Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards’ and Shrake and Rupley’s approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed / protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49-67-residue systems with high statistical accuracy, using only modest computational resources by today's standards.

The properties of the amyloid-beta peptide that lead to aggregation associated with Alzheimer's disease are not fully understood. This study aims at identifying conformational differences among four variants of full-length Abeta42 that are known to display very different aggregation properties. By extensive all-atom Monte Carlo simulations, we find that a variety of beta-sheet structures with distinct turns are readily accessible for full-length Abeta42. In the simulations, wild type (WT) Abeta42 preferentially populates two major classes of conformations, either extended with high beta-sheet content or more compact with lower beta-sheet content. The three mutations studied alter the balance between these classes. Strong mutational effects are observed in a region centered at residues 23-26, where WT Abeta42 tends to form a turn. The aggregation-accelerating E22G mutation associated with early onset of Alzheimer's disease makes this turn region conformationally more diverse, whereas the aggregation-decelerating F20E mutation has the reverse effect, and the E22G/I31E mutation reduces the turn population. Comparing results for the four Abeta42 variants, we identify specific conformational properties of residues 23-26 that might play a key role in aggregation.

The unfolding behavior of ubiquitin under the influence of a stretching force recently was investigated experimentally by single-molecule constant-force methods. Many observed unfolding traces had a simple two-state character, whereas others showed clear evidence of intermediate states. Here, we use Monte Carlo simulations to investigate the force-induced unfolding of ubiquitin at the atomic level. In agreement with experimental data, we find that the unfolding process can occur either in a single step or through intermediate states. In addition to this randomness, we find that many quantities, such as the frequency of occurrence of intermediates, show a clear systematic dependence on the strength of the applied force. Despite this diversity, one common feature can be identified in the simulated unfolding events, which is the order in which the secondary-structure elements break. This order is the same in two-and three-state events and at the different forces studied. The observed order remains to be verified experimentally but appears physically reasonable. all-atom model ͉ force-induced unfolding ͉ Monte Carlo simulation T he 76-residue protein ubiquitin fulfills many important regulatory functions in eukaryotic cells through its covalent attachment to other proteins (1, 2). In many cases, the ubiquitin tag consists of a chain of ubiquitin domains (polyubiquitin), which is formed by linkages between an exposed lysine side chain of the last ubiquitin of a growing chain and the C terminus of a new ubiquitin. The fate of a polyubiquitin-tagged protein depends on the linkage. For example, Lys-48-C-linked polyubiquitin marks the protein substrate for proteasomal degradation (3).Recently, Fernandez and coworkers (4-7) and Chyan et al. (8) investigated the mechanical properties of polyubiquitin by single-molecule force spectroscopy. It was shown that Lys-48-Clinked as well as end-to-end (N-C)-linked polyubiquitin can withstand a stretching force; the average unfolding force was 85 pN for Lys-48-C linkage and Ϸ200 pN for N-C linkage (4). In these experiments, the polyubiquitin chains were pulled with a constant velocity. In another experiment on N-C-linked polyubiquitin, the stretching force was kept constant (6). At constant force, the fraction of unfolded ubiquitin domains was found to show an approximately single-exponential time dependence, as expected if the unfolding of individual domains is a simple Markovian two-state process. Nevertheless, the unfolding of individual domains sometimes occurred through intermediate states. The precise nature of these different unfolding pathways, including the structure of the intermediate states, remains to be determined. We stress that these intermediates are states along forced unfolding trajectories. To what extent there are significant folding intermediates for small proteins is a debated (9, 10), but different, issue. Here, we use Monte Carlo (MC) simulations to examine the unfolding of ubiquitin under a constant stretching force in atomic detail. Our calculations are b...