Journal articles: '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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7

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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8

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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9

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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10

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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11

Ruszkowska, Agnieszka, Milosz Ruszkowski, Jacob P. Hulewicz, Zbigniew Dauter, and Jessica A. Brown. "Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples." Nucleic Acids Research 48, no. 6 (2020): 3304–14. http://dx.doi.org/10.1093/nar/gkz1222.

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Abstract Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A′-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3′-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.

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12

Carter, Joshua. "Starting and Growing a Gene-to-Structure Services Company." Structural Dynamics 12, no. 2_Supplement (2025): A329. https://doi.org/10.1063/4.0000635.

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Josh Carter is the CEO and owner of Helix BioStructures, LLC, a gene-to-structure services company specializing in protein production, biophysical characterization, X-ray crystallography, and cryo-EM. After obtaining his BSc in Biochemistry (2011) from Indiana University (Dann Lab), Josh joined Shamrock Structures, a structural biology CRO in Woodridge, IL. During his tenure at Shamrock, Josh furthered his passion for structural biology and gained new expertise and knowledge of business and the pharmaceutical industry. In 2017, Josh started Helix with a single service, X-ray data collection. Six years later, Josh has helped Helix grow to over 20 scientists working in a 6,000 sq. ft laboratory and providing high-quality services to academic and industrial clients. His passion for protein structures has grown substantially and is now passed on to Helix employees and customers.

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13

Melnyk, Viginia. "Soft Knitted Tensile Membrane Tensegrity Helix-Tower." Enquiry The ARCC Journal for Architectural Research 20, no. 2 (2023): 60–68. http://dx.doi.org/10.17831/enqarcc.v20i2.1155.

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This paper explores project-based research approach for using knitted textiles as a participating element in a tensegrity structural system. The design of the tensegrity Helix-Tower takes advantage of the emergent elastic properties of knit material and the self-stress, self-stabilizing characteristics of tensegrity structures. The paper outlines the workflow for working with knit materials, including the feedback loop between small studies, digital models, and simulations, and from small to large prototypes. The resulting prototype is a 2.74-meter (9-foot) helix structured tensegrity tower, which is lightweight, deployable, and at a small architectural scale. The assembly process for the final construction is simple and requires no tools. The research is novel in its exploration of using knit membranes in tensegrity structures, resulting in a structure that is ultimately more flexible and responsive to movement than traditional tensegrity structures. The design also provides more interactivity with human bodies and the environment. The paper examines the benefits of knitted membrane, including their heterogeneity and uneven stretching. Which provides softness, flexibility, and more movement to the structure. However, questions remain regarding the potential for other environmental factors such as wind or water. Future work includes exploring the potential and problems of knitted compared to other materials used in tensegrity structures and examining the incorporation of the design into real architectural elements.

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14

Rivas, Elena. "RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure." PLOS Computational Biology 19, no. 7 (2023): e1011262. http://dx.doi.org/10.1371/journal.pcbi.1011262.

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Many biologically important RNAs fold into specific 3D structures conserved through evolution. Knowing when an RNA sequence includes a conserved RNA structure that could lead to new biology is not trivial and depends on clues left behind by conservation in the form of covariation and variation. For that purpose, the R-scape statistical test was created to identify from alignments of RNA sequences, the base pairs that significantly covary above phylogenetic expectation. R-scape treats base pairs as independent units. However, RNA base pairs do not occur in isolation. The Watson-Crick (WC) base pairs stack together forming helices that constitute the scaffold that facilitates the formation of the non-WC base pairs, and ultimately the complete 3D structure. The helix-forming WC base pairs carry most of the covariation signal in an RNA structure. Here, I introduce a new measure of statistically significant covariation at helix-level by aggregation of the covariation significance and covariation power calculated at base-pair-level resolution. Performance benchmarks show that helix-level aggregated covariation increases sensitivity in the detection of evolutionarily conserved RNA structure without sacrificing specificity. This additional helix-level sensitivity reveals an artifact that results from using covariation to build an alignment for a hypothetical structure and then testing the alignment for whether its covariation significantly supports the structure. Helix-level reanalysis of the evolutionary evidence for a selection of long non-coding RNAs (lncRNAs) reinforces the evidence against these lncRNAs having a conserved secondary structure.

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15

Sawyer, L., L. A. Fothergill-Gilmore, and G. A. Russell. "The predicted secondary structure of enolase." Biochemical Journal 236, no. 1 (1986): 127–30. http://dx.doi.org/10.1042/bj2360127.

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The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turn for both chicken skeletal-muscle and yeast enolase sequences. The predicted secondary-structure content of the chicken enzyme is 27% alpha-helix and less than 10% beta-sheet, whereas in the yeast enolase a similar helix content but virtually no sheet are predicted. These results are in fair agreement with published experimental estimates of the amount of secondary structure in the yeast enzyme. The enzyme appears to be formed from three domains.

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16

Kaiden, Koichi, Tomoko Matsui та Shigeyuki Tanaka. "A Study of the Amide III Band by FT-IR Spectrometry of the Secondary Structure of Albumin, Myoglobin, and γ-Globulin". Applied Spectroscopy 41, № 2 (1987): 180–84. http://dx.doi.org/10.1366/000370287774986714.

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FT-IR spectrometry was applied to the identification of the secondary structure species of a living protein. The spectra of native myoglobin and albumin were obtained with methods using either KBr pellet or film formed on a KBr window from an aqueous solution. Pellet preparation of myoglobin and albumin caused the structure to change from α-helix to β-structure. The conformational changes that arise from heat denaturation of myoglobin, albumin, and γ-globulin were observed by the changes in the amide I, II, and III bands. The bands of the 1300, 1260, and 1235 cm−1 regions were respectively assigned to α-helix, disordered, and β-sheet structures. These band positions were substantiated by the spectra of β-lactoglobulin and α-casein. α-Helix structure probably changes to β-structure in the presence of alkali halide, and changes to disordered structure with heat denaturation in phosphate buffer solution. The secondary structure of a protein is further identified by use of the information obtained from the amide I, II, and III bands; the amide III band is especially important. Furthermore, it may be possible to characterize the species of secondary structures of proteins adsorbed on material surfaces.

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17

Zhu, Qi, Lunyu Ma, and Suresh K. Sitaraman. "Development of G-Helix Structure as Off-Chip Interconnect." Journal of Electronic Packaging 126, no. 2 (2004): 237–46. http://dx.doi.org/10.1115/1.1756148.

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Microsystem packages continue to demand lower cost, higher reliability, better performance and smaller size. Compliant wafer-level interconnects show great potential for next-generation packaging. G-Helix, an electroplated compliant wafer-level chip-to-substrate interconnect can facilitate wafer-level probing as well as wafer-level packaging without the need for an underfill. The fabrication of the G-Helix interconnect is similar to conventional IC fabrication process and is based on electroplating and photolithography. G-Helix interconnect has good mechanical compliance in the three orthogonal directions and can accommodate the differential displacement induced by the coefficient of thermal expansion (CTE) mismatch between the silicon die and the organic substrate. In this paper, we report the wafer-level fabrication of an area-arrayed G-Helix interconnects. The geometry effect on the mechanical compliance and electrical parasitics of G-Helix interconnects have been studied. Thinner and narrower arcuate beams with larger radius and taller post are found to have better mechanical compliance. However, it is also found that structures with excellent mechanical compliance may not have good electrical performance. Therefore, a trade off is needed. Using response surface methodology (RSM), an optimization has been done. Furthermore, reliability of the optimized G-helix interconnects in a silicon-on-organic substrate assembly has been assessed, which includes the package weight and thermo-mechanical analysis. The pitch size effect on the electrical and mechanical performance of G-Helix interconnects has also been studied.

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18

Tumanyan, V. G., A. A. Anashkina, I. V. Filatov, K. V. Smirnov, I. Yu Torshin, and N. G. Esipova. "Alanine: from the usual to the unexpected." Биофизика 68, no. 2 (2023): 213–17. http://dx.doi.org/10.31857/s0006302923020011.

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Data from the experiments provides a possibility to talk about anomalously large contribution of alanine to the stability of an alpha-helix and other protein conformations. Independent data (and also experimental ones) suggest that alanine plays an especially big role in stabilization of the alpha-helix. This can be seen through the positive contribution of alanine both to the entropy of the system and to the enthalpy. The high contribution of alanine to the enthalpy of formation of the alpha helix contradicts the generally accepted view that the entropy should decrease during the formation of regular structures in proteins. Among three types of helices in proteins, alanine stabilizes two secondary structures: the alpha helix and the left helix of polyproline II, and in the case of fibrillar proteins, alanine also stabilizes the beta sheet. The stabilizing effect of alanine on the alpha helix structure extends to both natively unfolded proteins and alpha helix-support conjugates. Thus, it is no exaggeration to say that formation of secondary structure relies on alanine. The revealed contradictions are of paradoxical nature and yet there is no interpretation of the above-mentioned findings (first of all, substantiation of the contribution of alanine to the enthalpy of fusion in terms of fundamental physics) so far to resolve them. Meanwhile, the data and comments presented in this work hold out the promise of progress in resolving the revealed contradictions.

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Doig, Andrew J., Charles D. Andrew, Duncan A. E. Cochran та ін. "Structure, stability and folding of the α-helix". Biochemical Society Symposia 68 (1 серпня 2001): 95–110. http://dx.doi.org/10.1042/bss0680095.

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Pauling first described the α-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 310-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or αL C-cap motif. The kinetics of α-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

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Matveenko, L. I., and A. I. Witzel. "The Jets of Quasars 3C 345 and 1803+784." Symposium - International Astronomical Union 194 (1999): 229–34. http://dx.doi.org/10.1017/s0074180900162047.

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We have studied the structures of AGN objects 3C345 and 1803+784. The objects have one sided jets with conic helix structure, determining step and diameter of the helix. The jets are surrounded by cocoon - thermal plasma, the transparency of which determines low frequency variability and absorption of the core emission.

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Lee, A. G. "Ca2+-ATPase structure in the E1 and E2 conformations: mechanism, helix–helix and helix–lipid interactions." Biochimica et Biophysica Acta (BBA) - Biomembranes 1565, no. 2 (2002): 246–66. http://dx.doi.org/10.1016/s0005-2736(02)00573-4.

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22

Buchko, Garry W., Adelinda Yee, Anthony Semesi, Peter J. Myler, Cheryl H. Arrowsmith, and Raymond Hui. "Solution-state NMR structure of the putative morphogene protein BolA (PFE0790c) fromPlasmodium falciparum." Acta Crystallographica Section F Structural Biology Communications 71, no. 5 (2015): 514–21. http://dx.doi.org/10.1107/s2053230x1402799x.

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Protozoa of the genusPlasmodiumare responsible for malaria, which is perhaps the most important parasitic disease to infect mankind. The emergence ofPlasmodiumstrains resistant to current therapeutics and prophylactics makes the development of new treatment strategies urgent. Among the potential targets for new antimalarial drugs is the BolA-like protein PFE0790c fromPlasmodium falciparum(Pf-BolA). While the function of BolA is unknown, it has been linked to cell morphology by regulating transcription in response to stress. Using an NMR-based method, an ensemble of 20 structures ofPf-BolA was determined and deposited in the PDB (PDB entry 2kdn). The overall topology of thePf-BolA structure, α1–β1–β2–η1–α2/η2–β3–α3, with the β-strands forming a mixed β-sheet, is similar to the fold observed in other BolA structures. A helix–turn–helix motif similar to the class II KH fold associated with nucleic acid-binding proteins is present, but contains an FXGXXXL signature sequence that differs from the GXXG signature sequence present in class II KH folds, suggesting that the BolA family of proteins may use a novel protein–nucleic acid interface. A well conserved arginine residue, Arg50, hypothesized to play a role in governing the formation of the C-terminal α-helix in the BolA family of proteins, is too distant to form polar contacts with any side chains in this α-helix inPf-BolA, suggesting that this conserved arginine may only serve a role in guiding the orientation of this C-terminal helix in some BolA proteins. A survey of BolA structures suggests that the C-terminal helix may not have a functional role and that the third helix (α2/η2) has a `kink' that appears to be conserved among the BolA protein structures. Circular dichroism spectroscopy shows thatPf-BolA is fairly robust, partially unfolding when heated to 353 K and refolding upon cooling to 298 K.

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Gangwar, Shanti P., Sita R. Meena, and Ajay K. Saxena. "Comparison of four different crystal forms of theMycobacterium tuberculosisESX-1 secreted protein regulator EspR." Acta Crystallographica Section F Structural Biology Communications 70, no. 4 (2014): 433–37. http://dx.doi.org/10.1107/s2053230x14004166.

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TheMycobacterium tuberculosisESX-1 secreted protein regulator (EspR, Rv3849) is the key protein that delivers bacterial proteins into the host cell during mycobacterial infection. EspR binds directly to theespACDoperon and is involved in transcriptional activation. In the current study,M. tuberculosisEspR has been crystallized and its X-ray structure has been determined at 3.3 Å resolution in aP3221 crystal form. EspR forms a physiological dimer in the crystal. Each EspR monomer contains an N-terminal helix–turn–helix DNA-binding domain and a C-terminal dimerization domain. The EspR structure in theP3221 crystal form was compared with previously determined EspR structures inP32,P21andP212121crystal forms. Structural comparison analysis indicated that the N-terminal helix–turn–helix domain of EspR acquires a rigid structure in the four crystal forms. However, significant structural differences were observed in the C-terminal domain of EspR in theP21crystal form when compared with theP3221 andP32crystal forms. The interaction, stabilization energy and buried surface area analysis of EspR in the four different crystal forms have provided information about the physiological dimer interface of EspR.

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Donnelly, Dan, and John B. C. Findlay. "Seven-helix receptors: structure and modelling." Current Opinion in Structural Biology 4, no. 4 (1994): 582–89. http://dx.doi.org/10.1016/s0959-440x(94)90221-6.

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Heinemann, Udo, Claudia Alings, and Michael Hahn. "Crystallographic studies of DNA helix structure." Biophysical Chemistry 50, no. 1-2 (1994): 157–67. http://dx.doi.org/10.1016/0301-4622(94)85028-3.

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Ruan, J. F., J. Yang, G. Q. Lv, G. S. Deng, and L. Liu. "Structure Optimization of Space Helix TWT Based on Thermal Analysis." Applied Mechanics and Materials 130-134 (October 2011): 1753–57. http://dx.doi.org/10.4028/www.scientific.net/amm.130-134.1753.

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The main components of a space helix TWT (traveling wave tube) are electron gun, helix slow-wave system and collector. Thermal issue is of great importance for space helix TWTs. High heat efficiency of cathode is required for electron gun, as well as high heat transmission capacity for slow-wave system and collector. Some structure optimization for the electron gun, slow-wave system and the collector of some type of space helix TWT has been proposed aiming the above purpose. To evaluate the structural optimization means, the related thermal analysis has been carried out using ANSYS software. The simulation results demonstrate that the structure optimization is effective. And the actual effect needs to be further studied.

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CHEN, ZHONG, and YING XU. "STRUCTURE PREDICTION OF HELICAL TRANSMEMBRANE PROTEINS AT TWO LENGTH SCALES." Journal of Bioinformatics and Computational Biology 04, no. 02 (2006): 317–33. http://dx.doi.org/10.1142/s0219720006001965.

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As the first step toward a multi-scale, hierarchical computational approach for membrane protein structure prediction, the packing of transmembrane helices was modeled at the residue and atom levels, respectively. For predictions at the residue level, the helix-helix and helix-membrane interactions were described by a set of knowledge-based energy functions. For predictions at the atom level, CHARMM19 force field was used. To facilitate the system to overcome energy barriers, the Wang–Landau method was employed, where a random walk is performed in the energy space with a uniform probability. Native-like structures were predicted at both levels for two model systems, each of which consists of two transmembrane helices. Interestingly, consistent results were obtained from simulations at the residue and atom levels for the same system, strongly suggesting the feasibility of a hierarchical approach for membrane protein structure predictions.

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De Meutter, Joëlle, and Erik Goormaghtigh. "Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration." European Biophysics Journal 50, no. 3-4 (2021): 613–28. http://dx.doi.org/10.1007/s00249-021-01502-y.

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AbstractFTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.

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Baker, A. T., J. A. M. Ramshaw, D. Chan, W. G. Cole та J. F. Bateman. "Changes in collagen stability and folding in lethal perinatal osteogenesis imperfecta. The effect of α1(I)-chain glycine-to-arginine substitutions". Biochemical Journal 261, № 1 (1989): 253–57. http://dx.doi.org/10.1042/bj2610253.

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The effect of glycine-to-arginine mutations in the alpha 1 (I)-chain on collagen triple-helix structure in lethal perinatal osteogenesis imperfecta was studied by determination of the helix denaturation temperature and by computerized molecular modelling. Arginine substitutions at glycine residues 391 and 667 resulted in similar small decreases in helix stability. Molecular modelling suggested that the glycine-to-arginine-391 mutant resulted in only a relatively small localized disruption to the helix structure. Thus the glycine-to-arginine substitutions may lead to only a small structural abnormality of the collagen helix, and it is most likely that the over-modification of lysine, poor secretion, increased degradation and other functional sequelae result from a kinetic defect in collagen helix formation resulting from the mutation.

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Welch, J. T., W. R. Kearney, and S. J. Franklin. "Lanthanide-binding helix-turn-helix peptides: Solution structure of a designed metallonuclease." Proceedings of the National Academy of Sciences 100, no. 7 (2003): 3725–30. http://dx.doi.org/10.1073/pnas.0536562100.

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Hu, Hai-Yu, Jun-Feng Xiang, Yong Yang, and Chuan-Feng Chen. "A Helix−Turn−Helix Supersecondary Structure Based on Oligo(phenanthroline dicarboxamide)s." Organic Letters 10, no. 1 (2008): 69–72. http://dx.doi.org/10.1021/ol702720q.

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Matsubara, Teruhiko, Mie Iida, Takeshi Tsumuraya, Ikuo Fujii, and Toshinori Sato. "Selection of a Carbohydrate-Binding Domain with a Helix−Loop−Helix Structure†." Biochemistry 47, no. 26 (2008): 6745–51. http://dx.doi.org/10.1021/bi8000837.

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Dolphin, Gunnar T., and Lars Baltzer. "The pH-dependent tertiary structure of a designed helix–loop–helix dimer." Folding and Design 2, no. 5 (1997): 319–30. http://dx.doi.org/10.1016/s1359-0278(97)00043-6.

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Lee, Jinwoo, and Kerney Jebrell Glover. "The transmembrane domain of caveolin-1 exhibits a helix–break–helix structure." Biochimica et Biophysica Acta (BBA) - Biomembranes 1818, no. 5 (2012): 1158–64. http://dx.doi.org/10.1016/j.bbamem.2011.12.033.

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Liu, Fei, Zhe Yu, Beibei Wang, and Bor-Sen Chiou. "Changes in Structures and Properties of Collagen Fibers during Collagen Casing Film Manufacturing." Foods 12, no. 9 (2023): 1847. http://dx.doi.org/10.3390/foods12091847.

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Collagen casing is an edible film, which is widely used in the industrial production of sausages. However, the detailed changes in the collagen fibers, from the raw material to the final collagen film, have rarely been reported. In this research, the changes in the collagen fibers during the manufacturing process, including the fiber arrangement, the triple-helix structure and the thermal stability, were investigated using scanning electron microscopy (SEM), thermogravimetric analysis (TGA), X-ray diffraction (XRD), differential scanning calorimetry (DSC) and Fourier-transform infrared (FTIR) spectroscopy. The relationship between the structure stability and the arrangement of the collagen fibers was also discussed. According to the SEM, XRD, TGA, DSC and FTIR results, the collagen fibers were depolymerized during the acid swelling and became uniformly aligned after the homogenization process. Degassing had no obvious effect on the triple-helix structure. Alkaline neutralization with ammonia destroyed the triple-helix structure, which could be partly reversed through the washing and soaking processes. During the final drying step, the depolymerized triple helix of the collagen fibers recombined to form new structures that showed decreased thermal stability. This study expands our knowledge about the behavior of collagen fibers during the industrial process of producing collagen biobased casings.

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Presnell, S. R., and F. E. Cohen. "Topological distribution of four-alpha-helix bundles." Proceedings of the National Academy of Sciences 86, no. 17 (1989): 6592–96. http://dx.doi.org/10.1073/pnas.86.17.6592.

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The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts.

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Montemayor, Eric J., Johanna M. Virta, Lauren D. Hagler, Steven C. Zimmerman, and Samuel E. Butcher. "Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking." Acta Crystallographica Section F Structural Biology Communications 75, no. 10 (2019): 652–56. http://dx.doi.org/10.1107/s2053230x19012172.

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The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U–U mismatch sandwiched between Watson–Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U–C/C–U) mismatches flanked by U–G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tandem pyrimidine mismatches are unusual and display sheared, cross-strand stacking geometries that locally constrict the helical width, a type of stacking previously associated with purines in internal loops. Thus, pyrimidine-rich regions of RNA have a high degree of structural diversity.

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Guo, Peng-Chao, Jin-Di Ma, Yong-Liang Jiang, et al. "Structure of Yeast Sulfhydryl Oxidase Erv1 Reveals Electron Transfer of the Disulfide Relay System in the Mitochondrial Intermembrane Space." Journal of Biological Chemistry 287, no. 42 (2012): 34961–69. http://dx.doi.org/10.1074/jbc.m112.394759.

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The disulfide relay system in the mitochondrial intermembrane space drives the import of proteins with twin CX9C or twin CX3C motifs by an oxidative folding mechanism. This process requires disulfide bond transfer from oxidized Mia40 to a substrate protein. Reduced Mia40 is reoxidized/regenerated by the FAD-linked sulfhydryl oxidase Erv1 (EC 1.8.3.2). Full-length Erv1 consists of a flexible N-terminal shuttle domain (NTD) and a conserved C-terminal core domain (CTD). Here, we present crystal structures at 2.0 Å resolution of the CTD and at 3.0 Å resolution of a C30S/C133S double mutant of full-length Erv1 (Erv1FL). Similar to previous homologous structures, the CTD exists as a homodimer, with each subunit consisting of a conserved four-helix bundle that accommodates the isoalloxazine ring of FAD and an additional single-turn helix. The structure of Erv1FL enabled us to identify, for the first time, the three-dimensional structure of the Erv1NTD, which is an amphipathic helix flanked by two flexible loops. This structure also represents an intermediate state of electron transfer from the NTD to the CTD of another subunit. Comparative structural analysis revealed that the four-helix bundle of the CTD forms a wide platform for the electron donor NTD. Moreover, computational simulation combined with multiple-sequence alignment suggested that the amphipathic helix close to the shuttle redox enter is critical for the recognition of Mia40, the upstream electron donor. These findings provide structural insights into electron transfer from Mia40 via the shuttle domain of one subunit of Erv1 to the CTD of another Erv1 subunit.

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Xu, Xiaojun, and Shi-Jie Chen. "Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction." Nucleic Acids Research 48, no. 12 (2020): 6503–12. http://dx.doi.org/10.1093/nar/gkaa463.

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Abstract An RNA global fold can be described at the level of helix orientations and relatively flexible loop conformations that connect the helices. The linkage between the helices plays an essential role in determining the structural topology, which restricts RNA local and global folds, especially for RNA tertiary structures involving cross-linked base pairs. We quantitatively analyze the topological constraints on RNA 3D conformational space, in particular, on the distribution of helix orientations, for pseudoknots and loop-loop kissing structures. The result shows that a viable conformational space is predominantly determined by the motif type, helix size, and loop size, indicating a strong topological coupling between helices and loops in RNA tertiary motifs. Moreover, the analysis indicates that (cross-linked) tertiary contacts can cause much stronger topological constraints on RNA global fold than non-cross-linked base pairs. Furthermore, based on the topological constraints encoded in the 2D structure and the 3D templates, we develop a 3D structure prediction approach. This approach can be further combined with structure probing methods to expand the capability of computational prediction for large RNA folds.

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Ashok, Kumar T. "CFSSP: Chou and Fasman Secondary Structure Prediction server." Wide Spectrum 1, no. 9 (2013): 15–19. https://doi.org/10.5281/zenodo.50733.

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CFSSP (Chou & Fasman Secondary Structure Prediction Server) is an online protein secondary structure prediction server. This server predicts regions of secondary structure from the protein sequence such as alpha helix, beta sheet, and turns from the amino acid sequence.The output of predicted secondary structure is also displayed in linear sequential graphical view based on the probability of occurrence of alpha helix, beta sheet, and turns. The method implemented in CFSSP is Chou-Fasman algorithm, which is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography. CFSSP is freely accessible via ExPASy server or directly from BioGem tools at http://www.biogem.org/tool/chou-fasman.

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Kumar, Hemant, Janet S. Finer-Moore, H. Ronald Kaback та Robert M. Stroud. "Structure of LacY with an α-substituted galactoside: Connecting the binding site to the protonation site". Proceedings of the National Academy of Sciences 112, № 29 (2015): 9004–9. http://dx.doi.org/10.1073/pnas.1509854112.

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The X-ray crystal structure of a conformationally constrained mutant of the Escherichia coli lactose permease (the LacY double-Trp mutant Gly-46→Trp/Gly-262→Trp) with bound p-nitrophenyl-α-d-galactopyranoside (α-NPG), a high-affinity lactose analog, is described. With the exception of Glu-126 (helix IV), side chains Trp-151 (helix V), Glu-269 (helix VIII), Arg-144 (helix V), His-322 (helix X), and Asn-272 (helix VIII) interact directly with the galactopyranosyl ring of α-NPG to provide specificity, as indicated by biochemical studies and shown directly by X-ray crystallography. In contrast, Phe-20, Met-23, and Phe-27 (helix I) are within van der Waals distance of the benzyl moiety of the analog and thereby increase binding affinity nonspecifically. Thus, the specificity of LacY for sugar is determined solely by side-chain interactions with the galactopyranosyl ring, whereas affinity is increased by nonspecific hydrophobic interactions with the anomeric substituent.

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Goward, C. R., L. I. Irons, J. P. Murphy, and T. Atkinson. "The secondary structure of protein G′, a robust molecule." Biochemical Journal 274, no. 2 (1991): 503–7. http://dx.doi.org/10.1042/bj2740503.

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The secondary structure of recombinant streptococcal Protein G' was predicted and compared with spectropolarimetric data. The predicted secondary structure consisted of 37 +/- 4% alpha-helix and 30 +/- 5% beta-sheet, whereas the values obtained from c.d. data were 29 +/- 2% alpha-helix and 41 +/- 3% beta-sheet. An alpha-helix-beta-sheet/turn-alpha-helix motif is conjectured to comprise the Fc-binding unit. The c.d. spectra in the near u.v. and far u.v. show that the Protein G' molecule is stable to heating at 100 degrees C and to extremes of pH (pH 1.5 to 11.0). The protein retained biological activity at these extremes. The molecule uncoils above pH 11.5 in a time-dependent fashion. Unfolding of the molecule in guanidinium chloride was monitored by c.d. and fluorescence emission; 3 M-guanidinium chloride was required to unfold the protein by 50%. The protein was completely unfolded in 5.5 M-guanidinium chloride and fully refolded with restoration of activity after removal of guanidinium chloride.

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Yesselman, Joseph D., Sarah K. Denny, Namita Bisaria, Daniel Herschlag, William J. Greenleaf, and Rhiju Das. "Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation." Proceedings of the National Academy of Sciences 116, no. 34 (2019): 16847–55. http://dx.doi.org/10.1073/pnas.1901530116.

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Structured RNAs and RNA complexes underlie biological processes ranging from control of gene expression to protein translation. Approximately 50% of nucleotides within known structured RNAs are folded into Watson–Crick (WC) base pairs, and sequence changes that preserve these pairs are typically assumed to preserve higher-order RNA structure and binding of macromolecule partners. Here, we report that indirect effects of the helix sequence on RNA tertiary stability are, in fact, significant but are nevertheless predictable from a simple computational model called RNAMake-∆∆G. When tested through the RNA on a massively parallel array (RNA-MaP) experimental platform, blind predictions for >1500 variants of the tectoRNA heterodimer model system achieve high accuracy (rmsd 0.34 and 0.77 kcal/mol for sequence and length changes, respectively). Detailed comparison of predictions to experiments support a microscopic picture of how helix sequence changes subtly modulate conformational fluctuations at each base-pair step, which accumulate to impact RNA tertiary structure stability. Our study reveals a previously overlooked phenomenon in RNA structure formation and provides a framework of computation and experiment for understanding helix conformational preferences and their impact across biological RNA and RNA-protein assemblies.

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Menéndez, O., H. Rawel, U. Schwarzenbolz, and T. Henle. "Effect of high hydrostatic pressure on the secondary structure of microbial transglutaminase." Czech Journal of Food Sciences 22, SI - Chem. Reactions in Foods V (2004): S295—S298. http://dx.doi.org/10.17221/10685-cjfs.

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Enzyme activity and corresponding secondary structure, measured by circular dichroism was analysed before und after treatment of microbial transglutaminase at different temperatures (40, 80°C) and pressures (0.1, 200, 400, 600 MPa). Irreversible enzyme inactivation was achieved at 80°C after 2 minutes at atmospheric pressure. Enzyme inactivation at 0.1, 200, 400, 600 MPa and 40°C followed first order kinetics. Increasing pressure reduced MTG activity, nevertheless the enzyme showed a residual activity of 50% after 12 min at 600 MPa. The analysis of the native enzyme exhibited well-defined proportions between α-helix, β-strand, β-turn and unordered structures. In contrast to heating, high-pressure treatment only at high levels induced significant decrease in the α-helix content, whereas β-strand substructures remained unaltered in both cases. Based on the known crystal structure of MTG it can be concluded that the active centre of the enzyme itself, which is located in an expanded β-strand domain, is relatively stable and pressure-induced inactivation is caused by a degradation of α-helix elements with corresponding influence on the tertiary structure.

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Kaukinen, Pasi, Vibhor Kumar, Kirsi Tulimäki, Peter Engelhardt, Antti Vaheri та Alexander Plyusnin. "Oligomerization of Hantavirus N Protein: C-Terminal α-Helices Interact To Form a Shared Hydrophobic Space". Journal of Virology 78, № 24 (2004): 13669–77. http://dx.doi.org/10.1128/jvi.78.24.13669-13677.2004.

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ABSTRACT The structure of the nucleocapsid protein of bunyaviruses has not been defined. Earlier we have shown that Tula hantavirus N protein oligomerization is dependent on the C-terminal domains. Of them, the helix-loop-helix motif was found to be an essential structure. Computer modeling predicted that oligomerization occurs via helix protrusions, and the shared hydrophobic space formed by amino acids residues 380-IILLF-384 in the first helix and 413-LI-414 in the second helix is responsible for stabilizing the interaction. The model was validated by two approaches. First, analysis of the oligomerization capacity of the N protein mutants performed with the mammalian two-hybrid system showed that both preservation of the helix structure and formation of the shared hydrophobic space are crucial for the interaction. Second, oligomerization was shown to be a prerequisite for the granular pattern of transiently expressed N protein in transfected cells. N protein trimerization was supported by three-dimensional reconstruction of the N protein by electron microscopy after negative staining. Finally, we discuss how N protein trimerization could occur.

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Sherieff, Aysha, M. Mohibbe Azam, and K. Sesha Maheswaramma. "3D STRUCTURE PREDICTION AND VISUALIZATION OF PROTEIN OF THE NOVEL STRAIN OF RHODOPSEUDOMONAS FAECALIS." International Journal of Advanced Research 11, no. 07 (2023): 678–90. http://dx.doi.org/10.21474/ijar01/17276.

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The secondary protein structure of Rhodopseudomonas faecalis was obtained from the partial protein sequence, protein analysis and domain prediction were characterized further using PSIPRED tool. Motifs were analyzed using Motif Scan-Prosite pattern tool. The 3D Structure prediction and visualization was performed using Phyre2 program, Galaxy Web and CASTp platforms. The visualization of the predicted and concrete structure of the protein was done using RASMOL. The results shows that the protein structure has sites for amidation, phosphorylation and myristylation along with 30% alpha helix and 19% beta strands, 310 helix , Pi helix, turns and bends with repeated 11 different aminoacids occurrence.

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De, Meutter Joëlle, and Erik Goormaghtigh. "Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration." European Biophysics Journal 53 (February 3, 2021): 613–28. https://doi.org/10.1007/s00249-021-01502-y.

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FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.

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Peti, Wolfgang, Margaret A. Johnson, Torsten Herrmann, et al. "Structural Genomics of the Severe Acute Respiratory Syndrome Coronavirus: Nuclear Magnetic Resonance Structure of the Protein nsP7." Journal of Virology 79, no. 20 (2005): 12905–13. http://dx.doi.org/10.1128/jvi.79.20.12905-12913.2005.

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ABSTRACT Here, we report the three-dimensional structure of severe acute respiratory syndrome coronavirus (SARS-CoV) nsP7, a component of the SARS-CoV replicase polyprotein. The coronavirus replicase carries out regulatory tasks involved in the maintenance, transcription, and replication of the coronavirus genome. nsP7 was found to assume a compact architecture in solution, which is comprised primarily of helical secondary structures. Three helices (α2 to α4) form a flat up-down-up antiparallel α-helix sheet. The N-terminal segment of residues 1 to 22, containing two turns of α-helix and one turn of 310-helix, is packed across the surface of α2 and α3 in the helix sheet, with the α-helical region oriented at a 60° angle relative to α2 and α3. The surface charge distribution is pronouncedly asymmetrical, with the flat surface of the helical sheet showing a large negatively charged region adjacent to a large hydrophobic patch and the opposite side containing a positively charged groove that extends along the helix α1. Each of these three areas is thus implicated as a potential site for protein-protein interactions.

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Yao, Yao. "Prion Interaction with Normal Protein in Topological Changing Secondary Structure to Aggregation." Advanced Emergency Medicine 9, no. 2 (2020): 53. http://dx.doi.org/10.18686/aem.v9i2.167.

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<p>Prion is a protein smaller than virus and it infects host in the absence of nucleic acid. The secondary structure of protein folds incorrectly from α-helices to β-sheets through breaking and re-formation of hydrogen bond. Structural analogy of α-helix and DNA double helix and comparing differences between α-helix and β-sheet show prion's infectivity and propagation. Aggregates of dimers and polymers generate β-amyloid fibril in Alzheimer's disease.</p>

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Su, Qiang, Feizhuo Hu, Xiaofei Ge, et al. "Structure of the human PKD1-PKD2 complex." Science 361, no. 6406 (2018): eaat9819. http://dx.doi.org/10.1126/science.aat9819.

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Mutations in two genes, PKD1 and PKD2, account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo–electron microscopy structure of truncated human PKD1-PKD2 complex assembled in a 1:3 ratio. PKD1 contains a voltage-gated ion channel (VGIC) fold that interacts with PKD2 to form the domain-swapped, yet noncanonical, transient receptor potential (TRP) channel architecture. The S6 helix in PKD1 is broken in the middle, with the extracellular half, S6a, resembling pore helix 1 in a typical TRP channel. Three positively charged, cavity-facing residues on S6b may block cation permeation. In addition to the VGIC, a five–transmembrane helix domain and a cytosolic PLAT domain were resolved in PKD1. The PKD1-PKD2 complex structure establishes a framework for dissecting the function and disease mechanisms of the PKD proteins.

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Journal articles on the topic 'Helix structure'

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