Molecular simulation of PcCel45A protein expressed from Aspergillus nidulans to understand its structure, dynamics, and thermostability

ÜNAL M. A., BOYACIOĞLU B., ÜNVER H., ELMALI A.

JOURNAL OF MOLECULAR MODELING, cilt.25, sa.11, 2019 (SCI-Expanded) identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 25 Sayı: 11
  • Basım Tarihi: 2019
  • Doi Numarası: 10.1007/s00894-019-4175-4
  • Dergi Adı: JOURNAL OF MOLECULAR MODELING
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Anahtar Kelimeler: Molecular dynamics, PCcel45A, FORCE-FIELD, GROMACS, CELLULOSE, ENZYMES, TUBERS
  • Ankara Üniversitesi Adresli: Evet

Özet

PACS and mathematical subject classification numbers as needed. Molecular dynamic simulation is a very usable tool to understand various factors, including structure temperature dependence, dynamics, and stability for protein structure. The three main components, namely endoglucanase, exoglucanase, and beta-glucosidase, effectively convert lignocellulosic biomass into fermentable sugar. Cellulose is the major component of plant cell walls and is the most abundant organic compound on the earth. Somewhat organisms can use cellulose as a food source, possessing cellulases (cellobiohydrolases and endoglucanases) that can catalyze the hydrolysis of the beta-(1,4) glycosidic bonds. In this work, we investigated conformational and structural properties of PcCel45A protein by changing at temperatures with 300 K, 333 K, and 352 K. We found that the ASN92 residue was the major contributor to the stability of structure; some other residues correlated significantly with thermal stability. We also compared the theoretical results of the current study with the experimental ones published in previous studies.