RICERCA ITALIANA     

Protein folding and aggregation: a theoretical-experimental approach

Università degli Studi di Padova

Abstract

The problem of protein folding, the process through which proteins fold into their native structures, lies at the heart of modern molecular and cellular biology: How does an unstructured chain of amino-acids fold into a well defined three-dimensional structure, the native state, where biological activity is performed? Understanding the physical mechanisms at the basis of protein folding is of the greatest importance in decoding genetic information and its functional implications, and in designing novel artificial proteins and new drugs for biomedical purposes.

Protein folding and the related biological activity ‘in vivo’ are not processes taking place in isolation. Biological activity is often associated with molecular recognition processes involving ligand/substrate binding to an active catalytic site present in the native structure, and more generally with interaction between different proteins. The cellular environment is indeed crowded with different kinds of protein molecules, each being expressed at different concentration levels. Enhanced concentration of a given protein molecule may induce a non correct folding (mis-folding) by driving the formation of stable insoluble aggregates, amyloid fibrils, known to be involved in the onset of many debilitating neurodegenerative diseases, such as Alzheimer’s, type-II diabetes, and spongiform encephalopathies. Aggregation mechanisms and the very structure of amyloid fibrils at the molecular level are beginning >>>

Principal Investigator

Amos Maritan Università degli Studi di PADOVA

Research Objectives

The sequencing of the human genome has been one of the greatest achievements of modern research. New genes (polymers of nucleotides) have been identified and a great deal of information is also available regarding the process, gene expression, by which genes are converted into proteins (polymers of amino acids), the ultimate product of genes. Thus in principle we should be able to identify virtually all proteins operating in the human body. Nevertheless there is a rather incomplete understanding of the process by which genetic information is converted into biological activity, the protein folding.

Understanding the mechanism by which a polypeptide chain folds into its unique functional native state is one of the most intriguing problems in molecular biology. The transient character of the molecular species populated along the folding pathway(s) makes their experimental identification and characterization extremely difficult. Furthermore the computational modelling of the protein folding process is challenging because of the large number of weak interactions between amino acids and the small difference in the free energy between the native state and the denaturated states. Over and above this fundamental significance, studies on protein folding have recently acquired medical relevance since it has been shown that formation of amyloid plaques, responsible for the onset of some neuro degenerative disorders, may be caused by alterations of the canonical folding >>>

First Results

The expected result from the Research Unit in Florence is the understanding of aggregation mechanisms involving partially folded intermediates populated during the folding process. The focus will be an overall description of the energy landscape of all possible conformations adopted by the PDZ2 domain, from the unfolded to the folded state through folding intermediates, but also from the monomeric states to amyloid fibrils through oligomeric intermediates. Similar results are expected in the case of the aggregation process taking place in the presence of physiologically relevant compounds with the aim of identifying generic rules that are more pertinent to the in vivo situation. The obtained data will be compared with those published for other systems with the aim of collecting a number of data sufficient for editing models of general validity. In this respect, the interaction with the URs of Padova and Bari and the ability of these URs to develop models to be tested against the experimental data obtained by the UR in Florence will be an essential part of the project.

The expected result from the Research Unit in Rome is the unveiling of the molecular events involved in the folding and the binding reaction of PDZ domains, and the correlation between the two processes. Particular attention will be devoted to the definition of the key determinants of the long-range network of weak interactions affecting ligand recognition, and their relationships to the folding >>>

Timescale

24 months

National and international background

Protein science represents an exciting frontier of research for applied and theoretical physics, requiring efforts, resources and expertises from different disciplines. On a fundamental point of view, proteins are heteropolymers composed of 20 different aminoacids, whose chemistry dictates the shape they assume and hence regulates their function. Many progresses towards the elucidation of protein folding (how proteins assume their three-dimensional shape) and protein function (how proteins perform their specific task in the cell), have been achieved in recent years. However, the protein folding problem is far from being solved. In addition, a number of human diseases depend crucially on the misfolding of proteins or small peptides: they are associated with the conversion of specific proteins or peptides from their soluble state into insoluble fibrillar aggregates generally referred to as amyloid fibrils. These include Alzheimer’s disease, Creutzfeldt-Jacob disease, type II diabetes and other systemic or neurodegenerative pathological conditions (Selkoe 2003, Bellotti et al. 2007). Amyloid fibrils share common morphological and structural characteristics which seem independent of the precursor proteins from which they are generated: a specific diameter of 7-13 nm, an extensive beta-sheet structure and the ability to bind specific dyes (Sunde & Blake 1997). This seems to suggest that amyloid formation is not a peculiar behaviour of specific aberrant proteins, but >>>