Category Archives: Chembiochem

Cell fueling and metabolic energy conservation in synthetic cells.

Cell fueling and metabolic energy conservation in synthetic cells.
Chembiochem. 2019 Aug 05;:
Authors: Sikkema HR, Gaastra BF, Pols T, Poolman B
Abstract
We aim for a blue print for synthesizing com… Continue reading

Posted in Chembiochem | Tagged | Leave a comment

Convergent cascade catalyzed by monooxygenase – alcohol dehydrogenase fusion applied in organic media.

Convergent cascade catalyzed by monooxygenase – alcohol dehydrogenase fusion applied in organic media.
Chembiochem. 2019 Feb 27;:
Authors: Huang L, Tang W, Röllig R, Aalbers FS, Fraaije MW, Kara S
Abstract
Continue reading

Posted in Chembiochem | Tagged | Leave a comment

The generation and exploitation of protein mutability landscapes for enzyme engineering.

The generation and exploitation of protein mutability landscapes for enzyme engineering.
Chembiochem. 2016 Jul 21;
Authors: Van Der Meer JY, Biewenga L, Poelarends GJ
Abstract
The increasing number of… Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Evidence for the Formation of an Enamine Species during Aldol and Michael-type Addition Reactions Promiscuously Catalyzed by 4-Oxalocrotonate Tautomerase.

Evidence for the Formation of an Enamine Species during Aldol and Michael-type Addition Reactions Promiscuously Catalyzed by 4-Oxalocrotonate Tautomerase.

Chembiochem. 2015 Feb 26;

Authors: Poddar H, Rahimi M, Geertsema EM, Thunnissen AM, Poelarends GJ

Abstract
The enzyme 4-oxalocrotonate tautomerase (4-OT), which has a catalytic N-terminal proline residue (Pro1), can promiscuously catalyze various carbon-carbon bond-forming reactions, including aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde, and Michael-type addition of acetaldehyde to a wide variety of nitroalkenes to yield valuable γ-nitroaldehydes. To gain insight into how 4-OT catalyzes these unnatural reactions, we carried out exchange studies in D2 O, and X-ray crystallography studies. The former established that H-D exchange within acetaldehyde is catalyzed by 4-OT and that the Pro1 residue is crucial for this activity. The latter showed that Pro1 of 4-OT had reacted with acetaldehyde to give an enamine species. These results provide evidence of the mechanism of the 4-OT-catalyzed aldol and Michael-type addition reactions in which acetaldehyde is activated for nucleophilic addition by Pro1-dependent formation of an enamine intermediate.

PMID: 25728471 [PubMed – as supplied by publisher]

Continue reading

Posted in Chembiochem | Leave a comment

Structure-Based Design of Potent Small-Molecule Binders to the S-Component of the ECF Transporter for Thiamine.

Structure-Based Design of Potent Small-Molecule Binders to the S-Component of the ECF Transporter for Thiamine.
Chembiochem. 2015 Feb 12;
Authors: Swier LJ, Monjas L, Guskov A, de Voogd AR, Erkens GB, Slotboom DJ, Hi… Continue reading

Posted in Chembiochem | Leave a comment

Aqueous oxidative Heck reaction as a protein-labeling strategy.

Related Articles
Aqueous oxidative Heck reaction as a protein-labeling strategy.
Chembiochem. 2014 Jan 24;15(2):209-12
Authors: Ourailidou ME, van der Meer JY, Baas BJ, Jeronimus-Stratingh M, Gottumukkala AL, Poelare… Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Proteasome Inhibitors with Photocontrolled Activity.

Proteasome Inhibitors with Photocontrolled Activity.
Chembiochem. 2014 Aug 14;
Authors: Hansen MJ, Velema WA, de Bruin G, Overkleeft HS, Szymanski W, Feringa BL
Abstract
Proteasome inhibitors are wide… Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Computational Library Design for Increasing Haloalkane Dehalogenase Stability.

Related Articles

Computational Library Design for Increasing Haloalkane Dehalogenase Stability.

Chembiochem. 2014 Jun 27;

Authors: Floor RJ, Wijma HJ, Colpa DI, Ramos-Silva A, Jekel PA, Szymański W, Feringa BL, Marrink SJ, Janssen DB

Abstract
We explored the use of a computational design framework for the stabilization of the haloalkane dehalogenase LinB. Energy calculations, disulfide bond design, molecular dynamics simulations, and rational inspection of mutant structures predicted many stabilizing mutations. Screening of these in small mutant libraries led to the discovery of seventeen point mutations and one disulfide bond that enhanced thermostability. Mutations located in or contacting flexible regions of the protein had a larger stabilizing effect than mutations outside such regions. The combined introduction of twelve stabilizing mutations resulted in a LinB mutant with a 23 °C increase in apparent melting temperature (Tm,app , 72.5 °C) and an over 200-fold longer half-life at 60 °C. The most stable LinB variants also displayed increased compatibility with co-solvents, thus allowing substrate conversion and kinetic resolution at much higher concentrations than with the wild-type enzyme.

PMID: 24976371 [PubMed – as supplied by publisher]

Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Biocatalytic and structural properties of a highly engineered halohydrin dehalogenase.

Related Articles

Biocatalytic and structural properties of a highly engineered halohydrin dehalogenase.

Chembiochem. 2013 May 10;14(7):870-81

Authors: Schallmey M, Floor RJ, Hauer B, Breuer M, Jekel PA, Wijma HJ, Dijkstra BW, Janssen DB

Abstract
Two highly engineered halohydrin dehalogenase variants were characterized in terms of their performance in dehalogenation and epoxide cyanolysis reactions. Both enzyme variants outperformed the wild-type enzyme in the cyanolysis of ethyl (S)-3,4-epoxybutyrate, a conversion yielding ethyl (R)-4-cyano-3-hydroxybutyrate, an important chiral building block for statin synthesis. One of the enzyme variants, HheC2360, displayed catalytic rates for this cyanolysis reaction enhanced up to tenfold. Furthermore, the enantioselectivity of this variant was the opposite of that of the wild-type enzyme, both for dehalogenation and for cyanolysis reactions. The 37-fold mutant HheC2360 showed an increase in thermal stability of 8 °C relative to the wild-type enzyme. Crystal structures of this enzyme were elucidated with chloride and ethyl (S)-3,4-epoxybutyrate or with ethyl (R)-4-cyano-3-hydroxybutyrate bound in the active site. The observed increase in temperature stability was explained in terms of a substantial increase in buried surface area relative to the wild-type HheC, together with enhanced interfacial interactions between the subunits that form the tetramer. The structures also revealed that the substrate binding pocket was modified both by substitutions and by backbone movements in loops surrounding the active site. The observed changes in the mutant structures are partly governed by coupled mutations, some of which are necessary to remove steric clashes or to allow backbone movements to occur. The importance of interactions between substitutions suggests that efficient directed evolution strategies should allow for compensating and synergistic mutations during library design.

PMID: 23585096 [PubMed – indexed for MEDLINE]

Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Recent advances in the study of enzyme promiscuity in the tautomerase superfamily.

Related Articles
Recent advances in the study of enzyme promiscuity in the tautomerase superfamily.
Chembiochem. 2013 May 27;14(8):917-26
Authors: Baas BJ, Zandvoort E, Geertsema EM, Poelarends GJ
Abstract
Cata… Continue reading

Posted in Chembiochem | Leave a comment

When the leader gets loose: in vivo biosynthesis of a leaderless prenisin is stimulated by a trans-acting leader peptide.

Related Articles

When the leader gets loose: in vivo biosynthesis of a leaderless prenisin is stimulated by a trans-acting leader peptide.

Chembiochem. 2012 Nov 5;13(16):2433-8

Continue reading

Posted in Chembiochem | Tagged | Leave a comment

Promiscuous catalysis of asymmetric Michael-type additions of linear aldehydes to β-nitrostyrene by the proline-based enzyme 4-oxalocrotonate tautomerase.

Related Articles

Promiscuous catalysis of asymmetric Michael-type additions of linear aldehydes to β-nitrostyrene by the proline-based enzyme 4-oxalocrotonate tautomerase.

Continue reading

Posted in Chembiochem | Tagged | Leave a comment

Total synthesis of (-)-doliculide, structure-activity relationship studies and its binding to F-actin.

Related Articles

Total synthesis of (-)-doliculide, structure-activity relationship studies and its binding to F-actin.

Chembiochem. 2012 Nov 26;13(17):2537-48

Authors: …

Continue reading

Posted in Chembiochem | Tagged | Leave a comment

An unexpected promiscuous activity of 4-oxalocrotonate tautomerase: the cis-trans isomerisation of nitrostyrene.

Related Articles

An unexpected promiscuous activity of 4-oxalocrotonate tautomerase: the cis-trans isomerisation of nitrostyrene.

Chembiochem. 2012 Sep 3;13(13):1869-73

Continue reading

Posted in Chembiochem | Tagged | Leave a comment

Dehalogenation of an anthropogenic compound by an engineered variant of the mouse cytokine macrophage migration inhibitory factor.

Related Articles
Dehalogenation of an anthropogenic compound by an engineered variant of the mouse cytokine macrophage migration inhibitory factor.
Chembiochem. 2012 Jun 18;13(9):1270-3
Authors: Wasiel AA, Baas BJ, Zandvoort E… Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Enhancement of the promiscuous aldolase and dehydration activities of 4-oxalocrotonate tautomerase by protein engineering.

Related Articles
Enhancement of the promiscuous aldolase and dehydration activities of 4-oxalocrotonate tautomerase by protein engineering.
Chembiochem. 2012 Jun 18;13(9):1274-7
Authors: Zandvoort E, Geertsema EM, Quax WJ, Poe… Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Directed evolution strategies for enantiocomplementary haloalkane dehalogenases: from chemical waste to enantiopure building blocks.

Directed evolution strategies for enantiocomplementary haloalkane dehalogenases: from chemical waste to enantiopure building blocks.

Chembiochem. 2012 Jan 2;13(1):137-48

Authors: …

Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Systematic screening for catalytic promiscuity in 4-oxalocrotonate tautomerase: enamine formation and aldolase activity.

Systematic screening for catalytic promiscuity in 4-oxalocrotonate tautomerase: enamine formation and aldolase activity.

Chembiochem. 2011 Mar 7;12(4):602-9

Authors: Zandvoort E,…

Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Functionalization of Oxidases with Peroxidase Activity Creates Oxiperoxidases: A New Breed of Hybrid Enzyme Capable of Cascade Chemistry.

Functionalization of Oxidases with Peroxidase Activity Creates Oxiperoxidases: A New Breed of Hybrid Enzyme Capable of Cascade Chemistry.

Chembiochem. 2011 Dec 23;

Authors: Winter…

Continue reading

Posted in Chembiochem | Tagged , | Leave a comment

Antibody-free detection of protein tyrosine nitration in tissue sections.

Antibody-free detection of protein tyrosine nitration in tissue sections.

Chembiochem. 2011 Sep 5;12(13):2016-20

Authors: Wisastra R, Poelstra K, Bischoff R, Maarsingh H, Haisma…

Continue reading

Posted in Chembiochem | Tagged , | Comments Off on Antibody-free detection of protein tyrosine nitration in tissue sections.