Experimental validation of molecular dynamics simulation ofD0
A replica-exchange simulation of 68 µs of mHIV-1-PR1-95in water is performed with 110 temperatures in the range from 300K to 500K, as described in the Materials and Methods. The degree of equilibration of the simulation seems acceptable, as testified by the good exchange between replicas (cf. Fig. S8) and by the convergence of the average contact map (cf. Fig. S9).
To validate the simulation, we calculated the average secondary chemical shifts from the simulated trajectory using Sparta+56and compared them with the experimental values extrapolated forD0 (Fig. 6). The Pearson’s correlation coefficients are r=0.68 for CA, r=0.63 for C’, r=0.67 for N and r=0.54 for HN (also cf. Fig. S10). Thus, the simulated data is in good agreement with the experimental values (p-value<10-5, as calculated from a random bootstrap of the data).