Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins*

1. Download : Download high-res image (51KB)
2. Download : Download full-size image

Highlights

• •Method for the analysis of response curves from thermal proteome profiling (TPP).
• •NPARC uses nonparametric statistics and provides false discovery-rate (FDR) control.
• •Increased proteome coverage and sensitivity to identify drug-binding proteins.

     

Peptide and amino acid glycation: new insights into the Maillard reaction.

Nonenzymatic glycation of proteins, peptides and other macromolecules (the Maillard reaction) has been implicated in a number of pathologies, most clearly in diabetes mellitus. but also in the normal processes of aging and neurodegenerative amyloid diseases such as Alzheimer's. In the early stage, glycation results in the formation of Amadori-modified proteins. In the later stages, advanced glycation end products (AGE) are irreversibly formed from Amadori products leading to the formation of reactive intermediates, crosslinking of proteins, and the formation of brown and fluorescent polymeric materials. Although, the glycation of structural proteins has been attributed a key role in the complications of diabetes, recent attention has been devoted to the physiological significance of glycated peptide hormones. This review focuses on the physico-chemical properties of the Amadori compounds of bioactive peptides of endogenous and exogenous origin, such as Leu-enkephalin and morphiceptin, investigated under different conditions as well as on novel pathways in the Maillard reaction observed from investigating intramolecular events in ester-linked glycopeptides.     

Advancing the use of morphometric data for estimating and managing common bottlenose dolphin (Tursiops truncatus) mass

Knowledge of a dolphin's body mass is central to establishing body condition, comparing across individuals, and designing successful management programs. In the present study, sex‐specific prediction equations for estimating body mass were generated from morphometrics (i.e., length and girth) and ages of bottlenose dolphins residing under professionally managed care. Measurements of wild dolphins in Sarasota Bay, Florida, were used to generate sex‐specific body mass reference ranges. Gompertz growth models were fitted to length measurements and age to compare growth across populations. From the regression analyses, the body mass of managed females (R² = 0.937), managed males (R² = 0.953), wild females (R² = 0.979), and wild males (R² = 0.972) were predicted with high levels of accuracy. Managed adults had similar or longer asymptotic lengths compared to their wild conspecifics. To apply this information, ZooMorphTrak, a mobile software application, was developed to provide a new resource for management. The “Approximate” feature was designed to approximate body mass based on user inputs of individual morphometrics. The “Management” feature compared a managed dolphin's known body mass with respect to body mass reference ranges generated from wild dolphins. ZooMorphTrak, developed by the Chicago Zoological Society, is available for download at http://itunes.apple.com .     

All-Atom Structural Models for Complexes of Insulin-Like Growth Factors IGF1 and IGF2 with Their Cognate Receptor

Type 1 insulin-like growth factor receptor (IGF1R) is a membrane-spanning glycoprotein of the insulin receptor family that has been implicated in a variety of cancers. The key questions related to molecular mechanisms governing ligand recognition by IGF1R remain unanswered, partly due to the lack of testable structural models of apo or ligand-bound receptor complexes. Using a homology model of the IGF1R ectodomain IGF1RΔβ, we present the first experimentally consistent all-atom structural models of IGF1/IGF1RΔβ and IGF2/IGF1RΔβ complexes. Our explicit-solvent molecular dynamics (MD) simulation of apo-IGF1RΔβ shows that it displays asymmetric flexibility mechanisms that result in one of two binding pockets accessible to growth factors IGF1 and IGF2, as demonstrated via an MD-assisted Monte Carlo docking procedure. Our MD-generated ensemble of structures of apo and IGF1-bound IGF1RΔβ agrees reasonably well with published small-angle X-ray scattering data. We observe simultaneous contacts of each growth factor with sites 1 and 2 of IGF1R, suggesting cross-linking of receptor subunits. Our models provide direct evidence in favor of suggested electrostatic complementarity between the C-domain (IGF1) and the cysteine-rich domain (IGF1R). Our IGF1/IGF1RΔβ model provides structural bases for the observation that a single IGF1 molecule binds to IGF1RΔβ at low concentrations in small-angle X-ray scattering studies. We also suggest new possible structural bases for differences in the affinities of insulin, IGF1, and IGF2 for their noncognate receptors.     

A Conservative Point Mutation in a Dynamic Antigen-binding Loop of Human Immunoglobulin λ6 Light Chain Promotes Pathologic Amyloid Formation

Immunoglobulin light chain (LC) amyloidosis (AL) is a life-threatening human disease wherein free mono-clonal LCs deposit in vital organs. To determine what makes some LCs amyloidogenic, we explored patient-based amyloidogenic and non-amyloidogenic recombinant LCs from the λ6 subtype prevalent in AL. Hydrogen-deuterium exchange mass spectrometry, structural stability, proteolysis, and amyloid growth studies revealed that the antigen-binding CDR1 loop is the least protected part in the variable domain of λ6 LC, particularly in the AL variant. N32T substitution in CRD1 is identified as a driver of amyloid formation. Substitution N32T increased the amyloidogenic propensity of CDR1 loop, decreased its protection in the native structure, and accelerated amyloid growth in the context of other AL substitutions. The destabilizing effects of N32T propagated across the molecule increasing its dynamics in regions ∼30 Å away from the substitution site. Such striking long-range effects of a conservative point substitution in a dynamic surface loop may be relevant to Ig function. Comparison of patient-derived and engineered proteins showed that N32T interactions with other substitution sites must contribute to amyloidosis. The results suggest that CDR1 is critical in amyloid formation by other λ6 LCs.     

Soft–part preservation in heteromorph ammonites from the Cenomanian–Turonian Boundary Event (OAE 2) in north–west Germany

Abstract: From thinly laminated marlstones of the Hesseltal Formation, representing the Late Cenomanian Oceanic Anoxic Event (OAE) 2, at Lengerich in the Teutoburger Wald (Westfalen, north‐west Germany), 17 sediment‐compacted baculitid ammonites with carbonised and partially phosphatised soft parts are recorded. Some preserve remains of the buccal mass, including jaws (occasionally articulated) and radulae, as well as of the cephalic cartilage, such as eye capsules. Such have not yet been recorded previously for the order Ammonoidea. In addition, originally unmineralised parts found preserved in these specimens include extensive portions of the digestive tract, the siphonal tube, false colour patterns (megastriae), as well as traces of what would appear to be the oviduct. At the same levels, patches with numerous isolated horny upper and rarer lower jaws as well as radulae occur; these may represent regurgitates or faeces of larger predators. The cephalopod remains described were deposited in an epicontinental setting, possibly at palaeodepths between 200 and 600 m. In this particular Late Cretaceous fossil Lagerstätte, upper jaws and anaptychi of ammonites rank among the commonest fossils.     

Hydrolysis of concentrated raw starch: A new very efficient α-amylase from Anoxybacillus flavothermus

A new α-amylase from Anoxybacillus flavothermus (AFA) was found to be effective in hydrolyzing raw starch in production of glucose syrup at temperatures below the starch gelatinization temperature. AFA is very efficient, leading to 77% hydrolysis of a 31% raw starch suspension. The final hydrolysis degree is reached in 2-3 h at starch concentrations lower than 15% and 8-24 h at higher concentrations. AFA is also very efficient in hydrolyzing the crystalline domains in the starch granule. The major A-type crystalline structure is more rapidly degraded than amorphous domains in agreement with the observed preferential hydrolysis of amylopectin. Amylose-lipid complexes are degraded in a second step, yielding amylose fragments which then re-associate into B-type crystalline structures forming the final α-amylase resistant fraction. The mode of action of AFA and the factors limiting complete hydrolysis are discussed in details.     

Males of the predatory mirid bug Macrolophus caliginosus exploit plant volatiles induced by conspecifics as a sexual synomone

The olfactory responses of male and female Macrolophus caliginosus Wagner (Heteroptera: Miridae) adults towards volatiles from green bean plants previously exposed to feeding by conspecifics and to direct odours from conspecifics were tested in a Y-tube olfactometer. Female M. caliginosus did not respond to volatiles from plants exposed to mirid feeding or to odours emitted directly by adult mirids. In contrast, male mirid bugs were attracted both to volatiles from plants previously exposed to feeding by conspecific females and to odours emitted by conspecifics only with a marginally significant preference for the former. The gas chromatography-mass spectrometry analysis showed that mirid feeding induced the release of 11 additional compounds as compared to the volatiles emitted from clean plants. Three of these substances (5-ethyl-2(5H)-furanone, Z-3-hexenyl tiglate, and E,E-α-farnesene) were released only after feeding by females. Furthermore, 21 compounds were identified in volatiles emitted directly by mirids, 12 of which were unique to the mirids (i.e., not present in clean plants or plants previously exposed to mirid feeding). The results suggest that female-specific herbivore-induced plant volatiles play a role as mate-finding cues by the male mirids. The ecological implications of the findings are discussed, and the term ‘sexual synomone’ is introduced.     

Land-use intensification systematically alters the size structure of aquatic communities in the Neotropics

Land-use and land-cover transitions can affect biodiversity and ecosystem functioning in a myriad of ways, including how energy is transferred within food-webs. Size spectra (i.e. relationships between body size and biomass or abundance) provide a means to assess how food-webs respond to environmental stressors by depicting how energy is transferred from small to larger organisms. Here, we investigated changes in the size spectrum of aquatic macroinvertebrates along a broad land-use intensification gradient (from Atlantic Forest to mechanized agriculture) in 30 Brazilian streams. We expected to find a steeper size spectrum slope and lower total biomass in more disturbed streams due to higher energetic expenditure in physiologically stressful conditions, which has a disproportionate impact on large individuals. As expected, we found that more disturbed streams had fewer small organisms than pristine forest streams, but, surprisingly, they had shallower size spectrum slopes, which indicates that energy might be transferred more efficiently in disturbed streams. Disturbed streams were also less taxonomically diverse, suggesting that the potentially higher energy transfer in these webs might be channelled via a few efficient trophic links. However, because total biomass was higher in pristine streams, these sites still supported a greater number of larger organisms and longer food chains (i.e. larger size range). Our results indicate that land-use intensification decreases ecosystem stability and enhances vulnerability to population extinctions by reducing the possible energetic pathways while enhancing efficiency between the remaining food-web linkages. Our study represents a step forward in understanding how land-use intensification affects trophic interactions and ecosystem functioning in aquatic systems.