Structural Bioinformatics: a new window to observe the protein universe

avviso seminario
SEMINARIO PROF. NERI NICCOLAI
Dipartimento di Biotecnologie, Chimica e Farmacia Università di Siena
GIOVEDÌ 8 GIUGNO, 2017 ORE 16:30 AULA CH-1
"Structural Bioinformatics: a new window to observe the protein universe"
Host: Prof. Delia Picone
 
Abstract
The large repertoire of structural information nowadays freely available for proteins has suggested us to try bioinformatic approaches for delineating fundamental mechanisms of Life at atomic resolution. Thus, by analysing a sub-set of Protein Data Bank protein structures comprising proteins not involved in interactions with any type of ligands, their surfaces appeared populated by amino acids with charged side chains. However, the fact that opposite charges were most frequently observed on protein surfaces, suggested possible mechanisms of long-distance protein-protein recruitment [1].
 
The fact that genetic code multiplicity rewards the 20 natural amino acids in a way that is not directly related to their abundance in proteins, forced us to find an alternative rationale accounting for the uneven redundancy of standard genetic code [2]. More recently, a non-redundant set of 629 protein-DNA adducts have been analysed in order to find how amino acid composition of protein-DNA interfaces can determine the sliding of proteins along DNA  rails [3].
 
References
 
1. Alocci D, Bernini A, Niccolai N. Atom depth analysis delineates mechanisms of protein intermolecular interactions. Biochem Biophys Res Commun. 2013, 436, 725-729.
2. Gardini S, Cheli S, Baroni S, Di Lascio G, Mangiavacchi G, Micheletti N, Monaco CL, Savini L, Alocci D, Mangani S, Niccolai N. On Nature's Strategy for Assigning Genetic Code Multiplicity. PLoS One. 2016, 11, e0148174.
3. Gardini S, Furini S, Santucci A, Niccolai N. A structural bioinformatics investigation on protein- DNA complexes delineates their modes of interaction. Mol Biosyst. 2017, 13, 1010-1017.

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