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At least 685 records · Page 38Linked to original sources
PubMed2006

Diproline templates as folding nuclei in designed peptides. Conformational analysis of synthetic peptide helices containing amino terminal Pro-Pro segments.

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (alphaR) conformation for the segment residues 2 to 5, stabilized by one 4-->1 hydrogen bond and two 5-->1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P(II)) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alphaR-alphaR conformation, whereas in the latter, a P(II)-alphaR structure is established. The conformational equilibrium shifts in favor of the P(II)-alphaR structure in solvents like methanol and DMSO. A significant population of the Pro(1)-Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro-Pro segment: trans alphaR-alphaR, trans P(II)-alphaR and cis P(II)-alphaR. Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alphaR-alphaR conformation followed by a helix. Modeling and energy minimization studies suggest that both P(II)-alphaR and alphaR-alphaR conformations have very similar energies in the model hexapeptide 1.

Base Sequence↗
PubMed1992

Conformational analysis of a dinucleotide photodimer with the aid of the genetic algorithm.

The solution structure of the photodimer cis,syn-dUp[]dT is derived with the aid of the genetic algorithm. The conformational space available for the molecule is sampled efficiently using the computer program DENISE and tested against a set of constraints available from nmr experiments. The dominant conformation in solution found with this approach can be described by the following combinations of sugar-phosphate backbone torsion angles: epsilon(t), zeta(t), alpha(+), beta(-ac), and gamma(t). The conformation of the sugars and glycosidic torsion angles are S type and syn, respectively. The cyclobutane ring and pyrimidines are puckered. In addition, other conformations that exist in equilibrium with the first are found. It is concluded that the cyclobutane-pyrimidine system is rigid, whereas the sugar-phosphate backbone is flexible. The solution structures are compared with the crystal structure of the strongly related cyano-ethyl ester of cis,syn-dTp[]dT.

Algorithms↗
PubMed1997

Selective multiple labeling strategy to obtain accurate NMR parameters for nucleic acids. Conformational analysis around the glycosidic bond.

A systematic synthesis of pyrimidine nucleosides with 13C-labels only at specific atoms in both the base and sugar moieties has been developed in order to obtain conformational information about the glycosidic bond through measurement of the accurate vicinal coupling constants between H1' and C2/C6. For this purpose, 13C labels at three positions, namely C1', C2, and C6, are essential. We have synthesized selectively multiply labeled nucleosides, such as [2, 1'-13C2]-thymidine, [2, 1'-13C2]-2'-deoxycytidine, [6, 1'-13C2]-thymidine, and [6, 1'-13C2]-2'-deoxycytidine. These nucleosides will be useful to determine the relative orientation of the base and sugar moieties.

Carbon Isotopes↗
PubMedDate not supplied

[Theoretical conformational analysis of a encephalitogenic peptide molecule and a study of the structure-activity relationship in a series of its analogs].

Semi-empirical energy calculations are used to determine all low-energy conformations of Trp-containing fragment 113-121 of myelin basic protein (experimental allergic encephalomyelitis inducing peptide). The computed conformations are compared with the results of physico-chemical experiments and data on biological testing of the encephalitogenic peptide analogs. The three computed structures are shown to be in a good agreement with the available experimental evidence. However, additional information is required to predict "biologically active" conformation of encephalitogenic peptide.

Animals↗
PubMed1989

Conformational analysis of d(C3G3), a B-family duplex in solution.

NMR and circular dichroism studies of the duplex formed by the self-complementary DNA hexanucleotide d(C3G3) indicate that it is a B-type structure but differs from standard B-form. An analysis of NMR coupling constants within the deoxyribose moieties yields a 70% or greater contribution from pseudorotation phase angles corresponding to the C3'-exo conformation, a conformation similar to the C2'-endo conformation associated with B-form DNA. Intranucleotide interproton distances are consistent with a B-form structure, but some internucleotide distances are intermediate between A- and B-form structures. Circular dichroism spectra have B-form characteristics but also include an unusual negative band at 282 nm. The solution spectroscopic results are in contrast with X-ray crystallographic studies which find A-form structures for similar sequences.

Circular Dichroism↗
PubMed1999

New strategy for the conformational analysis of carbohydrates based on NOE and 13C NMR coupling constants. Application to the flexible polysaccharide of Streptococcus mitis J22.

For complex oligosaccharides, which are relatively rigid with modest excursions from a single minimum energy conformation, it is straightforward to build conformational models from NOE data. Other oligosaccharides are more flexible with transitions between distinct minima separated by substantial energy barriers. We show that modeling based on scalar coupling data is superior to NOE-based modeling for the latter case. Long range 13C-13C and 13C-1H coupling constants measured for the heptasaccharide repeating subunit of the cell wall polysaccharide from Streptococcus mitis J22 are correlated with individual glycosidic dihedral angles, effectively uncoupling the degrees of freedom of the oligosaccharide and allowing a search for combinations of dihedral angles which are energetically reasonable, i.e., with no bad van der Waals contacts, and which can be combined to satisfy all the measured J values. Allowed values of the individual angles can then be combined to search for overall oligosaccharide conformations which contribute to the ensemble. We show that while the polysaccharide from S. mitis J22 is flexible, requiring multiple conformations, most of the flexibility is localized to a few bonds and only a rather small number of conformations is required to reproduce the experimental NOE and scalar coupling data.

Carbohydrate Conformation↗
PubMed1999

Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformational analysis and NMR spectroscopy--application to DNS1-c-[D-A2,bu2,Trp4,Leu5]enkephalin and DNS1-c-[D-A2bu2,Trp4,D-Leu5]enkephalin.

A method is proposed to determine the conformational equilibrium of flexible polypeptides in solution, using the data provided by NMR spectroscopy and theoretical conformational calculations. The algorithm consists of the following three steps: (i) search of the conformational space in order to find conformations with reasonably low energy; (ii) simulation of the NOE spectrum and vicinal coupling constants for each of the low energy conformations; and (iii) determining the statistical weights of the conformations, by means of the maximum-entropy method, in order to obtain the best fit of the averaged NOE intensities and coupling constants to the experimental quantities. The method has been applied to two cyclic enkephalin analogs: DNS1-c-[D-A2bu2,Trp4,Leu5]enkephalin (ENKL) and DNS1-c-[D-A2bu2,Trp4,D-Leu5]enkephalin (ENKD). NMR measurements were carried out in deuterated dimethyl sulfoxide. Two techniques were used in conformational search: the electrostatically driven Monte Carlo method (EDMC), which results in extensive search of the conformational space, but gives only energy minima, and the molecular dynamics method (MD), which results in a more accurate, but also more confined search. In the case of EDMC calculations, conformational energy was evaluated using the ECEPP/3 force field augmented with the SRFOPT solvation-shell model, while in the case of MD the AMBER force field was used with explicit solvent molecules. Both searches and subsequent fitting of conformational weights to NMR data resulted in similar conformations of the cyclic part of the peptides studied. For both ENKL and ENKD a common feature of the low-energy solution conformations is the presence of a type II' or type IV beta-turn at residues 3 and 4; the ECEPP/3 force field also gives a remarkable content of type III beta-turn. These beta-turns are tighter in the case of ENKL, which is reflected in different distributions of the D-A2bu(N gamma H)...D-A2bu(CO) and D-A2bu(N gamma H)...Gly3(CO) hydrogen-bonding distances, indicating that the D-A2bu(N gamma H) amide proton is more shielded from the solvent than in the case of ENKD. This finding conforms with the results of temperature coefficient data of the D-A2bu(N gamma H) proton. It has also been found that direct (MD) or Boltzmann (EDMC) averages of the observables do not exactly conform with the measured values, even when explicit solvent molecules are included. This suggests that improving force-field parameters might be necessary in order to obtain reliable conformational ensembles in computer simulations, without the aid of experimental data.

Algorithms↗