title: The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics.
abstract: Currently, considerable interest exists with regard to the dissociation of close packed aminoacids within proteins, in the course of unfolding, which could result in either wet or dry moltenglobules. The progressive disjuncture of residues constituting the hydrophobic core ofcyclophilin from L. donovani (LdCyp) has been studied during the thermal unfolding of the molecule, by molecular dynamics simulations. LdCyp has been represented as a surface contactnetwork (SCN) based on the surface complementarity (Sm) of interacting residues within themolecular interior. The application of Sm to side chain packing within proteins make it a very sensitive indicator of subtle perturbations in packing, in the thermal unfolding of the protein. Network based metrics have been defined to track the sequential changes in the disintegration ofthe SCN spanning the hydrophobic core of LdCyp and these metrics prove to be highly sensitive compared to traditional metrics in indicating the increased conformational (and dynamical) flexibility in the network. These metrics have been applied to suggest criteria distinguishing DMG, WMG and transition state ensembles and to identify key residues involved in crucial conformational/topological events during the unfolding process.
authors.affiliation: Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata, 700064 India.
authors.forename: Sourav
authors.initials: S
authors.lastname: Roy
authors.affiliation: Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata, 700064 India.
authors.forename: Sankar
authors.initials: S
authors.lastname: Basu
authors.affiliation: Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata, 700064 India.
authors.forename: Dipak
authors.initials: D
authors.lastname: Dasgupta
authors.affiliation: Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata, 700064 India.
authors.forename: Dhananjay
authors.initials: D
authors.lastname: Bhattacharyya
authors.affiliation: Saha Institute of Nuclear Physics, Sector 1, Block AF, Bidhannagar, Kolkata, 700064 India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Banerjee
mesh_terms: D021983:Cyclophilins / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D007893:Leishmania donovani / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D015800:Protozoan Proteins / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D015800:Protozoan Proteins; D021983:Cyclophilins