1,538 Works

IBDV VP5

Bhaskar Ganguly

Homology model of Arabidopsis thaliana nitrile-specifier protein 3 (AtNSP3)

Daniela Eisenschmidt-Bönn
Glucosinolates, a group of sulfur-rich thioglucosides found in plants of the order Brassicales, have attracted a lot of interest as chemical defenses of plants and health promoting substances in human diet. They are accumulated separately from their hydrolyzing enzymes, myrosinases, within the intact plant, but undergo myrosinase-catalyzed hydrolysis upon tissue disruption. This results in various biologically active products, e.g. isothiocyanates, simple nitriles, epithionitriles, and organic thiocyanates. While formation of isothiocyanates proceeds by a spontaneous rearrangement...

Herbaspirillum seropedicae Recombinase A, active form, L53Q mutant

In this work we have performed in vitro, in vivo and in silico studies of Recombinase A from Herbaspirillum seropedicae (HsRecA) - Uniprot AC Q9F672 -, both the wild type and the L53Q mutant. This mutation is located at the Make ATP Work motif (MAW) and impairs the ATPase and DNA-strand exchange activities, however, it does not affect the binding of ADP, ATP and ssDNA. At complementation studies of E. coli recA1 with the HsRecA...

Allosteres to Regulate Neurotransmitter Sulfonation

Catecholamine neurotransmitter levels in the synapses of the brain shape human disposition — cognitive flexibility, aggression, depression, reward seeking… — and manipulating these levels is a major objective of the pharmaceutical industry. Certain transmitters are extensively sulfonated — an inactivating modification catalyzed by human sulfotransferase 1A3 (SULT1A3). To our knowledge, sulfonation as therapeutic means of regulating transmitter activity has not been explored. Here we describe the discovery of a SULT1A3 allosteric site that can be...

Selenophosphate Synthetase 2 (SEPHS2)

Selenophosphate synthetase 2 (SEPHS2) synthesizes from selenide and ATP the selenophosphate that represents the selenium donor used to synthesize selenocysteine (Sec), which is co-translationally incorporated into the selenoproteins. Only few information are reported in literature about SEPHS2 involvement in cancer. Thus, it should be interesting to understand what is its functional role in cancer development and progression. In this work, since up to now no structure was experimentally determined for SEPHS2, we decided to analyze...

NS3 MutantH (JFH-1)

To gain an insight into mutation flexibility across sequence space of hepatitis C virus (HCV) genome, we created mutant libraries, differing from the parent sequence as well as each other by using a random mutagenesis approach; the proportion of mutations increased across these libraries with declining template amount or dATP concentration. Replication efficiency of full-genome mutant libraries ranged between 71 and 329 foci forming unit (FFU) per 105 Huh7.5 cells. Mutant libraries with low proportions...

SELENOPROTEIN K

SELK is a single-pass trans-membrane protein that resides in the endoplasmic reticulum membrane (ER) with a C-terminal domain exposed to the cytoplasm that is known to interact with different components of the endoplasmic reticulum associated to the protein degradation (ERAD) pathway. This protein is resulted to be up-expressed in hepatocellular carcinoma and in other cancers, therefore there is a need to analyze its structure-function relationships. In this work we performed a detailed analysis of the...

Structure of the 40S rRNA of Plasmodium falciparum by homology and de novo modeling

Motivation: Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed in which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input and thus increasing the speed of scientific discoveries. In this study, a...

Integrating mechanism-based screening paradigm into homology and de novo modeling exemplified by Mycobacterium Tuberculosis 30S ribosomal structure and its potential application as a screening target

Motivation: Mycobacterium tuberculosis, the causative agent of the tuberculosis, has infected more than a third of the world’s popula-tion to date. It is known to be substantially aggressive and highly resistant to current drugs that target it. Antibiotics such as viomycin and capreomycin have been shown to bind to functionally important regions of the bacterial ribosome thereby inhibiting the protein synthesis process which subsequently affects the bacterial cell viability. Current methods for studying drug interaction...

PipCoA ligase

Black pepper (Piper nigrum L.) is known for the high content of piperine, a cinnamoyl amide derivative regarded as largely responsible for the pungent taste of this widely used spice. Despite its long history and worldwide use, the biosynthesis of piperine and related amides has been enigmatic up to now. In this report we describe a specific piperic acid CoA ligase from immature green fruits of P. nigrum. The corresponding enzyme was cloned and functionally...

Compund 31 (CAY10684) docked Human Prostanoid E2 Receptor Subtype 4 (hEP4)

The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. Homology models were generated by threading for human and rat EP4 receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and...

Rivenprost docked Human Prostanoid E2 Receptor Subtype 4 (hEP4)

The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. Homology models were generated by threading for human and rat EP4 receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and...

PGE1 docked Human Prostanoid E2 Receptor Subtype 4 (hEP4)

The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. Homology models were generated by threading for human and rat EP4 receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and...

3D model of SARS-CoV-2 Helicase for pocket mapping

We have generated a 3D structure of the SARS-CoV-2 Helicase NSP13 (NTPase). The structure model has been used for the exploration of the potential binding cavities within promising Covid-19 proteins. After in silico modelling of these 3D structures, such a mapping enables the identification of the most relevant binding sites for which virtual screening simulations or de novo rational design should allow the identification of promising hits. This study provides a novel strategy for pocket...

Human MHC-I peptide-loading complex

The MHC-I peptide-loading complex (PLC) is a cornerstone of the human adaptive immune system, being responsible for processing antigens that allow killer T-cells to distinguish between healthy and compromised cells. Based on a recent low-resolution cryo-EM structure of this large membrane-bound protein complex, we report an atomistic model of the PLC and study its conformational dynamics on the multi-microsecond timescale using all-atom molecular dynamics (MD) simulations in explicit lipid bilayer and water environment.

Mycoplasma pneumoniae RNA polymerase

Structural biology performed inside cells can capture molecular machines in action within their native context. Here we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae. We combined whole-cell crosslinking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at sub-nanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA...

Mycoplasma pneumoniae ribosome

Structural biology performed inside cells can capture molecular machines in action within their native context. Here we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae. We combined whole-cell crosslinking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at sub-nanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA...

Structure prediction of transferrin receptor protein 1 (TfR1) by homology modelling, docking, and molecular dynamics simulation studies

Transferrin receptor protein 1 (TfR1) is an important molecule in anti-cancer therapy. Targeted delivery of such therapeutic compounds improves their cellular uptake and circulation time, thereby enhancing therapeutic efficacy.Drug designing is therefore used to engineer molecules with structures that facilitate specific interactions. However, this process requires a thorough knowledge of all the interactions, including the three-dimensional (3D) and quaternary structures (QS) of the interacting molecules. Since structural information is available for only a part of...

Model of G-alpha-i3 bound to the GIV GBA-motif

The activation of heterotrimeric G proteins is typically achieved by guanine nucleotide exchange factor (GEF) proteins that facilitate the exchange of GDP for GTP on G-alpha subunits. While this exchange activity is typically performed by G protein-coupled receptors (GPCRs), cytosolic non-receptor type GEFs have been more recently described as G-alpha activators. A subset of the described non-receptor GEFs contain a Galpha-Binding and Activating (GBA) motif. This short, evolutionarily conserved motif is known to confer nucleotide...

Bacillus subtilis YolD protein

The YolD family (that includes both Bacillus subtilis YolD (this model) and YqjX) is part of the WYL-like superfamily, predicted to have an SH3 β-barrel fold related to Sm domains. In our analysis, among the closest detected structural matches were E. coli YaeO, a Rho-specific inhibitor of transcription termination, and a cyanobacterial Hfq homolog. Model assessment showed that YqjX and YolD sequences are indeed compatible with the SH3 β-barrel structure. Interestingly, UmuD' has an all...

Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity

The DXO family of proteins participates in eukaryotic mRNA 5′-end quality control, removal of non-canonical NAD+ cap and maturation of fungal rRNA precursors. In this work, we characterize the Arabidopsis thaliana DXO homolog, DXO1. We demonstrate that the plant-specific modification within the active site negatively affects 5′-end capping surveillance properties of DXO1, but has only a minor impact on its strong deNADding activity. Unexpectedly, catalytic activity does not contribute to striking morphological and molecular aberrations...

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 NON-STRUCTURAL PROTEIN 2 (nsp2)

The structure of 'SARS-CoV-2 NON-STRUCTURAL PROTEIN 2 (nsp2)” is a part of the project “In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” (Baruah et al., 2020; In communication) based on the sequence analysis and complete coordinate structure prediction of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321.

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 ORF3a protein

The structure of 'SARS-CoV-2 ORF3a protein' is a part of the project “In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” (Baruah et al., 2020; In communication) based on the sequence analysis and complete coordinate structure prediction of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. (Citation: bioRxiv preprint doi: https://doi.org/10.1101/2020.05.23.104919)

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

The aim of this study was to use molecular modelling and simulation to investigate how cytochrome P450 1A1 and its redox partner, cytochrome P450 reductase, form an electron transfer competent complex in a phospholipid bilayer. We used a multiresolution computational approach, combining Brownian dynamics, coarse-grained and all-atom molecular dynamics simulations to model the complex. The structural parameters and electron transfer rates agree well with experimental data.

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