webPIPSA: a web server for the comparison of protein interaction properties

Richter, Stefan; Wenzel, Anne; Stein, Matthias; Gabdoulline, Razif R.; Wade, Rebecca C.

doi:10.1093/nar/gkn181

Cited by 89 publications

(92 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Electrostatic Potentials and Clustering-We used PoissonBoltzmann electrostatic calculations and homology modeling to quantitatively identify regions of conserved electrostatic character (35,36) in the Hha/YmoA family of proteins. Homology modeling was used to generate structures for the Hha homologues with unsolved structures based on PDB code 1JW2 using SWISS-MODEL (37).…”

Section: Volume 290 • Number 35 • August 28 2015mentioning

confidence: 99%

See 1 more Smart Citation

A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing

Cordeiro

García

Bernadó

et al. 2015

Journal of Biological Chemistry

View full text Add to dashboard Cite

Section: Volume 290 • Number 35 • August 28 2015mentioning

confidence: 99%

“…Similarity matrices were generated based on the electrostatic similarity index as defined elsewhere (35,36). Cumulative distributions of electrostatic conservation index (ECI) were calculated using (40),…”

Section: Volume 290 • Number 35 • August 28 2015mentioning

confidence: 99%

A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing

Cordeiro

García

Bernadó

et al. 2015

Journal of Biological Chemistry

View full text Add to dashboard Cite

“…Electrostatic potentials have then been calculated by solving the linearized form of the Poisson-Boltzmann equation using the software APBS Version 1.3 (97). Similarity indices were calculated using the webserver PIPSA (99). PIPSA calculates similarity indices using Equation 1,…”

mentioning

confidence: 99%

Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control

Kent

Loo

Melton

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

Many pectin methylesterases (PMEs) are expressed in plants to modify plant cell-wall pectins for various physiological roles. These pectins are also attacked by PMEs from phytopathogens and phytophagous insects. The de-methylesterification by PMEs of the O6-methyl ester groups of the homogalacturonan component of pectin, exposing galacturonic acids, can occur processively or non-processively, respectively, describing sequential versus single de-methylesterification events occurring before enzyme-substrate dissociation. The high resolution x-ray structures of a PME from Aspergillus niger in deglycosylated and Asn-linked N-acetylglucosamine-stub forms reveal a 10 2 ⁄ 3-turn parallel ␤-helix (similar to but with less extensive loops than bacterial, plant, and insect PMEs). Capillary electrophoresis shows that this PME is non-processive, halophilic, and acidophilic. Molecular dynamics simulations and electrostatic potential calculations reveal very different behavior and properties compared with processive PMEs. Specifically, uncorrelated rotations are observed about the glycosidic bonds of a partially de-methyl-esterified decasaccharide model substrate, in sharp contrast to the correlated rotations of processive PMEs, and the substrate-binding groove is negatively not positively charged.The heterogeneous polysaccharide pectin (1-4) is a key component of the plant cell wall (5). A host of enzymes, including pectin methylesterase (PME) 3 as well as endo-and exopolygalacturonases, modifies pectin fine-structure locally in space and time for purposes of plant-cell differentiation, cell adhesion/separation, growth, and development from roots to meristem, morphogenesis, seed and fruit development, and defense against pathogens (6 -16). PMEs hydrolyze the O6-methyl ester groups of the homogalacturonan (HG) chains that form the backbone of pectin (Fig. 1). As well as being ubiquitous in plants, and frequently manifesting in a staggering number of isoforms (more than 66 for Arabidopsis thaliana) (8, 10), PMEs are found in phytopathogenic bacteria and fungi (17-26) and in Archaea (especially Halobacteriaceae (27)), and they have also been observed in the genomes of several phytophagous insects (28 -30) and in human gut microflora (31). Recently, plant pollen PMEs have been identified as a key human allergen (32, 33). Bacterial and plant PMEs that have been functionally characterized are generally observed to be processive (34 -55), i.e. the enzyme binds to the HG substrate and then successively hydrolyzes a block of methyl ester groups before dissociating. In all cases characterized to date, the direction of processivity is from the non-reducing end of the HG chain toward the reducing end, as shown in Fig. 1. The degree of processivity (also called the action pattern) has been reported to be dependent on ionic strength and pH (56), and various classifications of PMEs exist (48,49,(57)(58)(59)(60). In general, processive PMEs have their isoelectric points, pI, and pH for optimum activity at near-neutral to basic pH, although ...

show abstract

“…5 compares the electrostatic surface of NLRP7 PYD with those of ASC, ASC2, and NLRP1. We used the Protein Interaction Property Similarity Analysis server (62) to quantify the similarities between the electrostatic surfaces of the PYDs from NLRP1, NLRP7, ASC, and ASC2. The Protein Interaction Property Similarity Analysis server uses the University of Houston Brownian Dynamics program to calculate the electrostatic potential of a protein.…”

mentioning

confidence: 99%

Three-dimensional Structure of the NLRP7 Pyrin Domain

Pinheiro

Proell

Eibl

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

The innate immune system provides an initial line of defense against infection. Nucleotide-binding domain-and leucine-rich repeat-containing protein (NLR or (NOD-like)) receptors play a critical role in the innate immune response by surveying the cytoplasm for traces of intracellular invaders and endogenous stress signals. NLRs themselves are multi-domain proteins. Their N-terminal effector domains (typically a pyrin or caspase activation and recruitment domain) are responsible for driving downstream signaling and initiating the formation of inflammasomes, multi-component complexes necessary for cytokine activation. However, the currently available structures of NLR effector domains have not yet revealed the mechanism of their differential modes of interaction. Here, we report the structure and dynamics of the N-terminal pyrin domain of NLRP7 (NLRP7 PYD) obtained by NMR spectroscopy. The NLRP7 PYD adopts a six-␣-helix bundle death domain fold. A comparison of conformational and dynamics features of the NLRP7 PYD with other PYDs showed distinct differences for helix ␣3 and loop ␣2-␣3, which, in NLRP7, is stabilized by a strong hydrophobic cluster. Moreover, the NLRP7 and NLRP1 PYDs have different electrostatic surfaces. This is significant, because death domain signaling is driven by electrostatic contacts and stabilized by hydrophobic interactions. Thus, these results provide new insights into NLRP signaling and provide a first molecular understanding of inflammasome formation.Eukaryotes have evolved an array of strategies, collectively referred to as the innate immune system, to directly detect pathogens and "danger signals." This efficient pathogen-associated molecular pattern detection enables eukaryotes to quickly eliminate intruders, thereby increasing the chance of survival. Inflammatory reactions via the innate immune system and cell death are related processes that utilize parallel signaling mechanisms and employ common molecular effectors.Many of these molecular effectors share a common structural fold, the death domain fold. The death domain superfamily consists of: 1) the death domain (DD) 2 itself (1, 2), 2) the death effector domain (3), 3) the caspase activation and recruitment domain (CARD) (4), and 4) the pyrin domain (5-7) (PYD, formerly called PAAD (8) or DAPIN (9)).The most recently discovered family of proteins that are essential for the regulation of the innate immune system are the NLRs. These intracellular proteins act as receptors and regulators of innate immunity and apoptosis (10 -12). NLRs have three distinct domains: 1) a C-terminal leucine-rich repeat domain, which is responsible for pathogen-associated molecular pattern recognition, 2) a central NOD-WH-SH domain (nucleotide-binding and oligomerization-winged helix-superhelical domain), also known as the NACHT domain, which is essential for multimerization of NLR receptors upon pathogenassociated molecular pattern recognition, and 3) an N-terminal effector domain, which links the NLR proteins to distinct downstream signaling pathways...

show abstract

webPIPSA: a web server for the comparison of protein interaction properties

Cited by 89 publications

References 22 publications

A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing

A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing

Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control

Three-dimensional Structure of the NLRP7 Pyrin Domain

Contact Info

Product

Resources

About