Computational Predictions of G Protein-Coupled Receptor Structures and Binding Sites

G protein-coupled receptors (GPCRs) are the largest family of proteins within the human genome. They consist of seven transmembrane (TM) helices, with a N-terminal region of varying length and structure on the extracellular side, and a C-terminus on the intracellular side. GPCRs are involved in transmitting extracellular signals to cells, and as such are crucial drug targets. Designing pharmaceuticals to target GPCRs is greatly aided by full-atom structural information of the proteins. In particular, the TM region of GPCRs is where small molecule ligands (much more bioavailable than peptide ligands) typically bind to the receptors. In recent years nearly thirty distinct GPCR TM regions have been crystallized. However, there are more than 1,000 GPCRs, leaving the vast majority of GPCRs with limited structural information. Additionally, GPCRs are known to exist in a myriad of conformational states in the body, rendering the static x-ray crystal structures an incomplete reflection of GPCR structures. In order to obtain an ensemble of GPCR structures, we have developed the GEnSeMBLE procedure to rapidly sample a large number of variations of GPCR helix rotations and tilts. The lowest energy GEnSeMBLE structures are then docked to small molecule ligands and optimized. The GPCR family consists of five subfamilies with little to no sequence homology between them: class A, B1, B2, C, and Frizzled/Taste2. Almost all of the GPCR crystal structures have been of class A GPCRs, and much is known about their conserved interactions and binding sites. In this work we particularly focus on class B1 GPCRs, and aim to understand that family’s interactions and binding sites both to small molecules and their native peptide ligands. Specifically, we predict the full atom structure and peptide binding site of the glucagon-like peptide receptor and the TM region and small molecule binding sites for eight other class B1 GPCRs: CALRL, CRFR1, GIPR, GLR, PACR, PTH1R, VIPR1, and VIPR2. Our class B1 work reveals multiple conserved interactions across the B1 subfamily as well as a consistent small molecule binding site centrally located in the TM bundle. Both the interactions and the binding sites are distinct from those seen in the more well-characterized class A GPCRs, and as such our work provides a strong starting point for drug design targeting class B1 proteins. We also predict the full structure of CXCR4 bound to a small molecule, a class A GPCR that was not closely related to any of the class A GPCRs at the time of the work.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

First principles based predictions of the toughness of a metal/oxide interface

We describe a first-principles-based strategy to predict the macroscopic toughness of a gamma-Ni(Al)/alpha-Al2O3 interface. Density functional theory calculations are used to ascertain energy changes upon displacing the two materials adjacent to the interface, with relaxation conducted over all atoms located within adjoining rows. Traction/displacernent curves are obtained from derivatives of the energy. Calculations are performed in mode I (opening), mode II (shear) and at a phase angle of 45 degrees. The shear calculations are conducted for displacements along < 110 > and < 112 > of the Ni lattice. A generalized interface potential function is used to characterize the results. Initial fitting to both the shear and normal stress results is required to calibrate the unknowns. Thereafter, consistency is established by using the potential to predict other traction quantities. The potential is incorporated as a traction/displacement function within a cohesive zone model and used to predict the steady-state toughness of the interface. For this purpose, the plasticity of the Ni alloy must be known, including the plasticity length scale. Measurements obtained for a gamma-Ni superalloy are used and the toughness predicted over the full range of mode mixity. Additional results for a range of alloys are used to demonstrate the influences of yield strength and length scale.

First principles based predictions of the toughness of a metal/oxide interface

We describe a first-principles-based strategy to predict the macroscopic toughness of a gamma-Ni(Al)/alpha-Al2O3 interface. Density functional theory calculations are used to ascertain energy changes upon displacing the two materials adjacent to the interface, with relaxation conducted over all atoms located within adjoining rows. Traction/displacernent curves are obtained from derivatives of the energy. Calculations are performed in mode I (opening), mode II (shear) and at a phase angle of 45 degrees. The shear calculations are conducted for displacements along < 110 > and < 112 > of the Ni lattice. A generalized interface potential function is used to characterize the results. Initial fitting to both the shear and normal stress results is required to calibrate the unknowns. Thereafter, consistency is established by using the potential to predict other traction quantities. The potential is incorporated as a traction/displacement function within a cohesive zone model and used to predict the steady-state toughness of the interface. For this purpose, the plasticity of the Ni alloy must be known, including the plasticity length scale. Measurements obtained for a gamma-Ni superalloy are used and the toughness predicted over the full range of mode mixity. Additional results for a range of alloys are used to demonstrate the influences of yield strength and length scale.