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At least 613 records · Page 34Linked to original sources
PubMed2001

The single strand conformational analysis of cattle and human single nucleotide polymorphisms may be biased towards specific sequence motifs that minimize local secondary structure of single strand DNA.

Single strand conformational polymorphisms (SSCP) resulting from point mutations were found to be associated preferentially with two DNA sequence motifs. These motifs are (1) three or more of the same base but in which the polymorphism is not due to length variation and (2) a region of polypurine or polypyrimidine bases. These motifs were identified after SSCP alleles from cattle were sequenced. The sequence difference and flanking sequence for each single nucleotide polymorphism are shown. The motifs were also found in SSCP from humans chosen at random from the literature, in which the alleles had been sequenced. There is a low level of complementarity of adjacent bases in these motifs and they should represent regions of low secondary structure in the single stranded DNA. Regions of high secondary structure, such as palindromes, were found in the same sample to have allelic variation that was not detected by SSC analysis. These results give a rule of thumb for selecting the particular part of a DNA fragment to be selected for testing for polymorphisms, but this rule clashes with rules used to design primers to amplify sequences using the PCR, namely, minimise hydrogen bonding within and between primers and reduce self-complementarity.

Alleles↗
PubMed2003

Conformational analysis of furanoid epsilon-sugar amino acid containing cyclic peptides by NMR spectroscopy, molecular dynamics simulation, and X-ray crystallography: evidence for a novel turn structure.

Sugar amino acids (SAAs) are useful building blocks for the design of peptidomimetics and peptide scaffolds. The three-dimensional structures of cyclic hybrid molecules containing the furanoid epsilon-SAA III and several amino acids were elucidated to study the preferred conformation of such an epsilon-SAA and its conformational influence on the backbone of cyclic peptides. NMR-based molecular dynamics simulations and empirical calculations of the cyclic tetramer 1, consisting of two copies of the SAA residue and two amino acids, revealed that it is conformationally restrained. The two SAA residues adopt different conformations. One of them forms an unusual turn, stabilized by an intraresidue nine-member hydrogen bond. The methylene functionalities of the other SAA residue are positioned in such a way that an intraresidue H bond is not possible. The X-ray crystal structure of 1 strongly resembles the solution conformation. Molecular dynamics calculations in combination with NMR analysis were also performed for compounds 2 and 3, which contain the RGD (Arg-Gly-Asp) consensus sequence and were previously shown to inhibit alpha(IIb)beta(3)-receptor-mediated platelet aggregation. The biologically most active compound 2 adopts a preferred conformation with the single SAA residue folded into the nine-member H bond-containing turn. Compound 3, containing an additional valine residue, as compared with compound 2, is conformational flexible. Our studies demonstrate that the furanoid epsilon-SAA III is able to introduce an unusual intraresidue hydrogen bond-stabilized beta-turn-like conformation in two of the three cyclic structures.

Amino Acids↗
PubMed1989

The influence of the side-chain sequence on the structure-activity correlations of immunomodulatory branched polypeptides. Synthesis and conformational analysis of new model polypeptides.

New branched polypeptides were synthesized for a detailed study of the influence of the side-chain structure on the conformation and biological properties. The first subset of polypeptides were prepared by coupling of tetrapeptides to poly[L-Lys]. These polymers contain either DL-Ala3-X [poly[Lys-(X-DL-Ala3)n]] or X-DL-Ala3 [poly[Lys-(DL-Ala3-X)n] (n less than or equal to 1)] tetrapeptide side chains. Another group of branched polymers comprise a mixture of DL-Alam and of DL-Alam-X oligomeric branches in a random distribution [poly[Lys-(DL-Alam-Xi)] (i less than 1, m approximately 3)]. In each subset the X = Leu or Phe derivatives were prepared. The N-protected tetrapeptides were synthesized by conventional liquid phase methods and were coupled as active esters. The degree of racemization was found relatively high both for active esters and coupled derivatives, when optically active amino acids were in the C-terminal position of the tetrapeptides. In the case of the poly[Lys-(Leu-DL-Ala3)n] derivative, comparative experiments were carried out using various methodical alterations. The highest stereochemical homogeniety could be achieved when the tetrapeptide active ester was synthesized by the "backing off" method. CD spectra of poly[Lys-(Xi-DL-Alam)] (i less than 1, m approximately 3) and of poly[Lys-(X-DL-Ala3)n] were analyzed and compared to those of poly[Lys-(DL-Alam-Xi)] and of poly[Lys-(DL-Ala3-X)n]. All measurements were performed in water solutions of varying pH values and ionic strengths. The data obtained suggest that branched polypeptides containing a mixture of two different types of oligomeric side chains (DL-Alam and DL-Alam-Xi or Xi-DL-Alam) distributed randomly adopt an almost identical conformation to those that comprise only the respective tetrapeptide (DL-Ala3-X or X-DL-Ala3) branches. The results also indicate that the tendency to form an ordered structure is determined by the identity and the position of the chiral amino acid X (Phe or Leu) in the side chain.

Adjuvants, Immunologic↗
PubMed2004

Conformation analysis and molecular mobility of ethylene and tetrafluoroethylene copolymer using solid-state 19F MAS and 1H --> 19F CP/MAS NMR spectroscopy.

The changes in the conformation and molecular mobility accompanied by a phase transition in the crystalline domain were analyzed for ethylene (E) and tetrafluoroethylene (TFE) copolymer, ETFE, using variable-temperature (VT) solid-state 19F magic angle spinning (MAS) and 1H --> 19F cross-polarization (CP)/MAS NMR spectroscopy. The shifts of the signals for fluorines in TFE units to higher frequency and the continuing decrease and increase in the T1rho(F) values suggest that conformational exchange motions exist in the crystalline domain between 42 and 145 degrees C. Quantum chemical calculations of magnetic shielding constants showed that the high-frequency shift of TFE units should be induced by trans to gauche conformational changes at the CH2-CF2 linkage in the E-TFE unit. Although the 19F signals of the crystalline domain are substantially overlapped with those of the amorphous domain at ambient probe temperature (68 degrees C), they were successfully distinguished by using the dipolar filter and spin-lock pulse sequences at 145 degrees C. The dipolar coupling constants for the crystalline domain, which can be estimated by fitting the dipolar oscillation behaviors in the 1H --> 19F CP curve, showed a significant decrease with increasing temperature from 42 to 145 degrees C. This is due to the averaging of 1H-19F dipolar interactions originating from the molecular motion in the crystalline domain. The increase in molecular mobility in the crystalline domain was clearly shown by VT T1rho(F) and 1H --> 19F CP measurements in the phase transition temperature range.

Algorithms↗
PubMed2001

Evaluation of NMR diffusion measurements for the conformational analysis of flexible peptides.

The use of diffusion coefficients measured with pulsed-field gradient NMR spectroscopy for the determination of the relative population of conformers in solutions of the human Growth Hormone peptide fragment, hGH(9-19), has been studied in aqueous and in trifluoroethanol (TFE)/ water solutions. The peptide is a good model compound for this study because it adopts a predominantly random coil conformation in aqueous solution and is helical in TFE. The results of the diffusion measurements suggest that the peptide exhibits predominantly random coil structures in aqueous solution and adopts a more helical conformation in solutions containing increasing mole fractions of TFE, consistent with the qualitative findings of the standard CD and NMR experiments to probe peptide conformation. These results indicate that diffusion coefficients measured with NMR can provide additional information about temperature- and solvent-induced changes in the extent of the helical conformer for hGH(9-19) in aqueous solution and in solutions containing various mole fraction of TFE, respectively.

Amino Acid Sequence↗
PubMed2000

Conformational analysis of endothelin-1 analogs with indolizidinone amino acids incorporated at the C-terminus.

In light of the fact that a beta-turn conformation at the C-terminus of endothelin-1 (ET-1) could be responsible for activity at the ET(B) receptor, the incorporation of (3S, 6S, 9S)-2-oxo-3-amino-1-azabicyclo[4.3.0]nonane-9-carboxylic acid (IAA) should provide an elegant method to establish whether a formyl group on Trp21 plays a role in stabilizing a beta-turn. Eight linear ET-1 analogs, four formylated and four nonformylated, ET-1-(Leu17-Asp18-IAA-Trp21); ET-1-(Leu17-IAA-Ile20-Trp21); ET-1-(Leu17-Asp18-Pro19-Ile20-Trp21) and ET-1-(Leu17-Asp 8-Ile19-Pro20-Trp21) have been analyzed by high-resolution nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Two-dimensional double quantum filtered correlation spectroscopy (DQFCOSY), total correlation spectroscopy (TOCSY) and nuclear Overhausen enhancement spectroscopy (NOESY) were resolved and analyzed for each molecule. Interspatial distance constraints were derived from the intensity of the NOESY connectivities, The formation of hydrogen bonding was monitored from the temperature-dependence of the NH chemical shifts. Molecular models calculated by means of distance geometry, simulated annealing and energy minimization, suggested a global elongated structure for the formylated analogs and a folded arrangement for the nonformylated derivatives, but no hydrogen bonding was detected at the C-terminus of ET-1 analogs.

Endothelin-1↗
PubMed1992

Conformational analysis of the melanin-concentrating hormone core by circular dichroic spectroscopy. Disulphide bridge and tyrosine contributions.

A detailed circular dichroic (CD) study of the conformational flexibility of the melanin-concentrating hormone core [MCH(5-14)] is reported. Variable pH (2-10) and temperature (-80 degrees to +80 degrees C) in aqueous media reveal that CD contributions from tyrosine, disulphide bridge and the amide backbone can be discriminated. Only below -10 degrees C does a preferred -S-S-conformation (P chirality, dihedral angle phi = 90 +/- 10 degrees) dominate. The amide backbone CD contribution varies over all temperatures (-80 degrees to +80 degrees C) providing evidence for a type-II beta-turn at low temperatures, with the emergence of a type-I beta-turn at higher temperatures. Tyrosine exhibits a special behaviour at pH 7. These conclusions are in broad agreement with published NMR studies. Nevertheless, the MCH(5-14) core is seen to be conformationally flexible in aqueous solution at ambient temperatures. Conformation differences are observed in a non-aqueous environment.

Amino Acid Sequence↗
PubMed2003

Synthesis, conformational analysis and free radical scavenging activity of some new spiropyranoquinolinones.

A series of novel spiroadamantyl- and spirocyclical substituted pyranoquinolin-2-ones were synthesized and the conformation of the pyran ring was investigated. The free radical scavenging activity of the synthesized compounds was determined by their interaction with the stable free radical 1,1-diphenyl-2-picrylhydrazyl (DPPH). All compounds tested scavenged the DPPH radical and among them derivatives possessing extended conjugation showed the highest activity.

Biphenyl Compounds↗
PubMedDate not supplied

[Theoretical conformational analysis of tripeptides. N-acetyl-L-alanyl-L-alanyl-L-alanyl methylamide].

The minimization procedure has been used for calculation of the local minimum conformations of threepeptide--Ac-(L-Ala)3-NHMe without intramolecular H-bonds. The significant energy deviations from additivity found, arising with increase backbone length to three links, can be considered as the evidence for mutual dependence of conformational states of the neighbouring and terminal amino acid residues. It have been shown that stability of alpha-helix form for alanine threepeptide in contrary to corresponding dipeptide is noticeably higher due to stabilizing effect of dispersion interactions. The results of calculations are compared with the data on conformational distrubution of the threepeptide fragments in proteins with known three dimensional structure. The important role of the backbone interaction in protein chain have been marked.

Alanine↗
PubMed2000

Conformational analysis of the Sd(a) determinant-containing tetrasaccharide and two mimics in aqueous solution by using 1H NMR ROESY spectroscopy in combination with MD simulations.

The conformational behaviour of the spacer-linked synthetic Sd(a) tetrasaccharide beta-D-GalpNAc-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)- beta-D-GlcpNAc-(1-->O)(CH2)5NH2 (1) and the two mimics beta-D-Galp-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)-bet a-D-GlcpNAc-(1-->O)(CH2)5NH2 (2) and beta-D-GlcpNAc-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)- beta-D-GlcpNAc-(1-->O)(CH2)5NH2 (3) were investigated by 1H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 1H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the beta-D-Hex(NAc)-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp fragments. The alpha-Neu5-Ac-(2-->3)-beta-D-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.

Carbohydrate Conformation↗
PubMed2004

Insight into the mechanism of internalization of the cell-penetrating carrier peptide Pep-1 through conformational analysis.

Recently, we described a new strategy for the delivery of proteins and peptides into mammalian cells, based on an amphipathic peptide of 21 residues, Pep-1, which was designed on the basis of a protein-interacting domain associated with a nuclear localization sequence and separated by a linker. This peptide carrier constitutes a powerful tool for the delivery of active proteins or peptides both in cultured cells and in vivo, without requiring any covalent coupling. We have examined the conformational states of Pep-1 in its free form and complexed with a cargo peptide and have investigated their ability to interact with phospholipids and the structural consequences of these interactions. From the conformational point of view, Pep-1 behaves significantly differently from other similarly designed cell-penetrating peptides. CD analysis revealed a transition from a nonstructured to a helical conformation upon increase of the concentration. Determination of the structure by NMR showed that in water, its alpha-helical domain extends from residues 4-13. CD and FTIR indicate that Pep-1 adopts a helical conformation in the presence of phospholipids. Adsorption measurements performed at the air-water interface are consistent with the helical form. Pep-1 does not undergo conformational changes upon formation of a particle with a cargo peptide. In contrast, we observe a partial conformational transition when the complex encounters phospholipids. We propose that the membrane crossing process involves formation of a transient transmembrane pore-like structure. Conformational change of Pep-1 is not associated with complexation with its cargo but is induced upon association with the cell membrane.

Air↗
PubMed1998

Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods.

Barnase, an extracellular endoribonuclease from Bacillus amyloliquefaciens, hydrolyses single-stranded RNA. Its very low catalytic activity toward GpN dinucleotides, where N stands for any nucleoside, is markedly increased when a phosphate is added to the 3'-end, as in GpNp. Here we investigate the conformational properties of GpA and GpAp in solution, in order to determine whether differences in these properties may be related to the changes in enzymatic activity. Two independent 1.3 ns molecular dynamics trajectories are generated for each dinucleotide in the presence of explicit water molecules and counter ions. These trajectories are analysed by monitoring molecular properties, such as the solvent accessible surface area, the distance and orientation between the bases, the behaviour of torsion angles and formation of intramolecular H-bonds. To identify relevant correlations between these parameters, statistical techniques, comprising multiple regression, clustering and discriminant analysis are used. Results show that GpA has a significant propensity to form folded conformations (approximately 50%), fostered by a small number of intramolecular H-bonds, whereas GpAp remains essentially extended. The latter behaviour seems to be due to an H-bond between the terminal phosphate and adenosine ribose group, which restricts rotation about the adenine Agamma angle. We also find that GpA folding is induced by a concerted motion of specific torsion angles, which is closely coupled to the formation of a network of flexible hydrogen bonds. Finally, on the basis of an expression for barnase KM, which incorporates the folded/extended conformational equilibria of the dinucleotide substrates, it is argued that our findings on the differences between these equilibria, can qualitatively rationalize the experimentally measured differences in enzymatic properties.

Bacterial Proteins↗
PubMed1994

Conformational analysis of a 139 base-pair DNA fragment containing a single-stranded break and its interaction with human poly(ADP-ribose) polymerase.

The conformational changes induced by the introduction of a central and unique single-stranded break in a 139 base-pair DNA duplex have been analysed by means of polyacrylamide gel electrophoresis, HPLC and dark-field electron microscopy. Compared to the control DNA, the disruption of the covalent sugar-phosphate backbone induces a retardation detected both by gel electrophoresis and anion exchange based HPLC. Electron microscopic visualization of the DNA molecules reveals that most of them present a central fracture at the position of the nick. Measures of the angle at the apex were very well fitted by a simple model of isotropic flexible junction assuming spatial Hooke's law and simple basic Boltzmann statistics. This amounts to using a folded Gaussian distribution. The fit yields an angle equilibrium value phi 0 = 122 degrees for the nicked fragment. The angle distribution could also result from an equilibrium between two forms of the molecule with isotropic flexibility at the nicked site: a stacked and a very flexible unstacked form. The majority of bound poly(ADP-ribose) polymerase, a zinc-finger enzyme involved in DNA break detection, was localized at the apex of the V-shaped DNA duplex, with an accentuation of its general V-shaped conformation (phi 0 = 102 degrees).

Base Sequence↗
PubMed1980

Conformational analysis of nucleoside and nucleotide antibiotics prossessing five-membered base rings. A comparison of the glycosyl barrier for purine, pyrimidine and imidazole rings.

The preferred conformations of the nucleosides comprising five-membered base rings viz., ribavirin, tetrazole, showdomycin and pyrazomycin and their 5'-nucleoside monophosphates have been explored by semiempirical potential energy calculations. The nature of the substituents on the five-membered base ring has been found to influence significantly the favoured glycosyl conformation and the hydrogen bonding between the base and the sugar. In the absence of any such hydrogen bonding, the imidazole nucleosides expectedly exhibit nearly 'free' rotation around the glycosyl bond for the commonly found C(3') endo and C(2') endo sugar ring conformations, thus increasing the probability of anti in equilibrium high-anti in equilibrium syn conformational interconversions as compared to common purine and pyrimidine nucleosides. However, the C(2') exo pucker imparts a high-energy barrier to glycosyl rotation, locking the base in the high-anti region. The conformation behaviour is significantly modified in the nucleoside 5'-monophosphates. The additional attractive interactions between the carboxamide and the phosphate groups favour the syn glycosyl conformation in the 5'-monophosphates of ribavirin as well as pyrazomycin smaller to guanosine 5'-monophosphate whereas the anti conformation is strongly favoured for the 5'-nucleotides of tetrazole and showdomycin similar to other common purine and pyrimidine nucleotides. The conformational properties of five-membered base ring nucleosides have a strong resemblance to purine nucleosides. Molecular modelling studies reveal that only the anti or high anti-glycosyl conformations of ribavirin can mimic the inosine base. It is suggested that experiments on the configurational isomers of ribavirin, viz., aravirin and cycloaravirin would conclusively establish the conformational specificity and biological function of ribavirin and analogues.

Amides↗