2011/07/18 by Kyle A. Beauchamp, Daniel L. Ensign, Rhiju Das +1 · 1 citation
Biochemistry, Genetics and Molecular Biology · Materials Science · Chemistry · #Protein Structure and Dynamics #Enzyme Structure and Function #RNA and protein synthesis mechanisms #Markov chain #Folding (DSP implementation) #Molecular dynamics #Triplet state #Protein folding #Energy transfer #Chemistry #Statistical physics #Chemical physics #Computer science #Physics #Molecule #Computational chemistry
paper · doi:10.1073/pnas.1010880108
openalex publication_date 2011/07/18 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
As the fastest folding protein, the villin headpiece (HP35) serves as an important bridge between simulation and experimental studies of protein folding. Despite the simplicity of this system, experiments continue to reveal a number of surprises, including structure in the unfolded state and complex equilibrium dynamics near the native state. Using 2.5 ms of molecular dynamics and Markov state models, we connect to current experimental results in three ways. First, we present and validate a novel method for the quantitative prediction of triplet-triplet energy transfer experiments. Second, we construct a many-state model for HP35 that is consistent with previous experiments. Finally, we predict contact-formation time traces for all 1,225 possible triplet-triplet energy transfer experiments on HP35.