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Relevant bibliographies by topics / Helix structure

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Academic literature on the topic 'Helix structure'

Author: Grafiati

Published: 5 June 2025

Last updated: 24 June 2025

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Journal articles on the topic "Helix structure"

1

Glennon, Madeline M., Krishna M. Shivakumar, Martina Zafferani, et al. "Structural Elucidation of an RNA Triple Helix in Complex with a Small Molecule." Structural Dynamics 12, no. 2_Supplement (2025): A354. https://doi.org/10.1063/4.0000660.

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Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA with a 3ʹ-terminal triple helix, which stabilizes and protects the RNA from degradation. This stabilization contributes to MALAT1 overaccumulation, promoting cancer and disease. The unique structure and function of the MALAT1 triple helix makes it an ideal target for small-molecule intervention. Yet, structural details regarding the interactions between the MALAT1 triple helix and a small molecule drug remain unclear. Herein, I aim to solve a 3D structure of the MALAT1 triple helix in complex with a diminazene (DMZ) small molecule: DMZp8. Single-particle cryo-electron microscopy (cryo-EM) is a technique most suitable for solving large macromolecular structures, yet can be applied to solve structures of small RNAs (&lt;50 kDa). Visualization of small RNAs is limited by the signal-to-noise ratio, hindering global resolution. To overcome these limitations, RNA scaffolding techniques graft an RNA-of-interest onto a larger, well-structured RNA scaffold. Herein, we grafted the MALAT1 triple helix onto two established RNA scaffolds: TTR-3 (PDB ID: 6WLK) and a circularly permuted version of the Tetrahymena ribozyme (TetP6B) (PDB ID: 8TJX). Thus far, we have solved a 3D structure of the apo MALAT1 triple helix-TTR-3 at 5.2 Å resolution. Additionally, optimal single-particle density and distribution was observed for the MALAT1 triple helix-TTR-3:DMZp8 complex at a 1:4 ratio. Promising single-particle conditions for the MALAT1 triple helix-TetP6B scaffold were achieved using a 1:25 ratio of the MALAT1 triple helix-TetP6B:DMZp8. A high-resolution structure of a small molecule bound to the MALAT1 triple helix will advance the rational design of small molecules selective for disease-promoting RNAs.

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Murre, Cornelis, Gretchen Bain, Marc A. van Dijk, et al. "Structure and function of helix-loop-helix proteins." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1218, no. 2 (1994): 129–35. http://dx.doi.org/10.1016/0167-4781(94)90001-9.

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Cook, William J., Nicholas Galakatos, William C. Boyar, Richard L. Walter, and Steven E. Ealick. "Structure of human desArg-C5a." Acta Crystallographica Section D Biological Crystallography 66, no. 2 (2010): 190–97. http://dx.doi.org/10.1107/s0907444909049051.

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The anaphylatoxin C5a is derived from the complement component C5 during activation of the complement cascade. It is an important component in the pathogenesis of a number of inflammatory diseases. NMR structures of human and porcine C5a have been reported; these revealed a four-helix bundle stabilized by three disulfide bonds. The crystal structure of human desArg-C5a has now been determined in two crystal forms. Surprisingly, the protein crystallizes as a dimer and each monomer in the dimer has a three-helix core instead of the four-helix bundle noted in the NMR structure determinations. Furthermore, the N-terminal helices of the two monomers occupy different positions relative to the three-helix core and are completely different from the NMR structures. The physiological significance of these structural differences is unknown.

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Shibasaki, Yoshikazu, Hiroshi Sakura, Fumimaro Takaku, and Masato Kasuga. "Insulin enhancer binding protein has helix-loop-helix structure." Biochemical and Biophysical Research Communications 170, no. 1 (1990): 314–21. http://dx.doi.org/10.1016/0006-291x(90)91276-x.

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Wang, Ting, Chu Wang, Size Zheng, et al. "Insight into the Mechanism of Internalization of the Cell-Penetrating Carrier Peptide Pep-1 by Conformational Analysis." Journal of Biomedical Nanotechnology 16, no. 7 (2020): 1135–43. http://dx.doi.org/10.1166/jbn.2020.2950.

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Different secondary structures of the pep-1 protein were blamed for transmembrane internalization process of drugs and drug deliveries. But which structure will be important for transmembrane delivery was still not clear. In this study, interactions between pep-1 and cell membranes were studied. Pep-1 in the buffer (Pep-1) and pep-1 on graphene (PDS/G) or they on graphene oxide (PDS/GO) were composed as the transmembrane delivery system to study the different secondary structure of pep-1 that influence for their transmembrane delivery. The curves of chirascan circular dichroism (CD) and all-atom discontinuous molecular dynamics (DMD) simulations illuminate that, in a buffer environment, most pep-1 formed 3–10 helix structures. Meanwhile, when Pep-1 composed graphene slice and formed PDS/G, 3–10 helix and alpha-helix structures can be found in small quantities. When they on graphene oxide and formed PDS/GO, coil or type II beta-turn structure can be found from most of the pep-1 and 3–10 helix structure disappeared. By using sum-frequency generation (SFG) vibrational spectroscopy, we found that pep-1 with 3–10 helix structures in buffer solutions damaged the lipid bilayer violently. PDS/G with less 3–10 helix structures will change the orientation of lipid bilayer effectively but slightly. Pep-1 with coil or type II Beta-turn in PDS/GO cannot influence the structure of lipid bilayers. Hemolysis experiments also proved that when pep-1 composed as PDS/G, they will change the orientation of the plasma membrane of red blood cells effectively but slightly. When they attach on the GO and formed PDS/GO, the plasma membrane of red blood cells cannot be influenced. In conclusion, 3–10 helix structures will be positively correlated with disturbance of membranes. These results will be effectively guided the clinic application of pep-1 as a transporter of the drug delivery system.

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Meguro, T., and I. Yamato. "Prediction of helix-turn-helix structure by Monte Carlo simulation." Seibutsu Butsuri 39, supplement (1999): S130. http://dx.doi.org/10.2142/biophys.39.s130_1.

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Purushothaman, N., and S. K. Ghosh. "Performance improvement of helix TWT using metamaterial helix-support structure." Journal of Electromagnetic Waves and Applications 27, no. 7 (2013): 890–900. http://dx.doi.org/10.1080/09205071.2013.792748.

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Okuyama, K. "Structure of collagen-helix motif." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (2008): C353. http://dx.doi.org/10.1107/s0108767308088727.

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Lee, Jung C., and Robin R. Gutell. "Helix Capping in RNA Structure." PLoS ONE 9, no. 4 (2014): e93664. http://dx.doi.org/10.1371/journal.pone.0093664.

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Brodsky, Barbara, and John A. M. Ramshaw. "The collagen triple-helix structure." Matrix Biology 15, no. 8-9 (1997): 545–54. http://dx.doi.org/10.1016/s0945-053x(97)90030-5.

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Dissertations / Theses on the topic "Helix structure"

1

Olofsson, Susanne. "Design, synthesis, structure, and dynamics of a polypeptide with supersecondary structure a helix-loop-helix dimer /." Göteborg : Dept. of Organic Chemistry, University of Göteborg, 1994. http://books.google.com/books?id=6AdrAAAAMAAJ.

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McGee, Christopher J. "DNA helix imperfections Structure and flexibility /." Related electronic resource: Current Research at SU : database of SU dissertations, recent titles available full text, 2006. http://proquest.umi.com/login?COPT=REJTPTU0NWQmSU5UPTAmVkVSPTI=&clientId=3739.

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Freeman, Jon Oliver. "Structure and behavior of four-helix bundle cavitein systems." Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/35327.

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This thesis will investigate the sequence to structure relationship of protein folding through the use of template assembled synthetic proteins (TASPs). A cavitand template will be used to bring together four de novo designed peptides to form a four-helix bundled TASP, referred to as a cavitein. The first chapter will detail the rationale behind de novo protein design and use of TASPs to study protein folding. Chapter 1 will also review past and current work relating to the design and structural characterization of synthetic de novo proteins. Chapter 2 will investigate the context dependency of leucine residues within the hydrophobic core of a cavitein. Single leu to ala substitutions resulted in similar destabilization of the cavitein. However, replacing the middle leucine compromised the structure and stability of the cavitein. It was concluded that the middle leucine acted as a linchpin within the peptide sequence. Chapter 3 will examine the first reported crystallization of a TASP. The crystal structure is revealed as a dimer. The cavitein (Q4) was thought to be monomeric. The chapter will compare the solution structures of both the parent and Q4 cavitein. It was found that both parent and Q4 have a weak dimer association at relatively high concentrations. Chapter 4 will discuss glutamine variants used to probe the tolerance of dimer crystallization with respect to sequence variation. The chapter uncovers a key lattice contact for cavitein dimer lattice nucleation and stabilization. Furthermore, in an attempt to control the oligomeric state of caviteins, Chapter 4 will also discuss histidine metal binding caviteins and disulfide caviteins. A cavitein designed to favor a dimer via histidine metal binding was synthesized and crystallized revealing a potential metal binding center. Caviteins designed to favor a monomer conformation were also designed involving either histidine metal binding or disulfide bridges. Both methods proved successful in their monomeric design as shown by solution characterization. Chapter 5 will conclude and summarize the work throughout this thesis. The chapter will also suggest future projects expanding on studies within this thesis as well as suggest other projects pertaining to cavitein research.

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Therien, James Patrick Daniel. "The Role of Transmembrane Domain Helix-Helix Interactions in the Function of Pentameric Ligand-Gated Ion Channels." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/35643.

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The pentameric ligand gated ion channel super family plays a central role in fast synaptic communication between neurons and at the neuromuscular junction. Extensive studies on the prototypic pLGIC, the Torpedo nicotinic acetylcholine receptor (nAChR) have revealed an exquisite lipid sensitivity, with the nAChR adopting a novel uncoupled conformation in membranes lacking activating anionic and neutral lipids. The lipid-exposed transmembrane alpha-helix, M4, in each homologous subunit likely acts as a lipid sensor. One model proposes that activating lipids promote M4 “binding” to the adjacent alpha-helices, M1 and M3, to enhance interactions between the M4 C-terminus and the Cys-loop of the agonist-binding domain, with such interactions promoting coupling between the agonist site and channel gate. The first part of my thesis indirectly tests this hypothesis by exploring the effects of membrane hydrophobic thickness on nAChR function. Specifically, I tested the hypothesis that thicker membranes, which should promote alignment of M4 parallel to M1/M3 and thus helix-helix interactions, favor a coupled conformation. Although I found that the nAChR is uncoupled in all membranes tested, regardless of hydrophobic thickness, thicker membranes promote transitions from uncoupled to ultimately the desensitized state over the minutes to hours time frame. In contrast to anionic lipids, which influence function primarily via a conformational selection mechanism, membrane hydrophobic thickness influences function via a kinetic mechanism - thick membranes lower the activation energy between uncoupled and coupled conformations to promote conformational transitions. In the second part of my thesis, I used the two prokaryotic homologs, GLIC and ELIC, to explore how amino acid interactions at the interface between M4 and M1/M3 influence channel activity. Alanine scanning mutagenesis of this interface shows that disruption of almost any interaction in GLIC leads to a loss of folding and/or function, while analogous mutations in ELIC typically lead to no change or produce gains in function. Sequence comparisons with other members of the pLGIC superfamily suggest that the transmembrane domains of GLIC and ELIC represent two distinct archetypes. Each archetype may strike a different balance between the need for strong M4 binding to M1/M3 to promote folding and pentamer assembly, and the need for weaker interactions that allow for greater conformational flexibility during function.

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Wilman, Henry R. "Computational studies of protein helix kinks." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:21225f0e-efed-49c6-af27-5d3fe78fa731.

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Kinks are functionally important structural features found in the alpha-helices of many proteins, particularly membrane proteins. Structurally, they are points at which a helix abruptly changes direction. Previous kink definition and identification methods often disagree with one another. Here I describe three novel methods to characterise kinks, which improve on existing approaches. First, Kink Finder, a computational method that consistently locates kinks and estimates the error in the kink angle. Second the B statistic, a statistically robust method for identifying kinks. Third, Alpha Helices Assessed by Humans, a crowdsourcing approach that provided a gold-standard data set on which to train and compare existing kink identification methods. In this thesis, I show that kinks are a feature of long -helices in both soluble and membrane proteins, rather than just transmembrane -helices. Characteristics of kinks in the two types of proteins are similar, with Proline being the dominant feature in both types of protein. In soluble proteins, kinked helices also have a clear structural preference in that they typically point into the solvent. I also explored the conservation of kinks in homologous proteins. I found examples of conserved and non-conserved kinks in both the helix pairs and the helix families. Helix pairs with non-conserved kinks generally have less similar sequences than helix pairs with conserved kinks. I identified helix families that show highly conserved kinks, and families that contain non-conserved kinks, suggesting that some kinks may be flexible points in protein structures.

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Geraghty, Robert. "Structure-function studies of analogues of FMRFamide in Helix aspersa." Thesis, Queen's University Belfast, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317504.

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Arwel, Lewis. "Peptide secondary structure mimetics : the alpha-helix and beta-turn." Thesis, University of St Andrews, 1998. http://hdl.handle.net/10023/15433.

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This thesis describes research undertaken in peptidomimetic chemistry, concerned with stabilisation of peptide secondary structure. The first section describes the successful synthesis of two triazepinediones for potential application as cis prolyl mimetics and/or β-turn mimetics. The first triazepinedione 64, carrying an N-phenyl substituent, was subjected to reductive conditions in an unsuccessful attempt to generate a cis prolyl peptide. The second triazepinedione 72 was designed as a Gly-cw Pro-Phe peptidomimetic. Its synthesis proceeded in 8 steps, via a chiral a-hydrazino acid. Triazepinedione 72 was extended from both the N and C termini, demonstrating that it could be incorporated into a peptide. The second section describes the design and attempted synthesis of an N-terminal template for stabilisation of a-helical structure in an attached peptide. Preliminary efforts to produce a Pro-Pro-Ala macrocycle 91 and a Pro-Pro-Pro ether macrocycle 98 were unsuccessful. Attempts to synthesise a Pro-Pro-Pro thioether macrocycle 112 resulted in formation of a cyclic dimer 122. The formation of this dimer was proposed to be due to excessive steric hindrance in the transition state to cyclisation. Attempts to stabilise the desired folded transition state by α-methylation of proline residues or hydrogen bonding did not allow synthesis of any of the desired monomeric cyclic material. A monomeric cyclic compound was finally obtained by increasing the flexibility of the linear precursor, affording a Pro-(2R)-Ala-Pro thioether macrocycle 151. X-Ray crystallography and 2D NMR studies established that this macrocycle lacked the required arrangement of carbonyl groups conducive to initiation of an α-helix. Further NMR studies of macrocycle-peptide conjugates suggested that the macrocycle exerted a conformational influence only over the first residue of the attached peptide. The carbonyl groups of the macrocycle were found to adopt a significant degree of α-helical geometry upon attachment of a C-terminal cationic trialkylammonium group.

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Tranter, Dale Brendan. "Role of α-helix packing in structure, stability and function in opsins". Thesis, University of Essex, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.537949.

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Martyna, Agnieszka. "Structure and function of the M2 amphipathic helix in influenza virus membrane scission." Thesis, University of Kent, 2016. https://kar.kent.ac.uk/56663/.

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Influenza A is an enveloped, negative sense RNA virus which causes annual epidemics and major pandemics. Assembly and budding of new viral particles is a complex and multistep process, of which many aspects remain unclear despite many years of research. The Influenza virus M2 protein is a homotetrameric transmembrane protein, containing three domains: ecto domain, transmembrane domain and cytoplasmic tail (CT). In the final stage of budding it has been shown that M2 mediates membrane scission through an amphipathic helix (AH), which is formed by the first 17 amino acids of the protein's CT, however the exact mechanism by which membrane scission is triggered was not known. Using a collection of biochemical and biophysical techniques we have investigated the structure of the M2 AH and assessed its function in viral assembly and budding. We have shown that the M2 AH is formed upon lipid binding and remains unstructured in solution. It preferentially binds to membranes with high positive membrane curvature, which is detected by sensing the associated lipid packing defects. There are many cationic residues in the polar face of the M2 AH which could interact with anionic lipid headgroups, however charged interactions do not significantly affect the M2 AH interactions with the membranes. When inserted into the membrane the M2 AH increases lipid ordering. The M2 AH also induces positive membrane curvature and mediates membrane scission, which is the last step of Influenza virus budding, allowing for release of newly formed virions in to the environment. Membrane scission is a crucial step not only in viral budding but also in many biological processes, such as endocytosis. Many proteins have been associated with cellular membrane scission; however, the underlying molecular details are still not known. We have shown that AHs in some cellular peptides, such as Arf 1, Endophillin A3 and Epsin 1, which mediate membrane scission in biological processes, appear to work in a similar manner to the M2 AH. They represent a new protein motif that is capable of sensing curvature, inducing curvature and altering membrane fluidity, thereby mediating membrane scission and therefore belong to a novel group of AHs.

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Graether, Steffen Peter. "The structure of type III and spruce budworm antifreeze proteins, globular versus beta-helix folds." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0021/NQ54414.pdf.

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Books on the topic "Helix structure"

1

Littlewood, Trevor D. Helix-loop-helix transcription factors. 3rd ed. Oxford University Press, 1998.

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Phelan, Glen. Double helix: The quest to uncover the structure of DNA. National Geographic, 2006.

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Sarma, Ramaswamy H. DNA double helix & the chemistry of cancer. Adenine Press, 1988.

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D, Watson James. The double helix: A personal account of the discovery of the structure of DNA. Scribner, 1998.

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Sylvia, Nasar, ed. The double helix: A personal account of the discovery of the structure of DNA. a Touchstone book, published by Simon & Schuster, 2001.

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Olby, Robert C. The path to the double helix: The discovery of DNA. Dover Publications, 1994.

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Ivano, Bertini, ed. Iron-sulfur proteins perovskites. Springer, 1995.

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Ivano, Bertini, ed. Bioinorganic chemistry. Springer-Verlag, 1995.

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9

Cotti, Giordano, Boris A. Dubrovin, and Davide Guzzetti. Helix Structures in Quantum Cohomology of Fano Varieties. Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-69067-9.

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Symposium, International Astronomical Union. New eyes to see inside the sun and stars: Pushing the limits of helio- and asteroseismology with new observations from the ground and from space : proceedings of the 185th Symposium of the International Astronomical Union, held in Kyoto, Japan, August 18-22, 1997. Kluwer, 1998.

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Book chapters on the topic "Helix structure"

1

Thévenin, Damien, and Tzvetana Lazarova. "Identifying and Measuring Transmembrane Helix–Helix Interactions by FRET." In Membrane Protein Structure and Dynamics. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-023-6_6.

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Porumb, Horea. "Triple-Helix Structure. The Triple-Helix-Forming Oligonucleotide." In Triple Helix Forming Oligonucleotides. Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-5177-5_2.

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Mirkin, Sergei M. "Structure and Biology of H DNA." In Triple Helix Forming Oligonucleotides. Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-5177-5_15.

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Mant, Colin T., Nian E. Zhou, and Robert S. Hodges. "The Role of Amphipathic Helices in Stabilizing Peptide and Protein Structure." In The Amphipathic Helix. CRC Press, 2024. https://doi.org/10.1201/9781003574378-5.

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Gan, Runyuan. "The Structure, Function and Evolution of the State and the Social System." In Helix Network Theory. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-8803-5_8.

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Gan, Runyuan. "The Meso-Level of the Economic System: The Dynamic Structure and Evolution of the Sector." In Helix Network Theory. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-8803-5_5.

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Gan, Runyuan. "The Micro-level of the Economic System: The Dynamic Structure and Evolution of the Firm." In Helix Network Theory. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-8803-5_4.

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Gan, Runyuan. "The Macro-level of the Economic System: The Dynamic Structure and Evolution of the National Economy." In Helix Network Theory. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-8803-5_7.

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Goormaghtigh, Erick, Véronique Cabiaux, and Jean-Marie Ruysschaert. "Polarized Attenuated Total Reflection Infrared Spectroscopy as a Tool to Investigate the Structure and Orientation of Amphipathic Peptides in a Lipid Bilayer." In The Amphipathic Helix. CRC Press, 2024. https://doi.org/10.1201/9781003574378-7.

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Tinoco, Ignacio, Phillip Cruz, Peter Davis, et al. "Z-RNA: A Left-Handed Double Helix." In Structure and Dynamics of RNA. Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5173-3_5.

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Conference papers on the topic "Helix structure"

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Pengchao Huang, Peizhang Zhou, Hui Xu, and Ying Zhu. "Simulation of loading helix structure." In 8th International Vacuum Electron Sources Conference and Nanocarbon (2010 IVESC). IEEE, 2010. http://dx.doi.org/10.1109/ivesc.2010.5644215.

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Ajith, Kumar M. M., and Sheel Aditya. "Tape-Helix Analysis of Shielded Planar Helix Slow-Wave Structure." In 2019 International Vacuum Electronics Conference (IVEC). IEEE, 2019. http://dx.doi.org/10.1109/ivec.2019.8744797.

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Shah, Waqar A., Sultan Shoaib, Qamarul Islam, and Muhammad Amin. "Wide band side fed bifilar helix antenna caged in passive quadrifilar helix structure." In 2010 IEEE Radio and Wireless Symposium (RWS). IEEE, 2010. http://dx.doi.org/10.1109/rws.2010.5434217.

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Aditya, S., M. Tan, R. Nair, C. Ang, C. Ang, and Q. Pham. "Confined Planar Helix: A Novel Waveguide Structure." In 2006 IEEE MTT-S International Microwave Symposium Digest. IEEE, 2006. http://dx.doi.org/10.1109/mwsym.2006.249467.

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Zhou, Heng, Tingyong Jiang, Zhen Liu, et al. "A double helix coaxial pulse compression structure." In 2021 IEEE International Workshop on Electromagnetics: Applications and Student Innovation Competition (iWEM). IEEE, 2021. http://dx.doi.org/10.1109/iwem53379.2021.9790530.

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Chakraborty, S., M. K. Alaria, and S. K. Ghosh. "Design of helix slow wave structure for X band helix TWT using multi-dispersion." In 2020 URSI Regional Conference on Radio Science ( URSI-RCRS). IEEE, 2020. http://dx.doi.org/10.23919/ursircrs49211.2020.9113576.

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HE, JING, and YONGGANG LU. "USING THE LENGTH CONSTRAINTS OF HELIX TO EVALUATE PROTEIN SECONDARY STRUCTURE PREDICTION FOR HELIX." In Proceedings of the International Conference. WORLD SCIENTIFIC, 2005. http://dx.doi.org/10.1142/9789812702098_0033.

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Gheorghita, Maria, and Stela Pripa. "The role of the triple helix in designing a viable regional innovation system." In 4th Economic International Conference "Competitiveness and Sustainable Development". Technical University of Moldova, 2022. http://dx.doi.org/10.52326/csd2022.14.

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This article focuses on triple helix collaboration to support the development of the regional innovation-driven economy - in particular on questions of strategic structures for regional collaboration in the triple helix of government, industry and knowledge institutions. Regional innovation activity is often studied through the prism of regional innovation systems. Strategic collaboration in the triple helix is seen as one of the most viable ways to stimulate regional innovation. This article presents the role of strategic structures in regional triple helix collaboration. with the aim of highlighting how triple helix actors can structure and implement fruitful collaboration to support innovation-led regional development.

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Naidu, Vemula Bhanu, Subrata Kumar Datta, and Lalit Kumar. "Novel Multi helix structure for high frequency application." In 2012 IEEE Thirteenth International Vacuum Electronics Conference (IVEC). IEEE, 2012. http://dx.doi.org/10.1109/ivec.2012.6262234.

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Rao, K. Venkateswara, Talur Chanakya, Vemula Bhanu Naidu, and Subrata Kumar Datta. "Investigation into a triangular-helix slow-wave structure." In 2014 IEEE International Vacuum Electronics Conference (IVEC). IEEE, 2014. http://dx.doi.org/10.1109/ivec.2014.6857605.

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Reports on the topic "Helix structure"

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Scavuzzo, Sebastian, Jonathan Cedeño, and Jaroslava Miksovska. In Silico Calculation of Interhelical Angles in NCS1. Florida International University, 2025. https://doi.org/10.25148/fiuurj.3.1.16.

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Proteins are important macromolecules responsible for a variety of processes in living organisms. One of the most important features of proteins is their ability to respond to environmental stimuli, such as changes in intracellular metal concentration by binding metal ions, which in turns triggers structural changes within the protein that can modify its function or allow the protein to participate in a signaling pathway. One such signaling protein is the so-called neuronal calcium sensor 1 protein or NCS1, which binds Ca2+ along with other abiogenic metals such as Li+, and the metal binding regulates NCS1 interactions with other intracellular partners. NCS1 binds Ca2+ ions through the EF-hands, consisting of a helix-loop-helix motif. The exact nature of the structural changes triggered by Ca2+ binding to the EF-hands in NCS1 is currently unknown. In an attempt to elucidate the nature of these structural changes, we performed a variety of molecular dynamics simulations on NCS1 in the calcium bound, lithium bound, and metal unbound states. We then calculated the angles between helices in EF-hands to determine if these angles change upon metal ion binding. Using the outputs of the molecular dynamics simulations, we developed a python script in house using MDAnalysis and Numpy libraries to select and calculate the angle between each alpha helix pair as a function of simulation time. Based on our calculations, the EF-hand interhelical angles change significantly upon metal binding and are even sensitive to the specific identity of the metal ion. This method of interhelical angle calculation can serve as an important tool for determining the nature of structural changes caused by the binding of ligand molecules to sensor proteins.

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2

Shai, Yechiel, Arthur Aronson, Aviah Zilberstein, and Baruch Sneh. Study of the Basis for Toxicity and Specificity of Bacillus thuringiensis d-Endotoxins. United States Department of Agriculture, 1996. http://dx.doi.org/10.32747/1996.7573995.bard.

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The report contains three parts which summarizes the three years achievements of the three participating research groups; The Weizmann group, Tel-Aviv group and Purdue group. The firs part describes the achievements obtained by Shai's group toward the elucidation of the mechanism of membrane insertion and the structural organization of the pores formed by the Cry3A and Cry1Ac B. thuringiensis d-endotoxins. For that purpose Shai's group synthesized, fluorescently labeled and structurally and functionally characterized peptides corresponding to the seven helices that compose the pore-forming domain of Cry3A toxin, including mutants peptides and the hairpin a4G-a5 of both Cry3A and Cry 1Ac toxins composed of a4, a5 and the loop connecting a4-a5. Among the synthesized peptides were three mutated a4 helices based on site directed mutagenesis done at Aronson's group that decreased or increased Cry 1Ac toxicity. The results of these studies are consistent with a situation in which only helices a4 anda5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like ribs of an umbrella (the "umbrella model"). In order to test this model Shai's group synthesized the helical hairpin a4<-->a5 of both Cry3A and Cry 1 Ac toxins, as well. Initial functional and structural studies showed direct correlation between the properties of the mutated helices and the mutated Cry1Ac. Based on Shai's findings that a4 is the second helix besides a5 that insert into the membrane, Aronson and colleagues performed extensive mutation on this helix in the CrylAc toxin, as well as in the loop connecting helices 4 and 5, and helix 3 (part two of the report). In addition, Aronson performed studies on the effect of mutations or type of insect which influence the oligomerization either the Cry 1Ab or Cry 1Ac toxins with vesicles prepared from BBMV. In the third part of the report Zilberstein's and Sneh's groups describe their studies on the three domains of Cry 1C, Cry 1E and crylAc and their interaction with the epithelial membrane of the larval midgut. In these studies they cloned all three domains and combinations of two domains, as well as cloning of the pore forming domain alone and studying its interaction with BBMV. In addition they investigated binding of Cry1E toxin and Cry1E domains to BBMV prepared from resistant (R) or sensitive larvae. Finally they initiated expression of the loop a4G<-->a5 Cry3A in E. coli to be compared with the synthetic one done by Shai's group as a basis to develop a system to express all possible pairs for structural and functional studies by Shai's group (together with Y. Shai).

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Storrs, R. W. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/6707762.

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4

Storrs, Richard Wood. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/10131755.

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