Correcting cis-trans-transgressions in macromolecular structure models

Many macromolecular X-ray and cryo-EM structure models deposited in the PDB contain biologically relevant small molecule ligands with unsaturated fatty acid acyl chains, whose cis-trans stereochemistry is incorrect. The molecules are either not properly defined in their stereochemical restraint files, or the proper stereochemistry is neglected during model building. Often, the same molecules appear in deposited models in both isomeric configurations, one of which is almost always incorrect, and the use of the same moiety (HET) identifier and restraint files in model refinement is wrong. We present case studies of frequently occurring molecules and a compilation of identified cases of C-C=C-C cis-trans geometry in the deposited structure models. Full listings of cis/trans torsion angles are provided for models with commonly occurring molecules to assist identification and correction of cis-trans errors and prevent inadvertent use of incorrect models. Caveats for users, advice for modellers and suggestions for remediation efforts with a simple but effective restraint file modification are provided.

The Constructions and Pyrolysis of 3D Kerogen Macromolecular Models: Experiments and Simulations

Kerogens are extracted from deep shales to study pyrolysis of deep shale samples. The 2D molecular models of kerogens are obtained by a series of physical and chemical experiments by which the macromolecular models of kerogens are constructed. Then, the reasonable 3D macromolecular models are established by molecular mechanics and global energy minimization. The effects of temperature and heating rate on the chemical kinetics of kerogen pyrolysis are studied using reactive force field (ReaxFF). The hybrid molecular dynamics/force-biased Monte Carlo (MD/fbMC) approach is used to simulate the pyrolytic process at the experimental temperature, which is lower than the conventional one. The gaseous products and residues obtained by the simulations agree with the experimental results, which means a reliable simulation method for pyrolysis at experimental temperature is provided. This study constructs the rational macromolecular models of kerogen by experiments, and proposes the mechanisms of typical reactions of kerogen pyrolysis, which may help in understanding the formation of shale oil and gas.