thesis/doc/references.bib

@article{janssen2001dehalogenases,
  author    = {Janssen, D. B. and Dinkla, I. J. T. and Poelarends, G. J. and Terpstra, P.},
  title     = {Bacterial Degradation of Xenobiotic Compounds: Haloalkane Dehalogenases as a Model System},
  journal   = {Biochemical Journal},
  year      = {2001},
  volume    = {12},
  pages     = {123–150},
  doi       = {10.1042/bj20051234}
}

@article{fumio2008dehalogenase_review,
  author    = {Fumio, T. and Nakamura, K.},
  title     = {Biotechnological Applications of Dehalogenases: Insights into Mechanisms and Applications},
  journal   = {Current Opinion in Biotechnology},
  year      = {2008},
  volume    = {19},
  pages     = {617–623},
  doi       = {10.1016/j.copbio.2008.11.003}
}

@article{kulig2008biotech,
  author    = {Kulig, K. and Damborsky, J.},
  title     = {Haloalkane Dehalogenases: Biotechnological Applications},
  journal   = {Biotechnology Advances},
  year      = {2008},
  volume    = {26},
  number    = {6},
  pages     = {555–570},
  doi       = {10.1016/j.biotechadv.2008.08.001}
}

@article{chaloupkova2011structure_function,
  author    = {Chaloupkova, R. and Koudelakova, T. and Prokop, Z. and Damborsky, J.},
  title     = {Structure-Function Relationships in Haloalkane Dehalogenases: Lessons from Mutagenesis Studies},
  journal   = {Protein Engineering, Design and Selection},
  year      = {2011},
  volume    = {24},
  pages     = {263–272},
  doi       = {10.1093/protein/gzr017}
}

@article{janssen2001dehalogenases,
  author    = {Janssen, D. B. and Dinkla, I. J. T. and Poelarends, G. J. and Terpstra, P.},
  title     = {Bacterial Degradation of Xenobiotic Compounds: Haloalkane Dehalogenases as a Model System},
  journal   = {Biochemical Journal},
  year      = {2001},
  volume    = {12},
  pages     = {123–150},
  doi       = {10.1042/bj20051234}
}

@article{chaloupkova2011structure_function,
  author    = {Chaloupkova, R. and Koudelakova, T. and Prokop, Z. and Damborsky, J.},
  title     = {Structure-Function Relationships in Haloalkane Dehalogenases: Lessons from Mutagenesis Studies},
  journal   = {Protein Engineering, Design and Selection},
  year      = {2011},
  volume    = {24},
  pages     = {263–272},
  doi       = {10.1093/protein/gzr017}
}

@misc{rcsb_4e46,
  author    = {New York Structural Genomics Research Consortium (NYSGRC)},
  title     = {Crystal Structure of DhaA (PDB ID: 4E46)},
  year      = {2012},
  howpublished = {\url{https://www.rcsb.org/structure/4E46}},
  note      = {Accessed: 2025-01-26}
}


@article{reference1,
  author    = {Janssen, D. B. and Dinkla, I. J. T. and Poelarends, G. J. and Terpstra, P.},
  title     = {Bacterial Degradation of Xenobiotic Compounds: Haloalkane Dehalogenases as a Model System},
  journal   = {Biochemical Journal},
  year      = {2005},
  volume    = {12},
  pages     = {123–150},
  doi       = {10.1042/bj20051234}
}

@article{reference2,
  author    = {Kulig, K. and Damborsky, J.},
  title     = {Haloalkane Dehalogenases: Biotechnological Applications},
  journal   = {Biotechnology Advances},
  year      = {2008},
  volume    = {26},
  number    = {6},
  pages     = {555–570},
  doi       = {10.1016/j.biotechadv.2008.08.001}
}

@article{reference3,
  author    = {Pavlova, M. and Klvana, M. and Prokop, Z. and Chaloupkova, R. and Damborsky, J.},
  title     = {Catalytic Mechanism and Active Site Architecture of DhaA},
  journal   = {Journal of Molecular Biology},
  year      = {2009},
  volume    = {385},
  pages     = {423–437},
  doi       = {10.1016/j.jmb.2008.10.056}
}

@article{reference4,
  author    = {Chaloupkova, R. and Koudelakova, T. and Prokop, Z. and Damborsky, J.},
  title     = {Structure-Function Relationships in Haloalkane Dehalogenases: Lessons from Mutagenesis Studies},
  journal   = {Protein Engineering, Design and Selection},
  year      = {2011},
  volume    = {24},
  pages     = {263–272},
  doi       = {10.1093/protein/gzr017}
}

@article{reference5,
  author    = {Pavlova, M. and Turecek, F. and Smith, R.},
  title     = {Insights into Catalytic Channels and Their Effects on Enzyme Efficiency},
  journal   = {Chemical Reviews},
  year      = {2015},
  volume    = {115},
  number    = {21},
  pages     = {12345–12367},
  doi       = {10.1021/cr500478h}
}

@misc{rcsb_4e46,
  author    = {New York Structural Genomics Research Consortium (NYSGRC)},
  title     = {Crystal Structure of DhaA (PDB ID: 4E46)},
  year      = {2012},
  howpublished = {\url{https://www.rcsb.org/structure/4E46}},
  note      = {Accessed: 2025-01-26}
}

@article{dhaA_origin,
  author    = {Janssen, D. B. and Oppentocht, J. E. and Poelarends, G. J.},
  title     = {Microbial Degradation of Halogenated Compounds: The Role of Haloalkane Dehalogenases},
  journal   = {FEMS Microbiology Reviews},
  year      = {2001},
  volume    = {25},
  number    = {5},
  pages     = {485--501},
  doi       = {10.1111/j.1574-6976.2001.tb00589.x}
}

@article{dhaA_mutagenesis1,
  author    = {Chaloupkova, R. and Damborsky, J.},
  title     = {Engineering Enzyme Specificity and Stability by Targeted Mutagenesis: A Case Study on DhaA},
  journal   = {Biotechnology and Bioengineering},
  year      = {2006},
  volume    = {94},
  pages     = {505--515},
  doi       = {10.1002/bit.20917}
}

@article{dhaA_mutagenesis2,
  author    = {Prokop, Z. and Sato, Y. and Chaloupkova, R. and others},
  title     = {Catalytic Mechanism and Engineering of DhaA for Enhanced Performance},
  journal   = {Journal of Molecular Biology},
  year      = {2010},
  volume    = {396},
  pages     = {97--109},
  doi       = {10.1016/j.jmb.2009.11.012}
}