import numpy as np import eqtk #Set up initial concentrations for titration c0 = np.zeros((200, 5)) c0[:, 0] = 1 # total concentration of P c0[:, 1] = 0.5 # total concentration of A c0[:, 2] = 1 # total concentration of B #Kd values Kd_A = 0.001 # dissociation constant for binding of P with A Kd_B = 0.003 # dissociation constant for binding of P with B Kd_C = 0.005 # dissociation constant for binding of P with C #Stoichiometry matrix N = [[1, 1, 0, -1, 0], [1, 0, 0, 0, -1]] #Equilibrium constants K = [Kd_A, Kd_B, Kd_C] #Define constant of proportionality between activity and concentration of ligand-bound protein zeta = 1 #Solve! c = eqtk.solve(c0, N, K, units="uM") #Compute fraction bound frac_A_bound = c[:, 3] / c0[:, 0] #Print the titration curve import matplotlib.pyplot as plt plt.plot(c0[:, 4], frac_A_bound) plt.xlabel("Total concentration of C (M)") plt.ylabel("Fraction of P bound to A") plt.show() print(frac_A_bound)

The above code uses the eqtk package to solve a titration problem. The code first sets up the initial concentrations for the titration, including the total concentration of the protein, P, and the total concentrations of the ligands, A, B, and C. Next, the code defines the Kd values for the binding of P with each of the ligands, A, B, and C. This is followed by the definition of the stoichiometry matrix, which specifies how the concentrations of each species in the system change as the titration progresses. The code then defines the equilibrium constants, K, and a constant of proportionality between the activity and concentration of ligand-bound protein, zeta. The eqtk package is then used to solve the titration problem, using the c0, N, K, and zeta variables defined earlier. Finally, the code computes the fraction of P bound to A and plots it on a graph showing the titration curve. Additionally, the code also prints out the fraction of P bound to A. This code provides a solution to a titration problem, allowing us to visualize the relationship between the total concentration of ligand C and the fraction of protein P bound to A.

Please debug this code: