Synthesis and structural investigations of functionalizable hybrid β-hairpin

The solution and solid state conformations of a designed β-hairpin containing functionalizable α,β-unsaturated γ-amino acids at the antiparallel β-strands and a single step transformation to its saturated γ-peptide analogue are studied.     

A rapid fluorescence-based assay for classification of iNKT cell activating glycolipids

Structural variants of α-galactosylceramide (αGC) that activate invariant natural killer T cells (iNKT cells) are being developed as potential immunomodulatory agents for a variety of applications. Identification of specific forms of these glycolipids that bias responses to favor production of proinflammatory vs anti-inflammatory cytokines is central to current efforts, but this goal has been hampered by the lack of in vitro screening assays that reliably predict the in vivo biological activity of these compounds. Here we describe a fluorescence-based assay to identify functionally distinct αGC analogues. Our assay is based on recent findings showing that presentation of glycolipid antigens by CD1d molecules localized to plasma membrane detergent-resistant microdomains (lipid rafts) is correlated with induction of interferon-γ secretion and Th1-biased cytokine responses. Using an assay that measures lipid raft residency of CD1d molecules loaded with αGC, we screened a library of ～200 synthetic αGC analogues and identified 19 agonists with potential Th1-biasing activity. Analysis of a subset of these novel candidate Th1 type agonists in vivo in mice confirmed their ability to induce systemic cytokine responses consistent with a Th1 type bias. These results demonstrate the predictive value of this novel in vitro assay for assessing the in vivo functionality of glycolipid agonists and provide the basis for a relatively simple high-throughput assay for identification and functional classification of iNKT cell activating glycolipids.     

From Valleys to Ridges: Exploring the Dynamic Energy Landscape of Single Membrane Proteins

Membrane proteins are involved in essential biological processes such as energy conversion, signal transduction, solute transport and secretion. All biological processes, also those involving membrane proteins, are steered by molecular interactions. Molecular interactions guide the folding and stability of membrane proteins, determine their assembly, switch their functional states or mediate signal transduction. The sequential steps of molecular interactions driving these processes can be described by dynamic energy landscapes. The conceptual energy landscape allows to follow the complex reaction pathways of membrane proteins while its modifications describe why and how pathways are changed. Single‐molecule force spectroscopy (SMFS) detects, quantifies and locates interactions within and between membrane proteins. SMFS helps to determine how these interactions change with temperature, point mutations, oligomerization and the functional states of membrane proteins. Applied in different modes, SMFS explores the co‐existence and population of reaction pathways in the energy landscape of the protein and thus reveals detailed insights into local mechanisms, determining its structural and functional relationships. Here we review how SMFS extracts the defining parameters of an energy landscape such as the barrier position, reaction kinetics and roughness with high precision.     

Mechanical properties of bovine rhodopsin and bacteriorhodopsin: possible roles in folding and function

Molecular interactions and mechanical properties that contribute to the stability and function of proteins are complex and of fundamental importance. In this study, we used single-molecule dynamic force spectroscopy (DFS) to explore the interactions and the unfolding energy landscape of bovine rhodopsin and bacteriorhodopsin. An analysis of the experimental data enabled the extraction of parameters that provided insights into the kinetic stability and mechanical properties of these membrane proteins. Individual structural segments of rhodopsin and bacteriorhodopsin have different properties. A core of rigid structural segments was observed in rhodopsin but not in bacteriorhodopsin. This core may reflect differences in mechanisms of protein folding between the two membrane proteins. The different structural rigidity of the two proteins may also reflect their adaptation to differing functions.     

Ab-initio study of electronic and elastic properties of B2-type ductile YM (M=Cu, Zn and Ag) intermetallics

A theoretical study of structural, electronic, elastic, thermal and mechanical properties of nonmagnetic intermetallics YM (M=Cu, Zn and Ag), which crystallize in CsCl-type structure, is performed using first principles density functional theory based on full potential linearized augmented plane wave (FP-LAPW) method. The calculations are carried out within the generalized gradient approximation (GGA) for the exchange correlation potential. The calculated ground state properties such as lattice constants, bulk modulus and elastic constants agree well with the experiment. From energy dispersion curves, it is found that these compounds are metallic in nature. The ductility of these intermetallics is determined by calculating the bulk to shear ratio B/G_H. The calculated results indicate that YAg is the most ductile amongst the present YM compounds. The results obtained are compared with the available experimental and theoretical results. The mechanical and thermal properties are predicted from the calculated values of elastic constants.     

Resonant soft X-ray reflectivity as a sensitive probe to investigate polished zinc sulphide surface

Resonant soft X-ray reflectivity measurements at and near the L₃ absorption edge of sulphur have been performed on mechanically polished zinc sulphide using Indus-1 synchrotron source. A sulphur rich surface (∼15 nm thick) consisting of two layers with gradient electron density distribution was uniquely determined. As compared to bulk ZnS, the top layer has ∼30-50% less electron density whereas, the intermediate layer has ∼10-18% less electron density. Conventional hard X-ray reflectivity measurement at Cu Kα wavelength also indicates low electron density (sulphur rich) surface of ZnS but the technique was found insensitive for unique determination of electron density distribution. Optical constants of ZnS in the soft X-ray region (100-250 eV) have been reported for the first time and were in good agreement with the theoretically reported values.     

Theoretical study of electronic structures and conduction properties of copolymers based on poly(cyclopentadienylene)

Various quasi-one-dimensional superlattices (copolymers) (AmBn)x of two novel donor-acceptor polymers PPDCF ([A]x) and PPDCN ([B]x) based on poly(cyclopentadienylene) (PPD) and belonging to the class of type II staggered superlattices were investigated using a negative factor counting method in the tight-binding approximation. Both PPDCF and PPDCN consist of a bicyclopentadienylene unit bridged by an electron-accepting group >C=CF2 in PPDCF and >C=C(CN)2 in PPDCN. The trends in the electronic structures and conduction properties of the copolymers (AmBn)x as a function of the block sizes m and n, arrangement of the units (periodic or random) in the copolymer chain, and length of the copolymer chain are discussed.     

Label-free fluorescence detection of the depurination activity of ribosome inactivating protein toxins

Development of a simple label-free fluorescence hybridization assay to monitor the depurination activity of toxic ribosome inactivating proteins by using a fluorescent ligand that specifically pseudo base pairs with a cytosine residue opposite an abasic site is described. This method could be potentially implemented in screening platforms for the discovery of small molecules that inhibit the activity of these toxins.