Biomedical subjects

Giulia Morra

Publications and source records attributed to Giulia Morra.

4 recordsLinked to original sources

PubMed2005

High performance workflow implementation for protein surface characterization using grid technology.

BACKGROUND: This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. METHODS: Workflows are very common in Bioinformatics because they allow to process large quantities of data by delegating the management of resources to the information streaming. Grid technology optimizes the computational load during the different workflow steps, dividing the more expensive tasks into a set of small jobs. RESULTS: Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications. The proposed workflow is implemented to integrate huge amounts of data and the results themselves must be stored into a relational database, which results as the added value to the global knowledge. CONCLUSION: A web interface has been developed to make this technology accessible to grid users. Once the workflow has started, by means of the simplified interface, it is possible to follow all the different steps throughout the data processing. Eventually, when the workflow has been terminated, the different features of the protein, like the amino acids exposed on the protein surface, can be compared with the data present in the output database.

Automation↗

PubMed2005

Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study.

Molecular dynamics (MD) simulations on a bacterial cytochrome c were performed to investigate the lifetime and fluctuations of backbone hydrogen bonds and to correlate these data with protection factors for hydrogen exchange measured by NMR spectroscopy (Bartalesi et al. in Biochemistry, 42:10923-10930, 2003). The MD simulations provide a consistent pattern in that long lifetimes of hydrogen bonds go along with small amplitude fluctuations. In agreement with experiments, differences in stability were found with a rather flexible N-terminal segment as compared with a more rigid C-terminal part. Protection factors of backbone hydrogen exchange correlate strongly with the number of contacts but also with hydrogen-bond occupancy, hydrogen-bond survival times, as well as the inverse of fluctuations of backbone atoms and hydrogen-bond lengths derived from MD simulation data. We observed a conformational transition in the C-terminal loop, and significant motion in the N-terminal loop, which can be interpreted as being the structural units involved in the onset of the protein unfolding process in agreement with experimental evidence on mitochondrial cytochrome c.

Amides↗

PubMed2003

Unfolding of the cold shock protein studied with biased molecular dynamics.

The cold shock protein from Bacillus caldolyticus is a small beta-barrel protein that folds in a two-state mechanism. For the native protein and for several mutants, a wealth of experimental data are available on stability and folding, so that it is an optimal system to study this process. We compare data from unfolding simulations (trajectories of 5 and up to 12 ns) obtained with a bias potential at room temperature and from unbiased thermal unfolding simulations with experimental data. The unfolding patterns derived from the trajectories starting from different native-like conformations and subject to different unfolding conditions agree. The transition state found in the simulations of unfolding is close to the native structure in agreement with experiment. Moreover, a lower value of the free energy barrier of unfolding was found for the mutant R3E than for the mutant E46A and the native protein, as indicated by experimental data. The first unfolding event involves the three-stranded beta-sheet whose decomposition corresponds to the transition state. In contrast to conclusions drawn from experiments, we found that the two-stranded beta-strand forms the most stable substructure, which decomposes very late in the unfolding process. However, assuming that this structure forms very early in the folding process, our findings would not contradict the experiments but require a different interpretation of them.

Bacterial Proteins↗

PubMed2003

Redox potential of quinones in photosynthetic reaction centers from Rhodobacter sphaeroides: dependence on protonation of Glu-L212 and Asp-L213.

The absolute values of the one-electron redox potentials of the two quinones (Q(A) and Q(B)) in bacterial photosynthetic reaction centers from Rhodobacter sphaeroides were calculated by evaluating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation at pH 7.0. The redox potential for Q(A) was calculated to be between -173 and -160 mV, which is close to the lowest measured values that are assumed to refer to nonequilibrated protonation patterns in the redox state Q(A)(-). The redox potential of quinone Q(B) is found to be about 160-220 mV larger for the light-exposed than for the dark-adapted structure. These values of the redox potentials are obtained if Asp-L213 is nearly protonated (probability 0.75-1.0) before and after electron transfer from Q(A) to Q(B), while Glu-L212 is partially protonated (probability 0.6) in the initial state Q(A)(-)Q(B)(0) and fully protonated in the final state Q(A)(0)Q(B)(-). Conversely, if the charge state of the quinones is varied from Q(A)(-)Q(B)(0) to Q(A)(0)Q(B)(-) corresponding to the electron transfer from Q(A) to Q(B), Asp-L213 remains protonated, while Glu-L212 changes its protonation state from 0.15 H(+) to fully protonated. In agreement with results from FTIR spectra, there is proton uptake at Glu-L212 going along with the electron transfer, whereas Asp-L213 does not change its protonation state. However, in our simulations Asp-L213 is considered to be protonated rather than ionized as deduced from FTIR spectra. The calculated redox potential of Q(A) shows little dependence on the charge state of Asp-L213, which is due to a strong coupling with the protonation state of Asp-M17 but increases by 50 mV if Glu-L212 changes from the ionized to the protonated charge state. Both are in agreement with fluorescence measurements observing the decay of SP(+)Q(A)(-) in a wide pH regime. The computed difference in redox potential of Q(B) in the light-exposed and dark-adapted structure was traced back to the hydrogen bond of Q(B) with His-L190 that is lost in the dark-adapted structure and the charge of the non-heme iron atom, which is closer to Q(B) in the light-exposed than in the dark-adapted structure.

Amino Acid Substitution↗