An overview of the Amber protein force fields, and how they were developed, can be found in: . Ponder and . Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Details on the ff14SB force field are here: . Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, . Hauser and C. Simmerling. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J. Chem. Theor. Comput. 11, 3696-3713 (2015). Similar information for nucleic acids is given by: . Cheatham, III and . Case. Twenty-five years of nucleic acid simulations. Biopolymers , 99, 969-977 (2013).
Evidence for crosstalk between the extrinsic and intrinsic pathways exists in the Fas signal cascade. In most cell types, caspase-8 catalyzes the cleavage of the pro-apoptotic BH3 -only protein Bid into its truncated form, tBid. BH-3 only members of the Bcl-2 family engage exclusively anti-apoptotic members of the family (Bcl-2, Bcl-xL), allowing Bak and Bax to translocate to the outer mitochondrial membrane, thus permeabilizing it and facilitating release of pro-apoptotic proteins such as cytochrome c and Smac/DIABLO , an antagonist of inhibitors of apoptosis proteins ( IAPs ).
AB - The α 7 acetylcholine receptor (AChR) mediates pre-and postsynaptic neurotransmission in the central nervous system and is a potential therapeutic target in neurodegenerative, neuropsychiatric and inflammatory disorders. We determined the crystal structure of the extracellular domain of a receptor chimera constructed from the human α 7 AChR and Lymnaea stagnalis acetylcholine binding protein (AChBP), which shares 64% sequence identity and 71% similarity with native Î ± 7. We also determined the structure with bound epibatidine, a potent AChR agonist. Comparison of the structures revealed molecular rearrangements and interactions that mediate agonist recognition and early steps in signal transduction in α 7 AChRs. The structures further revealed a ring of negative charge within the central vestibule, poised to contribute to cation selectivity. Structure-guided mutational studies disclosed distinctive contributions to agonist recognition and signal transduction in α 7 AChRs. The structures provide a realistic template for structure-aided drug design and for defining structure-function relationships of α 7 AChRs.