Protein structure by mechanical triangulation.
Ontology highlight
ABSTRACT:
SUBMITTER: Dietz H
PROVIDER: S-EPMC1360557 | biostudies-literature | 2006 Jan
REPOSITORIES: biostudies-literature
Publications
Protein structure by mechanical triangulation.
Dietz Hendrik H Rief Matthias M
Proceedings of the National Academy of Sciences of the United States of America 20060123 5
Knowledge of protein structure is essential to understand protein function. High-resolution protein structure has so far been the domain of ensemble methods. Here, we develop a simple single-molecule technique to measure spatial position of selected residues within a folded and functional protein structure in solution. Construction and mechanical unfolding of cysteine-engineered polyproteins with controlled linkage topology allows measuring intramolecular distance with angstrom precision. We dem ...[more]
Similar Datasets
Project description:A statistical test for the detection of inhomogeneity in metagenomic samples
| PRJEB12272 | ENA
Project description:Cell-shape changes associated with processes like cytokinesis and motility proceed on several-second timescales but are derived from molecular events, including protein-protein interactions, filament assembly, and force generation by molecular motors, all of which occur much faster [1-4]. Therefore, defining the dynamics of such molecular machinery is critical for understanding cell-shape regulation. In addition to signaling pathways, mechanical stresses also direct cytoskeletal protein accumulation [5-7]. A myosin-II-based mechanosensory system controls cellular contractility and shape during cytokinesis and under applied stress [6, 8]. In Dictyostelium, this system tunes myosin II accumulation by feedback through the actin network, particularly through the crosslinker cortexillin I. Cortexillin-binding IQGAPs are major regulators of this system. Here, we defined the short timescale dynamics of key cytoskeletal proteins during cytokinesis and under mechanical stress, using fluorescence recovery after photobleaching and fluorescence correlation spectroscopy, to examine the dynamic interplay between these proteins. Equatorially enriched proteins including cortexillin I, IQGAP2, and myosin II recovered much more slowly than actin and polar crosslinkers. The mobility of equatorial proteins was greatly reduced at the furrow compared to the interphase cortex, suggesting their stabilization during cytokinesis. This mobility shift did not arise from a single biochemical event, but rather from a global inhibition of protein dynamics by mechanical-stress-associated changes in the cytoskeletal structure. Mechanical tuning of contractile protein dynamics provides robustness to the cytoskeletal framework responsible for regulating cell shape and contributes to cytokinesis fidelity.
| S-EPMC4348339 | biostudies-literature
Project description:Triangulation is the practice of obtaining more reliable answers to research questions through integrating results from several different approaches, where each approach has different key sources of potential bias that are unrelated to each other. With respect to causal questions in aetiological epidemiology, if the results of different approaches all point to the same conclusion, this strengthens confidence in the finding. This is particularly the case when the key sources of bias of some of the approaches would predict that findings would point in opposite directions if they were due to such biases. Where there are inconsistencies, understanding the key sources of bias of each approach can help to identify what further research is required to address the causal question. The aim of this paper is to illustrate how triangulation might be used to improve causal inference in aetiological epidemiology. We propose a minimum set of criteria for use in triangulation in aetiological epidemiology, summarize the key sources of bias of several approaches and describe how these might be integrated within a triangulation framework. We emphasize the importance of being explicit about the expected direction of bias within each approach, whenever this is possible, and seeking to identify approaches that would be expected to bias the true causal effect in different directions. We also note the importance, when comparing results, of taking account of differences in the duration and timing of exposures. We provide three examples to illustrate these points.
| S-EPMC5841843 | biostudies-other
Project description:A strategy for responsively toughening an injectable protein hydrogel has been implemented by incorporating an associative protein as the midblock in triblock copolymers with thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) endblocks, producing materials with a low yield stress necessary for injectability and durability required for load-bearing applications post-injection. Responsive reinforcement triggered by PNIPAM association leads to significant increases in the gel's elastic modulus as well as its resistance to creep. The performance of these materials is a strong function of molecular design, with certain formulations reaching elastic moduli of up to 130 kPa, effectively reinforced by a factor of 14 over their low temperature moduli, and having stress relaxation times increased by up to a factor of 50. The nanostructural origins of these thermoresponsive enhancements were explored, demonstrating that large micellar cores, high PNIPAM volume fractions, and high densities of associating groups in the protein corona lead to the greatest reinforcement of the gel's elastic modulus. Gels with the largest micelles and the highest packing fractions also had the longest relaxation times in the reinforced state. These combined structure and mechanics studies reveal that control of both the micellar and protein networks is critical for making high performance gels relevant for biomedical applications.
| S-EPMC4321950 | biostudies-literature
Project description:An insulating myelin sheath ensures saltatory conduction of mechanosensory A afferents. Myelin damage results in the electrical instability of A fibers and the ability to generate pain in response to light touch/pressure (mechanical allodynia). We have hypothesized and then established that the release of T cell epitopes of myelin basic protein (MBP) enables nociceptive circuitry in myelinated fibers. Thus, mass spectrometry analysis of the rat sciatic nerve proteome followed by bioinformatics examination of the datasets revealed a loss of MBP and activation of T-helper cell signaling in the nerves undergoing chronic constriction injury (CCI). Matrix metalloproteinase-9 (MMP-9) proteolysis resulted in the MBP digest peptides, including the MBP84-104 and MBP68-86 regions, which exhibit prominent immunogenic epitopes. Myelin-forming Schwann cells and paranodal areas accumulated MHCII, MMP-9 and the degraded MBP at the sciatic nerve injury site. Administration of the immunodominant MBP84-104 and MBP68-86 peptides but not of the control peptides in a naïve rat sciatic nerve produced robust mechanical allodynia. Allodynia was accompanied by the T cell infiltration and an increase in MHCII, IL-17A and TNF- levels at the nerve injection site and the segmental ganglia. The pro-nociceptive activity of the synthetic MBP84-104 diminished in athymic nude rats lacking T cells. SB-3CT, an antagonist of MMP-9, inhibited mechanical allodynia, neuroinflammation and spinal sensitization after CCI. Collectively, our novel data implicate, for the first time, MMP-mediated cleavage of MBP and the resulting MBP digest fragments as a major cause of neuropathic pain. Gene extression profiling of total RNAs extracted from rat sciatic nerves, dorsal root ganglion and spinal cords after MBP84-104 peptide injection
2012-03-03 | E-GEOD-34868 | biostudies-arrayexpress
Project description:This work proposes a new approach to determine the spatial location and orientation of an object using measurements performed on the object itself. The on-board triangulation algorithm we outline could be implemented in lieu of, or in addition to, well-known alternatives such as Global Positioning System (GPS) or standard triangulation, since both of these correspond to significantly different geometric pictures and necessitate different hardware and algorithms. We motivate the theory by describing situations in which on-board triangulation would be useful and even preferable to standard methods. The on-board triangulation algorithm we outline involves utilizing dumb beacons which broadcast omnidirectional single frequency radio waves, and smart antenna arrays on the object itself to infer the direction of the beacon signals, which may be used for onboard calculation of the position and orientation of the object. Numerical examples demonstrate the utility of the method and its noise tolerance.
| S-EPMC5482487 | biostudies-literature
Project description:The origin and early dispersal of speakers of Transeurasian languages-that is, Japanese, Korean, Tungusic, Mongolic and Turkic-is among the most disputed issues of Eurasian population history1-3. A key problem is the relationship between linguistic dispersals, agricultural expansions and population movements4,5. Here we address this question by 'triangulating' genetics, archaeology and linguistics in a unified perspective. We report wide-ranging datasets from these disciplines, including a comprehensive Transeurasian agropastoral and basic vocabulary; an archaeological database of 255 Neolithic-Bronze Age sites from Northeast Asia; and a collection of ancient genomes from Korea, the Ryukyu islands and early cereal farmers in Japan, complementing previously published genomes from East Asia. Challenging the traditional 'pastoralist hypothesis'6-8, we show that the common ancestry and primary dispersals of Transeurasian languages can be traced back to the first farmers moving across Northeast Asia from the Early Neolithic onwards, but that this shared heritage has been masked by extensive cultural interaction since the Bronze Age. As well as marking considerable progress in the three individual disciplines, by combining their converging evidence we show that the early spread of Transeurasian speakers was driven by agriculture.
| S-EPMC8612925 | biostudies-literature
Project description:Laser triangulation (LT) is widely used in many fields due to its good stability, high resolution and fast speed. However, the accuracy in these applications suffers from severe constraints on the data acquisition accuracy of LT. To solve this problem, the optical triangulation principle, the object equation of the optical path relationship and the deviation of the laser spot centroid are applied to deduce a mathematical model. Therefore, the image sensor inclination errors can be quantitatively calculated, and the collected data are compensated in real time. Further, a threshold sub-pixel gray-gravity (GG) extraction algorithm is proposed; the gradient function and Gaussian fit algorithm are used to set thresholds to remove the impact of the spot edge noise area on the center location; and polynomial interpolation is employed to enhance the data density of the traditional GG method, thus improving the data acquisition accuracy of LT. Finally, the above methods are applied to on-machine measurement of the American Petroleum Institute (API) thread and the screw rotor, respectively. The experimental results prove that the proposed method can significantly improve the measurement accuracy of free-form curved surfaces using LT and that the improved laser spot center extraction algorithm is more suitable for free-form curved surfaces with smaller curvature and more uniform curvature changes.
| S-EPMC6209907 | biostudies-literature
Project description:Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with diseases appropriately distributed among populations. Our results indicate that ET can filter association results to improve our ability to discover disease loci.
| S-EPMC4818851 | biostudies-literature
Project description:Alphaviruses are spherical, enveloped RNA viruses primarily transmitted by mosquitoes, and cause significant arthritogenic and neurotropic disease in humans and livestock. Previous reports have shown that-in contrast to prototypical icosahedral viruses-alphaviruses incorporate frequent defects, and these may serve important functions in the viral life cycle. We confirm the genus-wide pleomorphism in live viral particles and extend our understanding of alphavirus assembly through the discovery of an alternate architecture of Eastern equine encephalitis virus (EEEV) particles. The alternate T = 3 icosahedral architecture differs in triangulation number from the classic T = 4 icosahedral organization that typifies alphaviruses, but the alternate architecture maintains the quasi-equivalence relationship of asymmetric units. The fusion spike glycoproteins are more loosely apposed in the T = 3 form with corresponding changes in the underlying capsid protein lattice. This alternate architecture could potentially be exploited in engineering alphavirus-based particles for delivery of alphaviral or other RNA.
| S-EPMC9780915 | biostudies-literature