Transition Path Times for the Folding of Nucleic Acids and Proteins Determined from Experimentally-Reconstructed Energy Landscape Profiles

Reconstruction of the Energy Landscape P

Reconstruction of the Energy Landscape Profile for Native Folding of Thepprion Protein from Single-Molecule Force Spectroscopy

✍ Liu, Xia; Yu, Hao; Nath Gupta, Amar; Neupane, Krishna; Brigley, Angela M.; Sosov 📂 Article 📅 2012 🏛 Biophysical Society 🌐 English ⚖ 37 KB

Energy landscape analysis of native fold

Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates

✍ Yu, H.; Gupta, A. N.; Liu, X.; Neupane, K.; Brigley, A. M.; Sosova, I.; Woodside 📂 Article 📅 2012 🏛 National Academy of Sciences 🌐 English ⚖ 880 KB

Determination of side-chain-rotamer and

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method

✍ Urszula Kozłowska; Adam Liwo; Harold A. Scheraga 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 381 KB 👁 1 views

## Abstract In this and the accompanying article, we report the development of new physics‐based side‐chain‐rotamer and virtual‐bond‐deformation potentials which now replace the respective statistical potentials used so far in our physics‐based united‐reside UNRES force field for large‐scale simula

Determination of side-chain-rotamer and

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field

✍ Urszula Kozłowska; Gia G. Maisuradze; Adam Liwo; Harold A. Scheraga 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 674 KB

## Abstract Using the harmonic‐approximation approach of the accompanying article and AM1 energy surfaces of terminally blocked amino‐acid residues, we determined physics‐based side‐chain rotamer potentials and the side‐chain virtual‐bond‐deformation potentials of 19 natural amino‐acid residues wit