Assembly and regulation of the mammalian mRNA processing body by Donald B. Bloch, Claire O. Sinow, Andrew J. Sauer, Benjamin H. P. Corman

“…The N-terminus of full-length PATL1 was required to mediate the interaction between EDC4 and DDX6. The C-terminal, alpha helix-domain- containing portion of EDC4 was sufficient to mediate interaction with DCP1a and CCHCR1. …”
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Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure by Webb-Robertson Bobbie-Jo, Bystroff Christopher

“…Here we show that a pairwise covariant sequence model does not predict alpha helix or beta strand significantly better overall than a profile-based model, but it does improve the prediction of certain loop motifs. …”
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YqiC of <it>Salmonella enterica </it>serovar Typhimurium is a membrane fusogenic protein required for mice colonization by Goldbaum Fernando A, García-Véscovi Eleonora, Aguirre Andes, Craig Patricio O, García-Angulo Víctor A, Carrica Mariela C, Cravero Silvio L

“…We found that YqiC shares biophysical and biochemical properties with <it>Brucella abortus </it>BMFP, the only previously characterized member of this group, such as a high alpha helix content, a coiled-coil domain involved in trimerization and a membrane fusogenic activity <it>in vitro</it>. …”
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Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. by Anna V Glyakina, Natalya S Bogatyreva, Oxana V Galzitskaya

“…Moreover, in the beta structure, the probability of formation of backbone hydrogen bonds is higher than that in the alpha helix for all residues of α+β proteins (the average probability is 0.73±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without proline) and α/β proteins, except for asparagine, aspartic acid, glycine, threonine, and serine (0.70±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without the proline residue). …”
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Identification of a small molecule that modifies MglA/SspA interaction and impairs intramacrophage survival of Francisella tularensis. by Algevis P Wrench, Christopher L Gardner, Claudio F Gonzalez, Graciela L Lorca

“…Further in vitro analyses, using size exclusion chromatography, indicated that quinacrine does not disrupt the heterodimer formation, however, changes in the alpha helix content were confirmed by circular dichroism. …”
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Nitric oxide reversibly binds the reduced [2Fe-2S] cluster in mitochondrial outer membrane protein mitoNEET and inhibits its electron transfer activity by Chelsey R. Fontenot, Zishuo Cheng, Huangen Ding

“…Structurally, the N-terminal domain of mitoNEET has a single transmembrane alpha helix that anchors the protein to mitochondrial outer membrane. …”
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Interaction of the Spo20 membrane-sensor motif with phosphatidic acid and other anionic lipids, and influence of the membrane environment. by Habib Horchani, Maud de Saint-Jean, Hélène Barelli, Bruno Antonny

“…Nevertheless, the lipid binding properties and the cellular localization of the Spo20 alpha-helix differed markedly from that of another amphipathic motif, Amphipathic Lipid Packing Sensor (ALPS), suggesting that even in the absence of stereo specific interactions, amphipathic helices can act as subcellular membrane targeting determinants in a cellular context.…”
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Assembly and regulation of the mammalian mRNA processing body. by Donald B Bloch, Claire O Sinow, Andrew J Sauer, Benjamin H P Corman

“…The N-terminus of full-length PATL1 was required to mediate the interaction between EDC4 and DDX6. The C-terminal, alpha helix-domain- containing portion of EDC4 was sufficient to mediate interaction with DCP1a and CCHCR1. …”
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Unconventional superconductivity induced in Nb films by adsorbed chiral molecules by H Alpern, E Katzir, S Yochelis, N Katz, Y Paltiel, O Millo

“…By applying scanning tunneling spectroscopy, we demonstrate that the singlet-pairing s-wave order parameter of Nb is significantly altered upon adsorption of chiral polyalanine alpha-helix molecules on its surface. The tunneling spectra exhibit zero-bias conductance peaks embedded inside gaps or gap-like features, suggesting the emergence of unconventional triplet-pairing components with either d-wave or p-wave symmetry at the Nb organic–molecules interface, as corroborated by simulations. …”
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Macrophage scavenger receptor A mediates adhesion to apolipoproteins A-I and E. by Neyen, C, Plüddemann, A, Roversi, P, Thomas, B, Cai, L, van der Westhuyzen, DR, Sim, R, Gordon, S

“…SR-A was found to recognize the exchangeable apolipoproteins A-I and E (apo A-I and apo E, respectively) in both lipid-free and lipid-associated form, suggesting the shared amphipathic alpha-helix as a potential recognition motif. Adhesion of RAW 264.7 macrophages to surfaces coated with apo A-I and apo E4 proved to be integrin-independent and could be blocked by anti-SR-A antibodies. …”

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. by Cox, K, Bond, P, Grottesi, A, Baaden, M, Sansom, MS

“…The first two eigenvectors (which account for &gt;50% of the protein motion) reveal that such motions are concentrated in the extracellular loops and, in the case of PagP, in the N-terminal alpha-helix. Residue profiles of the magnitude of motions corresponding to the first two eigenvectors are similar for the corresponding X-ray and NMR simulations, but the directions of these motions correlate poorly reflecting incomplete sampling on a approximately 10 ns timescale.…”

Competing intrachain interactions regulate the formation of beta-sheet fibrils in bovine PrP peptides. by Tahiri-Alaoui, A, Bouchard, M, Zurdo, J, James, W

“…The normal form (PrP(C)), rich in alpha-helix, converts into an aberrant beta-sheet-dominated form (PrP(Sc)), which seems to be at the center of the pathotoxic symptoms observed in TSEs. …”

The artificial zinc finger coding gene 'Jazz' binds the utrophin promoter and activates transcription. by Corbi, N, Libri, V, Fanciulli, M, Tinsley, J, Davies, K, Passananti, C

“…The entire zinc finger alpha-helix region, containing the amino acid positions that are crucial for DNA binding, was specifically chosen on the basis of the contacts more frequently represented in the available list of the 'code'. …”

Assessing the effects of time and spatial averaging in 15N chemical shift/15N-1H dipolar correlation solid state NMR experiments. by Straus, S, Scott, W, Watts, A

“…Three types of motion are considered: (a) Librational motion of the peptide planes in the alpha-helix; (b) rotation of the helix about its long axis; and (c) wobble of the helix about a nominal tilt angle. …”

Polarized Raman anisotropic response of collagen in tendon: towards 3D orientation mapping of collagen in tissues. by Leonardo Galvis, John W C Dunlop, Georg Duda, Peter Fratzl, Admir Masic

“…For out-of-plane molecular orientations alpha-helix structures display a decreased average intensity. …”
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Antibody recognition of the Pneumovirus fusion protein trimer interface. by Jiachen Huang, Darren Diaz, Jarrod J Mousa

“…MPV458 was co-crystallized with hMPV F, and the mAb primarily interacts with an alpha helix on the F2 region of the hMPV F protein. …”
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Bioinformatics Analysis Reveals Abundant Short Alpha-Helices as a Common Structural Feature of Oomycete RxLR Effector Proteins. by Wenwu Ye, Yang Wang, Yuanchao Wang

“…Moreover, we identified less alpha-helix-rich proteins from secretomes of several oomycete and fungal organisms in which RxLRs have not been identified, providing additional evidence that these organisms are unlikely to harbor RxLR-like proteins. …”
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In-silico characterisation and comparative mapping of yellow stripe like transporters in five grass species by M G MALLIKARJUNA, T NEPOLEAN, SHIKHA MITTAL, FIROZ HOSSAIN, J S BHAT, K M MANJAIAH, S MARLA, AMITHA CR MITHRA, P K AGRAWAL, A R RAO, H S GUPTA

“…Scondary structure analysis identified that, alpha helix and random coils were the most common structures of the YSL proteins. …”
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Structural Basis for the Interaction between p53 Transactivation Domain and the Mediator Subunit MED25 by Min-Sung Lee, Kyungeun Lim, Mi-Kyung Lee, Seung-Wook Chi

“…Taken together with the mutagenesis data, the refined structural model of MED25 ACID/p53TAD2 peptide complex showed that an amphipathic &alpha;-helix of p53TAD2 peptide bound an elongated hydrophobic groove of MED25 ACID. …”
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Estimated secondary structure propensities within V1/V2 region of HIV gp120 are an important global antibody neutralization sensitivity determinant. by Maxim Totrov

“…Recent X-ray structures revealed presence of well-defined tertiary structure within this domain but also demonstrated partial disorder and conformational heterogeneity.Correlations of neutralization sensitivity with the conformational propensities for beta-strand and alpha-helix formation over the entire folded V1/V2 domain as well as within sliding 5-residue window were investigated. …”
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