Asparagine and aspartate are known to adopt conformations in the left-handed alpha-helical region and other partially allowed regions of the Ramachandran plot more readily than any other non-glycyl amino acids. The reason for this preference has not been established. An examination of the local environments of asparagine and aspartic acid in protein structures with a resolution better than 1.5 ...

State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalcula...

We used UV resonance Raman (UVRR) spectroscopy exciting at ∼200 nm within the peptide bond π f π* transitions to selectively study the amide vibrations of peptide bonds during R-helix melting. The dependence of the amide frequencies on theirΨ Ramachandran angles and hydrogen bonding enables us, for the first time, to experimentally determine the temperature dependence of the peptide bond Ψ Rama...

Current practice of validating predicted protein structural model is knowledge-based where scoring parameters are derived from already known structures to obtain decision on validation out of this structure information. For example, the scoring parameter, Ramachandran Score gives percentage conformity with steric-property higher value of which implies higher acceptability. On the other hand, Fo...

MediaBroker is a distributed framework designed to support pervasive computing applications. Key contributions of MediaBroker are efficient and scalable data transport, data stream registration and discovery, an extensible system for data type description, and type-aware data transport that is capable of dynamically transforming data en route from source to sinks. Specifically, the architecture...

The focus of this paper is to offer a practical multi-radio mesh network architecture that can realize the benefits of multiple radios. Our architecture provides solutions to challenges in three key areas. The first is the construction of a split wireless router that enables modular wireless mesh routers to be constructed from commodity hardware. The second is the design of a centralized channe...

Observers see a white triangle on the top of three black disks; the white triangle appears lighter, although it has the same luminance of the white background. Also squared or irregular “anomalous” figures can be created (Kanizsa & Gerbino, 1987). Several competing explanations have been put forward for the effect (Dumais, & Bradley, 1976; Coren, 1991; Ramachandran & Rogers-Ramachandran, 2005),...

We used 204 nm excitation UV Resonance Raman (UVRR) spectroscopy to examine the effects of NaClO(4) on the conformation of poly-L-lysine (PLL). The presence of NaClO(4) induces the formation of α-helix, π-helix/bulge, and turn conformations. The dependence of the AmIII(3) frequency on the peptide Ψ Ramachandran angle allows us to experimentally determine the conformational population distributi...

UV resonance Raman (UVR) spectroscopy was used to examine the solution conformation of poly-L-lysine (PLL) and poly-L-glutamic acid (PGA) in their non-R-helical states. UVR measurements indicate that PLL (at pH ) 2) and PGA (at pH ) 9) exist mainly in a mixture of polyproline II (PPII) and a novel left-handed 2.51-helical conformation, which is an extended -strand-like conformation with Ψ ≈ +17...

We examined the 204-nm UV Raman spectra of the peptide XAO, which was previously found by Shi et al.'s NMR study to occur in aqueous solution in a polyproline II (PPII) conformation. The UV Raman spectra of XAO are essentially identical to the spectra of small peptides such as ala(5) and to the large 21-residue predominantly Ala peptide, AP. We conclude that the non-alpha-helical conformations ...