RICERCA ITALIANA     

Structural genomics of metalloproteins and of their functional interactions

Università degli Studi di Firenze

Abstract

This project aims at the determination of the structure of some metalloproteins that are involved in important biochemical processes and, whenever possible, at proposing structural models of their protein-protein interactions relevant for those processes.
Typically, proteins involved in copper-trafficking will be a major target of this project for their involvement in copper homeostasis and for the dependence of copper transfer upon specific protein-protein interactions. Some aspects of nickel trafficking will also be studied. Calcium-dependent signalling proteins will be another subject of study, as calcium binding induces conformational changes which allow protein-protein interactions to occur. Other interesting systems may attract our attention during the two years of this research. The structural characterization will be mainly performed by NMR with the help of X-ray spectroscopy (XAS) and by X-ray crystallography, whenever convenient. We plan to automate and speed up the solution structure determination procedures by NMR, and to develop software and hardware to study large proteins or large complexes. We will develop bioinformatics tools to select the metalloproteins to be studied and predict their functional role. We will also optimize the technologies for obtaining the targeted proteins through their heterologous expression. All these activities will contribute to push forward the frontier of biological sciences, by addressing the challenging problem of >>>

Principal Investigator

Ivano BERTINI Università degli Studi di FIRENZE

Research Objectives

Structural genomics projects started in 1998, aiming at the determination of the three-dimensional structure of all the proteins encoded into the sequenced genomes. However, it was soon apparent that the structure of an extensive number of proteins could be only modestly attractive by itself, and that prioritization of the proteins to be studied could be of primary importance. The Centre of Magnetic Resonance (CERM) of the University of Florence contributed since the beginning to structural genomics by focusing on selecting metalloproteins as primary targets.
Metalloproteins are proteins capable of binding one or more metal ions, which are required for their biological function, for the regulation of their activities, or for structural purposes. During the course of past research at CERM, partly financed in previous COFIN projects, we realized that the definition itself of a protein as a metalloprotein is not an obvious task. If a protein is purified with a metal ion, this does not necessarily mean that the protein binds a metal ion in vivo and, conversely, in the case a protein is isolated as demetallated, this does not mean that the protein is not a metalloprotein. We are finding that the assessment of whether a protein needs a metal ion for its function requires a good deal of biological knowledge, and that the latter can be largely assembled by means of thorough bioinformatics searches (see later). On the basis of bioinformatics searches and of thorough >>>

Timescale

24 months

National and international background

Genome sequencing has provided nearly complete lists of the macromolecules present in many organisms. As a consequence, worldwide initiatives have developed aimed at determining a large number of protein structures in a high throughput mode, and this new field of research was called "structural genomics" [1]. The benefits of combining three-dimensional structural information with genome information is based on the consideration that "function follows form". The first structural genomics projects started in USA in 1998 funded by NIH and DOE. Japan started a project of Structural Genomics at the Riken Institute in 1998 and, finally, in 2002 Europe had its own project named SPINE (Structural Proteomics in Europe). The definition "structural proteomics" was used to emphasyze how, with time, scientists have directed more and more attention to the identification of the role of proteins whose structure has to be determined, with increasing importance of target selection. We, as Center of Magnetic Resonance (CERM), were involved in the international debate on structural genomics from the very beginning (see http://www.oecd.org/dataoecd/24/31/2105118.pdf) with the specific task of dealing with the structure determination of metalloproteins, as we are a renowned lab operating in the field of metal ions in biology.
Many of the structural genomics projects focus on the development of new methods and technologies for high-throughput structure determination, with the main >>>