title: Theoretical study of conformational flexibility of tuftsin in vacuum and in aqueous environment.
abstract: Conformational flexibility of tuftsin molecule is studied using all-atom based atom-atom potential and systematic search, simulated annealing molecular dynamics (SAMD) and molecular dynamics (MD) techniques. Latter was carried out for 650 pico seconds (ps) using AMBER 4.0 with explicit water in TIP3P model. Number of inter-atomic distances and torsional angles were monitored during SAMD and MD simulation. We found that tuftsin molecule, irrespective of any starting conformation, assumes highly folded structure with strong electrostatic interaction between Lys-2 NH3 and Arg-4 carboxylic group and weak hydrogen bond between Lys-2 CO and Arg-4 NH atoms. It had distorted but stable conformation close to inverse gamma turn.
authors.affiliation: Department of Biophysics, All India Institute of Medical Sciences, New Delhi. kothekar@medinst.ernet.in
authors.forename: V
authors.initials: V
authors.lastname: Kothekar
authors.lastname: Ashish
authors.forename: D
authors.initials: D
authors.lastname: Gupta
authors.forename: R
authors.initials: R
authors.lastname: Kishore
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics; D014405:Tuftsin / Q000737:chemistry*; D014618:Vacuum; D014867:Water
chemical_list: D014867:Water; D014405:Tuftsin