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).