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Research Il Centro di Eccelenza di Biocristallografia ha le seguenti linee di ricerca:
1. Caratterizzazione cristallografica di complessi dell'enzima batterico maltodestrina fosforilasi con substrati inibitori e relativi studi di catalisi enzimatica mediante cristalli proteici volti ad indagare sul meccanismo catalitico presente nelle fosforilasi.
2. Determinazione strutturale della transcobalamina (forma bovina ed umana), la proteina di trasporto dei corrinoidi presente nel plasma dei mammiferi che permette l'uptake cellulare della vitamina B12. Studio finalizzato allo sviluppo di bioconiugati della B12 diagnostici e terapeutici verso cellule tumorali che presentano un elevato uptake di B12.
3. Determinazione della struttura mediante tecniche di diffrazione di raggi-X di mutanti di proteasi HIV resistenti ai farmaci attualmente utilizzati nella terapia anti-HIV complessati con nuovi inibitori.
4. Studio biocristallografici del complesso DNA-proteina costituito dal "Paired Domain" del fattore di trascrizione Pax8. essenziale per lo sviluppo regolare delle ghiandole tiroidee, con l'oligonucleotide corrispondente alla relativa sequenza consensus
5. Caratterizzazione degli epitopi antigenici presenti nelle proteine del virus dell'epatite C (HCV) e negli anticorpi IgG che producono una risposta autoimmunitaria caratteristica della patologia della crioglobulinemia mista di tipo II (CM II), un progetto svolto in collaborazione con il Centro di Riferimento Oncologico di Aviano nell'ambito dello studio di malattie associate all'infezione di virus HCV che degenerano in linfomi non-Hodgkin.
Scarica il file CEB-research-2007.ppt
| Workpackage 1 | Crystallisation and X-ray Structure Determination of Natural and Miniaturised Proteins |
Research line 1
Group leader: Prof. Lucio Randaccio
1. Synthesis, characterisation, the accurate X-ray analysis of cobalamins, by using synchrotronradiation, and theoretical calculations (in collaboration with Prof. Ching of the Department of Physics of the Kansas City Missouri University, USA).
2. Miniaturised proteins. Design, synthesis and characterisation of cobalt-peptide complexes (miniaturised B12 proteins), in the solid state and in solution; crystallisation and synchrotron X-ray structure of miniaturised iron proteins: hemo-protein models, which reproduce the characteristic sandwich structural motif helix-heme-helix of cytochromes c; di-iron protein models and their mutants, having the four-helix bundle motif of ferritin; iron-sulfur protein models of rubredoxin, based on a 11 residue peptide(in collaboration with Prof. DeGrado of the School of Medicine, University of Pennsylvania, USA).
3. New synthetic constrained peptides (in collaboration with both Prof. Yamada, Department of Chemistry, Konan University, Kobe, Japan and the Research Unit 1 of the Workpackage 3). Characterization of the redox properties of the above systems with electrochemical and spectro-electrochemical techniques.
Research line 2
Group leader: Prof. Silvano Geremia
1. Expression, crystallizsation and the X-ray structure determination of transport proteins such as the transcobalamin TCII ( in collaboration with prof. Petersen of the Aarhus University, DK).
2. Structural analysis of the zinc uptake regulator protein (ZUR) and the Atx1-COPZ;
3. Structural determination oof substrate- or -inhibitor complexes of enzymes such as the maltodextrin phosphorylase (in collaboration with Prof. L. Johnson, University of Oxford, UK) and of HIV-1 protease, in collaboration with the research line 1 of workpackage 2.
4. Expression, crystallisation and structural determination of redox proteins such as c-type cytochromes and blue copper proteins.
5. Crystallisation and structural determination of complexes with DNA of proteins involved in recognition and interaction with telomeric DNA.
| Workpackage 2 | Molecular modelling of enzymes, and computer-aided design and synthesis of inhibitors |
Research line 3
Group leader: Prof. Domenico Romeo
1. The synthesis, structure (to be run in collaboration with the Research Units of the Workpackage 1) and testing of new HIV-1 protease peptidomimetic inhibitors, characterised by a relatively low molecular weight and potentially endowed with high bioavailability. These inhibitors (Pn…P2-P1-[y-] P1'-P2'…Pn) are based on rational computer-aided design, followed by modular assembly of flanking residues onto presynthesised, nonhydrolasable central cores.
2. A somewhat alternative and innovative approach to the design and synthesis of HIV inhibitors based on the use of fullerenes, hydrophobic and inert spheroidal molecules which show interesting potentialities for biomedical applications. Fullerene derivatives with increased affinity for the HIV protease cavity can thus be designed and synthesised.
3. Computer-aided design of several analogues of known inhibitors, targeted against selected mutants of the HIV-1 protease, useful for tackling the emergence of viral resistance.
Research line 4
Group leader: Prof. Paolo Linda
1. Development of new, versatile biocatalysts is of great interest in the area of organic and medicinal chemistry: particularly, hydrolases, and among these lipases and amino-hydrolases for their generally excellent regio- and stereospecificity, and for their ability to accept structurally different substrates. Their use in organic solvents further broadens the scope for synthetically useful transformations. The problem is approached in the following steps: i) mechanistic study of enzyme-solvent-substrate interactions aimed at a fine-tuning of the reactivity of catalytic systems. Chemometrics will be used as a tool for this investigation ii) application of regio-, stereo- and chemoselective processes to the synthesis or modification of pharmaceutically and synthetically interesting molecules; iii) molecular modelling studies of the catalytic mechanism at the microscopic level.
2. De novo development of catalytic species able to perform the desired transformation.. Catalytic antibodies are a possible approach to the targeted design of novel catalytic proteins. In order to expand the range of available hydrolytic biocatalysts, antibodies will be prepared against phosphoesters, phosphonamides and the corresponding sulphonyl derivatives as transition-state analogues. This part of the project will require a close collaboration with the two Research Units of the Workpackage 1.The ultimate target of this part of the project is to study possible applications of this approach to the regio- and stereo-selective synthesis of pharmaceuticals.
Research line 5
Group leader: Prof. Gianni Del Sal
1. Understanding the regulation of p53 tumor suppressor and p53 related proteins (p73 and p63) functions through the characterization of post-translational modifications and protein interaction profiles.
2. Isolation and use of peptide aptamers, displayed from an inert scaffold protein, able to interfere in vivo with relevant protein complexes and therefore with their biological functions.
Research line 6
Group leader: Prof. Giorgio Manzini
1. Isolation and characterization of proteins interacting with telomeric-type single stranded DNA in collaboration with Dr. Andrea Scaloni, at the International Center for Mass Spectrometry of the National Research Council in Naples.
2. Determination of the cellular localization of these proteins, and their possible co-localization with already known telomere binding proteins, such as the factor TRF1.
3. Expression and purification of proteins in suitable amounts by recombinant methodology, principally finalized (but not only) to the preparation of single crystals of these proteins, alone and possibly in complex with DNA, for the determination of their tertiary structure, utilising the expertise of the Research Unit 2 of Workpackage 1.
4. Generation of deletion and substitution mutants of these proteins, aiming at clarifying the molecular basis of the remarkable specificity in these protein-DNA interactions, also by means of molecular modelling studies, in collaboration with Dr. Federico Fogolari (University of Verona) and the expertise of the Research Units of Workpackage 2.
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