The
study of protein conformations using molecular dynamics (MD)
simulations has been in place for decades. A major contribution to
the structural stability and native conformation of a protein is made
by the primary sequence and disulfide bonds formed during the folding
process. Here, we investigated μ-conotoxins GIIIA, KIIIA, PIIIA,
SIIIA, and SmIIIA as model peptides possessing three disulfide bonds.
Their NMR structures were used for MD simulations in a novel approach
studying the conformations between the folded and the unfolded states
by systematically breaking the distinct disulfide bonds and monitoring
the conformational stability of the peptides. As an outcome, the use
of a combination of the existing knowledge and results from the simulations
to classify the studied peptides within the extreme models of disulfide
folding pathways, namely the bovine pancreatic trypsin inhibitor pathway
and the hirudin pathway, is demonstrated. Recommendations for the
design and synthesis of cysteine-rich peptides with a reduced number
of disulfide bonds conclude the study.