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Derek N. Woolfson - One of the best experts on this subject based on the ideXlab platform.
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Coiled-Coil Design: Updated and Upgraded
Subcellular Biochemistry, 2017Co-Authors: Derek N. WoolfsonAbstract:α-Helical Coiled Coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural Coiled-Coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple Coiled Coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers. In turn, these provide a toolkit for directing the assembly of both natural proteins and more complex designs in protein engineering, materials science and synthetic biology. Moving on, the increased and improved use of computational design is allowing access to Coiled-Coil structures that are rare or even not observed in nature, for example α-helical barrels, which comprise five or more α-helices and have central channels into which different functions may be ported. This chapter reviews all of these advances, outlining improvements in our knowledge of the fundamentals of Coiled-Coil folding and assembly, and highlighting new Coiled Coil-based materials and applications that this new understanding is opening up. Despite considerable progress, however, challenges remain in Coiled-Coil design, and the next decade promises to be as productive and exciting as the last.
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ccbuilder an interactive web based tool for building designing and assessing Coiled Coil protein assemblies
Bioinformatics, 2014Co-Authors: Christopher W Wood, Marc Bruning, Amaurys Avila Ibarra, Gail J Bartlett, Andrew R Thomson, Richard B Sessions, Leo R Brady, Derek N. WoolfsonAbstract:Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the helical Coiled Coils. CCBuilder generates Coiled-Coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, Coiled-Coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 Coiled-Coil structures from the PDB, which cover496% of the known Coiled-Coil types, and by generating models for rarer and de novo Coiled-Coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://CoiledCoils.chm.bris.ac.uk/app/cc_builder/
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LOGICoil — Multi-state prediction of Coiled-Coil oligomeric state
Bioinformatics, 2012Co-Authors: Thomas L. Vincent, Peter Green, Derek N. WoolfsonAbstract:Motivation: The Coiled Coil is a ubiquitous �-helical protein-structure domain that directs and facilitates protein–protein interactions in a wide variety of biological processes. At the protein-sequence level, the Coiled Coil is readily recognized via a conspicuous heptad repeat of hydrophobic and polar residues. However, structurally Coiled Coils are more complicated, existing in a wide range of oligomer states and topologies. As a consequence, predicting these various states from sequence remains an unmet challenge. Results: This work introduces LOGICoil, the first algorithm to address the problem of predicting multiple Coiled-Coil oligomeric states from protein-sequence information alone. By covering 490% of the known Coiled-Coil structures, LOGICoil is a net improvement compared with other existing methods, which achieve a predictive coverage of � 31% of this population. This leap in predictive power offers better opportunities for genome-scale analysis, and analyses of
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cc a relational database of Coiled Coil structures
Nucleic Acids Research, 2009Co-Authors: Oliver D. Testa, Efrosini Moutevelis, Derek N. WoolfsonAbstract:We introduce the CC+ Database, a detailed, searchable repository of Coiled-Coil assignments, which is freely available at http://CoiledCoils.chm.bris.ac.uk/ccplus. Coiled Coils were identified using the program SOCKET, which locates Coiled Coils based on knobs-into-holes packing of side chains between α-helices. A method for determining the overall sequence identity of Coiled-Coil sequences was introduced to reduce statistical bias inherent in Coiled-Coil data sets. There are two points of entry into the CC+ Database: the ‘Periodic Table of Coiled-Coil Structures’, which presents a graphical path through Coiled-Coil space based on manually validated data, and the ‘Dynamic Interface’, which allows queries of the database at different levels of complexity and detail. The latter entry level, which is the focus of this article, enables the efficient and rapid compilation of subsets of Coiled-Coil structures. These can be created and interrogated with increasingly sophisticated pull-down, keyword and sequence-based searches to return detailed structural and sequence information. Also provided are means for outputting the retrieved Coiled-Coil data in various formats, including PyMOL and RasMol scripts, and Position-Specific Scoring Matrices (or amino-acid profiles), which may be used, for example, in protein-structure prediction.
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A periodic table of Coiled-Coil protein structures.
Journal of Molecular Biology, 2009Co-Authors: Efrosini Moutevelis, Derek N. WoolfsonAbstract:Abstract Coiled Coils are protein structure domains with two or more α-helices packed together via interlacing of side chains known as knob-into-hole packing. We analysed and classified a large set of Coiled-Coil structures using a combination of automated and manual methods. This led to a systematic classification that we termed a “periodic table of Coiled Coils,” which we have made available at http://CoiledCoils.chm.bris.ac.uk/ccplus/search/periodic_table . In this table, Coiled-Coil assemblies are arranged in columns with increasing numbers of α-helices and in rows of increased complexity. The table provides a framework for understanding possibilities in and limits on Coiled-Coil structures and a basis for future prediction, engineering and design studies.
Alexander Kros - One of the best experts on this subject based on the ideXlab platform.
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in situ modification of plain liposomes with lipidated Coiled Coil forming peptides induces membrane fusion
Journal of the American Chemical Society, 2013Co-Authors: Frank Versluis, Jens Voskuhl, Harshal Zope, Bartjan Van Kolck, Marien Bremmer, Tjerk Albregtse, Alexander KrosAbstract:Complementary Coiled Coil forming lipidated peptides embedded in liposomal membranes are able to induce rapid, controlled, and targeted membrane fusion. Traditionally, such fusogenic liposomes are prepared by mixing lipids and lipidated peptides in organic solvent (e.g., chloroform). Here we prepared fusogenic liposomes in situ, i.e., by addition of a lipidated peptide solution to plain liposomes. As the lipid anchor is vital for the correct insertion of lipidated peptides into liposomal membranes, a small library of lipidated Coiled Coil forming peptides was designed in which the lipid structure was varied. The fusogenicity was screened using lipid and content mixing assays showing that cholesterol modified Coiled Coil peptides induced the most efficient fusion of membranes. Importantly, both lipid and content mixing experiments demonstrated that the in situ modification of plain liposomes with the cholesterol modified peptides yielded highly fusogenic liposomes. This work shows that existing membranes c...
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Controlling the rate of Coiled Coil driven membrane fusion.
Chemical Communications, 2013Co-Authors: Tingting Zheng, Jens Voskuhl, Frank Versluis, Harshal Zope, Itsuro Tomatsu, Hana Robson Marsden, Alexander KrosAbstract:Sets of complementary lipidated Coiled-Coil forming peptides that fuse membrane fusion have been designed. The influence of the Coiled-Coil motif on the rate of liposome fusion was studied, by varying the number of heptad repeats. We found that an increased Coiled-Coil stability of complementary peptides translates into increased rates of membrane fusion of liposomes.
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Noncovalent triblock copolymers based on a Coiled-Coil peptide motif.
Journal of the American Chemical Society, 2008Co-Authors: Hana Robson Marsden, Alexander V. Korobko, Ellen N. M. Van Leeuwen, Emilie Pouget, Sandra J. Veen, Nico A. J. M. Sommerdijk, Alexander KrosAbstract:The formation of a noncovalent triblock copolymer based on a Coiled-Coil peptide motif is demonstrated in solution. A specific peptide pair (E and K) able to assemble into heteroCoiled Coils was chosen as the middle block of the polymer and conjugated to poly(ethylene glycol) (PEG) and polystyrene (PS) as the outer blocks. Mixing equimolar amounts of the polymer−peptide block copolymers PS−E and K−PEG resulted in the formation of Coiled-Coil complexes between the peptides and subsequently in the formation of the amphiphilic triblock copolymer PS−E/K−PEG. Aqueous self-assembly of the separate peptides (E and K), the block copolymers (PS−E and K−PEG), and equimolar mixtures thereof was studied by circular dichroism, dynamic light scattering, and cryogenic transmission electron microscopy. It was found that the noncovalent PS−E/K−PEG copolymer assembled into rodlike micelles, while in all other cases, spherical micelles were observed. Temperature-dependent studies revealed the reversible nature of the Coiled...
Sean Munro - One of the best experts on this subject based on the ideXlab platform.
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the golgin Coiled Coil proteins of the golgi apparatus
Cold Spring Harbor Perspectives in Biology, 2011Co-Authors: Sean MunroAbstract:Coiled-Coils are widely occurring protein structural motifs in which two or more α-helices wind around each other to form an extended rod-like structure. Proteins containing such structures are found in many parts of the cell, and play diverse roles including organizing centrosomes, chromatin, and synapses, or serving as molecular motors. As such there may seem little reason to consider them collectively beyond an interest in the structural and biophysical properties of the Coiled-Coil itself. However, the Golgi is unique amongst the cellular compartments in that several different large Coiled-Coil proteins are present on its cytoplasmic surface (Gillingham and Munro 2003; Lupashin and Sztul 2005; Short et al. 2005; Ramirez and Lowe 2009). A number of these share a similar organization in that most of the protein is predicted to form a Coiled-Coil, and that their carboxyl termini mediate attachment to Golgi membranes. They are generally ubiquitously expressed and well conserved in evolution, but their Coiled-Coil regions are relatively poorly conserved suggesting that much of their length serves as spacer. Given that 500 residues of Coiled-Coil is ∼75 nm in length then the proteins could extend for ∼100–400 nm. Some of the proteins have regions which appear likely to be unstructured and hence could serve as extensions or hinges to increase the proteins’ reach and flexibility (Oas and Endow 1994; Yamakawa et al. 1996). These shared features suggest that the proteins serve related functions on the Golgi. The term “golgin” is often applied to these proteins having been coined in early studies when several were found as human autoantigens (Fritzler et al. 1993), but the term lacks a clear definition. To provide a focus to this article, I will concentrate on “golgins” as defined by being a protein that is found primarily, if not exclusively, on the Golgi and is predicted to form a homodimeric parallel Coiled-Coil over most of its length. Proteins with shorter regions of Coiled-Coil are more likely to have roles distinct to the golgins, especially if further domains are present. Golgin Coiled-Coil proteins are found on the cis-face of the Golgi, around the rims of the stack and on the trans-face of the Golgi (Fig. 1). The human golgins are summarized in Table 1, along with their orthologs in model organisms and the rather confusing gene names inflicted by the Human Gene Nomenclature Committee. I discuss what is known about the individual proteins from each of the parts of the Golgi, and mention briefly the Golgi Coiled-Coil proteins that are probably not golgins. I then discuss how the golgins are regulated and how their properties might reflect a shared function in Golgi organization and traffic. Figure 1. The golgin Coiled-Coil proteins of humans. Table 1. The canonical golgins of the human Golgi and their orthologs.
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golgi Coiled Coil proteins contain multiple binding sites for rab family g proteins
Journal of Cell Biology, 2008Co-Authors: Rita Sinka, Alison K Gillingham, Vangelis Kondylis, Sean MunroAbstract:Vesicles and other carriers destined for the Golgi apparatus must be guided to the correct cisternae. Golgins, long Coiled-Coil proteins that localize to particular Golgi subdomains via their C termini, are candidate regulators of vesicle sorting. In this study, we report that the GRIP domain golgins, whose C termini bind the Arf-like 1 G protein on the trans-Golgi, can also bind four members of the Rab family of G proteins. The Rab2-, Rab6-, Rab19-, and Rab30-binding sites are within the Coiled-Coil regions that are not required for Golgi targeting. Binding sites for two of these Rabs are also present on two Coiled-Coil proteins of the cis-Golgi, the Drosophila melanogaster orthologues of GM130 and GMAP-210. We suggest an integrated model for a tentacular Golgi in which Coiled-Coil proteins surround the Golgi to capture and retain Rab-containing membranes, excluding other structures such as ribosomes. Binding sites for diverse Rabs could ensure that incoming carriers are captured on first contact and moved to their correct destination within the stack.
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long Coiled Coil proteins and membrane traffic
Biochimica et Biophysica Acta, 2003Co-Authors: Alison K Gillingham, Sean MunroAbstract:Protein transport between organelles is mediated by vesicles which must accurately dock and fuse with appropriate compartments. Over the past several years a large number of long Coiled-Coil proteins have been identified on the Golgi and on endosomes, mostly as auto-antigens in autoimmune disorders. Based on their restricted intracellular distributions and their predicted rod-like structure, these proteins have been proposed to play a role in tethering vesicles to target organelles prior to fusion. However, such proteins may also play a structural role, for example as components of a Golgi matrix, or as scaffolds for the assembly of other factors important for fusion. This review will examine what is known about the function of these large Coiled-Coil proteins in membrane traffic.
Olivier Lequin - One of the best experts on this subject based on the ideXlab platform.
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the c terminal domain of the uup protein is a dna binding Coiled Coil motif
Journal of Structural Biology, 2012Co-Authors: Ludovic Carlier, Sander A Haase, Monica Burgos Y Zepeda, Elie Dassa, Olivier LequinAbstract:Abstract The bacterial Uup protein belongs to the REG subfamily of soluble ATP-binding cassette (ABC) ATPases, and is implicated in precise excision of transposons. In Escherichia coli , the uup gene encodes a 72 kDa polypeptide that comprises two ABC domains, separated by a linker region, and a 12 kDa C-terminal domain (CTD). Uup binds double-stranded DNA with no sequence specificity, and we previously demonstrated that the CTD domain is a crucial region that participates in DNA-binding activity. We report herein the NMR structure of Uup CTD, consisting of an intramolecular antiparallel two-stranded Coiled Coil motif. Structural comparison with analogous Coiled Coil domains reveals that Uup CTD contains an atypical 3 10 -helix in the α-hairpin region that contributes to the hydrophobic core. Using NMR titration experiments, we identified residues of the CTD domain involved in the binding to double-stranded DNA. These residues are located on two opposite surfaces at the base of the Coiled Coil, formed by the N- and C-terminal extremities, where a strictly conserved proline residue induces an overwinding of the Coiled Coil. Finally, preliminary analysis of NMR spectra recorded on distinct Uup constructs precludes a fully flexible positioning of the CTD domain in full-length Uup. These structural data are the first reported for a non-ATPase domain within ABC REG subfamily.
Katja M. Arndt - One of the best experts on this subject based on the ideXlab platform.
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photocontrol of Coiled Coil proteins in living cells
Angewandte Chemie, 2010Co-Authors: Fuzhong Zhang, Katja M. Arndt, Katharina A Timm, Andrew G WoolleyAbstract:Light switching of the activity of a Coiled-Coil protein, the AP-1 transcription factor, in living cells was made possible by the introduction of a designed azobenzene-cross-linked dominant negative peptide, XAFosW (red and yellow in the picture). In the dark, XAFosW showed decreased helical content and decreased affinity for target Jun proteins (green); irradiation at 365 nm enhanced helicity and target affinity.
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Coiled Coil domains stability specificity and biological implications
ChemBioChem, 2004Co-Authors: Jody M Mason, Katja M. ArndtAbstract:The Coiled Coil is a common structural motif, formed by approximately 3 ± 5% of all amino acids in proteins. Typically, it consists of two to five -helices wrapped around each other into a left-handed helix to form a superCoil. Whereas regular -helices go through 3.6 residues for each complete turn of the helix, the distortion imposed upon each helix within a left-handed Coiled Coil lowers this value to around 3.5. Thus a heptad repeat occurs every two turns of the helix. 3] The Coiled Coil was first described by Crick in 1953. He noted that -helices pack together 20 away from parallel whilst wrapping around each other, with their side chains packing TMin a knobs-into-holes manner∫. The same year, Pauling and Corey put forward a model for -keratin. It was some 20 years later that the sequence of rabbit skeletal tropomyosin was published, and another twenty until the first structure of the leucine zipper motif was solved by Alber and co-workers. These last discoveries pushed the Coiled-Coil field into the spotlight, as it became apparent that they are found in important structures that are involved in crucial interactions such as transcriptional control. The most commonly observed type of Coiled Coil is left-handed; here each helix has a periodicity of seven (a heptad repeat), with anywhere from two (in designed Coiled Coils) to 200 of these repeats in a protein. This repeat is usually denoted (a-b-c-d-e-fg)n in one helix, and (a -b -c -d -e -f -g )n in the other (Figure 1). In this model, a and d are typically nonpolar core residues found at the interface of the two helices, whereas e and g are solventexposed, polar residues that give specificity between the two helices through electrostatic interactions. Similarly in righthanded Coiled Coils, an eleven-residue repeat is observed (undecatad repeat). 11] The apparent simplicity of the structure with its heptad periodicity has led to extensive studies. Here we aim to outline the importance of individual amino acids in maintaining -helical structure (intramolecular interactions) within individual helices, whilst promoting specific Coiled-Coil interactions (intermolecular interactions) of correct oligomeric state and orientation. The PV Hypothesis
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Protein fusions to Coiled-Coil domains.
Methods in Enzymology, 2000Co-Authors: Kristian M. Müller, Katja M. Arndt, Tom AlberAbstract:Publisher Summary Oligomerization plays key roles in protein function and regulation. As a consequence, powerful experimental tools have been created with defined, chimeric multimers made by genetic fusions to heterologous oligomerization domains. Coiled Coils provide versatile fusion partners. They are particularly small domains with predictable quaternary structure and adjustable stability. Numerous Coiled-Coil fusions have been constructed to achieve diverse experimental aims. The use of Coiled Coils to probe these functions will continue to grow with increasing knowledge of the principles of helical associations. In vivo applications that target natural Coiled-Coil domains offer particularly fruitful prospects. Expressing Coiled-Coil motifs alone or in combination with inactivating domains may be used increasingly to generate dominant negative proteins. Fusions to fluorescent molecules such as green fluorescent protein (GFP) can yield new methods to label Coiled-Coil structures. This chapter reviews the principles of Coiled-Coil structure and describes fusion domain sequences and their several applications.
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Considerations in the design and optimization of Coiled Coil structures.
Protein Engineering Protocols, 1Co-Authors: Jody M Mason, Kristian M. Müller, Katja M. ArndtAbstract:Coiled Coil motifs are, despite their apparent simplicity, highly specific, and play a significant role in the understanding of tertiary structure and its formation. The most commonly observed of the Coiled Coils, the parallel dimeric, is yet to be fully characterized for this structural class in general. Nonetheless, strict rules have emerged for the necessity of specific types of amino acids at specific positions. In this chapter, we discuss this system in light of existing Coiled Coil structures and in applying rules to Coiled Coils that are to be designed or optimized. Understanding and expanding on these rules is crucial in using these motifs, which play key roles in virtually every cellular process, to act as drug-delivery agents by sequestering other proteins that are not behaving natively or that have been upregulated (for example, by binding to Coiled Coil domains implicated in oncogenesis). The roles of the a and d "hydrophobic" core positions and the e and g "electrostatic" edge positions in directing oligomerization and pairing specificity are discussed. Also discussed is the role of these positions in concert with the b, c, and f positions in maintaining alpha-helical propensity, helix solubility, and dimer stability.