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Results for “Molecular Conformation”

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At least 19 recordsLinked to original sources

PubMed1975

Molecular conformation prostaglandin A1 monoclinic crystalline polymorph.

The molecular conformation of the monoclinic crystalline polymorph of prostaglandin A1 has been determined by X-ray diffraction techniques. The space group is P21 with a = 13.637(2), b = 7.567(1), c = 10.576(2) A, beta = 107.37(3) degrees; Dc = 1.073 g.cm-3 for Z = 2. The molecular conformation is characterized by the nearly parallel arrangement of the C1-C7 and C13-C20 side chains, with a general flattening of the overall structure when compared with the orthorhombic polymorph. The cyclopentenone moiety assumes a C8 envelope conformation with C8 and O9 displaced +0.29 A and -0.18 A from the C9-C10=C11-C12 plane respectively. Concerted, small varations of the torsion angles, primarily about the C8-C12, C14-C15 and C16-C17 bonds, bring the monoclinic and orthorhombic conformations into coincidence.

Models, Molecular↗

PubMed1992

Molecular conformation of ubiquitinated structures and the implications for regulatory function.

The molecular conformation of ubiquitinated structures and the validity of the N-end rule were examined by simulating the molecular mechanics to ascertain the global energy-minimized structure. We examined the chemical linkage involved in attaching the ubiquitin carboxyl terminus to the N-terminus of three different x-hexapeptides, where x is the amino group of the acceptor peptide--either valine, arginine or glutamic acid--(x-K linkage) and to the epsilon-amino group of lysine of the acceptor hexapeptide x-glu1-his2-lys3-gly4-lys5-val6 (K-K linkage) through the formation of an isopeptide bond. Changes in conformation and molecular stability of the multi-ubiquitinated structures were determined by energy-minimization procedures using the SYBYL program developed by Tripos Associates. In the x-K linkage, the ubiquitin molecule is stretched in the beta-pleated sheets and beta-turns while the alpha-helices expand, as the molecule continues to unfold linearly. In the K-K linkage, the ubiquitin molecules have turned into a u-shaped, semi-circular alignment, contracting into a compact, folded structure.

Amino Acid Sequence↗

PubMed1978

Molecular conformation of a halogen-free thyroxine analog: 4-Methoxy-3,5,3-trimethyl-L-thyronine N-acetyl ethyl ester.

The molecular conformation of the halogen-free thyroxine analog 4-methoxy-3,5,3'-trimethyl-L-thyronine -n-acetyl ethyl ester has been determined by x-ray diffraction techniques. The unsubstituted parent compound, trimethylthyronine, has significant biological activity in rat thymocyte tests when compared with the thyroid hormone 3,5,3'-triiodo-L-thyronine (T3). Although no activity data are available for the analog studied, it is presumed to be inactive because of the 4-methoxy blocking group. The observed conformation of this structure is similar to that found for the natural hormone T(3). The 3'-methyl group is distal, the overall conformation is cisoid, and the diphenyl ether conformation is twist-skewed. The results of this diffraction study show that methyl substituents are capable of maintaining the thyronine conformation required for hormonal activity; they suggest that iodine enhances hormone-protein binding because of the electronic effects it produces either by alteration of molecular charge distributions or by direct charge-transfer interactions with the serum or nuclear binding proteins.

Models, Molecular↗

PubMed1977

Intramolecular hydrogen bonding and molecular conformations of nucleosides. N (6)-dimethyl-2',3'-isopropylidene adenosine.

The physical properties of an adenosine derivative, N(6)-dimethyl-2',3'-O-isopropylidene adenosine, Derivative 1, which is capable of intramolecular hydrogen bond formation between base-ring and sugar exocyclic hydroxymethyl group, have been studied in solution by infrared, circular dichroic and nuclear magnetic resonance spectroscopy. Analysis of the 220 MHZ 1H NMR spectrum of Derivative 1 in C2HCl2 solution indicated an overwhelming preference for the gg conformation for rotation about the C(4')--C5') bond and a predominant conformation for rotation about the C(5')--O(5') bond in which OH(5') projects towards the base ring. The purine base ring was shown to be in a predominant syn conformation with respect to the sugar ring by 100 MHZ 1H nuclear Overhauser experiments, by analysis of 3J(13C,H1') magnitudes observed in proton-coupled 13C NMR experiments and by CD measurements. Combination of each conformation feature of Derivative 1 in non-polar solvents is consistent with the overall molecular conformation observed in the solid state in which intramolecular hydrogenbonding exists between purine N(3) and the sugar CH2OH group; the presence of a strong intramolecular hydrogen bond was observed by infrared spectroscopy. The sugar ring conformations of 2',3'-O-isopropylidene ribonucleosides were analysed in terms of the pseudorotational properties of the ring; the N and S conformations tend toward to C(2')-exo and C(3')-'exo conformations, respectively, compared to normal ribonucleosides (C(3')-endo and C(2')-endo, respectively). The presence of the hydrogen bond in the derivative is sufficient to promote the S-type conformations (approx. 80%--90%) compared to cases where such a strong hydrogen bond is unlikely to be present approx. 40--50%).

Adenosine↗

PubMed1992

Crystal structure and molecular conformation of achatin-I (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide containing a D-amino acid residue.

In order to investigate the active conformation of achatin-I (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide from the Achatina fulica ganglia, its crystal structure and molecular conformation were analysed by the X-ray diffraction method. Crystals from methanol/dioxane are monoclinic, space group P2(1) with a = 5.083(1), b = 9.125(1), c = 20.939(3) A, beta = 94.73(1) degrees. The structure was solved by direct methods and refined to R = 0.051 for 1714 independent reflections with /Fo/ greater than sigma (Fo). The molecule exists as a zwitterion with the Gly N-terminal end protonated and Asp beta-carboxyl deprotonated; the C-terminal of Asp is in a neutral state. The molecule takes a kind of beta turn structure with the D-Phe-Ala residues at the corner of the bend. This turn conformation is primarily formed by the strong intramolecular hydrogen bonds of NH(Gly)...O delta 1 (Asp) and NH(Asp)...O delta 1 (Asp) pairs, thus forming a 15-membered ring structure. Judging from the published data concerning the structure-activity relationship, this turn conformation may reflect an important feature related to the neuroexcitatory activity of achatin-I.

Amino Acid Sequence↗

PubMed1977

On the molecular conformation of human haemopexin. I. Reactivity of the tyrosine and tryptophan side chains.

The reactivity of the aromatic side chains of Tyr and Trp in human haemopexin were studied by chemical modifications and analysis of spectrophotometric titration curves. It has turned out that: 1. Under non-denaturing conditions the aromatic rings of Tyr resisted both acetylation and nitration. 2. Three indole groups of Trp reacted with the Koshland agent, without the native conformation of the protein being markedly affected (CD spectra). 3. Oxidation by N-bromosuccinimide split the peptide chain and the molecular conformation collapsed. 4. The Tyr residues could be placed into three classes, according to their pK values: 2 (or 1 in the haem-haemopexin complex) were normally accessible to titration, 5 were masked and the remaining 7 (or 8) were buried. 5. The spectrophotometric titration curve could not be analysed in terms of the Linderstrøm-Lang equation. The findings 1 to 3 refer to both haemopexin and its complex with haem; the spectrophotometric titration curves of the two molecules are very similar too. Consequently, the binding of haem is not associated with a profound alteration of the molecular architecture. The generally low reactivity of the side chains studied indicates that the hydrophobic peptide core of this glycoprotein is a compact one, very restricted in its contacts with the environment.

Circular Dichroism↗

PubMed1975