scholarly journals Engineering CGTase to improve synthesis of alkyl glycosides

Glycobiology ◽  
2020 ◽  
Author(s):  
Kazi Zubaida Gulshan Ara ◽  
Javier A Linares-Pastén ◽  
Jonas Jönsson ◽  
Maria Viloria-Cols ◽  
Stefan Ulvenlund ◽  
...  
Keyword(s):  
Double Mutant ◽  
Coupling Reaction ◽  
Fold Increase ◽  
Active Site Residues ◽  
Triple Mutant ◽  
Coupling Product ◽  
Alkyl Glycosides ◽  
Alkyl Glycoside ◽  
Dodecyl Maltoside ◽  
Elongation Process

Abstract Alkyl glycoside surfactants with elongated carbohydrate chains are useful in different applications due to their improved biocompatibility. Cyclodextrin glucanotransferases can catalyze the elongation process through the coupling reaction. However, due to the presence of a hydrophobic tail, the interaction between an alkyl glycoside acceptor and the active site residues is weaker than the interaction with maltooligosaccharides at the corresponding site. Here we report the mutations of F197, G263 and E266 near the acceptor subsites in the CGTase CspCGT13 from Carboxydocella sp. The results showed that substitutions of both F197 and G263 were important for the binding of acceptor substrate dodecyl maltoside during coupling reaction. The double mutant F197Y/G263A showed enhanced coupling activity and displayed a 2-fold increase of the primary coupling product using γ-cyclodextrin as donor when compared to wildtype CspCGT13. Disproportionation activity was also reduced, which was also the case for another double mutant (F197Y/E266A) that however not showed the corresponding increase in coupling. A triple mutant F197Y/G263A/E266A maintained the increase in primary coupling product (1.8-fold increase) using dodecyl maltoside as acceptor, but disproportionation was approximately at the same level as in the double mutants. In addition, hydrolysis of starch was slightly increased by the F197Y and G263A substitutions, indicating that interactions at both positions influenced the selectivity between glycosyl and alkyl moieties.

scholarly journals Complex Patterns of Protease Inhibitor Resistance among Antiretroviral Treatment-Experienced HIV-2 Patients from Senegal: Implications for Second-Line Therapy

2013 ◽  
Vol 57 (6) ◽  
pp. 2751-2760 ◽  
Author(s):  
Dana N. Raugi ◽  
Robert A. Smith ◽  
Selly Ba ◽  
Macoumba Toure ◽  
Fatou Traore ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protease Inhibitor ◽  
Fold Increase ◽  
Cross Resistance ◽  
Second Line ◽  
Triple Mutant ◽  
Second Line Therapy ◽  
Line Therapy ◽  
The Mean ◽  
Complex Patterns

ABSTRACTProtease inhibitor (PI)-based antiretroviral therapy (ART) can effectively suppress HIV-2 plasma load and increase CD4 counts; however, not all PIs are equally active against HIV-2, and few data exist to support second-line therapy decisions. To identify therapeutic options for HIV-2 patients failing ART, we evaluated the frequency of PI resistance-associated amino acid changes in HIV-2 sequences from a cohort of 43 Senegalese individuals receiving unboosted indinavir (n= 18 subjects)-, lopinavir/ritonavir (n= 4)-, or indinavir and then lopinavir/ritonavir (n= 21)-containing ART. Common protease substitutions included V10I, V47A, I54M, V71I, I82F, I84V, L90M, and L99F, and most patients harbored viruses containing multiple changes. Based on genotypic data, we constructed a panel of 15 site-directed mutants of HIV-2ROD9containing single- or multiple-treatment-associated amino acid changes in the protease-encoding region ofpol. We then quantified the susceptibilities of the mutants to the HIV-2 “active” PIs saquinavir, lopinavir, and darunavir using a single-cycle assay. Relative to wild-type HIV-2, the V47A mutant was resistant to lopinavir (6.3-fold increase in the mean 50% effective concentration [EC50]), the I54M variant was resistant to darunavir and lopinavir (6.2- and 2.7-fold increases, respectively), and the L90M mutant was resistant to saquinavir (3.6-fold increase). In addition, the triple mutant that included I54M plus I84V plus L90M was resistant to all three PIs (31-, 10-, and 3.8-fold increases in the mean EC50for darunavir, saquinavir, and lopinavir, respectively). Taken together, our data demonstrate that PI-treated HIV-2 patients frequently harbor viruses that exhibit complex patterns of PI cross-resistance. These findings suggest that sequential PI-based regimens for HIV-2 treatment may be ineffective.

scholarly journals Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol

2019 ◽  
Vol 295 (2) ◽  
pp. 597-609 ◽  
Author(s):  
Taeho Kim ◽  
Peter J. Stogios ◽  
Anna N. Khusnutdinova ◽  
Kayla Nemr ◽  
Tatiana Skarina ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Thermotoga Maritima ◽  
Fold Increase ◽  
Site Directed Mutagenesis ◽  
Bacillus Halodurans ◽  
Active Site Residues ◽  
Carbon Carbon Bond ◽  
Condensation Activity

Carbon–carbon bond formation is one of the most important reactions in biocatalysis and organic chemistry. In nature, aldolases catalyze the reversible stereoselective aldol addition between two carbonyl compounds, making them attractive catalysts for the synthesis of various chemicals. In this work, we identified several 2-deoxyribose-5-phosphate aldolases (DERAs) having acetaldehyde condensation activity, which can be used for the biosynthesis of (R)-1,3-butanediol (1,3BDO) in combination with aldo-keto reductases (AKRs). Enzymatic screening of 20 purified DERAs revealed the presence of significant acetaldehyde condensation activity in 12 of the enzymes, with the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli. The crystal structures of BH1352 and TM1559 at 1.40–2.50 Å resolution are the first full-length DERA structures revealing the presence of the C-terminal Tyr (Tyr224 in BH1352). The results from structure-based site-directed mutagenesis of BH1352 indicated a key role for the catalytic Lys155 and other active-site residues in the 2-deoxyribose-5-phosphate cleavage and acetaldehyde condensation reactions. These experiments also revealed a 2.5-fold increase in acetaldehyde transformation to 1,3BDO (in combination with AKR) in the BH1352 F160Y and F160Y/M173I variants. The replacement of the WT BH1352 by the F160Y or F160Y/M173I variants in E. coli cells expressing the DERA + AKR pathway increased the production of 1,3BDO from glucose five and six times, respectively. Thus, our work provides detailed insights into the molecular mechanisms of substrate selectivity and activity of DERAs and identifies two DERA variants with enhanced activity for in vitro and in vivo 1,3BDO biosynthesis.

scholarly journals Genetic interactions and functional analyses of the fission yeast gsk3 and amk2 single and double mutants defective in TORC1-dependent processes

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Charalampos Rallis ◽  
StJohn Townsend ◽  
Jürg Bähler
Keyword(s):  
Fission Yeast ◽  
Double Mutant ◽  
Genetic Interaction ◽  
Genetic Network ◽  
Cellular Growth ◽  
Regulatory Subunit ◽  
Triple Mutant ◽  
Network Information ◽  
Damage Repair ◽  
Dependent Processes

Abstract The Target of Rapamycin (TOR) signalling network plays important roles in aging and disease. The AMP-activated protein kinase (AMPK) and the Gsk3 kinase inhibit TOR during stress. We performed genetic interaction screens using synthetic genetic arrays (SGA) with gsk3 and amk2 as query mutants, the latter encoding the regulatory subunit of AMPK. We identified 69 negative and 82 positive common genetic interactors, with functions related to cellular growth and stress. The 120 gsk3-specific negative interactors included genes functioning in translation and ribosomes. The 215 amk2-specific negative interactors included genes functioning in chromatin silencing and DNA damage repair. Both amk2- and gsk3-specific interactors were enriched in phenotype categories related to abnormal cell size and shape. We also performed SGA screen with the amk2 gsk3 double mutant as a query. Mutants sensitive to 5-fluorouracil, an anticancer drug are under-represented within the 305 positive interactors specific for the amk2 gsk3 query. The triple-mutant SGA screen showed higher number of negative interactions than the double mutant SGA screens and uncovered additional genetic network information. These results reveal common and specialized roles of AMPK and Gsk3 in mediating TOR-dependent processes, indicating that AMPK and Gsk3 act in parallel to inhibit TOR function in fission yeast.

scholarly journals Rational Engineering of Hydratase from Lactobacillus Acidophilus Reveals Critical Residues Directing Substrate Specificity and Regioselectivity

2019 ◽  
Author(s):  
Bekir Engin Eser ◽  
Michal Poborsky ◽  
Rongrong Dai ◽  
Shigenobu Kishino ◽  
Anita Ljubic ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Substrate Specificity ◽  
Lactobacillus Acidophilus ◽  
Catalytic Efficiency ◽  
Fold Increase ◽  
Wild Type ◽  
Active Site Residues ◽  
Diverse Range ◽  
Preparative Scale ◽  
Conversion Rates

<div>Enzymatic conversion of abundant fatty acids (FAs) through fatty acid hydratases (FAHs) presents an environment-friendly and efficient route for production of high-value hydroxy fatty acids (HFAs). However, a limited diversity was achieved among HFAs to date with respect to chain length and hydroxy group position, due to high substrate- and regio-selectivity of hydratases. In this study, we compared two highly similar FAHs from <i>Lactobacillus acidophilus</i>: FA-HY2 has narrow substrate scope and strict regioselectivity, whereas FA-HY1 utilize longer chain substrates and hydrate various double bond positions. We reveal three active-site residues that play remarkable role in directing substrate specificity and regioselectivity of hydration. When these residues on FA-HY2 are mutated to the corresponding residues in FA-HY1, we observe a significant expansion of substrate scope and distinct shift and enhancement in hydration of double bonds towards omega-end of FAs. A three-residue mutant of FA-HY2 (TM-FA-HY2; T391S/H393S/I378P) displayed an impressive reversal of regioselectivity towards linoleic acid, shifting ratio of the HFA product regioisomers (10-OH:13-OH) from 99:1 to 12:88. Although kcat values are still low in comparison to wild-type FA-HY1, TM-FA-HY2 exhibited about 60-fold increase in catalytic efficiency (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub>) compared to wild-type FA-HY2. Important changes in regioselectivity were also observed with mutant enzymes for arachidonic acid and C18 PUFAs. In addition, TM-FA-HY2 variant exhibited high conversion rates for <i>cis</i>-5, <i>cis</i>-8, <i>cis</i>-11,<i> cis</i>-14, <i>cis</i>-17-eicosapentaenoic acid (EPA) and <i>cis</i>-8, <i>cis</i>-11, <i>cis</i>-14-eicosatrienoic acid (ETA) at preparative scale and enabled isolation of 12-hydroxy products with moderate yields. Furthermore, we demonstrated the potential of microalgae as a source of diverse FAs for HFA production. Our study paves the way for tailor-made FAH design and for efficient conversion of FA sources into diverse range of HFAs with high potential for various applications from polymer industry to medical field.</div><div><br></div>

scholarly journals Synthesis of New 1H-1,2,3-Triazole Analogs in Aqueous Medium via “Click” Chemistry: A Novel Class of Potential Carbonic Anhydrase-II Inhibitors

2021 ◽  
Vol 9 ◽  
Author(s):  
Satya Kumar Avula ◽  
Majid Khan ◽  
Sobia Ahsan Halim ◽  
Ajmal Khan ◽  
Samia Ahmed Al-Riyami ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Aqueous Medium ◽  
Coupling Reaction ◽  
Cross Coupling ◽  
Carbonic Anhydrase Ii ◽  
Polar Group ◽  
Active Site Residues ◽  
Cross Coupling Reaction ◽  
Inhibitory Potential

A series of novel 1H-1,2,3-triazole analogs (9a–j) were synthesized via “Click” chemistry and Suzuki–Miyaura cross-coupling reaction in aqueous medium. The compounds were evaluated for their carbonic anhydrase-II enzyme inhibitory activity in vitro. The synthesis of triazole 7a was accomplished using (S)-(-) ethyl lactate as a starting material. This compound (7a) underwent Suzuki–Miyaura cross-coupling reaction with different arylboronic acids in aqueous medium to afford the target molecules, 9a–j in good yields. All newly synthesized compounds were characterized by 1H NMR, 13C NMR, FT-IR, HRMS, and where applicable 19F NMR spectroscopy (9b, 9e, 9h, and 9j). The new compounds have shown moderate inhibition potential against carbonic anhydrase-II enzyme. A preliminary structure-activity relationship suggested that the presence of polar group at the 1H-1,2,3-triazole substituted phenyl ring in these derivatives (9a–j) has contributed to the overall activity of these compounds. Furthermore, via molecular docking, it was deduced that the compounds exhibit inhibitory potential through direct binding with the active site residues of carbonic anhydrase-II enzyme. This study has unraveled a new series of triazole derivatives as good inhibitors against carbonic anhydrase-II.

scholarly journals Kinetic Profile and Molecular Dynamic Studies Show that Y229W Substitution in an NDM-1/L209F Variant Restores the Hydrolytic Activity of the Enzyme toward Penicillins, Cephalosporins, and Carbapenems

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Alessandra Piccirilli ◽  
Fabrizia Brisdelli ◽  
Massimiliano Aschi ◽  
Giuseppe Celenza ◽  
Gianfranco Amicosante ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Antimicrobial Susceptibility ◽  
Double Mutant ◽  
Catalytic Mechanism ◽  
Catalytic Efficiency ◽  
Terminal Region ◽  
Site Directed Mutagenesis ◽  
Active Site Residues ◽  
Single Mutant ◽  
Remarkable Increase

ABSTRACT The New Delhi metallo-β-lactamase-1 (NDM-1) enzyme is the most common metallo-β-lactamase identified in many Gram-negative bacteria causing severe nosocomial infections. The aim of this study was to focus the attention on non-active-site residues L209 and Y229 of NDM-1 and to investigate their role in the catalytic mechanism. Specifically, the effect of the Y229W substitution in the L209F variant was evaluated by antimicrobial susceptibility testing, kinetic, and molecular dynamic (MD) studies. The Y229W single mutant and L209F-Y229W double mutant were generated by site-directed mutagenesis. The Km, kcat, and kcat/Km kinetic constants, calculated for the two mutants, were compared with those of (wild-type) NDM-1 and the L209F variant. Compared to the L209F single mutant, the L209F-Y229W double mutant showed a remarkable increase in kcat values of 100-, 240-, 250-, and 420-fold for imipenem, meropenem, benzylpenicillin, and cefepime, respectively. In the L209F-Y229W enzyme, we observed a remarkable increase in kcat/Km of 370-, 140-, and 80-fold for cefepime, meropenem, and cefazolin, respectively. The same behavior was noted using the antimicrobial susceptibility test. MD simulations were carried out on both L209F and L209F-Y229W enzymes complexed with benzylpenicillin, focusing attention on the overall mechanical features and on the differences between the two systems. With respect to the L209F variant, the L209F-Y229W double mutant showed mechanical stabilization of loop 10 and the N-terminal region. In addition, Y229W substitution destabilized both the C-terminal region and the region from residues 149 to 154. The epistatic effect of the Y229W mutation jointly with the stabilization of loop 10 led to a better catalytic efficiency of β-lactams. NDM numbering is used in order to facilitate the comparison with other NDM-1 studies.

Dermal and pulmonary inflammatory disease in E-selectin and P-selectin double-null mice is reduced in triple-selectin–null mice

Blood ◽  
2001 ◽  
Vol 98 (3) ◽  
pp. 727-735
Author(s):  
Robert G. Collins ◽  
Unsu Jung ◽  
Maricela Ramirez ◽  
Daniel C. Bullard ◽  
M. John Hicks ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Double Mutant ◽  
Pulmonary Inflammation ◽  
Embryonic Stem ◽  
Cervical Lymphadenopathy ◽  
Surface Expression ◽  
Mutant Mice ◽  
Triple Mutant ◽  
Adhesive Interactions ◽  
Factor Α

In the initial phase of an inflammatory response, leukocytes marginate and roll along the endothelial surface as a result of adhesive interactions between molecules on the endothelial cells and leukocytes. To evaluate the role of the 3 selectins (E, L, and P) in leukocyte rolling and emigration, a null mutation for L-selectin was introduced into previously described embryonic stem cells with null mutations in the genes for both E-selectin and P-selectin (E/P double mutants) to produce triple-selectin–null mice (E-selectin, L-selectin, and P-selectin [E/L/P] triple mutants). Triple-selectin homozygous mutant mice are viable and fertile and only rarely develop the severe mucocutaneous infections or pulmonary inflammation characteristic of E/P double-mutant mice. Surface expression of L-selectin was undetectable in triple-mutant mice on fluorescence-activated cell-sorter analysis of peripheral neutrophils. Pathological studies revealed moderate cervical lymphadenopathy and lymphoplasmacytic infiltrate, but these were less extensive than in E/P double-mutant mice. Neutrophil emigration during thioglycolate-induced peritonitis was significantly reduced at 4, 8, and 24 hours (35%, 65%, and 46% of wild-type values, respectively). Intravital microscopy of the cremaster muscle revealed almost no rolling at times up to 6 hours after exteriorization, with or without addition of tumor necrosis factor α. The small amount of residual rolling was dependent on α4-integrin. The occurrence of skin and pulmonary disease in E/P double-mutant mice but not E/L/P triple-mutant mice suggests that deficiency of L-selectin alters the inflammatory response in E/P mutants.

2-Tier Bacterial and In Vitro Selection of Active and Methotrexate-Resistant Variants of Human Dihydrofolate Reductase

2008 ◽  
Vol 13 (6) ◽  
pp. 504-514 ◽  
Author(s):  
Elena Fossati ◽  
Jordan P. Volpato ◽  
Lucie Poulin ◽  
Vanessa Guerrero ◽  
David-Antoine Dugas ◽  
...  
Keyword(s):  
Dihydrofolate Reductase ◽  
Active Site ◽  
Drug Target ◽  
In Vitro Selection ◽  
Fold Increase ◽  
Active Site Residues ◽  
20 Nm ◽  
Human Dihydrofolate Reductase ◽  
Selection Of

We report a rapid and reliable 2-tier selection and screen for detection of activity as well as drug-resistance in mutated variants of a clinically-relevant drug-target enzyme. Human dihydrofolate reductase point-mutant libraries were subjected to a 1st-tier bacterial complementation assay, such that bacterial propagation served as an indicator of enzyme activity. Alternatively, when selection was performed in the presence of the inhibitor methotrexate (MTX), propagation indicated MTX resistance. The selected variants were then subjected to a 2nd-tier in vitro screen in 96-well plate format using crude bacterial lysate. Conditions were defined to establish a threshold for activity or for MTX resistance. The 2nd-tier assay allowed rapid detection of the best variants among the leads and provided reliable estimates of relative reactivity, ( kcat) and IC50MTX. Screening saturation libraries of active-site positions 7, 15, 24, 70, and 115 revealed a variety of novel mutations compatible with reactivity as well as 2 novel MTX-resistant variants: V115A and V115C. Both variants displayed KiMTX = 20 nM, a 600-fold increase relative to the wild-type. We also present preliminary results from screening against further antifolates following simple modifications of the protocol. The flexibility and robustness of this method will provide new insights into interactions between ligands and active-site residues of this clinically relevant human enzyme. ( Journal of Biomolecular Screening 2008:504-514)

Structural requirements of KTS-disintegrins for inhibition of α1β1 integrin

2008 ◽  
Vol 417 (1) ◽  
pp. 95-101 ◽  
Author(s):  
Meghan C. Brown ◽  
Johannes A. Eble ◽  
Juan J. Calvete ◽  
Cezary Marcinkiewicz
Keyword(s):  
Cell Adhesion ◽  
Fold Increase ◽  
Specific Inhibition ◽  
Wild Type ◽  
Triple Mutant ◽  
Inhibitory Potency ◽  
Structural Requirements ◽  
Critical Residue ◽  
Blocking Activity

Obtustatin and viperistatin represent the shortest known snake venom monomeric disintegrins. In the present study, we have produced recombinant full-length wild-type and site-directed mutants of obtustatin to assess the role of the K21TS23 tripeptide and C-terminal residues for specific inhibition of the α1β1 integrin. Thr22 appeared to be the most critical residue for disintegrin activity, whereas substitution of the flanking lysine or serine residues for alanine resulted in a less pronounced decrease in the anti-α1β1 integrin activity of the disintegrin. The triple mutant A21AA23 was devoid of blocking activity towards α1β1 integrin-mediated cell adhesion. The potency of recombinant KTS-disintegrins also depended on the residue C-terminally adjacent to the active motif. Substitution of Leu24 of wild-type obtustatin for an alanine residue slightly decreased the inhibitory activity of the mutant, whereas an arginine residue in this position enhanced the potency of the mutant over wild-type obtustatin by 6-fold. In addition, the replacements L38V and P40Q may account for a further 25-fold increase in α1β1 inhibitory potency of viperistatin over KTSR-obtustatin.

scholarly journals Genetic Evidence that Small Maf Proteins Are Essential for the Activation of Antioxidant Response Element-Dependent Genes

2005 ◽  
Vol 25 (18) ◽  
pp. 8044-8051 ◽  
Author(s):  
Fumiki Katsuoka ◽  
Hozumi Motohashi ◽  
Tetsuro Ishii ◽  
Hiroyuki Aburatani ◽  
James Douglas Engel ◽  
...  
Keyword(s):  
Double Mutant ◽  
Antioxidant Response ◽  
Mutant Mice ◽  
Butylated Hydroxyanisole ◽  
Dependent Manner ◽  
Antioxidant Response Element ◽  
Triple Mutant ◽  
Response Element ◽  
Decisive Evidence ◽  
Mutant Cells

ABSTRACT While small Maf proteins have been suggested to be essential for the Nrf2-mediated activation of antioxidant response element (ARE)-dependent genes, the extent of their requirement remains to be fully documented. To address this issue, we generated mafG::mafF double-mutant mice possessing MafK as the single available small Maf. Induction of the NAD(P)H:quinone oxidoreductase 1 (NQO1) gene was significantly impaired in double-mutant mice treated with butylated hydroxyanisole, while other ARE-dependent genes were less affected. Similarly, in a keap1-null background, where many of the ARE-dependent genes are constitutively activated in an Nrf2-dependent manner, only a subset of ARE-dependent genes, including NQO1, were sensitive to a simultaneous deficiency in MafG and MafF. Examination of single and double small maf mutant cells revealed that MafK also contributes to the induction of ARE-dependent genes. To obtain decisive evidence, we established mafG::mafK::mafF triple-mutant fibroblasts that completely lack small Mafs and turned out to be highly susceptible to oxidative stress. We found that induction in response to diethyl maleate was abolished in a wider range of ARE-dependent genes in the triple-mutant cells. These data explicitly demonstrate that small Mafs play critical roles in the inducible expression of a significant portion of ARE-dependent genes.

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