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MD Simulations of (Membrane) Proteins

The continuous research efforts in Molecular Biophysics have provided an amazing number of solved protein structures. Whether obtained by NMR or X-rays diffraction from protein crystals, these structures are just snapshots of the proteins, often taken in an experimental condition that is far from the real cellular environment in which these proteins perform their function.

These limitations can be partly overcome by applying Molecular Dynamics simulation to the analysis of available protein structures. The field of research is rather mature, with over 40 years of developments and achievements, marked also by the massive employment of open-source software packages, readily available on almost all supercomputer centers in Europe and even on local clusters or desktop computers.

Although theoretical methods are robust, their validation strictly requires a careful comparison with experimental data: in addition, it is actually through this endless interplay between theory and experiments that major advances in molecular biophysics can be achieved. Therefore, all the systems investigated within this research line do feature an experimental counterpart, whether located in Trento or not.

We have developed a particular preference and experience for membrane proteins, but there are no limits: as far as there are reliable data to compare with, we are open to any collaboration with experimental groups around the world and (why not?) even beyond: the fantastic implications of extra-terrestrial life would open an entirely new dream playground for molecular biophysics…


  • D. Alberga, D. Trisciuzzi, G. Lattanzi, J. L. Bennett, A. S. Verkman, G. F. Mangiatordi, O. Nicolotti, Comparative Molecular Dynamics Study of Neuromyelitis Optica – Immunoglobulin G binding to Aquaporin-4 Extracellular Domains, Biochimica et Biophysica Acta (BBA) – Biomembranes 1859, 1326-1334 (2017)
  • G. F. Mangiatordi, D. Alberga, L. Pisani, D. Gadaleta, D. Trisciuzzi, R. Farina, A. Carotti, G. Lattanzi, M. Catto, O. Nicolotti, A rational approach to elucidate human monoamine oxidase molecular selectivity, Eur. J. Pharm. Sci. 101, 90-99 (2017)
  • G. F. Mangiatordi, D. Alberga, D. Trisciuzzi, G. Lattanzi and O. Nicolotti, Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future, Int. J. Mol. Sci. 17:E1119 (2016)
  • Z. Ghaemi, D. Alberga, P. Carloni, A. Laio and G. Lattanzi, Permeability coefficients of lipophilic compounds estimated by computer simulations, J. Chem. Theory Computation 12, 4093-4099 (2016)
  • P. Imbrici, L. Maggi, G. F. Mangiatordi, M. M. Dinardo, C. Altamura, R. Brugnoni, D. Alberga, G. Lauria Pinter, G. Ricci, G. Siciliano, R. Micheli, G. Annicchiarico, G. Lattanzi, O. Nicolotti, L. Morandi, P. Bernasconi, J.-F. Desaphy, R. Mantegazza and D. Conte Camerino, ClC-1 mutations in myotonia congenita patients: insights into molecular gating mechanisms and genotype–phenotype correlation, Journal of Physiology 593, 4181-4199 (2015)
  • G. F. Mangiatordi, D. Alberga, L. Siragusa, L. Goracci, G. Lattanzi and O. Nicolotti, Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields, Biochimica et Biophysica Acta (BBA) – Biomembranes 1848, 1462-1471 (2015)
  • F. Pisani, M. G. Mola, L. Simone, S. Rosito, D. Alberga, G. F. Mangiatordi, G. Lattanzi, O. Nicolotti, A. Frigeri, M. Svelto and G. P. Nicchia, Identification of a Point Mutation Impairing the Binding between Aquaporin-4 and the Neuromyelitis Optica Autoantibodies, The Journal of Biological Chemistry 289, 30578-30589 (2014)
  • D. Alberga, O. Nicolotti, G. Lattanzi, G. P. Nicchia, A. Frigeri, F. Pisani, V. Benfenati, G. F. Mangiatordi, A new gating site in human aquaporin-4: Insights from molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) – Biomembranes 1838, 3052-3060 (2014)
  • G. Cottone, G. Lattanzi, G. Ciccotti and R. Elber, Multiphoton absorption of myoglobin- nitric oxide complex: relaxation by D-NEMD of a stationary state, Journal of Physical Chemistry B 116, 3397-3410 (2012)