Proteins in vacuo: Denaturing and folding mechanisms studied with computer‐simulated molecular dynamics

I. Introduction 402 II. Experiments and Simulations: Background 403 III. Unfolding Studies 406 A. Centrifugal Unfolding of Neutral Proteins 407 B. Unfolding by Coulombic Repulsion 409 C. Unfolding by Screened van der Waals Attraction 411 IV. Refolding Studies 412 V. Closing Remarks 414 VI. Acknowledgments 415 Appendix 1. Molecular Shape Descriptors for Protein Backbones 416 Appendix 2. MD Simulations 417 References 419 Mounting evidence from experiments suggests that the native fold in solution is metastable in dehydrated proteins. Results from a number of experiments that use mass spectrometry indicate also that folding–unfolding transitions take place in protein ions even in the absence of water. These observations on anhydrous proteins call for a re‐evaluation of our understanding of the folding transition. In this context, computer‐assisted simulations are an important complementary tool. Here, we provide an overview of recent progress on the simulation of proteins in vacuo . In particular, we discuss the response of proteins and protein ions to perturbations that trigger unfolding and re‐folding transitions. By comparing the general patterns emerging from theory and experiment, we propose a series of new measurements that could help to validate, and improve, current simulation models.