An overview of our work

"The important thing I have learned over the years is the difference between taking one's work seriously and taking oneself seriously. The first is imperative and the second is disasterous."
–M. Fonteyn.

Our research is focused both on fundamental work on protein folding and, more recently, on studies oriented to elucidate the relation between protein folding, misfolding and disease in the framework of computer modelling and simulations. Our work addresses the following topics:

I. Kinetics & mechanisms of protein folding

The folding of small proteins is two-state, topology-dependent & highly cooperative

For the vast majority of small (i.e., proteins with less than 100 aa), single domain proteins, folding kinetics is typically well-described by a two-state model, suggesting that the only relevant milestons along the folding reaction are the unfolded state, the transition state, and the native fold. Furthermore, the folding rates of these small proteins span a remarkable million-fold range (see figure's top panel) and are mostly determined by the topology of the native fold, as measured by the contact order [1, 2] or other related metrics. A major goal of our simulations-based studies is that of understanding how native topology drives and controls the kinetics and mechanisms of protein folding. For example, we have investigated what is the relative role of local and long-range (LR) interactions in the folding kinetics of different native topologies. In doing so we have found that while LR interactions play a dominant role in determining the folding rates, irrespective of native topology, the dispersion of folding times, observed upon unbalancing the relative contribution of local and LR interactions to the protein's native energy, is critically dependent on the fold's topology [3].

Another characteristic trait of the folding of small proteins is its extraordinary thermodynamic cooperativity, which gives rise to the S-shaped form of protein experimental denaturation curves, and microscopically leads to a bi-modal distribution of molecules over any observable parameter at the so-called transition temperature (see figure's middle panel). While it is well accepted that such behaviour must rely on highly unusual energetics (involving non-additive multi-body effects, where the formation of one bond favours the formation of additional bonds - in fact this is the reason why the folding transition is termed cooperative), the exact nature of the interactions underlying protein folding cooperativity, and the relation of the latter with topology-dependent kinetics remains to be elucidated. In one of our initial efforts to understand protein folding cooperativity we have found that structures with predominantly local contacts (i.e., low CO and alpha-helix rich) are generally associated with a lack of cooperativity in the formation of tertiary bonds during folding [4]. More recently, we have shown that the folding kinetics of lattice polymers modified to render their folding more cooperative are, like those of small proteins, rapid and single-exponential, which underlies the existence a smooth energy landscape (see figure's bottom panel) [5].

In a related effort, we have investigated the role of protein sequence as a modulator of the nucleation mechanism. In order to do so we have compared a nucleation scenario that is exclusively driven by native topology with one that is driven by both primary structure (i.e. sequence) and topology. We found that the sequence's finer details tune the formation of the nucleus but its overall position along the protein chain is mostly driven by the fold's topology [6].

References

1. Topology, Stability, Sequence, and Length: Defining the Determinants of Two-State Protein Folding Kinetics
   Kevin W. Plaxco, Kim T. Simons, Ingo Ruczinski, and David Baker, Biochemistry 39, 11177-11183 (2000).


2. Topological complexity, contact order and protein folding rates
   P.F.N. Faísca & R.C. Ball, Journal of Chemical Physics117, 8587-8592 (2002) & Virtual Journal of Biological Physics Research 4 (9), November-1 (2002).


3. The Go model revisited: Native structure and the geometric coupling between local and long-range contacts
   P.F.N. Faísca, M.M. Telo da Gama & A. Nunes, Proteins: Structure, Function and Bioinformatics 60, 712-722 (2005).


4. Folding and form: Insights from lattice simulations
   P.F.N. Faísca, M.M. Telo da Gama & R.C. Ball, Physical Review E 69, 051917, 8 pp. (2004) & and Virtual Journal of Biological Physics Research 7 (11), June-1 (2004).


5. Cooperativity and the origins of rapid, single-exponential kinetics in protein folding
   P.F.N. Faísca & K.W. Plaxco, Protein Sci. 15, 1608-1618 (2006).


6. Nucleation phenomena in protein folding: The modulating role of protein sequence
   Rui D.M. Travasso, Patrícia F.N. Faísca & Margarida M. Telo da Gama, J. Phys.: Cond. Matt. 19, 15 pp. (2007) 285212.

II. The role of intermediate states in folding, misfolding & disease

There is plenty of evidence that intermediates are involved in the onset of the so-called amyloidoses

Folding intermediates are metastable conformations that are transiently populated during the folding reaction. Since the early 1990s, when is was firstly shown that the folding of small proteins follows a two-state kinetic paradigm, intermediates have been typically seen as relatively dull species mainly associated with the folding of large (>120 amino acids) proteins. Their exact role as folding helpers or folding breakers is, however, a matter of substantial debate as there is plentiful evidence for both scenarios. More recently, the recognition that intermediate species play a pivotal role in the onset of amyloidoses (e.g., Alzheimer's and Parkinson's diseases) by participating in the early stage of the aggregation process that leads to amyloid fibrils, has contributed to a renewed interest in these conformers. We are currently using Monte Carlo lattice simulations to explore the role of intermediate species in the folding of large proteins, and we are also using off-lattice Langevin Molecular Dynamics simulations to investigate the genesis and universal character of the early amyloid precursor.

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III. The physico-chemical triggers of amyloid formation

While in many cases there is an underlying genetic defect that facilitates, or triggers, the formation of amyloid, the existence of sporadic forms, which are indeed the most common forms of the amyloidogenic diseases, poses the challenge of understanding their molecular basis. In the last few years research in the field of protein misfolding established some sequence properties (e.g. high hydrophobicity, low net charge, ability to form beta strands) as important determinants of protein aggregation. We will use full atomistic Molecular Dynamics to explore the impact of amyloidogenic sequence properties in the unfolding dynamics of several target proteins with medical relevance.

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