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Analysis of open reading frames from Pyrococcus furiosus

Those who plan crystallization for structural genomics projects may be interested in recent analysis of the open reading frames of the genome sequence of P. furiosus.  The contour plot below shows the calculated isoelectric points against the calculated charge densities of the proteins.  As shown, there are three main clusters of proteins:  the top left cluster is rich in the amino acids ASP and GLU, the top right is dominated by LYS, while the bottom right cluster contains proteins with many ARG residues.  Over 2000 ORFs were used to construct the plot.

This information could be used to devise different crystallization strategies for the three clusters.  For example, research presented by M. Ries-Kautt at the recent ACA meeting and elsewhere suggests that different screening approaches should be used for positively and negatively charged proteins.

To calculate the molecular weight, isoelectric point etc. of an amino acid sequence, click here

For technical details, please contact Dr. Dennis L. Maeder: maeder@umbi.umd.edu

Ionic properties of Pfuriosus ORFs.gif (78277 bytes)

 

Remember, a small excess of one amino acid tends to dominate the landscape as it then has greater buffering capacity.

Click here for alternative plots:  IEP against frequency, charge density at IEP against frequency, frequency of ionic residues against IEP, and MW against IEP.

 

 

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