Solution properties and structure of proteins, nucleic acids, polysaccharides and macromolecules complexes

Summary:

Althoug the development of methodology is one of our main aims, we also intend to test and demonstrate the applicability of the procedures to relevant biological systems. For instance, we have considered DNA with various perspectives. Medium, coarse-grained models of the double helix can be constructed with beads representing nucleotides; these models can include the bending and torsional flexibility of the double helix, and their properties are evaluated with HYDRO or Brownian dynamics simulation. High-resolution atomic models of short, rigid oligonucleotides can be treated with HYDROPRO. Our methodologies also cover a wide variety of proteins, from small proteins treated with atomic detail, to large multisubunit proteins for which HYDROSUB is a useful tool

Some relevant publications:

• "The Molecular Weight Distribution and Conformation of Citrus Pectins in Solution Studied by Hydrodynamics". Carbohydrate Polymers 16, 1-15 (1991). [PDF]
• "Hydrodynamic Properties of a Double-Helical Model for DNA", Biophysical Journal, 66, 1573-1579, (1994). [PDF]
• "HYDRO: A Computer Software for the Prediction of Hydrodynamic Properties of Macromolecules", Biophysical Journal 67, 530-531, (1994). [PDF]
• "Simulation of the Conformation and Dynamics of a double-helical model for DNA". Biophysical Journal 73, 3142-3153 (1997). [PDF]
• "The Conformation of Serum Albumin in Solution. A Combined Phosphorescence Depolarization-Hydrodynamic Modeling Study". Biophysical Journal 80, 2422-2430 (2001). [PDF]
• "Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins". Biophysical Chemistry 63, 159-170 (2001). [PDF]
• "Calculation of hydrodynamic properties of small nucleic acids from their atomic structures". Nucleic Acids Research 30 (8), 1782-1788 (2002). [PDF]
• "Estimating domain orientation of two human antibody IgG4 chimeras by crystallohydrodynamics". European Biophysics Journal 32, 503-510 (2003). [PDF]

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