Predicting Peptide Binding Affinities to MHC Molecules Using a Modified Semi-Empirical Scoring Function

The Major Histocompatibility Complex (MHC) plays an important role in the human immune system. The MHC is involved in the antigen presentation system assisting T cells to identify foreign or pathogenic proteins. However, an MHC molecule binding a self-peptide may incorrectly trigger an immune response and cause an autoimmune disease, such as multiple sclerosis. Understanding the molecular mechanism of this process will greatly assist in determining the aetiology of various diseases and in the design of effective drugs. In the present study, we have used the Fresno semi-empirical scoring function and modify the approach to the prediction of peptide-MHC binding by using open-source and public domain software. We apply the method to HLA class II alleles DR15, DR1, and DR4, and the HLA class I allele HLA A2. Our analysis shows that using a large set of binding data and multiple crystal structures improves the predictive capability of the method. The performance of the method is also shown to be correlated to the structural similarity of the crystal structures used. We have exposed some of the obstacles faced by structure-based prediction methods and proposed possible solutions to those obstacles. It is envisaged that these obstacles need to be addressed before the performance of structure-based methods can be on par with the sequence-based methods

Experimente zur Dephosphorylierung von Rhodopsin aus Stäbchen Sussensegmenten (ROS) des Rindes

The light-activated phosphorylation of rhodopsin under in-vivo- and in-vitroconditions is known since a long time. On contrary little is known about dephosphorylation.The quantitative dephosphorylation of highly phosphorylated bovine rhodopsin is not yet described. I describe optimized conditions to dephosphorylate highly phosphorylated rhodopsin from bovine (PG 5 -6 mol/mol rhodopsin) quantitatively with different extracts from ROS or from the whole retina. Experiments, using "whole ROS" as a source for phosphatase(s) are shown. Further first results of experiments to purify phosphatase(s) from retina-extracts areshown. 1) I found phosphatase-activity in different extracts from ROS and from retina and in "whole ROS". Phosphatase (s) from ROS is (are) isotonically extracted, but hypotonic extracts contain slightly higher phosphatase-activity. About only 20 % of the activity remains in the pellets after extraction. Therefore phosphatase(s) seem(s) to be soluble protein(s) of the Rod Outer Segments. Activity of hypotonic retina-extract is about 60 times higher than the activity of ROS-extract. I discuss the possibility of the existence of different phosphatases in these different extracts. A quantitative dephosphorylation of rhodopsin with extracts from ROS or from retinaoccurs only in the presence of a nonionic detergent (Octylglucosid). In the absence of detergent phosphorylated rhodopsin is dephosphorylated to about 30 - 40 % only. I discuss increased activity in presence of detergent as a possible influence on the substrat or on the phosphatase(s) itself The results indicate an influence of the detergent on the phosphatase(s) but not on the substrat. The pH-optimum for the phosphatase-activity is at pH 5.7; therefore the phosphatase(s) is (are) adjoined to "acid phosphatases". Depending on temperature a considerable loss of phosphatase-activity in the extracts was found during the experiments. The loss of activity is highly depressed in presence of DTT. Several factors inhibit phosphatase-activity. An ionic strengh of about 250 mM NaCl inhibits the activity half-maximal. Sodiumphosphat inhibits halfmaximal at a concentration of 10 mM and ATP inhibits about 90 % at a concentration of 5 mM. Using "whole ROS" as a "phosphatase-source" I found in contrast to extracts no quantitative dephosphorylation of rhodopsin in the presence of detergent. "Whole [...