Improvement of Structure-Based Potentials for Protein Folding by Native and Nonnative Hydrogen Bonds

Search for the most stable folds of prot

Search for the most stable folds of protein chains: III. Improvement in fold recognition by averaging over homologous sequences and 3D structures

✍ D.S. Rykunov; M.Yu. Lobanov; A.V. Finkelstein 📂 Article 📅 2000 🏛 John Wiley and Sons 🌐 English ⚖ 180 KB 👁 1 views

Evidence for the Preservation of Native

Evidence for the Preservation of Native Inter- and Intra-Molecular Hydrogen Bonds in the Desolvated FK-Binding Protein·FK506 Complex Produced by Electrospray Ionization

✍ Jonathan T. S. Hopper, Andrew Rawlings, José P. Afonso, Deborah Channing, Robert 📂 Article 📅 2012 🏛 Elsevier Science 🌐 English ⚖ 455 KB

Structures of randomly generated mutants

Structures of randomly generated mutants of T4 lysozyme show that protein stability can be enhanced by relaxation of strain and by improved hydrogen bonding via bound solvent

✍ Philip Pjura; Brian W. Matthews 📂 Article 📅 1993 🏛 Cold Spring Harbor Laboratory Press 🌐 English ⚖ 606 KB

## Abstract The structures of three mutants of bacteriophage T4 lysozyme selected using a screen designed to identify thermostable variants are described. Each of the mutants has a substitution involving threonine. Two of the variants, Thr 26 → Ser (T26S) and Thr 151 → Ser (T151S), have increased r

Mapping the Structure of Folding Cores i

Mapping the Structure of Folding Cores in TIM Barrel Proteins by Hydrogen Exchange Mass Spectrometry: The Roles of Motif and Sequence for the Indole-3-glycerol Phosphate Synthase from Sulfolobus solfataricus

✍ Zhenyu Gu; Jill A. Zitzewitz; C. Robert Matthews 📂 Article 📅 2007 🏛 Elsevier Science 🌐 English ⚖ 999 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