Herein, the expression of recombinant cysteine-rich atypical buckwheat (Fagopyrum esculentum) aspartic protease (FeAPL1) in five Escherichia coli strains differing in their expression capabilities is presented. It was shown that the expression success depended highly on the choice of FeAPL1 fusion partner. His6-FeAPL1 was produced in large quantities as an insoluble protein localized in inclusi...

The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X-ray diffracti...

We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing th...

Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail...

The method of Probability Density Profile Analysis has been introduced previously as a tool to find a best match between a set of experimentally generated Residual Dipolar Couplings and a set of known protein structures. While it proved effective on small databases in identifying protein fold families, and for picking the best result from computational protein folding tool ROBETTA, for larger d...

The motion of particles and feeding currents created by micro-organisms due to a flagellum are considered. The calculations are pertinent to a range of sessile organisms, but we concentrate on a particular organism, namely Salpingoeca amphoridium (SA) (a choanoflagellate), due to the availability of experimental data (Pettitt, 2000). These flow fields are characterized as having very small Reyn...

The Rosetta data set opens the possibility of comparing a user microarray data set with a reference profile from the compendium (see [1]). However, explaining this comparison in terms of individual genes could be a daunting task because of the sheer number of genes. Thus, we postulate a new strategy of modeling microarray data in terms of functional genomic units (FGUs). A functional genomic un...

MOTIVATION Alternative splicing (AS) serves as a mechanism to create diversity among functional proteins. Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures. RESULTS A new cross-species gene identification and AS analysis system, PSEP, has been developed. The system is based on expressed sequence ta...