Studies of preferential solvation of peptides and proteins in solution

Chemical environment (pH, salts, co-solvents) plays an important role in the stabilization of secondary structure forming peptides and proteins in solution. The presence of co-solvent in aqueous solution can increase the structural stability as well as to promote denaturation or conformational changes. For this reason, atomic level understanding of protein solvation can provide useful insights into the mechanism of protein folding, aggregation, fibril formation etc. Among the co-solvents, alcohols, and in particular fluorinated ones, are commonly used as stabilizing or denaturing agents. Roccatano et al. have proposed new models of 1,1,1-trifluoroethanol (TFE) and 1,1,1,6,6,6-hexafluoropropan-2-ol (HFIP), to use for MD simulations. These models have successfully reproduced the experimentally observed increase of stability for different secondary structure forming peptides in TFE and HFIP/water mixtures. These encouraging results will allow us to make more detailed investigations of the effect of these solvents on peptides and proteins.

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Figure 1.

My recent investigation on the co-solvent effects, encompass the following aspects:

– Probing the effect of the chemical environmental agents on the structure of peptides and proteins by long time scale simulations. In particular, in collaboration with the group of Prof. U. Schwaneberg, I’m studying the effect of dimethyl sulfoxide on the dynamics of monooxygenase P450 BM3.

– Study of the effects of these agents on the conformational equilibrium of peptides (for example, fibrils forming peptides involved in neural-degenerative syndromes). In this case, I would like to explore the details of the secondary structure folding mechanism induced by the presence of these co-solvents.

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Figure 2: Detail of the interaction of DMSO molecules with the Heme iron in the P450 BM3

 

REFERENCES

  1. D. Roccatano Molecular dynamics simulations studies of biomolecules in non-aqueous and cosolvent mixture solutions. Current Peptide and Peptide Science. 9(4), 407-426, (2008).
  2. Kuper, T. S. Wong, D. Roccatano M. Wilmanns, U. Schwaneberg. Understanding the mechanism of organic co-solvent inactivation in heme monooxygenase P450 BM-3 JACS, 129, 5786-5787 (2007).
  3. Roccatano, T. S. Wong, U. Schwaneberg, M. Zacharias. Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study., Biopolymers, 83, 467-476 (2006).
  4. Roccatano, T. S. Wong, U. Schwaneberg, M. Zacharias. Structural and dynamical properties of cytochrome P450 BM3 in pure water and in DMSO/water mixture. Biopolymers, 78, 259-267 (2005).
  5. Di Teodoro, M. Aschi, A. Amadei, D. Roccatano, F. Malatesta, L. Ottaviano. Conformational and electronic properties of a microperoxidase in acqueous solution: A computational study. ChemPhysChem, 6, 681-689 (2005).

About Danilo Roccatano

I have a Doctorate in chemistry at the University of Roma “La Sapienza”. I led educational and research activities at different universities in Italy, The Netherlands, Germany and now in the UK. I am fascinated by the study of nature with theoretical models and computational. For years, my scientific research is focused on the study of molecular systems of biological interest using the technique of Molecular Dynamics simulation. I have developed a server (the link is in one of my post) for statistical analysis at the amino acid level of the effect of random mutations induced by random mutagenesis methods. I am also very active in the didactic activity in physical chemistry, computational chemistry, and molecular modeling. I have several other interests and hobbies as video/photography, robotics, computer vision, electronics, programming, microscopy, entomology, recreational mathematics and computational linguistics.
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