The usefulness of molecular dynamics to assess
the structural integrity of mutants containing several
mutations has been investigated. Our goal was to determine
whether molecular dynamics would be able to discriminate
mutants of a protein having a close–to–wild-type
fold, from those that are not folded under the same conditions.
We used as a model the B1 domain of protein G in which
we replaced the unique central α-helix by the sequence
of the second β-hairpin, which has a strong intrinsic
propensity to form this secondary structure in solution.
In the resulting protein, one-third of the secondary structure
has been replaced by a non-native one. Models of the mutants
were built based on the three-dimensional structure of
the wild-type GB1 domain. During 2 ns of molecular
dynamics simulations on these models, mutants containing
up to 10 mutations in the helix retained the native fold,
while another mutant with an additional mutation unfolded.
This result is in agreement with our circular dichroism
and NMR experiments, which indicated that the former mutants
fold into a structure similar to the wild-type, as opposed
to the latter mutant which is partly unfolded. Additionally,
a mutant containing six mutations scattered through the
surface of the domain, and which is unfolded, was also
detected by the simulation. This study suggests that molecular
dynamics calculations could be performed on molecular models
of mutants of a protein to evaluate their foldability,
prior to a mutagenesis experiment.