Статті в журналах: "Coiled-coil structure"

1

Kwon, Min Jee, Myeong Hoon Han, Joshua A. Bagley, Do Young Hyeon, Byung Su Ko, Yun Mi Lee, In Jun Cha, et al. "Coiled-coil structure-dependent interactions between polyQ proteins and Foxo lead to dendrite pathology and behavioral defects." Proceedings of the National Academy of Sciences 115, no. 45 (October 22, 2018): E10748—E10757. http://dx.doi.org/10.1073/pnas.1807206115.

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Neurodegenerative disorders, such as Huntington’s diseases and spinocerebellar ataxias (SCAs), are driven by proteins with expanded polyglutamine (polyQ) tracts. Recently, coiled-coil structures in polyQ regions of such proteins were shown to facilitate aggregate formation and ultimately lead to cell death. However, the molecular mechanism linking these structural domains to neuronal toxicity of polyQ proteins remains elusive. Here, we demonstrate that coiled-coil structures in the Q repeat region of SCA type 3 (SCA3) polyQ proteins confer protein toxicity inDrosophilaneurons. To functionally characterize coiled-coil structures in the Q repeat regions, we generated three structural variants of SCA3 polyQ proteins: (i) MJDtr-76Q, containing both α-helical coiled-coil and β-sheet hairpin structures in the Q repeat region; (ii) MJDtr-70Q_cc0, possessing only α-helical coiled-coil structures due to the incorporation of β-sheet–breaking residues (Q-to-N or Q-to-E mutations); and (iii) MJDtr-70Q_pQp, with no secondary structure due to the introduced proline residues (Q-to-P mutations). Through comparative analysis of these variants, we found that coiled-coil structures facilitated nuclear localization of SCA3 polyQ proteins and induced dendrite defects inDrosophiladendritic arborization neurons. Furthermore, genetic and functional screening identified the transcription factor Foxo as a target of polyQ proteins, and coiled-coil–mediated interactions of Foxo and polyQ proteins in the nucleus resulted in the observed dendrite and behavioral defects inDrosophila. These results demonstrate that coiled-coil structures of polyQ proteins are crucial for their neuronal toxicity, which is conferred through coiled-coil to coiled-coil interactions with the nuclear targets of these proteins.

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2

Vajda, Tamás, and András Perczel. "The clear and dark sides of water: influence on the coiled coil folding domain." Biomolecular Concepts 7, no. 3 (June 1, 2016): 189–95. http://dx.doi.org/10.1515/bmc-2016-0005.

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AbstractThe essential role of water in extra- and intracellular coiled coil structures of proteins is critically evaluated, and the different protein types incorporating coiled coil units are overviewed. The following subjects are discussed: i) influence of water on the formation and degradation of the coiled coil domain together with the stability of this conformer type; ii) the water’s paradox iii) design of coiled coil motifs and iv) expert opinion and outlook is presented. The clear and dark sides refer to the positive and negative aspects of the water molecule, as it may enhance or inhibit a given folding event. This duplicity can be symbolized by the Roman ‘Janus-face’ which means that water may facilitate and stimulate coiled coil structure formation, however, it may contribute to the fatal processes of oligomerization and amyloidosis of the very same polypeptide chain.

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3

Fu, Ruijiang, Wu-Pei Su, and Hongxing He. "Direct Phasing of Coiled-Coil Protein Crystals." Crystals 12, no. 11 (November 20, 2022): 1674. http://dx.doi.org/10.3390/cryst12111674.

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Coiled-coil proteins consisting of multiple copies of helices take part in transmembrane transportation and oligomerization, and are used for drug delivery. Cross-alpha amyloid-like coiled-coil structures, in which tens of short helices align perpendicular to the fibril axis, often resist molecular replacement due to the uncertainty to position each helix. Eight coiled-coil structures already solved and posted in the protein data bank are reconstructed ab initio to demonstrate the direct phasing results. Non-crystallographic symmetry and intermediate-resolution diffraction data are considered for direct phasing. The retrieved phases have a mean phase error around 30∼40°. The calculated density map is ready for model building, and the reconstructed model agrees with the deposited structure. The results indicate that direct phasing is an efficient approach to construct the protein envelope from scratch, build each helix without model bias which is also used to confirm the prediction of AlphaFold and RosettaFold, and solve the whole structure of coiled-coil proteins.

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4

Wilbur, Jeremy D., Peter K. Hwang, Frances M. Brodsky, and Robert J. Fletterick. "Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain." Acta Crystallographica Section D Biological Crystallography 66, no. 3 (February 12, 2010): 314–18. http://dx.doi.org/10.1107/s0907444909054535.

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Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington's disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coil domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility.

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5

Thomas, Jens M. H., Ronan M. Keegan, Daniel J. Rigden, and Owen R. Davies. "Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling." Acta Crystallographica Section D Structural Biology 76, no. 3 (February 25, 2020): 272–84. http://dx.doi.org/10.1107/s2059798320000443.

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The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.

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Caillat, Christophe, Alexander Fish, Dafni-Eleftheria Pefani, Stavros Taraviras, Zoi Lygerou, and Anastassis Perrakis. "The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins." Acta Crystallographica Section D Biological Crystallography 71, no. 11 (October 31, 2015): 2278–86. http://dx.doi.org/10.1107/s1399004715016892.

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GemC1, together with Idas and Geminin, an important regulator of DNA-replication licensing and differentiation decisions, constitute a superfamily sharing a homologous central coiled-coil domain. To better understand this family of proteins, the crystal structure of a GemC1 coiled-coil domain variant engineered for better solubility was determined to 2.2 Å resolution. GemC1 shows a less typical coiled coil compared with the Geminin homodimer and the Geminin–Idas heterodimer structures. It is also shown that both in vitro and in cells GemC1 interacts with Geminin through its coiled-coil domain, forming a heterodimer that is more stable that the GemC1 homodimer. Comparative analysis of the thermal stability of all of the possible superfamily complexes, using circular dichroism to follow the unfolding of the entire helix of the coiled coil, or intrinsic tryptophan fluorescence of a unique conserved N-terminal tryptophan, shows that the unfolding of the coiled coil is likely to take place from the C-terminus towards the N-terminus. It is also shown that homodimers show a single-state unfolding, while heterodimers show a two-state unfolding, suggesting that the dimer first falls apart and the helices then unfold according to the stability of each protein. The findings argue that Geminin-family members form homodimers and heterodimers between them, and this ability is likely to be important for modulating their function in cycling and differentiating cells.

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Alminaite, Agne, Vera Backström, Antti Vaheri, and Alexander Plyusnin. "Oligomerization of hantaviral nucleocapsid protein: charged residues in the N-terminal coiled-coil domain contribute to intermolecular interactions." Journal of General Virology 89, no. 9 (September 1, 2008): 2167–74. http://dx.doi.org/10.1099/vir.0.2008/004044-0.

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The nucleocapsid (N) protein of hantaviruses (family Bunyaviridae) is the most abundant component of the virion; it encapsidates genomic RNA segments and participates in viral genome transcription and replication, as well as in virus assembly. During RNA encapsidation, the N protein forms intermediate trimers and then oligomers via ‘head-to-head, tail-to-tail’ interactions. In previous work, using Tula hantavirus (TULV) N protein as a model, it was demonstrated that an intact coiled-coil structure of the N terminus is crucial for the oligomerization capacity of the N protein and that the hydrophobic ‘a’ residues from the second α-helix are especially important. Here, the importance of charged amino acid residues located within the coiled-coil for trimer formation and oligomerization was analysed. To predict the interacting surfaces of the monomers, the previous in silico model of TULV coiled-coils was first upgraded, taking advantage of the recently published crystal structure of the N-terminal coiled-coil of the Sin Nombre virus N protein. The results obtained using a mammalian two-hybrid assay suggested that conserved, charged amino acid residues within the coiled-coil make a substantial contribution to N protein oligomerization. This contribution probably involves (i) the formation of interacting surfaces of the N monomers (residues D35 and D38, located at the tip of the coiled-coil loop, and R63 appear particularly important) and (ii) stabilization of the coiled-coil via intramolecular ionic bridging (with E55 as a key player). It is hypothesized that the tips of the coiled-coils are the first to come into direct contact and thus to initiate tight packing of the three structures.

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Thomas, Jens M. H., Ronan M. Keegan, Jaclyn Bibby, Martyn D. Winn, Olga Mayans, and Daniel J. Rigden. "Routine phasing of coiled-coil protein crystal structures withAMPLE." IUCrJ 2, no. 2 (February 26, 2015): 198–206. http://dx.doi.org/10.1107/s2052252515002080.

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Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The programAMPLEcan solve crystal structures by molecular replacement usingab initiosearch models in the absence of an existent homologous protein structure.AMPLEhas been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable byab initiomethodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both theab initiomodelling and the use of ensemble search models contribute to the success ofAMPLEby comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement withAMPLEshould be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore,AMPLEmay be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

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Kuruba, Balaganesh, Marta Kaczmarek, Małgorzata Kęsik-Brodacka, Magdalena Fojutowska, Małgorzata Śliwinska, Alla S. Kostyukova, and Joanna Moraczewska. "Structural Effects of Disease-Related Mutations in Actin-Binding Period 3 of Tropomyosin." Molecules 26, no. 22 (November 19, 2021): 6980. http://dx.doi.org/10.3390/molecules26226980.

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Tropomyosin (Tpm) is an actin-binding coiled-coil protein. In muscle, it regulates contractions in a troponin/Ca2+-dependent manner and controls the thin filament lengths at the pointed end. Due to its size and periodic structure, it is difficult to observe small local structural changes in the coiled coil caused by disease-related mutations. In this study, we designed 97-residue peptides, Tpm1.164–154 and Tpm3.1265–155, focusing on the actin-binding period 3 of two muscle isoforms. Using these peptides, we evaluated the effects of cardiomyopathy mutations: I92T and V95A in Tpm1.1, and congenital myopathy mutations R91P and R91C in Tpm3.12. We introduced a cysteine at the N-terminus of each fragment to promote the formation of the coiled-coil structure by disulfide bonds. Dimerization of the designed peptides was confirmed by gel electrophoresis in the presence and absence of dithiothreitol. Using circular dichroism, we showed that all mutations decreased coiled coil stability, with Tpm3.1265–155R91P and Tpm1.164–154I92T having the most drastic effects. Our experiments also indicated that adding the N-terminal cysteine increased coiled coil stability demonstrating that our design can serve as an effective tool in studying the coiled-coil fragments of various proteins.

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Gáspári, Zoltán, and László Nyitray. "Coiled coils as possible models of protein structure evolution." BioMolecular Concepts 2, no. 3 (June 1, 2011): 199–210. http://dx.doi.org/10.1515/bmc.2011.015.

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AbstractCoiled coils are formed by two or more α-helices wrapped around one another. This structural motif often guides di-, tri- or multimerization of proteins involved in diverse biological processes such as membrane fusion, signal transduction and the organization of the cytoskeleton. Although coiled coil motifs seem conceptually simple and their existence was proposed in the early 1950s, the high variability of the motif makes coiled coil prediction from sequence a difficult task. They might be confused with intrinsically disordered sequences and even more with a recently described structural motif, the charged single α-helix. By contrast, the versatility of coiled coil structures renders them an ideal candidate for protein (re)design and many novel variants have been successfully created to date. In this paper, we review coiled coils in the light of protein evolution by putting our present understanding of the motif and its variants in the context of structural interconversions. We argue that coiled coils are ideal subjects for studies of subtle and large-scale structural changes because of their well-characterized and versatile nature.

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Bhairosing-Kok, Doreth, Flora S. Groothuizen, Alexander Fish, Shreya Dharadhar, Herrie H. K. Winterwerp, and Titia K. Sixma. "Sharp kinking of a coiled-coil in MutS allows DNA binding and release." Nucleic Acids Research 47, no. 16 (August 2, 2019): 8888–98. http://dx.doi.org/10.1093/nar/gkz649.

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Abstract DNA mismatch repair (MMR) corrects mismatches, small insertions and deletions in DNA during DNA replication. While scanning for mismatches, dimers of MutS embrace the DNA helix with their lever and clamp domains. Previous studies indicated generic flexibility of the lever and clamp domains of MutS prior to DNA binding, but whether this was important for MutS function was unknown. Here, we present a novel crystal structure of DNA-free Escherichia coli MutS. In this apo-structure, the clamp domains are repositioned due to kinking at specific sites in the coiled-coil region in the lever domains, suggesting a defined hinge point. We made mutations at the coiled-coil hinge point. The mutants made to disrupt the helical fold at the kink site diminish DNA binding, whereas those made to increase stability of coiled-coil result in stronger DNA binding. These data suggest that the site-specific kinking of the coiled-coil in the lever domain is important for loading of this ABC-ATPase on DNA.

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Ferron, François, David Blocquel, Johnny Habchi, Eric Durand, Marion Sevajol, Jenny Erales, Nicolas Papageorgiou, and Sonia Longhi. "Impact of crystal packing on coiled-coil flexibility." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1599. http://dx.doi.org/10.1107/s2053273314084009.

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The structural characterization of various constructs of the Measles virus (MeV) Phosphoprotein (P) multimerization domain (PMD) has brought to light significant discrepancies in the quaternary structure due to both crystal constraints and the flexible nature of this coiled-coil. Indeed, despite a conserved tetrameric parallel coiled-coil core, structural comparison unveiled significant deformations in the C-terminal extremities that even led to the partial unfolding of the coiled-coil. These deformations were induced by intermolecular interactions within the crystal, as well as by the crystallization condition. These deformations also suggest that PMD has the ability to adapt to external mechanical constrains. Using a combination of biophysical methods (size-exclusion chromatography, circular dichroism and small angle X-ray scattering), we assessed the differential flexibility of the C-terminal region of the MeV PMD in solution. Taken together, these results show that crystal packing can be used to "freeze" in a certain state, parts of proteins known to be in a dynamic folding-unfolding equilibrium. They also bring awareness that conclusions about function and mechanism based on analysis of a single crystal structure of a known dynamic protein can be easily biased, and they challenge to some extent the assumption that coiled-coil structures can be reliably predicted from the amino acid sequence.

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Jokar, Mojtaba, and Korosh Torabi. "Thermodynamics of a Coiled-Coil Protein Structure." Biophysical Journal 114, no. 3 (February 2018): 580a. http://dx.doi.org/10.1016/j.bpj.2017.11.3174.

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Hanukoglu, Israel, and Liora Ezra. "Proteopedia entry: Coiled-coil structure of keratins." Biochemistry and Molecular Biology Education 42, no. 1 (November 22, 2013): 93–94. http://dx.doi.org/10.1002/bmb.20746.

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Cheng, Haiyun Y., Anthony P. Schiavone, and Thomas E. Smithgall. "A Point Mutation in the N-Terminal Coiled-Coil Domain Releases c-Fes Tyrosine Kinase Activity and Survival Signaling in Myeloid Leukemia Cells." Molecular and Cellular Biology 21, no. 18 (September 15, 2001): 6170–80. http://dx.doi.org/10.1128/mcb.21.18.6170-6180.2001.

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ABSTRACT The c-fes locus encodes a 93-kDa non-receptor protein tyrosine kinase (Fes) that regulates the growth and differentiation of hematopoietic and vascular endothelial cells. Unique to Fes is a long N-terminal sequence with two regions of strong homology to coiled-coil oligomerization domains. We introduced leucine-to-proline substitutions into the coiled coils that were predicted to disrupt the coiled-coil structure. The resulting mutant proteins, together with wild-type Fes, were fused to green fluorescent protein and expressed in Rat-2 fibroblasts. We observed that a point mutation in the first coiled-coil domain (L145P) dramatically increased Fes tyrosine kinase and transforming activities in this cell type. In contrast, a similar point mutation in the second coiled-coil motif (L334P) was without effect. However, combining the L334P and L145P mutations reduced transforming and kinase activities by approximately 50% relative to the levels of activity produced with the L145P mutation alone. To study the effects of the coiled-coil mutations in a biologically relevant context, we expressed the mutant proteins in the granulocyte-macrophage colony-stimulating factor (GM-CSF)-dependent myeloid leukemia cell line TF-1. In this cellular context, the L145P mutation induced GM-CSF independence, cell attachment, and spreading. These effects correlated with a marked increase in L145P protein autophosphorylation relative to that of wild-type Fes. In contrast, the double coiled-coil mutant protein showed greatly reduced kinase and biological activities in TF-1 cells. These data are consistent with a role for the first coiled coil in the negative regulation of kinase activity and a requirement for the second coiled coil in either oligomerization or recruitment of signaling partners. Gel filtration experiments showed that the unique N-terminal region interconverts between monomeric and oligomeric forms. Single point mutations favored oligomerization, while the double point mutant protein eluted essentially as the monomer. These data provide new evidence for coiled-coil-mediated regulation of c-Fes tyrosine kinase activity and signaling, a mechanism unique among tyrosine kinases.

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Maerz, Anne L., Rob J. Center, Bruce E. Kemp, Bostjan Kobe, and Pantelis Poumbourios. "Functional Implications of the Human T-Lymphotropic Virus Type 1 Transmembrane Glycoprotein Helical Hairpin Structure." Journal of Virology 74, no. 14 (July 15, 2000): 6614–21. http://dx.doi.org/10.1128/jvi.74.14.6614-6621.2000.

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ABSTRACT Retrovirus entry into cells follows receptor binding by the surface-exposed envelope glycoprotein (Env) subunit (SU), which triggers the membrane fusion activity of the transmembrane (TM) protein. TM protein fragments expressed in the absence of SU adopt helical hairpin structures comprising a central coiled coil, a region of chain reversal containing a disulfide-bonded loop, and a C-terminal segment that packs onto the exterior of the coiled coil in an antiparallel manner. Here we used in vitro mutagenesis to test the functional role of structural elements observed in a model helical hairpin, gp21 of human T-lymphotropic virus type 1. Membrane fusion activity requires the stabilization of the N and C termini of the central coiled coil by a hydrophobic N cap and a small hydrophobic core, respectively. A conserved Gly-Gly hinge motif preceding the disulfide-bonded loop, a salt bridge that stabilizes the chain reversal region, and interactions between the C-terminal segment and the coiled coil are also critical for fusion activity. Our data support a model whereby the chain reversal region transmits a conformational signal from receptor-bound SU to induce the fusion-activated helical hairpin conformation of the TM protein.

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Hawkins, Rhoda J., and Tom C. B. McLeish. "Dynamic allostery of protein alpha helical coiled-coils." Journal of The Royal Society Interface 3, no. 6 (August 16, 2005): 125–38. http://dx.doi.org/10.1098/rsif.2005.0068.

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Alpha helical coiled-coils appear in many important allosteric proteins such as the dynein molecular motor and bacteria chemotaxis transmembrane receptors. As a mechanism for transmitting the information of ligand binding to a distant site across an allosteric protein, an alternative to conformational change in the mean static structure is an induced change in the pattern of the internal dynamics of the protein. We explore how ligand binding may change the intramolecular vibrational free energy of a coiled-coil, using parameterized coarse-grained models, treating the case of dynein in detail. The models predict that coupling of slide, bend and twist modes of the coiled-coil transmits an allosteric free energy of ∼2 k B T , consistent with experimental results. A further prediction is a quantitative increase in the effective stiffness of the coiled-coil without any change in inherent flexibility of the individual helices. The model provides a possible and experimentally testable mechanism for transmission of information through the alpha helical coiled-coil of dynein.

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Ahn, Jinsook, Soyeon Jeong, So-Mi Kang, Inseong Jo, Bum-Joon Park, and Nam-Chul Ha. "Separation of Coiled-Coil Structures in Lamin A/C Is Required for the Elongation of the Filament." Cells 10, no. 1 (December 31, 2020): 55. http://dx.doi.org/10.3390/cells10010055.

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Intermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, the crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the critical interaction. This study investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in the N-terminal of coil 1a and the C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in the elongation of IF proteins.

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Nefedova, Victoria V., Sergey Y. Kleymenov, Irina V. Safenkova, Dmitrii I. Levitsky, and Alexander M. Matyushenko. "Neurofilament Light Protein Rod Domain Exhibits Structural Heterogeneity." Biomolecules 14, no. 1 (January 9, 2024): 85. http://dx.doi.org/10.3390/biom14010085.

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Neurofilaments are neuron-specific proteins that belong to the intermediate filament (IFs) protein family, with the neurofilament light chain protein (NFL) being the most abundant. The IFs structure typically includes a central coiled-coil rod domain comprised of coils 1A, 1B, and 2, separated by linker regions. The thermal stability of the IF molecule plays a crucial role in its ability for self-association. In the current study, we investigated the thermal stability of NFL coiled-coil domains by analyzing a set of recombinant domains and their fusions (NFL1B, NFL1A+1B, NFL2, NFL1B+2, and NFLROD) via circular dichroism spectroscopy and differential scanning calorimetry. The thermal stability of coiled-coil domains is evident in a wide range of temperatures, and thermal transition values (Tm) correspond well between isolated coiled-coil domains and full-length NFL. NFL1B has a Tm of 39.4 °C, and its’ fusions, NFL1A+1B and NFL1B+2, have a Tm of 41.9 °C and 41.5 °C, respectively. However, in the case of NFL2, thermal denaturation includes at least two thermal transitions at 37.2 °C and 62.7 °C. These data indicate that the continuous α-helical structure of the coil 2 domain has parts with varied thermal stability. Among all the NFL fragments, only NFL2 underwent irreversible heat-induced denaturation. Together, these results unveil the origin of full-length NFL’s thermal transitions, and reveal its domains structure and properties.

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Del Priore, V., C. Heath, C. Snay, A. MacMillan, L. Gorsch, S. Dagher, and C. Cole. "A structure/function analysis of Rat7p/Nup159p, an essential nucleoporin of Saccharomyces cerevisiae." Journal of Cell Science 110, no. 23 (December 1, 1997): 2987–99. http://dx.doi.org/10.1242/jcs.110.23.2987.

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Rat7p/Nup159p is an essential nucleoporin of Sac-charomyces cerevisiae originally isolated in a genetic screen designed to identify yeast temperature-sensitive mutants defective in mRNA export. Here we describe a detailed structural-functional analysis of Rat7p/Nup159p. The mutation in the rat7-1 ts allele, isolated in the original genetic screen, was found to be a single base pair change that created a stop codon approximately 100 amino acids upstream of the actual stop codon of this 1,460 amino acid polypeptide, thus eliminating one of the two predicted coiled-coil regions located near the carboxyl terminus of the protein. These coiled-coil regions are essential since an allele lacking both coiled-coil regions was unable to support growth under any conditions. In contrast, no other region of the protein was absolutely required. The SAFG/PSFG repeat region in the central third of the protein was completely dispensable for growth at temperatures between 16 degrees C and 37 degrees C and cells expressing this mutant allele were indistinguishable from wild type. Deletion of the amino-terminal third of the protein, upstream from the repeat region, or the portion between the repeat region and the coiled-coils resulted in temperature-sensitivity, but the two alleles showed distinct phenotypes with respect to the behavior of nuclear pore complexes (NPCs). Taken together, our data suggest that Rat7p/Nup159p is anchored within the NPC through its coiled-coil region and adjacent sequences. In addition, we postulate that the N-terminal third of Rat7p/Nup159p plays an important role in mRNA export.

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López-García, Patricia, Melis Goktas, Ana E. Bergues-Pupo, Beate Koksch, Daniel Varón Silva, and Kerstin G. Blank. "Structural determinants of coiled coil mechanics." Physical Chemistry Chemical Physics 21, no. 18 (2019): 9145–49. http://dx.doi.org/10.1039/c9cp00665f.

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In shear geometry, the sequence–structure–mechanics relationship of rationally designed coiled coil heterodimers is determined by the helix propensity of the individual helices and the packing density at the hydrophobic core.

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Yao, Deqiang, Maia Cherney, and Miroslaw Cygler. "Structure of the N-terminal domain of the effector protein LegC3 fromLegionella pneumophila." Acta Crystallographica Section D Biological Crystallography 70, no. 2 (January 29, 2014): 436–41. http://dx.doi.org/10.1107/s139900471302991x.

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Legionella pneumophilasecretes over 300 effectors during the invasion of human cells. The functions of only a small number of them have been identified. LegC3 is one of the identified effectors, which is believed to act by inhibiting vacuolar fusion. It contains two predicted transmembrane helices that divide the protein into a larger N-terminal domain and a smaller C-terminal domain. The function of LegC3 has been shown to be associated primarily with the N-terminal domain, which contains coiled-coil sequence motifs. The structure of the N-terminal domain has been determined and it is shown that it is highly α-helical and contains a helical bundle followed by a long antiparallel coiled-coil. No similar protein fold has been observed in the PDB. A long loop at the tip of the coiled-coil distal from the membrane is disordered and may be important for interaction with an as yet unidentified protein.

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Then, Andre, Haotian Zhang, Bashar Ibrahim, and Stefan Schuster. "Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods." International Journal of Molecular Sciences 23, no. 15 (August 4, 2022): 8692. http://dx.doi.org/10.3390/ijms23158692.

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A coiled coil is a structural motif in proteins that consists of at least two α-helices wound around each other. For structural stabilization, these α-helices form interhelical contacts via their amino acid side chains. However, there are restrictions as to the distances along the amino acid sequence at which those contacts occur. As the spatial period of the α-helix is 3.6, the most frequent distances between hydrophobic contacts are 3, 4, and 7. Up to now, the multitude of possible decompositions of α-helices participating in coiled coils at these distances has not been explored systematically. Here, we present an algorithm that computes all non-redundant decompositions of sequence periods of hydrophobic amino acids into distances of 3, 4, and 7. Further, we examine which decompositions can be found in nature by analyzing the available data and taking a closer look at correlations between the properties of the coiled coil and its decomposition. We find that the availability of decompositions allowing for coiled-coil formation without putting too much strain on the α-helix geometry follows an oscillatory pattern in respect of period length. Our algorithm supplies the basis for exploring the possible decompositions of coiled coils of any period length.

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Thorn, Kurt S., Jeffrey A. Ubersax, and Ronald D. Vale. "Engineering the Processive Run Length of the Kinesin Motor." Journal of Cell Biology 151, no. 5 (November 27, 2000): 1093–100. http://dx.doi.org/10.1083/jcb.151.5.1093.

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Conventional kinesin is a highly processive molecular motor that takes several hundred steps per encounter with a microtubule. Processive motility is believed to result from the coordinated, hand-over-hand motion of the two heads of the kinesin dimer, but the specific factors that determine kinesin's run length (distance traveled per microtubule encounter) are not known. Here, we show that the neck coiled-coil, a structure adjacent to the motor domain, plays an important role in governing the run length. By adding positive charge to the neck coiled-coil, we have created ultra-processive kinesin mutants that have fourfold longer run lengths than the wild-type motor, but that have normal ATPase activity and motor velocity. Conversely, adding negative charge on the neck coiled-coil decreases the run length. The gain in processivity can be suppressed by either proteolytic cleavage of tubulin's negatively charged COOH terminus or by high salt concentrations. Therefore, modulation of processivity by the neck coiled-coil appears to involve an electrostatic tethering interaction with the COOH terminus of tubulin. The ability to readily increase kinesin processivity by mutation, taken together with the strong sequence conservation of the neck coiled-coil, suggests that evolutionary pressures may limit kinesin's run length to optimize its in vivo function.

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Wu, Shuai, Yunjiao He, Xianxiu Qiu, Wenchao Yang, Wenchao Liu, Xiaohua Li, Yan Li, et al. "Targeting the potent Beclin 1–UVRAG coiled-coil interaction with designed peptides enhances autophagy and endolysosomal trafficking." Proceedings of the National Academy of Sciences 115, no. 25 (June 4, 2018): E5669—E5678. http://dx.doi.org/10.1073/pnas.1721173115.

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The Beclin 1–Vps34 complex, known as “mammalian class III PI3K,” plays essential roles in membrane-mediated transport processes including autophagy and endosomal trafficking. Beclin 1 acts as a scaffolding molecule for the complex and readily transits from its metastable homodimeric state to interact with key modulators such as Atg14L or UVRAG and form functionally distinct Atg14L/UVRAG-containing Beclin 1–Vps34 subcomplexes. The Beclin 1–Atg14L/UVRAG interaction relies critically on their coiled-coil domains, but the molecular mechanism remains poorly understood. We determined the crystal structure of Beclin 1–UVRAG coiled-coil complex and identified a strengthened interface with both hydrophobic pairings and electrostatically complementary interactions. This structure explains why the Beclin 1–UVRAG interaction is more potent than the metastable Beclin 1 homodimer. Potent Beclin 1–UVRAG interaction is functionally significant because it renders UVRAG more competitive than Atg14L in Beclin 1 binding and is critical for promoting endolysosomal trafficking. UVRAG coiled-coil mutants with weakened Beclin 1 binding do not outcompete Atg14L and fail to promote endolysosomal degradation of the EGF receptor (EGFR). We designed all-hydrocarbon stapled peptides that specifically targeted the C-terminal part of the Beclin 1 coiled-coil domain to interfere with its homodimerization. One such peptide reduced Beclin 1 self-association, promoted Beclin 1–Atg14L/UVRAG interaction, increased autophagic flux, and enhanced EGFR degradation. Our results demonstrate that the targeting Beclin 1 coiled-coil domain with designed peptides to induce the redistribution of Beclin 1 among its self-associated form or Atg14L/UVRAG-containing complexes enhances both autophagy and endolysosomal trafficking.

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Zhang, Yuchen, Richard J. Alsop, Asfia Soomro, Fei-Chi Yang, and Maikel C. Rheinstädter. "Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair." PeerJ 3 (October 1, 2015): e1296. http://dx.doi.org/10.7717/peerj.1296.

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The hair is a filamentous biomaterial consisting of thecuticle, thecortexand themedulla, all held together by the cell membrane complex. Thecortexmostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of theα-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

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Xiao, Qiang, Dallin S. Ashton, Zachary B. Jones, Katherine P. Thompson, and Joshua L. Price. "Long-range PEG stapling: macrocyclization for increased protein conformational stability and resistance to proteolysis." RSC Chemical Biology 1, no. 4 (2020): 273–80. http://dx.doi.org/10.1039/d0cb00075b.

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Long-range stapling of two Asn-linked PEG oligomers via olefin metathesis substantially increases the conformational stability of the WW and SH3 domain tertiary structures and the GCN4 coiled-coil quaternary structure.

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Dames, Sonja A., Richard A. Kammerer, Ronald Wiltscheck, Jürgen Engel, and Andrei T. Alexandrescu. "NMR structure of a parallel homotrimeric coiled coil." Nature Structural & Molecular Biology 5, no. 8 (August 1998): 687–91. http://dx.doi.org/10.1038/90444.

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Dowling, L. M., W. G. Crewther та D. A. Parry. "Secondary structure of component 8c-1 of α-keratin. An analysis of the amino acid sequence". Biochemical Journal 236, № 3 (15 червня 1986): 705–12. http://dx.doi.org/10.1042/bj2360705.

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The amino acid sequence of component 8c-1 from alpha-keratin was analysed by using secondary-structure prediction techniques, homology search methods, fast Fourier-transform techniques to detect regularities in the linear disposition of amino acids, interaction counts to assess possible modes of chain aggregation and assessment of hydrophilicity distribution. The analyses show the following. The molecule has two lengths of coiled-coil structure, each about 20 nm long, one from residues 56-202 with a discontinuity from about residue 91 to residue 101, and the other from residues 219-366 with discontinuities from about residue 238 to residue 245 and at about residue 306. The acidic and basic residues in the coiled-coil segment between residues 102 and 202 show a 9,4-residue structural period in their linear disposition, whereas between residues 246 and 366 a period of 9.9 residues is observed in the positioning of ionic residues. Acidic and basic residues are out of phase by 180 degrees. Similar repeats occur in corresponding regions of other intermediate-filament proteins. The overall mean values for the repeats are 9.55 residues in the N-terminal region and 9.85 residues in the C-terminal region. The regions at each end of the protein chain (residues 1-55 and 367-412) are not alpha-helical and contain many potential beta-bends. The regions specified in have a significant degree of homology mainly due to a semi-regular disposition of proline and half-cystine residues on a three-residue grid; this is especially apparent in the C-terminal segment, in which short (Pro-Cys-Xaa)n regions occur. The coiled-coil segments of component 8c-1 bear a striking similarity to corresponding segments of other intermediate-filament proteins as regards sequence homology, structural periodicity of ionic residues and secondary/tertiary-structure predictions. The assessments of the probabilities that these homologies occurred by chance indicate that there are two populations of keratin filament proteins. The non-coiled-coil regions at each end of the chain are less hydrophilic than the coiled-coil regions. Ionic interactions between the heptad regions of components 8c-1 and 7c from the microfibrils of alpha-keratin are optimized when a coiled-coil structure is formed with the heptad regions of the constituent chains both parallel and in register.

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Ludwiczak, Jan, Aleksander Winski, Krzysztof Szczepaniak, Vikram Alva, and Stanislaw Dunin-Horkawicz. "DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences." Bioinformatics 35, no. 16 (January 2, 2019): 2790–95. http://dx.doi.org/10.1093/bioinformatics/bty1062.

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Abstract Motivation Coiled coils are protein structural domains that mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function. Results Here, we report DeepCoil, a new neural network-based tool for the detection of coiled-coil domains in protein sequences. In our benchmarks, DeepCoil significantly outperformed current state-of-the-art tools, such as PCOILS and Marcoil, both in the prediction of canonical and non-canonical coiled coils. Furthermore, in a scan of the human genome with DeepCoil, we detected many coiled-coil domains that remained undetected by other methods. This higher sensitivity of DeepCoil should make it a method of choice for accurate genome-wide detection of coiled-coil domains. Availability and implementation DeepCoil is written in Python and utilizes the Keras machine learning library. A web server is freely available at https://toolkit.tuebingen.mpg.de/#/tools/deepcoil and a standalone version can be downloaded at https://github.com/labstructbioinf/DeepCoil. Supplementary information Supplementary data are available at Bioinformatics online.

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Carter, Andrew P., and Ronald D. Vale. "Communication between the AAA+ ring and microtubule-binding domain of dyneinThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 1 (February 2010): 15–21. http://dx.doi.org/10.1139/o09-127.

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Dyneins are microtubule motors, the core of which consists of a ring of AAA+ domains. ATP-driven conformational changes of the AAA+ ring are used to drive the movement of a mechanical element (termed the linker domain) that provides the motor’s powerstroke and to change the affinity of the motor for microtubules (strong binding during the power stroke and weak binding to allow stepping and recocking of the linker domain). Dynein’s microtubule-binding domain (MTBD) is located at the end of a 10 nm long anti-parallel coiled coil (the stalk) and conformational changes that alter the affinity for microtubules must propagate through this coiled coil. A recent crystal structure of dynein’s MTBD sheds new light on how this long-range communication along a coiled coil might occur.

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Choi, Jin Hyeong, Jun Ho Noh, and Changsoon Choi. "Highly Elastically Deformable Coiled CNT/Polymer Fibers for Wearable Strain Sensors and Stretchable Supercapacitors." Sensors 23, no. 4 (February 20, 2023): 2359. http://dx.doi.org/10.3390/s23042359.

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Stretchable yarn/fiber electronics with conductive features are optimal components for different wearable devices. This paper presents the construction of coil structure-based carbon nanotube (CNT)/polymer fibers with adjustable piezoresistivity. The composite unit fiber is prepared by wrapping a conductive carbon CNT sheath onto an elastic spandex core. Owing to the helical coil structure, the resultant CNT/polymer composite fibers are highly stretchable (up to approximately 300%) without a noticeable electrical breakdown. More specifically, based on the difference in the coil index (which is the ratio of the coil diameter to the diameter of the fiber within the coil) according to the polymeric core fiber (spandex or nylon), the composite fiber can be used for two different applications (i.e., as strain sensors or supercapacitors), which are presented in this paper. The coiled CNT/spandex composite fiber sensor responds sensitively to tensile strain. The coiled CNT/nylon composite fiber can be employed as an elastic supercapacitor with excellent capacitance retention at 300% strain.

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Meseroll, Rebecca A., Patricia Occhipinti, and Amy S. Gladfelter. "Septin Phosphorylation and Coiled-Coil Domains Function in Cell and Septin Ring Morphology in the Filamentous Fungus Ashbya gossypii." Eukaryotic Cell 12, no. 2 (November 30, 2012): 182–93. http://dx.doi.org/10.1128/ec.00251-12.

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ABSTRACT Septins are a class of GTP-binding proteins conserved throughout many eukaryotes. Individual septin subunits associate with one another and assemble into heteromeric complexes that form filaments and higher-order structures in vivo . The mechanisms underlying the assembly and maintenance of higher-order structures in cells remain poorly understood. Septins in several organisms have been shown to be phosphorylated, although precisely how septin phosphorylation may be contributing to the formation of high-order septin structures is unknown. Four of the five septins expressed in the filamentous fungus, Ashbya gossypii , are phosphorylated, and we demonstrate here the diverse roles of these phosphorylation sites in septin ring formation and septin dynamics, as well as cell morphology and viability. Intriguingly, the alteration of specific sites in Cdc3p and Cdc11p leads to a complete loss of higher-order septin structures, implicating septin phosphorylation as a regulator of septin structure formation. Introducing phosphomimetic point mutations to specific sites in Cdc12p and Shs1p causes cell lethality, highlighting the importance of normal septin modification in overall cell function and health. In addition to discovering roles for phosphorylation, we also present diverse functions for conserved septin domains in the formation of septin higher-order structure. We previously showed the requirement for the Shs1p coiled-coil domain in limiting septin ring size and reveal here that, in contrast to Shs1p, the coiled-coil domains of Cdc11p and Cdc12p are required for septin ring formation. Our results as a whole reveal novel roles for septin phosphorylation and coiled-coil domains in regulating septin structure and function.

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Marin, E. P., та R. R. Neubig. "Lack of association of G-protein β2- and γ2-subunit N-terminal fragments provides evidence against the coiled-coil model of subunit-βγ assembly". Biochemical Journal 309, № 2 (15 липня 1995): 377–80. http://dx.doi.org/10.1042/bj3090377.

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The association between peptides from bovine G-protein beta 2- and gamma 2-subunits was studied by CD spectroscopy and cross-linking. Both peptides had approximately 25% stable alpha-helical structure at 25 degrees C, but there was no increase on mixing subunits as expected for coiled-coil formation. Also, disulphide cross-linking gave more beta 2 beta 2 homodimer than beta 2 gamma 2 heterodimer. These data do not support the proposed N-terminal coiled-coil model of beta gamma-subunit association.

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Di Palma, Francesco, Gian Luca Daino, Venkata Krishnan Ramaswamy, Angela Corona, Aldo Frau, Elisa Fanunza, Attilio V. Vargiu, Enzo Tramontano, and Paolo Ruggerone. "Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition." Antiviral Chemistry and Chemotherapy 27 (January 2019): 204020661988922. http://dx.doi.org/10.1177/2040206619889220.

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Ebola virus high lethality relies on its ability to efficiently bypass the host innate antiviral response, which senses the viral dsRNA through the RIG-I receptor and induces type I interferon α/β production. In the bypassing action, the Ebola virus protein VP35 plays a pivotal role at multiple levels of the RIG-I cascade, masking the viral 5′-triphosphorylated dsRNA from RIG-I, and interacting with other cascade components. The VP35 type I interferon inhibition is exerted by the C-terminal domain, while the N-terminal domain, containing a coiled-coil region, is primarily required for oligomerization. However, mutations at key VP35 residues L90/93/107A (VP35-3m) in the coiled-coil region were reported to affect oligomerization and reduce type I interferon antagonism, indicating a possible but unclear role of homo-oligomerization on VP35 interaction with the RIG-I pathway components. In this work, we investigated the VP35 dimerization thermodynamics and its contribution to type I interferon antagonism by computational and biological methods. Focusing on the coiled-coil region, we combined coarse-grained and all-atom simulations on wild type VP35 and VP35-3m homo-dimerization. According to our results, wild type VP35 coiled-coil is able to self-assemble into dimers, while VP35-3m coiled-coil shows poor propensity to even dimerize. Free-energy calculations confirmed the key role of L90, L93 and L107 in stabilizing the coiled-coil homo-dimeric structure. In vitro type I interferon antagonism studies, using full-length wild type VP35 and VP35-3m, revealed that VP35 homo-dimerization is an essential preliminary step for dsRNA binding, which appears to be the main factor of the VP35 RIG-I cascade inhibition, while it is not essential to block the other steps.

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Odgren, Paul R., Lawrence W. Harvie, and Edward G. Fey. "Phylogenetic occurrence of coiled coil proteins: Implications for tissue structure in metazoa via a coiled coil tissue matrix." Proteins: Structure, Function, and Genetics 24, no. 4 (April 1996): 467–84. http://dx.doi.org/10.1002/(sici)1097-0134(199604)24:4<467::aid-prot6>3.0.co;2-b.

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Drennan, Amanda C., Shivaani Krishna, Mark A. Seeger, Michael P. Andreas, Jennifer M. Gardner, Emily K. R. Sether, Sue L. Jaspersen, and Ivan Rayment. "Structure and function of Spc42 coiled-coils in yeast centrosome assembly and duplication." Molecular Biology of the Cell 30, no. 12 (June 2019): 1505–22. http://dx.doi.org/10.1091/mbc.e19-03-0167.

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Centrosomes and spindle pole bodies (SPBs) are membraneless organelles whose duplication and assembly is necessary for bipolar mitotic spindle formation. The structural organization and functional roles of major proteins in these organelles can provide critical insights into cell division control. Spc42, a phosphoregulated protein with an N-terminal dimeric coiled-coil (DCC), assembles into a hexameric array at the budding yeast SPB core, where it functions as a scaffold for SPB assembly. Here, we present in vitro and in vivo data to elucidate the structural arrangement and biological roles of Spc42 elements. Crystal structures reveal details of two additional coiled-coils in Spc42: a central trimeric coiled-coil and a C-terminal antiparallel DCC. Contributions of the three Spc42 coiled-coils and adjacent undetermined regions to the formation of an ∼145 Å hexameric lattice in an in vitro lipid monolayer assay and to SPB duplication and assembly in vivo reveal structural and functional redundancy in Spc42 assembly. We propose an updated model that incorporates the inherent symmetry of these Spc42 elements into a lattice, and thereby establishes the observed sixfold symmetry. The implications of this model for the organization of the central SPB core layer are discussed.

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Gong, Xinyu, Yingli Wang, Yuqian Zhou, and Lifeng Pan. "Structure of the WIPI3/ATG16L1 Complex Reveals the Molecular Basis for the Recruitment of the ATG12~ATG5-ATG16L1 Complex by WIPI3." Cells 13, no. 24 (December 20, 2024): 2113. https://doi.org/10.3390/cells13242113.

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Macroautophagy deploys a wealth of autophagy-related proteins to synthesize the double-membrane autophagosome, in order to engulf cytosolic components for lysosome-dependent degradation. The recruitment of the ATG12~ATG5-ATG16L1 complex by WIPI family proteins is a crucial step in autophagosome formation. Nevertheless, the molecular mechanism by which WIPI3 facilitates the recruitment of the ATG12~ATG5-ATG16L1 complex remains largely unknown. Here, we uncover that WIPI3 can directly interact with the coiled-coil domain of ATG16L1. By determining the crystal structure of WIPI3 in complex with ATG16L1 coiled-coil, we elucidate the molecular basis underpinning the specific recruitment of the ATG12~ATG5-ATG16L1 complex by WIPI3. Moreover, we demonstrate that WIPI2 and WIPI3 are competitive for interacting with ATG16L1 coiled-coil, and ATG16L1 and ATG2 are mutually exclusive in binding to WIPI3. In all, our findings provide mechanistic insights into the WIPI3/ATG16L1 interaction, and are valuable for further understanding the activation mechanism of the ATG12~ATG5-ATG16L1 complex as well as the working mode of WIPI3 in autophagy.

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Jacques, David, Cy Jeffries, Matthew Caines, Michael Lammers, Donna Mallery, Amanda Price, Stephen McLaughlin, Chris Johnson, Dmitri Svergun, and Leo James. "TRIM protein domain topology and implications for antiviral immunity." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C243. http://dx.doi.org/10.1107/s2053273314097563.

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The tripartite motif (TRIM) proteins are a large family of >100 members, several of which have important roles in antiviral immunity and innate immune signaling. TRIM5α associates with incoming HIV-1 capsids, interfering with controlled disassembly and targeting them for degradation by the proteasome. TRIM21 is a cytosolic antibody receptor, which also targets incoming viral capsids for proteasomal degradation. TRIM25 is also involved in innate immunity, being essential for the ubiquitination of RIG-I. Recent positive selection analysis has predicted another 10 TRIM proteins with antiviral activity. Despite the fact that TRIM5α, 21 and 25 play key roles in antiviral protection, their mechanism of action is incompletely understood. All three proteins share a similar domain architecture, comprising a RING, B Box, coiled coil and PRYSPRY domains. The RING domains are responsible for ubiquitin ligase activity, while the PRYSPRY domains determine target specificity. We have used a combination of crystallography and SAXS to generate the first complete model for a TRIM protein structure. Crystallographic studies of TRIM25 reveal a central elongated coiled-coil domain with an unusual right-handed twist. The dimer formed by the coiled-coil is antiparallel but is followed by additional helices that reverse the direction of the protein chain. This structure suggests that the N-terminal domains of each monomer are separated but the C terminal domains are maintained in proximity. Multi-angle light scattering (MALS), isothermal titration calorimetry (ITC) and SAXS analysis confirms that this dimer structure is present in solution. Furthermore, scattering studies on the tripartite motif of TRIM21, comprising RING, B Box and coiled-coil, demonstrate that the first two domains of each monomer are held 150-200 Å apart. Finally, SAXS measurement of a complex between intact TRIM21 and its ligand, IgG Fc, provides the first empirical structure of a complete TRIM protein.

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Cornillez-Ty, Cromwell T., and David W. Lazinski. "Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo." Journal of Virology 77, no. 19 (October 1, 2003): 10314–26. http://dx.doi.org/10.1128/jvi.77.19.10314-10326.2003.

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ABSTRACT Hepatitis delta virus expresses two essential proteins, the small and large delta antigens, and both are required for viral propagation. Proper function of each protein depends on the presence of a common amino-terminal multimerization domain. A crystal structure, solved using a peptide fragment that contained residues 12 to 60, depicts the formation of an octameric ring composed of antiparallel coiled-coil dimers. Because this crystal structure was solved for only a fragment of the delta antigens, it is unknown whether octamers actually form in vivo at physiological protein concentrations and in the context of either intact delta antigen. To test the relevance of the octameric structure, we developed a new method to probe coiled-coil structures in vivo. We generated a panel of mutants containing cysteine substitutions at strategic locations within the predicted monomer-monomer interface and the dimer-dimer interface. Since the small delta antigen contains no cysteine residues, treatment of cell extracts with a mild oxidizing reagent was expected to induce disulfide bond formation only when the appropriate pairs of cysteine substitution mutants were coexpressed. We indeed found that, in vivo, both the small and large delta antigens assembled as antiparallel coiled-coil dimers. Likewise, we found that both proteins could assume an octameric quaternary structure in vivo. Finally, during the course of these experiments, we found that unprenylated large delta antigen molecules could be disulfide cross-linked via the sole cysteine residue located within the carboxy terminus. Therefore, in vivo, the C terminus likely provides an additional site of protein-protein interaction for the large delta antigen.

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Taylor, Keenan C., Massimo Buvoli, Elif Nihal Korkmaz, Ada Buvoli, Yuqing Zheng, Nathan T. Heinze, Qiang Cui, Leslie A. Leinwand, and Ivan Rayment. "Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly." Proceedings of the National Academy of Sciences 112, no. 29 (July 6, 2015): E3806—E3815. http://dx.doi.org/10.1073/pnas.1505813112.

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The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report here that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. In addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.

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Nautiyal, Shivani, and Tom Alber. "Crystal structure of a designed, thermostable, heterotrimeric coiled coil." Protein Science 8, no. 1 (December 31, 2008): 84–90. http://dx.doi.org/10.1110/ps.8.1.84.

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43

Bassel-Duby, Rhonda, Anula Jayasuriya, Devjani Chatterjee, Nahum Sonenberg, Jacob V. Maizel, and Bernard N. Fields. "Sequence of reovirus haemagglutinin predicts a coiled-coil structure." Nature 315, no. 6018 (May 1985): 421–23. http://dx.doi.org/10.1038/315421a0.

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44

Sato, Yusuke, Ryutaro Shirakawa, Hisanori Horiuchi, Naoshi Dohmae, Shuya Fukai, and Osamu Nureki. "Asymmetric Coiled-Coil Structure with Guanine Nucleotide Exchange Activity." Structure 15, no. 2 (February 2007): 245–52. http://dx.doi.org/10.1016/j.str.2007.01.003.

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45

Hitchcock-DeGregori, Sarah E., Stephen F. Lewis, and Tony M. T. Chou. "Tropomyosin lysine reactivities and relationship to coiled-coil structure." Biochemistry 24, no. 13 (June 18, 1985): 3305–14. http://dx.doi.org/10.1021/bi00334a035.

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46

Lin, Xingcheng, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma, and José N. Onuchic. "Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill." Proceedings of the National Academy of Sciences 115, no. 34 (July 16, 2018): E7905—E7913. http://dx.doi.org/10.1073/pnas.1805442115.

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Influenza hemagglutinin (HA) mediates viral entry into host cells through a large-scale conformational rearrangement at low pH that leads to fusion of the viral and endosomal membranes. Crystallographic and biochemical data suggest that a loop-to-coiled-coil transition of the B-loop region of HA is important for driving this structural rearrangement. However, the microscopic picture for this proposed “spring-loaded” movement is missing. In this study, we focus on understanding the transition of the B loop and perform a set of all-atom molecular dynamics simulations of the full B-loop trimeric structure with the CHARMM36 force field. The free-energy profile constructed from our simulations describes a B loop that stably folds half of the postfusion coiled coil in tens of microseconds, but the full coiled coil is unfavorable. A buried hydrophilic residue, Thr59, is implicated in destabilizing the coiled coil. Interestingly, this conserved threonine is the only residue in the B loop that strictly differentiates between the group 1 and 2 HA molecules. Microsecond-scale constant temperature simulations revealed that kinetic traps in the structural switch of the B loop can be caused by nonnative, intramonomer, or intermonomer β-sheets. The addition of the A helix stabilized the postfusion state of the B loop, but introduced the possibility for further β-sheet structures. Overall, our results do not support a description of the B loop in group 2 HAs as a stiff spring, but, rather, it allows for more structural heterogeneity in the placement of the fusion peptides during the fusion process.

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47

Thomas, Jens, Ronan Keegan, Jaclyn Bibby, Martyn Winn, Olga Mayans, and Daniel Rigden. "Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C347. http://dx.doi.org/10.1107/s2053273314096521.

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Molecular Replacement (MR) is an increasingly popular route to protein structure solution. AMPLE[1] is a software pipeline that uses either cheaply obtained ab inito protein models, or NMR structures to extend the scope of MR, allowing it to solve entirely novel protein structures in a completely automated pipeline on a standard desktop computer. AMPLE employs a cluster-and-truncate approach, combined with multiple modes of side chain treatment, to analyse the candidate models and extract the consensual features most likely to solve the structure. The search models generated in this way are screened by MrBump using Phaser and Molrep and correct solutions are detected using main chain tracing and phase modification with Shelxe. AMPLE proved capable of processing rapidly obtained ab initio structure predictions into successful search models and more recently proved effective in assembling NMR structures for MR[2]. Coiled-coil proteins are a distinct class of protein fold whose structure solution by MR is not typically straightforward. We show here that AMPLE can quickly and routinely solve most coiled-coil structures using ab initio predictions from Rosetta. The predictions are generally not globally accurate, but by encompassing different degrees of truncation of clustered models, AMPLE succeeds by sampling across a range of search models. These sometimes succeed through capturing locally well-modelled conformations, but often simply contain small helical units. Remarkably, the latter regularly succeed despite out-of-register placement and poor MR statistics. We demonstrate that single structures derived from successful ensembles perform less well, and comparable ideal helices solve few targets. Thus, both modelling of distortions from ideal helical geometry and the ensemble nature of the search models contribute to success. AMPLE is a framework applicable to any set of input structures in which variability is correlated with inaccuracy. We also present preliminary data demonstrating structure solution of transmembrane helical structures using Rosetta modelling. We finally consider future sources of starting models which offer the hope that MR with AMPLE, in the absence of close homology between a known structure and the target, may soon be possible with larger proteins.

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Hoenger, A., S. Sack, M. Thormählen, A. Marx, J. Müller, H. Gross, and E. Mandelkow. "Image Reconstructions of Microtubules Decorated with Monomeric and Dimeric Kinesins: Comparison with X-Ray Structure and Implications for Motility." Journal of Cell Biology 141, no. 2 (April 20, 1998): 419–30. http://dx.doi.org/10.1083/jcb.141.2.419.

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We have decorated microtubules with monomeric and dimeric kinesin constructs, studied their structure by cryoelectron microscopy and three-dimensional image reconstruction, and compared the results with the x-ray crystal structure of monomeric and dimeric kinesin. A monomeric kinesin construct (rK354, containing only a short neck helix insufficient for coiled-coil formation) decorates microtubules with a stoichiometry of one kinesin head per tubulin subunit (α–β-heterodimer). The orientation of the kinesin head (an anterograde motor) on the microtubule surface is similar to that of ncd (a retrograde motor). A longer kinesin construct (rK379) forms a dimer because of the longer neck helix forming a coiled-coil. Unexpectedly, this construct also decorates the microtubule with a stoichiometry of one head per tubulin subunit, and the orientation is similar to that of the monomeric construct. This means that the interaction with microtubules causes the two heads of a kinesin dimer to separate sufficiently so that they can bind to two different tubulin subunits. This result is in contrast to recent models and can be explained by assuming that the tubulin–kinesin interaction is antagonistic to the coiled-coil interaction within a kinesin dimer.

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Pellegrino, Simone, Daniele de Sanctis, Sean McSweeney, and Joanna Timmins. "Expression, purification and preliminary structural analysis of the coiled-coil domain ofDeinococcus radioduransRecN." Acta Crystallographica Section F Structural Biology and Crystallization Communications 68, no. 2 (January 26, 2012): 218–21. http://dx.doi.org/10.1107/s1744309111055187.

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Deinococcus radioduranshas developed an efficient mechanism which allows the integrity of its entire genome to be fully restored after exposure to very high doses of ionizing radiation. Homologous recombination plays a crucial role in this process. RecN is a protein that belongs to the SMC-like protein family and is suggested to be involved in DNA repair. RecN is composed of a globular domain and an antiparallel coiled-coil region which connects the N- and C-termini. It has been suggested that dimerization of RecN occursviathe coiled-coil domain, but to date there is no structural or biochemical evidence for this. Here, SAXS studies and preliminary X-ray diffraction data of crystals of the purified coiled-coil domain of RecN are presented. The structure was solved by single-wavelength anomalous dispersion using SeMet derivatives, and preliminary electron-density maps support the rod-like model derived from the SAXS data. Model building and refinement are still ongoing.

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Hoh, François, Marilyne Uzest, Martin Drucker, Célia Plisson-Chastang, Patrick Bron, Stéphane Blanc, and Christian Dumas. "Structural Insights into the Molecular Mechanisms of Cauliflower Mosaic Virus Transmission by Its Insect Vector." Journal of Virology 84, no. 9 (February 24, 2010): 4706–13. http://dx.doi.org/10.1128/jvi.02662-09.

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ABSTRACT Cauliflower mosaic virus (CaMV) is transmitted from plant to plant through a seemingly simple interaction with insect vectors. This process involves an aphid receptor and two viral proteins, P2 and P3. P2 binds to both the aphid receptor and P3, itself tightly associated with the virus particle, with the ensemble forming a transmissible viral complex. Here, we describe the conformations of both unliganded CaMV P3 protein and its virion-associated form. X-ray crystallography revealed that the N-terminal domain of unliganded P3 is a tetrameric parallel coiled coil with a unique organization showing two successive four-stranded subdomains with opposite supercoiling handedness stabilized by a ring of interchain disulfide bridges. A structural model of virus-liganded P3 proteins, folding as an antiparallel coiled-coil network coating the virus surface, was derived from molecular modeling. Our results highlight the structural and biological versatility of this coiled-coil structure and provide new insights into the molecular mechanisms involved in CaMV acquisition and transmission by the insect vector.

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