Molecular Conformation of Adenosine 3′,5′-Monophosphonate Monohydrate

ADENOSINE 3′,5′-monophosphate (cyclic AMP) plays a role in many metabolic and genetic processes¹. To modify the biological activity of the natural metabolite, various analogues have been synthesized and studied². For example, the N(6) alkyl analogues possess not only greater but more specific biological activity¹ and the isosteric phosphonate analogue, where the 5′ oxygen atom is substituted by a methylene group also possesses biological activity (ref. 2 and J. G. Moffat, private communication). The crystal structure determination of the latter was undertaken to compare its stereochemistry with that of the natural compound, cyclic AMP³.     

GABA Binding to an Insect GABA Receptor: A Molecular Dynamics and Mutagenesis Study

RDL receptors are GABA-activated inhibitory Cys-loop receptors found throughout the insect CNS. They are a key target for insecticides. Here, we characterize the GABA binding site in RDL receptors using computational and electrophysiological techniques. A homology model of the extracellular domain of RDL was generated and GABA docked into the binding site. Molecular dynamics simulations predicted critical GABA binding interactions with aromatic residues F206, Y254, and Y109 and hydrophilic residues E204, S176, R111, R166, S176, and T251. These residues were mutated, expressed in Xenopus oocytes, and their functions assessed using electrophysiology. The data support the binding mechanism provided by the simulations, which predict that GABA forms many interactions with binding site residues, the most significant of which are cation-π interactions with F206 and Y254, H-bonds with E204, S205, R111, S176, T251, and ionic interactions with R111 and E204. These findings clarify the roles of a range of residues in binding GABA in the RDL receptor, and also show that molecular dynamics simulations are a useful tool to identify specific interactions in Cys-loop receptors.Abbreviations used: nACh, nicotinic acetylcholine; AChBP, acetylcholine binding protein; GABA, gamma-aminobutyric acid; MD, molecular dynamics; RDL, resistant to dieldrin; RMSD, root mean-square displacement; RMSF, root mean-square fluctuation     

Molecular Conformation of Alkaline Proteinase of Aspergillus sojae in Aqueous Solution

The molecular conformation of the alkaline proteinase of Aspergillus sojae in aqueous solution was investigated by the optical rotatory dispersion, Cotton effects, infra-red absorption spectra (amide I and V bands), ultraviolet difference spectra, etc. It is concluded that; (1) there are about 10 to 15% of the α-helix and a small amount of the β-structure in the enzyme molecule, but most parts of the peptide chain are present as the disordered structure; (2) the enzyme molecule is compactly folded even in the disordered parts; and (3) the two tryptophan residues involved in the peptide chain are burried in the interior of the molecule.     

截短型细胞毒素Gelonin的分子构象和生物活性

为了探索免疫络合物中具杀伤靶细胞的毒素,gelonin的结构与功能的关系,根据化学合成的gelonin基因序列和3维分子构象设计了N端区Gly,Leu,Asp和/或C端区Asp,Lys,Asp,Pro,Lys缺失的gelonin. 以重组质粒pE gel为模板,在相应引物存在下,用PCR法获得5′端区和/或3′端区碱基序列缺失的gelonin基因片段. 经克隆、表达和纯化得到3种截短型gelonin（G-N3、G-C5、G-N3C5）. CD谱和荧光谱表明,完整型gelonin（G-O）与截短型gelonin的分子构象有明显的差异.它们的构象变化与类DNase活性和抑制肿瘤细胞生长的能力均为G-O≥ G-N3＞G C5＞G-N3C5. 结果再一次证明了具有α+β型结构蛋白,gelonin的构象与生物活性的一致性.     

ZNC(C)PR的构象及分子动力学模拟

本文用分子动力学方法和质子间距约束结合建立了ZNC(C)PR的构象。质子间距是由二维核磁共振的NOE效应得到的。结果表明ZNC(C)PR分子的主链是伸展的,但Asn2的侧链与Arg5的侧链相互靠近,使整个分子成紧密结构。在所建模型的基础上,对ZNC(C)PR进行了分子动力学摸拟。发现第一位的焦谷氨酸环很灵活,这可能意味着焦谷氨酸环对ZNC(C)PR的活性并不重要,这与实验结果是一致的。     

Single-Strand Conformation Polymorphism for Molecular Variability Studies of Six Viroid Species

Coenzyme Q10 (CoQ10) is a popular food supplement. Earlier, we successfully produced CoQ10 in rice, which normally produces predominately CoQ9. Here we developed efficient production of CoQ10 in rice by introducing the gene for decaprenyl diphosphate synthase into rice sugary and shrunken mutants. These rices produced 1.3 to 1.6 times as much CoQ10 as the earlier enriched rice did.     

Probing the Conformation of FhaC with Small-Angle Neutron Scattering and Molecular Modeling

Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120–160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins.     

Probing the Conformation of FhaC with Small-Angle Neutron Scattering and Molecular Modeling

Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120–160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins.     

Crystal Structure and Molecular Conformation of the Cyclic Hexapeptide cyclo-(Gly-Aib-Gly)2

We have synthesized and crystallized the cyclic peptide (Gly-Aib-Gly) ₂. Its structure has been determined by conventional X-ray diffracti on methods. In the crystal it adopts a conformation with one β-turn (type I) and its mirror image at the other side of the ring. All conformation al angles are similar to those reported for these amino acid residues. In particular the Aib residue has a conformation intermediate between α- and 3₁₀-helical conformations. The ring is an adequate model for the β-turn conformation. A molecule of formic acid is found in the crystal which shows a very short hydrogen bond with one of the glycine carbonyl groups.     

Condensed State Molecular Dynamics in Sorbitol and Maltitol: Mobility Gradients and Conformation Transitions

Abstract

Molecular mobility in sorbitol and maltitol is studied in order to understand their differences near the junction between the α and β relaxations. The molecular dynamics simulations performed on the polyols in their bulk state give support to the ¹³C NMR results and imply that the mobility of a carbon atom located at the extremity of the chain is higher than that of any other carbon. Moreover, the difference in carbon atoms mobility is greater within the sorbitol moiety of maltitol than in sorbitol and seems intimately related to the junction temperature of the α and β relaxation processes. The reorientation of the C–H vectors as probed by NMR is shown to be mainly the effect of conformation transitions in the case of a carbon atom located at the end of the chain.     

Conformation of the Flavin Adenine Dinucleotide Cofactor FAD in DNA-Photolyase: A Molecular Dynamics Study

In order to gain insight into the light-driven repair of DNA by the enzyme DNA photolyase, the conformation of the photoactive cofactor FAD, a flavin adenine dinucleotide, has been studied by molecular dynamic simulations. In contrast to FAD in the gas phase and in water where the MD procedure yields various "open" I-shaped as well as "closed" U-shaped conformations, the calculations of FAD binding to the enzyme show essentially a single U-shaped conformation of this cofactor which, so far, is unique among FAD-carrying proteins. It is characteristic for this U-shaped conformation that the FAD components occupy opposite sides of the pocket in the surface of the protein which provides the binding site for the defect pyrimidine dimer structure on DNA. In fact, the calculated U-shaped conformation is very close to the one revealed by the X-ray structure analysis of DNA photolyase. Moreover, the simulations yield details on the binding of the photoactive isoalloxazine moiety and the dynamics of the amino acids forming the binding cavity of the enzyme.     

Molecular orbital studies on nucleoside analogs. II. Conformation of 6-azapyrimidine nucleosides.

PCILO (Perturbative Configuration Interaction using Localised Orbitals) computations have been carried out for three 6-azapyrimidine nucleosides, 6-azauridine, 6-azacytidine and 6-azathymidine, for both C(2')-endo and C(3')-endo pucker of the sugar ring. The results indicate a syn (chiCN=180 degrees) conformation followed by chiCN=90 degrees and gg conformation for C(3')-endo 6-aza analogs as compareed to the anti (chiCN=0 degrees) and gg conformation preferred by the corresponding pyrimidine nucleosides. For C(2')-endo sugar geometry, 6-azauridine and 6-azacytidine prefer, respectively, chiCN=0 degrees (anti) and phi C(4')-C(5')=60 degrees C (gg) and chiCN-240 degrees (syn) and phi C(4')-C(5')=120 degrees. The corresponding nucleosides, uridine and cytidine, show a preference for syn (chiCN=240 degrees) and gg and anti(chiCN=0 degrees) and gg , respectively. The X-ray crystallographic conformations of 6-azauridine and 6-azacytidine have been attributed to intermolecular hydrogen bonding and crystal packing forces. The results of PMR, CD and ORD studies on 6-azauridine and 6-azacytidine in aqueous solutions are in agreement with the PCILO predictions.     

Conformation of physalaemin

The conformational and spatial configuration of the biologically active undecapeptide physalaemin was studied using 350-MHz1H NMR. The NMR analyses suggested the existence of a strong hydrogen bond between the amide proton of the Phe7 and a carbonyl group in the N-terminal moiety, most likely the Pro4 one. Other bondings were postulated, involving the side-chain amine of Lys6 and the side-chain amide of Asn5 and respectively the side-chain carboxyl of Asp3 and the terminal amide carbonyl of Met-NH2. Thus unlike its shorter peptidic fragments, physalaemin exhibited a stable molecular structure in solution, giving some insight into the conformation required for interaction at the biological receptor of tachykinins.     

Conformation of dipeptides

The amide bond in L ,L - and L ,D -α-chloropropionylalanine methyl ester is shown to be trans by molar polarization and infrared spectroscopy. In these dipeptide diastereoisomer analogues, therefore, differences in physical properties, i.e., melting points, crystalline forms, gas chromatographic mobilities, etc., depend on preferred molecular conformations and not peptide bond configuration. Nuclear magnetic resonance spectra of both compounds were identical, indicating that no major chemical environment differences exist, which might have resulted from dissimilar side group interactions. Based on the data reported here and those of others, most dipeptide conformations can be eliminated because of contradiction with limits set by experimental or theoretical considerations. Of the remaining conformational possibilities, a single pair accounts for observed physical differences in dipeptide diastereoisomers, free or blocked. The preferred form contains α-hydrogens trans to each other and in the plane of the peptide bond. In this conformation, R¹–R² and amino–carboxyl distances are minimal in L ,D diastereomers and maximal in L ,L forms.     

Conformation of Prostaglandins

ALTHOUGH different prostaglandins^* may have different pharmacological effects, in general the compounds have the same qualitative action on a given cell type. Investigation^1,2 has revealed structure-activity correlations and the importance of the orientation of the 11 and 15 hydroxyl groups³ is recognized. Molecular model building together with structure-activity data have suggested that prostaglandins are one of a number of classes of drugs and hormones that seem to fit stereochemically into a pre-existing (for example, polypeptide-nucleotide) receptor site^4,5. The restraints applied to the prostaglandin molecule to fix it as a stable conformational isomer, or conformer, are little understood and we now wish to indicate the significance of this conformation with respect to interaction with biological membranes.