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Bassot, Claudio (2017) In silico analysis of membrane transport/permeability mechanisms. [Ph.D. thesis]

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Abstract (english)

Lipid membranes are a fundamental component of living cells, mediating the physical separation of intracellular components from the external environment, as well as the different cellular organelles from cytoplasm. Transmembrane transport proteins confer permeability to lipid membranes, which is essential for nutrient translocation and energy metabolism. Crystallography of transmembrane proteins is a particularly challenging problem. Due to their natural localization and chemical properties only a limited number of structures are to date available at atomic resolution. In silico analysis can be successfully applied to address the structure and to propose testable models of transporters and pores and of their function. My PhD work focused on two main models: Pendrin (SLC26A4) and the Permeability Transition Pore (PTP). These two systems allowed me to investigate different membrane types and permeation mechanisms, i.e. the plasma membrane-specific anion exchange (SLC26A4) and the inner mitochondrial membrane (IMM) unselective PTP.
Pendrin mutations are estimated to be the second most common genetic cause of human deafness, but a precise 3D structure of the protein is still missing. Aim of my work was to obviate the absence of structural information for pendrin transmembrane domain and to give a functional explanation for mutations collected in the MORL Deafness Variation Database. The human pendrin 3D model was inferred by homology with SLC26Dg and then validated analyzing the surface distribution of hydrophobic residues. The resulting high quality model was used to map 147 pathogenic human mutations. Three mutation clusters were found, while their localization suggested an innovative 14 transmembrane domain structure for pendrin.
The nature of PTP has long remained a mystery. In 2013 Giorgio et. al. suggested dimers of F1FO (F)-ATP synthase to form the pore, however the exact PTP composition and how can a pore form from the energy-conserving enzyme is still matter of debate. PTP opening is triggered by an increased Ca2+ concentration in the mitochondrial matrix, and is favored by oxidative stress. To shed light on PTP function, I investigated the effect of Ca2+ binding to the Me2+ binding site of the F1 domain of F-ATP synthase through molecular dynamics (MD) simulations. A similar approach was also applied to the F-ATP synthase β subunit mutation T163S, which alters the relative affinity for Mg2+ and Ca2+. Experimental data show that Ca2+ binding stiffens the complex structure and that the T163S mutation induces resistance to PTP opening. Further, catalytic site rearrangement induced from different ion occupancy, as well as the mutation T163S, yields relevant variation of the interaction between F1 domain and OSCP subunit. I suggest that an unstructured loop between residues 82-131 of the β subunit transmits the structural rearrangement originated into catalytic site to the OSCP subunit and then to the inner membrane through the rigid lateral stalk.
The critical role emerging for OSCP in the PTP regulation opens two parallel questions, i.e. (i) how the OSCP-mediated opening signal is transmitted to the trans-membrane region and (ii) what are the transmembrane PTP components. Variation in pore conductivity among species suggested that the putative pore-forming subunits may be different in different species. Sequence alignment was performed for all the subunits of F-ATP synthase, but we mainly focused on subunits e, g and b due to their localization in the complex and sequence conservation. Specific mutations affecting F-ATP synthase were collected and their functional effect is currently under analysis. In parallel, the presence and features of e, g and f subunits across eukaryotes was investigated by mean of phylogenetic analysis. Protein homologues of these specific subunits were found to be widespread in eukaryotes from yeast to plants while we found that Oomycetes lack subunits e and g and green algae subunit e. This observation suggest an ancient evolution for the F-ATP synthase dimerization subunits and possibly for the PTP. Further analysis and experimental validation are planned to clarify this aspect.

Abstract (italian)

Le membrane lipidiche sono una componente fondamentale delle cellule viventi, separano fisicamente le componenti intracellulari dall’ambiente esterno e i diversi organelli del citoplasma.
Le proteine di trasporto conferiscono permeabilità alle membrane lipidiche, proprietà essenziale per la traslocazione di nutrienti e la conservazione dell’energia.
La cristallografia di proteine transmembrana è problematica a causa della loro localizzazione e proprietà chimiche, e solo un numero piuttosto ridotto di strutture è disponibile. L’analisi in silico può essere applicata con successo per investigare le strutture e il funzionamento proporre modelli testabili di trasportatori e delle loro funzioni. Il lavoro del mio dottorato sì è focalizzato su due modelli: la pendrina (SLC26A4) e il poro di transizione di permeabilità (PTP). Questi due sistemi proteici mi hanno permesso di studiare due differenti tipi di membrana e meccanismi di permeabilità: la membrana plasmatica con scambio specifico di anioni (SLC26A4) e la membrana interna mitocondriale con la permeabilità non selettiva mitocondriale (PTP).
Le mutazioni della pendrina sono stimate essere la seconda causa genetica più comune della sordità umana, ma la struttura della proteina non è stata ancora determinata. Scopo del mio lavoro è stato quello di sopperire all’assenza di informazioni strutturali per il dominio transmembrana della pendrina e di dare una spiegazione funzionale per le mutazioni raccolte nel MORL Deafness Variation Database.
Il modello 3D della pendrina è basato sull’omologia con SLC26Dg (3) ed è stato validato analizzando la distribuzione sulla superfice dei residui idrofobici. L’alta qualità risultante dal modello è stata usata per mappare 147 mutazioni patologiche umane. Tre cluster di mutazioni sono stati trovati e la loro localizzazione suggerisce per pendrina un innovativa struttura a 14 domini transmembrana.
Anche la natura del PTP è rimasta a lungo misteriosa. Nel 2013 Giorgio et al. hanno suggerito che i dimeri di F1FO (F)-ATP sintasi formino il poro, tuttavia l’esatta composizione e il modo in cui il poro di transizione si possa formare è ancora materia di dibattito. L’apertura del PTP è innescata da un aumento della concentrazione di Ca2+ nella matrice mitocondriale ed è favorita dallo stress ossidativo. Per fare luce sul funzionamento del PTP ho studiato l’effetto del legame del Ca2+ al sito per i cationi divalenti (Me2+) nel dominio F1 attraverso la dinamica molecolare (MD). Un approccio simile è stato anche applicato alla mutazione T163S, che fa variare l’affinità relativa per Mg2+ e Ca2+. I dati sperimentali mostrano come la mutazione induca resistenza all’apertura del PTP. La MD ha dimostrato come il legame del Ca2+ irrigidisca la struttura del complesso. Il riarrangiamento del sito catalitico indotto dai differenti ioni che lo occupano, così come la mutazione T163S, causa rilevanti variazioni delle interazioni tra il dominio F1 e la subunità OSCP. Suggerisco che un loop non strutturato tra i residui 82-131 della subunità β trasmetta il riarrangiamento strutturale originato nel sito catalitico a OSCP e quindi alla membrana interna attraverso il rigido stalk laterale.
Il ruolo critico che emerge per OSCP nella regolazione del PTP apre due domande collegate: (i) come il segnale di apertura mediato da OSCP venga trasmesso alla regione trans-membrana e (ii) quali siano i componenti transmembrana del PTP.
Le variazioni di conduttanza del poro osservate in specie diverse suggeriscono che le subunità che formano il canale debbano avere delle differenze significative. E’ stato prodotto un allineamento di sequenze per tutte le subunità della F-ATP sintasi. I risultati preliminari ci hanno spinto a focalizzarci sulle subunità e, g e b a causa della loro localizzazione e conservazione di sequenza. Basandomi sugli allineamenti multipli ho suggerito mutazioni puntiformi per testare l’importanza di specifici residui ai fini dell’apertura del poro. In parallelo la presenza delle subunità e e g tra gli eucarioti è stata indagata attraverso un analisi filogenetica. Proteine omologhe di queste specifiche subunità sono presenti in tutti gli eucarioti: dai lieviti alle piante, tuttavia gli Oomiceti sono risultati mancanti delle subunità e e g e le alghe verdi della subunità e.
Questi risultati suggeriscono un’origine antica per le subunità di dimerizzazione della F-ATP sintasi e probabilmente anche del PTP. Per chiarire questo aspetto saranno necessarie ulteriori analisi e verifiche sperimentali.

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EPrint type:Ph.D. thesis
Tutor:Bernardi, Paolo
Supervisor:Tosatto, Silvio C. E.
Ph.D. course:Ciclo 29 > Corsi 29 > BIOSCIENZE E BIOTECNOLOGIE
Data di deposito della tesi:31 January 2017
Anno di Pubblicazione:31 January 2017
Key Words:Pendrin, ATP synthase, Permeability Transition Pore,
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/10 Biochimica
Struttura di riferimento:Dipartimenti > Dipartimento di Scienze Biomediche
Codice ID:10272
Depositato il:09 Nov 2017 12:09
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