title: De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.
abstract: For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures.
authors: Department of Applied Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
authors: Sota
authors: S
authors: Yagi
authors: Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan.
authors: Satoshi
authors: S
authors: Akanuma
authors: Department of Applied Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
authors: Manami
authors: M
authors: Yamagishi
authors: Department of Molecular Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
authors: Tatsuya
authors: T
authors: Uchida
authors: Department of Applied Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. Electronic address: yamagish@toyaku.ac.jp.
authors: Akihiko
authors: A
authors: Yamagishi
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D001665:Binding Sites; D004220:Disulfides / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry; D006422:Hemerythrin / Q000737:chemistry* / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D056968:Lac Repressors / Q000737:chemistry* / Q000378:metabolism; D007930:Leucine; D046912:Multiprotein Complexes; D011485:Protein Binding; D015202:Protein Engineering; D017510:Protein Folding; D060066:Protein Interaction Maps; D017433:Protein Structure, Secondary / Q000235:genetics*; D012416:Rubredoxins / Q000737:chemistry* / Q000378:metabolism; D012997:Solvents / Q000737:chemistry; D016944:Sulfolobus / Q000737:chemistry / Q000378:metabolism
chemical_list: D004220:Disulfides; D006422:Hemerythrin; D056968:Lac Repressors; D046912:Multiprotein Complexes; D012416:Rubredoxins; D012997:Solvents; C055857:rubrerythrins; D007930:Leucine
keywords: Coiled coil; Hydrophobic interaction; Ion pairing; Protein–protein interaction; Solubility