Web servers and services for electrostatics calculations with APBS and PDB2PQR

The activation of heterodimeric (α/β) integrin transmembrane receptors by cytosolic protein talin is crucial for regulating diverse cell-adhesion-dependent processes, including blood coagulation, tissue remodeling, and cancer metastasis. This process is triggered by the coincident binding of N-terminal FERM (four-point-one-protein/ezrin/radixin/moesin) domain of talin (talin-FERM) to the inner membrane surface and integrin β cytoplasmic tail, but how these binding events are spatiotemporally regulated remains obscure. Here we report the crystal structure of a dormant talin, revealing how a C-terminal talin rod segment (talin-RS) self-masks a key integrin-binding site on talin-FERM via a large interface. Unexpectedly, the structure also reveals a distinct negatively charged surface on talin-RS that electrostatically hinders the talin-FERM binding to the membrane. Such a dual inhibitory topology for talin is consistent with the biochemical and functional data, but differs significantly from a previous model. We show that upon enrichment with phosphotidylinositol-4,5-bisphosphate (PIP2) -a known talin activator, membrane strongly attracts a positively charged surface on talin-FERM and simultaneously repels the negatively charged surface on talin-RS. Such an electrostatic "pull-push" process promotes the relief of the dual inhibition of talin-FERM, which differs from the classic "steric clash" model for conventional PIP2-induced FERM domain activation. These data therefore unravel a new type of membrane-dependent FERM domain regulation and illustrate how it mediates the talin on/off switches to regulate integrin transmembrane signaling and cell adhesion.

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“…http://www.pymol. org), and the surface electrostatic potential was calculated with the program APBS [46].…”

Section: Crystallization Data Collection and Structure Determinationmentioning

confidence: 99%

A novel membrane-dependent on/off switch mechanism of talin FERM domain at sites of cell adhesion

et al. 2012

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“…The search region was defined interactively, and rotational flexibility was allowed for all ligand backbone bonds. Surface views were prepared with the program Chimera (35) using APBS and PDB2PQR for electrostatic calculations (48).…”

Section: Preparation Of Ide Mutants-ratmentioning

confidence: 99%

Anion Activation Site of Insulin-degrading Enzyme

Noinaj

Song

Bhasin

et al. 2012

Journal of Biological Chemistry

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Insulin-degrading enzyme (IDE) (insulysin) is a zinc metallopeptidase that metabolizes several bioactive peptides, including insulin and the amyloid ␤ peptide. IDE is an unusual metallopeptidase in that it is allosterically activated by both small peptides and anions, such as ATP. Here, we report that the ATPbinding site is located on a portion of the substrate binding chamber wall arising largely from domain 4 of the four-domain IDE. Two variants having residues in this site mutated, IDE K898A,K899A,S901A and IDE R429S , both show greatly decreased activation by the polyphosphate anions ATP and PPP i . IDE K898A,K899A,S901A is also deficient in activation by small peptides, suggesting a possible mechanistic link between the two types of allosteric activation. Sodium chloride at high concentrations can also activate IDE. There are no observable differences in average conformation between the IDE-ATP complex and unliganded IDE, but regions of the active site and C-terminal domain do show increased crystallographic thermal factors in the complex, suggesting an effect on dynamics. Activation by ATP is shown to be independent of the ATP hydrolysis activity reported for the enzyme. We also report that IDE K898A,K899A,S901A has reduced intracellular function relative to unmodified IDE, consistent with a possible role for anion activation of IDE activity in vivo. Together, the data suggest a model in which the binding of anions activates by reducing the electrostatic attraction between the two halves of the enzyme, shifting the partitioning between open and closed conformations of IDE toward the open form.

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“…Hydrogens, atomic charges, and radii were placed using the software PDB 2PQR Version 1.9 (97) using the parameters derived by the PARSE force field, which has been optimized for calculations in implicit solvent (98). 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).…”

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

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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 ...

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Web servers and services for electrostatics calculations with APBS and PDB2PQR

Cited by 261 publications

References 9 publications

A novel membrane-dependent on/off switch mechanism of talin FERM domain at sites of cell adhesion

A novel membrane-dependent on/off switch mechanism of talin FERM domain at sites of cell adhesion

Anion Activation Site of Insulin-degrading Enzyme

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

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