title: For the sequence YKGQ, the turn and extended conformational forms are separated by small barriers and the turn propensity persists even at high temperatures: implications for protein folding.
abstract: The folding of the sequence (21)DTVKLMYKGQPMTFR(35) from staphylococcal nuclease into a β-hairpin, nucleated by the turn region YKGQP, is known to be an early folding event. With YKGQ being the shortest sequence for a β-turn model and in view of its importance to the folding of staphylococcal nuclease, we investigated the thermodynamics of turn formation at a range of temperatures from 280 to 380 K, with a regular interval of 10 K. Eleven independent molecular dynamics simulations (under NPT conditions) were performed using the GROMACS package of programs and the OPLS-AA/L all-atom force field, each for a time period of 1 μs. Turn formation is supported by enthalpy at lower temperatures, while entropy supports it at higher temperatures. There are modest free energy barriers between turn and extended conformational ensembles. The turn propensity persists even at elevated temperatures. The role of proline in driving the turn formation has been re-examined, and it is inferred that the absence of proline does not affect turn propensity.
authors.affiliation: Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India.
authors.forename: Harpreet
authors.initials: H
authors.lastname: Kaur
authors.forename: Yellamraju U
authors.initials: YU
authors.lastname: Sasidhar
mesh_terms: D000595:Amino Acid Sequence; D057927:Hydrophobic and Hydrophilic Interactions; D008836:Micrococcal Nuclease / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D013696:Temperature; D013816:Thermodynamics
chemical_list: D010455:Peptides; D008836:Micrococcal Nuclease