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Genetically Engineered Protein Domains as Hydrogel Crosslinks
Published in Raphael M. Ottenbrite, Sung Wan Kim, Polymeric Drugs & Drug Delivery Systems, 2019
Chun Wang, Russell J. Stewart, Russell J. Stewart, Jindrich KopeČek
One unique feature of our design is the use of coiled-coil protein domains. In addition to temperature-induced volume transition and responsiveness to chelating agents, sensitivity toward other stimuli, such as pH, ionic strength, solvents, electric current, mechanical force, or specific recognition and binding with ligand, could also be built into the hydrogel system. This could be accomplished by incorporating protein domains with specially engineered sequences. Furthermore, certain physical properties of the hydrogels, such as viscosity, gelation temperature, elasticity, rigidity, porosity, and bioerodibility, can be similarly tailored. As one of the possible extensions of the work described here, all the “e” and “g” positions of the heptad repeats of a coiled-coil strand could be occupied by glutamic acid or by lysine residues. Electrostatic interaction between two of such strands would favor specific formation of a heterodimer. Polar residues, such as as-paragine, could be inserted at the hydrophobic interface to facilitate specific alignment and orientation of the two strands and to decrease overall stability. Compared with the hybrid hydrogels formed using TEK42 as crosslinkers, gels crosslinked by such heterodimeric coiled-coil domains would be expected to have better defined pore size, better crosslinking efficiency with less intramolecular crosslinker, and a lower dissociation temperature.
Structures
Published in Thomas M. Nordlund, Peter M. Hoffmann, Quantitative Understanding of Biosystems, 2019
Thomas M. Nordlund, Peter M. Hoffmann
One of the reasons keratin crystals do not readily form is an interaction we have discussed in general but not applied specifically to keratin. The lowest-level structure of an α keratin consists of α-helical domains that consist of amino acid repeats of a pattern of seven, ABCDEFG. A and D are hydrophobic amino acids. This “heptad” repeat is characteristic of sequences able to form coiled-coil structures.15 What structural consequences do these heptads have? One basic feature of the α helix is that there are about 3.6 residues per turn. This means that every fourth amino acid will be on the same side of the helix as the first but offset a bit. This offset will create a hydrophobic line that will wind around the outside of the helix. When two such α helices come near each other, the hydrophobic interaction will tend to make the two helices wind around each other—a helix of helices.
Virus-Based Nanobiotechnology
Published in Yubing Xie, The Nanobiotechnology Handbook, 2012
Magnus Bergkvist, Brian A. Cohen
Perhaps one of the most intriguing developments using CCMV assembly is the possibility to incorporate other proteins inside the VLP core. Comellas-Aragonés et al. (2007) demonstrated for the first time in 2007 that a single horseradish peroxidase (HRP) enzyme can be internalized and remain active. Their approach was to simply mix HRP with coat protein and use the conventional pH assembly process to entrap the enzyme (initially mixing at pH 7.5 and then dialyzing against lower pH buffer). Single-enzyme encapsulation was achieved by manipulating the coat protein:HRP ratio. It is useful to be able to manipulate the amount of protein being encapsulated; however, it could be hard to control this relying solely on increasing concentration. One way to improve the encapsulation efficiency is to incorporate self-recognizing peptides in the system. Pair motifs of self-assembling short coiled-coil peptides (seven amino acids) are frequently found in nature and tend to associate with high affinity. Minten et al. (2009a,2010) used a heterodimeric coiled-coil pair to realize controlled encapsulation of green fluorescent protein (GFP) in CCMV VLPs. They fused a short positively charged peptide (K-coil) to the coat protein while GFP were modified to contain a complimentary negatively charged coil (E-coil) (Figure 7.4). Upon mixing the recombinant proteins at pH 7.5 and then lowering pH to 5.0, VLPs containing as many as ~15 GFPs could be obtained consistently. In addition to GFP, lipase B from Pseudozyma antarctica has also been packaged with this approach to get a catalytically active VLP (Minten et al. 2011a). The pH-dependent assembly of CCMV is one reason why it is attractive as a nanocontainer; however, above pH ~7.5, it is not functional as it will disassemble into dimers. In an attempt to remedy this, Minten et al., as a continuation of their work, have included a coat protein with an N-terminal His-tag in addition to the coiled-coil peptides. After VLPs are formed at pH 5, Ni2+ is added to the solution, which causes the His-tags to associate and stabilize the structure when increasing the pH to 7.5 (Minten et al. 2011b). Improving the pH stability of CCMV VLPs opens up many possibilities in various application areas.
A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer
Published in Molecular Physics, 2018
Kazutomo Kawaguchi, Satoshi Nakagawa, Isman Kurniawan, Koichi Kodama, Muhammad Saleh Arwansyah, Hidemi Nagao
GCN4-pLI is one of the GCN4 leucine zipper mutants and a coiled-coil composed of four α-helices wrapped around each other to bury a hydrophobic core [1]. The formation of GCN4-pLI tetramer is dominated by both hydrophobic and electrostatic interaction between monomers. While the association of the tetramer is dominated by hydrophobic interaction, the helix orientation is dominated by the salt bridge arising from the electrostatic interaction between charged amino acid residues [2]. In their experiment, only all-parallel helices have been observed after 36 h because of the salt bridge between charged amino acid residues, although anti-parallel four-helix bundle conformations have been prepared in solution.
Self-organisation of rhombitruncated cuboctahedral hexagonal columns from an amphiphilic Janus dendrimer
Published in Molecular Physics, 2021
Ning Huang, Qi Xiao, Mihai Peterca, Xiangbing Zeng, Virgil Percec
There are three possible directions equivalent to [421] at the corner of the unit cell (yellow spheres) (Figure 10a upper). In addition, there are other three possible directions which are different but also equivalent to [421] that start from the body centre of the Pmn unit cell (yellow sphere) (Figure 10a lower). Due to the symmetry of the cubic lattice, the number of directions equivalent to [421] is 8 times the 6 directions mentioned in Figure 9a, which represents 48 directions in total (Figure 10b, c). Figure 10b illustrates the 48 directions that hexagonal arrays of columns form via the SOM effect. These directions are generated with hexagonal arrays of columns as shown in Figure 10c. This arrangement corresponds to a rhombitruncated cuboctahedron, that to the best of our knowledge, although more primitive than biological assemblies created from proteins, was never encountered in biology or in synthetic supramolecular chemistry. Bundles of α-helical proteins are widely available in biology. They were discovered simultaneously and independently by Pauling and Corey [110] and by Crick [111] and are known as coiled-coil α-helix protein structures. Recently, a periodic table of coiled-coil proteins was elaborated [112]. Mimics of three and four-bundles of helical columns were elaborated by our laboratory via complex multistep synthetic methods [16,17,113–116]. However, the simplicity of the SOM method for the design of bundles of helical columns organised in unprecedentedly complex architectures such as tetrahedral [63], orthogonal [62], distorted dodecahedral [65] and now in rhombitruncated cuboctahedral arrangement of hexagonal columns as shown in the present report (Figure 11) seems to exceed even the ability of biology, although with a much lower level of perfection. We would like to stress again that in view of the results reported here, the distorted dodecahedral morphology [65] will have to be reinvestigated. This will be done and reported in a different publication. Elucidating the mechanism of the SOM concept and extending it to other F-K phases will provide access, most probably, to even more complex architectures.