A quantum mechanical study of different concerted mechanisms of peptide release in the ribosome has been carried out using the M06-2X density functional. Reoptimization with MP2 has also been carried out for the stationary points of some selected mechanisms. The uncatalyzed processes in solution have been treated with the SMD solvation model. We conclude that the 2'-OH plays an important catalytic role and that it takes place via a zwitterionic transition state, this TS being stabilized by the presence of oxyanion holes or by the solvent. The comparison with our previous study on the peptide bond formation shows that both processes proceed via two different mechanisms, in such a way that the TS of the aminolysis has an ion-pair instead of a zwitterionic character. So, despite the limitations of the model we have used, we can conclude that there is catalytic promiscuity at the peptidyl transferase center (PTC) of the ribosome.
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http://dx.doi.org/10.1021/jp3110248 | DOI Listing |
J Chem Inf Model
January 2025
Industrial and Molecular Pharmaceutics, Purdue University, West Lafayette, Indiana 47907, United States.
Drug-drug interaction can lead to diminished therapeutic effects or increased toxicity, posing significant risks, especially in polypharmacy, and cytochrome P450 plays an indispensable role in this interaction. Cytochrome P450, responsible for the metabolism and detoxification of most drugs, metabolizes about 90% of Food and Drug Administration-approved drugs, making early detection of potential drug-drug interactions. Over the years, in-silico modeling has become a valuable tool for predicting drug-drug interactions.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
The Effective Fragment Potential (EFP) method, a polarizable quantum mechanics-based force field for describing non-covalent interactions, is utilized to calculate protein-ligand interactions in seven inactive cyclin-dependent kinase 2-ligand complexes, employing structural data from molecular dynamics simulations to assess dynamic and solvent effects. Our results reveal high correlations between experimental binding affinities and EFP interaction energies across all the structural data considered. Using representative structures found by clustering analysis and excluding water molecules yields the highest correlation (R2 of 0.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromso̷ N-9037, Norway.
We introduce a method for computing quantum mechanical forces through surface integrals over the stress tensor within the framework of the density functional theory. This approach avoids the inaccuracies of traditional force calculations using the Hellmann-Feynman theorem when applied to multiresolution wavelet representations of orbitals. By integrating the quantum mechanical stress tensor over surfaces that enclose individual nuclei, we achieve highly accurate forces that exhibit superior consistency with the potential energy surface.
View Article and Find Full Text PDFACS Cent Sci
January 2025
College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
Multicomponent reactions (MCRs), highly sought-after methods to produce atom-, step-, and energy-economic organic syntheses, have been developed extensively. However, catalytic asymmetric MCRs, especially those involving radical species, remain largely unexplored owing to the difficulty in stereoselectively regulating the extraordinarily high reactivity of open-shell radical species. Herein, we report a conceptually novel catalytic asymmetric three-component radical cascade reaction of readily accessible glycine esters, α-bromo carbonyl compounds and 2-vinylcyclopropyl ketones via synergistic photoredox/Brønsted acid catalysis, in which three sequential C-C (σ/π/σ) bond-forming events occurred through a radical addition/ring-opening/radical-radical coupling protocol, affording an array of valuable enantioenriched unnatural α-amino acid derivatives bearing two contiguous stereogenic centers and an alkene moiety in moderate to good yield with high diastereoselectivity, excellent enantioselectivity and good -dominated geometry under mild reaction conditions.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.
Atomic polarizabilities are considered to be fundamental parameters in polarizable molecular mechanical force fields that play pivotal roles in determining model transferability across different electrostatic environments. In an earlier work, the atomic polarizabilities were obtained by fitting them to the B3LYP/aug-cc-pvtz molecular polarizability tensors of mainly small molecules. Taking advantage of the recent PCMRESPPOL method, we refine the atomic polarizabilities for condensed-phase simulations using a polarizable Gaussian Multipole (pGM) force field.
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