Mean first passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding

We have analyzed dynamics on the complex free energy landscape of protein folding in the FOLD-X model, by calculating for each state of the system the mean first passage time to the folded state. The resulting kinetic map of the folding process shows that it proceeds in jumps between well-defined, local free energy minima. Closer analysis of the different local minima allows us to reveal secondary, parallel pathways as well as dead ends.Comment: 7 page

Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

<p>Abstract</p> <p>Background</p> <p>Empirical binding models have previously been investigated for the energetics of protein complexation (ΔG models) and for the influence of mutations on complexation (i.e. differences between wild-type and mutant complexes, ΔΔG models). We construct binding models to directly compare these processes, which have generally been studied separately.</p> <p>Results</p> <p>Although reasonable fit models were found for both ΔG and ΔΔG cases, they differ substantially. In a dataset curated for the absence of mainchain rearrangement upon binding, non-polar area burial is a major determinant of ΔG models. However this ΔG model does not fit well to the data for binding differences upon mutation. Burial of non-polar area is weighted down in fitting of ΔΔG models. These calculations were made with no repacking of sidechains upon complexation, and only minimal packing upon mutation. We investigated the consequences of more extensive packing changes with a modified mean-field packing scheme. Rather than emphasising solvent exposure with relatively extended sidechains, rotamers are selected that exhibit maximal packing with protein. This provides solvent accessible areas for proteins that are much closer to those of experimental structures than the more extended sidechain regime. The new packing scheme increases changes in non-polar burial for mutants compared to wild-type proteins, but does not substantially improve agreement between ΔG and ΔΔG binding models.</p> <p>Conclusion</p> <p>We conclude that solvent accessible area, based on modelled mutant structures, is a poor correlate for ΔΔG upon mutation. A simple volume-based, rather than solvent accessibility-based, model is constructed for ΔG and ΔΔG systems. This shows a more consistent behaviour. We discuss the efficacy of volume, as opposed to area, approaches to describe the energetic consequences of mutations at interfaces. This knowledge can be used to develop simple computational screens for binding in comparative modelled interfaces.</p

Excluded volume approximation to protein-solvent interaction. The solvent contact model.

Important properties of globular proteins, such as the stability of its folded state, depend sensitively on interactions with solvent molecules. Existing methods for estimating these interactions, such as the geometrical surface model, are either physically misleading or too time consuming to be applied routinely in energy calculations. As an alternative, we derive here a simple model for the interactions between protein atoms and solvent atoms in the first hydration layer, the solvent contact model, based on the conservation of the total number of atomic contacts, a consequence of the excluded-volume effect. The model has the conceptual advantage that protein-protein contacts and protein-solvent contacts are treated in the same language and the technical advantage that the solvent term becomes a particularly simple function of interatomic distances. The model allows rapid calculation of any physical property that depends only on the number and type of protein-solvent nearest-neighbor contacts. We propose use of the method in the calculation of protein solvation energies, conformational energy calculations, and molecular dynamics simulations

Advances in the INFN-Legnaro BNCT project for skin melanoma

The Legnaro National Laboratory is studying the construction of a specialised facility (SPES: Study and Production of Exotic Species) for Radioactive Ion Beams (RIB) originated by fission fragments produced by secondary neutrons. This facility will be characterised by moderate size, performance and cost and will allow also having intense neutron beams. It will allow for carrying out significant experiments and activities in both fundamental and applied nuclear physics (medicine, biology and Solid State); in particular, it will represent an attractive accelerator-based source for BNCT. The design is based on a high intensity proton LINAC as driver, which can deliver a proton beam in the energy range of 5 – 100 MeV with a beam power up to 3 MW. The full project will be developed in two phases. The first phase begin in 2001 and will be accomplished in five-seven years. During the first phase, most of the civil engineering, plants and enclosures are planned to be built together with the primary accelerator (up to 10 MeV, 300 kW protons), the neutron and RIBs production targets and the medical facility for the BNCT application. The BNCT project will use an intense 5 MeV proton beam to produce fast neutrons, which will be properly thermalised. The thermal and epithermal neutrons will be used for dosimetric, microdosimetric and radiobiological studies as well as for the skin melanoma treatment. In this paper we will present the state of art of this project