32 Works

SULT1E1_OHPCB1_E2_PAPS

Polychlorinated bisphenols are continuing to contaminate food chains globally where they concentrate in the tissues and disrupt the endocrine systems of species throughout the ecosphere. Hydroxylated PCBs (OH-PCBs) are major PCB metabolites and high affinity inhibitors of human estrogen sulfotransferase (SULT1E1), which sulfonates estrogens and thus prevents them from binding to and activating their receptors. It has been hypothesized that OH PCB inhibition of SULT1E1 contributes significantly to PCB-based endocrine disruption. Here, for the first...

In silico tertiary structure of DBP-1 from Hyposidra talaca nucleopolyhedrovirus (HytaNPV)

In silico tertiary structure prediction and evolutionary analysis of two DNA-binding proteins (DBP-1 and DBP-2) from Hyposidra talaca nucleopolyhedrovirus (HytaNPV)

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.

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.

The homology model of Rhodococcus fascians SPL using the structure of Agrobacterium fabrum FeS-BCP as the template

Lei Xu
We identified a novel class of proteins of the cryptochrome/photolyase family (CPF), which are shorter than most CPF proteins. We named this class of proteins Short Photolyase-Like (SPL). A member of SPL from Rhodococcus fascians (RfSPL) was selected, and its homology structural model was built with SWISS-MODEL using the known crystal structure of Agrobacterium fabrum FeS-BCP (AfPhrB, PDB ID: 4DJA) as the templates. Among the total of 406 residues of RfSPL, a fragment of 4-256...

PP102 Antimicrobial peptide from IBSD35

The endophyte, Paenibacillus peoriae IBSD35 was isolated from Milletttia pachycarpa Benth. and its fermentation broth was purified by ammonium sulfate precipitation and RP-HPLC. The fraction were further purified, checked with tricine SDS PAGE and gel overlay experiment to study its antimicrobial activity. The bioactive sample was sequenced with LC-MS proteomic analyse. The sequence were then submitted in Amino acids fasta format on structure homology-modelling server the ExPASy web server. The template were search and two...

NFT bound to E. coli NfsA

Andrew Christofferson
NfsA is a dimeric flavoprotein that catalyses the reduction of nitroaromatics and quinones by NADPH. This reduction is required for the activity of nitrofuran antibiotics. The crystal structure of free E. coli NfsA and several homologues have been determined previously, but there is no structure of the enzyme with ligands. We present here crystal structures of oxidised E. coli NfsA in the presence of several ligands, including the antibiotic nitrofurantoin. Nitrofurantoin binds with the furan...

Resveratrol-O-methyltransferase

We constructed a three-dimensional protein model of the resverartrol-O-methyltransferase (VvROMT) to modify its substrate-selectivity. VvROMT has the highest catalytic efficiency in di-methylating resveratrol to yield pterostilbene. By applying different in silico approaches, we identified four critical binding site residues. Then we rationally designed eight variants through comparison of the binding site residues with other stilbene OMTs. We successfully modified the native substrate-selectivity of VvROMT. Variant L117F/F311W showed the highest conversion to the monomethylated compound, pinostilbene.

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 ORF7a PROTEIN

The structure of 'SARS-CoV-2 ORF7a 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: https://www.biorxiv.org/content/10.1101/2020.05.23.104919v2

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 ENVELOPE PROTEIN

The structure of 'SARS-CoV-2 ENVELOPE 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:https://www.biorxiv.org/content/10.1101/2020.05.23.104919v2

In silico tertiary structure of DBP-2 from Hyposidra talaca nucleopolyhedrovirus (HytaNPV)

In silico tertiary structure prediction and evolutionary analysis of two DNA-binding proteins (DBP-1 and DBP-2) from Hyposidra talaca nucleopolyhedrovirus (HytaNPV)

MEIOB-SPATA22 human complex

During meiosis, programmed double strand breaks are repaired by homologous recombination (HR) to form crossovers that are essential to homologous chromosomes segregation. Single stranded DNA (ssDNA) containing intermediates are key features of HR which must be highly regulated. RPA, the ubiquitous ssDNA binding complex was thought to play similar roles during mitotic and meiotic HR until the recent discovery of MEIOB and its partner, SPATA22, two essential meiosis-specific proteins. Despite low sequence identity, remote homology...

Structural model of the human tRNA multisynthetase complex by cross-linking mass spectrometry

We have taken advantage of cross-linking mass spectrometry (XL-MS) to interrogate the quaternary structure of the human MSC. Using the MS-cleavable cross-linker, DSSO, 19 unique inter-protein cross-links spanning all MSC constituents, and 118 unique intra-protein cross-links, were observed in MSC isolated from human HEK293T cells. The cross-links established spatial relationships between constituent pairs, and between domains in individual constituents. The protein-protein interactions detected by XL-MS were further improved by docking, revealing for the first time...

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.

The homology model of Rhodococcus fascians SPL using the structure of Synechococcus elongatus photolyase as the template

Lei Xu
We identified a novel class of proteins of the cryptochrome/photolyase family (CPF), which are shorter than most CPF proteins. We named this class of proteins Short Photolyase-Like (SPL). A member of SPL from Rhodococcus fascians (RfSPL) was selected, and its homology structural model was built with SWISS-MODEL using the known crystal structure of Synechococcus elongatus class I CPD photolyase (SeCPDI, PDB ID: 1TEZ) as the templates. Among the total of 406 residues of RfSPL, a...

Structural model of the human tRNA multisynthetase complex by cross-linking mass spectrometry

We have taken advantage of cross-linking mass spectrometry (XL-MS) to interrogate the quaternary structure of the human MSC. Using the MS-cleavable cross-linker, DSSO, 19 unique inter-protein cross-links spanning all MSC constituents, and 118 unique intra-protein cross-links, were observed in MSC isolated from human HEK293T cells. The cross-links established spatial relationships between constituent pairs, and between domains in individual constituents. The protein-protein interactions detected by XL-MS were further improved by docking, revealing for the first time...

Defining a novel domain which provides an essential contribution to site-specific interaction of Rep protein with DNA

The essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA-protein cross-linking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the broad-host-range plasmid RK2, in addition to two winged helix domains, contains a third DNA binding...

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 ORF7b PROTEIN

The structure of 'SARS-CoV-2 ORF7b 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: https://www.biorxiv.org/content/10.1101/2020.05.23.104919v2

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 ORF10 PROTEIN

The structure of 'SARS-CoV-2 ORF10 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)

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 NON-STRUCTURAL PROTEIN 6 (nsp6)

The structure of 'SARS-CoV-2 NON-STRUCTURAL PROTEIN 6 (nsp6)” 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 NUCLEOCAPSID PHOSPHOPROTEIN

The structure of 'SARS-CoV-2 NUCLEOCAPSID PHOSPHOPROTEIN” 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 NON-STRUCTURAL PROTEIN 3 (nsp3)

The structure of 'SARS-CoV-2 NON-STRUCTURAL PROTEIN 3 (nsp3)” 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)

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 NON-STRUCTURAL PROTEIN 4 (nsp4)

The structure of 'SARS-CoV-2 NON-STRUCTURAL PROTEIN 4 (nsp4)” is a part of the project “In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” (Baruah et al., 2020; bioRxiv preprint doi: https://doi.org/10.1101/2020.05.23.104919) 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.

Registration Year

  • 2021
    32

Resource Types

  • Model
    32