Stereochemical errors and their implications for molecular dynamics simulations

<p>Abstract</p> <p>Background</p> <p>Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations.</p> <p>Results</p> <p>Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules.</p> <p>Conclusions</p> <p>Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.</p

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

SummaryA novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented. The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically correct. The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are introduced. The MDFF method is then used to obtain high-resolution structures of the E. coli ribosome in different functional states imaged by cryo-EM

Investigating the mechanisms of protein synthesis using multi-resolution structural data

The ribosome is a complex, dynamic molecular machine responsible for protein synthesis in all cells according to the genetic information. Recent breakthroughs in ribosome crystallography culminated with the 2009 Nobel Prize in Chemistry. Concomitantly, advances in cryo-electron microscopy (cryo-EM) enabled the determination of images of the ribosome trapped in functional states at ever increasing resolution. In order to study different aspects of ribosome function at the atomic level, we developed the molecular dynamics flexible fitting (MDFF) method that combines X-ray and cryo-EM data, furnishing atomic models of the ribosome corresponding to functional intermediates. The MDFF-derived atomic models, combined with molecular dynamics simulations and other computational techniques, allowed us to address different research questions presented in this thesis. First, we found how ribosome-induced changes in the structure of elongation factor Tu leads to its GTPase activation, a crucial step in the decoding of genetic information. Next, we investigated structural and regulatory aspects of ribosomes in complex with a protein-conducting channel, which transports certain nascent proteins across or into membranes. Another area of investigation was the recognition of a regulatory nascent chain by the ribosome, as well as the mechanism by which it leads to translational stalling. Finally, we studied intermediate states of translocation of messenger and transfer RNAs through the ribosome, reconciling data from cryo-EM and single-molecule experiments