Activation mechanism of the human Smoothened receptor

Bansal, Prateek; Dutta, Soumajit; Shukla, Diwakar

doi:10.1016/j.bpj.2023.03.007

Cited by 13 publications

(21 citation statements)

References 110 publications

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“…Later, Bansal et al also showed that this cation−π interaction is broken in active SMO by using an active SMO structure for preparing the system. 52 However, no such correlation has been observed in our data. This interaction was broken in the cholesterol-free system and in the system with cholesterol bound to both the CRD and the TMD.…”

Section: ■ Discussioncontrasting

confidence: 82%

“…A cation−π (ionic-lock) interaction between R451 in TM6 and W535 in TM7 (Supporting Information Figure S7), reported in some of the crystal and cryo-EM structures of SMO, has been hypothesized to characterize the cholesterol-free inactive state of SMO and has been suggested to break during its cholesterol-binding-induced transition to the active state. ,, This ionic-lock was monitored by measuring the distance between the COMs of the positively charged guanidine group of R451 and the indole group of W535. This distance was 0.44 nm in the modeled SMO structure, which was used for the preparation of all simulated systems.…”

Section: Resultsmentioning

confidence: 99%

“…The salt-bridge interactions between D473 (TM6), R400 (TM5), and E518 (TM7) constitute a D-R-E network 52 situated at the extracellular end of TMD (Supporting Information Figure S7). Variations in the distances between the COMs of the side chains of interacting residues, observed in the simulation trajectories of all of the systems, were examined to understand the role of cholesterol binding on the D-R-E network (Figure 8).…”

Section: The Primacy Of Interaction Shifts From D-r To E-r Within The...mentioning

confidence: 99%

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Putative Role of Cholesterol in Shaping the Structural and Functional Dynamics of Smoothened (SMO)

Kumari,

Mitra,

Bulusu

2023

J. Phys. Chem. B

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The smoothened (SMO) receptor belongs to the superfamily of class F G protein-coupled receptors (GPCRs) and is a potential drug target in several types of cancer. It has two ligand binding sites, respectively, in the cysteine-rich domain (CRD) and the transmembrane domain (TMD). It has been shown that cholesterol is important for its activation and function. However, the molecular-level understanding of SMO dynamics in the presence of cholesterol has not been explored in sufficient detail. In this work, we have carried out atomistic molecular dynamics simulations totaling 3.6 μs to analyze the effect of cholesterol binding to TMD and/or CRD on the structure and dynamics of the SMO receptor. Our results show that the presence of cholesterol in the CRD and TMD, respectively, alters the conformational dynamics of SMO differently. We reported that the reorganization of the D-R-E network at the extracellular end of the TMD is important for the high activity of SMO. In general, the transmembrane helices 5, 6, and 7 and helix 8 are most affected, which, in turn, leads to changes in the CRD and intracellular cytoplasmic domain (ICD) dynamics patterns depending on the presence or absence of cholesterol in the CRD and/or the TMD. We have also reported that the interaction of membrane lipids with SMO is different in different SMO states. These results agree with the experimental structural observations and data of cholesterol-bound and unbound structures of SMO and add to our molecular understanding of the SMO−cholesterol interaction.

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Section: ■ Discussioncontrasting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: The Primacy Of Interaction Shifts From D-r To E-r Within The...mentioning

confidence: 99%

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Putative Role of Cholesterol in Shaping the Structural and Functional Dynamics of Smoothened (SMO)

Kumari,

Mitra,

Bulusu

2023

J. Phys. Chem. B

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“…To perform adaptive sampling and markov state model (MSM) building (Discussed in the following sections), protein conformations in MD system need to be represented by the descriptors that can capture protein conformational changes. To find the descriptors, we have implemented residue-residue contact score (RRCS) analysis 66 , 67 . Using RRCS method, a score was assigned to each residue pair distances for a particular protein conformation which are more than one helical tern away.…”

Section: Methodsmentioning

confidence: 99%

“…Thus, to capture the entire protein conformational ensemble, adaptive sampling protocol was implemented 72 – 75 . Adaptive sampling is a well established sampling technique used for studying ligand binding 76 – 78 , protein conformational change 67 , 68 , 79 – 81 and ligand selectivity 82 . First, conformations obtained from MD simulations are expressed in terms of collective variables.…”

Section: Methodsmentioning

confidence: 99%

Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors

Dutta

Shukla

2023

Commun Biol

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Design of cannabinergic subtype selective ligands is challenging because of high sequence and structural similarities of cannabinoid receptors (CB1 and CB2). We hypothesize that the subtype selectivity of designed selective ligands can be explained by the ligand binding to the conformationally distinct states between cannabinoid receptors. Analysis of ~ 700 μs of unbiased simulations using Markov state models and VAMPnets identifies the similarities and distinctions between the activation mechanism of both receptors. Structural and dynamic comparisons of metastable intermediate states allow us to observe the distinction in the binding pocket volume change during CB1 and CB2 activation. Docking analysis reveals that only a few of the intermediate metastable states of CB1 show high affinity towards CB2 selective agonists. In contrast, all the CB2 metastable states show a similar affinity for these agonists. These results mechanistically explain the subtype selectivity of these agonists by deciphering the activation mechanism of cannabinoid receptors.

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Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations

et al. 2023

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The class Frizzled of G protein-coupled receptors (GPCRs), consisting of ten Frizzled (FZD1-10) paralogs and Smoothened, remains one of the most enigmatic GPCR families. This class mediates signaling predominantly through Disheveled (DVL) or heterotrimeric G proteins. However, the mechanisms underlying pathway selection are elusive. Here we employ a structure-driven mutagenesis approach in combination with an extensive panel of functional signaling readouts to investigate the importance of conserved state-stabilizing residues in FZD5 for signal specification. Similar data were obtained for FZD4 and FZD10 suggesting that our findings can be extrapolated to other members of the FZD family. Comparative molecular dynamics simulations of wild type and selected FZD5 mutants further support the concept that distinct conformational changes in FZDs specify the signal outcome. In conclusion, we find that FZD5 and FZDs in general prefer coupling to DVL rather than heterotrimeric G proteins and that distinct active state micro-switches in the receptor are essential for pathway selection arguing for conformational changes in the receptor protein defining transducer selectivity.

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Activation mechanism of the human Smoothened receptor

Cited by 13 publications

References 110 publications

Putative Role of Cholesterol in Shaping the Structural and Functional Dynamics of Smoothened (SMO)

Putative Role of Cholesterol in Shaping the Structural and Functional Dynamics of Smoothened (SMO)

Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors

Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations

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