Assessment of ab initio models of protein complexes by molecular dynamics

Determining how proteins interact to form stable complexes is of crucial importance, for example in the development of novel therapeutics. Computational methods to determine the thermodynamically stable conformation of complexes from the structure of the binding partners, such as RosettaDock, might potentially emerge to become a promising alternative to traditional structure determination methods. However, while models virtually identical to the correct experimental structure can in some cases be generated, the main difficulty remains to discriminate correct or approximately correct models from decoys. This is due to the ruggedness of the free-energy landscape, the approximations intrinsic in the scoring functions, and the intrinsic flexibility of proteins. Here we show that molecular dynamics simulations performed starting from a number top-scoring models can not only discriminate decoys and identify the correct structure, but may also provide information on an initial map of the free energy landscape that elucidates the binding mechanism.Author summary: Determining how proteins fold and form complexes is of crucial importance, for example in the development of novel therapeutics. Experimental determination of structures is costly and lengthy. Computational methods to determine the thermodynamically stable conformation of complexes from the structure of the binding partners are available and constantly improving. Such methods generate a large number of diverse conformations and rank them for their likelihood to be correct. Even a model very similar to the correct structure is rarely the top-scoring one, but, as in the examples presented here, only within the top ~10–100 (the exact number depends on the complexity of the structure, and could be much higher). Here we show through atomistic simulation that good models are kinetically stable and bad models most often are not. More surprisingly, we also see that some bad models spontaneously find the correct (i.e., experimentally determined) conformation. This is remarkable, and could become an additional tool to contribute to structure determination of protein complexes. Such a result can also be expected, because evolution sculpted the free energy landscape in a way that the biologically active state is not only the one of lowest free energy (i.e., the most likely state) but also robustly reachable and kinetically stable (i.e., at the bottom of a funnel on the free energy landscape).