Background: 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.
Results: 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.
Conclusions: 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.
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http://dx.doi.org/10.1186/1471-2105-12-190 | DOI Listing |
Molecules
January 2025
GSK Carbon Neutral Laboratories for Sustainable Chemistry, Jubilee Campus, University of Nottingham, Triumph Road, Nottingham NG7 2TU, UK.
The range of chemical databases available has dramatically increased in recent years, but the reliability and quality of their data are often negatively affected by human-error fidelity. The size of chemical databases can make manual data curation/checking of such sets time consuming; thus, automated tools to help this process are highly desirable. Herein, we propose the use of Graph Neural Networks (GNNs) to identifying potential stereochemical misassignments in the primary asymmetric catalysis literature.
View Article and Find Full Text PDFAcc Chem Res
January 2025
College of Chemistry, Sichuan University, Chengdu 610065, P. R. China.
Chirality
November 2024
Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São José do Campos, São Paulo, Brazil.
Fargesin is an important bioactive furofuran lignan isolated from different plant species. Despite presenting potent biological activities, its stereochemical characterization has relied mostly on empirical correlations of optical rotation, an approach considered risky that commonly leads to misassignments and error propagation. Additionally, the enantiomeric purity of fargesin isolates used for biological assays has not been previously investigated.
View Article and Find Full Text PDFCarbohydrates, vital components of biological systems, are well-known for their structural diversity. Nuclear Magnetic Resonance (NMR) spectroscopy plays a crucial role in understanding their intricate molecular arrangements and is essential in assessing and verifying the molecular structure of organic molecules. An important part of this process is to predict the NMR chemical shift from the molecular structure.
View Article and Find Full Text PDFAnal Chem
July 2024
Hubei Engineering Technology Research Centre of Energy Polymer Materials, Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, South-Central Minzu University, Wuhan 430074, P. R. China.
Both solitary and tandem applications of residual chemical shift anisotropy (RCSA) and residual dipolar coupling (RDC) show great potential for the structural and configurational determination of organic molecules. A critical component of both RDC and RCSA methodologies is the alignment medium, whose availability is limited, especially for RCSA measurement. Moreover, reported RDC and RCSA acquisitions mainly rely on two experiments conducted under two different conditions, which are relatively time-consuming and easily cause experimental errors.
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