Ab initio computational study of beta-cellobiose conformers using B3LYP/6-311++G**

The molecular structure of 27 conformers of beta-cellobiose were studied in vacuo through gradient geometry optimization using B3LYP density functionals and the 6-311++G** basis set. The conformationally dependent geometry changes and energies were explored as well as the hydrogen-bonding network. The lowest electronic energy structures found were not those suggested from available crystallographic and NMR solution data, where the glycosidic dihedral angles fall in the region (phi, psi) approximately (40 degrees, -20 degrees ). Rather, 'flipped' conformations in which the dihedral angles are in the range (phi, psi) approximately (180 degrees, 0 degrees ) are energetically more stable by approximately 2.5 kcal/mol over the 'experimentally accepted' structure. Further, when the vibrational free energy, deltaG, obtained from the calculated frequencies, is compared throughout the series, structures with (phi, psi) in the experimentally observed range still have higher free energy ( approximately 2.0 kcal/mol) than 'flipped' forms. The range of bridging dihedral angles of the 'normal' conformers, resulting from the variance in the phi dihedral is larger than that found in the 'flipped' forms. Due to this large flat energy surface for the normal conformations, we surmise that the summation of populations of these conformations will favor the 'normal' conformations, although evidence suggests that polar solvent effects may play the dominant role in providing stability for the 'normal' forms. Even though some empirical studies previously found the 'flipped' conformations to be lowest in energy, these studies have been generally discredited because they were in disagreement with experimental results. Most of the DFT/ab initio conformations reported here have not been reported previously in the ab initio literature, in part because the use of less rigorous theoretical methods, i.e. smaller basis sets, have given results in general agreement with experimental data, that is, they energetically favored the 'normal' forms. These are the first DFT/ab initio calculations at this level of theory, apparently because of the length and difficulty of carrying out optimizations at these high levels.     

The crystal and molecular structures of cellulose I and II

The paper describes molecular dynamics (MD) simulations on the crystal structures of the Iβ and II phases of cellulose. Structural proposals for each of these were made in the 1970s on the basis of X-ray diffraction data. However, due to the limited resolution of these data some controversies remained and details on hydrogen bonding could not be directly obtained. In contrast to structure factor amplitudes in X-ray diffraction, energies, as obtained from MD simulations, are very sensitive to the positions of the hydroxyl hydrogen atoms. Therefore the latter technique is very suitable for obtaining such structural details. MD simulations of the Iβ phase clearly shows preference for one of the two possible models in which the chains are packed in a parallel orientation. Only the parallel-down mode (in the definition of Gardner and Blackwell (1974) J Biopolym 13: 1975-2001) presents a stable structure. The hydrogen bonding consists of two intramolecular hydrogen bonds parallel to the glycosidic linkage for both chains, and two intralayer hydrogen bonds. The layers are packed hydrophobically. All hydroxymethyl group are positioned in the tg conformation. For the cellulose II form it was found that, in contrast to what seemed to emerge from the X-ray fibre diffraction data, both independent chains had the gt conformation. This idea already existed because of elastic moduli calculations and 13C-solid state NMR data. Recently, the structure of cellotetraose was determined. There appear to be a striking similarity between the structure obtained from the MD simulations and this cellotetraose structure in terms of packing of the two independent molecules, the hydrogen bonding network and the conformations of the hydroxymethyl group, which were also gt for both molecules. The structure forms a 3D hydrogen bonded network, and the contribution from electrostatics to the packing is more pronounced than in case of the Iβ structure. In contrast to what is expected, in view of the irreversible transition of the cellulose I to II form, the energies of the Iβ form is found to be lower than that of II by 1 kcal mol-1 per cellobiose. This revised version was published online in November 2006 with corrections to the Cover Date.     

Structural Factors that Distinguish Dopamine D1 and D2 Agonists

To determine the structural features responsible for their selectivity as dopamine D1 agonists, a conformational analysis has been performed on an analog of nomifensine, dihydrexidine, a benzergoline, and an isochroman using the MM2-87 program. The preferred three dimensional structure of the hydroxylated phenyl ring of the nomifensine analog was found to differ from the other compounds with a substantial energy barrier to achieving the planar conformation of the other compounds which may explain its weak potency for D1 receptors. The preferred three dimensional structures of dihydrexidine and the benzergoline were found to differ significantly despite their molecular similarity. These conformational differences were also evident in crystal structures of the compounds or their analogs. The hypothesis that an equatorial ammonium hydrogen (or amine lone pair) is required for D1 agonist selectivity was tested by performing calculations on N-methyl equatorial and N-methyl axial analogs of the compounds. Calculations were also performed on nonselective dopamine agonists (apomorphine and 5,6-diOH- and 6,7-diOH aminotetralin) and dopamine D2-selective agonists ((+)-PHNO and an analog of quinpirole). The energy difference for the N-methyl axial conformations (or their equivalent) were found to be relatively small for the nonselective agonists and more substantial for the D2-selective agonists. This suggests that D2-selectivity may be associated with the relative unfavorability of the N-methyl axial conformation and provides an explanation for the decreased potency of tertiary amine analogs of the D1-selective agonists. In the benzergoline, where the energy difference is computed to be smaller, the addition of the N-methyl group appears to have a smaller deleterious effect on D1 activity. An N-methyl axial conformation has also been observed for the benzergoline in the crystal state suggesting that this conformation is energetically accessible.     

Effects of Analogs of the Fungal Sexual Pheromone Sirenin on Male Gamete Motility in Allomyces macrogynus

The ability of various structural analogs of the sexual pheromone sirenin to attract male gametes of the aquatic fungus Allomyces macrogynus was determined. Previous studies had shown that several structural analogs and stereoisomers of natural l-sirenin were devoid of activity at physiological concentrations. We now report the discovery of a structural analog that exhibits biological activity indistinguishable from the natural pheromone. The bioassay system used to determine chemotaxis was calibrated using synthetic, racemic sirenin, which exhibited a threshold concentration for gamete attraction at an applied concentration of 10 picomolar. The new synthetic monohydroxy analog of sirenin also had a threshold concentration of 10 picomolar. In the process of developing a new total synthesis of sirenin, a variety of other analogs were prepared and tested. All of these analogs exhibited threshold concentrations at 1 micromolar or higher, although attraction at these higher concentrations still varied according to their structural resemblance to sirenin. Thus, the results of these studies demonstrate that the hydroxymethyl group attached to the six-membered ring of sirenin is not essential for biological activity at physiological concentrations. The studies with other analogs demonstrate that biological activity at any concentration involves a balance between hydrophilic hydroxyl groups and hydrophobic hydrocarbon groups in the structure.     

Calculations on crystal packing of a flexible molecule, Leu-enkephalin

Crystal packing calculations have been carried out on a substantial number of conformations of Leu-enkephalin; namely, those obtained both from crystal structures and from energy minimizations on isolated molecules, and with and without waters of crystallization. The known crystal structures represent the most energetically stable packings found. The conformations of the enkephalin molecules in the crystal are not the most stable for an isolated molecule; i.e. intermolecular interactions force the isolated molecule to change conformation in order to achieve a small packing volume and an optimal packing energy in the crystal. It is found that the packing energy of an enkephalin molecule is a reasonably smooth function of its molecular volume in the unit cell, if structures with intermolecular hydrogen bonding are excluded, and is substantially independent of other details of the molecular conformation or of the crystal packing. Hydrogen bonding provides additional stabilization of the crystal structure, and would likely permit crystallization of the system if it is sufficiently dense. Solvent molecules further stabilize the structure when they can also provide intermolecular hydrogen bonds.     

Base pair hydrogen bonds are essential for proofreading selectivity by the human mitochondrial DNA polymerase

We have characterized the role of Watson-Crick hydrogen bonding in the 3'-terminal base pair on the 3'-5' exonuclease activity of the human mitochondrial DNA polymerase. Nonpolar nucleoside analogs of thymidine (dF) and deoxyadenosine (dQ) were used to eliminate hydrogen bonds while maintaining base pair size and shape. Exonuclease reactions were examined using pre-steady state kinetic methods. The time dependence of removal of natural nucleotides from the primer terminus paired opposite the nonpolar analogs dF and dQ were best fit to a double exponential function. The double exponential kinetics as well as the rates of excision (3-6 s(-1) fast phase, 0.16-0.3 s(-1) slow phase) are comparable with those observed during mismatch removal of natural nucleotides even when the analog was involved in a sterically correct base pair. Additionally, incorporation of the next correct base beyond a nonpolar analog was slow (0.04-0.22 s(-1)), so that more than 95% of terminal base pairs were removed rather than extended. The polymerase responds to all 3'-terminal base pairs containing a nonpolar analog as if it were a mismatch regardless of the identity of the paired base, and kinetic partitioning between polymerase and exonuclease sites failed to discriminate between correct and incorrect base pairs. Thus, sterics alone are insufficient, whereas hydrogen bond formation is essential for proper proofreading selectivity by the mitochondrial polymerase. The enzyme may use the alignment and prevention of fraying provided by proper hydrogen bonding and minor groove hydrogen bonding interactions as critical criteria for correct base pair recognition.     

Hydrogen bonding in lignin: a Fourier transform infrared model compound study

Hydrogen bonding plays an important role in the thermal and mechanical properties of biopolymers. To investigate hydrogen bond formation in lignin, an abundant natural polymer found in plants, Fourier transform infrared (FTIR) analysis of various lignin model compounds was performed. Four monomeric model compounds and one dimeric model compound were studied under various conditions. FTIR analysis revealed aliphatic hydroxyl groups form stronger hydrogen bonds than phenolic hydroxyl groups. Further, the dimeric biphenyl-type structure formed significantly stronger intermolecular hydrogen bonds as compared to the other monomeric model compounds. Results from the model compound studies were used to explain the observed complex hydrogen-bonding system present in both softwood and hardwood technical lignins. Together with chemical analysis, we discuss the difference in hydrogen bonding between hardwood and softwood lignin and the observed differences in the glass transition temperature.     

Synthesis, conformation and biology of naphthoxylosides

Proteoglycans (PG) are polyanionic proteins consisting of a core protein substituted with carbohydrate chains, that is, glycosaminoglycans (GAG). The biosynthesis of GAG can be manipulated by simple xylosides carrying hydrophobic aglycons, which can enter the cell and initiate the biosynthesis. While the importance of the aglycon is well investigated, there is far less information on the effect of modifications in the xylose residue. We have developed a new synthetic protocol, based on acetal protection and selective benzylation, for modification of the three hydroxyl groups in xylose. Thus we have synthesized twelve analogs of 2-naphthyl β-d-xylopyranoside (XylNap), where each hydroxyl group has been epimerized or replaced by methoxy, fluoro, or hydrogen. To gain more information about the properties of xylose, conformational studies were made on some of the analogs. It was found that the (4)C(1) conformation is highly predominant, accompanied by a nonnegligible population of the (2)S(0) conformation. However, deoxygenation at C3 results in a large portion of the (1)C(4) conformation. The GAG priming ability and proliferation activity of the twelve analogs, were investigated using a matched pair of human breast fibroblasts and human breast carcinoma cells. None of the analogs initiated the biosynthesis of GAG, but an inhibitory effect on endogenous PG production was observed for analogs fluorinated or deoxygenated at C4. From our data it seems reasonable that all three hydroxyl groups in XylNap are essential for the priming of GAG chains and for selective toxicity for tumor cells.     

The role of tyrosine 67 in the cytochrome c heme crevice structure studied by semisynthesis.

Tyr-67 of mitochondrial cytochrome c is thought to be involved in important hydrogen bonding interactions in the hydrophobic heme pocket of the protein (Takano, T., Dickerson, R. E. (1981) J. Mol. Biol. 153:95-115). The role of this highly conserved residue in heme pocket stability was studied by comparing properties of semisynthetic (Phe-67) and (p-F-Phe-67) analogs with those of native cytochrome c and a "control" analog, (Hse-65)cytochrome c. The (Phe-67) and (p-F-Phe-67) analogs have well-developed 695-nm visible absorption bands and are active in a cytochrome c oxidase assay. The reduction potentials of both analogs are lower than the native protein by approximately 50 mV. Although both analogs bind imidazole with higher affinity than the native protein, only the (p-F-Phe-67) analog has a 3- to 5-fold lower binding constant for cyanide. Only the (Phe-67) analog was significantly more stable toward alkaline isomerization. These results are not consistent with stabilization of the native protein heme pocket via hydrogen bonding of Tyr-67 to Met-80. An alternative steric role for Tyr-67 is proposed in which the residue controls the heme reduction potential by limiting the number of internal H2O molecules in the heme pocket.     

Novel nonsecosteroidal vitamin D3 carboxylic acid analogs for osteoporosis, and SAR analysis

Novel vitamin D(3) analogs with carboxylic acid were explored, focusing on a nonsecosteroidal analog, LG190178, with a bisphenyl skeleton. From X-ray analysis of these analogs with vitamin D receptor (VDR), the carboxyl groups had very unique hydrogen bonding interactions in VDR and mimicked 1α-hydroxy group and/or 3β-hydroxy group of 1α,25-dihydroxyvitamin D(3). A highly potent analog, 6a, with good in vitro activity and pharmacokinetic profiles was identified from an SAR study. Compound 6a showed significant prevention of bone loss in a rat osteoporosis model by oral administration.     

Crystal structures of dihydroxyacetone and its derivatives

The crystal and molecular structures of three crystalline forms of the dihydroxyacetone dimer, C6H12O6, DHA-dimer: alpha (1a), beta (1b), and gamma (1c), the hydrated calcium chloride complex of dihydroxyacetone monomer, CaCl2(C3H6O3)(2) x H2O, CaCl2(DHA)2 x H2O (2a), the tetrahydrated calcium chloride complex of dihydroxyacetone monomer, CaCl2(C3H6O3) x 4H2O, CaCl2(DHA) x 4H2O (2b), the dihydroxyacetone monomer, C3H6O3, DHA (2c), and dihydroxyacetone dimethyl acetal, C5H12O4, (MeO)2DHA (3) are described. Compounds 1a and 2b crystallize in the triclinic system, and 1b,c, 2a,c, and 3 are monoclinic. Molecules of all forms of dihydroxyacetone dimer 1a,b, and 1c are the trans isomers, with the 1,4-dioxane ring in the chair conformation and the hydroxyl and hydroxymethyl groups in axial and equatorial dispositions, respectively. The Ca2+ ions in 2a and 2b are bridged by the carbonyl O atoms from two symmetry-related DHA molecules to form centrosymmetric dimers with Ca...Ca distance of 4.307(2)A in 2a and 4.330(2) and 4.305(2)A in two crystallographically independent dimers in 2b. DHA molecules coordinate to the Ca2+ ions by hydroxyl and carbonyl oxygen atoms. The eight-coordinate polyhedra of Ca2+ are completed by water molecule and Cl- ion in 2a and by four water molecules in 2b. The dihydroxyacetone molecules in 2a,b, and 2c are in an extended conformation, with both hydroxyl groups being synperiplanar (sp) to the carbonyl O atom. All hydroxyl groups in 2c (along with water molecules in 2a and 2b) are involved as donors in medium strong and weak intermolecular O-H...O hydrogen bonding. Some of them, as well as carbonyl O atoms or Cl- ions in 2a and 2b, act as acceptors in C-H...O (and C-H...Cl) hydrogen interactions.     

Conformation of 4-thio-l-lyxono-1,4-lactone in solution and in the crystalline state

The conformation in ²H₂O of 4-thio-l-lyxono-1,4-lactone (1) was studied by nuclear magnetic resonance spectroscopy, by means of homonuclear (J_1H,1H) and heteronuclear (J_1H,13C) coupling constants. The couplings were directly measured by a two-dimensional heteronucleus-coupled ω₁ hetero-half-filtered proton-proton correlation (HETLOC) experiment, which does not require ¹³C isotopic enrichment. In solution, the thiolactone ring of 1 adopts preferentially the E₃ conformation, and its hydroxymethyl group populates mainly the gt rotamer. The X-ray diffraction data of a single crystal of 1 indicates that also in the solid state the thiolactone ring adopts an E₃ conformation, with a puckering somewhat larger than that observed for aldono-1,4-lactones and furanose rings. The molecules are linked by hydrogen bonds, which form chains. Particularly, O-5 is fully engaged as donor and acceptor in hydrogen bonding and the rotameric conformation of the hydroxymethyl group of 1 is fixed in the tg form.     

Molecular and crystal structures of N-arylglycopyranosylamines formed by reaction between sulfanilamide and D-ribose, D-arabinose and D-mannose

The X-ray crystal structures of three monosaccharide derivatives prepared by the reaction of sulfanilamide with D-ribose, D-arabinose, and D-mannose have been determined. The derivatives are N-(p-sulfamoylphenyl)-alpha-D-ribopyranosylamine (1), N-(p-sulfamoylphenyl)-alpha-D-arabinopyranosylamine (2), and N-(p-sulfamoylphenyl)-beta-D-mannopyranosylamine monohydrate (3). The monosaccharide ring of 1 and 2 has the 1C4 conformation, stabilized in 1 by an intramolecular hydrogen bond from 0-2 to 0-4. Compound 3 has the 4C1 conformation at the monosaccharide ring and the gt conformation at the C-6-O-6 side chain. Occupancy of the water molecule in the crystal of 3 actually examined was 22%. The degree of interaction between sulfamoyl groups and monosaccharide moieties varies from structure to structure. The packing arrangement of 2 involves hydrogen bonding between sulfamoyl groups and monosaccharide hydroxyl groups, but interactions of this type are fewer in 1, and in 3 the hydrogen bonds are either strictly between monosaccharide hydroxyl groups or strictly between sulfamoyl groups. Pairs of hydrogen bonds (two-point contacts) link neighboring molecules in all three structures, between screw-axially related molecules in 1 and 2 and between translationally related molecules in 3. The contact in 3 defined by the O-3-H...O-5 and O-6-H...O-4 hydrogen bonds is found in several other N-aryl-beta-D-mannopyranosylamine crystal structures and is apparently an especially favorable mode of intermolecular interaction in these compounds.     

Membrane protein-lipid hydrogen bonding: evidence from protein kinase C, diglyceride, and tumor promotors

Membrane-bound proteins owe their retention and conformation in the lipid bilayer to hydrophobic peptide domains. Additional fixation, by protein-lipid hydrogen bonding, has been suggested, and recent reports on protein kinase C activation by diacylglycerol (DG) provide an unambiguous model for such bonding. The sn-1,2-diacylglycerol appears to donate a hydrogen bond from the sn-3 hydroxyl to the enzyme and to receive two hydrogen bonds, in the sn-1 and sn-2 ester CO groups, from the enzyme. This arrangement is confirmed in phorbol ester, a competitive inhibitor of DG for the kinase. This tumor promotor has a nearly identical spatial arrangement of hydrogen bond donor (9 alpha-OH) and acceptors (12 and 13 ester CO); so have two other tumor promotors, teleocidin and aplysiatoxin. There are reasons to believe that protein kinase C is not the only protein that is bound to membrane lipids by hydrogen bonding, and such bonding will have to be considered in membrane-associated events such as fusion, cross-membrane transport, or anesthesia.     

DFT study of alpha- and beta-D-galactopyranose at the B3LYP/6-311++G** level of theory

Forty-one conformations of alpha- and beta-d-galactopyranose were geometry optimized using the B3LYP density functional and 6-311++G** basis set. Full geometry optimization was performed on different ring geometries and different hydroxymethyl rotamers (gg/gt/tg). Analytically derived Hessians were used to calculate zero point energy, enthalpy, and entropy. The lowest energy and free-energy conformation found is the alpha-gg-(4)C(1)-c chair conformation, which is of lower electronic and free energy than the lowest energy alpha-d-glucopyranose conformer because of favorable hydrogen-bonding interactions. The in vacuo calculations showed considerable ( approximately 2.2kcal/mol) energetic preference for the alpha over the beta anomer for galactopyranose in both the (4)C(1) and (1)C(4) chair conformations. Results are compared to glucopyranose and mannopyranose calculations in vacuo. Boat and skew-boat forms were found that remained stable upon gradient optimization, although many starting conformations moved to other boat forms upon optimization. As with glucopyranose and mannopyranose, the orientation and interaction of the hydroxyl groups make the most significant contributions to the conformation-energy relationship in vacuo.     

N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol

We have prepared palmitoyl sphingomyelin (PSM) analogs in which either the 2-NH was methylated to NMe, the 3-OH was methylated to OMe, or both were methylated simultaneously. The aim of the study was to determine how such modifications in the membrane interfacial region of the molecules affected interlipid interactions in bilayer membranes. Measuring DPH anisotropy in vesicle membranes prepared from the SM analogs, we observed that methylation decreased gel-phase stability and increased fluid phase disorder, when compared to PSM. Methylation of the 2-NH had the largest effect on gel-phase instability (T(m) was lowered by ~7°C). Atomistic molecular dynamics simulations showed that fluid phase bilayers with methylated SM analogs were more expanded but thinner compared to PSM bilayers. It was further revealed that 3-OH methylation dramatically attenuated hydrogen bonding also via the amide nitrogen, whereas 2-NH methylation did not similarly affect hydrogen bonding via the 3-OH. The interactions of sterols with the methylated SM analogs were markedly affected. 3-OH methylation almost completely eliminated the capacity of the SM analog to form sterol-enriched ordered domains, whereas the 2-NH methylated SM analog formed sterol-enriched domains but these were less thermostable (and thus less ordered) than the domains formed by PSM. Cholestatrienol affinity to bilayers containing methylated SM analogs was also markedly reduced as compared to its affinity for bilayers containing PSM. Molecular dynamics simulations revealed further that cholesterol's bilayer location was deeper in PSM bilayers as compared to the location in bilayers made from methylated SM analogs. This study shows that the interfacial properties of SMs are very important for interlipid interactions and the formation of laterally ordered domains in complex bilayers.     

DFTr studies of five- and six-residue cyclic-β(1→4) cellulosic molecules

Density functional (DFT) conformational in vacuo studies of cellobiose have shown that ?_H‐anti conformations are low in energy relative to the syn forms, while the ψ_H‐anti forms are higher in energy. Further, as the cellulosic fragments became larger than a disaccharide and new hydrogen bonding interactions between multiple residues become available, stable low energy ?_H‐anti, and ψ_H‐anti cellulosic structures became possible. To test the stability of cyclic anti‐conformations, a number of β‐linked five‐ and six‐residue molecules were created and then energy optimized in solvent (water, n‐heptane) using the implicit solvation method COSMO at the B3LYP level of theory. The created symmetric cyclic structures were without distortion. Upon optimization some cyclic conformations were found to be of low energy when compared with linear five‐ and six‐residue chains, after correcting the energy for the exclusion of a water molecule upon cyclization. It was also obvious from the hydrogen bonding network formed above and below the plane of the cyclic structure that these structures could exhibit strong synergistic tendencies. The conformational energy preferences for clockwise “c” and counter‐clockwise “r” hydroxyl groups and preference for the hydroxymethyl rotamers is described. Because these structures contain energetically unfavorable flipped conformations in water, that is, dihedral angles of ～180°/0° or ～0°/180° in ?_H/ψ_H, it is clear that the synthesis of these compounds will be challenging. © 2012 Wiley Periodicals, Inc. Biopolymers 97:568–576, 2012.     

Decreased thermal stability of collagens containing analogs of proline or lysine

Fibroblasts were incubated with analogs of proline or lysine and the thermal stability of procollagen molecules containing the analogs was investigated using pepsin digestion at different temperatures as an enzymatic probe of conformation. The procollagens containing either 4-cis-hydroxy-l-proline, 3,4-dehydroproline, or 4,5-trans-dehydrolysine were less stable than normal procollagen and these abnormal collagens were largely in a non-triplehelical conformation within the cells at 37 °C. These results support the idea that procollagen molecules which are not in a triple-helical conformation are not secreted at a normal rate. Procollagens containing both 4,5-trans-dehydrolysine and a proline analog were much less stable than molecules containing a single type of analog. This result suggests that simultaneous administration of both types of analogs may have a greater effect on collagen accumulation in whole-animal experiments than administration of a single analog.     

Substrate properties of C'-methylnucleoside triphosphates in a reaction of RNA synthesis catalyzed by Escherichia coli RNA-polymerase

2 theta-C-methyl substituted and phosphonate analogs of UTP were prepared and together with the synthesized earlier 3'-C-methyl-UTP were investigated in the RNA synthesis reaction catalysed by Escherichia coli RNA-polymerase. Substrate properties of UTP analogs were studied in the presence of all natural triphosphates, in the absence of UTP and under conditions of soil substrate reaction. It was shown that UTP(3'CH3) is incorporated into the RNA chain and terminates further RNA elongation. Another analog UTP (2'CH3) may substitute natural UTP in RNA synthesis, but the effectivity of its incorporation is diminished. Phosphonate analog UTP(5'CH2) is a pseudoterminator of RNA synthesis. The conformational analysis of 2'- and 3'C-methylnucleosides by force-field method of calculation was carried out in order to find energetically forbidden conformations of these analogs due to the collision of bulky methyl group and a heterocyclic base. An attempt was made to fix the conformation of the substrate during its enzymatic transformation.     

Unique molecular conformation of aureobasidin A, a highly amide N-methylated cyclic depsipeptide with potent antifungal activity: X-ray crystal structure and molecular modeling studies.

A structural feature of aureobasidins, cyclic depsipeptide antibiotics produced by Aureobasidium pullulans R106, is the N-methylation of four out of seven amide bonds. In order to investigate possible relationship between the molecular conformation and the amide N-methylation, aureobasidin A (AbA), which exhibits the potent antifungal activity, was subjected to X-ray crystal analysis. The crystal, recrystallized from ether (orthorhombic, space group P2(1)2(1)2(1), a = 21.643 (3) A, b = 49.865(10) A, c = 12.427 (1) A, z= 8), contained two independent conformers per asymmetric unit and they took on a similar arrowhead-like conformation. The conformation consisted of three secondary structures of antiparallel beta-sheet, and beta- and gamma-turns, and was stabilized by three intramolecular and transannular N-H O=C hydrogen bonds. The beta-hydroxy-N-methyl-l-valine residue, which is indispensable for its bioactivity, was located at the tip of the corner. Since a nearly identical conformation has been observed for aureobasidin E, a related cyclic depsipeptide, this arrowhead-like conformation may be energetically stable and important for biological activity. The contribution of the amide N-methylation to the conformation was investigated by model building and energy calculations. The energy-minimizations of AbA analogs, in which some (one to four) of four N-methylated amide bonds were replaced with usual amide bond, led to some conformers which are fairly different from the arrowhead form of AbA, although they are stabilized by three intramolecular N-H...O=C hydrogen bonds. This result explains the reason why four out of the seven amide bonds have to be methylated to manifest biological activity, i.e. the high N-methylation of aureobasidin is necessary to form only one well-defined conformation.