Summary of key activities carried out by the Programme

Our group has continued to study disordered proteins in the centrosome. We found that (1) the centrosomal proteome is characterized by a larger fraction of disordered, coiled coil and phosphorylated residues than generic proteins of the same organism, (2) these three properties are correlated, and (3) they increase with the complexity of the organism, measured as the number of cell types. By comparing orthologous proteins, we found that disorder mainly increases in protein evolution through the acquisition of new modules that tend to contain a large fraction of disordered residues, while amino acid substitutions contribute very little to the flux of disorder (Preprint: Protein disorder in the centrosome correlates with complexity in cell types numberarticle in preparation).

We also have several side projects. First, we are studying protein flexibility, similar to that conferred by disorder but for globular proteins, by using our new elastic network model in torsion angle space (second revision submittedRef. Bast4). Second, we are studying protein structure evolution, in particular we investigated the relationship between changes of function and changes of sequence and structure in protein evolution (Ref.Bast1) and the cross-over between discrete (where hierarchical classification is possible) and continuous (network-like) protein structure space (Ref.Bast3). Third, still in the field of molecular evolution, we investigated the relationship between protein folding stability, mutation bias towards AT and population size, proposing a new explanation for the distribution of AT bias in bacterial species (Ref. Bast5 and Bast6). Fourth, Third, we developed a new method for sequence alignments that more accurately reproduces structural relationships between proteins (second revision submittedRef.Bast7). This method was applied for generating accurate homology models of centrosome domains. Last, we studied how mutualistic ecological interactions influence biodiversity in ecosystems, a work that suggests a possible pathway to the increase of complexity in biological systems (Ref. Bast2).

Bast4: Mendez R, Bastolla U. Torsional Network Model:Normal modes in torsion angle space better correlate with conformation changes in proteins. Phys. Rev. Lett. 2010; 104: 228103.

Bast5: Mendez R, Fritsche M, Porto M, Bastolla U. Mutation bias favors protein folding stability in the evolution of small populations. PLoS Comput Biol. 2010 May 6;6(5):e1000767.

Bast6: Sammet SG, Bastolla U, Porto M. Comparison of translation loads for standard and alternative genetic codes. BMC Evol Biol. 2010 Jun 14;10(1):178. [Epub ahead of print]

Bast7: Teichert F, Minning J, Bastolla U, Porto M. High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH. BMC Bioinformatics. 2010 May 14;11:251.

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