Problem 4.1. Consider a protein P which can bind to two different ligands, A and
ID: 150020 • Letter: P
Question
Problem 4.1. Consider a protein P which can bind to two different ligands, A and B as in the figure. The protein has a flexible loop which can be in any position allowed by the geometry of the protein, but when the ligand is bound to the loop the number of its allowed conformations is reduced, in order to make the bond. Specifically, when ligand A is bound the entire loop is forced to be in contact with the ligand, whereas when B is bound, only the first element of the loop is forced in the horizontal position Ligand A binds with energy _9eo, Ligand B with energy-Teo, where eo = (100kB)K Using a 2 dimensional lattice model, find the range of temperatures in which the protein will bind most likely to A, to B or will be dissociated. Assume that only lateral contacts are allowed to find all the positions of the loop examples of dissociated proteins LT. 3 protein bound to A protein bound to B Figure 1: Some conformations in which the protein can be found when dissociated (top)., bound to A (bottom left) or to B (bottom right)Explanation / Answer
The range of temperatures =>Eo/ energy=>100/9 to 100/7=>100/16=> 11 C to 14 C
The range is easy to find out.