Proteins have evolved not only under the pressure to fold rapidly and reversibly into a well-defined overall shape but also for being capable of harnessing thermal energy toward realizing specific structural fluctuations that are functionally oriented. Accordingly, our current understanding of proteins’ function emphasizes the dynamic nature of these biopolymers. Rather than focusing on a single molecular structure, we envision the native state as an ensemble encompassing many distinct structural states. It is the interconversion between these states that enables proteins to change their physico-chemical properties in a controlled fashion, examples of such interconversions are: the open and closed forms of the pore of an ion channel and the bound and unbound forms of an enzyme-substrate complex. Thus, understanding the function of a protein entails, in essence, studying its structural fluctuations and how these change in response to a change in some environment factor, e.g.transmembrane potential, pH, temperature etc. Our research is directed toward the development of methods to effectively describe the structural dynamics of proteins and to perform comparisons within and across distinct protein families.
L. Ponzoni, G. Polles, V. Carnevale, and C. Micheletti. SPECTRUS: a dimensionality reduction approach for identifying dynamical domains in protein complexes from limited structural datasets. Structure, 23:8, 1516-1525, 2015.
A. Zen, V. Carnevale, A. M. Lesk, and C. Micheletti. Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families. PROTEIN SCIENCE 17, 918 (2008).
V. Carnevale, F. Pontiggia, and C. Micheletti. Structural and dynamical alignment of enzymes with partial structural similarity. JOURNAL OF PHYSICS-CONDENSED MATTER 19 (2007).
V. Carnevale, S. Raugei, C. Micheletti, and P. Carloni. Convergent dynamics in the protease enzymatic superfamily. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 128, 9766 (2006).
V. Carnevale, C. Micheletti, F. Pontiggia and R. Potestio Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins. In A. Kolinski editor, Multiscale Approaches to Protein Modeling, Springer Verlag, 2010.
One of the widely accepted explanations of ion selectivity posits that selectivity filters and binding sites are finely tailored to mimic the structure of the first solvation shell of cations. Therefore, the structure of the solvation shell of the Na+ and K+ in aqueous solutions is of great biological relevance. One of my longstanding research interests concerns the physical chemistry of ion solvation. This research is mostly based on ab initioBorn-Oppenheimer molecular dynamics simulations. One of the major focuses of this research concerns the properties of aqua ions in confined (on the nano-scale) environments. The goal is to develop a conceptual framework appropriate to describe ions in protein cavities and in the pore of ion channels. Along these lines, in collaboration with the group of Eric Borguet (Temple University), a leading experimental group in the field of surface spectroscopy of water, we are investigating the properties of water and electrolytes in proximity of charged and hydrophobic interfaces.
A. Bankura, A. Karmakar, V. Carnevale, A Chandra, M.L. Klein Structure, Dynamics, and Spectral Diffusion of Water from First-Principles Molecular Dynamics, JOURNAL OF PHYSICAL CHEMISTRY C, doi:10.1021/jp506120t
S. Dewan, V. Carnevale, A. Bankura, A. Eftekhari-Bafrooei, G. Fiorin, M. L. Klein, E. Borguet. Structure of Water at Charged Interfaces: A Molecular Dynamics Study.LANGMUIR, 2014, 30(27), pp 8056–8065, doi:10.1021/la5011055.
A. Bankura, V. Carnevale, M. L. Klein Hydration structure of Na+and K+from ab initio molecular dynamics based on modern density functional theory. MOLECULAR PHYSICS, doi: 10.1080/00268976.2014.905721.
A. Bankura, V. Carnevale, M. L. Klein Hydration structure of salt solutions from ab initio molecular dynamics JOURNAL OF CHEMICAL PHYSICS 138, 014501 (2013).
V. Carnevale, S. Raugei. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation. JOURNAL OF CHEMICAL PHYSICS 131(22), 225103-225103 (2009).