scholarly journals Simple approach for ranking structure determining residues

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2136 ◽  
Author(s):  
Oscar D. Luna-Martínez ◽  
Abraham Vidal-Limón ◽  
Miryam I. Villalba-Velázquez ◽  
Rosalba Sánchez-Alcalá ◽  
Ramón Garduño-Juárez ◽  
...  

Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

2014 ◽  
Author(s):  
Zhongjin Yang ◽  
Keli Han ◽  
Marat Molyboga ◽  
Georgiy Molyboga

2012 ◽  
Vol 170-173 ◽  
pp. 847-852
Author(s):  
Peng Ming Jiang ◽  
Zhong Lei Yan ◽  
Peng Li

As the complexity of unsaturated soil theory, and it must have a long test period when we study the unsaturated soils, so the conventional design analysis software does not provide such analysis, so we can imagine that such a slope stability analysis does not accurately reflect the actual state of the slope. Based on the known soil moisture content,this paper use the soil water characteristic curve and strength theory of unsaturated soil to calculate the strength reduction parameters of soil which can calculate the stability of the soil slope when using the common calculation method. It is noticeable that this method can be extended and applied if we establish regional databases for this simple method, and these databases can improve the accuracy of the calculation of slope stability.


1989 ◽  
Vol 12 (4) ◽  
pp. 571-585
Author(s):  
E. Fachini ◽  
A. Maggiolo Schettini ◽  
G. Resta ◽  
D. Sangiorgi

We prove that the classes of languages accepted by systolic automata over t-ary trees (t-STA) are always either equal or incomparable if one varies t. We introduce systolic tree automata with base (T(b)-STA), a subclass of STA with interesting properties of modularity, and we give a necessary and sufficient condition for the equivalence between a T(b)-STA and a t-STA, for a given base b. Finally, we show that the stability problem for T(b)-ST A is decidible.


2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Anna Aviñó ◽  
Elena Cubero ◽  
Raimundo Gargallo ◽  
Carlos González ◽  
Modesto Orozco ◽  
...  

The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.


2013 ◽  
Vol 10 (5) ◽  
pp. 2867-2884 ◽  
Author(s):  
S. Wooldridge

Abstract. That corals skeletons are built of aragonite crystals with taxonomy-linked ultrastructure has been well understood since the 19th century. Yet, the way by which corals control this crystallization process remains an unsolved question. Here, I outline a new conceptual model of coral biomineralisation that endeavours to relate known skeletal features with homeostatic functions beyond traditional growth (structural) determinants. In particular, I propose that the dominant physiological driver of skeletal extension is night-time hypoxia, which is exacerbated by the respiratory oxygen demands of the coral's algal symbionts (= zooxanthellae). The model thus provides a new narrative to explain the high growth rate of symbiotic corals, by equating skeletal deposition with the "work-rate" of the coral host needed to maintain a stable and beneficial symbiosis. In this way, coral skeletons are interpreted as a continuous (long-run) recording unit of the stability and functioning of the coral–algae endosymbiosis. After providing supportive evidence for the model across multiple scales of observation, I use coral core data from the Great Barrier Reef (Australia) to highlight the disturbed nature of the symbiosis in recent decades, but suggest that its onset is consistent with a trajectory that has been followed since at least the start of the 1900s. In concluding, I outline how the proposed capacity of cnidarians (which includes modern reef corals) to overcome the metabolic limitation of hypoxia via skeletogenesis also provides a new hypothesis to explain the sudden appearance in the fossil record of calcified skeletons at the Precambrian–Cambrian transition – and the ensuing rapid appearance of most major animal phyla.


1954 ◽  
Vol 5 (4) ◽  
pp. 218-234 ◽  
Author(s):  
J. H. Preston

SummaryA simple method is developed for computing the trailing vorticity which arises when a non-uniform stream is turned.It is shown that, for a sudden and constant deflection of a non-uniform stream, no net trailing vorticity is set up in the exit flow and hence there is no secondary motion.In the case of an impulse cascade of finite dimensions with constant turning, it is found that the trailing vorticity has three distinct components—the passage vorticity and two components which appear as vortex sheets springing from the trailing edges of the aerofoils. It is shown that for small angles of deflection there is no net circulation associated with the trailing vorticity downstream, of the cascade, and it is inferred that this should still be so for large deflections.


BMC Biology ◽  
2017 ◽  
Vol 15 (1) ◽  
Author(s):  
Clive S. Barker ◽  
Irina V. Meshcheryakova ◽  
Alla S. Kostyukova ◽  
Peter L. Freddolino ◽  
Fadel A. Samatey

Nanomaterials ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2636
Author(s):  
Fenghui Cao ◽  
Jia Xu ◽  
Xinci Zhang ◽  
Bei Li ◽  
Xiao Zhang ◽  
...  

We developed a simple method to fabricate SiO2-sphere-supported N-doped CNTs (NCNTs) for electromagnetic wave (EMW) absorption. EMW absorption was tuned by adsorption of the organic agent on the precursor of the catalysts. The experimental results show that the conductivity loss and polarization loss of the sample are improved. Meanwhile, the impedance matching characteristics can also be adjusted. When the matching thickness was only 1.5 mm, the optimal 3D structure shows excellent EMW absorption performance, which is better than most magnetic carbon matrix composites. Our current approach opens up an effective way to develop low-cost, high-performance EMW absorbers.


2010 ◽  
Vol 88 (2) ◽  
pp. 269-290 ◽  
Author(s):  
Sarah Rauscher ◽  
Régis Pomès

Protein disorder is abundant in proteomes throughout all kingdoms of life and serves many biologically important roles. Disordered states of proteins are challenging to study experimentally due to their structural heterogeneity and tendency to aggregate. Computer simulations, which are not impeded by these properties, have recently emerged as a useful tool to characterize the conformational ensembles of intrinsically disordered proteins. In this review, we provide a survey of computational studies of protein disorder with an emphasis on the interdisciplinary nature of these studies. The application of simulation techniques to the study of disordered states is described in the context of experimental and bioinformatics approaches. Experimental data can be incorporated into simulations, and simulations can provide predictions for experiment. In this way, simulations have been integrated into the existing methodologies for the study of disordered state ensembles. We provide recent examples of simulations of disordered states from the literature and our own work. Throughout the review, we emphasize important predictions and biophysical understanding made possible through the use of simulations. This review is intended as both an overview and a guide for structural biologists and theoretical biophysicists seeking accurate, atomic-level descriptions of disordered state ensembles.


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