Chitin Research Revisited

Two centuries after the discovery of chitin, it is widely accepted that this biopolymer is an important biomaterial in many aspects. Numerous studies on chitin have focused on its biomedical applications. In this review, various aspects of chitin research including sources, structure, biosynthesis, chitinolytic enzyme, chitin binding protein, genetic engineering approach to produce chitin, chitin and evolution, and a wide range of applications in bio- and nanotechnology will be dealt with

Mutant CD4 Molecules with Improved Binding to HIV Envelope Protein gp120 Selected by Phage Display

AbstractPhage-display methodology has been used to select variant CD4 proteins exhibiting increased binding to the surface envelope glycoprotein, gp120, of Human Immunodeficiency Virus Type-1. To facilitate the selection, a library of mutant CD4 proteins was constructed by cloning a PCR-generated error prone population of the first two domains of CD4 into the phagemid expression vector pHEN1. Phage displaying CD4 in functional form were confirmed by Western blot with CD4-specific antibody and by phage ELISA on immobilized gp120. Biopanning of CD4 phage on immobilized gp120 followed by individual characterization identified five clones with increased binding to gp120. All of the selected variants had one or two amino acid substitutions within the V1 domain of CD4, notably at positions 15, 27, 30, 50, and 66 located in the strands surrounding the main binding loop. Variants which exhibited increased binding to recombinant gp120in vitrowere also shown to have an increased capacity for virus neutralization broadly in line with theirin vitrobinding activity

trp operon induction during the expression in E. coli of two IFN-γ sequences

AbstractTwo nucleotide sequences coding for mature human immune interferon (IFN-γ) and differing from each other by nine N-terminal nucleotides were expressed in E. coli under the control of a trp promoter. The longer gene variant after the ATG initiatory codon contained a TGT TAC TGC sequence, which was absent in the shorter gene. When expressed in E. coli under the direction of identical transcription and translation regulatory elements, these genes showed different susceptibility to induction

DEPCOD: a tool to detect and visualize co-evolution of protein domains

Abstract Proteins with similar phylogenetic patterns of conservation or loss across evolutionary taxa are strong candidates to work in the same cellular pathways or engage in physical or functional interactions. Our previously published tools implemented our method of normalized phylogenetic sequence profiling to detect functional associations between non-homologous proteins. However, many proteins consist of multiple protein domains subjected to different selective pressures, so using protein domain as the unit of analysis improves the detection of similar phylogenetic patterns. Here we analyze sequence conservation patterns across the whole tree of life for every protein domain from a set of widely studied organisms. The resulting new interactive webserver, DEPCOD (DEtection of Phylogenetically COrrelated Domains), performs searches with either a selected pre-defined protein domain or a user-supplied sequence as a query to detect other domains from the same organism that have similar conservation patterns. Top similarities on two evolutionary scales (the whole tree of life or eukaryotic genomes) are displayed along with known protein interactions and shared complexes, pathway enrichment among the hits, and detailed visualization of sources of detected similarities. DEPCOD reveals functional relationships between often non-homologous domains that could not be detected using whole-protein sequences. The web server is accessible at http://genetics.mgh.harvard.edu/DEPCOD.</jats:p

Triad of polar residues implicated in pH specificity of acidic mammalian chitinase

Acidic mammalian chitinase (AMCase) is a mammalian chitinase that has been implicated in allergic asthma. One of only two active mammalian chinases, AMCase, is distinguished from other chitinases by several unique features. Here, we present the novel structure of the AMCase catalytic domain, both in the apo form and in complex with the inhibitor methylallosamidin, determined to high resolution by X-ray crystallography. These results provide a structural basis for understanding some of the unique characteristics of this enzyme, including the low pH optimum and the preference for the β-anomer of the substrate. A triad of polar residues in the second-shell is found to modulate the highly conserved chitinase active site. As a novel target for asthma therapy, structural details of AMCase activity will help guide the future design of specific and potent AMCase inhibitors