Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches.

We present the application of a method for protein structure prediction to aid the determination of structure-function relationships by experiment. The structure prediction method was rigourously tested by making blind predictions at the third meeting on the Critical Assessment of Protein Structure methods (CASP3). The method is a combined hierarchical approach involving exhaustive enumeration of all possible folds of a small protein sequence on a tetrahedral lattice. A set of filters, primarily in the form of discriminatory functions, are applied to these conformations. As the filters are applied, greater detail is added to the models resulting in a handful of all-atom "final" conformations. Encouraged by the results at CASP3, we used our approach to help solve a practical biological problem: the prediction of the structure and function of the 67-residue C-terminal zinc-finger region of the DNA polymerase alpha-associated zinc-finger (PAZ) protein. We discuss how the prediction points to a novel function relative to the sequence homologs, in conjunction with evidence from experiment, and how the predicted structure is guiding further experimental studies. This work represents a move from the theoretical realm to actual application of structure prediction methods for gaining unique insight to guide experimental biologists.

Development of a capillary electrophoresis method for the characterization of collagens in cartilage tissue.

The use of capillary electrophoresis (CE) for the separation of peptides specific to type I and type II collagen is evaluated. The aim of this work is to develop a method to characterize cartilage, cartilage repair tissue, and tissue engineered cartilage. The analysis is dependent on the cleavage of collagen into constituent peptides by cyanogen bromide. A number of these peptides are specific to the collagen type. CE is evaluated for the separation of these specific peptides using uncoated and coated capillaries over a wide range of pH and buffer concentrations. Separation of peptides specific to type I and type II collagen is achieved using a Supelco CElect N capillary and a 100mM phosphate buffer at pH 6. Meniscal cartilage is characterized using this method. The proportion of type I collagen to type II collagen corresponds well with that reported by others and indicates the potential of this method for the characterization of cartilage.

Separation of biomolecules using supercritical fluid extraction.

Supercritical fluids are increasingly being used as a replacement for more conventional organic solvents in the extraction of biomolecules from a range of matrices. Supercritical fluid extraction of essential fatty acids from fish oils is discussed. Supercritical CO2 was used to fractionate two fatty acids, EPA and DHA from fish oil ethyl esters. EPA and DHA were obtained with a purity of 58% and 67% respectively from Sardine oil with an original composition of 17% and 12%.