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PubMed1994

Conformational analysis of CCK-B agonists using 1H-NMR and restrained molecular dynamics: comparison of biologically active Boc-Trp-(N-Me) Nle-Asp-Phe-NH2 and inactive Boc-Trp-(N-Me)Phe-Asp-Phe-NH2.

The tetrapeptide Boc-Trp-(N-Me)Nle-Asp-Phe-NH2 is a potent CCK-B agonist. Replacement in this analogue of the norleucine residue by a phenylalanine, to yield Boc-Trp-(N-Me) Phe-Asp-Phe-NH2, led to a 740-fold decrease in affinity whereas the same decrease in affinity was not observed in their nonmethylated counterparts. In order to ascertain the conformational preferences of these two N-methylated tetrapeptides, a study by two-dimensional (2D) nmr spectroscopy and molecular modeling was undertaken. The solution conformation of the two peptides was examined by 1H-nmr in a d6-DMSO/H2O (80:20) mixture. A cis-trans equilibrium, induced by N-methylation, was observed for both analogues, and the proton spectra of the two rotamers were fully characterized in each case. 1H-1H distance constraints, derived from 2D nuclear Overhauser effect spectroscopy and rotating frame nuclear Overhauser effect spectroscopy experiments, were used as inputs for subsequent restrained molecular dynamics simulations. Comparisons of the nmr and molecular modeling data point toward distinct conformational preferences for these two peptides with an opposite spatial orientation of the Trp residue, and could explain the large difference in their biological activities. Furthermore, the tridimensional structure of Boc-Trp-(N-Me)Nle-Asp-Phe-NH2 could serve as a model for the design of nonpeptide CCK-B agonists.

Amino Acid Sequence↗
PubMed1992

Binding of brevetoxins and ciguatoxin to the voltage-sensitive sodium channel and conformational analysis of brevetoxin B.

The marine toxins known generically as brevetoxins, as well as their structural relative ciguatoxin, are known as polyether ladder toxins, and bind uniquely to site 5 of the voltage-sensitive sodium channel. Rat brain synaptosome binding data show similarities in binding affinity for brevetoxins having the same structural (ladder) backbone, but different affinities between brevetoxins having different backbones. Ciguatoxin has a different backbone from the brevetoxins, but binds even more strongly to the same site. Could the flexibility of the backbone be related to their relative toxicities? As part of an effort to identify the common pharmacophore for the toxins, Monte Carlo methods were used to generate conformational models of the polyether ladder toxin brevetoxin B (PbTx-2) which shows significant flexibility at the juncture of the two 7-membered rings.

Animals↗
PubMed2002

Efficient formal total synthesis of physostigmine and physovenine: conformational analysis of key intermediates.

An efficient route for the formal total synthesis of physostigmine (1) and physovenine (2), alkaloids from 5-methoxyindole-3-acetonitrile, through a Grignard reagent 1,4-addition, is described. 2-Hydroxyindolenine 5, the key advanced intermediate for the synthetic targets, was converted either to esermethole (12) via a high-yielding (28%) seven-step sequence or to the C-ring oxygenated analogue 15 in a five-step sequence and 23% overall yield. (1)H NMR and molecular modeling analyses of esermethole (12) and the furoindolines 13 and 15 were used to deconvolute weighted time-average vicinal coupling constants to provide definite solution-state conformational preferences in CD(2)Cl(2) solvent.

Fabaceae↗
PubMed2005

Conformational analysis of heparin binding peptides.

A properly engineered biomaterial for dental/orthopaedic applications must induce specific responses from the osteoblasts at the implant site. A most desirable response is an efficient adhesion, as it represents the first phase in the cell/material interaction and the quality of this phase will influence the cell's capacity to organize into a new functional tissue. The four osteoblast-adhesive peptides discussed in this paper are mapped on the 339-364 sequence (339MAPRPSLAKKQRFRHRNRKGYRSQRG364) located in the primary heparin-binding site of human vitronectin (HVP). Adsorbed on a polystyrene scaffold, these peptides display different adhesive activities towards osteoblasts. In this paper we report on the structural analysis in solution of the peptides through NMR and computational techniques. We find that the peptides with the highest adhesive activities display a hydrophobic patch opposite to the charged surface candidate to interact with heparin. These findings suggest that the peptides might adsorb on the polystyrene support in a favourable orientation for their activity. Furthermore, molecular models obtained for the four peptides in solution were used in rigid docking simulations with a heparin model. Assuming that the peptide solution conformations are not very different from the polystyrene-adsorbed structures, the simulations reveal that peptide adhesive activity is also affected by the number of ionic interactions and spacing between charged residues.

Amino Acid Sequence↗
PubMed1995

Crystal structure and a twisted beta-sheet conformation of the tripeptide L-leucyl-L-leucyl-L-leucine monohydrate trimethanol solvate: conformation analysis of tripeptides.

In order to test the helical preference of short oligo-L-leucines, we crystallized the tripeptide L-leucyl-L-leucyl-L-leucine (LLL) and carried out x-ray diffraction studies of it (L-leucyl-L-leucyl-Lleucine)2. 3CH3OH. H2O, (C39H84N6O12), crystallized in the monoclinic system, space group P2(1), cell parameters: a = 12.031(2), b = 15.578(3), c = 14.087(2) A, alpha = 90 degrees, beta = 97.29(1) degrees, gamma = 90 degrees, V = 2618.6 A3, MW = 829.1, Dc = 1.051 g cm-3, R index of 0.057 for 4213 reflections (lambda CuK alpha = 1.5418 A) > 2 sigma. LLL takes up the beta-sheet rather than a helical conformation in the crystalline state. The three methanol molecules and the water molecule that constitute the solvent of crystallization form a network of hydrogen bonds to the LLL molecules and to one another. It is rather remarkable that though A and L have stronger helical preferences than G, neither AAA nor LLL form the crystalline helix but GAL does, indicating that the helical preferences depend on the sequence context. The residue L2 in molecule A and the residues L1 and L3 of molecule B do not show the preferred conformation for forming helices. Further, very remarkably, LLL exhibits a unique supersecondary feature of the protein folding topology, namely the twisted beta-sheet, whereas most short peptides show only the classical beta-sheet conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2004

Conformation analysis of glu181 and ser186 in the metarhodopsin I state.

Photoactivation of rhodopsin yields a photointermediate, metarhodopsin I, during the formation of the fully activated photointermediate, metarhodopsin II. It is proposed that Glu181 and Ser186, in the second extracellular loop, play important roles in the stabilization of the protonated Schiff base of metarhodopsin I. Glu181 and Ser186 form a network of hydrogen bonds mediated by a water molecule in the dark-state crystal structure of rhodopsin. On the other hand, the counter-ion of the protonated Schiff base, Glu113, is not involved in the hydrogen-bond network, as it is located further than hydrogen-bond distance from Ser186. Herein, the conformations and proton arrangements of the protonated form of Glu181 and Ser186 in the hydrogen-bond network have been investigated by molecular-dynamics calculations of the rhodopsin crystal structure as well as in the structural model of metarhodopsin I. In the metarhodopsin I model, Ser186 mediated the hydrogen-bond network between Glu113 and Glu181, changing the protein's conformation and creating a space by the outward motion of transmembrane segment 3, while the hydroxyl group of Glu181 was favored in the hydrogen-bond network. The hydrogen bond between Glu113 and Ser186 is thought to reduce the basicity of the carboxylate of Glu113, maintaining the protonated state of the Schiff base in the metarhodopsin I state. In the Glu181Gln mutant, the hydroxyl group of Ser186 favored the water molecule as a proton donor in the metarhodopsin I state, since the carbonyl group of the Gln residue was favored in the hydrogen-bond network. These results indicate that the Gln181 residue interferes with the hydrogen-bond between Glu113 and Ser186 in the metarhodopsin I state, facilitating the neutralization of the protonated Schiff base.

Crystallography, X-Ray↗
PubMedDate not supplied

Synthesis, characterization, and conformational analysis of DNA adducts from methylated anilines present in tobacco smoke.

The ability of a series of aromatic amines present in tobacco smoke (2-, 3-, and 4-methylaniline, 2,3- and 2,4-dimethylaniline) to bind to DNA has been investigated by reacting N-(acyloxy)arylamines with dG, dG nucleotides, and DNA. The predominant products from reactions with dG and the nucleotides were characterized as N-(deoxyguanosin-8-yl)arylamines by spectroscopic and HPLC methods. HPLC and spectroscopic analyses of the modified DNA indicated the same adducts. Analyses of the 1H and 13C NMR spectra suggested that the adducts containing a methyl substituent ortho to the arylamine nitrogen had a higher percentage of syn conformers. This observation was supported by theoretical simulation studies that indicated substantial percentages of low energy syn conformers, increasing with the substitution pattern in the order para < meta < ortho < ortho,para < ortho,meta. The results demonstrate that, although single-ring arylamines are considered weak carcinogens, their electrophilic N-acetoxy derivatives, which are plausible metabolic intermediates, react with DNA to yield covalent adducts structurally identical to those derived from carcinogenic polyarylamines, such as 2-aminofluorene and 4-aminobiphenyl. Furthermore, the conformational perturbation induced in DNA by the formation of the monoarylamine-DNA adducts, especially those with an ortho substituent, may contribute to the biological activities of these compounds.

Aniline Compounds↗
PubMed1978

The quantitation of nuclear Overhauser effect methods for total conformational analysis of peptides in solution. Application to gramicidin S.

The [1H:1H] nuclear Overhauser effects (NOE's) and spin-lattice relaxation times (T1's) are reported for the backbone protons of the decapeptide gramicidin S. Several methods for calculating interproton distances from these measurements are presented. Ratios of interproton distances were obtained from [1H:1H] NOE's and from the combination of [1H:1H]NOE'S and T1 values. Actual proton-proton distances were calculated from these ratios either by using the known distance between two geminal protons or distances derived from scalar coupling constants. The interproton distances calculated for gramicidin S are consistent with a II' beta-turn/antiparallel beta-sheet conformation.

Gramicidin↗
PubMed1993

Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization.

Dimerization of genomic RNA is a key step in the retroviral life cycle and has been postulated to be involved in the regulation of translation, encapsidation and reverse transcription. Here, we have derived a secondary structure model of nucleotides upstream from psi and of the gag initiation region of Mo-MuLV RNA in monomeric and dimeric forms, using chemical probing, sequence comparison and computer prediction. The 5' domain is extensively base-paired and interactions take place between U5 and 5' leader sequences. The U5-PBS subdomain can fold in two mutually exclusive conformations: a very stable and extended helical structure (E form) in which 17 of the 18 nucleotides of the PBS are paired, or an irregular three-branch structure (B form) in which 10 nucleotides of the PBS are paired. The dimeric RNA adopts the B conformation. The monomeric RNA can switch from the E to the B conformation by a thermal treatment. If the E to B transition is associated to dimerization, it may facilitate annealing of the primer tRNAPro to the PBS by lowering the free energy required for melting the PBS. Furthermore, dimerization induces allosteric rearrangements around the SD site and the gag initiation region.

Allosteric Regulation↗
PubMed2004

Conformational analysis: a tool for the elucidation of the antioxidant properties of ferulic acid derivatives in membrane models.

With the aim to search and design more effective and safe antioxidant molecules to be used as functional ingredients in cosmetic formulations for UV protection, we evaluated the antioxidant/radical scavenging activities of ferulic acid and of some alkyl ferulates in both acellular and cellular systems. Ferulic acid esters, equipotent as antioxidant in homogeneous phase, showed when tested in membranous systems (rat liver microsomes, rat erythrocytes) marked differences in antioxidant potency. The n-C(12) derivative was the most potent, followed by n-C(8), n-C(16) and branched C(8), and then by ferulic acid. A conformational study carried out by NMR and modelling, indicates that the different antioxidant activity of ferulates in membrane models is due to the different spatial conformation and arrangement of the side chain of the molecule, which governs the access and binding to the phospholipid bilayer, the modality of orientation of the scavenging/quenching nucleus (phenol moiety), and hence the overall antioxidant potency of the derivative. These results emphasize the need of analytical studies (NMR and molecular modelling) addressed to the knowledge of the conformational parameters in combination with conventional antioxidant testings for understanding the antioxidant behaviour of a molecule in a biological membrane/system.

Animals↗
PubMed1992

Taxonomy and conformational analysis of loops in proteins.

We propose a general classification scheme for loops, aperiodic segments of protein structure. In an effort to avoid the geometric complexity created by non-repeating phi psi angles, a morphologic definition that focuses upon the linearity and planarity of loops is utilized. Out of 432 loops (4 to 20 residues in length) extracted from 67 proteins, 205 are classified as linear (straps), 133 as non-linear and planar (omegas), and 86 as non-linear and non-planar (zetas). The remaining 8 are classified as compound loops because they contain a combination of strap, omega, and zeta morphologies. We introduce a structural alphabet as a shorthand notation for describing local conformation. The symbols of this alphabet are based on the virtual dihedral angle joining four consecutive alpha carbons. The notation is used to provide a compact description of loop motifs in phosphate binding and calcium binding proteins. Since similar loop conformations form similar "words", the structural sequence facilitates the search for common structural motifs in a family of loops. Contrary to the view of loops as "random coils", we find loops to have positional preferences for amino acid residues analogous to those previously described for beta-turns.

Amino Acid Sequence↗
PubMed2004

Synthesis of alkylated deoxynojirimycin and 1,5-dideoxy-1,5-iminoxylitol analogues: polar side-chain modification, sulfonium and selenonium heteroatom variants, conformational analysis, and evaluation as glycosidase inhibitors.

The syntheses of N-alkylated deoxynojirimycin and 1,5-dideoxy-1,5-iminoxylitol derivatives having either a D- or an L-erythritol-3-sulfate functionalized N-substituent are reported. The alkylating agent used was a cyclic sulfate derivative, whereby selective attack of the nitrogen atom at the least hindered primary center afforded the desired ammonium salt. In aqueous solution, these salts were configurationally labile at the ammonium center. Sulfonium and/or selenonium analogues of the ammonium salts were prepared by analogous reactions. The chalcogen salts were obtained as mixtures of diastereomers, separable in some cases, differing only in the stereochemistry at the configurationally stable sulfur or selenium atoms. Proof of configuration and conformation of each compound was obtained by detailed NMR experiments. The compounds are six-membered ring analogues of salacinol, a known sulfonium-salt glucosidase inhibitor. Evaluation of the target compounds for enzyme inhibition of the glucosidase enzyme glucoamylase G2 indicated that these compounds were either inactive or, at best, only weak inhibitors of maltose hydrolysis.

1-Deoxynojirimycin↗
PubMed2004

Conformational analysis of the biflavanoid GB2 and a polyhydroxylated flavanone-chromone of Cratoxylum neriifolium.

Three compounds, namely the interesting biflavanonol GB-2(naringenin 1-3, 11-8-dihydroquercetin, 1), 1-4',1-5,11-5,1-7,11-7-pentahydroxyflavanone(l-3,11-8)chromone [naringenin-(3 -8) 5,7-dihydroxychromone, 21 and stigmasterol, have been isolated from the leaves of Cratoxylum neriifolium Kurz. Compounds 1 and 2 show rotameric behavior due to the presence of a single bond between the highly substituted flavanone and flavanonol part and the flavanone and chromone part, respectively. Complete NMR spectral assignments of 1 and 2 have been done at 27 C and 90 C for the first time followed by a study of conformational behavior at room temperature by ROESY.

Clusiaceae↗
PubMed2005

CD spectral study of Dnp derivatives of amino acids and peptides for their configurational and conformational analysis.

Rules relating the stereochemistry of N-Dnp (Dnp: 2,4-dinitrophenyl) derivatives of alpha-amino acids and peptides and the sign of the Cotton effects at the longest wavelength band (ca. 400 nm) are surveyed. Some new data and insights concerning the CD spectra of Dnp-alpha-amino acids are included: i.e., the spectra of Dnp derivatives as the composite of the corresponding o-nitrophenyl and p-nitrophenyl derivatives; the crystal structure of Dnp-I-phenylalanine and its solid-state CD spectra; the CD spectra of Dnp-alpha-amino acids containing sulfur atom on their side chains; and the theoretical approach to the CD spectra using molecular orbital method-based calculation. Conformational analyses of cyclic and linear peptides by the CD spectra of their Dnp derivatives are also discussed.

2,4-Dinitrophenol↗
PubMed2005

Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain.

The Antennapedia homeodomain structure consists of four helices. The helices II and III are connected by a tripeptide that forms a turn, and constitute the well-known helix-turn-helix motif. The recognition helix penetrates the DNA major groove, gives specific protein-DNA contacts and forms direct, or water-mediated, intermolecular hydrogen bonds. It was suggested that helix III (and perhaps also helix IV) might represent the recognition helix of Antennapedia homeodomain, which makes contact with the surface of the major groove of the DNA. In an attempt to clarify the helix III capabilities of assuming an helical conformation when separated from the rest of the protein, we carried out the structural determination of the recognition helix III in different solvent media. The conformational study of fragments 42-53, where residues W48 and F49, not involved in the protein-DNA interaction, were substituted by two alanines, was conducted in sodium dodecyl sulfate (SDS), trifluoroethanol (TFE) and TFE/water, using circular dichroism, nuclear magnetic resonance (NMR) and distance geometry (DG) techniques. The fragment assumes a well-defined secondary structure in TFE and in TFE/water (90/10, v/v) with an alpha-helix encompassing residues 4-9, while in TFE/water (70/30, v/v) a less regular structure was found. The DG results in the micellar system evidence the presence of a distorted alpha-helical conformation involving residues 4-8. Our results reveal that the isolated Antennapedia recognition helix III tend to preserve in solution the alpha-helical conformation even if separated from the rest of the molecule.

Animals↗
PubMed1995

Conformational analysis of the Campylobacter jejuni porin.

The major outer membrane protein (MOMP) of Campylobacter jejuni was purified to homogeneity by selective solubilization and fast protein liquid chromatography. The amino acid composition of the MOMP indicates the presence of cysteine residues. The amino-terminal sequence, determined over 31 residues, shows no significant homology with any other porin from gram-negative bacteria except in a discrete region. Immunocross-reactivity between Escherichia coli OmpC and the MOMP was analyzed, and a common antigenic site between these two porins was identified with an anti-peptide antibody. From circular dichroism and immunological investigations, the existence of a stable folded monomer, containing a high level of beta-sheet secondary structure, is evident. Conformational analyses show the presence of a native trimeric state generated by association of the three folded monomers; the stability of this trimer is reduced compared with that of E. coli porins. This study clearly reveals that the C. jejuni MOMP is related to the family of trimeric bacterial porins.

Amino Acid Sequence↗
PubMed2004

Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring.

To provide insight into the polycyclization mechanism of squalene by squalene-hopene cyclase (SHC) from Alicyclobacilus acidocaldarius, some analogs of nor- and bisnorsqualenes were synthesized including the deuterium-labeled squalenes and incubated with the wild-type SHC, leading to the following inferences. (1) The deprotonation reaction for the introduction of the double bond of the hopene skeleton occurs exclusively from the Z-methyl group on the terminal double bond of squalene. (2) 3R-Oxidosqualene was folded in a boat conformation for the A-ring construction, while the 3S-form was in a chair structure. (3) The terminal two methyl groups are indispensable both for the formation of the 5-membered E-ring of the hopene skeleton and for the initiation of the polycyclization cascade, but the terminal Z-methyl group has a more crucial role for the construction of the 5-membered E-ring than the E-methyl group. (4) Some of the novel terpene skeletons, 36, 37, 39 and 40, were created from the analogs employed in this investigation.

Alkenes↗
PubMed2004

Conformational analysis: crystallographic, molecular mechanics and quantum chemical studies of C--H...O hydrogen bonding in the flexible bis(nosylate) derivative of catechol.

The single-crystal X-ray diffraction analysis of 2-[[(4-nitrophenoxy)sulfonyl]oxy]phenyl 4-nitrophenyl sulfate (4) reveals that an interesting intermolecular or extended structure (a one-dimensional hydrogen-bonded polymer) is formed because of pairs of intermolecular (aryl)C--H...O(nitro) hydrogen bonds between the C(2) symmetry monomer units. The axis of the hydrogen-bonded polymer runs co-linear with the [101] face diagonal of the monoclinic unit cell. Molecular mechanics calculations using a modified version of the MM+ force field and a random conformational search algorithm have been used to locate the important low-energy in vacuo conformations of (4). The MM-calculated conformation of (4) that most closely matches the X-ray structure lies some 26.5 kJ mol(-1) higher in energy than the global minimum-energy conformation, consistent with the notion that the crystallographically observed molecular architecture of (4) is a local energy minimum in the absence of its crystal lattice environment. Since the X-ray conformation of (4) was correctly calculated only when all of the neighbouring molecules in the crystal lattice were included in the simulation, hydrogen bonding and other non-bonded interactions in the crystal lattice clearly dictate the experimentally observed conformation of (4). Quantum chemical calculations (AM1 method) confirm the critical role played by the intermolecular (aryl)C--H...O(nitro) hydrogen bonds in controlling the crystallographically observed conformation of (4) and show that self-recognition in this system by hydrogen bonding is favoured on electrostatic grounds. Collectively, the molecular simulations suggest that because the lowest-energy molecular conformation of (4) does not permit the formation of an extended hydrogen-bonded 'supramolecular' structure, it is not the preferred conformation in the crystalline solid state.

Journal Article↗