Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm

Abstract

One of the major constraints limiting the use of abundantly available lignocellulosic biomass as potential feedstock for alcohol industry is the lack of C₆/C₅ co-sugar fermenting yeast. The present study explores a mutant yeast Pichia kudriavzevii BGY1-γm as a potential strain for bioconversion of glucose/xylose sugars of green biomass into ethanol under batch fermentation. The mutant strain having higher alcohol dehydrogenase activity (11.31%) showed significantly higher ethanol concentration during co-fermentation of glucose/xylose sugars (14.2%) as compared to the native strain. Based on 99% sequence similarity of ADH encoding gene from the mutant with the gene sequences from other yeast strains, the ADH enzyme was identified as ADH-1 type. The study reveals first three-dimensional model of ADH-1 utilizing glucose/xylose sugars from P. kudriavzevii BGY1-γm (PkADH mutant). The refined and validated model of PkADH mutant was used for molecular docking against the substrate (acetaldehyde) and product (ethanol). Molecular docking results showed that substrate and product exhibited a binding affinity of −4.55 and −4.5 kcal/mol with PkADH mutant. Acetaldehyde and ethanol interacted at the active site of PkADH mutant via hydrogen bonds (Ser42, His69 and Asp163) and hydrophobic interactions (Cys40, Ser42, His69, Cys95, Trp123 and Asp163) to form the stable protein–ligand complex. Molecular dynamics analysis revealed that PkADH-mutant acetaldehyde and PkADH-mutant ethanol complexes were more stable than PkADH mutant. MMPBSA binding energy confirmed that binding of substrate and product results in the formation of a lower energy stable protein–ligand complex.

Communicated by Ramaswamy H. Sarma

Keywords:

• Pichia kudriavzevii
• alcohol dehydrogenase
• co-fermentation
• molecular docking
• molecular dynamics

Acknowledgments

Thanks to Director Experiment Station, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India, for providing technical and financial support. This study made use of NMRbox: National Center for Biomolecular NMR Data Processing and Analysis, a Biomedical Technology Research Resource (BTRR), which is supported by NIH grant no. P41GM111135 (NIGMS).

Disclosure statement

No conflict of interest is reported by the authors