Models of biological macromolecules

Final Activity Report Summary - MOBIOMAC (Models of Biological Macromolecules)

The MOBIOMAC project has focused on several tools derived from theoretical physics and, in particular, from statistical mechanics for the investigation of molecules of biological relevance. Recent advances in experimental techniques have made it possible to obtain information on single molecules, rather than averaging over large collections of molecules (ensembles). Our research has been devoted to the application of analytical calculations, computer simulations and experimental data analysis on several molecules of biological relevance and/or polymers of direct technological interest.

The main objectives of the originally proposed project were divided in three research lines, comprising the description of biological systems which are able to use chemical energy to perform mechanical work (mechanochemical systems, research objective 1), the characterisation of biopolymers (DNA, actin or microtubules) in confining nano- or micro-tubes (research objective 2) and the investigation of simplified models for the description of protein structures and organic molecules in general (research objective 3).

The MOBIOMAC project resulted in an accurate study of theoretical models for the description of mechanochemical systems (research objective 1), in particular by collecting, organizing and studying the relevant literature to extend the previously proposed models for the interpretation of data from single molecule experiments on several mechanochemical systems (motor proteins, DNA translocation). These studies, performed in collaboration with the University of Padua (Italy) are expected to yield a full theoretical description of mechanochemical systems and form part of a new project coordinated by Dr Lattanzi and financed over the years 2006-2008 by the Italian Minister for University and Research (MIUR-COFIN2005).

The research objective 2 was carried out in collaboration with the Ludwig-Maximillians University in Munich (Germany) and the European Molecular Biology Laboratory in Heidelberg (Germany). A major achievement of the project is the full characterization of the physics of confined polymers, which constitutes the main topic of two scientific papers in preparation. Besides the intrinsic importance of the acquired theoretical tools, they are expected to provide a useful roadmap for experiments on biological filaments, in particular actin (which constitutes one of the main components of the cellular environment) and DNA. This result is particularly important since DNA confinement might substitute, in a close future, gel-electrophoresis, currently the leading technique in the complex process of DNA sequencing, ensuring a rapid screening of entire genomes in a reasonable time. In addition, the models studied in this context were applied to obtain a full investigation of the elastic properties of microtubules, other major constituents of the cellular architecture. Our research allowed the interpretation of the puzzling data on the different elastic parameters and obtained a remarkable attention within the biophysical community.

The research objective 3 led to a fruitful collaboration on synthetic organic conjugated polymers within the University of Bari (Department of Chemistry, Prof. Torsi): these polymers constitute a new class of material and have many technological implications, in particular as detectors of dangerous substances even at very low concentrations, or in the development of thin flexible screens. Our research introduced computer simulations in this context, which constitute a powerful tool to test new polymers prior to their chemical synthesis.

In addition, the project has focused on protein models, applied to two proteins of direct medical interest: the inhibiting factor 1 (IF1) and the F0F1-ATP synthase, both related to the cellular respiration. This part, carried out in collaboration with the Medical Research Council in Cambridge, United Kingdom, has been extended and financed by MIUR over the years 2006-2008.

Final Activity Report Summary - MOBIOMAC (Models of Biological Macromolecules)

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