Critical structural and functional roles for the N-terminal insertion sequence in surfactant protein B analogs. by Frans J Walther, Alan J Waring, Jose M Hernandez-Juviel, Larry M Gordon, Zhengdong Wang, Chun-Ling Jung, Piotr Ruchala, Andrew P Clark, Wesley M Smith, Shantanu Sharma, Robert H Notter

“…Here, we perform similar analyses on a Super Mini-B construct that has native SP-B residues (1-7) attached to the N-terminus of Mini-B, to test whether the N-terminal sequence is also involved in surfactant activity.FTIR spectra of Mini-B and Super Mini-B in either lipids or lipid-mimics indicated that these peptides share similar conformations, with primary alpha-helix and secondary beta-sheet and loop-turns. …”
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TLR9-mediated activation of dendritic cells by CD32 targeting for the generation of highly immunostimulatory vaccines by J. A. Sepulveda-Toepfer, Johannes Pichler, Kathrin Fink, Milica Sevo, Sonja Wildburger, Liesbeth Christiene Mudde-Boer, Christopher Taus, Geert Cornelius Mudde

“…Furthermore, the scFv in the WH is extended with a five-time heptad repeat (EVSALEK) alpha helix which allows for a coiled-coil complex formation with any immunogen also extended with another five-time heptad (KVSALKE) repeat. …”
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Streptococcus pneumoniae serotype 1 capsular polysaccharide induces CD8CD28 regulatory T lymphocytes by TCR crosslinking. by Janina Mertens, Mario Fabri, Alessandra Zingarelli, Torsten Kubacki, Sonja Meemboor, Laura Groneck, Jens Seeger, Martina Bessler, Helena Hafke, Margarete Odenthal, Joan G Bieler, Christoph Kalka, Jonathan P Schneck, Hamid Kashkar, Wiltrud M Kalka-Moll

“…Zwitterionic capsular polysaccharides (ZPS) of commensal bacteria are characterized by having both positive and negative charged substituents on each repeating unit of a highly repetitive structure that has an alpha-helix configuration. In this paper we look at the immune response of CD8(+) T cells to ZPSs. …”
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Assembly of Influenza hemagglutinin fusion peptide trimers in a phospholipid bilayer by coarse-grained simulations. by Francesca eCollu, Enrico eSpiga, Christian Douglas Lorenz, Franca eFraternali

“…Recently, possible structures for the fusion peptide (ranging from an inverted V shaped alpha-helical structure to an alpha-helical hairpin, or to a complete alpha-helix) and their implication in the membrane fusion initiation have been proposed. …”
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Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences. by Vinal V Lakhani, Feng Ding, Nikolay V Dokholyan

“…Additionally, by lengthening polyQ, the first N-terminal 17 residues are more likely to adopt a beta-sheet conformation rather than an alpha-helix conformation. Therefore, our molecular dynamics study provides a structural insight of XN1 misfolding and elucidates the possible role of the flanking sequences in XN1 aggregation.…”
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Sonification based de novo protein design using artificial intelligence, structure prediction, and analysis using molecular modeling by Yu, Chi Hua, Buehler, Markus J

“…We train a deep learning model whose architecture is composed of several long short-term memory units from data consisting of musical representations of proteins classified by certain features, focused here on alpha-helix rich proteins. Using the deep learning model, we then generate de novo musical scores and translate the pitch information and chain lengths into sequences of amino acids. …”
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Improving transmembrane protein prediction analysis using machine learning by Kazemian, Hassan

“…The research presents a novel evolutionary support vector machine (SVM) based alpha-helix transmembrane region prediction algorithm to solve the membrane helices in amino acid sequences. …”
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Heterologous amyloid seeding: revisiting the role of acetylcholinesterase in Alzheimer's disease. by Jean, L, Thomas, B, Tahiri-Alaoui, A, Shaw, M, Vaux, D

“…The hAChE C-terminal domain (T40, AChE(575-614)) is an exposed amphiphilic alpha-helix involved in enzyme oligomerisation, but it also contains a conformational switch region (CSR) with high propensity for conversion to non-native (hidden) beta-strand, a property associated with amyloidogenicity. …”

Viral RNA modulates the acid sensitivity of foot-and-mouth disease virus capsids. by Curry, S, Abrams, C, Fry, E, Crowther, J, Belsham, G, Stuart, D, King, A

“…Sequence analysis of the three subtypes identified several differences at the interface between pentamers and highlighted a His-alpha-helix dipole interaction which spans the pentamer interface and appears likely to influence the acid lability of the virus.…”

Three-dimensional solution structure and conformational plasticity of the N-terminal scavenger receptor cysteine-rich domain of human CD5. by Garza-Garcia, A, Esposito, D, Rieping, W, Harris, R, Briggs, C, Brown, M, Driscoll, P

“…The eCD5d1m structure is similar to other members of the scavenger receptor cysteine-rich superfamily, but the position of the lone alpha helix differs due to interactions with the unique N-terminal region of the domain. …”

Uridine(5')diphospho(1)-alpha-D-glucose. A binding study to glycogen phosphorylase b in the crystal. by Oikonomakos, N, Acharya, K, Stuart, D, Melpidou, A, McLaughlin, P, Johnson, L

“…The pyrophosphate is also well located with the glucose phosphate interacting with the main-chain NH groups at the start of the glycine-loop alpha helix and the uridine phosphate interacting through a water molecule with the 5'-phosphate of the cofactor pyridoxal phosphate and with the side chains of residues Tyr-573, Lys-574 and probably Arg-569. …”

Pre-labelling versus direct labelling of anthrax proteins for imaging of matrix metalloproteinases activity using DOTA-GA by Xavier, M-AE, Liu, S, Leppla, SH, Cornelissen, B

“…Comparison of the secondary structure content of LFn exposed to 37°C or 95°C, showed a loss of alpha helix content at higher temperatures. Cell uptake of both forms of [111In]In-DOTA-GA-LFn, labelled directly or indirectly, was significantly higher in MMP-positive cells, in the presence of PA-L1, compared to controls. …”

Comparative analysis of the noncollagenous NC1 domain of type IV collagen: identification of structural features important for assembly, function, and pathogenesis. by Netzer, K, Suzuki, K, Itoh, Y, Hudson, BG, Khalifah, R

“…Neural network secondary structure prediction on multiple aligned sequences revealed a subdomain core structure consisting of six hydrophobic beta-strands and one short alpha-helix with a significant hydrophobic moment. The existence of opposite charges in the alpha-helices may carry implications for intersubdomain interactions. …”

Structural and functional prediction of Leucosporidium antarcticum antifreeze protein (Afp1) by Zulkifli, Mohammad Fairuz

“…It also showed average score between 0.30-0.60 in the Verify3D analysis which is satisfying for a low percentage of similarity protein models. In the alpha helix segments, there were five major amino acids (serine, threonine, aspartic acid,asparagine and glutamine) which had high possibility to be bonded with the water molecule at the ice surface. …”
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Cloning and comparative protein modelling of two MADS-box genes, HsMADS1 and HsMADS2 isolated from Hibiscus sabdariffa L. var. UMKL (roselle) by Othman, Siti N., Yong, S. Y. C, Karjiban, Roghayeh Abedi, Shakri, Adibah

“…The putative functions of the genes based on BLAST searches and phylogenetic analyses suggested that 'HsMADS1' possibly involves in the expression of SEP gene in stem, leaf, bud and flower organs of roselle, whereas 'HsMADS2' may probably involve in the late expression of floral tissue for stem branching. The alpha helix rich structures of SRF-TF identified in the deduced amino acid sequences of HsMADS1 and HsMADS2 supported the involvement of both proteins in DNA binding and dimerisation.…”
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Membrane-bound Δ12 fatty acid desaturase (FAD12); From Brassica napus to E. coli expression system by Abd Halim, Nur Farah Anis, Mohamad Ali, Mohd Shukuri, Leow, Adam Thean Chor, Raja Abd Rahman, Raja Noor Zaliha

“…Analysis of circular dichroism (CD) showed FAD12 was made up of 47.3% and 0.9% of alpha-helix and β-sheet secondary structures. The predicted Tm value was 50.2 °C.…”

Structural determination of the complement inhibitory domain of Borrelia burgdorferi BBK32 provides insight into classical pathway complement evasion by Lyme disease spirochetes. by Jialei Xie, Hui Zhi, Ryan J Garrigues, Andrew Keightley, Brandon L Garcia, Jon T Skare

“…BBK32-C adopts an anti-parallel four-helix bundle fold with a fifth alpha-helix protruding from the helical core. The structure revealed that the three residues targeted in the BXK32-C chimera are surface-exposed, further supporting their potential relevance in C1r binding and inhibition. …”
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Revisiting the Role of ß-Tubulin in Drosophila Development: β-tubulin60D is not an Essential Gene, and its Novel Pin1 Allele has a Tissue-Specific Dominant-Negative Impact by Ramesh Kumar Krishnan, Naomi Halachmi, Raju Baskar, Anna Bakhrat, Raz Zarivach, Raz Zarivach, Adi Salzberg, Uri Abdu

“…Analyzing the ß-tubulin structure suggests that this E75K alteration destabilizes the alpha-helix structure and may also alter the GTP-Mg2+ complex binding capabilities. …”
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Effect of vesicle size on their interaction with class A amphipathic helical peptides by J A Gazzara, M C Phillips, S Lund-Katz, M N Palgunachari, J P Segrest, G M Anantharamaiah, W V Rodrigueza, J W Snow

“…Peptides 18A, Ac-18A-NH2, Ac-18R-NH2, 37pA, and 37aA have been designed to investigate the lipid-binding properties of the amphipathic alpha-helix structural motif that appears to modulate the lipid-binding properties of the exchangeable plasma apolipoproteins. …”
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Bioinformatic prediction and functional characterization of human KIAA0100 gene by He Cui, Xi Lan, Shemin Lu, Fujun Zhang, Wanggang Zhang

“…Besides, human KIAA0100 protein contained a signalpeptide, a transmembrane region, three types of secondary structures (alpha helix, extended strand, and random coil) , and four domains from mitochondrial protein 27 (FMP27). …”
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