Journal Article

Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

Sun, Xianqiang, Blumer, Kendall J, Bowman, Gregory R, Singh, Sukrit

2018

Overview

Activation of heterotrimeric G proteins is a key step in many signaling cascades. However, a complete mechanism for this process, which requires allosteric communication between binding sites that are ~30 Å apart, remains elusive. We construct an atomically detailed model of G protein activation by combining three powerful computational methods: metadynamics, Markov state models (MSMs), and CARDS analysis of correlated motions. We uncover a mechanism that is consistent with a wide variety of structural and biochemical data. Surprisingly, the rate-limiting step for GDP release correlates with tilting rather than translation of the GPCR-binding helix 5. β-Strands 1 – 3 and helix 1 emerge as hubs in the allosteric network that links conformational changes in the GPCR-binding site to disordering of the distal nucleotide-binding site and consequent GDP release. Our approach and insights provide foundations for understanding disease-implicated G protein mutants, illuminating slow events in allosteric networks, and examining unbinding processes with slow off-rates. Cells communicate with each other by exchanging chemical signals, which allow them to coordinate their activities and relay important information about their environment. Often, cells secrete specific signals into their surroundings, which are then picked up by a receiving cell that has the right receptors to recognize the message. Once the signal attaches to the receptor, its shape or activity changes, which in turn triggers cascades inside the cell to convey the signal, much like a circuit would. A group of proteins called heterotrimeric G-proteins play an important role in these pathways. They act as molecular switches inside the cells to help transmit signals from the outside of the cell to the inside. The proteins are made up of three parts, one of which is G-alpha. When G-alpha receives a signal from its receptor, it becomes activated. To turn on, G-alpha needs to release a molecule called GDP – which is bound to G-alpha when turned off – and instead bind to another molecule called GTP. However, it remains unclear how exactly GDP is released when it receives a signal from its receptor. Faulty G-alphas have been linked to many diseases, including cancer and heart conditions. However, current treatments do not currently target this part of G-protein signaling. To develop new drugs in the future, we first need a better understanding about the critical steps driving G-alpha activation, such as the release of GDP. Now, Sun, Singh et al. used computer simulations and mathematical models to investigate how G-alpha is activated, and to identify the structural changes underlying the release of GDP. The simulations allow to observe how the atoms within G-alpha behave and were obtained from citizen-scientist volunteers, who ran simulations on their personal computers using the Folding@home app. Together, they generated an enormous amount of data that would normally take over 150 years to collect with one computer. Subsequent analyses identified the critical atomic motions driving the release of GDP and a network of amino acids located within G-alpha. These amino acids allow G-alpha to act like a switch and connect the part that receives the signal from the receptor to the GDP-binding site. In the future, this model could serve as a platform for developing drugs that target G-alpha and shed more light into how signals are transmitted within our cells.

• Publisher: eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Allosteric properties / Allosteric Regulation / allostery / Binding Sites / Computational and Systems Biology / Computer applications / Entropy / G protein-coupled receptors / G proteins / GTP-Binding Protein alpha Subunits, Gq-G11 - chemistry / GTP-Binding Protein alpha Subunits, Gq-G11 - metabolism / GTP-Binding Proteins - chemistry / GTP-Binding Proteins - metabolism / Guanosine Diphosphate - chemistry / Guanosine Diphosphate - metabolism / Markov Chains / Markov state models / molecular dynamics / Molecular Dynamics Simulation / NMR / Nuclear magnetic resonance / Probability / Protein Structure, Secondary / Proteins / Receptors, G-Protein-Coupled - chemistry / Receptors, G-Protein-Coupled - metabolism / Structural Biology and Molecular Biophysics / Thermodynamics