Internal water channel formation in CXCR4 is crucial for Gi-protein coupling upon activation by CXCL12

Abstract

Chemokine receptor CXCR4 is a major drug target for numerous diseases because of its involvement in the regulation of cell migration and the developmental process. In this study, atomic-level molecular dynamics simulations were used to determine the activation mechanism and internal water formation of CXCR4 in complex with chemokine CXCL12 and Gi-protein. The results indicated that CXCL12-bound CXCR4 underwent transmembrane 6 (TM6) outward movement and a decrease in tyrosine toggle switch by eliciting the breakage of hydrophobic layer to form a continuous internal water channel. In the GDP-bound Gαi-protein state, the rotation and translation of the α5-helix of Gαi-protein toward the cytoplasmic pocket of CXCR4 induced an increase in interdomain distance for GDP leaving. Finally, an internal water channel formation model was proposed based on our simulations for CXCL12-bound CXCR4 in complex with Gαi-protein upon activation for downstream signaling. This model could be useful in anticancer drug development.

Valine-279 Deletion–Mutation on Arginine Vasopressin Receptor 2 Causes Obstruction in G-Protein Binding Site: A Clinical Nephrogenic Diabetes Insipidus Case and Its Sub-Molecular Pathogenic Analysis

“…This and previous results [ 37 ] are consistent with our MD simulations. Similar findings were confirmed by mutagenesis experiments and MD simulations, suggesting that the mutations at L244 6.40 P and L246 6.42 P of the chemokine receptor CXCR4 do not affect its CXCL12 ligand-binding but noticeably reduce the calcium flux, leading to CXCR4 inactivation [ 25 , 45 , 46 ]. Very recently, Wang et al reported a cryo-EM structure of AVP-AVPR2-G s complex [ 20 ].…”

“…A previous study has shown that apo AVPR2-WT has constitutive activity and its mutant (AVPR2-D136A) has 2- to 3-fold higher constitutive activity in the absence of agonists [ 26 ]. In addition, the outward dynamic movement of the transmembrane helix 6 (TM6), which enlarges the cytoplasmic region of GPCR to facilitate G-protein coupling, is key to GPCR activation [ 25 , 27 , 28 , 29 , 30 , 31 ].…”

“…Lennard–Jones and short-range Coulomb interactions were cut off at 1.4 and 1.0 nm, respectively. The detailed MD simulation equilibration procedures were in the following based on our previous studies [ 23 , 24 , 25 ]: (i) temperatures were gradually increased from 100 to 200 K, then to 310 K, and systems were run for 500 ps under each temperature. During these simulations, complex structures remained fully restrained ( k = 1000 kJ·mol −1 ·nm −2 ); (ii) at 310 K, restraints on the structure via the force constant k were gradually released starting from k = 500 kJ·mol −1 ·nm −2 to 250 kJ·mol −1 ·nm −2 , and then to 100 kJ·mol −1 ·nm −2 .…”

Combinatorial Virtual Screening Revealed a Novel Scaffold for TNKS Inhibition to Combat Colorectal Cancer

“…The MM/PBSA binding energies of the TNKS inhibitors were calculated using the GROMACS program tool g_mmpbsa [ 19 ]. More detailed settings of the free energy calculations were described in our previous studies [ 20 , 21 , 22 ].…”

Computer-aided discovery, design, and investigation of COVID-19 therapeutics

“…As a result, in some cases, MD simulations, which calculate more detailed interaction energies, are required for providing complementary to molecular docking and more reliable results [ 25 ]. MD simulations can be used independently for investigations of conformational changes of specific molecules over a period of time [ 26 27 ]. These simulations can also be applied to optimize the structures of final complexes from molecular docking and provide insights of the ligand binding mechanism [ 23 25 28 ].…”