Saturday, 2 April 2022

Covalents, patches and N-O-S bridges in PyRosetta

Crosslinked residues are common, but for sure make up for it by being simultaneously highly intriguing and highly technically problematic. Oddly, I seem to keep bumping into them. During my PhD a decade ago I saw a talk by the father of Kiwi structural biochemistry, Ted Baker, about a curious case where they found an isopeptide bonds hidden in their crystal density. In a postdoc I worked with isopeptide bonds —I blogged about isopeptide bonds in Rosetta four years ago. During the start of the pandemic I dis some covalent-docking of compounds with PyRosetta for the Covid Moonshoot project, which evolved into Fragmenstein. Most tools have a hard time with crosslinks. And last month the Twittersphere was abuzz with the news of lysine-hydroxylcysteine (N-O-S) bridges in protein.

PyMOL will strip LINK entries from PDBs on saving while NGL obeys only CONECT entries in PBDs. An exception is PyRosetta: it behaves very nicely with disulfides, isopeptide bonds ( cf. repo of PyRosetta code from Keeble et al.) and other crosslinks —mostly. As a result I thought I'd add a note on how to add them in PyRosetta.