De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs.
We present an approach for designing self-assembled nanostructures from naturally occurring building block segments obtained from native protein structures. We focus on structural motifs from left-handed beta-helical proteins. We selected 17 motifs. Copies of each of the motifs are stacked one atop the other. The obtained structures were simulated for long periods by using Molecular Dynamics to test their ability to retain their organization over time. We observed that a structural model based on the self-assembly of a motif from E. coli galactoside acetyltransferase produced a very stable tube. We studied the interactions that help maintain the conformational stability of the systems, focusing on the role of specific amino acids at specific positions. Analysis of these systems and a mutational study of selected candidates revealed that the presence of proline and glycine residues in the loops of beta-helical structures greatly enhances the structural stability of the systems.
Haspel
Nurit
N
School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Zanuy
David
D
Alemán
Carlos
C
Wolfson
Haim
H
Nussinov
Ruth
R
D000123:Acetyltransferases / Q000737:chemistry / Q000235:genetics; D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics; D005998:Glycine / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D049329:Nanostructures / Q000737:chemistry*; D011392:Proline / Q000737:chemistry; D017433:Protein Structure, Secondary / Q000235:genetics; D011506:Proteins / Q000737:chemistry* / Q000235:genetics
D029968:Escherichia coli Proteins; D011506:Proteins; D011392:Proline; D000123:Acetyltransferases; D005998:Glycine