Jan 2, 2007

2007 week 01: Articles in General Medicine

Study Sheds New Light On Rare Immunodeficiency Disease

USC researchers have determined the 3-D atomic structure of the Apo2 protein, the first of the APOBEC enzyme family to be described. The protein structure has guided them to a new understanding of what goes wrong on a molecular level in a rare, but serious immunodeficiency syndrome.

Solution structure of a small protein containing a fluorinated side chain in the core

We report the first high-resolution structure for a protein containing a fluorinated side chain... Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability.

BPPred: A Web-based computational tool for predicting biophysical parameters of proteins

We exploit the availability of recent experimental data on a variety of proteins to develop a Web-based prediction algorithm (BPPred) to calculate several biophysical parameters commonly used to describe the folding process. These parameters include the equilibrium m-values, the length of proteins, and the changes upon unfolding in the solvent-accessible surface area, in the heat capacity, and in the radius of gyration. We also show that the knowledge of any one of these quantities allows an estimate of the others to be obtained, and describe the confidence limits with which these estimations can be made. Furthermore, we discuss how the kinetic m-values, or the Beta Tanford values, may provide an estimate of the solvent-accessible surface area and the radius of gyration of the transition state for protein folding. Taken together, these results suggest that BPPred should represent a valuable tool for interpreting experimental measurements, as well as the results of molecular dynamics simulations.

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