Chapter 9
Microbial and Bioinformatics Approach
in Biofuel Production
Tuna Karaytuğ, Nihan Arabacı İstifli, and Erman Salih İstifli
Abstract Due to the increasing world population and ever developing technology,
the need and demand for energy are increasing day by day. In parallel with this, the
tendency to use renewable alternative energy sources instead of limited fossil fuel
reserves is increasing worldwide. Lignocellulosic biomasses which are abundant in
nature with renewable energy potential are preferred in biofuel production. These
raw biomaterials are transformed into forms that can be used in biofuel production
processes by various pretreatment techniques. The physical and chemical methods
commonly used in the pretreatment of the substrate have some limitations. However,
microbial methods for hydrolysis of biomass are quite remarkable. In this study, we
focused on the pretreatment of biomass and microbial enzymes used in biofuel
production process.
Furthermore, due to the increasing applications of molecular interaction simulations in this field, at a small scale, we demonstrate how the molecular docking
technique is able to reveal the interactions between the xylanase enzyme (both wild
type and mutant) isolated from Thermotoga petrophila RKU-1 and its substrate,
xylobiose. In conclusion, molecular interaction simulations (molecular docking and
molecular dynamics) contribute to the fields of bioengineering and genetics as
powerful bioinformatics tools and offer a unique opportunity to study, at the atomic
level, how enzyme-substrate affinity change as a result of induced mutations in the
protein structure.
Keywords Biofuel · Biomass pretreatment · Microbial enzymes · Cocktail
enzymes · Binding free energy · Molecular docking · Molecular dynamics
T. Karaytuğ
Department of Biology, Institute of Natural and Applied Sciences, Cukurova University, Adana,
Turkey
N. Arabacı İstifli (*) · E. S. İstifli
Department of Biology, Faculty of Arts and Sciences, Cukurova University, Adana, Turkey
© The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2021
M. Srivastava et al. (eds.), Bioenergy Research: Basic and Advanced Concepts, Clean
Energy Production Technologies, https://doi.org/10.1007/978-981-33-4611-6_9
257
Microbial and Bioinformatics Approach
in Biofuel Production
Tuna Karaytuğ, Nihan Arabacı İstifli, and Erman Salih İstifli
Abstract Due to the increasing world population and ever developing technology,
the need and demand for energy are increasing day by day. In parallel with this, the
tendency to use renewable alternative energy sources instead of limited fossil fuel
reserves is increasing worldwide. Lignocellulosic biomasses which are abundant in
nature with renewable energy potential are preferred in biofuel production. These
raw biomaterials are transformed into forms that can be used in biofuel production
processes by various pretreatment techniques. The physical and chemical methods
commonly used in the pretreatment of the substrate have some limitations. However,
microbial methods for hydrolysis of biomass are quite remarkable. In this study, we
focused on the pretreatment of biomass and microbial enzymes used in biofuel
production process.
Furthermore, due to the increasing applications of molecular interaction simulations in this field, at a small scale, we demonstrate how the molecular docking
technique is able to reveal the interactions between the xylanase enzyme (both wild
type and mutant) isolated from Thermotoga petrophila RKU-1 and its substrate,
xylobiose. In conclusion, molecular interaction simulations (molecular docking and
molecular dynamics) contribute to the fields of bioengineering and genetics as
powerful bioinformatics tools and offer a unique opportunity to study, at the atomic
level, how enzyme-substrate affinity change as a result of induced mutations in the
protein structure.
Keywords Biofuel · Biomass pretreatment · Microbial enzymes · Cocktail
enzymes · Binding free energy · Molecular docking · Molecular dynamics
T. Karaytuğ
Department of Biology, Institute of Natural and Applied Sciences, Cukurova University, Adana,
Turkey
N. Arabacı İstifli (*) · E. S. İstifli
Department of Biology, Faculty of Arts and Sciences, Cukurova University, Adana, Turkey
© The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2021
M. Srivastava et al. (eds.), Bioenergy Research: Basic and Advanced Concepts, Clean
Energy Production Technologies, https://doi.org/10.1007/978-981-33-4611-6_9
257