TY  - JOUR
A1  - Akhoon, Bashir A.
A1  - Singh, Krishna P.
A1  - Varshney, Megha
A1  - Gupta, Shishir K.
A1  - Shukla, Yogeshwar
A1  - Gupta, Shailendra K.
T1  - Understanding the Mechanism of Atovaquone Drug Resistance in Plasmodium falciparum Cytochrome b Mutation Y268S Using Computational Methods
JF  - PLOS ONE
N2  - The rapid appearance of resistant malarial parasites after introduction of atovaquone (ATQ) drug has prompted the search for new drugs as even single point mutations in the active site of Cytochrome b protein can rapidly render ATQ ineffective. The presence of Y268 mutations in the Cytochrome b (Cyt b) protein is previously suggested to be responsible for the ATQ resistance in Plasmodium falciparum (P. falciparum). In this study, we examined the resistance mechanism against ATQ in P. falciparum through computational methods. Here, we reported a reliable protein model of Cyt bc1 complex containing Cyt b and the Iron-Sulphur Protein (ISP) of P. falciparum using composite modeling method by combining threading, ab initio modeling and atomic-level structure refinement approaches. The molecular dynamics simulations suggest that Y268S mutation causes ATQ resistance by reducing hydrophobic interactions between Cyt bc1 protein complex and ATQ. Moreover, the important histidine contact of ATQ with the ISP chain is also lost due to Y268S mutation. We noticed the induced mutation alters the arrangement of active site residues in a fashion that enforces ATQ to find its new stable binding site far away from the wild-type binding pocket. The MM-PBSA calculations also shows that the binding affinity of ATQ with Cyt bc1 complex is enough to hold it at this new site that ultimately leads to the ATQ resistance.
KW  - molecular-dynamics simulations
KW  - HIV-1 protease
KW  - structure prediction
KW  - saccharomyces cerevisiae
KW  - I-tasser
KW  - inhibitors
KW  - binding
KW  - malaria
KW  - complex
KW  - protein-protein interactions
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114882
VL  - 9
IS  - 10
ER  - 
TY  - JOUR
A1  - Schwender, Joerg
A1  - Koenig, Christina
A1  - Klapperstueck, Matthias
A1  - Heinzel, Nicolas
A1  - Munz, Eberhard
A1  - Hebbelmann, Inga
A1  - Hay, Jordan O.
A1  - Denolf, Peter
A1  - De Bodt, Stefanie
A1  - Redestig, Henning
A1  - Caestecker, Evelyne
A1  - Jakob, Peter M.
A1  - Borisjuk, Ljudmilla
A1  - Rolletschek, Hardy
T1  - Transcript abundance on its own cannot be used to infer fluxes in central metabolism
JF  - Frontiers in Plant Science
N2  - An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux vs. transcript (metabolite). Metabolite profiling succeeded in identifying 79 intermediates within the central metabolism, some of which differed quantitatively between the two accessions and displayed a significant shift corresponding to flux. An RNA-Seq based transcriptome analysis revealed a large number of genes which were differentially transcribed in the two accessions, including some enzymes/proteins active in major metabolic pathways. With a few exceptions, differential activity in the major pathways (glycolysis, TCA cycle, amino acid, and fatty acid synthesis) was not reflected in contrasting abundances of the relevant transcripts. The conclusion was that transcript abundance on its own cannot be used to infer metabolic activity/fluxes in central plant metabolism. This limitation needs to be borne in mind in evaluating transcriptome data and designing metabolic engineering experiments.
KW  - oilseeds
KW  - lipid biosynthesis
KW  - heterotrophic arabidopsis cells
KW  - central carbon metabolism
KW  - gene-expression data
KW  - targeted metabolite profiling
KW  - central metabolism
KW  - flux balance analysis
KW  - C-13-metabolic flux analysis
KW  - Brassica napus
KW  - RNA-SEQ
KW  - developing oilseeds
KW  - saccharomyces cerevisiae
KW  - maize kernels
KW  - embryo
KW  - seed
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114586
SN  - 1664-462X
N1  - Funding information:
Bayer Crop Science NV; Deutsche Forschungsgemeinschaft [BO-1917/4-1]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division [DEACO298CH10886]
VL  - 5
ER  -