Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces.

Stephan Rauschenbach,Alyazan Albarghash,Ludger Harnau,Duy Le,Gordon Rinke,Sabine Abb,Rico Gutzler,Klaus Kern,Talat S Rahman,Michael Dürr

doi:10.1021/acsnano.6b06145

Abstract

Herein we report the fabrication of molecular nanostructures on surfaces via two-dimensional (2D) folding of the nine amino acid peptide bradykinin. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy is used to fabricate and investigate the molecular nanostructures. Subnanometer resolved images evidence the large conformational freedom of the molecules if thermal motion is inhibited and the formation of stable uniform dimers of only one specific conformation when diffusion can take place. Molecular dynamics modeling supported by density functional theory calculations give atomically precise insight into the induced-fit binding scheme when the folded dimer is formed. In the absence of solvent, we find a hierarchy of binding strength from polar to nonpolar, manifested in an inverted polar-nonpolar segregation which suppresses unspecific interactions at the rim of the nanostructure. The demonstrated 2D-folding scheme resembles many key properties of its native 3D counterpart and shows that functional, molecular nanostructures on surfaces fabricated by folding could be just as versatile and specific.

Highlights

I n protein folding, the biological self-assembly scheme that is the route to molecular functionality, a flexible amino acid (AA) sequence encodes one specific, functional conformation as well as the folding pathway to reach it within the vastness of possible conformations.[1]
BK (Figure 1a) is a nona-peptide which has been intensively studied since the discovery of its physiological effects in 1949.24 Many attempts were made to determine the structure of BK in different environments such as in solution by cyclic dichroism (CD) and NMR25 as well as in the gas phase by ion mobility spectroscopy[26,27] or optical spectroscopy.[28]
The great potential of polypeptide folding lies in the ability to encode the folding pathway and the final conformation in the sequence via a universal synthesis approach

Summary

Introduction

I n protein folding, the biological self-assembly scheme that is the route to molecular functionality, a flexible amino acid (AA) sequence encodes one specific, functional conformation as well as the folding pathway to reach it within the vastness of possible conformations.[1]. Structures fabricated by vacuum sublimation of molecular building blocks onto atomically defined surfaces in ultrahigh vacuum (UHV) allow for the investigation by scanning tunneling microscopy (STM) at subnanometer resolution.[4] This approach has proven to be instrumental for obtaining a thorough understanding of the complex interactions among the molecules and with the surface, because STM reveals detailed information on the atomic structure, the formation mechanism, and physical as well as chemical properties of molecular assemblies. It further bears the potential for an integration with other vacuum technologies for a controlled fabrication and analysis. Based on the subnanometer resolved images, we perform atomistic modeling through a combination of classical molecular dynamics (MD) simulations and density functional theory (DFT) calculations

Methods

Results

Discussion

Conclusion