Dynamics and Mechanism of Binding of Androstenedione to Membrane-Associated Aromatase

Abstract

Aromatase (CYP19A1) catalyzes the synthesis of estrogens from androgens and is an invaluable target of pharmacotherapy for estrogen-dependent cancers. CYP19A1 is also one of the most primordial human CYPs and, to the extent that its fundamental dynamics are conserved, is highly relevant to understanding those of the more recently evolved and promiscuous enzymes. A complementary approach employing molecular dynamics simulations and hydrogen–deuterium exchange mass spectrometry (HDX-MS) was employed to interrogate the changes in CYP19A1 dynamics coupled to binding androstenedione (ASD). Gaussian-accelerated molecular dynamics and HDX-MS agree that ASD globally suppresses CYP19A1 dynamics. Bimodal HDX patterns of the B′–C loop potentially arising from at least two conformations are present in free 19A1 only, supporting the possibility that conformational selection is operative. Random-acceleration molecular dynamics and adaptive biasing force simulations illuminate ASD’s binding pathway, predicting ASD capture in the lipid headgroups and a pathway to the active site shielded from solvent. Intriguingly, the predicted access channel in 19A1 aligns well with the steroid binding sites of other human sterol-oxidizing CYPs.

Gaussian accelerated molecular dynamics: Principles and applications

“…These results were further verified in animal cell culture experiments and in cancer patients. Overall, GaMD simulations elucidated the molecular mechanisms of ligand binding in EGFR mutations for treatment of nonsmall cell lung carcinomas, as well as many other protein–ligand interactions 55,56,73–76 …”

“…Overall, GaMD simulations elucidated the molecular mechanisms of ligand binding in EGFR mutations for treatment of nonsmall cell lung carcinomas, as well as many other protein-ligand interactions. 55,56,[73][74][75][76]…”

“…In this review, we will present the principles and the most recent applications of GaMD. Robust GaMD has been established for advanced simulation studies of a wide range of biomolecular systems, especially the protein-nucleic acid interactions [63][64][65] such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene-editing system, 66,67 protein-protein/peptide interactions, [68][69][70][71][72] protein-ligand binding, 55,56,[73][74][75][76] protein folding, 77 protein enzymes, 52,58,[78][79][80][81][82][83][84][85][86][87][88][89][90][91][92] membrane proteins (including GPCRs, 68,69,73,76,[93][94][95] ion channels, 53,96 and γ-secretase 97 ) and carbohydrates, [98][99][100]…”

Combining Small-Molecule Bioconjugation and Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) to Expose Allostery: the Case of Human Cytochrome P450 3A4

“…Paco et al have recently reported EX1 behavior in the B′ helix of P450 aromatase, noting that the bimodal isotope distribution was abolished in the presence of the substrate. 52 The observation of EX1 kinetics in the B′ helix of different CYPs could suggest the existence of a conserved dynamic feature that is sensitive to ligand binding. Moving forward, it will be interesting to examine the extent to which the conformational dynamics revealed in the present study are shared by other CYPs.…”

Long Range Communication between the Drug-Binding Sites and Nucleotide Binding Domains of the Efflux Transporter ABCB1

“…For determining significantly affected peptides, a 95% confidence interval based on the average of standard deviations across all peptides per sample was used as in previous cases of small changes in uptake. 27 , 40 , 41 Peptides with two or more significantly different timepoints and a sum percent deuteration greater than ±3 were determined as affected unless trends were inconsistent for highly overlapping peptides or different charge states.…”