Microsecond Dynamics During the Binding-induced Folding of an Intrinsically Disordered Protein

Tau is an intrinsically disordered protein implicated in many neurodegenerative diseases. The repeat domain fragment of tau, tau-K18, is known to undergo a disorder to order transition in the presence of lipid micelles and vesicles, in which helices form in each of the repeat domains. Here, the mechanism of helical structure formation, induced by a phospholipid mimetic, sodium dodecyl sulfate (SDS) at sub-micellar concentrations, has been studied using multiple biophysical probes. A study of the conformational dynamics of the disordered state, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS) has indicated the presence of an intermediate state, I, in equilibrium with the unfolded state, U. The cooperative binding of the ligand (L), SDS, to I has been shown to induce the formation of a compact, helical intermediate (IL₅) within the dead time (∼37 µs) of a continuous flow mixer. Quantitative analysis of the PET-FCS data and the ensemble microsecond kinetic data, suggests that the mechanism of induction of helical structure can be described by a U ↔ I ↔ IL₅ ↔ FL₅ mechanism, in which the final helical state, FL₅, forms from IL₅ with a time constant of 50–200 µs. Finally, it has been shown that the helical conformation is an aggregation-competent state that can directly form amyloid fibrils.     

A current view on Tau protein phosphorylation in Alzheimer's disease

The functions of the neuronal microtubule-associated protein Tau in the central nervous system are regulated by manifold posttranslational modifications at more than 50 sites. Tau in healthy neurons carries multiple phosphate groups, mostly in its microtubule assembly domain. Elevated phosphorylation and aggregation of Tau are widely considered pathological hallmarks in Alzheimer’s disease (AD) and other tauopathies, triggering the quest for Tau posttranslational modifications in the disease context. However, the phosphorylation patterns of physiological and pathological Tau are surprisingly similar and heterogenous, making it difficult to identify specific modifications as therapeutic targets and biomarkers for AD. We present a concise summary of - and view on - important previous and recent advances in Tau phosphorylation analysis in the context of AD.     

基于低相干光干涉的眼睛光学生物参数测量研究

目的 眼睛的光学生物参数中的眼轴长度（AL）和角膜曲率半径（CR）可以作为预防和监测眼球近视的两个重要参数。为了提高测量眼轴长度的速度与精度和同步实现角膜曲率高精度动态测量，本文提出一种基于低相干光干涉技术眼睛光学生物参数测量的系统。方法 该系统使用旋转光学延迟线快速改变参考光的光程，利用曲率半径为8 mm的标准件标定人眼角膜顶点到靶环之间的距离，利用角膜的干涉信号对相机和数据采集卡进行触发实现同步采集，从而实现眼轴长度的快速测量和精准定位靶环到角膜顶点之间的距离，同时保证成像系统的放大倍率恒定和数据的实时采集。结果 实验结果表明，这种低相干光干涉测量系统，可以实时测量眼轴长度和角膜曲率半径，眼轴长度误差低于40 μm，人眼角膜曲率半径方差为2.082 36×10^-2 μm。结论 该系统能够快速、精准地测量AL和CR，可在近视的预防和监测中发挥重要作用。     

Conformation of ring single-stranded DNA measured by DNA origami structures

Measuring the mechanical properties of single-stranded DNA (ssDNA) is a complex challenge that has been addressed lately by different methods. We measured the persistence length of ring ssDNA using a combination of a special DNA origami structure, a self-avoiding ring polymer simulation model, and nonparametric estimation statistics. The method overcomes the complexities set forth by previously used methods. We designed the DNA origami nano structures and measured the ring ssDNA polymer conformations using atomic force microscopy. We then calculated their radius of gyration, which was used as a fitting parameter for finding the persistence length. As there is no simple formulation for the radius of gyration distribution, we developed a simulation program consisting of a self-avoiding ring polymer to fit the persistence length to the experimental data. ssDNA naturally forms stem-loops, which should be taken into account in fitting a model to the experimental measurement. To overcome that hurdle, we found the possible loops using minimal energy considerations and used them in our fitting procedure of the persistence length. Due to the statistical nature of the loops formation, we calculated the persistence length for different percentages of loops that are formed. In the range of 25–75% loop formation, we found the persistence length to be 1.9–4.4 nm, and for 50% loop formation we get a persistence length of 2.83 ± 0.63 nm. This estimation narrows the previously known persistence length and provides tools for finding the conformations of ssDNA.     

BAmSA: Visualising transmembrane regions in protein complexes using biotinylated amphipols and electron microscopy

Membrane protein (MP) complexes play key roles in all living cells. Their structural characterisation is hampered by difficulties in purifying and crystallising them. Recent progress in electron microscopy (EM) have revolutionised the field, not only by providing higher-resolution structures for previously characterised MPs but also by yielding first glimpses into the structure of larger and more challenging complexes, such as bacterial secretion systems. However, the resolution of pioneering EM structures may be difficult and their interpretation requires clues regarding the overall organisation of the complexes. In this context, we present BAmSA, a new method for localising transmembrane (TM) regions in MP complexes, using a general procedure that allows tagging them without resorting to neither genetic nor chemical modification. Labels bound to TM regions can be visualised directly on raw negative-stain EM images, on class averages, or on three-dimensional reconstructions, providing a novel strategy to explore the organisation of MP complexes.     

A Simplified Mass-Transfer Model for Visual Pigments in Amphibian Retinal-Cone Outer Segments

When radiolabeled precursors and autoradiography are used to investigate turnover of protein components in photoreceptive cone outer segments (COSs), the labeled components—primarily visual pigment molecules (opsins)—are diffusely distributed along the COS. To further assess this COS labeling pattern, we derive a simplified mass-transfer model for quantifying the contributions of advective and diffusive mechanisms to the distribution of opsins within COSs of the frog retina. Two opsin-containing regions of the COS are evaluated: the core axial array of disks and the plasmalemma. Numerical solutions of the mass-transfer model indicate three distinct stages of system evolution. In the first stage, plasmalemma diffusion is dominant. In the second stage, the plasmalemma density reaches a metastable state and transfer between the plasmalemma and disk region occurs, which is followed by an increase in density that is qualitatively similar for both regions. The final stage consists of both regions slowly evolving to the steady-state solution. Our results indicate that autoradiographic and cognate approaches for tracking labeled opsins in the COS cannot be effective methodologies for assessing new disk formation at the base of the COS.     

The pulse of the tree is under genetic control: eucalyptus as a case study

The pulse of the tree (diurnal cycle of stem radius fluctuations) has been widely studied as a way of analyzing tree responses to the environment, including the phenotypic plasticity of tree–water relationships in particular. However, the genetic basis of this daily phenotype and its interplay with the environment remain largely unexplored. We characterized the genetic and environmental determinants of this response, by monitoring daily stem radius fluctuation (dSRF) on 210 trees from a Eucalyptus urophylla × E. grandis full‐sib family over 2 years. The dSRF signal was broken down into hydraulic capacitance, assessed as the daily amplitude of shrinkage (DA), and net growth, estimated as the change in maximum radius between two consecutive days (ΔR). The environmental determinants of these two traits were clearly different: DA was positively correlated with atmospheric variables relating to water demand, while ΔR was associated with soil water content. The heritability for these two traits ranged from low to moderate over time, revealing a time‐dependent or environment‐dependent complex genetic determinism. We identified 686 and 384 daily quantitative trait loci (QTL) representing 32 and 31 QTL regions for DA and ΔR, respectively. The identification of gene networks underlying the 27 major genomics regions for both traits generated additional hypotheses concerning the biological mechanisms involved in response to water demand and supply. This study highlights that environmentally induced changes in daily stem radius fluctuation are genetically controlled in trees and suggests that these daily responses integrated over time shape the genetic architecture of mature traits.     

Assessing the effectiveness of foraging radius models for seabird distributions using biotelemetry and survey data

Relatively simple foraging radius models have the potential to generate predictive distributions for a large number of species rapidly, thus providing a cost-effective alternative to large-scale surveys or complex modelling approaches. Their effectiveness, however, remains largely untested. Here we compare foraging radius distribution models for all breeding seabirds in Ireland, to distributions of empirical data collected from tracking studies and aerial surveys. At the local/colony level, we compared foraging radius distributions to GPS tracking data from seabirds with short (Atlantic puffin Fratercula arctica, and razorbill Alca torda) and long (Manx shearwater Puffinus puffinus, and European storm-petrel Hydrobates pelagicus) foraging ranges. At the regional/national level, we compared foraging radius distributions to extensive aerial surveys conducted over a two-year period. Foraging radius distributions were significantly positively correlated with tracking data for all species except Manx shearwater. Correlations between foraging radius distributions and aerial survey data were also significant, but generally weaker than those for tracking data. Correlations between foraging radius distributions and aerial survey data were benchmarked against generalised additive models (GAMs) of the aerial survey data that included a range of environmental covariates. While GAM distributions had slightly higher correlations with aerial survey data, the results highlight that the foraging radius approach can be a useful and pragmatic approach for assessing breeding distributions for many seabird species. The approach is likely to have acceptable utility in complex, temporally variable ecosystems and when logistic and financial resources are limited.     

Aggregation-Prone Motifs in Human Immunoglobulin G

Therapeutic antibodies of many different IgG subclasses (IgG1, IgG2 and IgG4) are used in the treatment of various cancers, rheumatoid arthritis and other inflammatory and infectious diseases. These antibodies are stored for long durations under high concentrations as required in the disease treatment. Unfortunately, these antibodies aggregate under these storage conditions, leading to a decrease in antibody activity and raising concerns about causing an immunological response. Thus, there is a tremendous need to identify the aggregation-prone regions in different classes of antibodies. We use the SAP (spatial-aggregation-propensity) technology based on molecular simulations to determine the aggregation-prone motifs in the constant regions of IgG1 classes of antibodies. Mutations engineered on these aggregation-prone motif regions led to antibodies of enhanced stability. Fourteen aggregation-prone motifs are identified, with each motif containing one to seven residues. While some of these motifs contain residues that are neighbors in primary sequence, others contain residues that are far apart in primary sequence but are close together in the tertiary structure. Comparison of the IgG1 sequence with those of other subclasses (IgG2, IgG3 and IgG4) showed that these aggregation-prone motifs are largely preserved among all IgG subclasses. Other broader classes of antibodies (IgA1, IgD, IgE and IgM), however, differed in these motif regions. The aggregation-prone motifs identified were therefore common to all IgG subclasses, but differ from those of non-IgG classes. Moreover, since the motifs identified are in the constant regions, they are applicable for all antibodies within the IgG class irrespective of the variable region. Thus, the motif regions identified could be modified on all IgGs to yield antibodies of enhanced stability.     

红松天然种群邻体影响半径

以天然红松种群为研究对象,采用生长方程回归分析、分段拟合判定的方法,探讨不同坡位红松邻体影响半径的变化．结果表明,红松树种邻体干扰指数与生长量呈显著负相关（R^2为0．61～0．89）,相关程度因邻体影响范围和坡位而异,R^2达到最大值所对应的影响范围即为邻体影响半径;对红松树种进行邻体干扰指数与影响范围的线性分段拟合,邻体干扰指数随影响范围的增加而增加,其在一定的范围内上升较快,而超出该范围则上升幅度变缓,其转折点所对应的影响范围即为邻体影响半径,线性回归显著（R^2为0．41～0．55）;不同坡位的邻体影响半径有一定的差异,表现为下坡位=上坡位〉中坡位．