Native topology determines force-induced unfolding pathways in globular proteins

Single-molecule manipulation techniques reveal that stretching unravels ind ividually folded domains in the muscle protein titin and the extracellular matrix protein tenascin. These elastic proteins contain tandem repeats of f olded domains with beta-sandwich architecture. Herein, we propose by stretc hing two model sequences (S1 and S2) with four-stranded beta-barrel topolog y that unfolding forces and pathways in folded domains can be predicted by using only the structure of the native state. Thermal refolding of S1 and S Z in the absence of force proceeds in an all-or-none fashion. In contrast, phase diagrams in the force-temperature (f,T) plane and steered Langevin dy namics studies of these sequences, which differ in the native registry of t he strands, show that S1 unfolds in an all-or-none fashion, whereas unfoldi ng of S2 occurs via an obligatory intermediate. Force-induced unfolding is determined by the native topology. After proving that the simulation result s for S1 and S2 can he calculated by using native topology alone, we predic t the order of unfolding events in Ig domain (Ig27) and two fibronectin ill type domains ((9)FnIII and (10)FnIII). The calculated unfolding pathways f or these proteins, the location of the transition states, and the pulling s peed dependence of the unfolding forces reflect the differences in the way the strands are arranged in the native states. We also predict the mechanis ms of force-induced unfolding of the coiled-coil spectrin (a three-helix bu ndle protein) for all 20 structures deposited in the Protein Data Bank. Our approach suggests a natural way to measure the phase diagram in the (f,C) plane, where C is the concentration of denaturants.