scholarly journals Trading off stability against activity in extremophilic aldolases

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Markus Dick ◽  
Oliver H. Weiergräber ◽  
Thomas Classen ◽  
Carolin Bisterfeld ◽  
Julia Bramski ◽  
...  
Keyword(s):  
Network Analysis ◽  
Rational Design ◽  
Enzyme Stability ◽  
Disulfide Bridge ◽  
High Turnover ◽  
Dimer Interface ◽  
Constraint Network ◽  
Hyperthermophilic Enzymes ◽  
Monomeric Proteins ◽  
Hyperthermophilic Organisms

Abstract Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms. We present the first crystal structures of psychrophilic DERAs, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts. Conversion into monomeric proteins showed that the native dimer interface contributes to stability only in the hyperthermophilic enzymes. Nevertheless, introduction of a disulfide bridge in the interface of a psychrophilic DERA did confer increased thermostability, suggesting a strategy for rational design of more durable enzyme variants. Constraint network analysis revealed particularly sparse interactions between the substrate pocket and its surrounding α-helices in psychrophilic DERAs, which indicates that a more flexible active center underlies their high turnover numbers.

scholarly journals Rational design of new NO and redox sensitivity into connexin26 hemichannels

Open Biology ◽  
2015 ◽  
Vol 5 (2) ◽  
pp. 140208 ◽  
Author(s):  
Louise Meigh ◽  
Daniel Cook ◽  
Jie Zhang ◽  
Nicholas Dale
Keyword(s):  
Redox Potential ◽  
Rational Design ◽  
Salt Bridge ◽  
Disulfide Bridge ◽  
Wild Type ◽  
No Donors ◽  
Bridge Formation ◽  
Redox Sensitivity ◽  
Intracellular Redox

CO 2 directly opens hemichannels of connexin26 (Cx26) by carbamylating K125, thereby allowing salt bridge formation with R104 of the neighbouring subunit in the connexin hexamer. The formation of the inter-subunit carbamate bridges within the hexameric hemichannel traps it in the open state. Here, we use insights derived from this model to test whether the range of agonists capable of opening Cx26 can be extended by promoting the formation of analogous inter-subunit bridges via different mechanisms. The mutation K125C gives potential for nitrosylation on Cys125 and formation of an SNO bridge to R104 of the neighbouring subunit. Unlike wild-type Cx26 hemichannels, which are insensitive to NO and NO 2 − , hemichannels comprising Cx26 K125C can be opened by NO 2 − and NO donors. However, NO 2 − was unable to modulate the doubly mutated (K125C, R104A) hemichannels, indicating that an inter-subunit bridge between C125 and R104 is required for the opening action of NO 2 − . In a further test, we introduced two mutations into Cx26, K125C and R104C, to allow disulfide bridge formation across the inter-subunit boundary. These doubly mutated hemichannels open in response to changes in intracellular redox potential.

scholarly journals Engineering a Pseudo-26-kDa Schistosoma Glutathione Transferase from bovis/haematobium for Structure, Kinetics, and Ligandin Studies

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1844
Author(s):  
Neo Padi ◽  
Blessing Oluebube Akumadu ◽  
Olga Faerch ◽  
Chinyere Aloke ◽  
Vanessa Meyer ◽  
...  
Keyword(s):  
Glutathione Transferase ◽  
Specific Activity ◽  
Enzyme Stability ◽  
Competitive Inhibitor ◽  
Spectroscopic Studies ◽  
Complete Sequence ◽  
Detoxification Enzymes ◽  
Ligand Docking ◽  
Sequence Information ◽  
Dimer Interface

Glutathione transferases (GSTs) are the main detoxification enzymes in schistosomes. These parasitic enzymes tend to be upregulated during drug treatment, with Schistosoma haematobium being one of the species that mainly affect humans. There is a lack of complete sequence information on the closely related bovis and haematobium 26-kDa GST isoforms in any database. Consequently, we engineered a pseudo-26-kDa S. bovis/haematobium GST (Sbh26GST) to understand structure–function relations and ligandin activity towards selected potential ligands. Sbh26GST was overexpressed in Escherichia coli as an MBP-fusion protein, purified to homogeneity and catalyzed 1-chloro-2,4-dinitrobenzene-glutathione (CDNB-GSH) conjugation activity, with a specific activity of 13 μmol/min/mg. This activity decreased by ~95% in the presence of bromosulfophthalein (BSP), which showed an IC50 of 27 µM. Additionally, enzyme kinetics revealed that BSP acts as a non-competitive inhibitor relative to GSH. Spectroscopic studies affirmed that Sbh26GST adopts the canonical GST structure, which is predominantly α-helical. Further extrinsic 8-anilino-1-naphthalenesulfonate (ANS) spectroscopy illustrated that BSP, praziquantel (PZQ), and artemisinin (ART) might preferentially bind at the dimer interface or in proximity to the hydrophobic substrate-binding site of the enzyme. The Sbh26GST-BSP interaction is both enthalpically and entropically driven, with a stoichiometry of one BSP molecule per Sbh26GST dimer. Enzyme stability appeared enhanced in the presence of BSP and GSH. Induced fit ligand docking affirmed the spectroscopic, thermodynamic, and molecular modelling results. In conclusion, BSP is a potent inhibitor of Sbh26GST and could potentially be rationalized as a treatment for schistosomiasis.

scholarly journals Plant purple acid phosphatases - genes, structures and biological function.

2003 ◽  
Vol 50 (4) ◽  
pp. 1245-1256 ◽  
Author(s):  
Mariusz Olczak ◽  
Bronisława Morawiecka ◽  
Wiesław Watorek
Keyword(s):  
Disulfide Bridge ◽  
Acid Phosphatases ◽  
Amino Acid Residues ◽  
Disulfide Bridges ◽  
Inorganic Pyrophosphate ◽  
Manganese Ion ◽  
Substrate Preferences ◽  
Purple Acid Phosphatases ◽  
Single Polypeptide ◽  
Monomeric Proteins

The properties of plant purple acid phosphatases (PAPs), metallophosphoesterases present in some bacteria, plants and animals are reviewed. All members of this group contain a characteristic set of seven amino-acid residues involved in metal ligation. Animal PAPs contain a binuclear metallic center composed of two irons, whereas in plant PAPs one iron ion is joined by zinc or manganese ion. Among plant PAPs two groups can be distinguished: small PAPs, monomeric proteins with molecular mass around 35 kDa, structurally close to mammalian PAPs, and large PAPs, homodimeric proteins with a single polypeptide of about 55 kDa. Large plant PAPs exhibit two types of structural organization. One type comprises enzymes with subunits bound by a disulfide bridge formed by cysteines located in the C-terminal region around position 350. In the second type no cysteines are located in this position and no disulfide bridges are formed between subunits. Differences in structural organisation are reflected in substrate preferences. Recent data reveal in plants the occurrence of metallophosphoesterases structurally different from small or large PAPs but with metal-ligating sequences characteristic for PAPs and expressing pronounced specificity towards phytate or diphosphate nucleosides and inorganic pyrophosphate.

Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge at the Dimer–Dimer Interface

2003 ◽  
Vol 334 (4) ◽  
pp. 811-821 ◽  
Author(s):  
Alexandra Bjørk ◽  
Bjørn Dalhus ◽  
Dimitrios Mantzilas ◽  
Vincent G.H. Eijsink ◽  
Reidun Sirevåg
Keyword(s):  
Malate Dehydrogenase ◽  
Disulfide Bridge ◽  
Dimer Interface

Engineering of ωTransaminase for Effective Production of Chiral Amines

2020 ◽  
Vol 17 (6) ◽  
pp. 2827-2832
Author(s):  
Mitra Mirzaei ◽  
Per Berglund
Keyword(s):  
Active Site ◽  
Rational Design ◽  
Enzyme Stability ◽  
Building Blocks ◽  
Site Directed Mutagenesis ◽  
Saturation Mutagenesis ◽  
Rational Approach ◽  
Chiral Amines ◽  
Enzyme Specificity ◽  
Screening Assay

ωTransaminases are pyridoxal-5-phosphat (PLP) dependent enzymes having the ability to catalyze the transference of an amino group to a keto compound. These enzymes are used for production of chiral amines which are important building blocks in pharmaceutical industry. There is often a need to improve enzyme properties such as enzyme stability, enzyme specificity and to decrease substrate-product inhibition. Here, protein engineering was applied to improve the enzyme activity of the enzyme from Chromobacterium violaceum Rational-design and site-directed mutagenesis were applied on position of (W60) in the active site of the enzyme. Different mutated enzyme variants such as W60H, W60F and W60Y were made. Also, the enantiopreference of the wild type enzyme was reversed to produce (R)-chiral amines. For this aim, a screening assay was followed by semi-rational approach and saturation mutagenesis in the active site of the enzyme. Creating the mutated enzyme libraries resulted to obtaining two enzyme variants. Their properties were low enantiopreference towards formations of (R)-enantiopreference and low specific constant ratio between fast and slow enantiomers (Evalue around one).

scholarly journals In SilicoRational Design and Systems Engineering of Disulfide Bridges in the Catalytic Domain of an Alkaline α-Amylase from Alkalimonas amylolytica To Improve Thermostability

2013 ◽  
Vol 80 (3) ◽  
pp. 798-807 ◽  
Author(s):  
Long Liu ◽  
Zhuangmei Deng ◽  
Haiquan Yang ◽  
Jianghua Li ◽  
Hyun-dong Shin ◽  
...  
Keyword(s):  
Systems Engineering ◽  
Rational Design ◽  
Catalytic Domain ◽  
Disulfide Bridge ◽  
Biochemical Properties ◽  
Bridge Engineering ◽  
High Catalytic Activity ◽  
Disulfide Bridges ◽  
Wild Type ◽  
Triple Mutant

ABSTRACTHigh thermostability is required for alkaline α-amylases to maintain high catalytic activity under the harsh conditions used in textile production. In this study, we attempted to improve the thermostability of an alkaline α-amylase fromAlkalimonas amylolyticathroughin silicorational design and systems engineering of disulfide bridges in the catalytic domain. Specifically, 7 residue pairs (P35-G426, Q107-G167, G116-Q120, A147-W160, G233-V265, A332-G370, and R436-M480) were chosen as engineering targets for disulfide bridge formation, and the respective residues were replaced with cysteines. Three single disulfide bridge mutants—P35C-G426C, G116C-Q120C, and R436C-M480C—of the 7 showed significantly enhanced thermostability. Combinational mutations were subsequently assessed, and the triple mutant P35C-G426C/G116C-Q120C/R436C-M480C showed a 6-fold increase in half-life at 60°C and a 5.2°C increase in melting temperature compared with the wild-type enzyme. Interestingly, other biochemical properties of this mutant also improved: the optimum temperature increased from 50°C to 55°C, the optimum pH shifted from 9.5 to 10.0, the stable pH range extended from 7.0 to 11.0 to 6.0 to 12.0, and the catalytic efficiency (kcat/Km) increased from 1.8 × 104to 2.4 × 104liters/g · min. The possible mechanism responsible for these improvements was explored through comparative analysis of the model structures of wild-type and mutant enzymes. The disulfide bridge engineering strategy used in this work may be applied to improve the thermostability of other industrial enzymes.

scholarly journals Characterizing Activity and Thermostability of GH5 Cellulase Chimeras from Mesophilic and Thermophilic Parents

2018 ◽  
Author(s):  
Fei Zheng ◽  
Josh V. Vermaas ◽  
Jie Zheng ◽  
Yuan Wang ◽  
Tao Tu ◽  
...  
Keyword(s):  
Thermal Properties ◽  
Rational Design ◽  
Enzyme Stability ◽  
Catalytic Efficiency ◽  
Industrial Applications ◽  
Essential Property ◽  
Tim Barrel ◽  
Dynamics Simulations ◽  
Temperature Optima ◽  
Hybrid Enzymes

ABSTRACTCellulases from glycoside hydrolase (GH) family 5 are key enzymes in the degradation of diverse polysaccharide substrates and are used in industrial enzyme cocktails to break down biomass. The GH5 family shares a canonical (βα)8-barrel structure, where each (βα) module is essential for the enzyme stability and activity. Despite their shared topology, the thermostability of GH5 enzymes can vary significantly, and highly thermostable variants are often sought for industrial applications. Based on a previously characterized thermophilic GH5 cellulase from Talaromyces emersonii (TeEgl5A, with an optimal temperature of 90°C), we created ten hybrid enzymes with the mesophilic cellulase from Prosthecium opalus (PoCel5) to determine which elements are responsible for enhanced thermostability. Five of the expressed hybrid enzymes exhibit enzyme activity. Two of these hybrids exhibited pronounced increases in the temperature optima (10 and 20°C), T50 (15 and 19°C), Tm (16.5 and 22.9°C), and extended half life, t1/2 (~240- and 650-fold at 55°C) relative to the mesophilic parent enzyme, and demonstrated improved catalytic efficiency on selected substrates. The successful hybridization strategies were validated experimentally in another GH5 cellulase from Aspergillus nidulans (AnCel5), which demonstrated a similar increase in thermostability. Based on molecular dynamics simulations (MD) of both PoCel5 and TeEgl5A parent enzymes as well as their hybrids, we hypothesize that improved hydrophobic packing of the interface between α2 and α3 is the primary mechanism by which the hybrid enzymes increase their thermostability relative to the mesophilic parent PoCel5.IMPORTANCEThermal stability is an essential property of enzymes in many industrial biotechnological applications, as high temperatures improve bioreactor throughput. Many protein engineering approaches, such as rational design and directed evolution, have been employed to improve the thermal properties of mesophilic enzymes. Structure-based recombination has also been used to fuse TIM-barrel fragments and even fragments from unrelated folds, to generate new structures. However, there are not many research on GH5 cellulases. In this study, two GH5 cellulases, which showed TIM-barrel structure, PoCel5 and TeEgl5A with different thermal properties were hybridized to study the roles of different (βα) motifs. This work illustrates the role that structure guided recombination can play in helping to identify sequence function relationships within GH5 enzymes by supplementing natural diversity with synthetic diversity.

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