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

Idit      Buch; Chung-Jung      Tsai; Haim      J. Wolfson; Ruth      Nussinov

doi:10.2174/092986611794653996

Abstract

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.

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