3,797 results on '"coiled coil"'
Search Results
152. Cohesin ATPase activities regulate DNA binding and coiled-coil configuration
- Author
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Xingya, Xu, Ryuta, Kanai, Li, Wang, Mitsuhiro, Yanagida, Xingya, Xu, Ryuta, Kanai, Li, Wang, and Mitsuhiro, Yanagida
- Abstract
The cohesin complex is required for sister chromatid cohesion and genome compaction. Cohesin coiled coils (CCs) can fold at break sites near midpoints to bring head and hinge domains, located at opposite ends of coiled coils, into proximity. Whether ATPase activities in the head play a role in this conformational change is yet to be known. Here, we dissected functions of cohesin ATPase activities in cohesin dynamics in Schizosaccharomyces pombe. Isolation and characterization of cohesin ATPase temperature-sensitive (ts) mutants indicate that both ATPase domains are required for proper chromosome segregation. Unbiased screening of spontaneous suppressor mutations rescuing the temperature lethality of cohesin ATPase mutants identified several suppressor hotspots in cohesin that located outside of ATPase domains. Then, we performed comprehensive saturation mutagenesis targeted to these suppressor hotspots. Large numbers of the identified suppressor mutations indicated several different ways to compensate for the ATPase mutants: 1) Substitutions to amino acids with smaller side chains in coiled coils at break sites around midpoints may enable folding and extension of coiled coils more easily; 2) substitutions to arginine in the DNA binding region of the head may enhance DNA binding; or 3) substitutions to hydrophobic amino acids in coiled coils, connecting the head and interacting with other subunits, may alter conformation of coiled coils close to the head. These results reflect serial structural changes in cohesin driven by its ATPase activities potentially for packaging DNAs., source:https://www.pnas.org/doi/full/10.1073/pnas.2208004119
- Published
- 2022
153. Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain
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Jocelyn C. Newton, Nicolas L. Fawzi, John M. Sedivy, Mandar T. Naik, Grace Y. Li, Gerwald Jogl, and Eileen L. Murphy
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Genome instability ,Coiled coil ,0303 health sciences ,Messenger RNA ,biology ,DNA damage ,Chemistry ,Biophysics ,Retrotransposon ,Articles ,Cell biology ,Open Reading Frames ,03 medical and health sciences ,Cytosol ,Open reading frame ,Long Interspersed Nucleotide Elements ,0302 clinical medicine ,Protein Domains ,Chaperone (protein) ,biology.protein ,Humans ,RNA, Messenger ,030217 neurology & neurosurgery ,Molecular Chaperones ,030304 developmental biology - Abstract
Long interspersed nuclear element-1 (L1) is a retrotransposable element that autonomously replicates in the human genome, resulting in DNA damage and genomic instability. Activation of L1 in senescent cells triggers a type I interferon response and age-associated inflammation. Two open reading frames encode an ORF1 protein functioning as messenger RNA chaperone and an ORF2 protein providing catalytic activities necessary for retrotransposition. No function has been identified for the conserved, disordered N-terminal region of ORF1. Using microscopy and NMR spectroscopy, we demonstrate that ORF1 forms liquid droplets in vitro in a salt-dependent manner and that interactions between its N-terminal region and coiled-coil domain are necessary for phase separation. Mutations disrupting blocks of charged residues within the N-terminus impair phase separation, whereas some mutations within the coiled-coil domain enhance phase separation. Demixing of the L1 particle from the cytosol may provide a mechanism to protect the L1 transcript from degradation.
- Published
- 2021
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154. Supercoiling Structure-Based Design of a Trimeric Coiled-Coil Peptide with High Potency against HIV-1 and Human β-Coronavirus Infection
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Keliang Liu, Shuai Xia, Huan Wang, Yue Li, Shanshan Huo, Chao Wang, Rong Xiang, Lu Lu, Qian Wang, Qinwen Jiang, Qing Li, Qiaoshuai Lan, Fei Yu, Xinling Wang, Ruiying Liang, and Shibo Jiang
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viruses ,Peptide ,Trimer ,Microbial Sensitivity Tests ,Gp41 ,medicine.disease_cause ,Antiviral Agents ,01 natural sciences ,Cell Line ,Structure-Activity Relationship ,03 medical and health sciences ,Viral envelope ,Drug Discovery ,medicine ,Humans ,Potency ,030304 developmental biology ,Coronavirus ,chemistry.chemical_classification ,Coiled coil ,0303 health sciences ,Dose-Response Relationship, Drug ,virus diseases ,HIV Envelope Protein gp41 ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,chemistry ,Drug Design ,HIV-1 ,Biophysics ,Molecular Medicine ,DNA supercoil ,Coronavirus Infections ,Peptides - Abstract
Hexameric structure formation through packing of three C-terminal helices and an N-terminal trimeric coiled-coil core has been proposed as a general mechanism of class I enveloped virus entry. In this process, the C-terminal helical repeat (HR2) region of viral membrane fusion proteins becomes transiently exposed and accessible to N-terminal helical repeat (HR1) trimer-based fusion inhibitors. Herein, we describe a mimetic of the HIV-1 gp41 HR1 trimer, N3G, as a promising therapeutic against HIV-1 infection. Surprisingly, we found that in addition to protection against HIV-1 infection, N3G was also highly effective in inhibiting infection of human β-coronaviruses, including MERS-CoV, HCoV-OC43, and SARS-CoV-2, possibly by binding the HR2 region in the spike protein of β-coronaviruses to block their hexameric structure formation. These studies demonstrate the potential utility of anti-HIV-1 HR1 peptides in inhibiting human β-coronavirus infection. Moreover, this strategy could be extended to the design of broad-spectrum antivirals based on the supercoiling structure of peptides.
- Published
- 2021
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155. A De Novo‐Designed Artificial Metallopeptide Hydrogenase: Insights into Photochemical Processes and the Role of Protonated Cys
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Dhanashree Selvan, Sreya Malayam Parambath, Ashley E. Williams, Leigh Anna Hunt, Nathan I. Hammer, and Saumen Chakraborty
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Hydrogenase ,General Chemical Engineering ,Protonation ,02 engineering and technology ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Article ,Electron transfer ,Biomimetic Materials ,Environmental Chemistry ,General Materials Science ,Reactivity (chemistry) ,Photosensitizer ,Cysteine ,Binding site ,Coiled coil ,Chemistry ,Photochemical Processes ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,General Energy ,Drug Design ,Protons ,0210 nano-technology - Abstract
Hydrogenase enzymes produce H(2) gas, which can be a potential source of alternative energy. Inspired by the [NiFe] hydrogenases, we report the construction of a de novo designed artificial hydrogenase (ArH). The ArH is a dimeric coiled coil where two cysteine (Cys) residues are introduced at tandem a/d positions of a heptad to create a tetrathiolato Ni binding site. Spectroscopic studies show that Ni binding significantly stabilizes the peptide producing electronic transitions characteristic of Ni-thiolate proteins. The ArH produces H(2) photocatalytically, demonstrating a bell-shaped pH-dependence on activity. Fluorescence lifetimes and transient absorption spectroscopic studies are undertaken to elucidate the nature of pH-dependence, and to monitor the reaction kinetics of the photochemical processes. pH titrations are employed to determine the role of protonated Cys on reactivity. Combined, we find that a fine balance between solution acidity and the electron transfer steps need to be maintained such that the yield of reduced photosensitizer can be maximized to produce the Ni(I)-peptide and the Ni(II)-H(−) intermediate (Ni-R) is protonated by a Cys (pK(a)~6.4) to produce H(2).
- Published
- 2021
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156. A Stutter in the Coiled-Coil Domain of Escherichia coli Co-chaperone GrpE Connects Structure with Function
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Ishu Saraogi, Vaibhav V Karekar, Upasana S. Potteth, and Tulsi Upadhyay
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Coiled coil ,biology ,Chemistry ,Mutant ,medicine.disease_cause ,Biochemistry ,Nucleotide exchange factor ,Co-chaperone ,Förster resonance energy transfer ,Chaperone (protein) ,biology.protein ,medicine ,Biophysics ,Protein folding ,Escherichia coli - Abstract
In bacteria, the co-chaperone GrpE acts as a nucleotide exchange factor and plays an important role in controlling the chaperone cycle of DnaK. The functional form of GrpE is an asymmetric dimer, consisting of a non-ideal coiled coil. Partial unfolding of this region during heat stress results in reduced nucleotide exchange and disrupts protein folding by DnaK. In this study, we elucidate the role of non-ideality in the coiled-coil domain of Escherichia coli GrpE in controlling its co-chaperone activity. The presence of a four-residue stutter introduces nonheptad periodicity in the GrpE coiled coil, resulting in global structural changes in GrpE and regulating its interaction with DnaK. Introduction of hydrophobic residues at the stutter core increased the structural stability of the protein. Using an in vitro FRET assay, we show that the enhanced stability of GrpE resulted in an increased affinity for DnaK. However, these mutants were unable to support bacterial growth at 42°C in a grpE-deleted E. coli strain. This work provides valuable insights into the functional role of a stutter in GrpE in regulating the DnaK-chaperone cycle during heat stress. More generally, our findings illustrate how stutters in a coiled-coil domain regulate structure-function trade-off in proteins.
- Published
- 2021
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157. Structure and Function of Viral Glycoproteins in Membrane Fusion
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Weissenhorn, Winfried, Holzenburg, Andreas, editor, and Bogner, Elke, editor
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- 2002
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158. Cytadherence and the Cytoskeleton
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Balish, Mitchell F., Krause, Duncan C., Razin, Shmuel, editor, and Herrmann, Richard, editor
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- 2002
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159. Protein-Protein Interaction Mapping: Experimental
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Palzkill, Timothy
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- 2002
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160. Solving the Structure of Collagen
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Rich, A., Aggeli, Amalia, Boden, Neville, and Zhang, Shuguang
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- 2002
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161. A rational approach to de novo design of α-helical proteins
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Miao, Zhen-Wei, Li, Xiang-Qun, Li, Chong-Xi, Xu, Xiao-Jie, Tang, You-Qi, Xu, Xiao-Jie, editor, Ye, Yun-Hua, editor, and Tam, James P., editor
- Published
- 2002
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162. The matrilins: A novel family of extracellular adaptor proteins
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Paulsson, Mats, Klatt, Andreas R., Kobbe, Birgit, Nitsche, D. Patric, Wagener, Raimund, Hascall, Vincent C., editor, and Kuettner, Klaus E., editor
- Published
- 2002
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163. Miniantibodies
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Lindner, Peter, Plückthun, Andreas, Kontermann, Roland, editor, and Dübel, Stefan, editor
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- 2001
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164. Single-Molecule Dynamics Associated with Protein Folding and Deformations of Light-Harvesting Complexes
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Talaga, D. S., Jia, Y., Bopp, M. A., Sytnik, A., DeGrado, W. A., Cogdell, R. J., Hochstrasser, R. M., Schäfer, F. P., editor, Toennies, J. P., editor, Zinth, W., editor, Rigler, Rudolf, Orrit, Michel, and Basché, Thomas
- Published
- 2001
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165. Transmembrane Signal Transduction in Two‐Component Systems: Piston, Scissoring, or Helical Rotation?
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Gushchin, Ivan and Gordeliy, Valentin
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ALLOSTERIC regulation , *CELLULAR signal transduction , *CHEMORECEPTORS , *HISTIDINE kinases , *PHOTOTAXIS - Abstract
Allosteric and transmembrane (TM) signaling are among the major questions of structural biology. Here, we review and discuss signal transduction in four‐helical TM bundles, focusing on histidine kinases and chemoreceptors found in two‐component systems. Previously, piston, scissors, and helical rotation have been proposed as the mechanisms of TM signaling. We discuss theoretically possible conformational changes and examine the available experimental data, including the recent crystallographic structures of nitrate/nitrite sensor histidine kinase NarQ and phototaxis system
Np SRII:Np HtrII. We show that TM helices can flex at multiple points and argue that the various conformational changes are not mutually exclusive, and often are observed concomitantly, throughout the TM domain or in its part. The piston and scissoring motions are the most prominent motions in the structures, but more research is needed for definitive conclusions. [ABSTRACT FROM AUTHOR]- Published
- 2018
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166. Peptide-Mediated Liposome Fusion: The Effect of Anchor Positioning.
- Author
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Crone, Niek S. A., Minnee, Dirk, Kros, Alexander, and Boyle, Aimee L.
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LIPOSOMES , *PEPTIDES , *MEMBRANE fusion , *CIRCULAR dichroism , *HOMODIMERS , *POLYETHYLENE glycol - Abstract
A minimal model system for membrane fusion, comprising two complementary peptides dubbed "E" and "K" joined to a cholesterol anchor via a polyethyleneglycol spacer, has previously been developed in our group. This system promotes the fusion of large unilamellar vesicles and facilitates liposome-cell fusion both in vitro and in vivo. Whilst several aspects of the system have previously been investigated to provide an insight as to how fusion is facilitated, anchor positioning has not yet been considered. In this study, the effects of placing the anchor at either the N-terminus or in the center of the peptide are investigated using a combination of circular dichroism spectroscopy, dynamic light scattering, and fluorescence assays. It was discovered that anchoring the "K" peptide in the center of the sequence had no effect on its structure, its ability to interact with membranes, or its ability to promote fusion, whereas anchoring the 'E' peptide in the middle of the sequence dramatically decreases fusion efficiency. We postulate that anchoring the 'E' peptide in the middle of the sequence disrupts its ability to form homodimers with peptides on the same membrane, leading to aggregation and content leakage. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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167. C CBuilder 2.0: Powerful and accessible coiled-coil modeling.
- Author
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Wood, Christopher W. and Woolfson, Derek N.
- Abstract
The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3-5% of all known protein-encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy-to-use web application, called CCBuilder 2.0, for modeling and optimizing both α-helical coiled coils and polyproline-based collagen triple helices. This has many applications from providing models to aid molecular replacement for X-ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo 'dark matter' protein structures. CCBuilder 2.0 is available as a web-based application, the code for which is open-source and can be downloaded freely. . Lay Summary We have created CCBuilder 2.0, an easy to use web-based application that can model structures for a whole class of proteins, the α-helical coiled coil, which is estimated to account for 3-5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more-applied research including designing and engineering novel proteins that have potential applications in biotechnology. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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168. Is Five Percent Too Small? Analysis of the Overlaps between Disorder, Coiled Coil and Collagen Predictions in Complete Proteomes
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Zoltán Gáspári
- Subjects
intrinsically disordered protein ,coiled coil ,collagen triple helix ,cross-prediction ,proteome size ,Microbiology ,QR1-502 - Abstract
Identification of intrinsic disorder in proteins and proteomes has revealed important novel aspects of protein function and interactions. However, it has been pointed out that several oligomeric fibrillar protein motifs such as coiled coils and collagen triple helical segments can also identified as intrinsically disordered. This feature has not yet been investigated in more detail at the proteome level. The present work aims at the identification and quantification of such overlaps in full proteomes to assess their significance in large-scale studies of protein disorder. It was found that the percentage of cross-predicted residues is around 5% in the human proteome and is generally near that value in other metazoan ones but shows remarkable variation in different organisms. In particular, smaller proteomes are increasingly prone to such cross-predictions, thus, especially the analysis of viral proteomes requires the use of specific prediction tools.
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- 2014
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169. Deviations in conformational rearrangements of thin filaments and myosin caused by the Ala155Thr substitution in hydrophobic core of tropomyosin.
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Karpicheva, Olga E., Sirenko, Vladimir V., Rysev, Nikita A., Simonyan, Armen O., Borys, Danuta, Moraczewska, Joanna, and Borovikov, Yurii S.
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TROPOMYOSINS , *ACTIN , *MYOSIN , *PROTEINS , *CHEMICAL reactions - Abstract
Effects of the Ala155Thr substitution in hydrophobic core of tropomyosin Tpm1.1 on conformational rearrangements of the components of the contractile system (Tpm1.1, actin and myosin heads) were studied by polarized fluorimetry technique at different stages of the actomyosin ATPase cycle. The proteins were labelled by fluorescent probes and incorporated into ghost muscle fibres. The substitution violated the blocked and closed states of thin filaments stimulating abnormal displacement of tropomyosin to the inner domains of actin, switching actin on and increasing the relative number of the myosin heads in strong-binding state. Furthermore, the mutant tropomyosin disrupted the major function of troponin to alter the distribution of the different functional states of thin filaments. At low Ca 2 + troponin did not effectively switch thin filament off and the myosin head lost the ability to drive the spatial arrangement of the mutant tropomyosin. The information about tropomyosin flexibility obtained from the fluorescent probes at Cys190 indicates that this tropomyosin is generally more rigid, that obviously prevents tropomyosin to bend and adopt the appropriate conformation required for proper regulation. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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170. Design of silk proteins with increased heme binding capacity and fabrication of silk-heme materials.
- Author
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Rapson, Trevor D., Liu, Jian-Wei, Sriskantha, Alagacone, Musameh, Mustafa, Dunn, Christopher J., Church, Jeffrey S., Woodhead, Andrea, Warden, Andrew C., Riley, Mark J., Harmer, Jeffrey R., Noble, Christopher J., and Sutherland, Tara D.
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HEME , *SILK , *NITRIC oxide , *CHEMICAL detectors , *HETEROGENEOUS catalysts , *BINDING sites - Abstract
In our previous studies, heme was bound into honeybee silk to generate materials that could function as nitric oxide sensors or as recoverable heterogeneous biocatalysts. In this study, we sought to increase the heme-binding capacity of the silk protein by firstly redesigning the heme binding site to contain histidine as the coordinating residue and secondly, by adding multiple histidine residues within the core of the coiled coil core region of the modified silk protein. We used detergent and a protein denaturant to confirm the importance of the helical structure of the silk for heme coordination. Aqueous methanol treatment, which was used to stabilize the materials, transformed the low-spin, six-coordinate heme to a five-coordinate high-spin complex, thus providing a vacant site for ligand binding. The optimal aqueous methanol treatment time that simultaneously maintains the helical protein structure and stabilizes the silk material without substantial leaching of heme from the system was determined. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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171. Identification, biochemical characterization and crystallization of the central region of human ATG16L1.
- Author
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Archna, Archna and Scrima, Andrea
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PROTEIN-protein interactions , *AUTOPHAGY , *PROTEIN crystallography - Abstract
ATG16L1 plays a major role in autophagy. It acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. The ATG12~ATG5-ATG16L1 complex is one of the key complexes involved in autophagosome formation. Human ATG16L1 comprises 607 amino acids with three functional domains named ATG5BD, CCD and WD40, where the C-terminal WD40 domain represents approximately 50% of the full-length protein. Previously, structures of the C-terminal WD40 domain of human ATG16L1 as well as of human ATG12~ATG5 in complex with the ATG5BD of ATG16L1 have been reported. However, apart from the ATG5BD, no structural information for the N-terminal half, including the CCD, of human ATG16L1 is available. In this study, the authors aimed to structurally characterize the N-terminal half of ATG16L1. ATG16L111-307 in complex with ATG5 has been purified and crystallized in two crystal forms. However, both crystal structures revealed degradation of ATG16L1, resulting in crystals comprising only full-length ATG5 and the ATG5BD of ATG16L1. The structures of ATG5-ATG5BD in two novel crystal forms are presented, further supporting the previously observed dimerization of ATG5-ATG16L1. The reported degradation points towards a high instability at the linker region between the ATG5BD and the CCD in ATG16L1. Based on this observation and further biochemical analysis of ATG16L1, a stable 236-amino-acid subfragment comprising residues 72-307 of the N-terminal half of ATG16L1, covering the residual, so far structurally uncharacterized region of human ATG16L1, was identified. Here, the identification, purification, biochemical characterization and crystallization of the proteolytically stable ATG16L172-307 subfragment are reported. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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172. A Conserved Leucine Zipper Motif in Gammaherpesvirus ORF52 Is Critical for Distinct Microtubule Rearrangements.
- Author
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Loftus, Matthew S., Verville, Nancy, and Kedes, Dean H.
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LEUCINE zippers , *KAPOSI'S sarcoma-associated herpesvirus , *MICROTUBULE-associated proteins , *GENE expression , *CYTOSKELETON , *GENETICS of virus diseases - Abstract
Productive viral infection often depends on the manipulation of the cytoskeleton. Herpesviruses, including rhesus monkey rhadinovirus (RRV) and its close homolog, the oncogenic human gammaherpesvirus Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 (KSHV/HHV8), exploit microtubule (MT)-based retrograde transport to deliver their genomes to the nucleus. Subsequently, during the lytic phase of the life cycle, the maturing viral particles undergo orchestrated translocation to specialized regions within the cytoplasm, leading to tegumentation, secondary envelopment, and then egress. As a result, we hypothesized that RRV might induce changes in the cytoskeleton at both early and late stages of infection. Using confocal imaging, we found that RRV infection led to the thickening and acetylation of MTs emanating from the MT-organizing center (MTOC) shortly after viral entry and more pronounced and diffuse MT reorganization during peak stages of lytic gene expression and virion production. We subsequently identified open reading frame 52 (ORF52), a multifunctional and abundant tegument protein, as being the only virally encoded component responsible for these cytoskeletal changes. Mutational and modeling analyses indicated that an evolutionarily conserved, truncated leucine zipper motif near the N terminus as well as a strictly conserved arginine residue toward the C terminus of ORF52 play critical roles in its ability to rearrange the architecture of the MT cytoskeleton. Taken together, our findings combined with data from previous studies describing diverse roles for ORF52 suggest that it likely binds to different cellular components, thereby allowing context-dependent modulation of function. IMPORTANCE A thorough understanding of the processes governing viral infection includes knowledge of how viruses manipulate their intracellular milieu, including the cytoskeleton. Altering the dynamics of actin or MT polymerization, for example, is a common strategy employed by viruses to ensure efficient entry, maturation, and egress as well as the avoidance of antiviral defenses through the sequestration of key cellular factors. We found that infection with RRV, a homolog of the human pathogen KSHV, led to perinuclear wrapping by acetylated MT bundles and identified ORF52 as the viral protein underlying these changes. Remarkably, incoming virions were able to supply sufficient ORF52 to induce MT thickening and acetylation near the MTOC, potentially aiding in the delivery viral genomes to the nucleus. Although the function of MT alterations during late stages of infection requires further study, ORF52 shares functional and structural similarities with alphaherpesvirus VP22, underscoring the evolutionary importance of MT cytoskeletal manipulations for this virus family. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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173. Membrane-spanning α-helical barrels as tractable protein-design targets.
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Niitsu, Ai, Heal, Jack W., Fauland, Kerstin, Thomson, Andrew R., and Woolfson, Derek N.
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GLOBULAR proteins , *MEMBRANE proteins , *PROTEIN structure , *BIOLOGICAL membranes , *EUKARYOTIC cells - Abstract
The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined threedimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The a-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix--helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels--that is, symmetric bundles of five or more helices with central accessible channels--there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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174. Suppressor Analysis of the Fusogenic Lambda Spanins.
- Author
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Cahill, Jesse, Rajaure, Manoj, Holt, Ashley, Moreland, Russell, O'Leary, Chandler, Kulkarni, Aneesha, Sloan, Jordan, and Ry Young
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- *
ESCHERICHIA coli , *ALLELES , *PROTEINS , *ESCHERICHIA - Abstract
The final step of lysis in phage λ infections of Escherichia coli is mediated by the spanins Rz and Rz1. These proteins form a complex that bridges the cell envelope and that has been proposed to cause fusion of the inner and outer membranes. Accordingly, mutations that block spanin function are found within coiled-coil domains and the proline-rich region, motifs essential in other fusion systems. To gain insight into spanin function, pseudorevertant alleles that restored plaque formation for lysis-defective mutants of Rz and Rz1 were selected. Most second-site suppressors clustered within a coiled-coil domain of Rz near the outer leaflet of the cytoplasmic membrane and were not allele specific. Suppressors largely encoded polar insertions within the hydrophobic core of the coiled-coil interface. Such suppressor changes resulted in decreased proteolytic stability of the Rz double mutants in vivo. Unlike the wild type, in which lysis occurs while the cells retain a rod shape, revertant alleles with second-site suppressor mutations supported lysis events that were preceded by spherical cell formation. This suggests that destabilization of the membrane-proximal coiled coil restores function for defective spanin alleles by increasing the conformational freedom of the complex at the cost of its normal, all-or-nothing functionality. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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175. Molecular modeling of the tetramerization domain of human potassium channel Kv10.2 in different oligomeric states.
- Author
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Novoseletsky, V., Volyntseva, A., Shaitan, K., and Sokolova, O.
- Abstract
A voltage-gated potassium channel Kv10.2 is expressed in the nervous system, but its functions and involvement in the development of human disease remain poorly understood. Mutant forms of the Kv10.2 channel were found in patients with epileptic encephalopathy and autism. Molecular modeling of the channel spatial structure is an important tool for gaining knowledge about the molecular aspects of the channel functioning and mechanisms responsible for pathogenesis. In the present work, molecular modeling of the helical fragment of the human Kv10.2 (hEAG2) C-terminal domain in dimeric, trimeric, and tetrameric forms was performed. The stability of all forms was confirmed by molecular dynamics simulation. Contacts and interactions, stabilizing the structure, were identified. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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176. Dissecting the Binding Interface of the Septin Polymerization Enhancer Borg BD3.
- Author
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Castro, Danielle K.S.V., Rosa, Higor V.D., Mendonça, Deborah C., Cavini, Italo A., Araujo, Ana P.U., and Garratt, Richard C.
- Subjects
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POLYMERIZATION , *SEPTINS , *BIOLOGICAL membranes , *PEPTIDES , *CELL cycle proteins - Abstract
[Display omitted] • We provide a detailed description of how the Borg-BD3 domain interacts with septins. • Both SEPT6 and SEPT7 CTDs are needed for Borg3-BD3 to boost septin polymerization. • Borg-BD3 requires an extended coiled coil to interact with SEPT6-SEPT7. • Mutations to key septin residues validate the AF2 model for the ternary complex. The molecular basis for septin filament assembly has begun to emerge over recent years. These filaments are essential for many septin functions which depend on their association with biological membranes or components of the cytoskeleton. Much less is known about how septins specifically interact with their binding partners. Here we describe the essential role played by the C-terminal domains in both septin polymerization and their association with the BD3 motif of the Borg family of Cdc42 effector proteins. We provide a detailed description, at the molecular level, of a previously reported interaction between BD3 and the NC-interface between SEPT6 and SEPT7. Upon ternary complex formation, the heterodimeric coiled coil formed by the C-terminal domains of the septins becomes stabilized and filament formation is promoted under conditions of ionic strength/protein concentration which are not normally permissible, likely by favouring hexamers over smaller oligomeric states. This demonstrates that binding partners, such as Borg's, have the potential to control filament assembly/disassembly in vivo in a way which can be emulated in vitro by altering the ionic strength. Experimentally validated models indicate that the BD3 peptide lies antiparallel to the coiled coil and is stabilized by a mixture of polar and apolar contacts. At its center, an LGPS motif, common to all human Borg sequences, interacts with charged residues from both helices of the coiled coil (K368 from SEPT7 and the conserved E354 from SEPT6) suggesting a universal mechanism which governs Borg-septin interactions. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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177. CC + : A searchable database of validated coiled coils in PDB structures and AlphaFold2 models.
- Author
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Kumar P, Petrenas R, Dawson WM, Schweke H, Levy ED, and Woolfson DN
- Subjects
- Protein Structure, Secondary, Protein Domains, Protein Conformation, alpha-Helical, Software, Proteome
- Abstract
α-Helical coiled coils are common tertiary and quaternary elements of protein structure. In coiled coils, two or more α helices wrap around each other to form bundles. This apparently simple structural motif can generate many architectures and topologies. Coiled coil-forming sequences can be predicted from heptad repeats of hydrophobic and polar residues, hpphppp, although this is not always reliable. Alternatively, coiled-coil structures can be identified using the program SOCKET, which finds knobs-into-holes (KIH) packing between side chains of neighboring helices. SOCKET also classifies coiled-coil architecture and topology, thus allowing sequence-to-structure relationships to be garnered. In 2009, we used SOCKET to create a relational database of coiled-coil structures, CC
+ , from the RCSB Protein Data Bank (PDB). Here, we report an update of CC+ following an update of SOCKET (to Socket2) and the recent explosion of structural data and the success of AlphaFold2 in predicting protein structures from genome sequences. With the most-stringent SOCKET parameters, CC+ contains ≈12,000 coiled-coil assemblies from experimentally determined structures, and ≈120,000 potential coiled-coil structures within single-chain models predicted by AlphaFold2 across 48 proteomes. CC+ allows these and other less-stringently defined coiled coils to be searched at various levels of structure, sequence, and side-chain interactions. The identified coiled coils can be viewed directly from CC+ using the Socket2 application, and their associated data can be downloaded for further analyses. CC+ is available freely at http://coiledcoils.chm.bris.ac.uk/CCPlus/Home.html. It will be updated automatically. We envisage that CC+ could be used to understand coiled-coil assemblies and their sequence-to-structure relationships, and to aid protein design and engineering., (© 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)- Published
- 2023
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178. EPR Spectroscopic Ruler: the Method and its Applications
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Xiao, Wenzhong, Shin, Yeon-Kyun, Berliner, Lawrence J., editor, Eaton, Gareth R., editor, and Eaton, Sandra S., editor
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- 2000
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179. The MAP Kinase Cascade That Includes MAPKKK-Related Protein Kinase NPK1 Controls a Mitotic Process in Plant Cells
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Nishihama, Ryuichi, Machida, Yasunori, Hennig, W., editor, Nover, L., editor, Scheer, U., editor, and Hirt, Heribert, editor
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- 2000
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180. Summary and Conclusion
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Wang, Jianpeng and Wang, Jianpeng
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- 2016
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181. Structural characterization of the self‐association domain of swallow
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Nikolaus M. Loening and Elisar Barbar
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Coiled coil ,0303 health sciences ,Chemistry ,030302 biochemistry & molecular biology ,Dynein ,RNA-Binding Proteins ,Nuclear magnetic resonance spectroscopy ,Immunoglobulin light chain ,Biochemistry ,Domain (software engineering) ,03 medical and health sciences ,Drosophila melanogaster ,Protein structure ,Protein sequencing ,Protein Domains ,Biophysics ,Animals ,Drosophila Proteins ,Protein Multimerization ,Protein Structure Reports ,Molecular Biology ,030304 developmental biology - Abstract
Swallow, a 62 kDa multidomain protein, is required for the proper localization of several mRNAs involved in the development of Drosophila oocytes. The dimerization of Swallow depends on a 71-residue self-association domain in the center of the protein sequence, and is significantly stabilized by a binding interaction with dynein light chain (LC8). Here, we detail the use of solution-state nuclear magnetic resonance spectroscopy to characterize the structure of this self-association domain, thereby establishing that this domain forms a parallel coiled-coil and providing insight into how the stability of the dimerization interaction is regulated.
- Published
- 2021
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182. Coiled coil-based therapeutics and drug delivery systems
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Sajjad Naeimipour, Daniel Aili, Robert Selegård, and Johanna Utterström
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Coiled coil ,0303 health sciences ,Computer science ,Superhelix ,Proteins ,Pharmaceutical Science ,Nanotechnology ,02 engineering and technology ,Molecular systems ,Farmaceutiska vetenskaper ,021001 nanoscience & nanotechnology ,Drug uptake ,Pharmaceutical Sciences ,03 medical and health sciences ,Drug Delivery Systems ,Targeted drug delivery ,Electromagnetic coil ,Drug delivery ,Peptide ,Self-assembly ,Therapeutic ,Folding ,Dimerization ,Conjugation ,Nanostructure ,Humans ,Protein Multimerization ,0210 nano-technology ,Drug carrier ,030304 developmental biology - Abstract
Coiled coils are characterized by an arrangement of two or more alpha-helices into a superhelix and one of few protein motifs where the sequence-to-structure relationship to a large extent have been decoded and understood. The abundance of both natural and de novo designed coil coils provides a rich molecular toolbox for self assembly of elaborate bespoke molecular architectures, nanostructures, and materials. Leveraging on the numerous possibilities to tune both affinities and preferences for polypeptide oligomerization, coiled coils offer unique possibilities to design modular and dynamic assemblies that can respond in a predictable manner to biomolecular interactions and subtle physicochemical cues. In this review, strategies to use coiled coils in design of novel therapeutics and advanced drug delivery systems are discussed. The applications of coiled coils for generating drug carriers and vaccines, and various aspects of using coiled coils for controlling and triggering drug release, and for improving drug targeting and drug uptake are described. The plethora of innovative coiled coil-based molecular systems provide new knowledge and techniques for improving efficacy of existing drugs and can facilitate development of novel therapeutic strategies. (c) 2020 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http:// creativecommons.org/licenses/by/4.0/). 1. Introduction 27 2. The coiled coil motif 27 3. Coiled coils and coiled coil-hybrids for drug delivery and therapeutics 30 3.1. Coiled coils in liposome drug delivery systems 30 3.2. Lipidated coiled coils for assembly of virus-like particles 31 3.3. Coiled coil nanoparticles 31 3.4. Coiled coil nanocarriers 33 3.5. Coiled coil polymer-hybrids 33 3.6. Coiled coil-based hydrogels 36 3.7. Coiled coil inorganic nanoparticle hybrids 37 3.8. Coiled coils combined with cell penetrating peptides 37 3.9. Coiled coils for improved targeting 38 Funding Agencies|Swedish Foundation for Strategic Research (SFF)Swedish Foundation for Strategic Research [FFL15-0026, RMX18-0039]; Swedish Government Strategic Research Area inMaterials Science on Functional Materials at Linkoping University [2009-00971]; Knut and Alice Wallenberg FoundationKnut & Alice Wallenberg Foundation [KAW 2016.0231]; Swedish Research CouncilSwedish Research CouncilEuropean Commission [2017-04475]; Cancer Foundation [17 0534]
- Published
- 2021
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183. Modification of the pH Dependence of Assembly of Yeast Cargo Receptor Emp47p Coiled-Coil Domains: Computational Design and Experimental Mutagenesis
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Eiji Kurimoto, Koichi Kato, Akifumi Oda, and Tomoki Nakayoshi
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Coiled coil ,Saccharomyces cerevisiae Proteins ,010304 chemical physics ,Chemistry ,Mutagenesis ,Mutant ,Protonation ,Saccharomyces cerevisiae ,Hydrogen-Ion Concentration ,010402 general chemistry ,01 natural sciences ,Yeast ,0104 chemical sciences ,Surfaces, Coatings and Films ,Molecular dynamics ,Residue (chemistry) ,Protein Domains ,0103 physical sciences ,Materials Chemistry ,Side chain ,Biophysics ,Physical and Theoretical Chemistry - Abstract
The coiled-coil domains of the putative yeast cargo receptors Emp46p and Emp47p (Emp46pcc and Emp47pcc) assemble into heterocomplexes at neutral pH. Upon lowering the pH, the complex dissociates and reassembles into homo-oligomers. A glutamate residue (E303) located on the hydrophobic surface of Emp46pcc serves as the pH-sensing switch for assembly and segregation, and we have suggested that its side chains are protonated in the heterocomplex, even at neutral pH. To examine this hypothesis, we constructed two structural models in which the side chains of E303 were negatively charged or protonated and analyzed the effects of these charged states on the structure of the heterocomplex using molecular dynamics (MD) simulations. The calculated structures suggested the side chains of E303 to be protonated in the heterocomplex, even at neutral pH. Based on these computational results, the pH dependence of Emp47pcc homo-oligomer assembly was experimentally modified by a glutamate mutation on its hydrophobic surface. The Q306E mutant of Emp47pcc underwent a structural transition at physiological pH. Our results suggest a method for modifying pH-dependent protein-protein interactions.
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- 2021
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184. Recombinant expression of computationally designed peptide-bundlemers in Escherichia coli
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Darrin J. Pochan, Jeffery G. Saven, Christopher J. Kloxin, Zvi Kelman, Nairiti Sinha, and Grethe V. Jensen
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0106 biological sciences ,0301 basic medicine ,Biocompatible Materials ,Bioengineering ,Peptide ,medicine.disease_cause ,01 natural sciences ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,chemistry.chemical_compound ,010608 biotechnology ,Escherichia coli ,Peptide synthesis ,medicine ,Computational design ,chemistry.chemical_classification ,Coiled coil ,Recombinant expression ,Proteins ,General Medicine ,Combinatorial chemistry ,Nanostructures ,030104 developmental biology ,chemistry ,Peptides ,Biotechnology - Abstract
Computational design of fully artificial peptides is extensively researched by material scientists and engineers for the construction of novel nanostructures and biomaterials. Such design has yielded a peptide-based building block or bundlemer, a coiled coil peptide assembly that undergoes further physical-covalent interactions to form 1D, 2D and, potentially, 3D hierarchical assemblies and displays targeted and biomimetic material properties. Recombinant expression is a convenient, flexible tool to synthesize such artificial and modified peptides in large quantities while also enabling economical synthesis of isotopically labeled peptides and longer protein-like artificial peptides. This report describes the protocol for recombinant expression of a 31-amino acid, computationally designed bundlemer-forming peptide in Escherichia coli. Peptide yields of 10 mgs per liter of media were achieved which highlights complementary advantages of recombinant expression technique relative to conventional laboratory-scale synthesis, such as solid-phase peptide synthesis.
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- 2021
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185. Allosteric Inhibition of the Epidermal Growth Factor Receptor
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Julie K.-L. Sinclair, Alanna Schepartz, Deepto Mozumdar, Kim Quach, and Wesley E. Robertson
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Coiled coil ,Mutation ,biology ,Chemistry ,Kinase ,Activator (genetics) ,Cell Membrane ,Allosteric regulation ,medicine.disease_cause ,Biochemistry ,Cell biology ,ErbB Receptors ,Structure-Activity Relationship ,T790M ,Cell Line, Tumor ,medicine ,biology.protein ,Humans ,Amino Acid Sequence ,Epidermal growth factor receptor ,Protein Kinase Inhibitors ,EGFR inhibitors - Abstract
We previously reported a family of hydrocarbon-stapled peptides designed to interact with the epidermal growth factor receptor (EGFR) juxtamembrane (JM) segment, blocking its ability to form a coiled coil dimer that is essential for receptor activation. These hydrocarbon-stapled peptides, most notably E1S, decreased the proliferation of cell lines that express wild-type EGFR (H2030 and A431) as well as those expressing the oncogenic mutants EGFR L858R (H3255) and L858R/T790M (H1975). Although our previous investigations provided evidence that E1S interacted with EGFR directly, the location and details of these interactions were not established. Here we apply biochemical and cross-linking mass spectrometry tools to better define the interactions between E1S and EGFR. Taken with previously reported structure-activity relationships, our results support a model in which E1S interacts simultaneously with both the JM and the C-lobe of the activator kinase, effectively displacing the JM of the receiver kinase. Our results also reveal potential interactions between E1S and the N-terminal region of the C-terminal tail. We propose a model in which E1S inhibits EGFR by both mimicking and inhibiting JM coiled coil formation. This model could be used to design novel, allosteric (and perhaps nonpeptidic) EGFR inhibitors.
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- 2021
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186. Engineering soluble artificial epidermal growth factor receptor mimics capable of spontaneous in vitro dimerization
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May H. Abdel Aziz, Kendall Cooper, Ramsha Imran, Allison Sunderhaus, Manon Nassar, Dustin P. Patterson, and Amanda Goudelock
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0106 biological sciences ,0301 basic medicine ,Bioengineering ,Spodoptera ,Protein Engineering ,01 natural sciences ,Applied Microbiology and Biotechnology ,Receptor tyrosine kinase ,03 medical and health sciences ,010608 biotechnology ,Sf9 Cells ,Animals ,Epidermal growth factor receptor ,Receptor ,Coiled coil ,biology ,Kinase ,Chemistry ,Fusion protein ,Recombinant Proteins ,ErbB Receptors ,030104 developmental biology ,Protein kinase domain ,biology.protein ,Biophysics ,Dimerization ,Vesicle localization ,Biotechnology - Abstract
Epidermal growth factor receptor (EGFR) is a clinically validated target for a multitude of human cancers. The receptor is activated upon ligand binding through a critical dimerization step. Dimerization can be replicated in vitro by locally concentrating the receptor kinase domains on the surface of lipid-based vesicles. In this study we investigated the use of coiled coils to induce spontaneous receptor kinase domain dimerization in vitro to form non-membrane-bound artificial receptor mimics in solution. Two engineered forms of EGFR kinase domain fused to coiled coil complementary peptides were designed to self-associate upon mixing. Two fusion protein species (P3-EGFR and P4-EGFR) independently showed the same activity and polymerization profile known to exist with EGFR kinase domains. Upon mixing the two species, coiled coil heterodimers were formed that induced EGFR association to form dimers of the kinase domains. This was accompanied by 11.5-fold increase in the phosphorylation rate indicative of kinase domain activation equivalent to the levels achieved using vesicle localization and mimicking in vivo ligand-induced activation. This study presents a soluble tyrosine kinase receptor mimic capable of spontaneous in vitro activation that can facilitate functional and drug discovery studies for this clinically important receptor class.
- Published
- 2021
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187. Diversity, structure and function of the coiled‐coil domains of plant NLR immune receptors
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Meng Han, Yule Liu, and Junzhu Wang
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0106 biological sciences ,0301 basic medicine ,Coiled coil ,Programmed cell death ,Cell Death ,Effector ,NLR Proteins ,Plant Science ,Plants ,Biology ,01 natural sciences ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology ,Cell biology ,Structure and function ,03 medical and health sciences ,030104 developmental biology ,Immune system ,Protein Domains ,Receptors, Immunologic ,Receptor ,Function (biology) ,Plant Proteins ,010606 plant biology & botany - Abstract
Plant nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen avirulence effectors and activate defense responses. Nucleotide-binding, leucine-rich repeat receptors are classified into coiled-coil (CC)-containing and Toll/interleukin-1 receptor (TIR)-containing NLRs. Recent advances suggest that NLR CC domains often function in signaling activation, especially for induction of cell death. In this review, we outline our current understanding of NLR CC domains, including their diversity/classification and structure, their roles in cell death induction, disease resistance, and interaction with other proteins. Furthermore, we provide possible directions for future work.
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- 2021
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188. Origin of the Surprising Mechanical Stability of Kinesin’s Neck Coiled Coil
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Yi-Zhao Geng, Qing Ji, Hui Zhang, Shu-Xia Liu, and Gang Lü
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Coiled coil ,Materials science ,010304 chemical physics ,Protein Stability ,Shear force ,Kinesins ,Hydrogen Bonding ,01 natural sciences ,Protein Structure, Secondary ,Computer Science Applications ,Contact force ,Motor protein ,Molecular dynamics ,Protein structure ,Protein Domains ,0103 physical sciences ,Ultimate tensile strength ,Perpendicular ,Computer Simulation ,Physical and Theoretical Chemistry ,Composite material ,Hydrophobic and Hydrophilic Interactions - Abstract
Kinesin-1 is a motor protein moving along a microtubule with its two identical motor heads dimerized by two neck linkers and a coiled-coil stalk. When both motor heads bind the microtubule, an internal strain is built up between the two heads, which is indispensable to ensure proper coordination of the two motor heads during kinesin-1's mechanochemical cycle. The internal strain forms a tensile force along the neck linker that tends to unwind the neck coiled coil (NCC). Experiments showed that the kinesin-1's NCC has a high antiunwinding ability compared with conventional coiled coils, which was mainly attributed to the enhanced hydrophobic pressure arising from the unconventional sequence of kinesin-1's NCC. However, hydrophobic pressure cannot provide the shearing force which is needed to balance the tensile force on the interface between two helices. To find out the true origin of the mechanical stability of kinesin-1's NCC, we perform a novel and detailed mechanical analysis for the system based on molecular dynamics simulation at an atomic level. We find that the needed shearing force is provided by a buckle structure formed by two tyrosines which form effective steric hindrance in the presence of tensile forces. The tensile force is balanced by the tensile direction component of the contact force between the two tyrosines which forms the shearing force. The hydrophobic pressure balances the other component of the contact force perpendicular to the tensile direction. The antiunwinding strength of NCC is defined by the maximum shearing force, which is finally determined by the hydrophobic pressure. Kinesin-1 uses residues with plane side chains, tryptophans and tyrosines, to form the hydrophobic center and to shorten the interhelix distance so that a high antiunwinding strength is obtained. The special design of NCC ensures exquisite cooperation of steric hindrance and hydrophobic pressure that results in the surprising mechanical stability of NCC.
- Published
- 2021
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189. Triangular in Vivo Self-Assembling Coiled-Coil Protein Origami
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Sabina Božič Abram, Roman Jerala, Jana Aupič, Helena Gradišar, and Adam Round
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Protein Conformation, alpha-Helical ,0301 basic medicine ,Nanostructure ,Materials science ,Protein domain ,resveratrol ,Protein Engineering ,01 natural sciences ,Biochemistry ,enzyme clustering ,mevalonate ,03 medical and health sciences ,Polyhedron ,Protein structure ,Protein Domains ,udc:577 ,Escherichia coli ,Genes, Synthetic ,Coiled coil ,Fusion ,coiled coil ,010405 organic chemistry ,Proteins ,Articles ,General Medicine ,Protein engineering ,Nanostructures ,0104 chemical sciences ,Crystallography ,030104 developmental biology ,Molecular Medicine ,biosynthesis ,Protein Multimerization ,Linker - Abstract
Coiled-coil protein origami (CCPO) polyhedra are designed self-assembling nanostructures constructed from coiled coil (CC)-forming modules connected into a single chain. For testing new CCPO building modules, simpler polyhedra could be used that should maintain most features relevant to larger scaffolds. We show the design and characterization of nanoscale single-chain triangles, composed of six concatenated parallel CC dimer-forming segments connected by flexible linker peptides. The polypeptides self-assembled in bacteria in agreement with the design, and the shape of the polypeptides was confirmed with small-angle X-ray scattering. Fusion with split-fluorescent protein domains was used as a functional assay in bacteria, based on the discrimination between the correctly folded and misfolded nanoscale triangles comprising correct, mismatched, or truncated modules. This strategy was used to evaluate the optimal size of linkers between CC segments which comprised eight amino acid residues.
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- 2021
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190. Conformational control in a photoswitchable coiled coil
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Justin M. Torner and Paramjit S. Arora
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Models, Molecular ,Coiled coil ,Materials science ,Metals and Alloys ,Proteins ,General Chemistry ,Photochemical Processes ,Protein Engineering ,Protein Structure, Secondary ,Article ,Catalysis ,Protein tertiary structure ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Materials Chemistry ,Ceramics and Composites ,Protein recognition ,Biophysics - Abstract
The coiled coil is a common protein tertiary structure intimately involved in mediating protein recognition and function. Due to their structural simplicity, coiled coils have served as attractive scaffolds for the development of functional biomaterials. Herein we describe the design of conformationally-defined coiled coil photoswitches as potential environmentally-sensitive biomaterials.
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- 2021
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191. User-defined, temporal presentation of bioactive molecules on hydrogel substrates using supramolecular coiled coil complexes
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M. Gregory Grewal, Christopher B. Highley, Rachel A. Letteri, and Vincent P. Gray
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chemistry.chemical_classification ,Coiled coil ,Scaffold ,Chemistry ,Biomolecule ,Biomedical Engineering ,Supramolecular chemistry ,Hydrogels ,Peptide ,Extracellular Matrix ,Polyethylene Glycols ,Self-healing hydrogels ,Biophysics ,Click chemistry ,General Materials Science ,Hyaluronic Acid ,Peptides ,RGD motif - Abstract
The ability to spatiotemporally control the presentation of relevant biomolecules in synthetic culture systems has gained significant attention as researchers strive to recapitulate the endogenous extracellular matrix (ECM) in vitro. With the biochemical composition of the ECM constantly in flux, the development of platforms that allow for user-defined control of bioactivity is desired. Here, we reversibly conjugate bioactive molecules to hydrogel-based substrates through supramolecular coiled coil complexes that form between complementary peptides. Our system employs a thiolated peptide for tethering to hydrogel surfaces (T-peptide) through a spatially-controlled photomediated click reaction. The complementary association peptide (A-peptide), containing the bioactive domain, forms a heterodimeric coiled coil complex with the T-peptide. Addition of a disruptor peptide (D-peptide) engineered specifically to target the A-peptide outcompetes the T-peptide for binding, and removes the A-peptide and the attached bioactive motif from the scaffold. We use this platform to demonstrate spatiotemporal control of biomolecule presentation within hydrogel systems in a repeatable process that can be extended to adhesive motifs for cell culture. NIH 3T3 fibroblasts seeded on hyaluronic acid hydrogels and polyethylene glycol-based fibrous substrates supramolecularly functionalized with an RGD motif demonstrated significant cell spreading over their nonfunctionalized counterparts. Upon displacement of the RGD motif, fibroblasts occupied less area and clustured on the substrates. Taken together, this platform enables facile user-defined incorporation and removal of biomolecules in a repeatable process for controlled presentation of bioactivity in engineered culture systems.
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- 2021
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192. Rapid construction of fluorescence quenching-based immunosensor Q-bodies using α-helical coiled-coil peptides
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Akihito Inoue, Takanobu Yasuda, Tetsuya Kitaguchi, and Hiroshi Ueda
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Protein Conformation, alpha-Helical ,Coiled coil ,chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Metals and Alloys ,Peptide ,Biosensing Techniques ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Fluorescence ,Catalysis ,Antibody fragments ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Antigen ,α helical ,Fluorescence Resonance Energy Transfer ,Materials Chemistry ,Ceramics and Composites ,Biophysics ,Peptides - Abstract
Here, we report a rapid and efficient method to fabricate Quenchbodies (Q-bodies) that can detect targets with antigen-dependent fluorescence augmentation using a stable coiled-coil peptide pair, E4 and K4 (coiled Q-body, CQ-body). The CQ-body allowed antigen detection not only in buffer but also in 50% plasma. Furthermore, we describe FRET-type CQ-bodies using a dual-coloured K4 peptide, which allowed a more precise antigen quantification. Lastly, successful fabrication of nanobody-based CQ-body shows its applicability to a range of antibody fragments.
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- 2021
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193. Liposome fusion with orthogonal coiled coil peptides as fusogens: the efficacy of roleplaying peptides
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Alexander Kros, Patrick van der Est, Geert A. Daudey, G. J. Agur Sevink, Ankush Singhal, Meng-Jie Shen, and Aimee L. Boyle
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chemistry.chemical_classification ,Coiled coil ,Chemistry ,Heptad repeat ,Liposome ,chemistry ,Vesicle ,Drug delivery ,Biophysics ,Peptide ,Biological membrane ,General Chemistry ,Asparagine - Abstract
Biological membrane fusion is a highly specific and coordinated process as a multitude of vesicular fusion events proceed simultaneously in a complex environment with minimal off-target delivery. In this study, we develop a liposomal fusion model system with specific recognition using lipidated derivatives of a set of four de novo designed heterodimeric coiled coil (CC) peptide pairs. Content mixing was only obtained between liposomes functionalized with complementary peptides, demonstrating both fusogenic activity of CC peptides and the specificity of this model system. The diverse peptide fusogens revealed important relationships between the fusogenic efficacy and the peptide characteristics. The fusion efficiency increased from 20% to 70% as affinity between complementary peptides decreased, (from KF ≈ 108 to 104 M−1), and fusion efficiency also increased due to more pronounced asymmetric role-playing of membrane interacting ‘K’ peptides and homodimer-forming ‘E’ peptides. Furthermore, a new and highly fusogenic CC pair (E3/P1K) was discovered, providing an orthogonal peptide triad with the fusogenic CC pairs P2E/P2K and P3E/P3K. This E3/P1k pair was revealed, via molecular dynamics simulations, to have a shifted heptad repeat that can accommodate mismatched asparagine residues. These results will have broad implications not only for the fundamental understanding of CC design and how asparagine residues can be accommodated within the hydrophobic core, but also for drug delivery systems by revealing the necessary interplay of efficient peptide fusogens and enabling the targeted delivery of different carrier vesicles at various peptide-functionalized locations., We developed a liposomal fusion model system with specific recognition using a set of heterodimeric coiled coil peptide pairs. This study unravels important structure–fusogenic efficacy relationships of peptide fusogens.
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- 2021
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194. De novodesigned coiled coils as scaffolds for lanthanides, including novel imaging agents with a twist
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Alexandra M Webster and Anna F. A. Peacock
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Coiled coil ,Lanthanide ,Coordination sphere ,Chemistry ,Metal binding ,Metals and Alloys ,Nanotechnology ,Sequence (biology) ,General Chemistry ,Protein engineering ,Plasma protein binding ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Materials Chemistry ,Ceramics and Composites ,Peptide sequence - Abstract
For much of their history, lanthanides were thought to be biologically inert. However, the last decade has seen the discovery and development of the field of native lanthanide biochemistry. Lanthanides exhibit a variety of interesting photophysical properties from which many useful applications derive. The development of effective functional lanthanide complexes requires control of their coordination sphere; something proteins manage very effectively through their 3D metal-binding sites. α-Helical coiled coil peptides are miniature scaffolds which can be designed de novo and can retain the favourable properties of larger proteins within a much simplified system. Metal binding sites, including those which bind lanthanides can be engineered into the coiled coil sequence. This review will highlight the opportunities presented by the use of coiled coil peptides as scaffolds for lanthanide binding and the potential to control the coordination environment by simple modifications to peptide sequence. Designed lanthanide coiled coils offer opportunities to gain greater insight into native lanthanide biochemistry as well as to develop new functional complexes, including imaging agents.
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- 2021
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195. Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins
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E. Sitkiewicz, Stanislaw Dunin-Horkawicz, G. Goch, Maciej Jasiński, Ewa Lewicka, Jan Ludwiczak, B. Swiderska, Grazyna Jagura-Burdzy, Malgorzata Adamczyk, H. Nieznanska, and Roza Szatkowska
- Subjects
Microbiology (medical) ,Cell division ,Transcription, Genetic ,In silico ,Stability functions ,lcsh:QR1-502 ,Biology ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Plasmid ,Bacterial Proteins ,Escherichia coli ,Protein–DNA interaction ,Computer Simulation ,Cytoskeleton ,030304 developmental biology ,Coiled coil ,0303 health sciences ,Binding Sites ,030306 microbiology ,DNA-protein interaction ,Self-assembly ,Cell biology ,Coiled-coil proteins ,DNA binding site ,DNA-Binding Proteins ,Cytoskeletal Proteins ,chemistry ,Conjugation, Genetic ,Broad-host-range plasmids ,Brownian motion ,DNA ,Plasmids ,Research Article - Abstract
Background DNA binding KfrA-type proteins of broad-host-range bacterial plasmids belonging to IncP-1 and IncU incompatibility groups are characterized by globular N-terminal head domains and long alpha-helical coiled-coil tails. They have been shown to act as transcriptional auto-regulators. Results This study was focused on two members of the growing family of KfrA-type proteins encoded by the broad-host-range plasmids, R751 of IncP-1β and RA3 of IncU groups. Comparative in vitro and in silico studies on KfrAR751 and KfrARA3 confirmed their similar biophysical properties despite low conservation of the amino acid sequences. They form a wide range of oligomeric forms in vitro and, in the presence of their cognate DNA binding sites, they polymerize into the higher order filaments visualized as “threads” by negative staining electron microscopy. The studies revealed also temperature-dependent changes in the coiled-coil segment of KfrA proteins that is involved in the stabilization of dimers required for DNA interactions. Conclusion KfrAR751 and KfrARA3 are structural homologues. We postulate that KfrA type proteins have moonlighting activity. They not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and positioning in the cells before cell division, involving thermal energy.
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- 2021
196. Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor
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Miao Yu, Jody M. Mason, Barry J. Kappel, Jim A. Rotolo, and Lila Ghamsari
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0301 basic medicine ,fos related antigen-1 ,protein-protein interactions ,activator protein-1 ,Context (language use) ,Peptide ,protein-fragment complementation assay ,Computational biology ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Biochemistry ,Protein–protein interaction ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,Protein-fragment complementation assay ,Transcriptional regulation ,Peptide library ,Molecular Biology ,Transcription factor ,chemistry.chemical_classification ,Computational design ,coiled coil ,030102 biochemistry & molecular biology ,Chemistry ,peptide libraries ,030104 developmental biology ,Chemistry (miscellaneous) ,Intracellular - Abstract
To date, most research into the inhibition of oncogenic transcriptional regulator, Activator Protein 1 (AP-1), has focused on heterodimers of cJun and cFos. However, the Fra1 homologue remains an important cancer target. Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts. To do so the isCAN computational tool was used to rapidly screen >75 million peptide library members, narrowing the library size by >99.8% to one accessible to intracellular PCA selection. The resulting 131 072-member library was predicted to contain high quality binders with both a high likelihood of target engagement, while simultaneously avoiding homodimerization and off-target interaction with Jun homologues. PCA screening was next performed to enrich those members that meet these criteria. In particular, optimization was achieved via inclusion of options designed to generate the potential for compromised intermolecular contacts in both desired and non-desired species. This is an often-overlooked prerequisite in the conflicting design requirement of libraries that must be selective for their target in the context of a range of alternative potential interactions. Here we demonstrate that specificity is achieved via a combination of both hydrophobic and electrostatic contacts as exhibited by the selected peptide (Fra1W). In vitro analysis of the desired Fra1–Fra1W interaction further validates high Fra1 affinity (917 nM) yet selective binding relative to Fra1W homodimers or affinity for cJun. The isCAN → PCA based multidisciplinary approach provides a robust screening pipeline in generating target-specific hits, as well as new insight into rational peptide design in the search for novel bZIP family inhibitors., Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts.
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- 2021
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197. Designed protein- and peptide-based hydrogels for biomedical sciences
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Eunjung Lee, Jeewon Lee, Wonkyung Ahn, Jong-Hwan Lee, and Soo Rin Kim
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Coiled coil ,chemistry.chemical_classification ,Biocompatibility ,biology ,Chemistry ,Biomedical Engineering ,Proteins ,Fibroin ,Biocompatible Materials ,Hydrogels ,Nanotechnology ,Peptide ,General Chemistry ,General Medicine ,Tissue engineering ,Drug Design ,Self-healing hydrogels ,biology.protein ,Animals ,Humans ,General Materials Science ,Peptides ,Resilin ,Macromolecule - Abstract
Proteins are fundamentally the most important macromolecules for biochemical, mechanical, and structural functions in living organisms. Therefore, they provide us with diverse structural building blocks for constructing various types of biomaterials, including an important class of such materials, hydrogels. Since natural peptides and proteins are biocompatible and biodegradable, they have features advantageous for their use as the building blocks of hydrogels for biomedical applications. They display constitutional and mechanical similarities with the native extracellular matrix (ECM), and can be easily bio-functionalized via genetic and chemical engineering with features such as bio-recognition, specific stimulus-reactivity, and controlled degradation. This review aims to give an overview of hydrogels made up of recombinant proteins or synthetic peptides as the structural elements building the polymer network. A wide variety of hydrogels composed of protein or peptide building blocks with different origins and compositions - including β-hairpin peptides, α-helical coiled coil peptides, elastin-like peptides, silk fibroin, and resilin - have been designed to date. In this review, the structures and characteristics of these natural proteins and peptides, with each of their gelation mechanisms, and the physical, chemical, and mechanical properties as well as biocompatibility of the resulting hydrogels are described. In addition, this review discusses the potential of using protein- or peptide-based hydrogels in the field of biomedical sciences, especially tissue engineering.
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- 2021
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198. High-affinity antigen association to cationic liposomes via coiled coil-forming peptides induces a strong antigen-specific CD4+ T-cell response
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Leboux, R. J.T., Benne, N., van Os, W. L., Bussmann, J., Kros, A., Jiskoot, W., Slütter, B., Immunologie, Dep Farmaceutische wetenschappen, Pharmaceutics, Immunologie, Dep Farmaceutische wetenschappen, and Pharmaceutics
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Pharmaceutical Science ,Peptide ,02 engineering and technology ,030226 pharmacology & pharmacy ,03 medical and health sciences ,0302 clinical medicine ,Antigen ,In vivo ,Cationic liposome ,Lipid bilayer ,Coiled coil peptide ,chemistry.chemical_classification ,Coiled coil ,Liposome ,Chemistry ,Vaccination ,General Medicine ,021001 nanoscience & nanotechnology ,In vitro ,CD4 T-cell ,Liposomes ,Antigen association ,Biophysics ,0210 nano-technology ,Biotechnology - Abstract
Liposomes are widely investigated as vaccine delivery systems, but antigen loading efficiency can be low. Moreover, adsorbed antigen may rapidly desorb under physiological conditions. Encapsulation of antigens overcomes the latter problem but results in significant antigen loss during preparation and purification of the liposomes. Here, we propose an alternative attachment method, based on a complementary heterodimeric coiled coil peptide pair pepK and pepE. PepK was conjugated to cholesterol (yielding CPK) and pepE was covalently linked to model antigen OVA323 (yielding pepE-OVA323). CPK was incorporated in the lipid bilayer of cationic liposomes (180 nm in size). Antigen was associated more efficiently to functionalized liposomes (Kd 166 nM) than to cationic liposomes (Kd not detectable). In vivo co-localization of antigen and liposomes was strongly increased upon CPK-functionalization (35% -> 80%). CPK-functionalized liposomes induced 5-fold stronger CD4+ T-cell proliferation than non-functionalized liposomes in vitro. Both formulations were able to induce strong CD4+ T-cell expansion in mice, but more IFN-y and IL-10 production was observed after immunization with functionalized liposomes. In conclusion, antigen association via coiled coil peptide pair increased co-localization of antigen and liposomes, increased CD4+ T-cell proliferation in vitro and induced a stronger CD4+ T-cell response in vivo.
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- 2021
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199. Solution Structure of the Severe Acute Respiratory Syndrome-Coronavirus Heptad Repeat 2 Domain in the Prefusion State*
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Susanna Hakansson-McReynolds, Michael Caffrey, Shaokai Jiang, and Lijun Rong
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Models, Molecular ,Repetitive Sequences, Amino Acid ,Viral protein ,Protein Conformation ,viruses ,Hemagglutinins, Viral ,Trimer ,Biology ,medicine.disease_cause ,Crystallography, X-Ray ,Biochemistry ,Protein structure ,Viral Envelope Proteins ,Viral entry ,medicine ,Humans ,skin and connective tissue diseases ,Molecular Biology ,Coronavirus ,Coiled coil ,chemistry.chemical_classification ,Membrane Glycoproteins ,Cell Biology ,Virology ,Cell biology ,Heptad repeat ,chemistry ,Severe acute respiratory syndrome-related coronavirus ,Solubility ,Protein Structure and Folding ,Spike Glycoprotein, Coronavirus ,Glycoprotein ,Viral Fusion Proteins - Abstract
The envelope glycoprotein, termed the spike protein, of severe acute respiratory syndrome coronavirus (SARS-CoV) is known to mediate viral entry. Similar to other class 1 viral fusion proteins, the heptad repeat regions of SARS-CoV spike are thought to undergo conformational changes from a prefusion form to a subsequent post-fusion form that enables fusion of the viral and host membranes. Recently, the structure of a post-fusion form of SARS-CoV spike, which consists of isolated domains of heptad repeats 1 and 2 (HR1 and HR2), has been determined by x-ray crystallography. To date there is no structural information for the prefusion conformations of SARS-CoV HR1 and HR2. In this work we present the NMR structure of the HR2 domain (residues 1141-1193) from SARS-CoV (termed S2-HR2) in the presence of the co-solvent trifluoroethanol. We find that in the absence of HR1, S2-HR2 forms a coiled coil symmetric trimer with a complex molecular mass of 18 kDa. The S2-HR2 structure, which is the first example of the prefusion form of coronavirus envelope, supports the current model of viral membrane fusion and gives insight into the design of structure-based antagonists of SARS.
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- 2021
200. Enhancing Antimicrobial Peptide Potency through Multivalent Presentation on Coiled-Coil Nanofibrils
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Christian Roth, Beate Koksch, Dorian J. Mikolajczak, and Chaitanya Kumar Thota
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chemistry.chemical_classification ,Coiled coil ,Scaffold ,Circular dichroism ,Chemistry ,medicine.drug_class ,Organic Chemistry ,Antibiotics ,Peptide ,Context (language use) ,Antimicrobial ,Biochemistry ,Drug Discovery ,Biophysics ,medicine ,Mode of action - Abstract
[Image: see text] Antibiotic-resistant microbes have become a global health threat. New delivery systems that enhance the efficacy of antibiotics and/or overcome the resistances can help combat them. In this context, we present FF03, a fibril-forming α-helical coiled-coil peptide that functions as an efficient scaffold for the multivalent presentation of the weakly cationic antimicrobial peptide (AMP) IN4. The resulting IN4-decorated FF03 coiled-coil fibrils (FF03 + IN4) are nonhemolytic and noncytotoxic and show enhanced antimicrobial activity relative to unconjugated IN4 and standard antibiotics against several bacterial strains. Scanning electron microscopy analysis shows that FF03 + IN4 nanofibers disrupt methicillin-resistant Staphylococcus aureus membranes, indicating a surface-level mode of action. Furthermore, transmission electron microscopy and circular dichroism studies indicate that decoration of the FF03 scaffold with IN4 does not alter the secondary-structure propensity or fibril-forming properties of FF03. Thus, the approach reported herein provides a new peptidic scaffold for the multivalent presentation of AMPs to obtain nonhemolytic and noncytotoxic antimicrobial systems with improved efficacy relative to the unconjugated AMP analogues.
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- 2020
- Full Text
- View/download PDF
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