Literatura científica selecionada sobre o tema "Coiled-coil structure"
Crie uma referência precisa em APA, MLA, Chicago, Harvard, e outros estilos
Consulte a lista de atuais artigos, livros, teses, anais de congressos e outras fontes científicas relevantes para o tema "Coiled-coil structure".
Ao lado de cada fonte na lista de referências, há um botão "Adicionar à bibliografia". Clique e geraremos automaticamente a citação bibliográfica do trabalho escolhido no estilo de citação de que você precisa: APA, MLA, Harvard, Chicago, Vancouver, etc.
Você também pode baixar o texto completo da publicação científica em formato .pdf e ler o resumo do trabalho online se estiver presente nos metadados.
Artigos de revistas sobre o assunto "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, n.º 45 (22 de outubro de 2018): E10748—E10757. http://dx.doi.org/10.1073/pnas.1807206115.
Texto completo da fonteResumo:
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.
2
Vajda, Tamás, e András Perczel. "The clear and dark sides of water: influence on the coiled coil folding domain". Biomolecular Concepts 7, n.º 3 (1 de junho de 2016): 189–95. http://dx.doi.org/10.1515/bmc-2016-0005.
Texto completo da fonteResumo:
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.
3
Fu, Ruijiang, Wu-Pei Su e Hongxing He. "Direct Phasing of Coiled-Coil Protein Crystals". Crystals 12, n.º 11 (20 de novembro de 2022): 1674. http://dx.doi.org/10.3390/cryst12111674.
Texto completo da fonteResumo:
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.
4
Wilbur, Jeremy D., Peter K. Hwang, Frances M. Brodsky e Robert J. Fletterick. "Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain". Acta Crystallographica Section D Biological Crystallography 66, n.º 3 (12 de fevereiro de 2010): 314–18. http://dx.doi.org/10.1107/s0907444909054535.
Texto completo da fonteResumo:
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.
5
Thomas, Jens M. H., Ronan M. Keegan, Daniel J. Rigden e 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, n.º 3 (25 de fevereiro de 2020): 272–84. http://dx.doi.org/10.1107/s2059798320000443.
Texto completo da fonteResumo:
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.
6
Caillat, Christophe, Alexander Fish, Dafni-Eleftheria Pefani, Stavros Taraviras, Zoi Lygerou e 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, n.º 11 (31 de outubro de 2015): 2278–86. http://dx.doi.org/10.1107/s1399004715016892.
Texto completo da fonteResumo:
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.
7
Alminaite, Agne, Vera Backström, Antti Vaheri e 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, n.º 9 (1 de setembro de 2008): 2167–74. http://dx.doi.org/10.1099/vir.0.2008/004044-0.
Texto completo da fonteResumo:
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.
8
Thomas, Jens M. H., Ronan M. Keegan, Jaclyn Bibby, Martyn D. Winn, Olga Mayans e Daniel J. Rigden. "Routine phasing of coiled-coil protein crystal structures withAMPLE". IUCrJ 2, n.º 2 (26 de fevereiro de 2015): 198–206. http://dx.doi.org/10.1107/s2052252515002080.
Texto completo da fonteResumo:
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.
9
Kuruba, Balaganesh, Marta Kaczmarek, Małgorzata Kęsik-Brodacka, Magdalena Fojutowska, Małgorzata Śliwinska, Alla S. Kostyukova e Joanna Moraczewska. "Structural Effects of Disease-Related Mutations in Actin-Binding Period 3 of Tropomyosin". Molecules 26, n.º 22 (19 de novembro de 2021): 6980. http://dx.doi.org/10.3390/molecules26226980.
Texto completo da fonteResumo:
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.
10
Gáspári, Zoltán, e László Nyitray. "Coiled coils as possible models of protein structure evolution". BioMolecular Concepts 2, n.º 3 (1 de junho de 2011): 199–210. http://dx.doi.org/10.1515/bmc.2011.015.
Texto completo da fonteResumo:
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.
Teses / dissertações sobre o assunto "Coiled-coil structure"
1
Gutwin, Karl N. (Karl Nickolai). "Computational prediction of coiled-coil interaction structure specificity". Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/47880.
Texto completo da fonteResumo:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2009.Page 224 blank.
Includes bibliographical references.
The alpha-helical coiled coil is a protein sequence and structural motif that consists of two or more helices in a parallel or antiparallel orientation supercoiling around a central axis. Coiled coils have been observed in a wide range of protein families, and many studies have focused on their sequence and structural diversity over the past half-century. In particular, the observation that coiled coils can be involved in determining protein-protein interactions and protein architectures has prompted the developments of methods to predict the structure of a coiled-coil complex from sequence information alone. In this thesis, I discuss the development of a structurally annotated database of coiled-coil sequence useful for training statistics-based methods of coiled-coil structure prediction. This database was used to retrain and stringently cross-validate the Multicoil method of predicting coiled-coil oligomerization state. In addition, I describe recent work using implicit and explicit structure models to predict dimeric coiled-coil orientation and alignment. Improvements to existing models, insight into coiled-coil structure determinants, and the future of coiled-coil prediction are also discussed.
by Karl N. Gutwin.
Ph.D.
2
Allan, Robert Douglas. "Computational analysis and experimental characterisation of natural antiparallel coiled-coil motifs". Thesis, University of Sussex, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343369.
Texto completo da fonte
3
Odgren, Paul R. "Molecular Characterization of Mitofilin, a Novel, Mitochondrial, Coiled Coil Protein, and the Relationship Between Organism Complexity and Coiled Coil Protein-Mediated Structure: A Dissertation". eScholarship@UMMS, 1995. https://escholarship.umassmed.edu/gsbs_diss/28.
Texto completo da fonteResumo:
In the course of experiments designed to identify and characterize structural proteins of the nuclear matrix, one antibody was generated which recognized an extraction-resistant cytoplasmic protein. This antibody was used as the starting point in the cloning and molecular characterization of a novel protein of the inter-membrane space of the mitochondrion which has been named mitofilin. Mitofilin is expressed in all human cell types, and murine homologues also exist. Mitofilin associates only with mitochondria and not with other membrane-bounded organelles such as Golgi or endoplasmic reticulum. This observation has been confirmed both by biochemical fractionation and multi-label fluorescence microscopy. Recombinant mitofilin, purified to homogeneity by affinity chromatography and preparative electrophoresis, was used to raise second-generation antibodies. Results of Western blot and immunofluorescence microscopy experiments, identical to those obtained using the original monoclonal antibody, verify the cloning and biochemical characterization. The mitofilin polypeptide contains several regions which are predicted to interact by forming coiled coils; a mitochondrial targeting signal; and a hydrophobic, membrane-spanning domain. During the course of this work, a sequence match was found with a cDNA reported by Icho, et al (1994) for a mRNA preferentially expressed in heart muscle, which they have called HMP. Evidence is presented which contradicts those authors' contention that HMP is a kinesin-like motor protein.
In the course of these investigations, methods were developed to detect and quantitate the expression of solubilization-resistant proteins of the nuclear matrix and the nuclear matrix-intermediate filament scaffold. This was accomplished by combining SDS-PAGE, high sensitivity chemiluminescent Western blots, and scanning densitometry. Sensitivity in the picogram range was obtained, and reproducibility was assessed. For semi-quantitative measurements of protein expression in tissue samples, cell number was normalized by measurement of lamin B, the major protein of the nuclear envelope. Results of screening several cell and tissue types for the expression of mitofilin and for the nuclear matrix proteins NuMA, the nucleoporin tpr, and lamin B are presented. These preliminary data suggest a potential connection of over-expression of NuMA, tpr, and mitofilin with ovarian carcinoma. In addition, quantitative analysis of mitofilin expression in a variety of human cell types was done using purified recombinant protein antigen as the standard.
The presence of coiled coil domains in these and other proteins associated with cellular sub-structures gave rise to the third area of investigation described here. Experimental observations of the nuclear matrix-intermediate filament scaffold (NMIF), a tissue-wide structure greatly enriched in coiled coil proteins, led to the following hypothesis: that the differentiated cell and tissue architecture which characterizes Metazoa has evolved through the propagation and selective expression of genes encoding a wide variety of coiled coil proteins, and the integration of the gene products into a tissue-wide matrix based on coiled coil interactions. This hypothesis was explored by computer searches of sequence data files. The GenBank phylogenetic sequence files were examined with a heptad repeat analysis program to assess the occurrence of coiled coil proteins. how heptad repeat domains are organized within these proteins, and what structural/functional categories they comprised. Of 102,007 proteins analyzed, 5.95% (6074) contained coiled coil domains: 1.26% (1289) contained "extended" (> 75 amino acid) domains. While the frequency of proteins containing coiled coils was surprisingly constant among all biota, extended coiled coil proteins were 4-fold more frequent in the animal kingdom, and may reflect early events in the divergence of plants and animals. Structure/function categories of extended coils also revealed phylogenetic differences. In pathogens and parasites, many extended coiled coil proteins are external and bind host proteins. In animals, the majority of extended coiled coil proteins were identified as constituents of two categories: 1) myosins and motors, or 2) components of the NMIF. This scaffold, produced by sequential extraction of epithelial monolayers in situ, contains only 1-2% of the cell mass while accurately retaining morphological features of living epithelium. The NMIF incorporates many proteins with extensive, interrupted coiled coil forming domains. The increased occurrence of this type of protein in Metazoa compared to plants or protists supports the hypothesis that a tissue-wide matrix of coiled coil interactions underlies metazoan differentiated cell and tissue structure.
4
Shen, Wei Tirrell David A. Tirrell David A. "Structure, dynamics, and properties of artificial protein hydrogels assembled through coiled-coil domains /". Diss., Pasadena, Calif. : California Institute of Technology, 2005. http://resolver.caltech.edu/CaltechETD:etd-05132005-114413.
Texto completo da fonte
5
Makarov, Alexandr. "New insights into the structure and assembly of nuclear lamins from chemical cross-linking and mass spectrometry". Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28872.
Texto completo da fonteResumo:
Now that the functioning of microtubules and the actin cytoskeleton has been worked out in enormous detail, the next important task is defining the structure of intermediate filaments that are far behind the other two major skeletal networks due to their inherent resistance to most structural techniques. The evolution of novel structural approaches for flexible proteins is making this possible now. In my thesis I will aim to elucidate the structure and assembly principles of lamin A nuclear intermediate filament protein. To study lamin A, I principally employed chemical cross-linking that allows the capturing of full-length protein structures in solution. I combined this with mass spectrometry approaches to identify cross-linked residues at the various stages of lamin A assembly that were additionally tracked with SILAC labelling and rotary metal shadowing TEM. Unlike previous cross-linking studies on intermediate filaments I use a zero-length self-excluding cross-linking agent EDC that is better tailored for investigation of the polar interactions between multiple unstructured or otherwise flexible charged sequences of lamins. Using this composite approach I interrogated lamin A dimeric and tetrameric assemblies. I elucidated hinge-like properties of the L12 and found indications that L1 and the region containing coil 2A and L2 and the beginning of coil 2B possess properties of linker-like flexibility and of predicted linear α-helical bundle and could act as molecular springs or compression buffers for the nuclear intermediate filaments. Further I confirm the role of the N-terminal unstructured region in lamin A assembly and for the first time show similar role for the C-terminal unstructured region flanking the rod domain of lamin A. Collected data strongly supports the model where both positively charged unstructured regions participate in extensive interaction with acidic rod termini and act as molecular bridges between these in the head-to-tail interface, confirming the uniformity of this principle between cytoplasmic and nuclear intermediate filaments. Formation of these bridges requires conformational change likely happening due to proline residues in the mitotic phosphorylation sites. Finally I suggest a mechanism of regulation of the order of assembly unique to the nuclear intermediate filament where C-terminal unstructured region blocks lateral interactions until it is tethered to the head-to-tail interface. Collected data on the dynamic behaviour of the C-terminal unstructured region and its ability to tether lamin A Ig domain may have far reaching implications for filament assembly and regulation of binding of hundreds of lamin A partner proteins presenting an important step in our understanding of relationship between lamin A structure and function and how altering the former could lead to disease.
6
Chang, Eric P. "The Rational Design of Coiled-Coil Peptides towards Understanding Protein-Crystal Interactions and Amorphous-to-Crystalline Transitions". Bowling Green State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1363258701.
Texto completo da fonte
7
Smith, Mason Scott. "Measuring the Interaction and Cooperativity Between Ionic, Aromatic, and Nonpolar Amino Acids in Protein Structure". BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7443.
Texto completo da fonteResumo:
Protein folding studies have provided important insights about the key role of non-covalent interactions in protein structure and conformational stability. Some of these interactions include salt bridges, cation-π, and anion-Ï€ interactions. Understanding these interactions is crucial to developing methods for predicting protein secondary, tertiary, quaternary structure from primary sequence and understanding protein-protein interactions and protein-ligand interactions. Several studies have described how the interaction between two amino acid side chains have a substantial effect on protein structure and conformational stability. This is under the assumption that the interaction between the two amino acids is independent of surrounding interactions. We are interested in understanding how salt bridges, cation-π, and anion-π interactions affect each other when they are in close proximity. Chapter 1 is a brief introduction on noncovalent interactions and noncovalent interaction cooperativity. Chapter 2 describes the progress we have made measuring the cooperativity between noncovalent interactions involving cations, anions and aromatic amino acids in a coiled-coil alpha helix model protein. Chapter 3 describes cooperativity between cation, anion, and nonaromatic hydrophobic amino acids in the context of a coiled-coil alpha helix. In chapter 4 we describe a strong anion-π interaction in a reverse turn that stabilizes a beta sheet model protein. In chapter 5 we measure the interaction between a cysteine linked maleimide and two lysines in a helix and show that it is a general strategy to stabilize helical structure.
8
Behrens, Caroline Anna Julie [Verfasser], Karin [Akademischer Betreuer] Kühnel, Michael [Akademischer Betreuer] Thumm, Markus [Akademischer Betreuer] Zweckstetter e Marina [Akademischer Betreuer] Rodnina. "Crystal Structure and Characterization of the SCOC Coiled Coil Domain / Caroline Anna Julie Behrens. Gutachter: Michael Thumm ; Markus Zweckstetter ; Marina Rodnina. Betreuer: Karin Kühnel". Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2014. http://d-nb.info/1054821992/34.
Texto completo da fonte
9
Fitzgerald, Amanda Ann. "Folding and Assembly of Multimeric Proteins: Dimeric HIV-1 Protease and a Trimeric Coiled Coil Component of a Complex Hemoglobin Scaffold: A Dissertation". eScholarship@UMMS, 2007. https://escholarship.umassmed.edu/gsbs_diss/341.
Texto completo da fonteResumo:
Knowledge of how a polypeptide folds from a space-filling random coil into a biologically-functional, three-dimensional structure has been the essence of the protein folding problem. Though mechanistic details of DNA transcription and RNA translation are well understood, a specific code by which the primary structure dictates the acquisition of secondary, tertiary, and quarternary structure remains unknown. However, the demonstrated reversibility of in vitroprotein folding allows for a thermodynamic analysis of the folding reaction. By probing both the equilibrium and kinetics of protein folding, a protein folding mechanism can be postulated. Over the past 40 years, folding mechanisms have been determined for many proteins; however, a generalized folding code is far from clear. Furthermore, most protein folding studies have focused on monomeric proteins even though a majority of biological processes function via the association of multiple subunits. Consequently, a complete understanding of the acquisition of quarternary protein structure is essential for applying the basic principles of protein folding to biology.
The studies presented in this dissertation examined the folding and assembly of two very different multimeric proteins. Underlying both of these investigations is the need for a combined analysis of a repertoire of approaches to dissect the folding mechanism for multimeric proteins. Chapter II elucidates the detailed folding energy landscape of HIV-1 protease, a dimeric protein containing β-barrel subunits. The folding of this viral enzyme exhibited a sequential three-step pathway, involving the rate-limiting formation of a monomeric intermediate. The energetics determined from this analysis and their applications to HIV-1 function are discussed. In contrast, Chapter III illustrates the association of a coiled coil component of L. terrestriserythrocruorin. This extracellular hemoglobin consists of a complex scaffold of linker chains with a central ring of interdigitating coiled coils. Allostery is maintained by twelve dodecameric hemoglobin subunits that dock upon this scaffold. Modest association was observed for this coiled coil, and the implications of this fragment to linker assembly are addressed.
These studies depict the complexity of multimeric folding reactions. Chapter II demonstrates that a detailed energy landscape of a dimeric protein can be determined by combining traditional equilibrium and kinetic approaches with information from a global analysis of kinetics and a monomer construct. Chapter III indicates that fragmentation of large complexes can show the contributions of separate domains to hierarchical organization. As a whole, this dissertation highlights the importance of pursuing mulitmeric protein folding studies and the implications of these folding mechanisms to biological function.
10
Xu, Zeren. "Le rôle et les mécanismes de l'assemblage de REMORIN". Electronic Thesis or Diss., Bordeaux, 2024. http://www.theses.fr/2024BORD0307.
Texto completo da fonteResumo:
Les remorines (REMs) sont des protéines multifonctionnelles qui jouent des rôles essentiels dans l'immunité des plantes, le développement et la symbiose en s'associant à la membrane plasmique et en séquestrant des lipides spécifiques dans des nanodomaines membranaires fonctionnels. Ces protéines sont classées dans une famille multigénique avec six groupes caractérisés par des compositions distinctes de domaines de protéines. Tous les membres de la famille des REMs partagent une ancre membranaire C-terminale (REM-CA), un domaine d'homo-oligomérisation, et une région N-terminale intrinsèquement désordonnée (IDR) de longueur variable. De manière unique, les REMs contournent la voie sécrétoire pour cibler la membrane et se localisent dans distincts nanodomaines en fonction de leur groupe phylogénétique. Dans cette étude, nous avons combiné la spectroscopie de Résonance Magnétique Nucléaire (RMN), les calculs de structure de protéines et des simulations avancées de dynamique moléculaire (MD) pour révéler les propriétés de structuration et de dynamiques des REMs. Nous avons découvert que les REMs forment des dimères stables pré-structurés en coiled-coil dans le cytosol, qui agissent comme des unités modulables pour cibler des nanodomaines. Ces dimères présentent, avant l'association avec la membrane, une charge positive de la surface en forme de code-barres, dépendante des REMs. En outre, les REM-CA montrent des variations en structures et dynamiques au sein de la famille, fournissant une plateforme sélective pour l’association avec les phospholipides lors du contact avec la membrane. L'IDR N-terminale forme un ensemble structural flexible en forme de « fuzzy coat » autour du coeur coiled-coil. Les ancres C-terminales créent une avidité à travers des interactions électrostatiques multivalentes entre les groupes des lipides anioniques et la surface chargée positivement du dimère, indiquant un mécanisme synergique entre REM-CA et le domaine coiled-coil pour ségréguer les nanodomaines lipides-protéines. La RMN du solide et les simulations MD à gros grain de REMs sur la membrane lipidique ont également révélé le comportement distinct des REM-CA lorsqu'ils sont associés aux lipides de la membrane. Nous observons des différences dans les profils d'association des REM-CA et des coiled-coils chargés à la membrane, en fonction des charges de surface du dimère et des lipides présents dans la membrane. La stabilité du coiled-coil et l'intensité de l'association à la membrane sont modulées par les groupement des tête chargées des lipides présents à la surface de la membrane. Ces découvertes améliorent notre compréhension des mécanismes moléculaires sous-jacents au rôle des REMs dans l'organisation de la membrane des plantes, des localisations séléctives des REMs dans les nanodomaines des membranes et des facteurs structurales contribuant aux différentes fonctions des remorines. Cette recherche propose une base pour de futures études visant à élucider les comportements complexes des REMs associés aux membranes et les ajustement des structures lors des mécanismes de signalisation et de défense cellulairesRemorins are multifunctional proteins that play vital roles in plant immunity, development, and symbiosis by associating with the plasma membrane and sequestering specific lipids into functional membrane nanodomains. These proteins are classified into a multigenic family with six groups characterized by distinct protein-domain compositions. All remorin family members share a C-terminal membrane anchor (REM-CA), a homo-oligomerization domain, and the N-terminal is an intrinsically disordered region (IDR) of variable length. Uniquely, REMs bypass the secretory pathway for membrane targeting and localize to different nanodomains based on their phylogenetic group. In this study, we combined Nuclear Magnetic Resonance (NMR) spectroscopy, protein structure calculations, and advanced molecular dynamics (MD) simulations to reveal the structural and dynamic properties of REMs. We discovered that remorins form stable pre-structured coiled-coil dimers in the cytosol, which act as tunable nanodomain-targeting units. These dimers feature a REM-dependent barcode-like positive surface charge before membrane association. Furthermore, the REM-CAs exhibit structural and dynamic variations across the family, providing a selective platform for phospholipid binding upon membrane contact. The N-terminal IDR forms a flexible fuzzy structural ensemble around the coiled-coil core. The C-terminal anchors create avidity through multivalent electrostatic interactions between anionic lipid headgroups and the positively charged dimer surface, supporting a synergistic mechanism between REM-CA and the coiled-coil domain to segregate lipid-protein nanodomains. Solid-state NMR and coarse-grained MD simulations further revealed the distinct behavior of REM-CAs when associated to the lipid membrane. We observe differences in membrane association profiles of the REM-CAs and of the charged coiled-coils dependent on the dimer surface charges and dependent on the lipids present in the membrane. Coiled-coil stability and the intensity of membrane association is tuned by the lipid headgroups on the membrane surface. The insights enhance our understanding of the molecular mechanisms underlying the role of remorins in membrane organization in plants, the distinct localizations of remorins in membrane nanodomains and the structural factors contributing to the different remorin functions. This research lays the groundwork for future studies to elucidate the complex behaviors of membrane-associated REMs and their structural tuning during cellular signaling and defense mechanisms
Capítulos de livros sobre o assunto "Coiled-coil structure"
1
Fowlkes, D. M., N. T. Mullis, C. M. Comeau e G. R. Crabtree. "Fibrinogen evolution - The structure and evolution of fibrinogen: The coiled coil region". In Structural variants and interactions, editado por A. Henschen e B. Henssel, 11–22. Berlin, Boston: De Gruyter, 1985. http://dx.doi.org/10.1515/9783110855951-003.
Texto completo da fonte
2
Lee, Myung Kyu, Jeong Kon Seo, Hee Kyung Kim, Ju Hyun Cho e Kil Lyong Kim. "Higher Anti-HIV-1 Activity of Peptides Derived from gp41 Carboxyl-Terminal Coiled Coil Structure of HIV-1 89.6 Strain". In Peptides: The Wave of the Future, 585–86. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0464-0_271.
Texto completo da fonte
3
Sapperstein, Stephanie K., e M. Gerard Waters. "p115". In Guidebook to the Cytoskeletal and Motor Proteins, 538–40. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780198599579.003.00163.
Texto completo da fonteResumo:
Abstract The mammalian intra-Golgi transport factor p 115 and the Saccharomyces cerevisiae ER to Golgi transport factor Uso 1 p are members of a novel family of proteins required for intracellular protein transport. These proteins possess a distinctive globular head/coiled-coil tail structure, reminiscent of myosin II, with three regions of high homology in the primary sequence. The available biochemical and genetic data suggest that p 115 is required for efficient docking of intracellular transport vesicles at the target compartment. The precise mechanism by which p 115 carries out this function remains to be determined.
4
Longtine, Mark S., e John R. Pringle. "Septins". In Guidebook to the Cytoskeletal and Motor Proteins, 359–64. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780198599579.003.00115.
Texto completo da fonteResumo:
Abstract The septins are a family of filament-forming proteins that have been identified in a variety of fungi and animals (including mammals), but not yet in plants; each organism investigated has multiple septin family members (see reviews). All known septins contain a P-loop motif that is presumably involved in nucleotide binding, and most but not all, are predicted to contain a coiled-coil structure near the carboxyl-terminus that is probably involved in protein-protein interactions. The septins localize primarily to the cell cortex, including the division site, and they have important roles in (at least) cytokinesis, morphogenesis, and cell-wall biogenesis. The septins appear to function at least in part by serving as a template for localizing and organizing other molecules at the cell surface; the relationship between septin function and filament formation remains unclear.
5
Kilmartin, John V. "Yeast spindle pole body proteins". In Guidebook to the Cytoskeletal and Motor Proteins, 275–80. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780198599579.003.0091.
Texto completo da fonteResumo:
Abstract Spindle pole body proteins are a diverse set of low abundance proteins. A large fraction including two of the main structural components, Spc11 Op and Spc42p, have coiled coil regions, Kart p has a transmembrane domain, and Cdc31 p is a calcium-binding calmodulin-like protein.
6
Lupas, Andrei. "[30] Prediction and analysis of coiled-coil structures". In Methods in Enzymology, 513–25. Elsevier, 1996. http://dx.doi.org/10.1016/s0076-6879(96)66032-7.
Texto completo da fonte
7
Woolfson, Derek N. "The Design of Coiled-Coil Structures and Assemblies". In Fibrous Proteins: Coiled-Coils, Collagen and Elastomers, 79–112. Elsevier, 2005. http://dx.doi.org/10.1016/s0065-3233(05)70004-8.
Texto completo da fonte
8
Hasson, Tama. "Myosin VII". In Guidebook to the Cytoskeletal and Motor Proteins, 448–50. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780198599579.003.00135.
Texto completo da fonteResumo:
Abstract Myosin Vila is an unconventional myosin implicated in deafness syndromes in mouse and human. It has a conserved N-terminal motor domain, a light chain-binding neck region, which may associate with five calmodulin light chains, and a C-terminal tail comprised of coiled coil and a direct repeat of two motifs termed the Myth domain and the talin-like domain. These structural domains target myosin Vila to the actin cytoskeleton and to membrane domains in inner ear hair cells, retina, and testis.
Trabalhos de conferências sobre o assunto "Coiled-coil structure"
1
Greenwood, Jacob R., e Wyatt Felt. "SPIRA Coils: Soft Self-Sensing Pneumatic Integrated Retractable Actuator Coils". In ASME 2023 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2023. http://dx.doi.org/10.1115/detc2023-109473.
Texto completo da fonteResumo:
Abstract This paper introduces a novel self-sensing coiled actuator called a “SPIRA Coil.” This soft pneumatic actuator is formed from thin sheets of PET plastic that are laminated into a coil shape that unfurls like a “party horn” when inflated. Many soft actuators require large pressure to create only modest strains. SPIRA Coils, in contrast, can easily be designed and fabricated to extend over dramatic distances with relatively low working pressures. In this work, some of the actuators with a coiled outer diameter of approximately 2 cm were able to extend 60 cm with less than 5 kPa. The internal structure of a SPIRA Coil is formed by two layers of metalized PET that separate in the extended portion of the actuator. Where the coiled portion of the actuator begins, the sheets come together, closing an electrical circuit. By measuring the resistance of the circuit, the extended length of the actuator can be determined. The paper presents and experimentally validates easy-to-use design models for the actuator’s self-retracting spring stiffness, its pneumatic extension force, and its internal length-sensing electrical resistance. Testing of the self-sensing capabilities demonstrated that the embedded sensor can be used repeatably and accurately to determine the actuator length, with virtually no hysteresis (R2 = 0.996).
2
Ueno, H., T. Yasunaga, C. Shingyoji, T. Yamaguchi e K. Hirose. "Dynein Pulls Microtubules Without Rotating Its Stalk". In ASME 2009 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2009. http://dx.doi.org/10.1115/sbc2009-206430.
Texto completo da fonteResumo:
Dynein is a motor protein that hydrolyses ATP and moves toward the minus end of a microtubule (MT). A dynein molecule has one to three heavy chains, each consisting of three domains: a head, a stalk and a tail. ATP is bound and hydrolysed in the head, which has a ring-like structure composed of 6 AAA+ domains. The stalk is an antiparallel coiled-coil, 10–15 nm long, and has a nucleotide-dependent MT-binding domain at the tip (1) (Fig. 1). It has been proposed that the nucleotide-dependent binding affinity of the tubulin-binding site at the tip of the stalk is modulated by the two alpha helices in the coiled-coil sliding over each other (2). However, it is not known how a dynein molecule moves along a microtubule (MT).
3
Beljkas, Milan, Jelena Rebić, Milica Radan, Teodora Đikić, Slavica Oljačić e Katarina Nikolic. "3D-Quantitative Structure-Activity Relationship and design of novel Rho-associated protein kinases-1 (ROCK1) inhibitors". In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.584b.
Texto completo da fonteResumo:
Rho-associated coiled-coil kinases (ROCKs) are involved in essential cellular functions such as adhesion, contraction, motility, proliferation, and cell survival/apoptosis. Four ROCK inhibitors have already been approved by the FDA and are used to treat glaucoma (ripasudil and netarsudil), cerebral vasospasm (fasudil), and graft-versus-host disease (belumosudil). Recent studies have focused on exploring the role of ROCK kinase inhibitors in cancer treatment and the development of new ROCK inhibitors. The main objective of this study was to identify critical structural features relevant to the inhibition of ROCK1 using a ligand-based 3D-QSAR (3D quantitative structure-activity relationship) method. The 3D-QSAR model for ROCK1 was created and validated using internal and external validation parameters (R2, Q2, R2pred, rm 2, r/2m, rm̅̅2̅ and ∆r2m). The main structural features that correlate with the inhibition of ROCK1 were identified (e.g., heterocycle with hydrogen donor group like nitrogen atom) and further structural modifications of the ROCK1 inhibitors that contribute to increased activity were proposed (removal of the amino group of the oxadiazole, modification of the substituents of the phenyl ring).
4
Buehler, Markus J., e Zhao Qin. "Structure Prediction and Nanomechanical Properties of Human Vimentin Intermediate Filament Dimers". In ASME 2009 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2009. http://dx.doi.org/10.1115/sbc2009-204824.
Texto completo da fonteResumo:
Intermediate filaments (IFs), in addition to microtubules (MTs) and microfilaments (MFs), are one of the three major components of the cytoskeleton in eukaryotic cells. As the basic building block of IFs, the properties of the IF dimmer re crucial to fully understand the molecular basis for the properties of the IF network in cells. However, the structure of IF dimers remains unknown, which has thus far prevented the elucidation of its nanomechanical properties, in particular molecular-level mechanisms of deformation. Here we present the development of a full atomistic molecular model of the vimentin dimmer, a coiled-coil structure consisting of four alpha-helixes (AHs). The structure is found to be stable in molecular dynamics simulation after an extensive equilibration process. After careful structure prediction, the behavior of the IF dimer under mechanical stress is investigated; including studies of changing the pulling velocity and a detailed analysis of the associated deformation and rupture mechanisms. Most notably, we observe a transition of AHs to beta-sheets (BSs) under mechanical deformation, as has been observed indirectly in earlier experimental studies. Our result helps to better understand the structure and fracture mechanism of this important protein filament.
5
Ahmad, Syed Hamza, Saad Yousuf Khokhar, Rameez Anwar, Arif Yousuf, Aziz Ur Rehman, Abdul Asad, Muhammad Salman Saeed, Sameer Mustafa Noor e Irfan Nazir. "Successful Application of Engineered Loss Control Solution thru Drill Bits and Coil Tubing in a Naturally Fractured Limestone and High-Temperature Ultra Low-Pressure Sandstone". In PAPG/SPE Pakistan Section Annual Technical Symposium and Exhibition. SPE, 2023. http://dx.doi.org/10.2118/217365-ms.
Texto completo da fonteResumo:
Abstract Loss circulation has been a serious concern for drilling and workover operations, especially in depleting brownfields, leading to huge financial and time losses. In addition to the loss of expensive drilling/completion fluid, it also causes several other drilling problems including wellbore stability and stuck drill strings which themselves require additional resources and time for the continuation of operations safely. Extensive research has been performed by engineers since the advent of modern drilling techniques, however, LCM (loss circulation materials) in practice today still have operational and technical limitations. Commonly used materials are loaded with solids to plug off the formation limiting their application via drilling strings (especially with advanced BHAs containing directional drilling and MWD tools). Similar challenges are common during rigless workover operations using coiled tubing (CT) for well intervention solutions. To address the challenges related to solid-laden fluid pumping, a temperature-activated anionic polymer is formulated when combined with a carboxylate complex cross-linking agent, it produces a rubber-like ringing gel structure. It works by entering the porous media and permanently reducing permeability while improving the wellbore stability by strengthening the formation, instead of simply plugging the sand face as in conventional LCM and Cement Plug Solutions. In addition to being a solids-free solution, the product is also in-soluble with acid, making it more robust for workover operations. This paper presents two case studies of the successful application of engineered LCM solutions in drilling and workover operations. In Case A, the product was deployed via drill bit where the string got stuck due to total losses and coarse CaCO3 could not be pumped via drill string to cure losses creating the risk of losing the string downhole. Polymer-based LCM (non-acid soluble) was pumped via drill string to effectively seal off the fractures in a naturally fractured loss zone, reinforced with Bond Enhancer to increase structure robustness to sustain hydrostatic column thus allowing successful resumption of circulation in the first attempt eventually leading to release the stuck drill string. In another case, the product was designed and placed via Coil Tubing (CT) to seal off a High-Temperature Ultra-low Pressure depleted sandstone formation to sustain ~ 3500 psi differential pressure to safely perforate the deeper zone and allowing the operator to add reserves while avoiding rig workover. This approach highlights the ‘limitations of application’ of conventional Loss control material. The methodology adopted to overcome conduit and BHA challenges in drilling and rigless operations provide a new area of opportunities for designing ringing gels to meet desired isolation objectives within present operational limitations.
6
Ishikawa, Masa-aki, Hiroshi Oiwa, Kosuke Sakai, Yuichi Murai, Shin-ichi Toda, Kiyoshi Tamayama e Fujio Yamamoto. "Flow Structure and Pressure Loss of Two-Phase Flow in Helically Coiled Tubes". In ASME/JSME 2003 4th Joint Fluids Summer Engineering Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/fedsm2003-45376.
Texto completo da fonteResumo:
In the steam generator of the prototype FBR (Fast Breeder Reactor) in Japan, heat exchange tubes of helical coil type are utilized. The gas-liquid two-phase flows in the helical coil tube have different characteristic from straight tubes due to the effects of centrifugal acceleration in the curved tubes. In our study, the interfacial structure of the gas-liquid two-phase flows in the helical coil tube is visualized to provide the flow pattern map. Simultaneously, the pressure loss and its local fluctuation are measured in order to investigate the dynamic characteristics of the two-phase flow appearing in the helical coil tube. The result reveals that the bubbly flow regime extends and the stratified flow vanishes compared the gas-liquid flow in a horizontal straight tube. Moreover, the slug flow has asymmetric structure due to the effect of centrifugal acceleration. On the contrary the pressure loss is basically not remarkably different from the straight tube except the fact that the pressure has a high fluctuation component.
7
Zhu, Guangyu, e Hongye Zhu. "Numerical Simulation of Interfacial Phenomenon of Air-Water Adiabatic Intermittent Flow in Helically Coiled Tubes". In 2016 24th International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/icone24-60221.
Texto completo da fonteResumo:
Helically coiled tube are widely used as the basic heat transfer elements in steam generators of the next generation reactors, such as HTR-PM (High Temperature Gas-cooled Reactor), IRIS (International Reactor Innovative and Secure) and SMART (System-integrated Modular Advanced Reactor), because of the advantages in reducing space, enhancing heat transfer, accommodating thermal stress and preventing two-phase flow instabilities. Owing to the presence of gravity and centrifugal force that being perpendicular to the main flow, two-phase flow in helically coiled tubes has different features with either vertical flow or horizontal flow. To ensure safety and reliability of the plant, it is necessary to carry out detail investigation on the two-phase flow phenomena and mechanisms in helically coiled tubes. However, less research has been carried out on this subject than on straight tubes. In this work, the upward air-water slug and plug flows in helically coiled tubes have been numerically analyzed based on the computational fluid dynamics (CFD) techniques. Three dimension models of helically coiled tubes with inner diameter of 16 mm, coil diameter of 0.1 and 0.4m, pitch of 0.08 and 0.16m are constructed, for which the structural meshes are generated by software ANSYS ICEM. The gas-liquid interface is captured by the volume of fluid (VOF) approach adopting geo-reconstruction scheme for interface interpolation, which is solved by a pressure-based transient solver in the commercial CFD software ANSYS FLUENT 14.5. Bubble chord length, slug/plug frequency, bubble velocity and void fraction under different superficial velocities have been investigated. The numerical results meet well with the pictures recorded by a high speed camera. It is revealed that in slug regime, the bubbles mainly migrate towards the top and inner wall of the tube due to the combined action of gravity and centrifugal force, leading to a highly asymmetrical internal phase distributions. Meanwhile, the secondary flow in the cross section introduced by the centrifugal force enhances the turbulence and prevents small bubbles to coalescent into enlarged bubbles. Accordingly the intermittent flow regime in helically coiled tubes is narrower than that in straight horizontal tubes. Furthermore, the influences of geometrical parameters on phase distribution characteristics are predicted. The results show that the bubble length will increase along with the increase of the coil diameter or the pitch of the helically coiled tube. And the bubble frequency will increase with the decreasing of the tube coil diameter.
8
Passos, R., e C. German. "Lessons Learned from Hydrate Plug Dissociation During an Acid Stimulation in an Ultra-Deepwater, High GOR, Pre-Salt Well in Brazil". In Offshore Technology Conference Brasil. OTC, 2023. http://dx.doi.org/10.4043/32830-ms.
Texto completo da fonteResumo:
Abstract An acid stimulation was performed in an ultra-deepwater pre-salt Brazil well to improve its productivity. The formation of hydrate plugs was a critical concern, as the stimulation requires water injection to neutralize the acid, and this well has a high GOR. Even with a risk of hydrate formation, acid stimulation is proven to be effective in recovering the production potential. However, experience with gas wells is still in the learning process with low best practices reported in the literature. The intention of this paper is to present a case history and the lessons learned during an acid stimulation in a high GOR well, in which the gas production was greater than anticipated leading to the formation of a massive hydrate plug, noted while the coiled tubing was being pulled and became stuck. The hydrate risk analysis and the steps taken to release the coiled tubing will be presented, and the discussion will include the following: Hydrate risk analysis from the acid stimulation program: as the subsea valves remain locked open during the rig operation, gas continuously migrates from the reservoir into the well leading to a high risk of hydrate formation during the water injection steps, requiring a bullhead with base oil to mitigate this risk. Also, a detailed evaluation of the risk of hydrate formation during the well startup will be discussed, as the high volume of water injected to neutralize the acid requires artificial lift to produce this effluent, in the case the only option was gas lift, the combination of high BSW% effluent and gas lift leads to a high risk of hydrate formation.Troubleshooting to dissociate the hydrate: After the hydrate identification some attempts to dissociate were taken, the effective one being a gas flush from the FPSO to the Rig, injecting gas to the well through the service line to lift the drilling fluid from the work over riser to the Rig, therefore reducing the pressure until being outside of the hydrate stable zone, making possible to pull the coil tubing in an inhibited liquid environment, in the case MEG 50%, to avoid hydrate reassociation. The figure below illustrates the steps of hydrate risk assessment during well startup: i) above 10% BSW the fluid temperature puts the subsea system inside the hydrate formation zone; ii) the evaluation of the best suitable thermodynamic hydrate inhibitor available to avoid hydrate reassociation and to move the system to outside the hydrate formation zone; iii) the gas flush to move outside of the stable hydrate formation zone at sea level depth, showing that the option was valid to dissociate a hydrate formed at this depth. This case history discusses an acid stimulation in a high GOR well, in ultra-deep water, offshore Brazil. The lessons learned in this operation will be discussed to propose a structured guideline for hydrate mitigation during acid stimulation jobs in high GOR wells, from the risk analysis before the operation until the well restart, including hydrate dissociation options.