Search results for "conformation"
showing 10 items of 1414 documents
Sequence-specific and DNA structure-dependent interactions of Escherichia coli MutS and human p53 with DNA
2013
Many proteins involved in DNA repair systems interact with DNA that has structure altered from the typical B-form helix. Using magnetic beads to immobilize DNAs containing various types of structures, we evaluated the in vitro binding activities of two well-characterized DNA repair proteins, Escherichia coli MutS and human p53. E. coli MutS bound to double-stranded DNAs, with higher affinity for a G/T mismatch compared to a G/A mismatch and highest affinity for larger non-B-DNA structures. E. coli MutS bound best to DNA between pH 6 and 9. Experiments discriminated between modes of p53-DNA binding, and increasing ionic strength reduced p53 binding to nonspecific double-stranded DNA, but had…
Bile acid–amino acid ester conjugates: gelation, structural properties, and thermoreversible solid to solid phase transition
2010
Design, synthesis, and gelation properties of three novel biocompatible bile acid–L-methionine methyl ester conjugates are presented. Two of the conjugates have been shown to undergo self-assembly leading to organogelation in certain aromatic solvents. The properties of these gels have been investigated by conventional methods typical for molecular gel studies along with 13C CPMAS NMR spectroscopic studies of the native gel. In addition, properties in solid and solution states for all three compounds have been investigated, and single crystal X-ray structures of all compounds determined. Furthermore, powder X-ray diffraction studies have revealed that compound 1 undergoes a dynamic and reve…
Complexes of tryptophan dipeptides with the R2Sn(IV)2+ ion (R=Me, Ph): Spectroscopic studies, solution properties and structural implications
1995
Tryptophan dipeptides such as L-tryptophyl-L-alanine (H 2 TrpAla), L-tryptophyl-L-tyrosine (H 2 TrpTyr), L-tryptophyl-L-tryptophan (H 2 TrpTrp), along with L-histidyl-L-tyrosine (H 2 HisTyr), were reacted with R 2 SnO (R=Me, Ph) yielding the corresponding complexes. The complexes have been characterized by IR and 119 Sn Mossbauer spectroscopy in the solid state and by 1 H and 13 C NMR in CD 3 OD solutions. Monomeric species were detected, with the tin atom arranged in a pentacoordinated trigonal-bipyramidal structure. The dipeptides are coordinated via the terminal amino group, deprotonated peptide nitrogen and terminal carboxylate group. No side-chain appears to be involved in bonding. Det…
Synthesis, crystal structure and molecular conformation of the tBuCO-D,L-Ala-Δz-Phe-NhiPr α,β-unsaturated dipeptide
2009
The crystal structure of the tBuCO-D,L-Ala-delta Z-Phe-NHiPr dipeptide has been solved by X-ray diffraction. The peptide crystallizes in monoclinic space group P2(1)/c with a = 13.445 (3) A, b = 35.088 (4) A, c = 14.755 (3) A, beta = 116.73 (1) degree, Z = 12 and dc = 1.151 g.cm-3. The three independent molecules per asymmetric unit accommodate a beta II-folded conformation, but only one of them contains the typical i + 3----i interaction characterizing a beta-turn. In the other two molecules, the N...O distance exceeds 3.2 A, a value generally considered the upper limit for hydrogen bonds in peptides. In solution, the beta II-turn conformation is largely predominant.
Synthesis of cyclic dipeptide templates, their incorporation into peptides and studies on their conformational and biological properties.
2009
This study investigated the diastereoselective synthesis of three dipeptide templates 1, 2 and 3, which may be regarded as conformationally restricted analogs of H-Gly-Xaa-OH, in which Xaa constitutes an aromatic amino acid. Bond formation between α-C of Gly and the aromatic moiety was achieved by proton-catalyzed intramolecular electrophilic aromatic substitution. The absolute configuration of the dipeptide templates was determined by single-crystal X-ray crystallography or by nuclear Overhauser enhancement measurements. A protective group strategy was elaborated to allow their incorporation into peptide sequences by liquid phase as well as by solid-phase peptide synthesis. The templates w…
Conformational investigation of α,β-dehydropeptides. IX. N-Acetyl-(E)-α,β-dehydrobutyrine N′-methylamide: stereoelectronic properties from infrared a…
2009
The Fourier transform infrared spectra of Ac-(E)-deltaAbu-NHMe were analyzed to determine the predominant solution conformation(s) of this (E)-alpha,beta-dehydropeptide-related compound and the electron density perturbation in its amide groups. The measurements were performed in dichloromethane and acetonitrile in the region of mode vs (N-H), amide I, amide II and vs (C(alpha)=Cbeta). The equilibrium geometrical parameters, calculated by a method based on the density functional theory with the B3LYP functional and the 6-31G* basis set, were used to support spectroscopic interpretation and gain some deeper insight into the molecule. The experimental and theoretical data were compared with th…
Complexation of C-methyl pyrogallarene with small quaternary and tertiary alkyl ammonium cations
2007
Complexation properties of pyrogallarene 1 towards small quaternary and tertiary alkyl ammonium cations were studied in gas phase, solution and in solid state. In gas phase both dimeric capsules and monomeric 1 : 1 complexes of all cations 2a+–d+ are detected but only in the case of 2a+ is the abundance of the capsule form higher than the monomeric 1 : 1 complex. A similar trend is observed in NMR experiments, which reveal a favourable dimeric complex for 2a+ and a weaker dimeric complex for 2b+ but only monomeric complexes for 2c+ and 2d+. Also in solid state, 2a+ and 2b+ form capsules when crystallized from MeOH while 2c+ and 2d+ form dimeric 1 : 1 complexes. As a reference, hetero-confor…
Sequence of a new tRNALeu(U∗AA) from brewer's yeast
1991
The nucleotide sequence of a new tRNA(Leu)(anticodon U*AA) from Saccharomyces cerevisiae which could recognize exclusively the UUA codon has been determined. Its primary structure is: pGGAGGGUUGm2GCac4CGAGDGmGDCDAAGGCm2(2)GGCAGACmUU*AAm1GA++ + psi CUGUUGGACGGUUGUCCGm5CGCGAGT psi CGm1A(orA)ACCUCGCAUCCUUCACCA. This tRNA has a large extraloop and contains 15 modified nucleotides. So far it is the third isoacceptor tRNA for leucine in yeast. It has 61% homology with tRNA(Leu)(anticodon m5CAA) and 63% homology with tRNA(Leu)(anticodon UAG), the two other known yeast tRNAs(Leu).
Ferrocenyl-Labeled Sugar Amino Acids: Conformation and Properties
2012
Novel organometallic sugar amino acid conjugates 1–5 have been prepared by amide coupling of O-protected N-acetylmuramic acid and iso-muramic acid (2-[3-amino-2, 5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxypropanoic acid) with 1-aminoferrocene, 1-aminoferrocene-1′-carboxylic acid (H-Fca-OH), or 1, 1′-diaminoferrocene, respectively. The influence of the ferrocenyl moiety and presence of additional remote potential hydrogen atom acceptors and donors at the ferrocenyl core on the conformation and lipophilicity is investigated by TLC, IR, NMR, and CD spectroscopic methods augmented by density functional calculations. Furthermore, the redox potential of the ferrocene/ferrocenium couple is tuned by…
Association of model peptides and dehydropeptides: N-acetyl-l-alanine- and dehydroalanine N′,N′-dimethylamides
2005
Abstract The comparative studies on the association of Ac-ΔAla-NMe 2 and Ac- l -Ala-NMe 2 in carbon tetrachloride were performed by the analysis of their average molecular weight, dipole moments and FTIR spectra. To aid spectroscopic interpretation and gain some deeper insight into the nature of associates, the geometries of the minimum energy of the dimers of Ac-ΔAla-NMe 2 and Ac- l -Ala-NMe 2 were calculated by the B3LYP/6-31+G** method. The average molecular weight in the studied concentration range, for the ΔAla and l -Ala peptide, as determined by the osmometric method, did not exceed 1.5 and 1.2 of the monomeric mass, respectively. Accordingly, the percentage of the monomeric form (α)…