De novo structure generation using chemical shifts for proteins with high‐sequence identity but different folds

Abstract

Proteins with high-sequence identity but very different folds present a special challenge to sequence-based protein structure prediction methods. In particular, a 56-residue three-helical bundle protein (GA 95 ) and an a/b-fold protein (GB 95 ), which share 95% sequence identity, were targets in the CASP-8 structure prediction contest. With only 12 out of 300 submitted server-CASP8 models for GA 95

Polymorphic Triple β-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid β42 Peptide

“…Highly polymorphic protein structures pose challenges for computational prediction and experimental identification. The information contained in NMR chemical shifts has already been demonstrated to assist in pro- tein fold prediction and identification (40). Our work focuses on the misfolded A␤ aggregate conformations.…”

A structurally dynamic N-terminal region drives function of the staphylococcal peroxidase inhibitor (SPIN)

“…The secondary structure of SPIN was predicted using the TALOS-N platform (18,19). Likewise, the CS-Rosetta Server (Rosetta v3.8, CSRosetta Toolbox v3.3) was used to generate 40,000 independent models for three-dimensional structure of SPIN (40,41) consistent with the chemical shift data. This approach was used because the NMR spectra collected on SPIN were not sufficient to permit experimental determination of its structure.…”

An improved algorithm for MFR fragment assembly

“…This has been demonstrated using the CHESHIRE algorithm (Cavalli et al 2007), which uses secondary structure information and secondary chemical shift derived backbone conformations together with Monte Carlo structure generation or the CS-ROSETTA methodology (Shen et al 2008(Shen et al , 2009(Shen et al , 2010 which combines mining the PDB database for homologous peptide fragments using the MFR approach with the Monte Carlo type fragment assembly of this MFR fragment library by the ROSETTA software system (Simons et al 1999;Rohl et al 2004;Leaver-Fay et al 2011).…”