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06:23 EST 23rd February 2019 | BioPortfolio

Helix Opco, LLC PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Helix Opco, LLC articles that have been published worldwide.

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Showing "Helix Opco" PubMed Articles 1–25 of 380

Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics.

De novo designed helix-loop-helix peptide foldamers containing cis-2-aminocyclopentanecarboxylic acid residues were evaluated for their conformational stability and possible use in enzyme mimetic development. The correlation between hydrogen bond network size and conformational stability was demonstrated through CD and NMR spectroscopies. Molecules incorporating a Cys/His/Glu triad exhibited enzyme-like hydrolytic activity.


Not as easy as π: an insertional residue does not explain the π-helix gain-of-function in two component FMN reductases.

The π-helix located at the tetramer interface of two-component FMN-dependent reductases contributes to the structural divergence from canonical FMN-bound reductases within the NADPH:FMN reductase family. The π-helix in the SsuE FMN-dependent reductase of the alkanesulfonate monooxygenase system has been proposed to be generated by the insertion of a Tyr residue in the conserved α4-helix. Variants of Tyr118 were generated, and their X-ray crystal structures determined, to evaluate how these alterations af...

Tug-of-War in a Dynamic Helical Peptide: Solvent-Induced Helix-Helix Transition of a Lactam-Bridged Peptide Composed of Point- and Axial Chiralities Remote from Each Other.

The dynamic axial chirality of oligopeptide-bound 2,2'-bipyridine (bpy) residues can be remote-controlled and diastereoselectively locked. A right-handed (P)-310-helix is first induced in the dynamic helical oligopeptide by an L-valine (L-Val) far from the bpy moiety and the induced axial bpy chirality is diastereoselectively dioxidized. The resulting L-Val-containing linear oligopeptides at the 3,3'-positions retain their (P)-310-helices independent of the axial chirality (aR or aS) of the N-terminal N,N'-...


A novel linear epitope crossing Group 1 and Group 2 influenza A viruses located in the helix A of HA2 derived from H7N9.

In this research, four monoclonal antibodies (mAbs) were first generated as an immunogen by using the GST fusion protein that carries the fusion peptide and helix A derived from H7N9 influenza A virus (IAV). These mAbs could react with HA of H7N9, H3N2, and H9N2 with neutralizing activity. A novel linear epitope recognized by these mAbs was identified by peptide-based ELISA, and this epitope was located in TAADYKSTQSAIDQITGKLN at the C terminus of the helix A of H7N9. 3 A11, which is one of the four mAbs,...

Molecular Modeling for Structural Insights Concerning the Activation Mechanisms of F1174L and R1275Q Mutations on Anaplastic Lymphoma Kinase.

Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase involved in various cancers. In its basal state, the structure of ALK is in an autoinhibitory form stabilized by its A-loop, which runs from the N-lobe to the C-lobe of the kinase. Specifically, the A-loop adopts an inhibitory pose with its proximal A-loop helix (αAL-helix) to anchor the αC-helix orientation in an inactive form in the N-lobe; the distal portion of the A-loop is packed against the C-lobe to block the peptide substrate from bind...

Why does RNA collapse? The importance of water in a simulation study of helix-junction-helix systems.

Using computer simulations we consider the balance of thermodynamic forces that collapse RNA. A model helix-junction-helix (HJH) construct is used to investigate the transition from an extended to a collapsed conformation. Conventional Molecular Dynamics and Milestoning simulations are used to study the free energy profile of the process for two ion concentrations. We illustrate that HJH folds to a collapsed state with two types of counter ions (Mg2+ and K+). By dissecting the free energy landscape into ene...

Twisting Ultrathin Au Nanowires into Double Helices.

Previously, double helix nanowire was reported by coating Pd/Pt/Au onto Au-Ag alloy nanowire. Here, straight oleylamine-stabilized ultrathin Au nanowires with single crystalline fcc lattice are surprisingly converted into double helix helices upon reacting with Ag in tetrahydrofuran (THF). The obtained Au-Ag helical nanowires contain lattice distinctively different from the fcc lattice and are different in many aspects with the previous system. The discovery may expand the scope of nanoscale double helix fo...

Isolated collagen mimetic peptide assemblies have stable triple-helix structures.

The origin of the triple-helix structure and high stability of collagen has been debated for many years. As models of the triple helix and building blocks for new biomaterials, collagen mimetic peptide (CMP) assemblies have been deeply studied in the condensed phase. In particular, it was found that hydroxylation of proline, an abundant post-translational modification in collagen, increases its stability. Two main hypotheses emerged to account for this behavior: 1) intra-helix stereoelectronic effects, and ...

Sequence-controlled Stimuli-responsive Single-Double Helix Conversion between 1:1 and 2:2 Chloride-Foldamer Complexes.

The primary sequence in biopolymers carries the information to direct folded secondary structures, modulate their stabilities, and control the resultant functions. Our ability to encode such information into non-biological oligomers and polymers, however, is still limited. Here, we describe a C2 symmetric aryl-triazole foldamer that assembles into a chloride-templated 2:2 double helix and the discovery that its interconversion with the simpler 1:1 single helix can be driven by solvent quality, temperature, ...

A seven-helix protein constitutes stress granules crucial for regulating translation during human-to-mosquito transmission of Plasmodium falciparum.

The complex life-cycle of the human malaria parasite Plasmodium falciparum requires a high degree of tight coordination allowing the parasite to adapt to changing environments. One of the major challenges for the parasite is the human-to-mosquito transmission, which starts with the differentiation of blood stage parasites into the transmissible gametocytes, followed by the rapid conversion of the gametocytes into gametes, once they are taken up by the blood-feeding Anopheles vector. In order to pre-adapt to...

Presence of Intra-helical Salt-Bridge in Loop E Half-Helix Can Influence the Transport Properties of AQP1 and GlpF Channels: Molecular Dynamics Simulations of In Silico Mutants.

Major intrinsic protein (MIP) superfamily contains water-transporting AQP1 and glycerol-specific GlpF belonging to two major phylogenetic groups, namely aquaporins (AQPs) and aquaglyceroporins (AQGPs). MIP channels have six transmembrane helices (TM1 to TM6) and two half-helices (LB and LE). LE region contributes two residues to the aromatic/arginine (Ar/R) selectivity filter (SF) within the MIP channel. Bioinformatics analyses have shown that all AQGPs have an intra-helical salt-bridge (IHSB) in LE half-he...

Occupancies in the DNA-Binding Pathways of Intrinsically Disordered Helix-Loop-Helix Zipper Proteins.

Quantifying the stability of intermediates along parallel molecular pathways is often hampered by the limited experimental resolution of ensemble methods. In biology however, such intermediates may represent important regulatory targets, thus calling for strategies to map their abundance directly. Here, we use single-molecule Foerster resonance energy transfer (FRET) to quantify the occupancies of intermediates along two parallel DNA-binding pathways of the basic helix-loop-helix leucine-zipper (bHLH-LZ) do...

Molecular Design of Sequence-minimized, Structure-optimized, and Hydrocarbon-stapled Helix-Helix Interactions in the Trimer-of-Hairpins Motif of Pediatric Pneumonia RSV-F Protein.

The respiratory syncytial virus fusion (RSV-F) protein is a primary target for vaccine and drug development against respiratory infection and pediatric pneumonia. The RSV-F core forms a trimer-of-hairpins (TOH) motif in post-fusion conformation, which is characterized by a six-helix bundle (6HB) where the three N-terminal HRn helices define a central coiled-coil, while three C-terminal HRc helices pack on the coiled-coil surface in an antiparallel manner. Here, one tightly packed HRn-HRc helix-helix interac...

Overexpression of OsbHLH107, a member of the basic helix-loop-helix transcription factor family, enhances grain size in rice (Oryza sativa L.).

Grain size, which is determined by grain length, grain width, and grain thickness, is an important determinant for grain yield in rice. Identification and characterization of new genes that are associated with grain size will be helpful for the improvement of grain yield in rice.

Generation and probing of 3D helical lattices with tunable helix pitch and interface.

We propose a method for generation of tunable three-dimensional (3D) helical lattices with varying helix pitch. In order to change only the lattice helix pitch, a periodically varying phase along the propagation direction is added to the central beam - one of the interference beams for lattice construction. The phase periodicity determines the helix pitch, which can be reconfigured at ease. Furthermore, a helical lattice structure with an interface (domain wall) is also achieved by changing the phase struct...

A transient helix in the disordered region of dynein light intermediate chain links the motor to structurally diverse adaptors for cargo transport.

All animal cells use the motor cytoplasmic dynein 1 (dynein) to transport diverse cargo toward microtubule minus ends and to organize and position microtubule arrays such as the mitotic spindle. Cargo-specific adaptors engage with dynein to recruit and activate the motor, but the molecular mechanisms remain incompletely understood. Here, we use structural and dynamic nuclear magnetic resonance (NMR) analysis to demonstrate that the C-terminal region of human dynein light intermediate chain 1 (LIC1) is intri...

Hsp90 Mediates Membrane Deformation and Exosome Release.

Hsp90 is an essential chaperone that guards proteome integrity and amounts to 2% of cellular protein. We now find that Hsp90 also has the ability to directly interact with and deform membranes via an evolutionarily conserved amphipathic helix. Using a new cell-free system and in vivo measurements, we show this amphipathic helix allows exosome release by promoting the fusion of multivesicular bodies (MVBs) with the plasma membrane. We dissect the relationship between Hsp90 conformation and membrane-deformin...

12/10-helix in mixed b-peptides alternating bicyclic and acyclic b-amino acids: probing the relationship between bicyclic side chain and helix stability.

12/10-helices constitute suitable templates to design original objects. Nevertheless, they often suffer from a weak stability in polar solvents since they exhibit a mixed hydrogen-bond network resulting in a small macrodipole. In this work, we developed stable and functionalizable 12/10-helices alternating the highly constrained b2,3,3-trisubstituted bicyclic amino acid (S)-ABOC and acyclic substituted β-homologated proteinogenic amino acid (L-b3-hAA). Using NMR, we showed that such mixed b-peptides displa...

Discovery of the First Small Molecule Ligands for MALAT1 by Tuning an RNA-Binding Scaffold.

Structural studies of the 3'-end of the oncogenic long non-coding RNA Metastasis-associated Lung Adenocarcinoma Transcript 1 (MALAT1) revealed a unique triple helix structure. This structure enables accumulation of the transcript, and high levels of MALAT1 are found in several cancers. Here, we synthesize a small molecule library based on an RNA-binding scaffold, diphenylfuran (DPF), screen it against a variety of nucleic acid constructs, and demonstrate for the first time that the MALAT1 triple helix can b...

Deprotonation of a Single Amino Acid Residue Induces Significant Stability in an α-Helical Heteropeptide.

Stability of secondary structural elements is an integral component of a structurally stable protein. Presence of protons in the residue sequence and their immediate environment play a significant role in conformational stability. In this study, we show that removing a proton from a single amino acid residue significantly increases the stability of an α-helical heteropeptide in comparison with the unprotonated form. Far-UV circular dichroism spectroscopy, fluorescence spectroscopy, fluorescence energy tran...

Cooperation of helix insertion and lateral pressure to remodel membranes.

Nature has developed different protein mediated mechanisms to remodel cellular membranes. One of the proteins that is implicated in these processes is α-synuclein (αS). Here we investigate if besides αS's membrane bound amphipathic helix the disordered, solvent exposed tail of the protein contributes to membrane reshaping. We produced αS variants with elongated or truncated disordered solvent exposed domains. We observe a transformation of opaque multi lamellar vesicle solutions into non-scattering solu...

Concentration levels of cadmium and lead in the raw and processed meat of Helix pomatia snails.

This work reports on cadmium and lead contaminations in the edible snail Helix pomatia harvested in Poland. One hundred and 24 samples of Helix pomatia meat collected from seven provinces (voivodeships) of Poland were analyzed for their trace metal levels by graphite furnace atomic absorption spectrometry (GFAAS). The research was conducted in 2 stages. The 1st stage analyzed snail meat prior to any further technological treatment (raw meat). In the 2nd stage, the trace element levels were measured in meat ...

Basic helix-loop-helix gene family: Genome wide identification, phylogeny, and expression in Moso bamboo.

Studies have shown that basic helix-loop-helix (bHLH) transcription factors play important roles in plant growth and survival, and response to various biotic/abiotic stresses. We identified a total of 448 bHLH genes. These genes were classified into 21 bHLH subfamilies, and most genes in a given subfamily had similar gene structures and conserved motifs. We identified 176 homologous pairs in the three species. We calculated Ka, Ks, and Ka/Ks to analyze the replication relationships among the three species. ...

Long- and short-range structural characteristics of pea starch modified by autoclaving, α-amylolysis, and pullulanase debranching.

Pea starch (S) was modified by autoclaving (A), α-amylolysis (E), and pullulanase debranching (P), the effect of pretreatments including autoclaving and α-amylolysis on the structural modifications to the pullulanase debranched starch was investigated. All processed pea starch was transformed from a C- to a B-type crystalline structure. The power law exponent (α) ranging from 1.85 to 2.64 suggested the existence of mass fractal structure. Compared with native starch, all treatments applied caused an enha...

Clade Ib basic helix-loop-helix transcription factor, bHLH101, acts as a regulatory component in photo-oxidative stress responses.

The accumulation of reactive oxygen species (ROS) leads to oxidative damage; however, ROS also acts as signaling molecules. We previously demonstrated that the inducible silencing of thylakoid membrane-bound ascorbate peroxidase Arabidopsis plants (IS-tAPX) accumulated HO in their chloroplasts, resulting in the clarification of ROS-responsive genes. In IS-tAPX plants, the transcript levels of the basic helix-loop-helix (bHLH) transcription factor bHLH101, which belongs to clade Ib bHLH, were down-regulated....


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