In situ Studies of Peptide and Protein Assemblies at the Solid-Liquid Interface

At the interface between science and engineering, there is the field of biomimicry: Innovations inspired by the observation of natural, evolutionary optimized biological structures and processes. To understand the challenges of biomimicry, the concept of âMolecular Tectonicsâ is particularly useful. It describes how different self-assembling processes are spatially and dynamically integrated to form successively more complex structures. This integration makes it difficult to isolate the underlying mechanisms, which are often on the scale of individual molecules. Molecular biomimicry therefore critically depends on the observation of natural systems at the molecular scale. Advances in scanning probe microscopy have enabled the study of molecular self-assembly in unprecedented detail. However, many of these advances critically depend on the use of Ultra High Vacuum (UHV) conditions. To study natural systems at the molecular scale, a transition from UHV towards solvated systems is required. In the first part of this thesis, small synthetic peptides are used as model system for molecular self-assembly. The self-assembly of peptides at interfaces has been studied by systematically varying the chemical structure and deposition method. By using ElectroSpray Ion Beam Deposition (ES-IBD) as well as in situ drop casting, the self-assembly at the solid-vacuum interface (UHV conditions) and at the solid-liquid interface was directly compared. This comprehensive study on the effect of solvent, structure and deposition method on the assembly of peptides at gas-solid and solid-liquid biointerfaces has shown that the same AcFA5K peptide can organize into various structures, from Î²-sheets to tubular and globular assemblies, depending on their local environment. The study of molecular self-assembly was extended to 2D protein crystals. By using high-speed and high-resolution and Atomic Force Microscopy (AFM), it was possible to resolve both spatially and dynamically the mechanisms involved in S-layer self-assembly at the solid-liquid interface, such as monomer adsorption, condensation into high-density clusters, crystallization and finally conformational changes of existing S-layer crystals. In the second part of this thesis, the integration of different self-assembling systems is explored and their functional properties are investigated. It combines the concepts of self-assembly and molecular tectonics. Self-assembled striped PS-b-PEO block copolymer (BCP) thin film substrates were used to confine and align S-layer self-assembly, without affecting the internal structure. Furthermore, the nucleation rate and S-layer growth was greatly enhanced on PS-b-PEO substrates, compared to the pure PS or PEO constituents. The hierarchical use of different self-assembling systems can be seen as a functional approach to the concept of molecular tectonics. The catalytic properties of S-layers regarding the formation of CaCO3 were studied. By studying the catalytic properties of S-layers ex vivo, their role can be investigated independently from the internal metabolism of their parent bacteria. Synchrotron based in situ X-ray Absorption Spectroscopy (XAS) and AFM are combined with continuous flow conditions, demonstrating that S-layers are able to stabilize amorphous forms of CaCO3 and catalyze the nucleation of calcite at extremely low supersaturations.

Stimuli-responsive nanostructured surfaces

Ana Maria Popa

The coupling of stimuli-responsive macromolecules to nanostructured surfaces opens the perspective for the fabrication and integration of "smart" micro- and nano-electro-mechanical systems (MEMS&NEMS) in which the smallest motile unit is the polymeric chain. The goal of this work was to develop thermoresponsive, durable nanoporous surfaces as a first step toward the fabrication of functional nanocontainers and nanovalves. The proposed strategy involves in a first step the design and implementation of a clean-room compatible, reproducible and up-scalable method for defining organized nanoporous arrays in MEMS compatible surfaces, such as silicon, silicon oxide and silicon nitride. The main objective of the second step was the covalent immobilization of responsive macromolecules on the obtained structures, as to provide the later with a "smart" behavior. The nanostructuring step was realized by block-copolymer assisted lithography. This newly developed technique enables the definition of nanoscale features on semiconductor substrates over large surface areas and in a cost effective manner. A novel method for patterning thin metal films by a lift-off approach, using spin coated block-copolymer micelles monolayers as a template, was investigated. The obtained nanoporous mask was used as resist for the structuring of hard substrates in plasma-assisted processes and structures with aspect ratios as high as 1:10 were be obtained. By using different block-copolymer micelles and spin-coating conditions, the proposed approach enables the variation of the nanopores' diameter from 40 to 80 nm and a surface coverage between 11.7% and 25.5 % in an independent manner. This technique was successfully integrated in a standard microfabrication process for the batch production of thin nanoporous silicon nitride membranes. The 100 nm thick membranes span over thousands of square micrometers and present porosities higher than 109 pores/cm2. They are thus competitive in terms of porosity with the commercially available polymeric membranes. In addition they are two orders of magnitude thinner than polymeric membranes, this making them extremely interesting for applications where permeation rate or response time is important. The rapid flow of water soluble small molecular species through the nanopores was demonstrated in a qualitative manner in this work. Another series of investigations targeted the functionalization of the available nanoporous surfaces with responsive molecules. Poly(N-isopropyl acrylamide) (PNIPAAM) was chosen as a model system. Its coupling to silicon surfaces by a "grafting-to" approach from melt, using an epoxy-functionalized silane as anchoring layer was studied. The analysis of the yielded grafting density showed results superior to those obtained by classic grafting-to approaches. The relation between the polymer's weight and its responsiveness was investigated in liquid media by atomic force microscopy and by dynamic force spectroscopy. Polymers with more than 500 monomers in the back bone were shown to exhibit enhanced responsiveness. Additionally, two bioengineered polymers from the class of elastin-like polymers (ELPs) were investigated as possible candidates for the fabrication of stimuli responsive nanovalves. The molecules were synthesized in collaboration with the Bioforge group (Universidad de Valladolid, Spain) and details of the bioproduction process are presented. A method for the covalent photoattachment of macromolecules using a benzophenone-functionalized silane, was tested in this work. First the capacity of the benzophenone silane to graft synthetic thermo-responsive polymers such as PNIPAAM was demonstrated. The temperature-induced morphology change of the photografted PNIPAAM was not affected by this anchoring strategy and was monitored by tapping AFM in liquid media. The investigations were then extended to the photo-immobilization of ELPs on nanoporous silicon surfaces and the XPS measurements revealed the success of this step. However no conformation modification of the proteins could be evidenced by tapping-mode AFM in liquid media under different ionic strengths.

EPFL2009

Characterization of Solid-Liquid Interfaces with High-Resolution Atomic Force Microscop

Maria Ricci

Solid-liquid interfaces are ubiquitous. Despite the unquestioned relevance, many scientific research fields rely on simplified or macroscopic descriptions, discarding the molecular nature of the constituents. However, it is the specific molecular interactions and the complex chemistry in the interfacial region that are fundamental in phenomena such as heterogeneous catalysis, electrochemistry, crystal growth, membrane transport and body-antibody recognition. In particular, the models used to describe the so-called electrical double layer of ionic distributions at charged surfaces in liquid, are based on continuum assumptions. For example, the Gouy-Chapman-Stern model assumes that a dense, homogenously distributed layer with a thickness of a hydrated ion (referred to as the "Stern layer"), is adsorbed onto the charged surface, proceeded by an exponentially decaying diffuse ionic cloud, in which ions are point charges in a continuous dielectric media. In this thesis, I will first illustrate how the assumption of a homogeneous ion lateral density in the Stern Layer fails to describe the actual solid-water interface of several relevant surfaces. Then I will show how the lateral organization of the ions indeed plays a role as important as the vertical modulation of the charge distribution. This is because the molecular nature of the ions, the surface, and the water molecules themselves each contribute to the precise lateral organization of the constituents. As result, the ions can reside on discrete surface sites, defined both laterally and vertically in space. Moreover, the water-mediated interaction can impart a correlation in the reciprocal lateral distribution of the ions. To achieve this level of description, high-resolution atomic force microscopy (AFM) is used. Unlike most of other experimental techniques, AFM is able to characterize interfaces locally at the atomic/molecular level. In fact, in the AFM small-amplitude regime, detection of even single ions adsorbed at the surface of the solid is possible by measuring the perturbation they induce on the local solvation environment. This capability represents an invaluable tool for the exploration of phenomena occurring at the Stern layer of solid-liquid interfaces. Following, I will investigate the properties of several solid-aqueous interfaces in the presence of different ionic concentrations and species, ranging from hard (mica) to soft systems such as organic self-assembled monolayers, lipid bilayers, and the dynamic surface restructuring of calcite when covered with fatty acid molecules. The experimental study, combined with molecular dynamic simulations, reveals a water-induced ion-ion attractive interaction for some ionic species. These results show that water alone is the driving force to induce order within the Stern layer, creating hydration-correlation effects on mica, self-assembled monolayers and possibly lipid bilayers. The local modulation of the hydration properties of the surface is fundamental to highly dynamic systems such as calcite, where steps act as nucleating points for the processes of dissolution and growth. The specific interaction of foreign ions and fatty acids modify these processes as well as the equilibrium between the crystal and the solution. This thesis provides clear experimental evidence of new mechanisms developing at solid-liquid interfaces paving the way for a deeper and more conscious understanding of the colloidal properties of materials.

EPFL2015

Scanning tunneling microscopy on large bio-molecular systems on surfaces

Sebastian Koslowski

The ever growing demand for the development of new technologies and materials has led to extensive studies inspired by biological functional complexes. Peptides with their outstanding ability to efficiently self-assemble can express a broad spectrum of intriguing functionalities. A key question in mimicking their assembly and function is the precise understanding of the specific interactions between the contained amino acids on the level of a sub-molecular length scale. An excellent tool to probe samples at these length scales is available with scanning tunneling microscopy (STM) and its operation under the controlled conditions of ultra-high vacuum (UHV) and low temperature. Within this thesis it is demonstrated how high-resolution studies by STMin combination with a controlled sample preparation by electrospray ion beam deposition (ES-IBD) under UHV conditions allows for the structural determination of peptides on surfaces. Furthermore the results presented here contribute to the development of a method capable of directly identifying individual amino acids within a peptide sequence. The structural and electronic properties of molecules on surfaces crucially depend on their interaction with the underlying substrate. Implementing a thin dielectric layer on the metallic surface, electronically decouples molecules from the substrate and enables an unperturbed observation of the molecular electronic structure. In Chapter 2 the properties of hexagonal boron nitride (h-BN) on Rh(111) as decoupling layer are assessed on behalf of the structural and electronic properties of the molecular model system pentacene adsorbed on it. In a second part of this chapter the discovery and the characterization of a new phase of h-BN/Rh(111) is described. In Chapter 3, we gained insight into the properties of amino acids on metal surfaces by utilizing the capability of the STM to probe the structure and the electronic characteristics in high resolution imaging and scanning tunneling spectroscopy (STS). As a second important aspect of this chapter, the modification of STM tips with amino acids is investigated as a method to enhance the structural and electronic resolution. An experimental protocol allowing to adhere amino acids on the STM tip be could developed. Using functional STM tips in STS experiments on amino acids enabled the observation of specific molecular resonances. An obstacle in investigating large bio-polymers, such as natural peptides, is their high structural complexity and conformational freedom. Therefore the utilization of custom designed synthetic sequences tailored towards a specific property is a good approach. In Chapter 4 studies performed on two synthetic peptide sequences deposited by ES-IBD on an Au(111) surface are discussed. The first sequence assembled in ordered two-dimensional networks. A folded gas-phase conformation could be utilized to rationalize the observed structures in the networks. Subsequently it was shown that the self-assembly behavior of the peptide could be steered towards chain-like assemblies by modifying the sequence at the peptide C-terminal. Using specific amino acid functionalized STM tips a sensitivity towards an amino acid of the same type in the peptide sequence could be observed. Thereby a partial sequencing of the synthetic peptide was enabled.

EPFL2017