44 Works

Model of the Rabies virus L protein

A homology-based model of the RABV L protein was generated based on the structure of the vesicular stomatitis virus (VSV) L protein (PDB id: 5A22).

Model of the Rabies virus L terminal de novo initiation complex

A homology-based model of the RABV L terminal de novo initiation complex was generated based on the vesicular stomatitis virus (VSV) L terminal de novo initiation complex (Molecular Archive id: ma-5k432).

Mouse Eugenol Odorant Receptor

Molecular interactions of odorants with their olfactory receptors (ORs) are of central importance for the ability of the mammalian olfactory system to detect and discriminate a vast variety of odors with a limited set of receptors. How a particular OR binds and distinguishes different odorant molecules remains largely unknown on a structural basis. Here we investigated this question for the mouse eugenol receptor (mOR-EG). By screening a large odorant library, we discovered a wide range...

Bacillus subtilis YqjX protein

The YolD family (that includes both Bacillus subtilis YolD and YqjX (this model)) 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...

Multidrug transporter AcrD of E. coli

Resistance-Nodulation-cell Division (RND) transporters AcrB and AcrD of Escherichia coli expel a wide range of substrates out of the cell in conjunction with AcrA and TolC, contributing to the onset of bacterial multidrug resistance. AcrB is the best characterized RND transporter, and its structure has been solved by several labs both without and with bound substrates and inhibitors. AcrD, a close homolog of AcrB, shares an overall sequence identity of nearly 66% (similarity ~80%) but...

CYP21A2Bruque2016

A model of the human CYP21A2 protein based on the structure of the bovine CYP21A2 (PDB ID: 3QZ1) was generated using MODELLER version 9.11 including heme cofactor explicitly. Amino acid sequence was taken from UniProt (NP_000491.4) while alignments were performed with MEGA 4 software. A significant improvement of the model was obtained by manually displacing L129 in the automatic alignment and iterative loop refinement. The use of multiple templates of other proteins of the CYP...

Homology model of ANR from Pseudomonas aeruginosa

Pseudomonas aeruginosa is a deadly opportunistic human pathogen. The organism codes for different virulence factors and among them is HCN synthesized by HCN synthase enzyme. the enzyme is encoded by the hcnABC operon. It is to be noted that the expression of the genes of the hcnABC operon are regulated by LasR, ANR and RhlR proteins. ANR protein belongs to the FNR family. It works in anaerobic condition. It binds to the promoter DNA as...

Models of transcription factor LasR

Pseudomonas aeruginosa, an opportunistic human pathogen can attack human patients suffering from different diseases like AIDS, cancer, cystic fibrosis, etc. The organism codes for a virulent factor called Hydrogen Cyanide (HCN). HCN is encoded by an operon called hcnABC operon. The expressions of the hcnABC operon are carried out by binding of LasR protein with the corresponding promoter DNA region of the hcnABC operon. Till date no studies have been performed to analyze the molecular...

Factor VIII/von Willebrand Factor Complex

Paul Clinton Spiegel
Blood coagulation factor VIII forms a tight complex with von Willebrand Factor in circulation, which protects factor VIII from proteolytic degradation and increases its half-life. The region of von Willebrand Factor that binds to factor VIII is the N-terminal TIL'E' domain. In this model, we combined two structures: the 3.2 Å X-ray crystal structure of factor VIII and the NMR-determined structure of TIL'E'. The putative complex was computationally docked together with RosettaDock as part of...

11-deoxy-PGE2 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...

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 ORF 14 PROTEIN

The structure of 'SARS-CoV-2 ORF 14 protein” is a part of the manuscript “Sequence analysis and structure prediction of SARS-CoV-2 accessory proteins 9b and ORF14: evolutionary analysis indicates close relatedness to bat coronavirus” (Baruah et al., 2020; ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.12424958.v1) based on the sequence analysis and complete coordinate structure prediction of UniProtkB reviewed sequence data.

Complex between HIV-1 integrase and human mitochondrial lysyl-tRNA synthetase

Replication of human immunodeficiency virus type 1 (HIV-1) requires the packaging of tRNALys,3 from the host cell into the new viral particles. The GagPol viral polyprotein precursor associates with mitochondrial lysyl-tRNA synthetase in a complex with tRNALys, an essential step of the viral life cycle to capture the primer RNA necessary to initiate reverse transcription in the virions. The C-terminal integrase moiety of GagPol is known to be essential for its association with GagPol. In...

Model of the Rabies virus L protein

A homology-based model of the RABV L protein was generated based on the structure of the vesicular stomatitis virus (VSV) L protein (PDB id: 5A22). In this model, Zn2+ binding site geometry is optimized.

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...

Registration Year

  • 2020
    44

Resource Types

  • Model
    44