Physical Principles of Biomolecular Recognition, Self-Assembly and Regulation

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Interactions between various biological helices control protein folding and assembly, DNA packing, protein-DNA interactions, connective tissue formation and stability, and many other processes responsible for normal function and pathology in living organisms. By combining several experimental techniques (UV-VIS, fluorescence, and FTIR spectroscopy, x-ray diffraction, calorimetry, etc.) with rigorous physical theories, we continued to advance our understanding of these most basic molecular recognition reactions. Our most significant achievements during the past year were: (1) Our study of a mouse model of osteogenesis Imperfecta (OI) revealed that (a) Although G349C substitution in a1(I) chain of type I collagen results in moderate to severe (lethal) OI, by itself the mutation has absolutely no effect on collagen-collagen interactions in tendons and demineralized bones, on in vitro fibrillogenesis, and on the protein stability. (b) The subtle changes in interactions, fibrillogenesis and protein stability, observed in some but not all mutant animals, appear to be related to difference in posttranslational protein overmodification rather than to different levels of mutant protein expression. (c) The extent of the overmodification depends strongly on the animal age. (2) We started a systematic study of the relationship between temperature dependence of collagen fibrillogenesis and thermal stability of the protein. Our preliminary results indicate that the protein is metastable rather than stable at physiological temperature. It appears that initial stages of unfolding are the trigger for self assembly of the protein into fibers where it is protected from denaturation. (3) We started investigation of human type I collagen with an unusual mutation that leads to chain register disruption, recently discovered by the group of Dr. Marini (HDB/NICHD). We described the effect of this mutation on the stability and in vitro fibrillogenesis of the protein. (4) We developed a theory that describes the effect of base pair sequence on electrostatic interaction between DNA duplexes. We found that this interaction can lead to an effective sequence recognition and pairing of 50-200 bp DNA fragments. This may explain the puzzling observation of such local pairing between intact fragments of duplex, nucleosome-free DNA in cells. It was reported in the literature that such pairing precedes homologous recombination and that it is independent of RecA family proteins.