ct401087a_si_001.pdf (412.29 kB)
Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins
journal contribution
posted on 2015-12-17, 02:32 authored by Sai J. Ganesan, S. MatysiakWe present a generic solvated coarse-grained
protein model that
can be used to characterize the driving forces behind protein folding.
Each amino acid is coarse-grained with two beads, a backbone, and
a side chain. Although the backbone beads are modeled as polar entities,
side chains are hydrophobic, polar, or charged, thus allowing the
exploration of how sequence patterning determines a protein fold.
The change in orientation of the atoms of the coarse-grained unit
is captured by the addition of two oppositely charged dummy particles
inside the backbone coarse-grained bead. These two dummy charges represent
a dipole that can fluctuate, thus introducing structural polarization
into the coarse-grained model. Realistic α/β content is
achieved de novo without any biases in the force
field toward a particular secondary structure. The dipoles created
by the dummy particles interact with each other and drive the protein
models to fold into unique structures depending on the amino acid
patterning and presence of capping residues. We have also characterized
the role of dipole–dipole and dipole–charge interactions
in shaping the secondary and supersecondary structure of proteins.
Formation of helix bundles and β-strands are also discussed.