MS-EVB
(Multi-state Empirical Valence Bond)
Development and application of a unique Molecular dynamics (MD) simulation methodology for studying proton transport ("translocation") in biomolecular systems is of utmost importance. Proton translocation is a process of fundamental importance in biology, which generally occurs via proton shuttling over significant distances (ten or more Angstroms) through intervening water molecules and ionizable amino acid residues. This shuttling process creates an enormous challenge for standard MD simulations because of the dynamically changing bonding topologies occurring over numerous molecular groups. However, by virtue of our Multi-state Empirical Valence Bond (MS-EVB) approach, this challenge has now been met so that explicit proton transport can now be simulated using the MD method.
CcO
(Cytochrome c Oxidase)
CcO, the membrane -bound terminal enzyme of the respiratory chain, catalyzes the reduction of oxygen to water in a process coupled to translocation of protons across the cell membrane. Our current research interest lays in modeling of explicit proton translocation through one of the proton-conducting pathways: the D-pathway.
gA
Gramicidin A
Gramicidin A, being the smallest ion channel known with detailed structures so far, is an ideal model channel for studying proton transport (PT) through a single water wire inside the channel. Our current research interest is to investigate PT through a single water wire and the influence from the membrane in PT process through gA.