Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

Ion implantation of organic thin films and electronic devices

Organic semiconductors have great promise in the field of electronics due to their low cost in term of fabrication on large areas and their versatility to new devices, for these reasons they are becoming a great chance in the actual technologic scenery. Some of the most important open issues related to these materials are the effects of surfaces and interfaces between semiconductor and metals, the changes caused by different deposition methods and temperature, the difficulty related to the charge transport modeling and finally a fast aging with time, bias, air and light, that can change the properties very easily. In order to find out some important features of organic semiconductors I fabricated Organic Field Effect Transistors (OFETs), using them as characterization tools. The focus of my research is to investigate the effects of ion implantation on organic semiconductors and on OFETs. Ion implantation is a technique widely used on inorganic semiconductors to modify their electrical properties through the controlled introduction of foreign atomic species in the semiconductor matrix. I pointed my attention on three major novel and interesting effects, that I observed for the first time following ion implantation of OFETs: 1) modification of the electrical conductivity; 2) introduction of stable charged species, electrically active with organic thin films; 3) stabilization of transport parameters (mobility and threshold voltage). I examined 3 different semiconductors: Pentacene, a small molecule constituted by 5 aromatic rings, Pentacene-TIPS, a more complex by-product of the first one, and finally an organic material called Pedot PSS, that belongs to the branch of the conductive polymers. My research started with the analysis of ion implantation of Pentacene films and Pentacene OFETs. Then, I studied totally inkjet printed OFETs made of Pentacene-TIPS or PEDOT-PSS, and the research will continue with the ion implantation on these promising organic devices.

Scaled down physical properties of semiconductor nanowires for nanoelectronics scaling up

Semiconductor nanowires (NWs) are one- or quasi one-dimensional systems whose physical properties are unique as compared to bulk materials because of their nanoscaled sizes. They bring together quantum world and semiconductor devices. NWs-based technologies may achieve an impact comparable to that of current microelectronic devices if new challenges will be faced. This thesis primarily focuses on two different, cutting-edge aspects of research over semiconductor NW arrays as pivotal components of NW-based devices. The first part deals with the characterization of electrically active defects in NWs. It has been elaborated the set-up of a general procedure which enables to employ Deep Level Transient Spectroscopy (DLTS) to probe NW arrays’ defects. This procedure has been applied to perform the characterization of a specific system, i.e. Reactive Ion Etched (RIE) silicon NW arrays-based Schottky barrier diodes. This study has allowed to shed light over how and if growth conditions introduce defects in RIE processed silicon NWs. The second part of this thesis concerns the bowing induced by electron beam and the subsequent clustering of gallium arsenide NWs. After a justified rejection of the mechanisms previously reported in literature, an original interpretation of the electron beam induced bending has been illustrated. Moreover, this thesis has successfully interpreted the formation of NW clusters in the framework of the lateral collapse of fibrillar structures. These latter are both idealized models and actual artificial structures used to study and to mimic the adhesion properties of natural surfaces in lizards and insects (Gecko effect). Our conclusion are that mechanical and surface properties of the NWs, together with the geometry of the NW arrays, play a key role in their post-growth alignment. The same parameters open, then, to the benign possibility of locally engineering NW arrays in micro- and macro-templates.

Caratterizzazione genomica di virus influenzali suini in Italia mediante next generation sequencing

I sottotipi H1N1, H1N2 e H3N2 di influenza A virus sono largamente diffusi nella popolazione suina di tutto il mondo. Nel presente lavoro è stato sviluppato un protocollo di sequenziamento di c.d. nuova generazione, su piattaforma Ion Torrent PGM, idoneo per l’analisi di tutti i virus influenzali suini (SIV). Per valutare l’evoluzione molecolare dei SIV italiani, sono stati sequenziati ed analizzati mediante analisi genomica e filogenetica un totale di sessantadue ceppi di SIV appartenenti ai sottotipi H1N1, H1N2 e H3N2, isolati in Italia dal 1998 al 2014. Sono stati evidenziati in sei campioni due fenomeni di riassortimento: tutti i SIV H1N2 esaminati presentavano una neuraminidasi di derivazione umana, diversa da quella dei SIV H1N2 circolanti in Europa, inoltre l’emoagglutinina (HA) di due isolati H1N2 era originata dal riassortimento con un SIV H1N1 avian-like. L’analisi molecolare dell’HA ha permesso di rivelare un’inserzione di due amminoacidi in quattro SIV H1N1 pandemici e una delezione di due aminoacidi in quattro SIV H1N2, entrambe a livello del sito di legame con il recettore cellulare. E’ stata inoltre evidenziata un’elevata omologia di un SIV H1N1 con ceppi europei isolati negli anni ’80, suggerendo la possibile origine vaccinale di questo virus. E’ stato possibile, in aggiunta, applicare il nuovo protocollo sviluppato per sequenziare un virus influenzale aviare altamente patogeno trasmesso all’uomo, direttamente da campione biologico. La diversità genetica nei SIV esaminati in questo studio conferma l’importanza di un continuo monitoraggio della costellazione genomica dei virus influenzali nella popolazione suina.