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The impact of this difference is clearly illustrated in the present manuscript in which unfolding times and mechanisms vary non-monotonically with the applied pulling force magnitude. Notably, this is not the case for force-induced unfolding in which the extended stretch (and unfolded) configuration is as unique as the folded state, providing yet another motivation to investigate long helix unfolding. Unfolded short helices have vast conformational space from which to sample, much larger than the conformational space of the folded state. Fourth, the process of pulling by force is fundamentally different from the unfolding of short helices. While pulling experiments вЂ“ have been used for some time to probe mechanical properties of bio macromolecules, here we examine, via computations, the feasibility of using a single-molecule pulling-experiment to investigate the early events in the unfolding of a relatively long, helical structure. Third, the helixвЂ™s longer length potentially permits a new type of experiment directly probing the moleculeвЂ™s mechanical properties, namely single-molecule pulling-experiments. Such an initial crack in the basic building block of a motor is critical to the motorвЂ™s overall stability under load and, thus, likely to be important to their function. Here, we specifically explore the onset of mechanical instability in long helices in which the first вЂњcrackвЂќ is observed.

Second, the central role that long helices play in the proper functioning of motor proteins renders the study of their mechanical properties to be particularly important. While studies of short helices are strongly influenced by end effects, studies of long helices may enable the definition and calculation of an вЂњaverageвЂќ helical residue that is approximately invariant to translation (in the helical sense) far from the helix edges. For a number of reasons, it is intriguing to investigate the physical, biological and mechanical properties of these longer helices, in addition to the well-studied short helices.ДЇirst, it is difficult to extract from short helices the general and average properties of a single amino acid that are useful in phenomenological models of helix folding. For example, molecular motors-like kinesin вЂ“ and myosin вЂ“-use order of magnitude longer helices as key components to вЂњwalkвЂќ along cytoskeletal proteins to transmit energy and to conduct work. However, significantly longer helices are also found in vivo that are making important and unique contributions in the field of molecular biophysics. It is, therefore, not surprising that most of the experiments and simulations on the properties of helices focus on relatively short helical peptides of about 20 amino acids or less. Typical helices found in proteins in vivo are short (~10вЂ“20 amino acids), a necessary restriction to support compact three-dimensional shapes of proteins. Introduction Alpha helices are fundamental building blocks of protein folds.ДЄs structure elements frequently found in globular proteins, they continue to attract considerable attention in experiments вЂ“, theory, and simulations,вЂ“. Hydrogen bonds are much faster coarse variables (by about 2 orders of magnitude) compared to backbone torsional transition, which gates unfolding and thereby provides the appropriate coarse variable for the initiation of unfolding. Consistent prediction of about ~5ns for the time of a single amino-acid unfolding event are obtained. Coarse variables are examined at different levels of resolution the rate of unfolding illustrates remarkable stability under changes in the coarsening. Network analysis and selection of MaxFlux pathways illustrate that load impacts unfolding mechanisms in addition to time scales.ДЄt relatively high (100pN) load levels, the principal intermediate is the 3 10-helix, while at relatively low (10pN) levels the ПЂ-helix is significantly populated, albeit not as an unfolding intermediate. Dense kinetic networks are constructed that, with Milestoning analysis, provide the overall kinetics of early breakage events. Transitions of individual amino acids (averaged over the helixвЂ™s interior residues) are examined and its surrounding hydrogen bonds are considered.

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RF-X Software with InterLink-X Controller. A helix length of ~100 amino acids is considered as a model for typical helices found in molecular machines and as a model that minimizes end effects for early events of unfolding. Initial events of helix breakage as a function of load are considered using Molecular Dynamics simulations and Milestoning analysis.

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