1,557 Works

Xenorhabdus nematophila RelE toxin

TAG protein model

JYOTI SINGH TOMAR

Xn-RelT toxin from X. nematophila in complex with RNA substrate.

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...

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