Surface Of Helix Research Articles

Fiber dispersion and breakage in deep screw channel during processing of long fiber-reinforced polypropylene

Long glass fiber-reinforced thermoplastics are usually processed by pultruded granules, but glass fiber rovings were used to process long glass fiber-reinforced thermoplastics in this study. This article investigated the dispersion and breakage of fibers during extrusion processing of long glass fiber-reinforced polypropylene containing 30 wt% glass fibers at a certain processing conditions. For this study, the morphology of the surface and polished cross-section of helices was observed by digital photography, as was the morphology of the remaining fiber after burning. On this basis, the fiber/polymer system behavior in the screw channel and the dispersion mechanism of the fiber bundles were analyzed. Moreover, scanning electron microscopy (SEM) was used to observe individual fiber cross-sections to analyze the mechanism of fiber breakage. Finally, the effect of processing conditions such as temperature, screw speed and fiber content on fiber length and dispersion was studied. The results show that the fiber agglomerates composed of fiber bundles form near the barrel surface at the fiber feed point and then undergo three main stages: compression, impregnation, and dispersion. The fiber bundles separate into daughter bundles and individual fibers in different parts of the screw channel. In addition, the results indicate that the fibers can suffer tensile fracture and bending fracture during the extrusion processing. Finally, this paper includes suggestions for improving fiber bundle dispersion and reducing fiber breakage.

Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations.

A complex of the phosphorylated kinase-inducible domain (pKID) with its interacting domain (KIX) is a model system for studies of mechanisms by which intrinsically unfolded proteins perform their functions. These mechanisms are not fully understood. Using an efficient coarse-grained model, ab initio simulations were performed of the coupled folding and binding of the pKID to the KIX. The simulations start from an unbound, randomly positioned and disordered pKID structure. During the simulations the pKID chain and its position remain completely unrestricted, while the KIX backbone is limited to near-native fluctuations. Ab initio simulations of such large-scale conformational transitions, unaffected by any knowledge about the bound pKID structure, remain inaccessible to classical simulations. Our simulations recover an ensemble of transient encounter complexes in good agreement with experimental results. We find that a key folding and binding step is linked to the formation of weak native interactions between a preformed nativelike fragment of a pKID helix and KIX surface. Once that nucleus forms, the pKID chain may condense from a largely disordered encounter ensemble to a natively bound and ordered conformation. The observed mechanism is reminiscent of a nucleation-condensation model, a common scenario for folding of globular proteins.

Peculiarities and mechanism of surface topography changes in photochromic cholesteric oligomer-based films

Detailed investigations of surface topography peculiarities for two cholesteric mixtures with photovariable helix pitch are presented. The mixtures were prepared by doping cholesteric cyclosiloxane with two chiral-photochromic substances possessing different handedness. Both chiral-photochromic dopants are susceptible to UV light-induced E-Z isomerization and changing of their helical twisting power. UV irradiation allows one to change the helix pitch values of the mixtures in a wide spectral range (~350–740 nm). AFM investigation reveals the specific peculiarities of the surface topography of the mixtures’ films (formation of “fingerprint like” topography or circular, spiralized domains depending on helix pitch). Quantitative analysis of the geometry of the domains (size and cross sections) allows one to find the correlations between photo- and thermally induced helix pitch values and surface features of the films. The handedness of the dopants does not affect surface relief topography. A mechanism has been suggested to explain the topographical changes under helix untwisting, which occurs upon slow cooling of mixtures films.

Helix surfaces in the Berger sphere

We characterize helix surfaces in the Berger sphere, that is surfaces which form a constant angle with the Hopf vector field. In particular, we show that, locally, a helix surface is determined by a suitable 1-parameter family of isometries of the Berger sphere and by a geodesic of a 2-torus in the 3-dimensional sphere.

PEDAL CURVES OF TANGENT SURFACES OF BIHARMONIC B-GENERAL HELICES ACCORDING TO BISHOP FRAME IN HEISENBERG GROUP Heis³

In this paper, we study pedal curves of tangent surfaces of biharmonic B-general helices according to Bishop frame in the Heisenberg group Heis³. We give necessary and sufficient conditions for B-general helices to be biharmonic according to Bishop frame. We characterize this pedal curves in the Heisenberg group Heis³. Additionally, we illustrate our main theorem.

The helix surface of sugar ring for tetrahydrofuran

The present calculations of three geometry conformation for tetrahydrofuran (THF, C4H8O) using density functional theory lead to the energy level sequence E(C1) E(Cs) E(C2v), where, both the geometry symmetry C2v and Cs are probably a transition structure. The C1 symmetry is the equilibrium conformation, for its energy is the lowest one and it is only possible without the negative harmonic frequency. In C1 conformation, the 4 of carbon atoms C and oxygen atom O constitute a curved surface or the helix surface. The tetrahydrofuran molecule can be as a simple prototype of deoxyribose and has been reviving a quite deal of interest in radiation damage research. It is well known that the sugar ring of deoxyribose is considered as a plane in most of the references. If the equilibrium conformation of THF is C1 symmetry with the helix surface, and for the same reason, the sugar ring of deoxyribose would be also the helix surface; this probably causes the double helix of DNA. It is hardly believed that the sugar ring is a plane in deoxyribose.

Parallel surfaces to normal ruled surfaces of general helices in the sol space Sol³

In this paper, parallel surfaces to normal ruled surface of general helices in the Sol³ are studied. Also, explicit parametric equations of parallel surfaces to normal ruled surface of general helices in the Sol³ are found.

One parameter family of b-m₁ developable surfaces of biharmonic new type b-slant helices according to Bishop frame in the sol space Sol³

In this paper, we study inextensible flows of b-m₁ developable surfaces of biharmonic new type b-slant helix in the Sol³. We characterize one parameter family of the b-m₁ developable surfaces in terms of their Bishop curvatures.

The C‐terminal domain of the transcriptional regulator BldD from Streptomyces coelicolor A3(2) constitutes a novel fold of winged‐helix domains

BldD regulates transcription of key developmental genes in Streptomyces coelicolor. While the N-terminal domain is responsible for both dimerization and DNA binding, the structural and functional roles of the C-terminal domain (CTD) remain largely unexplored. Here, the solution structure of the BldD-CTD shows a novel winged-helix domain fold not compatible with DNA binding, due to the negatively charged surface and presence of an additional helix. Meanwhile, a small elongated groove with conserved hydrophobic patches surrounded by charged residues suggests that the BldD-CTD could be involved in protein-protein interactions that provide transcriptional regulation.

Hepatitis C Virus RNA Replication and Virus Particle Assembly Require Specific Dimerization of the NS4A Protein Transmembrane Domain

Hepatitis C virus (HCV) NS4A is a single-pass transmembrane (TM) protein essential for viral replication and particle assembly. The sequence of the NS4A TM domain is highly conserved, suggesting that it may be important for protein-protein interactions. To test this hypothesis, we measured the potential dimerization of the NS4A TM domain in a well-characterized two-hybrid TM protein interaction system. The NS4A TM domain exhibited a strong homotypic interaction that was comparable in affinity to glycophorin A, a well-studied human blood group antigen that forms TM homodimers. Several mutations predicted to cluster on a common surface of the NS4A TM helix caused significant reductions in dimerization, suggesting that these residues form an interface for NS4A dimerization. Mutations in the NS4A TM domain were further examined in the JFH-1 genotype 2a replicon system; importantly, all mutations that destabilized NS4A dimers also caused defects in RNA replication and/or virus assembly. Computational modeling of NS4A TM interactions suggests a right-handed dimeric interaction of helices with an interface that is consistent with the mutational effects. Furthermore, defects in NS4A oligomerization and virus particle assembly of two mutants were rescued by NS4A A15S, a TM mutation recently identified through forward genetics as a cell culture-adaptive mutation. Together, these data provide the first example of a functionally important TM dimer interface within an HCV nonstructural protein and reveal a fundamental role of the NS4A TM domain in coordinating HCV RNA replication and virus particle assembly.

Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices

BackgroundSince membrane protein structures are challenging to crystallize, computational approaches are essential for elucidating the sequence-to-structure relationships. Structural modeling of membrane proteins requires a multidimensional approach, and one critical geometric parameter is the rotational angle of transmembrane helices. Rotational angles of transmembrane helices are characterized by their folded structures and could be inferred by the hydrophobic moment; however, the folding mechanism of membrane proteins is not yet fully understood. The rotational angle of a transmembrane helix is related to the exposed surface of a transmembrane helix, since lipid exposure gives the degree of accessibility of each residue in lipid environment. To the best of our knowledge, there have been few advances in investigating whether an environment descriptor of lipid exposure could infer a geometric parameter of rotational angle.ResultsHere, we present an analysis of the relationship between rotational angles and lipid exposure and a support-vector-machine method, called TMexpo, for predicting both structural features from sequences. First, we observed from the development set of 89 protein chains that the lipid exposure, i.e., the relative accessible surface area (rASA) of residues in the lipid environment, generated from high-resolution protein structures could infer the rotational angles with a mean absolute angular error (MAAE) of 46.32˚. More importantly, the predicted rASA from TMexpo achieved an MAAE of 51.05˚, which is better than 71.47˚ obtained by the best of the compared hydrophobicity scales. Lastly, TMexpo outperformed the compared methods in rASA prediction on the independent test set of 21 protein chains and achieved an overall Matthew’s correlation coefficient, accuracy, sensitivity, specificity, and precision of 0.51, 75.26%, 81.30%, 69.15%, and 72.73%, respectively. TMexpo is publicly available at http://bio-cluster.iis.sinica.edu.tw/TMexpo.ConclusionsTMexpo can better predict rASA and rotational angles than the compared methods. When rotational angles can be accurately predicted, free modeling of transmembrane protein structures in turn may benefit from a reduced complexity in ensembles with a significantly less number of packing arrangements. Furthermore, sequence-based prediction of both rotational angle and lipid exposure can provide essential information when high-resolution structures are unavailable and contribute to experimental design to elucidate transmembrane protein functions.

Poly(ethylene glycol) Conjugation Stabilizes the Secondary Structure of α-Helices by Reducing Peptide Solvent Accessible Surface Area

We investigate the effect of poly(ethylene glycol) (PEG) side-chain conjugation on the conformational behavior of an α-helix using molecular dynamics simulations in explicit solvents of varying hydrophobicity. Our simulations illustrate an increase in peptide helicity with increasing PEG molecular weight in the range ~400 to 1800 Da. The data with varying PEG contour lengths as well as constant force pulling simulations that allow control over the end-to-end length of PEG indicate a strong inverse correlation between peptide helicity and solvent accessible surface area (SASA). A residue-based mapping analysis reveals that the formation of a protecting PEG shell around peptide helix in water is facilitated by two distinct mechanisms that depend on the solvent environment. First, cationic residues such as lysine interact favorably with PEG due to strong polar interactions with PEG oxygen atoms. Additionally, we find that hydrophobic residues interact strongly with PEG to reduce their SASA in polar solvents by polymer shielding. Our simulations illustrate that these two mechanisms that involve side-chain chemistry and solvent polarity govern the preferred conformation of PEG on the helix surface and thus the stability of peptide secondary structure. These findings elucidate the molecular mechanisms underpinning recent experimental findings on the stability and conformational dynamics of protein-PEG conjugates.

Membrane Partitioning of the Pore-Forming Domain of Colicin A. Role of the Hydrophobic Helical Hairpin

The colicins are bacteriocins that target Escherichia coli and kill bacterial cells through different mechanisms. Colicin A forms ion channels in the inner membranes of nonimmune bacteria. This activity resides exclusively in its C-terminal fragment (residues 387–592). The soluble free form of this domain is a 10 α-helix bundle. The hydrophobic helical hairpin, H8–H9, is buried inside the structure and shielded by eight amphipathic surface helices. The interaction of the C-terminal colicin A domain and several chimeric variants with lipidic vesicles was examined here by isothermal titration calorimetry. In the mutant constructions, natural sequences of the hydrophobic helices H8 and H9 were either removed or substituted by polyalanine or polyleucine. All the constructions fully associated with DOPG liposomes including the mutant that lacked helices H8 and H9, indicating that amphipathic rather than hydrophobic helices were the major determinants of the exothermic binding reactions. Alanine is not specially favored in the lipid-bound form; the chimeric construct with polyalanine produced lower enthalpy gain. On the other hand, the large negative heat capacities associated with partitioning, a characteristic feature of the hydrophobic effect, were found to be dependent on the sequence hydrophobicity of helices H8 and H9.

Simulation Study for the Effects of Rotational Speed on Performance of Full Metal Single Screw Pump

Rotational speed is one of the important parameters that impact lifting capacity of full-metal single screw pump .Firstly using the finite volume method to establish a full-metal single screw pump 3D model, secondly using FLUENT software to calculate outlet pressure changes with different series of rotational speed value of the pump in condition of the same inlet pressure .Lastly drawing outlet pressure change curves to evaluate the concrete effect of rotational speed on the performance of the pump. The results indicate that the lifting capacity of the pump and pressure bearing capacity of single stage increase with the rotational speed increasing. The centrifugal performance of the full metal single screw pump is more obvious. So it needs to give full consideration to the effect of rotational speed on characteristics of screw pump in the process of screw pump designing and using, especially the selection of pump series and rotational speed .Increasing the rotational speed of the screw pump can not only reduce the pump series and the structural size, but also can reduce the load torque, improve the reliability of drive system.Now,most of traditional rubber stator is cast one layer rubber that is of double helix surface in the metal enclosure, which can be used together with the metal rotor whose outer surface is plated by hard chrome, while working, the stator can be easily damaged because of the swelling, temperature expansion, and easy to aging of the rubber. As the stator is connected with the tubing, while the stator is damaged and we need to replace a new one, we should disassemble both the poles and string, and it leads to a high cost and the stator can not be used any more, which is apparently a great waste of resource. Besides, that the rubber in the inner surface is hard to clear is also one reason leading to the useless of the stator[1]. Full-metal single screw pump can avoid these shortcomings for its stator and rotor are made of metal materials and they take way of clearance fit. This can ensure the screw pump develops the higher working efficiency in normal operation. However the full-metal single screw pump developed quite late, its theoretical study and basic theory is less and not mature[2]. Rotational speed is the main parameter in the designing and using of full metal screw pump ,so in order to help improve the screw pump performance and for further study of the basic theory of metal screw pump, this paper will focus on the study of effect of rotational speed on the pump performance .

Structural Determinants of Ubiquitin Conjugation in Entamoeba histolytica

Ubiquitination is important for numerous cellular processes in most eukaryotic organisms, including cellular proliferation, development, and protein turnover by the proteasome. The intestinal parasite Entamoeba histolytica harbors an extensive ubiquitin-proteasome system. Proteasome inhibitors are known to impair parasite proliferation and encystation, suggesting the ubiquitin-proteasome pathway as a viable therapeutic target. However, no functional studies of the E. histolytica ubiquitination enzymes have yet emerged. Here, we have cloned and characterized multiple E. histolytica ubiquitination components, spanning ubiquitin and its activating (E1), conjugating (E2), and ligating (E3) enzymes. Crystal structures of EhUbiquitin reveal a clustering of unique residues on the α1 helix surface, including an eighth surface lysine not found in other organisms, which may allow for a unique polyubiquitin linkage in E. histolytica. EhUbiquitin is activated by and forms a thioester bond with EhUba1 (E1) in vitro, in an ATP- and magnesium-dependent fashion. EhUba1 exhibits a greater maximal initial velocity of pyrophosphate:ATP exchange than its human homolog, suggesting different kinetics of ubiquitin activation in E. histolytica. EhUba1 engages the E2 enzyme EhUbc5 through its ubiquitin-fold domain to transfer the EhUbiquitin thioester. However, EhUbc5 has a >10-fold preference for EhUba1∼Ub compared with unconjugated EhUba1. A crystal structure of EhUbc5 allowed prediction of a noncovalent "backside" interaction with EhUbiquitin and E3 enzymes. EhUbc5 selectively engages EhRING1 (E3) to the exclusion of two HECT family E3 ligases, and mutagenesis indicates a conserved mode of E2/RING-E3 interaction in E. histolytica.

Structural basis of specific interactions of Lp-PLA2 with HDL revealed by hydrogen deuterium exchange mass spectrometry.

Lipoprotein-associated phospholipase A(2) (Lp-PLA(2)), specifically Group VIIA PLA(2), is a member of the phospholipase A(2) superfamily and is found mainly associated with LDL and HDL in human plasma. Lp-PLA(2) is considered as a risk factor, a potential biomarker, a target for therapy in the treatment of cardiovascular disease, and evidence suggests that the level of Lp-PLA(2) in plasma is associated with the risk of future cardiovascular and stroke events. The differential location of the enzyme in LDL/HDL lipoproteins has been suggested to affect Lp-PLA(2) function and/or its physiological role and an abnormal distribution of the enzyme may correlate with diseases. Although a mutagenesis study suggested that a surface helix (residues 362-369) mediates the association between Lp-PLA(2) and HDL, the molecular details and mechanism of association has remained unknown. We have now employed hydrogen deuterium exchange mass spectrometry to characterize the interaction between recombinant human Lp-PLA(2) and human HDL. We have found that specific residues 113-120, 192-204, and 360-368 likely mediate HDL binding. In a previous study, we showed that residues 113-120 are important for Lp-PLA(2)-liposome interactions. We now find that residues 192-204 show a decreased deuteration level when Lp-PLA(2) is exposed to apoA-I, but not apoA-II, the most abundant apoproteins in HDL, and additionally, residues 360-368 are only affected by HDL.The results suggest that apoA-I and phospholipid membranes play crucial roles in Lp-PLA(2) localization to HDL.

Structure and mechanism of the CRISPR associated complex for antiviral defense (CASCADE)

The CRISPR/Cas prokaryotic adaptive immune system archives fragments of virus‐derived DNA within a hosts CRISPR loci. The CRISPR loci are then transcribed, processed, and loaded into 2 distinct complexes, CMR and CASCADE, that respectively target destruction of complementary invading RNA and DNA in subsequent infections. We report structural and functional characterization of the evolutionarily conserved components of CASCADE. Cas7 (aka Csa2), the dominant CASCADE protein, co‐purifies with Cas6‐processed CRISPR‐RNA (crRNA) and smaller amounts of Cas5a. TEM studies of the nucleoprotein complex reveal that Cas7 assembles along crRNA with right handed helical symmetry. The crystal structure of Cas7 unexpectedly revealed a decorated RNA‐recognition motif (RRM) and two additional domains present as insertions in the RRM. Biochemical and ribonuclease protection assays, mutational analysis, particle symmetry and modeling studies collectively indicate that the crRNA is bound nonspecifically along the inside surface of this central Cas7 helix, which is capped at the 5′ and 3′ ends by Cas5a and Cas6, respectively. Importantly, we identify similarities between CASCADE and the RecA/DNA complex that strongly suggest mechanistic similarities between CASCADE mediated recognition of invading DNA by crRNA, and RecA catalyzed strand invasion and D‐loop formation during DNA double strand break repair. Supported by the National Science Foundation (MCB‐0920312).

Sequence Selective Recognition of Double Helical RNA Using Nucleobase‐Modified PNA

The important role that non‐coding RNA plays in cell biology makes it an attractive target for molecular recognition. The surface of an RNA helix is relatively uniform, dominated by negatively charged phosphates and presents little opportunity for the traditional shape selective molecular recognition. We envisioned that a hydrogen bond mediated major groove triple helix formation could provide the most straightforward sequence selective recognition of double helical RNA. Using isothermal titration calorimetry we show that peptide nucleic acids, as short as six nucleobases, bind very strongly (Ka > 107) and sequence selectively to polypurine tract of double helical RNA. The data suggest that the binding mode is a sequence selective triple helix formation. Although RNA does not have long polypurine tracts, it is common to find stretches of seven and more purines interrupted by one or two pyrimidines in microRNAs and ribosomal RNAs. We found that such pyrimidine interruptions in the polypurine tracts of biologically relevant RNAs can be recognized in a sequence specific manner using nucleobase‐modified PNA under physiologically relevant conditions. Our results have implications for development of biochemical probes to study function of non‐coding RNAs and design of novel therapeutic approaches based on sequence selective inhibition of microRNAs. Supported by NIH R01 GM071461

Structure, Dynamics, and Antimicrobial and Immune Modulatory Activities of Human LL-23 and Its Single-Residue Variants Mutated on the Basis of Homologous Primate Cathelicidins

LL-23 is a natural peptide corresponding to the 23 N-terminal amino acid residues of human host defense cathelicidin LL-37. LL-23 demonstrated, compared to LL-37, a conserved ability to induce the chemokine MCP-1 in human peripheral blood mononuclear cells, a lack of ability to suppress induction of the pro-inflammatory cytokine TNF-α in response to bacterial lipopolysaccharides (LPS), and reduced antimicrobial activity. Heteronuclear multidimensional nuclear magnetic resonance (NMR) characterization of LL-23 revealed similar secondary structures and backbone dynamics in three membrane-mimetic micelles: SDS, dodecylphosphocholine (DPC), and dioctanoylphosphatidylglycerol. The NMR structure of LL-23 determined in perdeuterated DPC contained a unique serine that segregated the hydrophobic surface of the amphipathic helix into two domains. To improve our understanding, Ser9 of LL-23was changed to either Ala or Val on the basis of homologous primate cathelicidins. These changes made the hydrophobic surface of LL-23 continuous and enhanced antibacterial activity. While identical helical structures did not explain the altered activities, a reduced rate of hydrogen-deuterium exchange from LL-23 to LL-23A9 to LL-23V9 suggested a deeper penetration of LL-23V9 into the interior of the micelles, which correlated with enhanced activities. Moreover, these LL-23 variants had discrete immunomodulatory activities. Both restored the TNF-α dampening activity to the level of LL-37. Furthermore, LL-23A9, like LL-23, maintained superior protective MCP-1 production, while LL-23V9 was strongly immunosuppressive, preventing baseline MCP-1 induction and substantially reducing LPS-stimulated MCP-1 production. Thus, these LL-23 variants, designed on the basis of a structural hot spot, are promising immune modulators that are easier to synthesize and less toxic to mammalian cells than the parent peptide LL-37.

Interactions Between the Isolated DHPR β1A Subunit and the Type 1 Ryanodine Receptor

Excitation-contraction (EC) coupling in skeletal muscle proceeds in the absence of an influx of external calcium ions. This suggests that there is a physical interaction between the dihydropyridine receptor (DHPR) voltage sensor in the surface/transverse tubule membrane and the skeletal muscle ryanodine receptor (RyR1) calcium release channel in the membrane of the intracellular sarcoplasmic reticulum. The α1s and β1a subunit of the DHPR, as well as RyR1 are essential for skeletal EC coupling, but the mechanism of their interaction remains undefined. One scenario, that α1s subunit communicates with RyR1 via the β1a subunit, is supported by studies of EC coupling in intact cells as well as by interactions between the three proteins in vitro. We have described interactions between the critical region of the α1s subunit and the SH3 domain of the β1a subunit (Karunsekara et al. Biophys Abstract 2011) and between RyR1 and the full length β1a subunit or the 35 residue C-terminal tail of β1a (V490 - M524) (Rebbeck et al. Biophys J. 2011;100:922-30). We have also reported that a hydrophobic heptad repeat implicated by others in β1a interactions with RyR1 is not required for the in vitro interactions (Rebbeck et al., Biophysics abstract 2011). We now focus on a “hydrophobic triplet” (L496, L500 and W503) in the β1a C-tail that is aligned along one surface of an alpha helix and is separated from the extreme C-terminus by 21 residues. Individual substitution of L496, L500 or W503 with alanine abolished the ability of the peptide to increase channel activity at +40mV, although residual activation remained −40mV. Substitution of the three residues rendered the peptide inactive at both potentials, indicating that all three residues are required for this protein-protein interaction between the β1a C-tail and RyR1.