Knowledge-based interaction potentials for proteins.

We discuss the derivation of atomic-level potentials of mean force from the known protein structures and their applicability for structural evaluation applications. In the derivation process, rigorous density estimation methodology is used to estimate the probability density functions (PDFs) for the distributions of interatomic distances in the protein structures. Potentials of mean force are then derived from these density functions using simple Boltzmann's relation. We also test the potentials against pairs of current and superseded protein structures in the Protein Data Bank. Using PDF potentials to evaluate each structure pair, we are able to identify, with high accuracy, which of the two structures is of higher resolution or better quality. This result shows that the PDF potentials are sensitive to details in protein structures as the current and superseded atomic coordinates generally do not differ by more than 1 A in root-mean-square deviation, and that the PDF potentials could potentially be used for X-ray structure refinement and protein structure prediction.     

Apical cell surface expression of rat dipeptidyl peptidase IV in transfected Madin-Darby canine kidney cells.

Dipeptidyl peptidase IV (DPPIV) is a type II membrane glycoprotein that is predominantly localized to the apical plasma membrane in various epithelial cells. In order to understand in more detail the biogenesis and sorting of DPPIV, the cDNA for rat DPPIV was inserted into a mammalian plasmid expression vector so that DPPIV expression was driven by a control region composed of the SV40 early promoter region fused to the enhancer of the Rous sarcoma virus. Madin-Darby canine kidney cells transfected with this construct were found to express the DPPIV protein. In these transfected cells, the majority of DPPIV was present on the apial cell surface. This observation suggests that the information for apical surface localization is inherent in the DPPIV molecule itself and that this sorting information is decipherable in the epithelial cells of a different species. DPPIV is transported efficiently from the endoplasmic reticulum to the Golgi apparatus as assessed by pulse-chase experiments. Furthermore, evidence is presented which suggests that the majority of DPPIV is sorted intracellularly to the apical cell surface. The same protein has, however, been reported to be sorted by an indirect pathway through transcytosis from the basolateral to the apical cell surface in hepatocytes (Bartles, J.R., Feracci, H., M., Stinger, B., and Hubbard, A.L. (1987) J. Cell Biol. 105, 1241-1251). This study suggests that the same protein can take two different pathways in different cell types for its correct apical cell surface localization.