Knowledge‐based protein secondary structure assignment

Abstract

We have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers as a standard-of-truth. Comparison to the currently most widely used technique DSSP by Kabsch and Sander (Biopolymers 22:2577-2637, 1983) shows that STRIDE and DSSP assign secondary structural states in 58 and 31% of 226 protein chains in our data sample, respectively, in greater agreement with the specific residue-by-residue definitions provided by the discoverers of the structures while in 11% of the chains, the assignments are the same. STRIDE delineates every 11th helix and every 32nd strand more in accord with published assignments.

High‐Resolution Crystal Structure of a Lasso Peptide

“…A stereochemical analysis of the final peptide structure [18,19] shows that it generally obeys empirically derived parameter ranges for peptide structures [20] with regard to bond lengths, bond and dihedral angles, as well as being consistent with usually observed peptide conformations. All residues fall within most favorable regions of the Ramachandran plot except Trp 13, which falls just outside allowed regions with (f,y) = (À858,À1478).…”

A framework for exhaustively mapping functional missense variants

“…This includes secondary structure, solvent accessibility, burial in interfaces with different interaction partners and involvement in hydrogen bonds or salt bridges with interaction partners. Secondary structures were calculated using Stride (Frishman & Argos, 1995). Solvent accessibility and interface burial were calculated using the GETAREA tool (Fraczkiewicz & Braun, 1998) on the following PDB entries: for UBE2I: 3UIP (Gareau et al , 2012); 4W5V (Boucher et al unpublished); 3KYD (Olsen et al , 2010); 2UYZ (Knipscheer et al , 2007); 4Y1L (Alontaga et al , 2015); for SUMO1: 2G4D (Xu et al , 2006); 2IO2 (Reverter & Lima, 2006); 3KYD (Olsen et al , 2010); 3UIP (Gareau et al , 2012); 2ASQ (Song et al , 2005); 4WJO (Cappadocia et al , 2015); 4WJQ (Cappadocia et al , 2015); 1WYW (Baba et al , 2005); for calmodulin: 3G43 (Fallon  et al , 2009); 4DJC (Sarhan et al , 2012); and for TPK1: 3S4Y (Baker et al , 2001).…”

Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations

“…All runs, except the control runs, were performed at 500 K. Secondary structure was assigned with the program STRIDE. 65 Residues in b-sheet are shown in gray, helical motifs are represented in dark gray, and residues in nonregular or other secondary structure are shown in white.…”

“…64 Secondary structure was assigned with the program STRIDE. 65 Hydrogen bonds were defined for donor (D) ÁÁÁ acceptor (A) distances shorter than 3.2 Å and DÁÁÁHÁÁÁA angles deviating less than 35 from linearity. Pairwise distances between all heavy non-neighbor atoms were calculated for each conformation in the trajectories; two residues were considered to be in contact when at least one heavy atom of one residue was within 4.2 Å of a heavy atom of another residue.…”