Indirect
Readout in Protein-Peptide Recognition: A
Different Story from Classical Biomolecular Recognition
Hua Yu
Peng Zhou
Maolin Deng
Zhicai Shang
10.1021/ci5000246.s001
https://acs.figshare.com/articles/journal_contribution/Indirect_Readout_in_Protein_Peptide_Recognition_A_Different_Story_from_Classical_Biomolecular_Recognition/2270401
Protein-peptide interactions are
prevalent and play essential roles
in many living activities. Peptides recognize their protein partners
by direct nonbonded interactions and indirect adjustment of conformations.
Although processes of protein-peptide recognition have been comprehensively
studied in both sequences and structures recently, flexibility of
peptides and the configuration entropy penalty in recognition did
not get enough attention. In this study, 20 protein-peptide complexes
and their corresponding unbound peptides were investigated by molecular
dynamics simulations. Energy analysis revealed that configurational
entropy penalty introduced by restriction of the degrees of freedom
of peptides in indirect readout process of protein-peptide recognition
is significant. Configurational entropy penalty has become the main
content of the indirect readout energy in protein-peptide recognition
instead of deformation energy which is the main source of the indirect
readout energy in classical biomolecular recognition phenomena, such
as protein–DNA binding. These results provide us a better understanding
of protein-peptide recognition and give us some implications in peptide
ligand design.
2014-07-28 00:00:00
readout energy
peptide ligand design
Configurational entropy penalty
configurational entropy penalty
biomolecular recognition phenomena
configuration entropy penalty