Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca.

The banana lectin from Musa paradisiaca, MW 29.4 kDa, has been isolated, purified and crystallized. The trigonal crystals contain one dimeric molecule in the asymmetric unit.

A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6 A resolution using sulfur-SAS at 1.54 A wavelength.

The crystal structure of the triple mutant K53,56,120M of bovine pancreatic phospholipase A(2) has been redetermined using sulfur single-wavelength anomalous scattering. The synchrotron data were collected at lambda = 1.54 A and the crystal diffracted to 1.

A FAST pattern matching algorithm.

The advent of digital computers has made the routine use of pattern-matching possible in various applications. This has also stimulated the development of many algorithms. In this paper, we propose a new algorithm that offers improved performance compared to those reported in the literature so far.

BSDD: Biomolecules Segment Display Device--a web-based interactive display tool.

An interactive web-based display tool, Biomolecules Segment Display Device (BSDD), has been developed to search for and visualize a user-defined motif or fragment among the protein structures available in the Protein Data Bank (PDB). In addition, the tool works for the structures available in a selected sub-set of non-homologous protein structures (25% and 90% sequence identity). The graphics package RASMOL has been incorporated as an interface to visualize the three-dimensional structure of the user-defined motif.

Neonatal distraction surgery for micrognathia reduces obstructive apnea and the need for tracheotomy.

The objective of the study was to assess the effectiveness of neonatal mandibular distraction in treatment of obstructive sleep apnea in the perinatal period in preventing a tracheotomy. This was a prospective study of 17 infants at two centers with severe micrognathia who demonstrated obstructive sleep apnea refractory to conservative therapy. Age at surgery varied from 5 to 120 days.

X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules.

The structure of the DNA binding protein from starved cells from Mycobacterium smegmatis has been determined in three crystal forms and has been compared with those of similar proteins from other sources. The dodecameric molecule can be described as a distorted icosahedron. The interfaces among subunits are such that the dodecameric molecule appears to have been made up of stable trimers.

A randomized, multicenter masked comparison trial of poractant alfa (Curosurf) versus beractant (Survanta) in the treatment of respiratory distress syndrome in preterm infants.

We compared the onset of clinical response and safety of two surfactants, poractant alfa (Curosurf, Chiesi Pharmaceuticals, Parma, Italy) and beractant (Survanta, Ross Laboratories, Columbus, OH), for treatment of respiratory distress syndrome (RDS) in preterm infants weighing 750 to 1750 g at birth and <35 weeks gestation. The study was performed as a 20-center prospective, randomized, masked comparison trial. Preterm infants (n = 293) with RDS were randomized to receive an initial dose of either 100 (n = 96) or 200 (n = 99) mg/kg of poractant alfa or 100 ( n = 98) mg/kg of beractant.

A Cost Minimization Comparison of Two Surfactants-Beractant and Poractant alfa-Based Upon Prospectively Designed, Comparative Clinical Trial Data.

Objectives: To compare the pharmacoeconomic profiles of beractant (Survanta(®), Ross Laboratories, Columbus, Ohio) and poractant alfa (Curosurf(®), DEY LP, Napa, CA) via a cost-minimization analysis.

Methods: This analysis was based upon clinical data from two previously published studies (Speer C, et al. Arch Dis Child 1995;72: F8-13; and Ramanathan R, et al.

LySDB - Lysozyme Structural DataBase.

LySDB (Lysozyme Structural DataBase) is an integrated database containing 740 three-dimensional structures of lysozyme available in the Protein Data Bank. The database can be used to visualize the three-dimensional structure of the entire protein model or the substructures in which the user is interested (for example, insertions and deletions of amino acids) using the three-dimensional atomic coordinates. The database is provided with a search engine with several useful built-in facilities.

THGS: a web-based database of Transmembrane Helices in Genome Sequences.

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB).

Crystallization and preliminary X-ray diffraction analysis of Mycobacterium smegmatis Dps.

Three crystal forms of a DNA-binding protein from stationary phase cells (Dps) of Mycobacterium smegmatis have been grown. They are hexagonal, tetragonal and cubic. The structure of the cubic form, which has one subunit in the asymmetric unit, has been solved using the molecular-replacement method.

Extended application of an LC-MS/MS method for the analysis of vesnarinone and its metabolites in human urine and dialysate fluid.

Vesnarinone, a positive inotropic drug developed for congestive heart failure, and its metabolites (OPC-8230, OPC-18136, OPC-18137) were analyzed in human dialysate and urine (plus an additional metabolite: OPC-18692 in urine) samples using a modification to a previously published LC-MS/MS assay for the analysis of human plasma and urine samples. OPC-8192, a structural analogue of vesnarinone, was used as the internal standard. The analytes of interest were extracted from human dialysate or urine by a solid phase extraction method using a pre-conditioned C-18 extraction column.

Side-chain conformation angles of amino acids: effect of temperature factor cut-off.

The paper presents the analysis of the side-chain conformation angles of amino acids in 90% non-identical protein structures. The analysis has been carried out using 113,699 residues, which is higher compared to the previous studies. In the present study, one more quality check, namely, temperature factor cut-off, has been introduced in addition to resolution and R-factor cut-offs.

Crystal structures of the free and anisic acid bound triple mutant of phospholipase A2.

Phospholipase A2 catalyses the hydrolysis of the ester bond of 3-sn-phosphoglycerides. Here, we report the crystal structures of the free and anisic acid-bound triple mutant (K53,56,120M) of bovine pancreatic phospholipase A2. In the bound triple mutant structure, the small organic molecule p-anisic acid is found in the active site, and one of the carboxylate oxygen atoms is coordinated to the functionally important primary calcium ion.

The crystal structure of 1,2,3,4,6-penta-O-benzoyl-alpha-D-mannopyranose: observation of C-H...pi interaction as a surrogate to O-H...O interaction of a free sugar.

The crystal structure of the title compound was determined by X-ray crystallography. The compound crystallized in the orthorhombic space group P2(1)2(1)2(1) with four molecules in the unit cell with a=9.170(2), b=9.

Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study.

The structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secondary site A, and secondary site B. In these structures and in the two structures reported earlier, Gal or GalNAc occupy the primary site with the anomeric carbon pointing towards secondary site A. The alpha-substituents, when present, interact, primarily hydrophobically, with secondary site A which has variable geometry.

Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications.

Single-stranded DNA-binding protein (SSB) is an essential protein necessary for the functioning of the DNA replication, repair and recombination machineries. Here we report the structure of the DNA-binding domain of Mycobacterium tuberculosis SSB (MtuSSB) in four different crystals distributed in two forms. The structure of one of the forms was solved by a combination of isomorphous replacement and anomalous scattering.

Supramolecular structures of 2-cyano-3-dimethylamino-N-(4-methylphenyl)acrylamide and 2-cyano-3-dimethylamino-N-(2-methoxyphenyl)acrylamide.

In the title compounds, C(13)H(15)N(3)O, (I), and C(13)H(15)N(3)O(2), (II), the dihedral angles between the planes of the phenyl ring and the amide group are 4.1 (1) and 20.7 (1) degrees, respectively.

SSEP: Secondary structural elements of proteins.

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the alpha-helical segments and beta-strand fragments of varying lengths.

SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules.

SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows the users to save the three-dimensional atomic coordinates of the symmetry equivalent molecules in the local machine. The widely recognized graphics program RasMol has been deployed to visualize the reference (input atomic coordinates) and the symmetry equivalent molecules.

CAP: conformation angles package-displaying the conformation angles of side chains in proteins.

Summary: A graphics package has been developed to display all side chain conformation angles of the user selected residue in a given protein structure. The proposed package is incorporated with all the protein structures (solved using X-ray diffraction and NMR spectroscopy) available in the Protein Data Bank. The package displays the multiple conformations adopted by a single amino acid residue whose structure is solved and refined at very high resolution.

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.

Observation of additional calcium ion in the crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A2.

Phospholipase A(2) catalyses hydrolysis of the ester bond at the C2 position of 3-sn-phosphoglycerides. Here we report the 1.9A resolution crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A(2).

Ramachandran plot on the web.

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output.

Demand for, access to and use of community mental health care: lessons from a demonstration project in India and Pakistan.

Background: A widely promoted model of mental health care and prevention appropriate to many low-income countries is one that is integrated into the local primary health care system.

Aims: To examine the influence of health-seeking behaviours (demand-side factors) and the access to/availability of services (supply-side factors) on local service utilisation patterns for people with common mental disorders.

Method: Two rural catchment populations outside Bangalore (India) and Rawalpindi (Pakistan), one with the standard primary health care system, the other with additional mental health care training and support, were screened for common mental disorders.