Mutation Space of Spatially Conserved Amino Acid Sites in Proteins

The mutation space
of spatially conserved (MSSC) amino acid residues
is a protein structural quantity developed and described in this work.
The MSSC quantifies how many mutations and which different mutations,
i.e., the mutation space, occur in each amino acid site in a protein.
The MSSC calculates the mutation space of amino acids in a target
protein from the spatially conserved residues in a group of multiple
protein structures. Spatially conserved amino acid residues are identified
based on their relative positions in the protein structure. The MSSC
examines each residue in a target protein, compares it to the residues
present in the same relative position in other protein structures,
and uses physicochemical criteria of mutations found in each conserved
spatial site to quantify the mutation space of each amino acid in
the target protein. The MSSC is analogous to scoring each site in
a multiple sequence alignment but in three-dimensional space considering
the spatial location of residues instead of solely the order in which
they appear in a protein sequence. MSSC analysis was performed on
example cases, and it reproduces the well-known observation that,
regardless of secondary structure, solvent-exposed residues are more
likely to be mutated than internal ones. The MSSC code is available
on GitHub: “https://github.com/Cantu-Research-Group/Mutation_Space”.