Wilmanns M

References (5)

Title : Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex - Pinotsis_2023_Nat.Commun_14_7649
Author(s) : Pinotsis N , Kruger A , Tomas N , Chatziefthymiou SD , Litz C , Mortensen SA , Daffe M , Marrakchi H , Antranikian G , Wilmanns M
Ref : Nat Commun , 14 :7649 , 2023
Abstract : The identification and characterization of enzyme function is largely lacking behind the rapidly increasing availability of large numbers of sequences and associated high-resolution structures. This is often hampered by lack of knowledge on in vivo relevant substrates. Here, we present a case study of a high-resolution structure of an unusual orphan lipase in complex with an endogenous C18 monoacylglycerol ester reaction intermediate from the expression host, which is insoluble under aqueous conditions and thus not accessible for studies in solution. The data allowed its functional characterization as a prototypic long-chain monoacylglycerol lipase, which uses a minimal lid domain to position the substrate through a hydrophobic tunnel directly to the enzyme's active site. Knowledge about the molecular details of the substrate binding site allowed us to modulate the enzymatic activity by adjusting protein/substrate interactions, demonstrating the potential of our findings for future biotechnology applications.
ESTHER : Pinotsis_2023_Nat.Commun_14_7649
PubMedSearch : Pinotsis_2023_Nat.Commun_14_7649
PubMedID: 38012138

Title : The crystal structure of mycobacterial epoxide hydrolase A - Schulz_2020_Sci.Rep_10_16539
Author(s) : Schulz EC , Henderson SR , Illarionov B , Crosskey T , Southall SM , Krichel B , Uetrecht C , Fischer M , Wilmanns M
Ref : Sci Rep , 10 :16539 , 2020
Abstract : The human pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis resulting in over 1 million fatalities every year, despite decades of research into the development of new anti-TB compounds. Unlike most other organisms M. tuberculosis has six putative genes for epoxide hydrolases (EH) of the alpha/beta-hydrolase family with little known about their individual substrates, suggesting functional significance for these genes to the organism. Due to their role in detoxification, M. tuberculosis EH's have been identified as potential drug targets. Here, we demonstrate epoxide hydrolase activity of M. thermoresistibile epoxide hydrolase A (Mth-EphA) and report its crystal structure in complex with the inhibitor 1,3-diphenylurea at 2.0 resolution. Mth-EphA displays high sequence similarity to its orthologue from M. tuberculosis and generally high structural similarity to alpha/beta-hydrolase EHs. The structure of the inhibitor bound complex reveals the geometry of the catalytic residues and the conformation of the inhibitor. Comparison to other EHs from mycobacteria allows insight into the active site plasticity with respect to substrate specificity. We speculate that mycobacterial EHs may have a narrow substrate specificity providing a potential explanation for the genetic repertoire of epoxide hydrolase genes in M. tuberculosis.
ESTHER : Schulz_2020_Sci.Rep_10_16539
PubMedSearch : Schulz_2020_Sci.Rep_10_16539
PubMedID: 33024154
Gene_locus related to this paper: myct3-g7cf24

Title : Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers - Mokrushina_2020_Proc.Natl.Acad.Sci.U.S.A_117_22841
Author(s) : Mokrushina YA , Golovin AV , Smirnov IV , Chatziefthimiou SD , Stepanova AV , Bobik TV , Zalevsky AO , Zlobin AS , Konovalov KA , Terekhov SS , Stepanov AV , Pipiya SO , Shamborant OG , Round E , Belogurov AA, Jr. , Bourenkov G , Makarov AA , Wilmanns M , Xie J , Blackburn GM , Gabibov AG , Lerner RA
Ref : Proc Natl Acad Sci U S A , 117 :22841 , 2020
Abstract : Quantum mechanics/molecular mechanics (QM/MM) maturation of an immunoglobulin (Ig) powered by supercomputation delivers novel functionality to this catalytic template and facilitates artificial evolution of biocatalysts. We here employ density functional theory-based (DFT-b) tight binding and funnel metadynamics to advance our earlier QM/MM maturation of A17 Ig-paraoxonase (WTIgP) as a reactibody for organophosphorus toxins. It enables regulation of biocatalytic activity for tyrosine nucleophilic attack on phosphorus. The single amino acid substitution l-Leu47Lys results in 340-fold enhanced reactivity for paraoxon. The computed ground-state complex shows substrate-induced ionization of the nucleophilic l-Tyr37, now H-bonded to l-Lys47, resulting from repositioning of l-Lys47. Multiple antibody structural homologs, selected by phenylphosphonate covalent capture, show contrasting enantioselectivities for a P-chiral phenylphosphonate toxin. That is defined by crystallographic analysis of phenylphosphonylated reaction products for antibodies A5 and WTIgP. DFT-b analysis using QM regions based on these structures identifies transition states for the favored and disfavored reactions with surprising results. This stereoselection analysis is extended by funnel metadynamics to a range of WTIgP variants whose predicted stereoselectivity is endorsed by experimental analysis. The algorithms used here offer prospects for tailored design of highly evolved, genetically encoded organophosphorus scavengers and for broader functionalities of members of the Ig superfamily, including cell surface-exposed receptors.
ESTHER : Mokrushina_2020_Proc.Natl.Acad.Sci.U.S.A_117_22841
PubMedSearch : Mokrushina_2020_Proc.Natl.Acad.Sci.U.S.A_117_22841
PubMedID: 32859757

Title : Evolution of catalytic centers of antibodies by virtual screening of broad repertoire of mutants using supercomputer - Golovin_2017_Dokl.Biochem.Biophys_475_245
Author(s) : Golovin AV , Smirnov IV , Stepanova AV , Zalevskiy AO , Zlobin AS , Ponomarenko NA , Belogurov AA , Knorre VD , Hurs EN , Chatziefthimiou SD , Wilmanns M , Blackburn GM , Khomutov RM , Gabibov AG
Ref : Dokl Biochem Biophys , 475 :245 , 2017
Abstract : It is proposed to perform quantum mechanical/molecular dynamics calculations of chemical reactions that are planned to be catalyzed by antibodies and then conduct a virtual screening of the library of potential antibody mutants to select an optimal biocatalyst. We tested the effectiveness of this approach by the example of hydrolysis of organophosphorus toxicant paraoxon using kinetic approaches and X-ray analysis of the antibody biocatalyst designed de novo.
ESTHER : Golovin_2017_Dokl.Biochem.Biophys_475_245
PubMedSearch : Golovin_2017_Dokl.Biochem.Biophys_475_245
PubMedID: 28864894

Title : On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths - Mueller-Dieckmann_2007_Acta.Crystallogr.D.Biol.Crystallogr_63_366
Author(s) : Mueller-Dieckmann C , Panjikar S , Schmidt A , Mueller S , Kuper J , Geerlof A , Wilmanns M , Singh RK , Tucker PA , Weiss MS
Ref : Acta Crystallographica D Biol Crystallogr , 63 :366 , 2007
Abstract : 23 different crystal forms of 19 different biological macromolecules were examined with respect to their anomalously scattering substructures using diffraction data collected at a wavelength of 2.0 A (6.2 keV). In more than 90% of the cases the substructure was found to contain more than just the protein S atoms. The data presented suggest that chloride, sulfate, phosphate or metal ions from the buffer or even from the purification protocol are frequently bound to the protein molecule and that these ions are often overlooked, especially if they are not bound at full occupancy. Thus, in order to fully describe the macromolecule under study, it seems desirable that any structure determination be complemented with a long-wavelength data set.
ESTHER : Mueller-Dieckmann_2007_Acta.Crystallogr.D.Biol.Crystallogr_63_366
PubMedSearch : Mueller-Dieckmann_2007_Acta.Crystallogr.D.Biol.Crystallogr_63_366
PubMedID: 17327674
Gene_locus related to this paper: manes-hnl