Molecular Dynamics of Monomeric IAPP in Solution: A Study of IAPP in Water at the Percolation Transition

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Chapter, Introduction:
The word protein was coined by the Swedish scientist Jöns Berzelius in 1838 to describe a certain class of molecules and their importance.1,2 In fact, it derives from the Greek word proteØoc of primary importance which in turn derives from the word protoc first. 3,4 After almost 150 years, one can read the opening sentence of the first chapter of the book on the structure and molecular properties of proteins by Creighton 5 Virtually every property that characterizes a living organism is affected by proteins. Proteins: Structure and Molecular Properties, Creighton (1993) and only wonder how much there still is to discover, in order to fully understand how these organic molecules, constituting living organisms, function. What is fascinating about proteins is the multitude of roles they have within living organisms, from enzymatic catalysis to transport and storage, and from functions as complex as biogenesis to being simply structural, just to mention a few primary functions carried out by proteins. In other words, each cell carries out ist activities through the expression of ist genes by means of ist working molecules, i.e., the proteins. How many proteins are encoded by a simple unicellular eukaryote like saccharomyces cerevisiae? The predicted number expressed by this yeast genome is 6200 (as can be found on Table 7.3 in Molecular Cell Biology by Lodish et al. (2000)). But what is even more astonishing is the fact that thousands of primary structures are linear chains consisting of a combination of only twenty amino acids. A protein can thus be considered a word, determined by a sequence of letters of the alphabet that has a meaning.6 Once the sequence of amino acids has been found, the adventure begins! The reason is that many times the function of the protein is still unknown. In fact, the primary structure of the object of this study, i.e., islet amyloid polypeptide (IAPP), is known, albeit ist biological function remains unclear. Moreover, the functionality of proteins and peptides depends on the native conformation, which for IAPP is also still unknown. IAPP seems to be involved in the regulation of the glucose metabolism, since it is cosecreted with insulin from pancreatic b-cells. Ist physiological role is unclear. Although pancreatic amyloid deposits in the islets of Langerhans have been found in more than 95% of the type II diabetes patients, the causal relationship between amyloid formation and the disease is still largely unknown.7 10 The conditions at which it aggregates are also still unclear; in fact, the human IAPP (hIAPP) sequence in healthy individuals is identical to that found in individuals who suffer from non-insulin-dependent diabetes. On the other hand, other variants, presenting a sequence identity of at least 80% such as rodent IAPP (rIAPP), do not aggregate. Moreover, healthy hIAPP-transgenic mice, which release hIAPP and insulin in a regulated manner, do not present any islet amyloid deposits either. Hence, the primary structure of hIAPP alone is not sufficient to cause amyloid formation. In fact, islet amyloid deposits were found only in mice that presented dysfunctional b-cells. One of the characteristics of the deposits formed by amyloidogenic precursor proteins, such as IAPP, is the proximity of the insoluble deposits to where the protein is produced.11 Owing to the complexity of living organisms and all the open questions surrounding them, it would be impossible to determine the biological function of IAPP only through MD simulations. In vitro experiments on hIAPP are particularly demanding, as it forms insoluble aggregates within minutes, compared to other amyloidogenic peptides that take 1 to 3 days, like Ab, responsible for the amyloid deposits in Alzheimer s Disease. The difficulty lies in the identification of the intermediate states that occur when the peptide undergoes a conformational transition from random coil to an aggregation-prone conformati