Number Of Secondary Structures Research Articles

On the stability of a pair of vortex rings

The growth of perturbations subject to the Crow instability along two vortex rings of equal and opposite circulation undergoing a head-on collision is examined. Unlike the planar case for semi-infinite line vortices, the zero-order geometry of the flow (i.e. the ring radius, core thickness and separation distance) and by extension the growth rates of perturbations vary in time. The governing equations are therefore temporally integrated to characterize the perturbation spectrum. The analysis, which considers the effects of ring curvature and the distribution of vorticity within the vortex cores, explains several key flow features observed in experiments. First, the zero-order motion of the rings is accurately reproduced. Next, the predicted emergent wavenumber, which sets the number of secondary vortex structures emerging after the cores come into contact, agrees with experiments, including the observed increase in the number of secondary structures with increasing Reynolds number. Finally, the analysis predicts an abrupt transition at a critical Reynolds number to a regime dominated by a higher-frequency, faster-growing instability mode that may be consistent with the experimentally observed rapid generation of a turbulent puff following the collision of rings at high Reynolds numbers.

Structural Characteristics and Antioxidant Mechanism of Donkey-Hide Gelatin Peptides by Molecular Dynamics Simulation.

This study aimed to explore the structural characteristics and antioxidant mechanism of donkey-hide gelatin peptides. After hydrolysis and ultrafiltration treatment, five gelatin peptides with different molecular weights (MWs) were obtained. Amino acid analysis showed that gelatin peptides with different MWs contained a large number of amino acids, including G, P, E, N, A, and R, and differences were noted in the content of various amino acids. Fourier transform infrared spectroscopy and circular dichroism revealed that these gelatin peptides differed in terms of the peak strength of functional groups and number of secondary structures. Moreover, 26 pentapeptides/hexapeptides were identified. Among them, we investigated by molecular docking how PGPAP, which has the best antioxidant activity, may interact with the Keap1 protein. The results showed that the PGPAP-Keap1 complex had a stable conformation, and Arg415, Gly462, Phe478, and Tyr572 were the key residues involved in the binding of the peptide PGPAP to Keap1. Our results demonstrated that PGPAP could serve as a bioactive peptide with antioxidant activity.

A new strategy for cellulases application in high temperature industrial scenarios with syringic acid assisting

AbstractIn the process of bioethanol production, more stable and active cellulase in high temperature condition is required. In this study, syringic acid was applied in cellulase hydrolysis system. At 70°C, TvEG3 activity increased 201.36%, CtBglA activity decreased 72.79% by syringic acid. With syringic acid assisting, TvEG3 thermostability was improved, CtBglA thermostability was reduced. Syringic acid scarcely affected CtCBH. In hydrolysis system with the cellulases containing TvEG3, CtCBH, and CtBglA, the reducing sugar yield improved by 28.37% with syringic acid assisting. With the molecular dynamic simulation in syringic acid system, the backbone root‐mean‐square deviation (RMSD) and the residue root‐mean‐square fluctuation (RMSF) of TvEG3, CtCBH reduced, while the RMSD and RMSF of CtBglA increased. The reduction in the number of secondary structures, especially α‐helix, caused the structure of CtBglA in the presence of syringic acid to collapse at high temperature. More secondary structures in TvEG3 and more α‐helix in CtCBH in the presence of syringic acid make them more stable at high temperatures. These means syringic acid can stabilize TvEG3 and CtCBH structure, destabilize CtBglA structure at high temperature. In summary, this study not only provides insight into cellulase hydrolysis at high temperature with syringic acid assisting but also demonstrates the promoting mechanism of syringic acid.

Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies.

Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments and a set of traces of secondary structures in three-dimensional space. In order to enhance accuracy in ranking secondary structure topologies, we explored a method that combines three sources of information: a set of sequence segments in 1D, a set of amino acid contact pairs in 2D, and a set of traces in 3D at the secondary structure level. A test of fourteen cases shows that the accuracy of predicted secondary structures is critical for deriving topologies. The use of significant long-range contact pairs is most effective at enriching the rank of the maximum-match topology for proteins with a large number of secondary structures, if the secondary structure prediction is fairly accurate. It was observed that the enrichment depends on the quality of initial topology candidates in this approach. We provide detailed analysis in various cases to show the potential and challenge when combining three sources of information.

The Advances of Electrospun Nanofibers in Membrane Technology

Electrospinning is a simple and versatile technique that relies on the electrostatic repulsion between surface charges to continuously draw nanofibers from a viscoelastic fluid. Electrospinning can generate nanofibers with a number of secondary structures. Surface and/or interior of nanofibers can be functionalized with molecular species or nanoparticles during or after an electrospinning process to obtain desirable results. In a short period, elecrospun nanofiber membranes (ENMs) have gained popularity due to the facile fabrication, interconnectivity and large area/volume ratio. However, ENMs’ pore sizes are intrinsically very large fractions of micrometer to few macrometer, which makes modification of surface chemistry and especially reduction of the ENM pore size indispensable for wider applications of ENMs for membrane separation processes. The modification of nanofibers has been applied widely to give them improved properties. This review paper will provide the progress have recently made on the modification of ENMs to enhance their performance in various membrane separation processes.

Using different grain-size granular mixtures (quartz and K-feldspar sand) in analogue extensional models

We have performed a series of sandbox models addressing the influence of sand mixtures (quartz and feldspar sand in different proportions) with different grain-size on the development of normal faults. The overall model evolution suggests that fault orientation, width of the deformed area, and average subsidence are not significantly influenced by the different sand mixtures. Conversely, the number of secondary structures, mean fault length, and average fault dip are strongly dependent on the material and grain-size. Modelling results suggest that a Log-normal distribution of fault length and segment length distribution betst describes the experimental fault populations, particularly when the amount of fine-grained (K-feldspar) sand is ~30%. The length distribution and the number of faults are related, specifically with increasing the amount of the K-feldspar sand (i.e., higher the amount of fine-grained material) the shorter the minimum detectable fault length. This behavior is described by a Log-normal distribution, with a few long faults and many intermediate to short faults. We thus suggest that (for length ratios of 10−5 to 2 10−6) a sand-mixture composed of 70% quartz sand and 30% K-feldspar sand is the one (among those we have tested) that provides the best compromise in terms of frictional properties, density, structural detail, number and length distribution of the faults, easiness of use, and general behavior.

Electrospun Nanofibers: New Concepts, Materials, and Applications.

Electrospinning is a simple and versatile technique that relies on the electrostatic repulsion between surface charges to continuously draw nanofibers from a viscoelastic fluid. It has been applied to successfully produce nanofibers, with diameters down to tens of nanometers, from a rich variety of materials, including polymers, ceramics, small molecules, and their combinations. In addition to solid nanofibers with a smooth surface, electrospinning has also been adapted to generate nanofibers with a number of secondary structures, including those characterized by a porous, hollow, or core-sheath structure. The surface and/or interior of such nanofibers can be further functionalized with molecular species or nanoparticles during or after an electrospinning process. In addition, electrospun nanofibers can be assembled into ordered arrays or hierarchical structures by manipulation of their alignment, stacking, and/or folding. All of these attributes make electrospun nanofibers well-suited for a broad spectrum of applications, including those related to air filtration, water purification, heterogeneous catalysis, environmental protection, smart textiles, surface coating, energy harvesting/conversion/storage, encapsulation of bioactive species, drug delivery, tissue engineering, and regenerative medicine. Over the past 15 years, our group has extensively explored the use of electrospun nanofibers for a range of applications. Here we mainly focus on two examples: (i) use of ceramic nanofibers as catalytic supports for noble-metal nanoparticles and (ii) exploration of polymeric nanofibers as scaffolding materials for tissue regeneration. Because of their high porosity, high surface area to volume ratio, well-controlled composition, and good thermal stability, nonwoven membranes made of ceramic nanofibers are terrific supports for catalysts based on noble-metal nanoparticles. We have investigated the use of ceramic nanofibers made of various oxides, including SiO2, TiO2, SnO2, CeO2, and ZrO2, as supports for heterogeneous catalysts based on noble metals such as Au, Pt, Pd, and Rh. On the other hand, the diameter, composition, alignment, porosity, and surface properties of polymeric nanofibers can be engineered in a controllable fashion to mimic the hierarchical architecture of an extracellular matrix and help manipulate cell behaviors for tissue engineering and regenerative medicine. To this end, we can mimic the native structure and morphology of the extracellular matrix in tendon using uniaxially aligned nanofibers; we can use radially aligned nanofibers to direct the migration of cells from the periphery to the center in an effort to speed up wound healing; and we can also use uniaxially aligned nanofibers to guide and expedite the extension of neurites for peripheral nerve repair. Furthermore, we can replicate the anatomic structures at the tendon-to-bone insertion using nanofiber scaffolds with graded mineral coatings. In this Account, we aim to demonstrate the unique capabilities of electrospun nanofibers as porous supports for heterogeneous catalysis and as functional scaffolds for tissue regeneration by concentrating on some of the recent results.

Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea

Wong's theory of the genetic code's origin states that because of historical constraints, codon assignment depends on the relation between precursor and derivative amino acids, a result of the coevolutionary process between amino acids' biosynthetic pathways and tRNAs. Based on arguments supporting the assumption that natural selection favors more stable and thus functionally constrained structures, we tested whether precursor and derivative tRNAs are equally evolved by measuring their structural parameters, thermostability and molecular plasticity. We also estimated the extent to which precursor and derivative tRNAs differ within Archaea. We used Archaea sequences of both precursor and derivative tRNAs in order to examine the plastic repertoires or sets of suboptimal structures at a defined free energy interval. We grouped secondary structures according to their helix nesting and adjacency using abstract shapes analysis. This clustering enabled us to infer a consensus sequence for all shapes that fit the clover leaf secondary structure [Giegerich, R., et al., Nucleic Acids Res 2004; 32 (16): 4843–51.]. This consensus sequence was then folded in order to retrieve a set of suboptimal structures. For each pair of precursor and derivative tRNAs, we compared these plastic repertoires based on the number of secondary structures, the thermostability of the minimum free energy structure and two structural parameters (base pair propensity ( P) and mean length of helical stem structures ( S)), which were measured for every representative secondary structure [Schultes, E.A., et al., J Mol Evol 1999; 49 (1): 76–83.]. We found that derivative tRNAs have fewer numbers of shapes, higher thermostability and more stable parameters than precursor tRNAs, a fact in full agreement with Wong's coevolution theory of the genetic code.