Quantitative single-molecule localization microscopy combined with rule-based modeling reveals ligand-induced TNF-R1 reorganization toward higher-order oligomers

We report on the assembly of tumor necrosis factor receptor 1 (TNF-R1) prior to ligand activation and its ligand-induced reorganization at the cell membrane. We apply single-molecule localization microscopy to obtain quantitative information on receptor cluster sizes and copy numbers. Our data suggest a dimeric pre-assembly of TNF-R1, as well as receptor reorganization toward higher oligomeric states with stable populations comprising three to six TNF-R1. Our experimental results directly serve as input parameters for computational modeling of the ligand-receptor interaction. Simulations corroborate the experimental finding of higher-order oligomeric states. This work is a first demonstration how quantitative, super-resolution and advanced microscopy can be used for systems biology approaches at the single-molecule and single-cell level.

Electrochemical single-molecule transistors with optimized gate coupling

Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids. These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ξ, of unity. This compares to a much lower gate coupling parameter of 0.2 for the equivalent aqueous gating system. This study shows that ionic liquids are far more effective media for gating the conductance of single molecules than either solid-state three-terminal platforms created using nanolithography, or aqueous media.

Surface-enhanced resonance Raman scattering: Single-molecule detection in a Langmuir-Blodgett monolayer

Surface-enhanced resonance Raman scattering (SERRS) is used for single-molecule detection from spatially resolved 1-mum(2) sections of a Langmuir-Blodgett (LB) monolayer deposited onto a Ag film. The target molecule, his (benzimidazo) thioperylene (BZP), is dispersed in an arachidic acid monomolecular layer containing one BZP molecule per mum(2) which is also the probing area of the Raman microscope. For concentrated samples (attomole quantities in the field of view), average SERRS, surface-enhanced fluorescence (SEF), and Raman imaging, including line mapping and global images at different temperatures, were recorded. Single-molecule SERRS spectra, obtained using an LB monolayer, present changes in bandwidth and relative intensities, highlighting the properties of single-molecule SERRS that are lost in average SERRS measurements of mixed LB monolayers obtained at the same temperatures. Also, the dilute system phenomenon of blinking is discussed with regard to results obtained from LB monolayers. The dilution process used in the single-molecule LB SERRS work is independently supported by fluorescence results obtained from very dilute solutions with monomer concentrations down to 10(-12) M.

Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Single molecule electron transfer dynamics in complex environments

We propose a new theoretical approach to study the kinetics of the electron transfer (ET) under the dynamical influence of the complex environments with the first passage times (FPT) of the reaction events. By measuring the mean and high order moments of FPT and their ratios, the full kinetics of ET, especially the dynamical transitions across different temperature zones, is revealed. The potential applications of the current results to single molecule electron transfer are discussed.

Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier. The ratio between first-passage-time moments is proposed to be a good variable to quantitatively probe these kinetic changes. The temperature-dependent kinetics is consistent with the strange kinetics found in folding dynamics experiments. The potential applications of the current results to single-molecule protein folding are discussed.

Surface-enhanced resonance Raman scattering as an analytical tool for single molecule detection

A perylene derivative, n-(n-butyl)-n'-(4-aminobutyl) perylene-3,4,9,10-tetracarboxylic acid diimide (simplified as nBu-PTCD-(CH2)(4)-NH2) has been chosen as the target molecule for studies involving single molecule detection (SMD) using Raman scattering. The enhancement of the Raman signal is the result of the multiplicative effects of two phenomena, resonance Raman scattering (RRS) and surface-enhanced Raman scattering (SERS), which leads to the resulting surface-enhanced resonance Raman scattering (SERRS) process. The SERRS spectra from a single molecule have been collected using both silver and gold colloids. The SMD detection of the fundamental vibrational frequencies characteristic of nBu-PTCD-(CH2)(4)-NH2 is complemented with the detection of some overtones and combinations from ring stretching modes at the single molecule level. The background characterization of the ensemble vibrational spectroscopy of the target perylene and its SERRS is also presented, which includes the UV-vis absorption, experimental and calculated Raman scattering and infrared absorption, and molecular organization using reflection-absorption infrared spectroscopy (RAIRS).

SERS mapping in langmuir-blodgett films and single-molecule detection

Plasmon-enhanced spectroscopic techniques have expanded single-molecule detection (SMD) and are revolutionizing areas such as bio-imaging and single-cell manipulation. Surface-enhanced (resonance) Raman scattering (SERS or SERRS) combines high sensitivity with molecularfingerprint information at the single-molecule level. Spectra originating from single-molecule SERS experiments are rare events, which occur only if a single molecule is located in a hot-spot zone. In this spot, the molecule is selectively exposed to a significant enhancement associated with a high, local electromagnetic field in the plasmonic substrate. Here, we report an SMD study with an electrostatic approach in which a Langmuir film of a phospholipid with anionic polar head groups (PO 4 -) was doped with cationic methylene blue (MB), creating a homogeneous, two-dimensional distribution of dyes in the monolayer. The number of dyes in the probed area of the Langmuir-Blodgett (LB) film coating the Ag nanostructures established a regime in which single-molecule events were observed, with the identification based on direct matching of the observed spectrum at each point of the mapping with a reference spectrum for the MB molecule. In addition, advanced fitting techniques were tested with the data obtained from micro-Raman mapping, thus achieving real-time processing to extract the MB single-molecule spectra. © 2013 Society for Applied Spectroscopy.

Multiscale sensing of antibody - antigen interactions by organic transistors and single-molecule force spectroscopy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Each one teaches one: characterizing active forms of proteins by single molecule force spectroscopy

This Ph.D. candidate thesis collects the research work I conducted under the supervision of Prof.Bruno Samor´ı in 2005,2006 and 2007. Some parts of this work included in the Part III have been begun by myself during my undergraduate thesis in the same laboratory and then completed during the initial part of my Ph.D. thesis: the whole results have been included for the sake of understanding and completeness. During my graduate studies I worked on two very different protein systems. The theorical trait d’union between these studies, at the biological level, is the acknowledgement that protein biophysical and structural studies must, in many cases, take into account the dynamical states of protein conformational equilibria and of local physico-chemical conditions where the system studied actually performs its function. This is introducted in the introductory part in Chapter 2. Two different examples of this are presented: the structural significance deriving from the action of mechanical forces in vivo (Chapter 3) and the complexity of conformational equilibria in intrinsically unstructured proteins and amyloid formation (Chapter 4). My experimental work investigated both these examples by using in both cases the single molecule force spectroscopy technique (described in Chapter 5 and Chapter 6). The work conducted on angiostatin focused on the characterization of the relationships between the mechanochemical properties and the mechanism of action of the angiostatin protein, and most importantly their intertwining with the further layer of complexity due to disulfide redox equilibria (Part III). These studies were accompanied concurrently by the elaboration of a theorical model for a novel signalling pathway that may be relevant in the extracellular space, detailed in Chapter 7.2. The work conducted on -synuclein (Part IV) instead brought a whole new twist to the single molecule force spectroscopy methodology, applying it as a structural technique to elucidate the conformational equilibria present in intrinsically unstructured proteins. These equilibria are of utmost interest from a biophysical point of view, but most importantly because of their direct relationship with amyloid aggregation and, consequently, the aetiology of relevant pathologies like Parkinson’s disease. The work characterized, for the first time, conformational equilibria in an intrinsically unstructured protein at the single molecule level and, again for the first time, identified a monomeric folded conformation that is correlated with conditions leading to -synuclein and, ultimately, Parkinson’s disease. Also, during the research work, I found myself in the need of a generalpurpose data analysis application for single molecule force spectroscopy data analysis that could solve some common logistic and data analysis problems that are common in this technique. I developed an application that addresses some of these problems, herein presented (Part V), and that aims to be publicly released soon.

The effect of osmolytes on protein fold stability at the single-molecule level

By pulling and releasing the tension on protein homomers with the Atomic Force Miscroscope (AFM) at different pulling speeds, dwell times and dwell distances, the observed force-response of the protein can be fitted with suitable theoretical models. In this respect we developed mathematical procedures and open-source computer codes for driving such experiments and fitting Bell’s model to experimental protein unfolding forces and protein folding frequencies. We applied the above techniques to the study of proteins GB1 (the B1 IgG-binding domain of protein G from Streptococcus) and I27 (a module of human cardiac titin) in aqueous solutions of protecting osmolytes such as dimethyl sulfoxide (DMSO), glycerol and trimethylamine N-oxide (TMAO). In order to get a molecular understanding of the experimental results we developed an Ising-like model for proteins that incorporates the osmophobic nature of their backbone. The model benefits from analytical thermodynamics and kinetics amenable to Monte-Carlo simulation. The prevailing view used to be that small protecting osmolytes bridge the separating beta-strands of proteins with mechanical resistance, presumably shifting the transition state to significantly higher distances that correlate with the molecular size of the osmolyte molecules. Our experiments showed instead that protecting osmolytes slow down protein unfolding and speed-up protein folding at physiological pH without shifting the protein transition state on the mechanical reaction coordinate. Together with the theoretical results of the Ising-model, our results lend support to the osmophobic theory according to which osmolyte stabilisation is a result of the preferential exclusion of the osmolyte molecules from the protein backbone. The results obtained during this thesis work have markedly improved our understanding of the strategy selected by Nature to strengthen protein stability in hostile environments, shifting the focus from hypothetical protein-osmolyte interactions to the more general mechanism based on the osmophobicity of the protein backbone.

Single-Molecule Junctions Based on Nitrile-Terminated Biphenyls: A Promising New Anchoring Group

We present a combined experimental and theoretical study of the electronic transport through single-molecule junctions based on nitrile-terminated biphenyl derivatives. Using a scanning tunneling microscope-based break-junction technique, we show that the nitrile-terminated compounds give rise to well-defined peaks in the conductance histograms resulting from the high selectivity of the N-Au binding. Ab initio calculations have revealed that the transport takes place through the tail of the LUMO. Furthermore, we have found both theoretically and experimentally that the conductance of the molecular junctions is roughly proportional to the square of the cosine of the torsion angle between the two benzene rings of the biphenyl core, which demonstrates the robustness of this structure-conductance relationship.