2 research outputs found
Unraveling the Interplay of Extracellular Domain Conformational Changes and Parathyroid Hormone Type 1 Receptor Activation in Class B1 G Protein-Coupled Receptors: Integrating Enhanced Sampling Molecular Dynamics Simulations and Markov State Models
Parathyroid
hormone (PTH) type 1 receptor (PTH1R), as a typical
class B1 G protein-coupled receptor (GPCR), is responsible for regulating
bone turnover and maintaining calcium homeostasis, and its dysregulation
has been implicated in the development of several diseases. The extracellular
domain (ECD) of PTH1R is crucial for the recognition and binding of
ligands, and the receptor may exhibit an autoinhibited state with
the closure of the ECD in the absence of ligands. However, the correlation
between ECD conformations and PTH1R activation remains unclear. Thus,
this study combines enhanced sampling molecular dynamics (MD) simulations
and Markov state models (MSMs) to reveal the possible relevance between
the ECD conformations and the activation of PTH1R. First, 22 intermediate
structures are generated from the autoinhibited state to the active
state and conducted for 10 independent 200 ns simulations each. Then,
the MSM is constructed based on the cumulative 44 μs simulations
with six identified microstates. Finally, the potential interplay
between ECD conformational changes and PTH1R activation as well as
cryptic allosteric pockets in the intermediate states during receptor
activation is revealed. Overall, our findings reveal that the activation
of PTH1R has a specific correlation with ECD conformational changes
and provide essential insights for GPCR biology and developing novel
allosteric modulators targeting cryptic sites
Unraveling the atomic mechanisms underlying glyphosate insensitivity in EPSPS: implications of distal mutations
5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS), as an indispensable enzyme in the shikimate pathway, is the specific target of grasser killer glyphosate (GPJ). GPJ is a competitive inhibitor of phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. A novel Ls-EPSPS gene variant discovered from Liliaceae, named ELs-EPSPS, includes five distal mutations, E112V, D142N, T351S, D425G, and R496G, endowing high GPJ insensitivity. However, the implicit molecular mechanism of the enhanced tolerance/insensitivity of GPJ in ELs-EPSPS is not fully understood. Herein, we try to interpret the hidden molecular mechanism using computational methods. Computational results reveal the enhanced flexibility of apo EPSPS upon mutations. The enhanced affinity of the initial binding substrate shikimate-3-phosphate (S3P), and the higher probability of second ligands PEP/GPJ entering the pocket are observed in the ELs-EPSPS-S3P system. Docking and MD results further confirmed the decreased GPJ-induced EPSPS inhibition upon mutations. And, the alterations of K98 and R179 side-chain orientations upon mutations are detrimental to GPJ binding at the active site. Additionally, the oscillation of side chain K98, in charge of PEP location, improves the proximity effect for substrates in the dual-substrate systems upon mutations. Our results clarify that the enhanced GPJ tolerance of EPSPS is achieved from decreased competitive inhibition of GPJ at the atomic perspective, and this finding further contributes to the cultivation of EPSPS genes with higher GPJ tolerance/insensitivity and a mighty renovation for developing glyphosate-resistant crops. Communicated by Ramaswamy H. Sarma</p