The tendency for replacements at a given residue position varies appreciably. Single amino acid substitutions are not the only differences
between homologous proteins. Larger steps are insertions and deletions of single residues or stretches of residues, which affect
not only side chains but also the main chain. Insertions and deletions cause great difficulties in sequence comparisons of distantly
related proteins.
In such cases knowledge of the three-dimensional protein structures helps considerably.
It reveals in general that internal residues vary slowly, whereas the differences between homologous proteins (amino acid
changes or deletions and insertions of chain loops) accumulate on the surface.
Consequently, the sequences of distantly related proteins can be aligned on the basis of residues that are geometrically at corresponding
positions in the tertiary structures..
2) Short life time of rising proteins
Intermediary structures must have short life time in proteins folding, the activation barrier for the next produtive state
shouldn't be large.
3) Partial unfolding The transport of one protein
from one cellular compartment to another, only can occur wheter if it can unfold itself sufficiently to cross the membrane
cell chanel.
4) Easy dismounting One example are the colagen molecules
which can be degraded over controled way to remodel tissues.