Evaluating the role of trypsin in silk degumming: An in silico approach.
J Biotechnol
; 359: 35-47, 2022 Nov 20.
Article
en En
| MEDLINE
| ID: mdl-36126805
ABSTRACT
The trypsin being universal enzyme forming family of proteases catalyzes the hydrolysis of proteins into amino acids and regenerates the serine hydroxyl an active site. The trypsin enzyme from D. saccharalis, uses sericin as its preferred substrate. Presence of catalytic triad (serine, aspartic acid and histidine) at the substrate binding site of this enzyme is very important for the catalytic activity. In the current study, the interacting mechanism between the substrate sericin protein and enzyme trypsin protein were explored by integrating various computational approaches including physico-chemical properties, biophysical properties, dynamics, gene ontology, molecular docking, protein - protein interactions, binding free energy calculation and structural motifs were studied. The evolutionary study performed by MEGA X showed that trypsin protein sequence (ALE15212.1) is closely related to cocoonase protein sequence (ADG26770.1) from Antheraea pernyi. 3-D models of trypsin and sericin proteins were predicted using I-TASSER and further validated by PROCHECK, and ProSAweb softwares. The predicted trypsin structure model was assigned E.C. no. 3.4.21.4 which refers hydrolytic mechanism. Gene Ontology predicted by QuickGO showed that trypsin has serine hydrolase activity (GO 00017171), and part of proteolysis (GO 0006508) as well as protein metabolic process (GO0019538) actvity. Molecular docking studies between trypsin and sericin proteins were conducted by the HADDOCK 2.4 having best docked protein complex with Z-score - 1.9. 2D and 3D protein-protein interaction was performed with LIGPLOT+ and HAWKDOCK, PDBsum, respectively. The amino acid residues interacting across proteins interface are sericin_chain A representing "Ser133, Tyr214, Thr188, Thr243, Ser225, Ser151, Ser156, His294, Arg293, Gly296â³ and trypsin_chain B "Lys120, Tyr246, Asn119, Glu239, Ser62, Tyr194, Ile197, Ser171, Tyr169, Gly170â³. Based on our results trypsin shows similarity with cocoonase and presumably trypsin can be used as an alternative source in cocoon degumming.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Seda
/
Sericinas
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
J Biotechnol
Asunto de la revista:
BIOTECNOLOGIA
Año:
2022
Tipo del documento:
Article