamin D) had a low biological activity and was a rather weak activator of the genomic signal transduction pathway. 19-Nor-trans-decalin-1,25(OH)2-vitamin D3 (19-nor-TD-vitamin D), characterized by the presence of a trans-fused decalin CD-ring system, was 10-fold more potent than the parent compound and was a potent activator of the genomic signal transduction pathway. Surprisingly, the previtamin, 19-nor-trans-decalin-1,25(OH)2-previtamin D3 (19-nor-TD-previtamin D), was as potent as 1,25(OH)2D3 in inhibiting cell proliferation and inducing cell differentiation and represents the first previtamin structure with pronounced vitamin D-like activity. Furthermore, this compound interacted as efficiently as 1,25(OH)2D3 with the vitamin D receptor (VDR), retinoid X receptor (RXR), coactivators, and DNA, which illustrated its potent ability to activate the genomic signal transduction pathway. Analysis of the transactivation potency of 12 VDR point mutants after stimulation with 19-nor-TD-previtamin D revealed that this analog used the same contact points within the receptor as did 1,25(OH)2D3. This could be confirmed by modeling analysis of this compound in the ligand binding pocket of VDR. In conclusion, a previtamin D3 analog is presented with genomic activities equivalent to 1,25(OH)2D3.

Molecular mechanics study of endohedral fullerene complexes with small molecules

Molecular mechanics calculations using CFF91, ESFF and CVFF force fields have been carried out for endohedral complexes of fullerenes C 60, C 70, C 76 (of D 2 and T d symmetry), C 80 (of C 2v , C 2v′ , D 2 , D 3 , D 5d , D 5h and I h symmetry), C 82 (of C 2v , two isomers of C 3v , three isomers of C 2 , and three isomers of C s symmetry), with several hydrocarbons, ketones, amines and other small molecules. The results obtained depend on the force field applied. Nevertheless, they indicate that much bigger fullerenes are needed to obtain complexes of practical importance.

Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force field

When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high-resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least-square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X-ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010–1025, 2001

Synthesis, X-ray crystallographic structures of thio substituted N-acetyl N'-methylamide alanine and evaluation of sp sulfur parameters of the CFF91 force field.

Acetyl thioalanine N-methyl (Ac-Alat-NHMe) and thioacetyl alanine N-methyl (Act-Ala-NHMe) were synthesized, crystallized and their X-ray diffraction structures determined for the first time. Both molecules adopted beta-sheet conformations and showed similar hydrogen bonding patterns with one molecular surface forming two oxo hydrogen bonds and the other forming two thio hydrogen bonds. The crystal structure data for the two thioamides provided a validation of the thioamide parameters for the newly derived CFF91 force field because the observed crystal (phi, psi) angles were situated in the global minimum regions of the theoretical (phi, psi) map predicted using the parameters. In addition, the parameters were further validated because conformational energy minimization of the crystal structure produced low deviations in unit cell dimensions, bond lengths, bond angles and torsional angles, and a 120-ps molecular dynamics simulation also gave a low deviation for the most probable N-H...S=C bond distance.

Conformational analysis of thiopeptides: (ϕ,ψ) maps of thio‐substituted dipeptides

AbstractNoncoded amino acids such as isobutyric acid have been used extensively in the process of drug design and protein engineering. This article focuses on a noncoded amino acid where the oxygen in the peptide unit is replaced with a sp2 sulfur. It was hypothesized that the conformational space as well as the conformational preferences of thiopeptides will be more restricted and altered by the bulkier atom with different electrostatic properties. In vacuo conformational minima as well as associated energies for the thio‐substituted alanine dipeptides were calculated at the ab initio HF/6‐31G* level. When the bulkier sulfur atom acts as a hydrogen bond acceptor in the C5 conformation or in the C\documentclass{article}\pagestyle{empty}\begin{document}$^{\mathrm{axial}}_{7}$\end{document} and C\documentclass{article}\pagestyle{empty}\begin{document}$^{\mathrm{equatorial}}_{7}$\end{document} conformations, the hydrogen bond lengths are much longer than that of normal peptides. Consequently, the ϕ, ψ dihedral angles of the C5, C\documentclass{article}\pagestyle{empty}\begin{document}$^{\mathrm{axial}}_{7}$\end{document}, and C\documentclass{article}\pagestyle{empty}\begin{document}$^{\mathrm{equatorial}}_{7}$\end{document} conformations change to accommodate the longer hydrogen bonds. The thiopeptide group is a poorer hydrogen bond acceptor and a better hydrogen bond donor than the normal peptide group. Therefore, thio‐substitution at the amino terminal leads to disfavoring of the C7 conformations relative to the C5 conformations and thio‐substitution at the carboxyl terminal leads to favoring of the C7 conformations relative to the C5 conformation. To simulate the conformations in solution, (ϕ,ψ) conformational energy maps were calculated for the glycine and alanine dipeptides at various dielectric constants using the CFF91 force field with our previously derived parameters for the thioamide group. The results show that thio‐substitution does restrict the conformations available to amino acids residues in peptides. Thio substitution at the amino terminal introduces unfavorable interactions near ϕ=−120 and 120, where there are increased overlaps between Sn−1Hβ, and Sn−1Cβ atoms, respectively. Thio substitution at the carboxyl terminal restricts the conformations near ψ=60, −60, and 180, which correspond with increase overlaps between SnCβ, SnHβ′ and SnNn atoms, respectively. The effects of dithio substitutions of either the alanine or the glycine dipeptides are similar to the combined effects of the two single thio substitutions. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1026–1037, 2001

Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force field

AbstractWhen a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio‐substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high‐resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least‐square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X‐ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010–1025, 2001

Molecular mechanics calculations of molecular and chiral recognition by cyclodextrins. Is it reliable? The selective complexation of decalins by β-cyclodextrin

Molecular mechanics calculations are frequently used to rationalize experimental findings concerning molecular and chiral recognition by cyclodextrins although the reliability of the method in general and the influence of choice of the parameters in particular has not almost been analyzed. In this work molecular and chiral recognition of decalin isomers by β-cyclodextrin was studied using amber, cvff, cff91, and mmx force fields and five values of dielectric constant ϵ=1, 2, 4, 10, 20. Most calculations yielded consistently lower stability of the complex with trans-decalin. However, in most cases the absolute value of the energy difference between the stabilization energies of the complexes with the latter isomer and the one with cis-decalin closer to it, |ΔΔ E molec|, characterizing molecular recognition was found smaller than the corresponding value involving cis-decalin enantiomers, |ΔΔ E chir|=|Δ E M- cis −Δ E P- cis |, characterizing chiral recognition. The calculations indicate no preference for complexation with either M- cis or P- cis decalin enantiomer. Therefore, we believe that MM is not suitable for reliable analysis of chiral recognition by cyclodextrins. Although the ϵ value of 1 was found unreliable for molecular mechanics calculations using all FF under study, our preliminary results of molecular dynamics calculations in water for the complexes of camphor and pinene enantiomers with α-cyclodextrin using the latter value yielded qualitatively correct results.

Modeling of the transition temperature for the helical denaturation of α‐keratin intermediate filaments

AbstractSimulations of the stability of the secondary and tertiary structure of the α‐keratin intermediate filament (IF) monomeric unit of wool are reported. Based on the assumed secondary structure three segments of the primary structure were selected: 1A, L12, and a part of 2B. Starting with an ideal α‐helical conformation for each IF‐segment, molecular dynamics simulations were carried out on the atomistic level at various temperatures in vaccum using the CFF91 force field. In either simulation the expected destabilization of the helical structure with increasing simulation temperature was observed. By use of different procedures of analysis, transition temperatures for the α‐helical denaturation were determined that are significantly higher for the supposedly α‐helical segments 1A and 2B than for the linker segment L12. The different stabilities of segments 1A and L12 were further verified through simulations in water environment that show the linker segment to be non‐helical at room temperature. The lower transition temperature of segment L12 confirms the expectation that its amino acid sequence leads to increased conformational flexibility. The mobility of the water molecules surrounding the IF‐segment is found to be significantly decreased by protein/water interactions.

Quantum chemical evaluation of the knee angle in the (5,5) - (9,0) coiled carbon tubule

The knee angle of the (5,5) - (9,0) coiled carbon tubule was determined by the semi-empirical complete neglect of differential overlap technique and was found to be . The construction of this achiral knee is described by a simple formalism based on the heptagon - pentagon pair. The use of molecular mechanics techniques gave values of and with the CVFF and CFF91 force fields, respectively.

Comparison of two force fields in MD‐simulations of α‐helical structures in keratins

AbstractMolecular dynamic (MD) simulations based on two different force fields, CVFF and CFF91, were carried out in order to check their feasibility for the structural investigation of the wool intermediate filament (IF) monomeric unit. Selecting an ideal α‐helix as start conformation, all MD‐simulations with CVFF in vaccum show the α‐helix to be unstable. Independently of the amino acid sequence of the α‐helix, a new helical structure with a larger diameter arises during the MD‐simulation, due to a shift of the intrahelical hydrogen bonds. However in simulations with surrounding water the α‐helix remains stable throughout the simulations with the CVFF force field. In contrast to this, MD‐simulations in vaccume based on the CFF91 force field are able to determine different stabilities for the α‐helical start conformation of various IF‐segments, that agree well with secondary structure predictions. The simulation results obtained with CFF91 in vacuum can like wise be verified using an explicit water environment. We found that higher partial charges attributed to the atoms of the amide groups that form the intrahelical hydrogen bonds are the reason for the superiority of the CFF91 force field.

Conformational studies and electronic structures of tamoxifen and toremifene and their allylic carbocations proposed as reactive intermediates leading to DNA adduct formation.

Toremifene, a compound which differs from tamoxifen by the substitution of a chlorine atom for a hydrogen atom in the ethyl group, is significantly less potent than tamoxifen in causing DNA adduct formation in rats. To examine the relationship of the DNA adduct-forming ability of these compounds with their physicochemical properties such as stable conformation and chemical reactivity, we carried out molecular mechanics, molecular dynamics, and quantum mechanics calculations for the two compounds. For tamoxifen, six stable conformers were identified by conformational search with CFF91 force field. Molecular dynamics simulations showed that these were often interconverted within 1.0 ns. On the other hand, although the conformation of stable conformers and dynamical behavior of toremifene were almost the same as those of tamoxifen, a few conformations were slightly different from those of tamoxifen owing to the effect of the chlorine atom at chloroethyl group. In addition, the stability of the allylic carbocation, which had been proposed as the reactive intermediate leading to DNA adduct formation, was calculated with both semiempirical and density functional methods. Results showed that the carbocation intermediate of toremifene was less stable than that of tamoxifen by 4-5 kcal/mol, suggesting that toremifene was less frequently activated to the intermediate than tamoxifen. Furthermore, the carbocation intermediates of two other tamoxifen derivatives, 4-iodotamoxifen and droxifene, which show no DNA adduct-forming ability, were also less stable compared with that of tamoxifen. These calculated results suggest a close relation between the stability of the proposed carbocation intermediate and DNA adduct-forming ability.

Molecular Self-Assemblies. 5. Analysis of the Vector Properties of Hydrogen Bonding in Crystal Engineering

Kitaigorodskii's aufbau principle (KAP) is used to analyze hydrogen bonding as a vector for the packing of molecules in the crystalline solid state. Using the CFF91 force field to compute the molecule−molecule interaction potential, we find that the signature for hydrogen bonding of N−H and O−H donor groups with N or O acceptors is a positive value for the nonbonded van der Waals term of the hydrogen atom involved in the H-bond. The H-bond may occur as a vector in any one or more of the four stages of KAP. We categorize these vectors as types 1−4 with 16 possible subtypes depending upon the number of KAP stages in which the H-bond appears. Within the constraints of the force field description, the H-bond then becomes a specific vector contribution to the packing of one or more substructures of the complete crystal. Of the 16 possible vector subtypes we illustrate 12 of them using crystal structure data from the Cambridge Structural Database. Knowing the vector subtype, we show how it is possible to locate the local minima representing the packing geometry of the substructures using Monte Carlo simulation methods. The establishment of quantitative signatures for vector types within KAP substructures and their relationship to crystal engineering is discussed.

Investigation of α‐keratin intermediate filament structure by molecular dynamic simulation

AbstractMolecular dynamic simulations are carried out in order to investigate the stability of the secondary and tertiary structure of the intermediate filaments monomer unit of wool. Based on the assumed secondary structure three segments of the primary structure are selected: 1A, L1,2 and a part of 2B. With the ideal α‐helix as start conformation, the simulations are carried out with the MD‐algorithm of DISCOVER 2.9.0 (BIOSYM, 1993) and the CFF91 force field for 500 ps at different temperatures in vacuum. In either simulation a destabilization of the helical structure with an increase of the simulation temperature is observed. By monitoring the length distribution of the axially oriented (O···H)‐hydrogen bonds, which stabilize the helical structure, transition temperatures for the α‐helical denaturation are determined. The supposedly α‐helical segments 1A and 2B show significantly higher transition temperatures than segment L1,2. This lower temperature confirms the expectation from the amino acid sequence that the linker segment shows more conformational flexibility and is nonhelical at room temperature.