Modeling amide-I vibrations of alanine dipeptide in solution by using neural network protocol.
Spectrochim Acta A Mol Biomol Spectrosc
; 268: 120675, 2022 Mar 05.
Article
em En
| MEDLINE
| ID: mdl-34890871
ABSTRACT
Infrared spectroscopy is a powerful tool for the understanding of molecular structure and function of polypeptides. Theoretical interpretation of IR spectra relies on ab initio calculations may be very costly in computational resources. Herein, we developed a neural network (NN) modeling protocol to evaluate a model dipeptide's backbone amide-I spectra. DFT calculations were performed for the amide-I vibrational motions and structural parameters of alanine dipeptide (ALAD) conformers in different micro-environments ranging from polar to non-polar ones. The obtained backbone dihedrals, C = O bond lengths and amide-I frequencies of ALAD were gather together for NN architecture. The applications of built NN protocols for the prediction of amide-I frequencies of ALAD in other solvation conditions are quite satisfactory with much less computational cost comparing with electronic structure calculations. The results show that this cost-effective way enables us to decipher the polypeptide's dynamic secondary structures and biological functions with their backbone vibrational probes.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Dipeptídeos
/
Amidas
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Spectrochim Acta A Mol Biomol Spectrosc
Assunto da revista:
BIOLOGIA MOLECULAR
Ano de publicação:
2022
Tipo de documento:
Article