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Order Tubulavirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
At the same time, Papavoine et al. (1998) determined the 3D structure of the M13 protein p8, solubilized in detergent micelles, by heteronuclear multidimensional NMR and restrained molecular dynamics. The protein consisted therefore of two α-helices, running from residues 8–16 and 25–45, respectively. These two helices were connected by a flexible and distorted helical hinge region. The authors commented that the p8 structural properties resembled a flail, in which the hydrophobic helix (residues 25 to 45) was the handle and the other, amphipathic, helix was the swingle. In this metaphor, the hinge region was the connecting piece of leather (Papavoine et al. 1998).
Dopamine Receptors, Signaling Pathways, and Drugs
Published in Nira Ben-Jonathan, Dopamine, 2020
The GPCRs are characterized by a seven-transmembrane α-helical configuration, predicted to form three extracellular loops (ECLs) and three intracellular loops (ICLs). The transmembrane loops are flanked by an extracellular N-terminus and an intracellular C-terminus (Figure 2.1). Most GPCRs have two cysteines that form an intramolecular disulfide bridge between the first and second ECLs. This bridge enhances the stability of the receptor and is involved in facilitating ligand binding and receptor activation. The helices are arranged in a circular orientation within the membrane plane. In many receptors, a crevice in the middle of the helices contains the ligand-binding site, which is accessible to ligands from the extracellular side. Binding of an agonist induces conformational changes in the cytoplasmic face of the receptor, enabling the linkage of the receptor to G proteins and their activation. In addition, activated receptors can become associated with GRKs and interact with β-arrestins. All the above changes are followed by activation of several downstream signaling cascades and are often accompanied by receptor desensitization, internalization and degradation [4,5], as is discussed in more detail in a later section.
RNA
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
The adjacent 3′ replicase domain contained about 1100 nucleotides. The hairpins in this protein-coding domain were much longer and more irregular than in the 3′ untranslated region. Both domains were defined by long-distance interactions. The secondary structure was not a collection of hairpin structures connected by single-stranded regions. Rather, the RNA stretches between the stem−loop structures were all involved in an extensive array of long-distance interactions that contracted the molecule to a rigid structure in which all hairpins were predicted to have a fixed position with respect to each other. A general feature of the model was that the helices tend to be organized in four-way junctions with little or no unpaired nucleotides between them. As a result, there was a potential for coaxial stacking of adjacent stems (Beekwilder et al. 1995).
Affinity-controlled capture and release of engineered monoclonal antibodies by macroporous dextran hydrogels using coiled-coil interactions
Published in mAbs, 2023
Seyed Farzad Baniahmad, Romane Oliverio, Ines Obregon-Gomez, Alma Robert, Anne E.G. Lenferink, Elena Pazos, Nick Virgilio, Xavier Banquy, Gregory De Crescenzo, Yves Durocher
Affinity peptides are versatile tunable tools that can be easily expressed as tags on recombinant proteins. This strategy ensures the efficient tagging of the protein since no extra conjugation step is required and removes the need for an additional purification step. Coiled-coil peptides are commonly used affinity systems derived from the coiled-coil structure, which is one of the most abundant naturally occurring motifs for protein folding and assembly.17 Structurally, this oligomerization motif consists of two or more α helices wrapped around each other. It is commonly found in many proteins involved in cellular activities, including transcription, muscle contractions, or viral fusion mechanisms.23–25 The fingerprint of this structure is a repeat of a seven-residue motif (heptad), the number of which can vary from 200 in naturally occurring fibrous proteins to only two heptads in a de novo designed synthetic coiled-coil.26 The E/K coiled coil is a de-novo-designed coiled-coil in which the Ecoil and Kcoil peptides, heptads: EVSALKE (Ecoil) and KVSALEK (Kcoil), form a highly specific, heterodimeric coiled-coil interaction with a high affinity, shown to be sufficiently strong in physiological conditions.27,28
Analysis of a Novel Mexican Variant of the HBB Gene Associated with β-Thalassemia Using Bioinformatic Tools
Published in Hemoglobin, 2021
Octavio Martínez Villegas, Diana Mendoza-Meléndez, Rocio Trueba-Gómez, Fany Rosenfeld-Mann, Héctor A. Baptista-González, Higinio Estrada-Juárez
The two types of Hb chains have 75.0% α helices as a secondary structure, with seven and eight segments, respectively. Hydrogen bonds stabilize the helical sections within this protein [2]. The eight helices of the β chain are named with the letters A to H [2]. The amino acid residues that make up each helix are identified as follows: the position of the residue in the protein, and in parentheses the letter of the helix and the position within it and its name in a three-letter code [2,3]. In the β chain, the residues 30(B12)Arg, 33(B15)Val, 34(B16)Val, 108(G10)Asn, 112(G14)Cys, 124(H2)Pro, 125(H3)Pro, 127(H5)Gln and 128(H6)Ala, are necessary to form the α1β1 dimer, and the heme group is also suspended between the E and F helices [4]. The ferrous ion of the heme group is linked in parallel to the N of proximal histidine 92 and distal histidine 63 [2] and at the same time is protected by a valine residue. The nonpolar vinyl groups of the heme group are found in the hydrophobic interior of the cavity, whereas the charged polar porphyrin groups are oriented toward the hydrophilic surface of the subunit [1]. Therefore, deletion or substitution of critical amino acids prevents the formation of αβ subunits and leads to a functional loss of half of the β strands [1].
Resistant starch, microbiome, and precision modulation
Published in Gut Microbes, 2021
Peter A. Dobranowski, Alain Stintzi
Starch’s supramolecular structure begins with pairs of amylopectin branch chains and amylose chains intertwining to form crystalline double helices. At amylopectin junction points (i.e. α-1,6 bonds), amorphous regions are thermodynamically favored over helices. Helices can either be dense and orthorhombic (A-type) or open and hexagonal (B-type).17 Alternating amorphous and crystalline lamellae are thought to form 20–500 nm intermediary structures called “blocklets”18,19 with amorphous amylose forming an intermolecular matrix or “glue” between blocklets.20 Recent in silico modeling proposes that the blocklet architecture follows phyllotaxic rules, whereby interlocking crystalline platelets form ellipsoid fractals.21 Depending on the amylopectin branching density and chain lengths, blocklets might be more amorphous (“defective blocklets”) or crystalline (“normal blocklets”).18,22 Blocklets arrange into arrays of alternating crystalline and semi-crystalline concentric rings, disrupted by amorphous channels and veins.19,20,22,23 Foresti and colleagues elegantly demonstrated that amorphous layers are preferentially degraded by soluble α-amylase, leaving behind a crystalline skeleton.24 Overall, blocklet type and arrangement are associated with surface smoothness, porosity, and resistance to hydrolysis.