CADB: Conformation Angles DataBase of proteins

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/.     

The Genome Sequence DataBase (GSDB): meeting the challenge of genomic sequencing.

The genome sequence database (GSDB) is a complete, publicly available relational database of DNA sequences and annotation maintained by the National Center for Genome Resources (NCGR) under a Cooperative Agreement with the US Department of Energy (DOE). GSDB provides direct, client- server access to the database for data contributions, community annotation and SQL queries. The GSDB Annotator, a multi-platform graphic user interface, is freely available. Automatically updated relational replicates of GSDB are also freely available.     

The genome sequence DataBase

The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information. Several notable changes have occurred in the past year: GSDB stopped accepting data submissions from researchers; ownership of data submitted to GSDB was transferred to GenBank; sequence analysis capabilities were expanded to include Smith-Waterman and Frame Search; and Sequence Viewer became available to Mac users. The content of GSDB remains up-to-date because publicly available data is acquired from the International Nucleotide Sequence Database Collaboration databases (IC) on a nightly basis. This allows GSDB to continue providing researchers with the ability to analyze, query and retrieve nucleotide sequences in the database. GSDB and its related tools are freely accessible from the URL: http://www.ncgr.org     

Conformational Transitions in Poly d(CGCGCGTTAATT)

Abstract

Conformational studies on poly d(CGCGCGTTAATT) in solution by circular dichroism spectroscopy are reported. The polynucleotide exhibits B conformation in sodium chloride solution and on addition of NiCl₂ a B-Z transition is observed. NiCl₂ titrations carried out in the presence of 5M NaCl show a midpoint of transition at 2.25 mM NiCl₂ and a complete (maximum conversion to Z form) transition at 16 mM NiCl₂. In 60% alcohol the polynucleotide remains in B conformation. The polynucleotide isomerizes into ψ and A conformations in the presence of spermidine and spermine respectively. The thermodynamic parameters calculated from the melting profiles using a two state model show that the polynucleotide is almost equally stable in its B and Z conformations.     

The Genome Sequence DataBase (GSDB): improving data quality and data access.

In 1997 the primary focus of the Genome Sequence DataBase (GSDB; www. ncgr.org/gsdb ) located at the National Center for Genome Resources was to improve data quality and accessibility. Efforts to increase the quality of data within the database included two major projects; one to identify and remove all vector contamination from sequences in the database and one to create premier sequence sets (including both alignments and discontiguous sequences). Data accessibility was improved during the course of the last year in several ways. First, a graphical database sequence viewer was made available to researchers. Second, an update process was implemented for the web-based query tool, Maestro. Third, a web-based tool, Excerpt, was developed to retrieve selected regions of any sequence in the database. And lastly, a GSDB flatfile that contains annotation unique to GSDB (e.g., sequence analysis and alignment data) was developed. Additionally, the GSDB web site provides a tool for the detection of matrix attachment regions (MARs), which can be used to identify regions of high coding potential. The ultimate goal of this work is to make GSDB a more useful resource for genomic comparison studies and gene level studies by improving data quality and by providing data access capabilities that are consistent with the needs of both types of studies.     

Conformational Studies of Nucleic Acids: III. Empirical Multiple Correlation Functions for Nucleic Acid Torsion Angles

Abstract

There are seven significantly variable torsion angles in each monomer unit of a polynucleotide. Because of this, it is computationally infeasible to consider the energetics of all conformations available to a nucleic acid without the use of simplifications. In this paper, we develop functions suggested by and regression fit to crystallographic data which allow three of these torsion angles, α (03′-P-05′-C5′), δ (C5′-C4′-C3′-03′) and ε (C4′-C3′-03′-P), to be calculated as dependent variables of those remaining. Using these functions, the seven independent torsions are reduced to four, a reduction in complexity sufficient to allow an examination of the global conformational energetics of a nucleic acid for the remaining independent torsion angles. These functions are the first to quantitatively relate a dependent nucleic acid torsion angle to several different independent angles. In all three cases the data are fit reasonably well, and in one case, α, the fit is exceptionally good, lending support for the suitability of the functions in conformational searches. In addition, an examination of the most significant terms in each of the correlation functions allows insight into the physical basis for the correlations.     

Conformational study of asialo-GM1 (GA1) ganglioside

In order to investigate the significance of preferred conformations of the saccharide for the steric orientation and recognition of glycosphingolipids at the membrane surface, the conformational free energy calculations were carried out on the asialo-GM1 [GA1; β-D -Gal(1 → 3) β-D -GalNAc(1 → 4) β-D -Gal(1 → 4) β-D -Glc-O-ceramide] using a new program CONCARB (CONformational study program for CARBohydrate) in the unhydrated and hydrated states. The overall backbone conformation of GA1 appears nearly to be extended with a little bent at the glycosidic II–III linkage, in which two pyranose rings of Gal(IV)-GalNAc-(III) moiety orient approximately perpendicular to those of Gal(II)-Glc(I) moiety. This is consistent with the structures deduced from high-sensitivity differential scanning calorimetry experiments and the nmr study on GA1. The calculated glycosidic torsion angles of the lowest free energy conformation of GA1 in the hydrated state are in accord with the structures of relevant oligosaccharides deduced from nmr experiments and hard sphere exoanomeric calculations. A comparison of the values of glycosidic torsion angles ϕ and π of GA1 and its constituent oligosaccharides indicates that the overall backbone conformation of each oligosaccharide is retained when the oligosaccharide chain becomes longer. This implies that the short-range interactions between the nearest-neighbored saccharides are of significant importance in stabilizing the overall backbone conformation of GA1 in both the unhydrated and hydrated states. The different orientation and hydrogen bonds of hydroxymethyl and hydroxyl groups from one oligosaccharide to another suggest that the medium- and long-range interactions are also of consequence. Hydration seems to affect significantly the conformation of these groups, but not to perturb remarkably the overall backbone conformation of GA1. © 1997 John Wiley & Sons, Inc. Biopoly 42: 19–35, 1997     

Conformational change of the L-shaped tRNA(Phe) molecule

Fluorophore of proflavine was introduced onto the 3'-terminal ribose moiety of yeast tRNA(Phe). The distance between the fluorophore and the fluorescent Y base in the anticodon of yeast tRNA(Phe) was measured by a singlet-singlet energy transfer. Conformational changes of tRNA(Phe) with binding of tRNA(2Glu), which has the anticodon UUC complementary to the anticodon GAA of tRNA(Phe), were investigated. The distance obtained at the ionic strength of 100 mM K+ and 10 mM Mg2+ is very close to the distance from x-ray diffraction, while the distance obtained in the presence of tRNA(2Glu) is significantly smaller. Further, using a fluorescent probe of 4-bromomethyl-7-methoxycoumarin introduced onto pseudouridine residue psi 55 in the T psi C loop of tRNA(Phe), Stern-Volmer quenching experiments for the probe with or without added tRNA(2Glu) were carried out. The results showed greater access of the probe to the quencher with added tRNA(2Glu). These results suggest that both arms of the L-shaped tRNA structure tend to bend inside with binding of tRNA(2Glu) and some structural collapse occurs at the corner of the L-shaped structure.     

Conformational fluctuation in palladium(II)-methyl aldopentopyranoside complexes

Four methyl d-pentopyranosides (β-Ara, α-Lyx, β-Rib, β-Xyl), as well as Me-β-l-Ara, some of them residing in a well-defined conformation in the solution state (Ara, Xyl) and some showing pronounced chair inversion in solution (Lyx, Rib), form bidentate chelates of the general formula [Pd(chxn)(LH₋₂)-κO,O′] and [Pd(tmen)(LH₋₂)-κO,O′], chxn = (R,R)-cyclohexane-1,2-diamine, tmen = N,N,N′,N′-ethane-1,2-diamine and L = glycoside, with Pd^IIN₂-type metal probes. The dynamic behaviour of the free glycosides is maintained in their chelates, the only case where the metal is bonded by a cis-vicinal diol function. Thus, one fluctuating chelate was detected with the lyxopyranoside in the κO^2,3 binding mode, and two fluctuating chelates were found for the ribopyranoside (κO^2,3 and κO^3,4). No fluctuating chelate was found for the arabinopyranoside (the free arabinopyranoside being non-fluctuating as well), or for the xylopyranoside (no cis-vicinal diol function). In addition, syn-diaxial chelation (κO^2,4) was observed for the ribopyranoside and the xylopyranoside. The spectroscopic results were supplemented by X-ray analyses.     

Conformational transitions of poly(dA-dT)poly(dA-dT) in ethanolic solutions.

Examination of circular dichroic and phosphorus nuclear magnetic resonance spectra showed that poly(dA-dT)-poly(dA-dT) exhibited an ethanol-induced transition to the A form in an Na+ containing medium like natural DNAs. A mere replacement of the Na+ by Cs+ counterions meant that the polynucleotide was with a little cooperativity transformed into a novel conformation displaying a deep negative band in the long wavelength part of the CD spectrum. The presence of very low concentration of Cs2+ shifted the midpoint of the transition to a lower content of ethanol.     

Conformational study of N(epsilon)-(carboxymethyl)lysine adducts of recombinant gammaC-crystallin

N -(carboxymethyl)lysine, an advanced glycation end product, is present in the human lens. The effects of CML formation on protein conformation and stability were studied using the recombinant C-crystallin as a model. Conformational change was studied by spectroscopic measurements such as fluorescence and circular dichroism. Conformational stability was determined by unfolding with heat. The results indicated that no conformational change was observed due to CML formation, but conformational stability decreased. These observations can be explained in terms of the relatively stable structure of -crystallin, especially when compared with other crystallins. The lens nucleus is rich in -crystallin and its stable conformation can assist -crystallin sustained insults and remain soluble.     

Conformational properties of DNA containing (CCA)n and (TGG)n trinucleotide repeats

We have used CD spectroscopy, polyacrylamide gel electrophoresis, and UV absorption spectroscopy to study conformational properties of DNA fragments containing (CCA)n and (TGG)n repeats, which are the most length-polymorphic microsatellite sequences of the human genome. The (CCA)n fragments are random single strands at neutral and alkaline pH but they fold into intramolecular intercalated cytosine tetraplexes at mildly acid pH values. More acid values stabilize intermolecular tetraplex formation. The behavior of (TGG)n repeats is more complex. They form hairpins or antiparallel homoduplexes in low salt solutions which, however, are transformed into parallel-stranded guanine tetraplexes at physiological KCl concentrations. Their molecularity depends on the repeat number: (TGG)4 associates into an octameric complex, (TGG)8 forms tetramolecular complexes. (TGG)n with odd repeat numbers (5, 7, and 9) generate bimolecular and tetramolecular tetraplexes. The only (TGG)7 folds into an intramolecular tetraplex at low KCl concentrations, which is antiparallel-stranded. Moreover, the (TGG)(n) fragments provide various mutually slipped conformers whose population increases with salt concentration and with the increasing repeat number. However, the self-structures of both strands disappear in the presence of the complementary strand because both (TGG)n and (CCA)n prefer to associate into the classical heteroduplex. We suppose that the extreme conformational variability of the DNA strands stands behind the length polymorphism which the (CCA)n/(TGG)n repeats exhibit in the human genome.