Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target by Masoud Foroutan, Ali Dalir Ghaffari, Shahrzad Soltani, Hamidreza Majidiani, Ali Taghipour, Mohamad Sabaghan

“…The findings revealed that the CDPK4 protein comprised 30.14% and 34.97% alpha-helix, 59.84% and 53.54% random coils, and 10.02% and 11.49% extended strand with SOPMA and GOR4 tools, respectively. …”
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In silico Analysis and Molecular Modeling of RNA Polymerase, Sigma S (RpoS) Protein in Pseudomonas aeruginosa PAO1 by Mansour Sedighi, Mohsen Moghoofei, Ebrahim Kouhsari, Abazar Pournajaf, Behzad Emadi, Masoud Tohidfar, Mehrdad Gholami

“…Secondary structure analysis predicted that random coil is the predominant structure followed by extended alpha helix. The three-dimensional (3D) structure was modeled using SWISS-MODEL Workspace. …”
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Molecular interaction studies of trimethoxy flavone with human serum albumin. by Mahesh Gokara, Babu Sudhamalla, Damu G Amooru, Rajagopal Subramanyam

“…The HSA conformation was altered upon binding of TMF to HSA with decrease in alpha-helix and an increase in beta-sheets and random coils suggesting partial unfolding of protein secondary structure. …”
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Diabetes without Overt Cardiac Disease Is Associated with Markers of Abnormal Repolarization: A Case-Control Study by Tomer Stahi, Keren Kaminer, Itay Shavit, Udi Nussinovitch

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Computational evaluation of the effect of processing on the trypsin and alpha‐amylase inhibitor from Ragi (Eleusine coracana) seed by Shannon Fenwick, Sai Kranthi Vanga, Andrea DiNardo, Jin Wang, Vijaya Raghavan, Ashutosh Singh

“…Thermal processing alone has also affected the second alpha helix of the molecule. Overall, the SEFs of 1 V/nm are found to have resulted in the most secondary structure deviations in terms of root mean square deviation and radius of gyration.…”
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The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function. by JP Segrest, MK Jones, H De Loof, CG Brouillette, YV Venkatachalapathi, GM Anantharamaiah

“…Site-directed mutagenesis and other molecular biology-based techniques are now available for probing the amphipathic alpha helix structural motif in the exchangeable apolipoproteins. …”
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Putative LysM Effectors Contribute to Fungal Lifestyle by Marta Suarez-Fernandez, Ana Aragon-Perez, Luis Vicente Lopez-Llorca, Federico Lopez-Moya

“…Additionally, molecular docking shows that the NAcGl binding sites of Pc123 Lys 2, 3 and 4 are adjacent to an alpha helix. Putative LysM effectors from fungal endophytes, such as Pc123, differ from those of plant pathogenic fungi. …”
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Leishmanolysin gp63: Bioinformatics evidences of immunogenic epitopes in Leishmania major for enhanced vaccine design against zoonotic cutaneous leishmaniasis by Morteza Shams, Hassan Nourmohammadi, Gholam Basati, Ghazaaleh Adhami, Hamidreza Majidiani, Esfandiar Azizi

“…The secondary structure encompassed 48.67% random coil, 31.4% alpha helix and 19.93% extended strand. Ramachandran analysis of the refined model showed 98.5% and 100% of residues in favored and allowed regions, respectively. …”
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Effect of particle lipid content on the structure of insect lipophorins. by RO Ryan, CM Kay, K Oikawa, H Liu, R Bradley, DG Scraba

“…The VHDLp-E apolipoproteins are an exception in that, while having the same alpha-helix content as HDLp-W1 and HDLp-W2, they contain less beta-structure and correspondingly more random coil. …”
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In silico prediction of the functional and structural consequences of the non-synonymous single nucleotide polymorphism A122V in bovine CXC chemokine receptor type 1 by A. F. Guzzi, F. S. L. Oliveira, M. M. S. Amaro, P. F. Tavares-Filho, J. E. Gabriel

“…The A122V polymorphism exerted tolerable and non-deleterious effects on the polymorphic CXCR1, and the predictive structural model for polymorphic CXCR1 revealed an alpha helix spatial structure typical of a receptor transmembrane polypeptide. …”
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Construction of novel repeat proteins with rigid and predictable structures using a shared helix method by Suk-Jun Youn, Na-Young Kwon, Ji Hyun Lee, Jin Hong Kim, Jinwoo Choi, Hayyoung Lee, Jie-Oh Lee

“…We describe a simple and efficient method for connecting two proteins via a fused alpha helix that is formed by joining two preexisting helices into a single extended helix. …”
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N-terminal amino acids of bovine alpha interferons are relevant for the neutralization of their antiviral activity by J.B. Barreto Filho, P.R.S. Eiras, R.R. Golgher

“…According to the three-dimensional structure described for human and murine IFNs, these amino acids are located in the alpha helix A; amino acids 16 and 19 of the bovine IFNs would be expected to be exposed and could bind to the antibody directly. …”
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A Amazônia Central e seus peixes by William I. Fink, Sara V. Fink

“…Mudanças cíclicas no nível da água e flutuações associadas à disponibilidade de oxigênio são dois fatores que exercem considerável influência sobre a biologia dos peixes da Amazônia Central Os locais de coleta do "Alpha Helix" Fase IV são sucintamente descritos. A sistemática e evolução da maioria dos grupos de peixes do Amazonas são muito pouco conhecidas; a incapacidade para identificar todos os peixes examinados e a falta de hipóteses evolucionárias de parentesco bem demonstradas para basear as comparações apresentam problemas para o biólogo comparativo. …”
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Characterization of 2'-fluoro-RNA aptamers that bind preferentially to disease-associated conformations of prion protein and inhibit conversion. by Rhie, A, Kirby, L, Sayer, N, Wellesley, R, Disterer, P, Sylvester, I, Gill, A, Hope, J, James, W, Tahiri-Alaoui, A

“…To understand the molecular basis of these properties and to distinguish specific from non-specific aptamer-PrP interactions, we studied deletion mutants of bovine PrP in denatured, alpha-helix-rich and beta-sheet-rich forms. We provide evidence that, like scrapie-associated fibrils (SAF), the beta-oligomer of PrP bound to SAF-93 with at least 10-fold higher affinity than did the alpha-form. …”

Naturally occurring A pocket polymorphism in HLA-B*2703 increases the dependence on an accessory anchor residue at P1 for optimal binding of nonamer peptides. by Griffin, T, Yuan, J, Friede, T, Stevanovic, S, Ariyoshi, K, Rowland-Jones, S, Rammensee, H, Colbert, R

“…Computer modeling of B*2703 reveals movement of a water molecule and the alpha1 alpha-helix to allow His at position 59 to maintain important hydrogen bonds with the peptide N terminus in the A pocket. …”

A RASSF1A polymorphism restricts p53/p73 activation and associates with poor survival and accelerated age of onset of soft tissue sarcoma. by Yee, K, Grochola, L, Hamilton, G, Grawenda, A, Bond, E, Taubert, H, Wurl, P, Bond, G, O'Neill, E

“…Secondary protein structure prediction studies suggest that an alpha helix containing the ATM recognition site is disrupted in the serine isoform of RASSF1A (RASSF1A-p.133Ser). …”

Molecular determinants for subcellular localization of the severe acute respiratory syndrome coronavirus open reading frame 3b protein. by Freundt, E, Yu, L, Park, E, Lenardo, M, Xu, X

“…Following nuclear localization, ORF 3b traffics to the outer membrane of mitochondria via a predicted amphipathic alpha-helix. Additionally, ORF 3b contains a consensus nuclear export sequence, and we demonstrate that nuclear export and thus mitochondrial translocation are dependent on a leptomycin B-sensitive nuclear export mechanism. …”

Molecular identification and bactericidal function analysis of NK-lysin from black sea bass (Centropristis striata) by Xiaowan Ma, Yongze Xing, Hongtao Liu, Dewei Cheng, Xuyang Chen, Ying Qiao, Shengping Zhong

“…Scanning electron microscopy analysis revealed that CsNKl-26 and CsNKl-28 played their bactericidal roles using the classical alpha-helix antimicrobial peptide route. These results illustrate the immune functions of CsNKl against V. harveyi, and they can be applied to developing disease control methods for fish.…”
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Genome-wide exploration of sugar transporter (sweet) family proteins in Fabaceae for Sustainable protein and carbon source. by Nisha Singh, Megha Ujinwal, Sapna Langyan, R Z Sayyed, Hesham Ali El Enshasy, Ahmed A Kenawy

“…Secondary structure analysis shown that these proteins are richer in alpha-helix (40%) than extended strand (30%) and random coil (25%), respectively. …”
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Physico-Chemical and Antifungal Properties of a Trypsin Inhibitor from the Roots of Pseudostellaria heterophylla by Xixi Cai, Xiaoli Xie, Nanyan Fu, Shaoyun Wang

“…The PHTI contained 3.7% α-helix, 42.1% β-sheets, 21.2% β-turns, and 33% disordered structures, which showed similarity with several Kunitz-type trypsin inhibitors. …”
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