A Refined Model of the Thyrotropin-Releasing Hormone (TRH) Receptor Binding Pocket. Novel Mixed Mode Monte Carlo/Stochastic Dynamics Simulations of the Complex between TRH and TRH Receptor

• Published in: Biochemistry (Easton) 1996-06, Vol.35 (24), p.7651-7663
• Main Authors: Laakkonen, Liisa J, Guarnieri, Frank, Perlman, Jeffrey H, Gershengorn, Marvin C, Osman, Roman
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Animals; Calorimetry; Computer Simulation; Mice; Models, Molecular; Models, Structural; Molecular Sequence Data; Monte Carlo Method; Protein Conformation; Protein Structure, Secondary; Receptors, Thyrotropin-Releasing Hormone - chemistry; Receptors, Thyrotropin-Releasing Hormone - metabolism; Software; Stochastic Processes; Thyrotropin-Releasing Hormone - chemistry; Thyrotropin-Releasing Hormone - metabolism
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi952203j

Previous mutational and computational studies of the thyrotropin-releasing hormone (TRH) receptor identified several residues in its binding pocket [see accompanying paper, Perlman et al. (1996) Biochemistry 35, 7643−7650]. On the basis of the initial model constructed with standard energy minimization techniques, we have conducted 15 mixed mode Monte Carlo/stochastic dynamics (MC−SD) simulations to allow for extended sampling of the conformational states of the ligand and the receptor in the complex. A simulated annealing protocol was adopted in which the complex was cooled from 600 to 310 K in segments of 30 ps of the MC−SD simulations for each change of 100 K. Analysis of the simulation results demonstrated that the mixed mode MC−SD protocol maintained the desired temperature in the constant temperature simulation segments. The elevated temperature and the repeating simulations allowed for adequate sampling of the torsional space of the complex with successful conservation of the general structure and good helicity of the receptor. For the analysis of the interaction between TRH and the binding pocket, TRH was divided into four groups consisting of pyroGlu, His, ProNH2, and the backbone. The pairwise interaction energies of the four separate portions of TRH with the corresponding residues in the receptor provide a physicochemical basis for the understanding of ligand−receptor complexes. The interaction of pyroGlu with Tyr106 shows a bimodal distribution that represents two populations:  one with a H-bond and another without it. Asp195 was shown to compete with pyroGlu for the H-bond to Tyr106. Simulations in which Asp195 was interacting with Arg283, thus removing it from the vicinity of Tyr106, resulted in a stable H-bond to pyroGlu. In all simulations His showed a van der Waals attraction to Tyr282 and a weak electrostatic repulsion from Arg306. The ProNH2 had a strong and frequent H-bonding interaction with Arg306. The backbone carbonyls show a frequent H-bonding interaction with the OH group of Tyr282 and strong, often multiple, interactions with Arg306. Three structures, which maintained these interactions simultaneously, were selected as candidates for ligand−receptor complexes. These show persistent interactions of TRH with Ile109 and Ile116 in HX 3 and with Tyr310 and Ser313 in HX 7, which will be tested to refine the structure of the ligand−receptor complex. The superposition of the three structures shows the extent of structural flexibility of