Self-avoiding walk model for proteins

We study a model for the backbone of proteins on a square lattice which consists of the path traced out by a self-avoiding walk (SAW) on the lattice and bridges not belonging to sites on the SAW but connecting nearest neighbor sites of the SAW. We calculated the fractal dimensiond _w for random walk on this model and found thatd _w2.6, in disagreement with a recent suggestion thatd _w should be 2.     

BIODEGRADABLE POLYMERS WITH A PHOSPHORYL-CONTAINING BACKBONE:TISSUE ENGINEERING AND CONTROLLED DRUG DELIVERY APPLICATIONS

This review provides a glimpse of the potential of the biodegradable phos-phoryl-containing polymers in medical applications. Undoubtedly these polymerspossess unique properties that are yet to be fully understood. Many areas warrantfurther investigation and much optimization remains to be done. The fascinatingchemistry of phosphorus poses interesting hurdles but at the same time leavesample room for polymer scientists to exercise their creativity in designinginteresting biomaterials. As the mutual understanding between basic and clinicalscientists on the need of medical devices and the capabilities of these newbiomaterials expands, imaginative application of new biomaterials to other medi-cal applications can be expected.     

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873–875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194–10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis.     

Acoustic wave transmission through piezoelectric structured materials

This paper deals with the transmission of acoustic waves through multilayered piezoelectric materials. It is modeled in an octet formalism via the hybrid matrix of the structure. The theoretical evolution with the angle and frequency of the transmission coefficients of ultrasonic plane waves propagating through a partially depoled PZT plate is compared to finite element calculations showing that both methods are in very good agreement. The model is then used to study a periodic stack of 0.65PMN-0.35PT/0.90PMN-0.10PT layers. The transmission spectra are interpreted in terms of a dispersive behavior of the critical angles of longitudinal and transverse waves, and band gap structures are analysed. Transmission measurements confirm the theoretical calculations and deliver an experimental validation of the model.