Biophysical Properties of Biomolecules: Homework 9 on Binding due June 7, 2013 1.

tRNA Complexes (15 pts) Read and use the table below (Proteins by Creighton), pg. 344 to answer the following: a) Draw the reaction profile indicating relative populations between all three states (separated, encounter complex, and folded complex) at relatively low and high tRNA concentration with concentration of synthetase fixed at 1pM.

b) Now sketch the initial rate, kinitial, of tRNA-tRNA synthetase(Ser) folded complex formation as a function of tRNA concentration (i.e. kinitial vs. [tRNA]). (I.e., dont solve the equations analytically. Hints: think in terms of kinetic partitioning, limiting cases, when is it concentration dependent? Remember kobs = kforward + kback).

2. Infinite Salt Bridges (20 points) i) Into a protein, one introduces 2 salt bridges (with no other changes). Calculate the increase in the macroscopic stability (total population of all native molecules relative to all unfolded molecules) assuming the equilibrium constant for each salt bridge is three times what it is in native unfolded 3K eq the unfolded state (i.e., K eq , with Keq = [bridge made]/[bridge broken]) and that each salt bridge can form independently of the other salt bridge in both the folded and unfolded states (four states: [no bonds], [Bond #1], [Bond #2], [both Bond # 1 and Bond # 2]. native Answer in terms . of G Keq

native ii) Recalculate G Keq for the situation where the bridges form sequentially, in a specific

states total, [no bonds] [Bond #1] [both Bond # 1 and Bond # 2]. order (three

iii) Redo i) and ii) for the general case of n salt bridges.