Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field.
In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector. A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained.
CNR-Institute of Chemistry of Organometallic Compounds-UOS Pisa, Pisa, Italy. sapeptides@gmail.com
Susanna
S
Monti
Alessandro
A
Corozzi
Peter
P
Fristrup
Kaushik L
KL
Joshi
Yun Kyung
YK
Shin
Peter
P
Oelschlaeger
Adri C T
AC
van Duin
Vincenzo
V
Barone
D005998:Glycine / Q000737:chemistry*; D007700:Kinetics; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012996:Solutions
D010455:Peptides; D011506:Proteins; D012996:Solutions; D005998:Glycine