Importanza del tipo di aminoacido e degli atomi coinvolti nel legame peptidico nella struttura tridimensionale delle proteine.

Importanza dei legami non-covalenti in Biologia

Note sul ripiegamento delle proteine.

Non covalent bonds
The Chemical Components of a Cell
Hydrogen bonds
Van der Waals bond
Hydrophobic effect
Surface tension
The Chemistry of Water

Water

Approfondimenti sulla membrana plasmatica (1): Lipidi saturi e insaturi. Fosfogliceridi (glicerolipidi): ruolo e caratteristiche delle teste e delle code. Colesterolo: ruolo nell'impermeabilizzazione e fluidità delle membrane. Sfingolipidi: sfingosina, ceramidi, sfingomielina (fosfolipide), glicosfingolipidi: classi (cerebrosidi, solfatidi, globosidi, gangliosidi) e ruolo. Asimmetria dei lipidi nella membrana e sua importanza biologica.

Materiale sul colesterolo e sugli sfingolipidi (complementare al materiale da studiare sui Testi suggeriti)

Lipids (altro sito)

Cell membranes

Cell membranes (sito didattico di Nature) [DA ENTRARE CON CREDENZIALI DI ATENEO]

Biological Membranes and the Cell Surface

Structure of the plasma membrane

Glycoforum

Glycosphingolipids: Structure, Localization and Metabolism

Biological Functions of Membrane Glycolipids

Approfondimenti sulla membrana plasmatica (2): Proteine associate con la membrana plasmatica: proteine integrali, proteine periferiche, proteine collegate ad ancore lipidiche (acidi grassi sature, gruppi prenilici - insaturi). Importanza delle ancore lipidiche per reclutare versola membrana proteine spesso coinvolte nella trasduzione di segnali.

Diapositive sulle proteine di membrana (vedi anche Alberts)

Glicocalice. (1): Glicoproteine N-linked e O-linked .Mucine.

Diapositive sul glicocalice: 1a parte

Seminario: Regioni "Variable number of tandem repeat” (VNTR) ricche di residui glicosilati nelle mucine; Alterazione delle mucine nei tumori

Membrane proteins

β-barrel membrane proteins

Glycosaminoglycan Chains (GAGs) and Glycolipids

Glicocalice. (2) Proteoglicani della membrana plasmatica; tipi e ruoli dei glicosaminoglicani. Ruolo dei proteoglicani di membrana nella risposta a fattori di crescita e differenziamento.

Diapositive sui proteoglicani di membrana.

Introduzione ai rafts lipidici. L'evoluzione del modello del mosaico fluido negli ultimi 40 anni. Tipi diversi di lipidi di membrana. glicerolipidi, sfingolipidi, colesterolo); particolare attenzione alle "teste polari" degli sfingolipidi e in particolare alla posizione di residui di galattosio nei cerebrosidi e gangliosidi [galattosio: coinvolto nell'interazione con domini tipo V3 in virus, precursorii di proteine prioniche e di placche di amiloide].

Sito con informazioni e immagini interessanti sui Proteoglicani in particolare quelli di di membrana [SERVIRA' ANCHE PER LE LEZIONI SULLA MATRICE EXTRACELLULARE].

OPEN ACCESS PAPER: Nicolson GL. The Fluid-Mosaic Model of Membrane Structure: still relevant to understanding the structure, function and dynamics of biological membranes after more than 40 years. Biochim Biophys Acta. 2014 Jun;1838(6):1451-66.

Rafts lipidici, segue. Organizzazione e stabilizzazione dei componenti dei rafts. Tipi di rafts, Caveolae.

Diapositive sull'introduzione ai rafts lipidici.

Seminario: Ruolo degli sfingolipidi nell modellamento della forma di alcune proteine. Caratteristiche dei domini tipo V3 che legano gli sfingolipidi presenti in proteine molto diversificate.Importanza dell'idrossilazione dell'acido grasso che lega la sfingosina e dell'isomero beta-galattosio per il legame specifico proteina-sfingolipide.

Diapositive sull'interazione di proteine con sfingolipidi.

Lipid raft

Simons K, Sampaio JL. Membrane organization and lipid rafts. Cold Spring Harb. Perspect Biol. 2011 Oct 1;3(10):a004697.

Fantini J. How sphingolipids bind and shape proteins: molecular basis of
lipid-protein interactions in lipid shells, rafts and related biomembrane
domains. Cell Mol Life Sci. 2003 Jun;60(6):1027-32.

Kai Simons (MPI) Part 1: The role of lipids in organizing the cellular traffic.

Kai Simons (MPI) Part 2: Lipid rafts as a membrane organizing principle

Rafts lipidici, segue: Ruolo dei rafts nella trasduzione dei segnali

Seminario 1: Ruolo dei rafts nell'invasione di tossine batteriche, virus (ad es. HIV-1), formazione di aggregati proteici patologici (proteina prionica, Alzheimer)

Diapositive infezione da virus e formazione aggregati proteici patologici

Seminario 2: Trasduzione di segnale nei rafts durante l'attivazione di linfociti B, T, mast-cells

Diapositive Trasduzione dei segnali (x esame) e attivazione linfociti (seminari)

Lavoro Fantini su HIV, prioni, Alzheimer (2002)

Lavoro di Fantini (2010) sulla regolazione della formazione di amiloide mediato da colesterolo e sfinglipidi.

Ectosomes (Cocucci, Meldolesi, 2011)

Endosomes

Exosomes

x altri lavori disponibili in .pdf Vedi lezione 19.5.2014 anno scorso

Microvescicole : (2) Genesi degli exosomi. Ruolo dei corpi multivescicolari (endosomi tardivi) nella genesi degli exosomi.

Diapositive 1a parte vescicole extracellulari

Microvescole (3): tipi di sostanze trasportate, importanza degli miRNA e mRNA trasportati, sistemi di ancoraggio ad altre cellule, scambio di informazioni.

Diapositive 2a parte vescicole extracellulari

Microvescicole (4): Seminari su campi della ricerca/clinica dove lo studio delle microvescicole è molto avanzato.

Adesione cellulare: Introduzione: Adesione omofilica e eterofilica. Principali famiglie: caderine, selettine, superfamiglia delle immunoglobuline e integrine. Giunzioni di membrana e molecole di adesione coinvolte nei desmosomi a cintura, desmosomi a borchia, emi-desmosomi e adesioni focali.

Molecole di adesione, Caderine: 1a parte: moduli extracellulari e intracellulari; caderine classiche (1a parte)

Cell adhesion molecules

Adhesion molecules

Cadherins

Cadherins (un altro sito)
Cadherin superfamily

Regulated adhesion as a driving force of gastrulation movements

Halbleib JM, Nelson WJ. Cadherins in development: cell adhesion, sorting, and tissue morphogenesis. Genes Dev. 2006 Dec 1;20(23):3199-214.

Molecole di adesione: caderine, segue: caderine classiche e non-classiche. Importanza delle proteine citoplasmatiche nel colelgamento al citoscheletro di actina o dei filamenti intermedi. Modulazione dell'adesione e trasduzione del segnale associata alle caderine.

Diapositive sulle caderine.

SEMINARI

1. Transizione epitelio-mesenchimale e mesenchima-epiteliale:

Trasparenti EMT/MET a colori

Trasparenti EMT/MET binaco e nero

2. Struttura dei capillari sanguigni normali e tumorali. Ruolo della VE-caderina

Diapositive: 2° seminario

Epithelial-mesenchymal transition

Epithelium–Mesenchyme Transitions Are Crucial Morphogenetic Events Occurring During Early Development

Epithelial-Mesenchymal Transitions in Human Cancer

Kalluri R. EMT: when epithelial cells decide to become mesenchymal-like cells. J Clin Invest. 2009 Jun;119(6):1417-9.

Kalluri R, Weinberg RA. The basics of epithelial-mesenchymal transition. J Clin Invest. 2009 Jun;119(6):1420-8.

Thiery JP, Sleeman JP. Complex networks orchestrate epithelial-mesenchymal transitions. Nat Rev Mol Cell Biol. 2006 Feb;7(2):131-42.

M.E. Herna´ndez-Caballero (2013). Molecular Mechanisms of Metastasis: Epithelial-Mesenchymal Transition, Anoikis and Loss of Adhesion, Carcinogenesis, Dr. Kathryn Tonissen (Ed.), ISBN: 978-953-51-0945-7, InTech, DOI: 10.5772/55399.

VE-cadherin

Molecular organization of endothelial AJs.

The role of adherens junctions and VE-cadherin in the control of vascular permeability

Adhesion in the stem cell niche: biological roles and regulation [disponibile lavoro in .pdf]

Meccanotrasduzione associata alle caderine.

Molecole di adesione, segue: Selectine: Lectine [seminario], selectine (lectine di tipo C) E-, L- e P-, tipi di ligandi. Importanza dell'adesione transiente.

Diapositive sulle selectine.

SITO IMPORTANTE: Glycoforum
Lectins
Selectins
C-type lectins

Adult neural stem/precursor cells recapitulate lymphocyte-like pathways for selective homing into inflamed areas of the CNS after intravenous injection.

Beyond glycogenes

Selectin-mediated cell recognition and its structural basis

Molecole di adesione, segue: Superfamiglia delle immunoglobuline: Domini tipo immunoglobulinico (Ig-like) e domini di tipo III della fibronectina; interazioni omofiliche ed eterofiliche; ICAMs, N-CAMs, V-CAM, PECAM. Importanza dell'acido polisialico delle N-CAM durante lo sviluppo embrionale.

Diapositive sulle molecole di adesione della superfamiglia delle immunoglobuline

The immunoglobulin (Ig) gene family of molecules.

The Immunoglobulin Gene Superfamily

N-CAMs Mediate Ca2+-Independent Homophilic Cell-Cell Adhesion.

Neuronal cell adhesion molecules of the immunoglobulin superfamily.

I-type lectins: I-type lectins are glycan-binding proteins that belong to the immunoglobulin superfamily (IgSF), excluding antibodies and T-cell receptors.... the Siglec family of sialic acid–binding lectins is the only well-characterized group of I-type lectins, both structurally and functionally..

CD Antigens

Integrins
Beta-2 integrins (Univ of Virginia)

Arnaout MA, Mahalingam B, Xiong JP. Integrin structure, allostery, and bidirectional signaling. Annu Rev Cell Dev Biol. 2005;21:381-410.

Goswami S.: Importance of integrin receptors in the field of pharmaceutical & medical science, Advances in Biological Chemistry, 2013, 3, 224-252

Molecole di adesione: Integrine, segue: Ruolo delle integrine nella trasduzione dei segnali. Legame con il citoscheletro dei filamenti intermedi.

Diapositive sulle integrine (contiene anche diapositive che verranno illustrate il 16.4.2015)

Introduzione alla matrice extracellulare.

Diapositive dell'introduzione alla matrice (anche con argomenti che verranno trattati nella prossima lezione)

Seminario: Moduli e domini della proteine

Fibronectin and Integrin: vedi filmato stretching fibronectina (importante anche per capitolo della Matrice Extracellulare)

Ruolo delle integrine nell'estravasione dei leucociti dai vasi sanguigni verso tessuti infiammati.

Introduzione alla ME, segue: ruolo come depositaria di fattori di crescita

Collageni: Introduzione: composizione, sintesi, collageni fibrillari e associati ai collageni fibrillari

Collageni, segue: tipi, processi di biosintesi (pro-collagene) e assemblaggio, organizzazione della deposizione dei vari collageni nella matrice. Patologie associate.

Seminario: Collageni di membrana e proteine simili al collagene.

Diapositive sui collageni

Elastina: composizione, formazione di fibrille, importanza dei legami incrociati bi- e tetrafunzionali fra le varie molecole di elastina; importanza della fibrillina
Differenze tra collagene ed elastina.

Diapositive sull'elastina.

Introduzione ai Glicosaminoglicani e proteoglicani della matrice. L'acido ialuronico (ora designato come ialuronato ("hyaluran")): un GAG  evoluzionariamente molto antico e importante.Sintesi dell'ialuronato sulla membrana plasmatica (notare che non si svolge nell'apparato di Golgi come avviene per gli altri glicosaminoglicani). 

Sculture di Julian Foos: collagene e non solo

Collagen
Collagen: The Fibrous Proteins of the Matrix
O-LINKED GLYCANS IN COLLAGENS

Type IV collagen network formation
Water-Soluble Vitamins Function As Coenzymes

Elastic fibers

Marfan's Syndrome: Michael Phelps blessing or curse?
Paganini, How The Great Violinist Was Helped By A Rare Medical Condition

Glicosaminoglicani e proteoglicani, segue: Eparina. Proteoglicani: struttura e funzioni. Perlecano e lamina basale.Aggrecano e  cartilagine. Ruolo dei proteoglicani nell'idratazione della matrice e nei legami a proteine e peptidi biologicamente attivi.

Diapositive sui GAGs e proteoglicani della matrice.

Glicoproteine della matrice: Importanza della struttura multimodulare. Fibronectina (struttura e funzione)

Secondary and tertiary structure of hyaluronan in aquous solution. Some biological consequences.

Proteoglycans
Glycosaminoglycans and Proteoglycans

Basement membrane proteogycans
Perlecan
Cartilage
Aggrecan

Fibronectin
Fibronectin, an Extracellular Adhesion Molecule

Glicoproteine della matrice: Laminina: struttura e ruolo nella lamina basale

Diapositive sulle glicoproteine della matrice: fibronectina e laminina

Seminario: struttura, ruolo e ligandi cellulari di nidogeno/entactina, trombospondina, tenascina, fattore di von Willebrand, secreted protein acidic and rich in cysteine (SPARC) /osteopontina.

Diapositive su altre glicoproteine della matrice.

Lamina/membrana basale: componenti (laminina, collagene di tipo IV, perlecano, agrina): ruolo strutturale e modulatore dell'attività delle cellule che su di essa poggiano.

Diapositive sulla lamina basale

Introduzione alla degradazione della matrice extracellulare.

Diapositive sull'introduzione alla degradazione della matrice.

Laminin

Lavori molto interessanti:

• LeBleu VS, Macdonald B, Kalluri R. Structure and function of basement membranes. Exp Biol Med (Maywood). 2007 Oct;232(9):1121-9. 

• Yurchenco PD. Basement membranes: cell scaffoldings and signaling platforms. Cold Spring Harb Perspect Biol. 2011 Feb 1;3(2). doi:pii: a004911. 10.1101/cshperspect.a004911.

• Miner JH. Glomerular basement membrane composition and the filtration barrier. Pediatr Nephrol. 2011 Sep;26(9):1413-7.
  
  
  Matsuo I, Kimura-Yoshida C. Extracellular distribution of diffusible growth factors controlled by heparan sulfate proteoglycans during mammalian
  embryogenesis. Philos Trans R Soc Lond B Biol Sci. 2014 Dec 5;369(1657).
  

Proteinasi della matrice, continuazione:

Serina proteasi e loro inibitori "Serpine" Attivatori del plasminogeno di tipo urochinasi e tissutale.

Diapositive sulle serina proteasi.

Seminario: Sistemi della coagolazione e fibrinolisi; sistema e del complemento; sistema delle chinine: importanza della callicreina nella crescita tumorale.

Diapositive sui seminari riguardanti le serina proteasi.

Metalloproteasi della matrice: Ruolo dei vari domini: dominio autoinibitorio, dominio catalitico, dominio tipo emopexina. Metallo proteasi della matrice secrete oppure legate alle membrane (MT-MMPs) e loro inibitori tissutali (TIMPs). Proteine ADAMs e importanza nel rilascio di ectodomini di proteine di membrana. Proteine ADAMTs e degradazione dei proteoglicani.

Diapositive sulle MMPs, TIMPs, ADAMs, ADAMTs

Seminari sui tipi di MMPs e ruolo delle MMPs nei tumori e nello'infiammazione.

Diapositive seminari MMPs

Serine protease

Enzyme Catalysis: The Serine Proteases

Serine proteases

Serpins

The Clotting Process Must Be Precisely Regulated

Murphy & Arhtur: Danger outside the cell. The extracellular matrix and diesease.

Role of Matrix Metalloproteinases in Cancer

Lavori disponibili in .pdf:

1) Egeblad M, Werb Z. New functions for the matrix metalloproteinases in cancer progression.Nat Rev Cancer. 2002 Mar;2(3):161-74.

Matrix metalloproteinases (MMPs) have long been associated with cancer-cell invasion and metastasis. This provided the rationale for clinical trials of MMP inhibitors, unfortunately with disappointing results. We now know, however, that the MMPs have functions other than promotion of invasion, have substrates other than components of the extracellular matrix, and that they function before invasion in the development of cancer. With this knowledge in hand, can we rethink the use of MMP inhibitors in the clinic?

2) Nagase H, Visse R, Murphy G. Structure and function of matrix metalloproteinases and TIMPs.Cardiovasc Res. 2006 Feb 15;69(3):562-73.

Matrix metalloproteinases (MMPs), also called matrixins, function in the extracellular environment of cells and degrade both matrix and non-matrix proteins. They play central roles in morphogenesis, wound healing, tissue repair and remodelling in response to injury, e.g. after myocardial infarction, and in progression of diseases such as atheroma, arthritis, cancer and chronic tissue ulcers. They are multi-domain proteins and their activities are regulated by tissue inhibitors of metalloproteinases (TIMPs). This review introduces the members of the MMP family and discusses their domain structure and function, proenyme activation, the mechanism of inhibition by TIMPs and their significance in physiology and pathology.

3) Khokha R, Murthy A, Weiss A. Metalloproteinases and their natural inhibitors in inflammation and immunity. Nat Rev Immunol. 2013 Sep;13(9):649-65.
Over the past 50 years, steady growth in the field of metalloproteinase biology has shown that the degradation of extracellular matrix components represents only a fraction of the functions performed by these enzymes and has highlighted their  fundamental roles in immunity. Metalloproteinases regulate aspects of immune cell development, effector function, migration and ligand-receptor interactions. They  carry out ectodomain shedding of cytokines and their cognate receptors. Together  with their endogenous inhibitors TIMPs (tissue inhibitor of metalloproteinases),  these enzymes regulate signalling downstream of the tumour necrosis factor receptor and the interleukin-6 receptor, as well as that downstream of the epidermal growth factor receptor and Notch, which are all pertinent for inflammatory responses. This Review discusses the metalloproteinase family as a crucial component in immune cell development and function.

Peptidi bioattivi derivati dalla degradazione della matrice: Matrichine e matricriptine. Definizione, meccanismi di formazione, effetti biologici. Agenti antiangiogenetici (endostatina, angiostatina).

Diapositive su matrichine (contiene seminario sulle matrichine derivate da diversi componenti della matrice)

Seminari:

1. Matrichine derivate dai vari componenti della matrice.

2. Angiogenesi tumorale.

Diapositive seminario angiogenesi tumorale.

Beginning of angiogenesis research: http://www.ncbi.nlm.nih.gov/books/NBK13877/

Angiogenesis Inhibitors

Articoli interessanti

Wells JM, Gaggar A, Blalock JE. MMP generated matrikines. Matrix Biol. 2015. Jan 28.

Carmeliet P. Angiogenesis in health and disease. Nat Med. 2003 Jun;9(6):653-60.

Articoli con .pdf disponibili:

1) Ricard-Blum S, Salza R.: Matricryptins and matrikines: biologically active fragments of the extracellular matrix. Exp Dermatol. 2014 Jul;23(7):457-63.

Numerous extracellular proteins and glycosaminoglycans (GAGs) undergo limited enzymatic cleavage resulting in the release of fragments exerting biological activities, which are usually different from those of the full-length molecules. In this review, we define matrikines and matricryptins, which are bioactive fragments released from the extracellular matrix proteins, proteoglycans and GAGs and report their major biological activities. These fragments regulate a number of physiopathological processes including angiogenesis, cancer, fibrosis, inflammation, neurodegenerative diseases and wound healing. The challenges to translate these fragments from molecules biologically active in vitro and in experimental models to potential drugs are discussed in the last part of the review.

2) Bix G, Iozzo RV. Matrix revolutions: "tails" of basement-membrane components with angiostatic functions. Trends Cell Biol. 2005 Jan;15(1):52-60.
Angiogenesis, the creation of neovasculature from native blood vessels, is a prerequisite for many physiological and pathological processes. Recently, C-terminal tail fragments of several basement-membrane proteins such as endostatin, tumstatin and endorepellin have been shown to inhibit angiogenesis. Although there seems to be little or no homology among them, a common theme is that these fragments modulate endothelial cells by distinct interactions with integrins and activate distinct intracellular signaling cascades that often lead  to disruption of the actin cytoskeleton. In this article, we focus on recent advances regarding the mechanism of action of these angiostatic fragments and the emerging concept of similarities among them, with the underlying premise that appreciating these similarities might lead to improved therapeutics.

3) Ricard-Blum S, Ballut L. Matricryptins derived from collagens and proteoglycans. Front Biosci. 2011 Jan 1;16:674-97.

Controlled proteolysis of extracellular matrix components releases bioactive fragments or unmasks cryptic sites that play key roles in controlling various physio-pathological processes including angiogenesis, tissue remodeling, wound healing, inflammation, tumor growth, and metastasis. We review here the structure and mechanisms of release of i) the proteolytic fragments (matricryptins) cleaved from collagens, proteoglycans and glycosaminoglycans, and ii) the matricryptic sites existing in these molecules. The cell surface receptors and the signaling pathways they trigger to exert their biological activities is discussed with the  major physio-pathological processes they control. Their involvement in autoimmune and inherited diseases is reported. Most matricryptins issued from collagens, proteoglycans and glycosaminoglycans exhibit anti-angiogenic and anti-tumor properties and their use as potential drugs and as potential disease markers is discussed. Perspectives for identifying the common structural features, if any, of the matricryptins and their use in combination with chemotherapy and radiotherapy in the treatment of cancer are presented.

4) Burgess JK, Weckmann M. Matrikines and the lungs. Pharmacol Ther. 2012 Jun;134(3):317-37.

The extracellular matrix is a complex network of fibrous and nonfibrous molecules that not only provide structure to the lung but also interact with and regulate the behaviour of the cells which it surrounds. Recently it has been recognised that components of the extracellular matrix proteins are released, often through the action of endogenous proteases, and these fragments are termed matrikines. Matrikines have biological activities, independent of their role within the extracellular matrix structure, which may play important roles in the lung in health and disease pathology. Integrins are the primary cell surface receptors, characterised to date, which are used by the matrikines to exert their effects on cells. However, evidence is emerging for the need for co-factors and other receptors for the matrikines to exert their effects on cells. The potential for matrikines, and peptides derived from these extracellular matrix protein fragments, as therapeutic agents has recently been recognised. The natural role of these matrikines (including inhibitors of angiogenesis and possibly inflammation) make them ideal targets to mimic as therapies. A number of these peptides have been taken forward into clinical trials. The focus of this review will be to summarise our current understanding of the role, and potential for highly relevant actions, of matrikines in lung health and disease.

APPENA USCITO:

García-Pardo A, Opdenakke G.: Nonproteolytic functions of matrix metalloproteinases in pathology and insights for the development of novel therapeutic inhibitors. Metalloproteinases In Medicine 2015:2 19–28.

Structural selectivity – in fact, the lack thereof – has been invoked as an explanation for the failure of matrix metalloproteinase (MMP) inhibitors as oncology drugs. However, functional selectivity is needed to develop a good drug. In addition, many drugs (including in oncology) act by interfering with signaling functions. The present market of successful biologicals contains many monoclonal antibodies, such as signaling inhibitors, with antitumor necrosis factor (anti-TNF) being the flagship of an armada. However, aside from its many pathogenic functions, TNF also plays physiological (ie, beneficial) roles. As long as the inhibition of detrimental functions supersedes the negative side effects, anti-TNF will be used. For such reasons, it is critical to know all the functions of MMPs, ideally before inhibitors are used as drugs. Here, we briefly summarize the known catalytic MMP functions and focus on the noncatalytic roles of these proteins, with an emphasis on their signaling effects. Indeed, recent studies have addressed the biology of multimolecular signaling complexes containing MMPs and the tissue inhibitors of metalloproteinases. These complexes are observed in solution (eg, as heteromers or homomultimers) and at the cell surfaces (eg, as docking complexes and signaling receptors). Consequently, a good understanding of the broader contexts – from the molecular, to the cellular and tissue levels – in which such molecular complexes operate will provide essential insights into direct new drug developments. This is exemplified with clinical and recent preclinical successes.

Il Corso è terminato. Spero di essere riuscita a rendervi interessanti gli argomenti che abbiamo affrontato.