Nanoscale insight into silk-like protein self-assembly: Effect of design and number of repeat units
| Autor: | Paul van der Schoot, Jamoliddin Razzokov, M. Saber Naderi |
|---|---|
| Přispěvatelé: | Sub Algemeen Theoretical Physics, Theoretical Physics, Soft Matter and Biological Physics |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
silk-like protein
Protein Structure Secondary Dimer Silk Biophysics Trimer 02 engineering and technology Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Protein Structure Secondary Accessible surface area Hydrophobic effect chemistry.chemical_compound Tetramer Silk/chemistry Structural Biology Biology Molecular Biology silk like protein Physics Hydrogen Bonding implicit solvent self-assembly Cell Biology Conformational entropy 021001 nanoscience & nanotechnology Random coil 0104 chemical sciences Solvents/chemistry Crystallography Chemistry Monomer chemistry Solvents 0210 nano-technology Hydrophobic and Hydrophilic Interactions replica exchange molecular dynamics fiber |
| Zdroj: | Physical Biology, 15(6). IOP PUBLISHING LTD Physical Biology, 15(6):066010. Institute of Physics Physical biology |
| ISSN: | 1478-3967 |
| Popis: | By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are beta-roll and beta-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock beta-sheet protein, the monomer and the dimer melt as well, although for the beta-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming beta-rolls and beta-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly. According to our simulations, the beta-roll and beta-sheet aggregates must be approximately equally stable. |
| Databáze: | OpenAIRE |
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