A graph-theoretic approach to quantitative structure—activity/reactivity studies

Characterization of molecular species based on the use of suitable graph invariants (graph paths, in particular) can provide a quantitative means of encoding structure; the technique is complementary to commoner approaches to studies of quantitative structure— activity relationships. Graph path encoding is here applied to quantitative studies of relationships between molecular structures and biological activity; the examples are the rates of various substrate reactions with hexoldnase, and the potential opiate-like activity of enkephalin analogs.     

Graph-theoretical analysis of molecular properties. Isomeric variations in nonanes

Paths of length two and three appear to dominate variations in isomers of alkanes when various physical and chemical molecular properties are compared. The regularities previously observed for octanes have been fully examined for the set of 35 nonane isomers C₉H₂₀. Such examinations are facilitated by construction of appropriate grid graphs with paths of length two and three, respectively, representing molecules and connecting such points along the grid axes. By ordering structures in the two-dimensional coordinate plane, various trends and regular changes in the relative magnitudes for the selected thermodynamic properties have been traced to molecular connectivity and topology.     

Mass spectra of some naturally occurring stictane triterpenoids and their trimethylsilyl derivatives

The mass spectra of ten di- and tri-oxygenated stictane triterpenoids and their trimethylsilyl derivatives have been studied in detail. Gas chromatography mass spectrometry of the TMS derivatives on OV-17 and OV-101 columns provided useful separations and identifications of mixtures of stictanes triterpenoids in lichen extracts. The major fragmentations involve ring C, but specific cleavages in rings A, B and E are also observed which allow the substitution pattern of the skeleton to be readily determined. The formation of an intense [M – C₅H₁₁?]⁺ ion for 22α-OTMS stictanes appears specific to their ring E configuration.     

Channel Flow Cell Studies of the Inhibiting Action of Gypsum on the Dissolution Kinetics of Calcite: A Laboratory Approach with Implications for Field Monitoring

The rate of dissolution of surface-treated calcite crystals in aqueous acidic solution has been studied using an adaptation of the channel flow cell method with microdisc electrode detection. Surface treatments of calcite with sulfuric acid lead to the nucleation of gypsum overgrowths, which reduce the rate of dissolution of calcite. Rate constants for untreated calcite and calcite pretreated with sulfuric acid conditions of 0.01 M for 1 h, 0.05 M for 5 h, and 0.1 M for 21 h are found to be 0.035, 0.018, 0.006, and 0.004 cm s(-1), respectively. Deterioration of calcite materials caused by acid deposition was investigated by field exposure of untreated and sulfate pretreated calcite rocks under urban conditions for 12 months. The rate constant for both pretreated and untreated calcite exposed to weathering is 0.003 cm s(-1). This suggests that calcite self-passivates the surface from further reaction when exposed to acid deposition. However, surface studies indicate that the surface undergoes erosion and dissolution before passivation. Pretreatment of the surface with sulfate protects the surface from acid deposition so it remains less reactive toward acid compared with untreated calcite. Copyright 2001 Academic Press.     

Design of a calcium-binding protein with desired structure in a cell adhesion molecule

Ca2+, "a signal of life and death", controls numerous cellular processes through interactions with proteins. An effective approach to understanding the role of Ca2+ is the design of a Ca2+-binding protein with predicted structural and functional properties. To design de novo Ca2+-binding sites in proteins is challenging due to the high coordination numbers and the incorporation of charged ligand residues, in addition to Ca2+-induced conformational change. Here, we demonstrate the successful design of a Ca2+-binding site in the non-Ca2+-binding cell adhesion protein CD2. This designed protein, Ca.CD2, exhibits selectivity for Ca2+ versus other di- and monovalent cations. In addition, La3+ (Kd 5.0 microM) and Tb3+ (Kd 6.6 microM) bind to the designed protein somewhat more tightly than does Ca2+ (Kd 1.4 mM). More interestingly, Ca.CD2 retains the native ability to associate with the natural target molecule. The solution structure reveals that Ca.CD2 binds Ca2+ at the intended site with the designed arrangement, which validates our general strategy for designing de novo Ca2+-binding proteins. The structural information also provides a close view of structural determinants that are necessary for a functional protein to accommodate the metal-binding site. This first success in designing Ca2+-binding proteins with desired structural and functional properties opens a new avenue in unveiling key determinants to Ca2+ binding, the mechanism of Ca2+ signaling, and Ca2+-dependent cell adhesion, while avoiding the complexities of the global conformational changes and cooperativity in natural Ca2+-binding proteins. It also represents a major achievement toward designing functional proteins controlled by Ca2+ binding.     

BOLD--a biological O-linked glycan database

Glycans can be O-linked to proteins via the hydroxyl group of serine, threonine, tyrosine, hydroxylysine or hydroxyproline. Sometimes the glycan is O-linked to the hydroxyl group via a phosphodiester bond. The core monosaccharide residue may be N-acetylgalactosamine, N-acetylglucosamine, galactose, glucose, fucose, mannose, xylose or arabinose. These O-linked glycans can remain as a monosaccharide, but often a complex structure is built up by stepwise addition of monosaccharides. Monosaccharides known to be added include galactose, N-acetylglucosamine, fucose, N-acetylneuraminic acid, N-glycolylneuraminic acid and 2-keto-3-deoxynonulosonic acid. O-linked glycans can also contain sulfate and phosphate residues. This leads to the possibility of the existence of numerous O-glycan structures. The biological O-linked database (BOLD) is a relational database that contains information on O-linked glycan structures, their biological sources (with a link to the SWISS-PROT protein database), the references in which the glycan was described (with a link to MEDLINE), and the methods used to determine the glycan structure. The database provides a valuable resource for glycobiology researchers interested in O-linked oligosaccharide structures that have been previously described on proteins from different species and tissues.