Engineering of a fungal nitrilase for improving catalytic activity and reducing by-product formation in the absence of structural information

2016 ◽  
Vol 6 (12) ◽  
pp. 4134-4141 ◽  
Author(s):  
Jin-Song Gong ◽  
Heng Li ◽  
Zhen-Ming Lu ◽  
Xiao-Juan Zhang ◽  
Qiang Zhang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Structural Information ◽  
Product Formation ◽  
Rational Engineering ◽  
Engineering Approach

Semi-rational engineering approach was employed to improve the catalytic activity and reduce the by-product formation of fungal nitrilase.

Significantly increased catalytic activity of Candida antarctica lipase B for the resolution of cis-(±)-dimethyl 1-acetylpiperidine-2,3-dicarboxylate

2018 ◽  
Vol 8 (18) ◽  
pp. 4718-4725 ◽  
Author(s):  
Jiang-Wei Shen ◽  
Jia-Mei Qi ◽  
Xiao-Jian Zhang ◽  
Zhi-Qiang Liu ◽  
Yu-Guo Zheng
Keyword(s):  
Catalytic Activity ◽  
Binding Pocket ◽  
Candida Antarctica ◽  
Candida Antarctica Lipase B ◽  
Candida Antarctica Lipase ◽  
Lipase B ◽  
Rational Engineering ◽  
Engineering Approach

Structure-based semi-rational engineering approach was applied to alter the binding pocket and substrate channel for enhancing the activity of CALB towards moxifloxacin chiral intermediate.

scholarly journals Effect of Iterative Use of Methylcyclohexane as a Hydrogen Carrier on Catalytic Activity and By-product Formation

2019 ◽  
Vol 62 (2) ◽  
pp. 67-73 ◽  
Author(s):  
Xieli CUI ◽  
Mika ISHII ◽  
Taku TSUJIMURA ◽  
Takaaki TANIGUCHI ◽  
Yasushi HASHIMOTO ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Product Formation ◽  
Hydrogen Carrier

scholarly journals Strategies in megasynthase engineering – fatty acid synthases (FAS) as model proteins

2017 ◽  
Vol 13 ◽  
pp. 1204-1211 ◽  
Author(s):  
Manuel Fischer ◽  
Martin Grininger
Keyword(s):  
Fatty Acid ◽  
Bioactive Compounds ◽  
Assembly Line ◽  
Structural Information ◽  
Natural Compounds ◽  
Polyketide Synthases ◽  
Therapeutic Applications ◽  
Rational Engineering ◽  
Fatty Acid Synthases

Megasynthases are large multienzyme proteins that produce a plethora of important natural compounds by catalyzing the successive condensation and modification of precursor units. Within the class of megasynthases, polyketide synthases (PKS) are responsible for the production of a large spectrum of bioactive polyketides (PK), which have frequently found their way into therapeutic applications. Rational engineering approaches have been performed during the last 25 years that seek to employ the “assembly-line synthetic concept” of megasynthases in order to deliver new bioactive compounds. Here, we highlight PKS engineering strategies in the light of the newly emerging structural information on megasynthases, and argue that fatty acid synthases (FAS) are and will be valuable objects for further developing this field.

Investigation of axial ligand effects on catalytic activity of manganese porphyrin, evidence for the importance of hydrogen bonding in cytochrome-P450 model reactions

2014 ◽  
Vol 18 (05) ◽  
pp. 354-365 ◽  
Author(s):  
Elnaz Mesbahi ◽  
Nasser Safari ◽  
Mahin Gheidi
Keyword(s):  
Hydrogen Bonding ◽  
Catalytic Activity ◽  
Product Formation ◽  
Axial Ligand ◽  
Active Species ◽  
Manganese Porphyrin ◽  
Axial Ligands ◽  
Epoxidation Reaction ◽  
Phenyl Rings ◽  
Hydroxy Groups

Various nitrogenous bases, such as imidazoles, pyridines and amines were employed as axial ligands in epoxidation reaction of cyclooctene bytetra-n-butylammonium hydrogen monopersulfate (n- Bu 4 NHSO 5), in the presence of Mn ( III )-tetrakis(2,3-dimethoxyphenyl)porphyrin-acetate ( T (2,3- OMeP ) PorMnOAc ). T (2,3- OMeP ) PorMnOAc is a fairly stable catalyst, with the ability of producing hydrogen bonding. High epoxidation yield of 85 ± 6% was obtained in the presence of imidazole axial ligand with 100% selectivity in 30 min. Higher conversion of around 100% was obtained by pyridine axial base, while selectivity was reduced to 69%. Further epoxidation reactions were also performed using Mn ( III )-Tetrakis(2,3-dihydroxyphenyl)porphyrin-acetate ( T (2,3- OHP ) PorMnOAc ) as catalyst. In addition to the usual electronic and steric effects, it is proposed that the catalytic activity depends on the existence and kind of hydrogen bonding between the axial base and the ortho-methoxy or hydroxy groups on the phenyl rings of manganese porphyrin. The cis to trans ratio of cis-stilbene oxide formed by imidazole and pyridine axial bases were obtained as 7.5 and 2.5 respectively. In addition GC-Ms and UV-vis studies were employed to find the nature of active species and product formation. Our DFT calculations disclosed that pyridine hydrogen bonding with moiety of the macrocycle rings strongly affects the relative energies of S/Q spin states in [ T (2,3- OMeP ) PorMn V ( O )( Py )]+, in that it results in the longer Mn – O bond and reactivity toward substrates.

scholarly journals Development of an integrated structural biology platform specialized for sub-100 kDa protein complexes to support biologics discovery and rational engineering

2021 ◽  
Author(s):  
Yuri Iozzo ◽  
Yu Qiu ◽  
Albert Xu ◽  
Anna Park ◽  
Maria Wendt ◽  
...  
Keyword(s):  
Decision Making ◽  
Structural Biology ◽  
Structural Information ◽  
Protein Complexes ◽  
Rapid Development ◽  
Protein Structures ◽  
Cost Effective ◽  
Particle Orientation ◽  
Dynamics Simulation ◽  
Rational Engineering

Developing a biologic medicine requires successful decision making at each step of selection, optimization, and/or combination of the right candidates at early research stages. Knowing the structural information and binding pattern between drug target and discovery candidates greatly increases the possibility of success. With the cryo-EM resolution revolution and rapid development of computational software, we have evaluated and integrated different tools in structural biology and the computation field and established a highly cost-effective platform, which allows us to obtain fast and accurate structural information for biologics projects with a close to 100% success rate and as fast as weeks turn-around time. Here we report four case studies selected from over 40 different protein structures and share how we integrate cryo-EM structure determination, computational structure modeling, and molecular dynamics simulation. With proper decision making and strategic planning, the platform allows us to obtain quality results within days to weeks, including sub-100 kDa complexes which are usually considered as a challenge due to their small size. Our utilization of this differential approach and use of multiple software packages, allows to manage priorities and resources to achieve goals quickly and efficiently. We demonstrate how to effectively overcome particle orientation bias by altering complex composition. In several of our examples, we use glycan density to facilitate interpretation of low-resolution 3D reconstruction and epitope mapping. Protein information plays an important role in our cryo-EM projects, especially in cases where we see significant challenges in obtaining high-resolution 3D maps.

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