scholarly journals Molecular Mechanism of Interaction Between Fatty Acid Delta 6 Desaturase and Acyl-CoA by Computational Prediction

2021 ◽  
Author(s):  
Jie Cui ◽  
Haiqin Chen ◽  
Xin Tang ◽  
Hao Zhang ◽  
YongQ Chen ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Three Dimensional ◽  
Computational Prediction ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Mechanism Of Interaction ◽  
Membrane Bound ◽  
Micromonas Pusilla ◽  
Substrate Binding Sites ◽  
Delta 6 Desaturase

Abstract Enzyme catalyzed desaturation of intracellular fatty acids plays an important role in various physiological and pathological processes related to lipids. Limited to the multiple transmembrane domains, it is difficult to obtain their three-dimensional structure of fatty acid desaturases. So how they interact with their substrates is unclear. Here, we predicted the complex of Micromonas pusilla delta 6 desaturase (MpFADS6) with the substrate linoleinyl-CoA (ALA-CoA) by trRosetta software and docking poses by Dock 6 software. The potential enzyme-substrate binding sites were anchored by analysis of the complex. Then, site-directed mutagenesis and activity verification clarified that W290, W224, and F352 were critical residues of the substrate tunnel and directly bonded to ALA-CoA. H94 and H69 were indispensable for transporting electrons with heme. H452, N445, and H358 significantly influenced the recognition and attraction of MpFADS6 to the substrate. These findings provide new insights and methods to determine the structure, mechanisms and directed transformation of membrane-bound desaturases.

Elucidation of the paratope of scFv-8H9D4, a PAI-1 neutralizing antibody derivative

2003 ◽  
Vol 89 (01) ◽  
pp. 74-82 ◽  
Author(s):  
Koen Verbeke ◽  
Ann Gils ◽  
Jean-Marie Stassen ◽  
Paul Declerck
Keyword(s):  
Rational Design ◽  
Three Dimensional ◽  
Neutralizing Antibody ◽  
Plasminogen Activator Inhibitor ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Single Chain ◽  
Plasminogen Activator Inhibitor 1 ◽  
Activator Inhibitor ◽  
Pai 1

SummaryInterfering with increased levels of plasminogen activator inhibitor-1 (PAI-1) might offer new therapeutic strategies for a variety of cardiovascular diseases. Inactivation of PAI-1 can be accomplished by a number of monoclonal antibodies (MA), including MA-8H9D4. In a previous study, a single-chain variable fragment (scFv-8H9D4) was cloned and found to have the same properties as the parental MA-8H9D4. In the present study, we identified the residues of scFv-8H9D4 that contribute significantly to the paratope. The complementarity determining region 3 from the heavy (H3) and the light (L3) chain were analysed through site-directed mutagenesis. Out of twelve mutations, only four residues appeared to contribute to the paratope. The affinity of scFv-8H9D4-H3-L97D for PAI-1 was 38-fold decreased (KA = 4.8 ± 0.2 × 107 M–1 vs. 1.8 ± 0.7 × 109 M–1 for scFv-8H9D4) whereas scFv-8H9D4-H3-R98Y did not bind to PAI-1. The affinities of scFv-8H9D4-L3-Y91S and scFv-8H9D4-L3-F94D for PAI-1 were 9- and 5-fold reduced, respectively, whereas the combined mutation resulted in an 86-fold decreased affinity (KA = 2.1 ± 0.2 × 107 M–1).In accordance with the affinity data, these mutants had no, or a reduced, PAI-1 inhibitory capacity, confirming that these four particular residues form the major interaction site of scFv-8H9D4 with PAI-1. In combination with the three-dimensional structure, these data contribute to the rational design of PAI-1 neutralizing compounds.

Mutagenesis of the borage Δ6 fatty acid desaturase

2000 ◽  
Vol 28 (6) ◽  
pp. 636-638 ◽  
Author(s):  
O. Sayanova ◽  
F. Beaudoin ◽  
B. Libisch ◽  
P. Shewry ◽  
J. Napier
Keyword(s):  
Fatty Acid ◽  
Consensus Sequence ◽  
Fatty Acid Desaturase ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
The Third ◽  
Membrane Bound ◽  
Fusion Domain ◽  
Δ6 Desaturase

The consensus sequence of the third histidine box of a range of Δ5, Δ6, Δ8 and sphingolipid desaturases differs from that of the membrane-bound non-fusion Δ12 and Δ15 desaturases in the presence of glutamine instead of histidine. We have used site-directed mutagenesis to determine the importance of glutamine and other residues of the third histidine box and created a chimaeric enzyme to determine the ability of the Cyt b5 fusion domain from the plant sphingolipid desaturase to substitute for the endogenous domain of the Δ6 desaturase.

scholarly journals Three-dimensional structure of fatty-acid-binding protein from bovine heart

1991 ◽  
Vol 199 (2) ◽  
pp. 271-276 ◽  
Author(s):  
Anke MULLER-FAHRNOW ◽  
Ursula EGNER ◽  
T. Alwyn JONES ◽  
Heinz RUDEL ◽  
Friedrich SPENER ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Binding Protein ◽  
Binding Protein ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Fatty Acid Binding ◽  
Three Dimensional Structure ◽  
Acid Binding Protein ◽  
Bovine Heart

scholarly journals Functional Analysis of the Carbohydrate-Binding Domains of Erwinia chrysanthemi Cel5 (Endoglucanase Z) and an Escherichia coli Putative Chitinase

1999 ◽  
Vol 181 (15) ◽  
pp. 4611-4616 ◽  
Author(s):  
Helen D. Simpson ◽  
Frederic Barras
Keyword(s):  
Escherichia Coli ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Site Directed Mutagenesis ◽  
Erwinia Chrysanthemi ◽  
Dimensional Structure ◽  
Carbohydrate Binding ◽  
Binding Domains ◽  
Cellulose Binding

ABSTRACT The Cel5 cellulase (formerly known as endoglucanase Z) fromErwinia chrysanthemi is a multidomain enzyme consisting of a catalytic domain, a linker region, and a cellulose binding domain (CBD). A three-dimensional structure of the CBDCel5 has previously been obtained by nuclear magnetic resonance. In order to define the role of individual residues in cellulose binding, site-directed mutagenesis was performed. The role of three aromatic residues (Trp18, Trp43, and Tyr44) in cellulose binding was demonstrated. The exposed potential hydrogen bond donors, residues Gln22 and Glu27, appeared not to play a role in cellulose binding, whereas residue Asp17 was found to be important for the stability of Cel5. A deletion mutant lacking the residues Asp17 to Pro23 bound only weakly to cellulose. The sequence of CBDCel5 exhibits homology to a series of five repeating domains of a putative large protein, referred to as Yheb, from Escherichia coli. One of the repeating domains (Yheb1), consisting of 67 amino acids, was cloned from the E. coli chromosome and purified by metal chelating chromatography. While CBDCel5 bound to both cellulose and chitin, Yheb1 bound well to chitin, but only very poorly to cellulose. The Yheb protein contains a region that exhibits sequence homology with the catalytic domain of a chitinase, which is consistent with the hypothesis that the Yheb protein is a chitinase.

scholarly journals Quantitative Computational Prediction of the Consensus B-cell Epitopes of 2019-nCoV

2020 ◽  
Vol 1 (1) ◽  
pp. 42-47
Author(s):  
Raúl Isea
Keyword(s):  
B Cell ◽  
Three Dimensional ◽  
Similarity Index ◽  
Computational Prediction ◽  
Dimensional Structure ◽  
Spike Glycoprotein ◽  
B Cell Epitopes ◽  
Three Dimensional Structure ◽  
Mathematical Algorithms

The goal of this paper is to obtain the numerical consensus of B cell epitopes from the three-dimensional structure of the prefusion spike glycoprotein of the new betacoronavirus that could lead to the development of a vaccine to 2019-nCoV. In order to do that, we first calculated the B-cell epitopes that are predicted using fourteen different mathematical algorithms. Later, we obtained the consensus of B-cell epitopes according to the Similarity Index, and finally selecting the best candidates according to the results of a function called <F> which is evaluated for the glycoprotein. The best candidates that we obtained in order to design a vaccine are SSANNCT, PLQSYGFQPT, TESNKKFLP, NNSYEC, AENS, LPDPSK and YDPLQPE.

scholarly journals The three-dimensional structure of a helix-less variant of intestinal fatty acid-binding protein

1998 ◽  
Vol 7 (6) ◽  
pp. 1332-1339 ◽  
Author(s):  
Ruth A. Steele ◽  
Daniel A. Emmert ◽  
Jeff Kao ◽  
Michaele E. Hodson ◽  
Carl Frieden ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Binding Protein ◽  
Binding Protein ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Fatty Acid Binding ◽  
Three Dimensional Structure ◽  
Acid Binding Protein

Three-dimensional Structure of Membrane-bound Annexin V

1994 ◽  
Vol 238 (2) ◽  
pp. 199-213 ◽  
Author(s):  
Dieter Voges ◽  
Robert Berendes ◽  
Alexander Burger ◽  
Pascal Demange ◽  
Wolfgang Baumeister ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Annexin V ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Membrane Bound

scholarly journals The Vanadium Iodoperoxidase from the Marine Flavobacteriaceae Species Zobellia galactanivorans Reveals Novel Molecular and Evolutionary Features of Halide Specificity in the Vanadium Haloperoxidase Enzyme Family

2014 ◽  
Vol 80 (24) ◽  
pp. 7561-7573 ◽  
Author(s):  
Jean-Baptiste Fournier ◽  
Etienne Rebuffet ◽  
Ludovic Delage ◽  
Romain Grijol ◽  
Laurence Meslet-Cladière ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Content Type ◽  
Bacterial Phyla ◽  
Iodide Oxidation ◽  
Enzyme Family ◽  
Evolutionary Features ◽  
Eukaryotic Species ◽  
Monomeric Structure

ABSTRACTVanadium haloperoxidases (VHPO) are key enzymes that oxidize halides and are involved in the biosynthesis of organo-halogens. Until now, only chloroperoxidases (VCPO) and bromoperoxidases (VBPO) have been characterized structurally, mainly from eukaryotic species. Three putative VHPO genes were predicted in the genome of the flavobacteriumZobellia galactanivorans, a marine bacterium associated with macroalgae. In a phylogenetic analysis, these putative bacterial VHPO were closely related to other VHPO from diverse bacterial phyla but clustered independently from eukaryotic algal VBPO and fungal VCPO. Two of these bacterial VHPO, heterogeneously produced inEscherichia coli, were found to be strictly specific for iodide oxidation. The crystal structure of one of these vanadium-dependent iodoperoxidases, Zg-VIPO1, was solved by multiwavelength anomalous diffraction at 1.8 Å, revealing a monomeric structure mainly folded into α-helices. This three-dimensional structure is relatively similar to those of VCPO of the fungusCurvularia inaequalisand ofStreptomycessp. and is superimposable onto the dimeric structure of algal VBPO. Surprisingly, the vanadate binding site of Zg-VIPO1 is strictly conserved with the fungal VCPO active site. Using site-directed mutagenesis, we showed that specific amino acids and the associated hydrogen bonding network around the vanadate center are essential for the catalytic properties and also the iodide specificity of Zg-VIPO1. Altogether, phylogeny and structure-function data support the finding that iodoperoxidase activities evolved independently in bacterial and algal lineages, and this sheds light on the evolution of the VHPO enzyme family.

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