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Symmetry-Based Self-Assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers

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We construct nanotubes using native protein structures and their native associations from structural databases. The construction is based on a shape-guided symmetric self-assembly concept. Our strategy involves fusing judiciouslyselected oligomerization domains via peptide linkers. Linkers are inherently flexible, hence their choice is critical: they should position the domains in three-dimensional space in the desired orientation while retaining their own natural conformational tendencies; however, at the same time, retain the construct stability. Here we outline a design scheme which accounts for linker flexibility considerations, and present two examples. The first is HIV-1 capsid protein, which in vitro self-assembles into nanotubes and conical capsids, and its linker exists as a short flexible loop. The second involves novel nanotubes construction based on antimicrobial homodimer Magainin 2, employing linkers of distinct lengths and flexibility levels. Our strategy utilizes the abundance of unique shapes and sizes of proteins and their building blocks which can assemble into a vast number of combinations, and consequently, nanotubes of distinct morphologies and diameters. Computational design and assessment methodologies can help reduce the number of candidates for experimental validation. This is an invited paper for a special issue on protein dynamics, here focusing on flexibility in nanotube design based on protein building blocks.

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Keywords: Building blocks; Carr-Purcell-Meiboom-Gill (CPMG); ClpP protein; EXSY; Nuclear Spin Relaxation; Nuclear magnetic resonance; RDC data encodes; SMN Tudor domain; Slow Protein Dynamic; chemical shift anisotropy (CSA); ligand binding and catalysis; molecular dynamics simulations; nanotube design; oligomerization domain; paramagnetic relaxation enhancement; protein dynamics; relaxation dispersion; residual dipolar coupling; self-assembly; symmetry; transverse relaxation optimized spectroscopy (TROSY)

Document Type: Research Article

Publication date: 2011-04-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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