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81.
Multiscale modeling of cellular actin filaments: from atomistic molecular to coarse-grained dynamics
Deriu MA Shkurti A Paciello G Bidone TC Morbiducci U Ficarra E Audenino A Acquaviva A 《Proteins》2012,80(6):1598-1609
In this article, we present a computational multiscale model for the characterization of subcellular proteins. The model is encoded inside a simulation tool that builds coarse-grained (CG) force fields from atomistic simulations. Equilibrium molecular dynamics simulations on an all-atom model of the actin filament are performed. Then, using the statistical distribution of the distances between pairs of selected groups of atoms at the output of the MD simulations, the force field is parameterized using the Boltzmann inversion approach. This CG force field is further used to characterize the dynamics of the protein via Brownian dynamics simulations. This combination of methods into a single computational tool flow enables the simulation of actin filaments with length up to 400 nm, extending the time and length scales compared to state-of-the-art approaches. Moreover, the proposed multiscale modeling approach allows to investigate the relationship between atomistic structure and changes on the overall dynamics and mechanics of the filament and can be easily (i) extended to the characterization of other subcellular structures and (ii) used to investigate the cellular effects of molecular alterations due to pathological conditions. 相似文献
82.
The DNA damage checkpoint is a surveillance mechanism activated by DNA lesions and devoted to the maintenance of genome stability. It is considered as a signal transduction cascade, involving a sensing step, the activation of a set of protein kinases and the transmission and amplification of the damage signal through several phosphorylation events. In budding yeast many players of this pathway have been identified. Recent work showed that G1 and G2 checkpoint activation in response to UV irradiation requires prior recognition and processing of UV lesions by nucleotide excision repair (NER) factors that likely recruit checkpoint proteins near the damage. However, another report suggested that NER was not required for checkpoint function. Since the functional relationship between repair mechanisms and checkpoint activation is a very important issue in the field, we analyzed, under different experimental conditions, whether lesion processing by NER is required for checkpoint activation. We found that DNA damage checkpoint can be triggered in an NER-independent manner only if cells are subjected to liquid holding after UV treatment. This incubation causes a time-dependent breakage of DNA strands in NER-deficient cells and leads to partial activation of the checkpoint kinase. The analysis of the genetic requirements for this alternative activation pathway suggest that it requires Mec1 and the Rad17 complex and that the observed DNA breaks are likely to be due to spontaneous decay of damaged DNA. 相似文献
83.
Stiffness and fraction of Myosin motors responsible for active force in permeabilized muscle fibers from rabbit psoas 总被引:1,自引:0,他引:1 下载免费PDF全文
The stiffness of the single myosin motor (epsilon) is determined in skinned fibers from rabbit psoas muscle by both mechanical and thermodynamic approaches. Changes in the elastic strain of the half-sarcomere (hs) are measured by fast mechanics both in rigor, when all myosin heads are attached, and during active contraction, with the isometric force (T0) modulated by changing either [Ca2+] or temperature. The hs compliance is 43.0+/-0.8 nm MPa-1 in isometric contraction at saturating [Ca2+], whereas in rigor it is 28.2+/-1.1 nm MPa-1. The equivalent compliance of myofilaments is 21.0+/-3.3 nm MPa-1. Accordingly, the stiffness of the ensemble of myosin heads attached in the hs is 45.5+/-1.7 kPa nm-1 in isometric contraction at saturating [Ca2+] (e0), and in rigor (er) it rises to 138.9+/-21.2 kPa nm-1. Epsilon, calculated from er and the lattice molecular dimensions, is 1.21+/-0.18 pN nm-1. epsilon estimated, using a thermodynamic approach, from the relation of T0 at saturating [Ca2+] versus the reciprocal of absolute temperature is 1.25+/-0.14 pN nm-1, similar to that estimated for fibers in rigor. Consequently, the ratio e0/er (0.33+/-0.05) can be used to estimate the fraction of attached heads during isometric contraction at saturating [Ca2+]. If the osmotic agent dextran T-500 (4 g/100 ml) is used to reduce the lateral filament spacing of the relaxed fiber to the value before skinning, both e0 and er increase by approximately 40%. Epsilon becomes approximately 1.7 pN nm-1 and the fraction and the force of myosin heads attached in the isometric contraction remain the same as before dextran application. The finding that the fraction of myosin heads attached to actin in an isometric contraction is 0.33 rules out the hypothesis of multiple mechanical cycles per ATP hydrolyzed. 相似文献
84.
Contribution of crop model structure,parameters and climate projections to uncertainty in climate change impact assessments 总被引:2,自引:0,他引:2 下载免费PDF全文
Fulu Tao Reimund P. Rötter Taru Palosuo Carlos Gregorio Hernández Díaz‐Ambrona M. Inés Mínguez Mikhail A. Semenov Kurt Christian Kersebaum Claas Nendel Xenia Specka Holger Hoffmann Frank Ewert Anaelle Dambreville Pierre Martre Lucía Rodríguez Margarita Ruiz‐Ramos Thomas Gaiser Jukka G. Höhn Tapio Salo Roberto Ferrise Marco Bindi Davide Cammarano Alan H. Schulman 《Global Change Biology》2018,24(3):1291-1307
Climate change impact assessments are plagued with uncertainties from many sources, such as climate projections or the inadequacies in structure and parameters of the impact model. Previous studies tried to account for the uncertainty from one or two of these. Here, we developed a triple‐ensemble probabilistic assessment using seven crop models, multiple sets of model parameters and eight contrasting climate projections together to comprehensively account for uncertainties from these three important sources. We demonstrated the approach in assessing climate change impact on barley growth and yield at Jokioinen, Finland in the Boreal climatic zone and Lleida, Spain in the Mediterranean climatic zone, for the 2050s. We further quantified and compared the contribution of crop model structure, crop model parameters and climate projections to the total variance of ensemble output using Analysis of Variance (ANOVA). Based on the triple‐ensemble probabilistic assessment, the median of simulated yield change was ?4% and +16%, and the probability of decreasing yield was 63% and 31% in the 2050s, at Jokioinen and Lleida, respectively, relative to 1981–2010. The contribution of crop model structure to the total variance of ensemble output was larger than that from downscaled climate projections and model parameters. The relative contribution of crop model parameters and downscaled climate projections to the total variance of ensemble output varied greatly among the seven crop models and between the two sites. The contribution of downscaled climate projections was on average larger than that of crop model parameters. This information on the uncertainty from different sources can be quite useful for model users to decide where to put the most effort when preparing or choosing models or parameters for impact analyses. We concluded that the triple‐ensemble probabilistic approach that accounts for the uncertainties from multiple important sources provide more comprehensive information for quantifying uncertainties in climate change impact assessments as compared to the conventional approaches that are deterministic or only account for the uncertainties from one or two of the uncertainty sources. 相似文献
85.
86.
Esposito Francesco Memoli Valeria Panico Speranza Claudia Trifuoggi Marco Di Natale Gabriella Maisto Giulia 《Plant and Soil》2019,436(1-2):517-526
Plant and Soil - The aims of this research were: i) to compare Cr, Cu, Ni and Pb concentrations in Quercus ilex L. leaves collected at urban/industrial and urban areas; ii) to investigate the main... 相似文献
87.
Chaldakov GN Beltowsky J Ghenev PI Fiore M Panayotov P Rančič G Aloe L 《Cell biology international》2012,36(3):327-330
Human adipose tissue is partitioned into two large depots (subcutaneous and visceral), and many small depots associated with internal organs, e.g. heart, blood vessels, major lymph nodes, pancreas, prostate gland and ovaries. Since the adipose 'Big Bang' led to the discovery of leptin (Zhang, Proenca, Maffei, Barone, Leopold and Friedman, Nature 1994;372:425-32), adipose tissue has been seen not merely as a lipid store, but as a secretory - endocrine and paracrine - organ, particularly in the pathogenesis of a number of diseases. Accordingly, two major sub-fields of adipobiology have emerged, viz. adipoendocrinology and adipoparacrinology, the latter herein being illustrated by PAAT (periadventitial adipose tissue) in vascular walls. A long-standing paradigm holds that the vascular wall consists of three coats, tunica intima, tunica media and tunica adventitia. It is now imperative that 'to further elucidate vascular function, we should no longer, as hitherto, separate adventitia and PAAT from the vascular wall, but keep them attached and in place, and subject to thorough examination' (Chaldakov, Fiore, Ghenev, Stankulov and Aloe, Int Med J 2000;7:43-9; Chaldakov, Stankulov and Aloe, Atherosclerosis 2001;154:237-8; Chaldakov GN, Stankulov IS, Fiore M, Ghenev PI and Aloe L, Atherosclerosis 2001;159:57-66). From the available data, we propose that it is time to rethink about vascular wall composition, and suggest that the PAAT may be considered the fourth and outermost vascular coat, hence, tunica adiposa (regarding the proximal segment of coronary artery, it is the innermost part of the EAT (epicardial adipose tissue) situated around the coronary adventitia). Its significance in the pathogenesis and therapy of CMDs (cardiometabolic diseases), particularly atherosclerosis and hypertension, requires further basic, translational and clinical studies. 相似文献
88.
Biedendieck R Beine R Gamer M Jordan E Buchholz K Seibel J Dijkhuizen L Malten M Jahn D 《Applied microbiology and biotechnology》2007,74(5):1062-1073
Fructosyltransferases, like the Lactobacillus reteri levansucrase, are important for the production of new fructosyloligosaccharides. Various His6- and Strep-tagged variants of this enzyme were recombinantly produced and exported into the growth medium using the Gram-positive
bacterium Bacillus megaterium. Nutrient-rich growth medium significantly enhanced levansucrase production and export. The B. megaterium signal peptide of the extracellular esterase LipA mediated better levansucrase export compared to the one of the penicillin
amidase Pac. The combination of protein export via the LipA signal peptide with the coexpression of the signal peptidase gene
sipM further increased the levansucrase secretion. Fused affinity tags allowed the efficient one-step purification of the recombinant
proteins from the growth medium. However, fused peptide tags led to slightly decreased secretion of tested fusion proteins.
After upscaling 2 to 3 mg affinity tagged levansucrase per liter culture medium was produced and exported. Up to 1 mg of His6-tagged and 0.7 mg of Strep-tagged levansucrase per liter were recovered by affinity chromatography. Finally, the purified
levansucrase was shown to synthesize new fructosyloligosaccharides from the novel donor substrates d-Gal-Fru, d-Xyl-Fru, d-Man-Fru, and d-Fuc-Fru.
R. Biedendieck and R. Beine contributed equally to this work. 相似文献
89.
Niyati Jain Christopher E. Morgan Brittany D. Rife Marco Salemi Blanton S. Tolbert 《The Journal of biological chemistry》2016,291(5):2331-2344
Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3′ acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein. 相似文献
90.
Scandura Massimo Iacolina Laura Capitani Claudia Gazzola Andrea Mattioli Luca Apollonio Marco 《European Journal of Wildlife Research》2011,57(4):949-958
We investigated local gene flow in a high-density wolf (Canis lupus) population of the Italian Apennines, where no effective barrier to wolf dispersal was present. From 1998 to 2004 we examined
wolf carcasses and non-invasively collected samples, focusing on three mountain districts, separated by two valleys, where
wolf packs showed high spatial stability. Using nine autosomal microsatellites we successfully genotyped 177 samples, achieving
the identification of 74 wolves. Genetic relatedness steeply decreased with increasing distance between sampling areas, thus
suggesting that short-distance interpack migration is infrequent in this population. In addition, no individual from a central
pack under intensive monitoring was sampled in the range of the surrounding packs over a 4-year period. The limited short-distance
gene flow resulted in a cryptic genetic structure, which was revealed by Bayesian analysis. A different genetic cluster was
found in each of the three mountain areas, and a small proportion of first-generation immigrants was detected. Overall, the
present study suggests that local genetic differentiation in Italian wolves might arise from high spatial stability of packs
and can be favoured by a combination of long-range dispersal, the attitude to mate between unrelated individuals and a high
young mortality rate. 相似文献