Conserved Amino Acid Residues that Affect Structural Stability of Candida boidinii Formate Dehydrogenase

Bulut, Huri; Yüksel, Büşra; Gul, Mehmet; Eren, Meryem; Karataş, Ersin; Kara, Nazlı; Yilmazer, Berin; Koçyiğit, Abdürrahim; Labrou, Nikolaos E.; Bi̇nay, Barış

doi:10.1007/s12010-020-03429-0

Cited by 6 publications

(10 citation statements)

References 22 publications

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“…Studies have reported that conserved residues might play important roles in directing the activity of a certain enzyme. [21][22][23] To exclude conserved residues from the entrance region and choose the optimal size of the randomization site and minimize the labor-determining screening effort, conservation analysis was performed using the ConSurf Server. 24 Five amino acid residues (bPhe41, bMet46, bLeu127, bPro128, and bAla129) with conservation grades lower than seven were chosen as hotspots for mutant library construction (Fig.…”

Section: And S2 †)mentioning

confidence: 99%

Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis

Cheng

Pepłowski

et al. 2022

Chem. Sci.

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Section: And S2 †)mentioning

confidence: 99%

Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis

Cheng

Pepłowski

et al. 2022

Chem. Sci.

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“…Full-length wild-type CbFDH gene was cloned into pET-23a (+) bacterial expression vector with a C-terminal hexahistidine-tag as previously described by Bulut et al [4]. The plasmid was transformed into the competent E. coli BL21 Rosetta-2 strain.…”

Section: Transformation Expression Purification and Crystallizationmentioning

confidence: 99%

“…Many prokaryotic and eukaryotic organisms express NAD + -dependent FDH enzymes with similar structural and kinetic properties [3]. However, many studies have focused on the Candida boidinii NAD +dependent FDH (CbFDH) due to its remarkable stability and activity [4].…”

Section: Introductionmentioning

confidence: 99%

Structural and Dynamic Characterization of Candida boidinii Formate Dehydrogenase by High-Resolution X-ray Crystallography

Gul¹,

Yüksel²,

Bulut³

et al. 2022

Preprint

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Candida boidinii NAD+-dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential applications in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. In this study, we present an atomic X-ray crystal structure of the apo CbFDH to 1.4 Å resolution determined at cryogenic temperature at the Turkish Light Source, “Turkish DeLight”. This structure offers a comprehensive view of the apo enzyme's dynamics, filling the gaps in our understanding from previous studies. Also, comparison of our high-resolution apo and previously available holo enzyme structures reveals major conformational changes of this dynamic enzyme in the absence and presence of the coenzyme and substrate/inhibitor complexes. Collectively all these information may provide invaluable insights into future protein engineering efforts that could enhance enzymatic activity and stability, potentially increasing its efficiency and effectiveness of CbFDH in industrial processes.

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“…Use of directed evolution to design more stable enzymes is now common. With this method, mutant libraries are created by random changes, and the most promising variants are subjected to further rounds of evolution [81][82][83][84][85]. Rational approach based on molecular dynamic (MD) and QM/MM simulations may help in identifying and redesigning variants with increased stability [86].…”

Section: Enzyme Engineeringmentioning

confidence: 99%

From Enzyme Stability to Enzymatic Bioelectrode Stabilization Processes

et al. 2021

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Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.

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Conserved Amino Acid Residues that Affect Structural Stability of Candida boidinii Formate Dehydrogenase

Cited by 6 publications

References 22 publications

Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis

Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis

Structural and Dynamic Characterization of Candida boidinii Formate Dehydrogenase by High-Resolution X-ray Crystallography

From Enzyme Stability to Enzymatic Bioelectrode Stabilization Processes

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