Loop prediction for a GPCR homology model: Algorithms and results

We present loop structure prediction results of the intracellular and extracellular loops of four G‐protein‐coupled receptors (GPCRs): bovine rhodopsin (bRh), the turkey β1‐adrenergic (β1Ar), the human β2‐adrenergic (β2Ar) and the human A2a adenosine receptor (A2Ar) in perturbed environments. We used the protein local optimization program, which builds thousands of loop candidates by sampling rotamer states of the loops' constituent amino acids. The candidate loops are discriminated between with our physics‐based, all‐atom energy function, which is based on the OPLS force field with implicit solvent and several correction terms. For relevant cases, explicit membrane molecules are included to simulate the effect of the membrane on loop structure. We also discuss a new sampling algorithm that divides phase space into different regions, allowing more thorough sampling of long loops that greatly improves results. In the first half of the paper, loop prediction is done with the GPCRs' transmembrane domains fixed in their crystallographic positions, while the loops are built one‐by‐one. Side chains near the loops are also in non‐native conformations. The second half describes a full homology model of β2Ar using β1Ar as a template. No information about the crystal structure of β2Ar was used to build this homology model. We are able to capture the architecture of short loops and the very long second extracellular loop, which is key for ligand binding. We believe this the first successful example of an RMSD validated, physics‐based loop prediction in the context of a GPCR homology model. Proteins 2013. © 2012 Wiley Periodicals, Inc.