Specificity of Furanoside–Protein Recognition through Antibody Engineering and Molecular Modeling

Recognition of furanosides (five‐membered ring sugars) by proteins plays important roles in host–pathogen interactions. In comparison to their six‐membered ring counterparts (pyranosides), detailed studies of the molecular motifs involved in the recognition of furanosides by proteins are scarce. Here the first in‐depth molecular characterization of a furanoside–protein interaction system, between an antibody (CS‐35) and cell wall polysaccharides of mycobacteria, including the organism responsible for tuberculosis is reported. The approach was centered on the generation of the single chain variable fragment of CS‐35 and a rational library of its mutants. Investigating the interaction from various aspects revealed the structural motifs that govern the interaction, as well as the relative contribution of molecular forces involved in the recognition. The specificity of the recognition was shown to originate mainly from multiple CH–π interactions and, to a lesser degree, hydrogen bonds formed in critical distances and geometries.     

Poly(bis‐2,2,2‐trifluoroethoxymethyl oxetane): Multiple crystal phases,crystallization‐induced surface topological complexity and enhanced hydrophobicity

Semicrystalline poly(bis‐trifluoroethoxymethyl)oxetane, P(B‐3FOx), was prepared by cationic ring‐opening polymerization at ?5 °C with M_n up to 21 kDa. Differences in cooling rates from the melt have substantial effects on crystal phase, percent crystallinity, surface topography, and wetting behavior. DSC and WAXD show that cooling from the melt at slow rates (<5 °C/min) gives α‐P(B‐3FOx) with ΔH_f = 22–27 J/g. Quenching from the melt results in β‐P(B‐3FOx) for which a mesophase structure is suggested. β‐P(B‐3FOx) melts at 53 °C followed by recrystallization to α‐P(B‐3FOx). Solution casting from THF results in third phase, γ‐P(B‐3FOx). TM‐AFM and SEM imaging for α‐P(B‐3FOx) showed that cold crystallization at 25 °C brought about increased crystallinity and surface topologies characterized by sharp asperities and lath‐shaped crystals. Spontaneous surface roughening of α‐P(B‐3FOx) results in a discontinuous three‐phase contact line with water and an increase in water sessile drop contact angle from 106° to 136°. The ～30° increase in water contact angle was attributed primarily to a topological change from a relatively smooth surface (Wenzel state) to an asperity‐rich surface yielding a discontinuous three‐phase contact line (composite of Wenzel and Cassie‐Baxter state). The oleophobicity for this polymer, which contains only a single ? CF₃ end group on each side chain, compares favorably with more highly fluorinated acrylates. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1022–1034, 2010     

Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff

Docking algorithms that aim to be applicable to a broad range of ligands suffer reduced accuracy because they are unable to incorporate ligand‐specific conformational energies. Here, we develop a set of Carbohydrate Intrinsic (CHI) energy functions that quantify the conformational properties of oligosaccharides, based on the values of their glycosidic torsion angles. The relative energies predicted by the CHI energy functions mirror the conformational distributions of glycosidic linkages determined from a survey of oligosaccharide‐protein complexes in the protein data bank. Addition of CHI energies to the standard docking scores in Autodock 3, 4.2, and Vina consistently improves pose ranking of oligosaccharides docked to a set of anticarbohydrate antibodies. The CHI energy functions are also independent of docking algorithm, and with minor modifications, may be incorporated into both theoretical modeling methods, and experimental NMR or X‐ray structure refinement programs. © 2013 Wiley Periodicals, Inc.     

Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species

Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of natural plant populations. We have employed an enrichment strategy for microsatellite isolation by using multi-enzymes digestion, microsatellite oligoprobes, and streptavidin magnetic beads in Sesamum (Sesamum indicum L.). More than 200 SSR motifs were detected (SSR motifs ??2 repeat units or 6?bp); 80?% of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10?bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60 Sesamum germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs.