No abstract

Realistic mechanistic pictures of β-hairpin formation, offering valuable insights into some of the key early events in protein folding, are accessible through short designed polypeptides as they allow atomic-level scrutiny through simulations. Here, we present a detailed picture of the dynamics and mechanism of β-hairpin formation of Chignolin, a de novo decapeptide, using extensive, unbiased molecular dynamics simulations. The results provide clear evidence for turn-directed broken-zipper folding and reveal details of turn nucleation and cooperative progression of turn growth, hydrogen-bond formations, and eventual packing of the hydrophobic core. Further, we show that, rather than driving folding through hydrophobic collapse, cross-strand side-chain packing could in fact be rate-limiting as packing frustrations can delay formation of the native hydrophobic core prior to or during folding and even cause relatively long-living misfolded or partially folded states that may nucleate aggregative events in more complex situations. The results support the increasing evidence for turn-centric folding mechanisms for β-hairpin formation suggested recently for GB1 and Peptide 1 based on experiments and simulations but also point to the need for similar examinations of polypeptides with larger numbers of cross-strand hydrophobic residues.

The basic unit in microtubules is alphabeta-tubulin, a heterodimer consisting of an alpha- and a beta-tubulin monomer. The mechanical characteristics of the dimer as well as of the individual monomers may be used to obtain new insight into the microtubule tensile properties. In the present work, we evaluate the elastic constants of each monomer and the interaction force between them by means of molecular dynamics simulations. Molecular models of alpha-, beta-, and alphabeta-tubulins were developed starting from the 1TUB.pdb structure from the RCSB database. Simulations were carried out in a solvated environment by using explicit water molecules. In order to measure the monomers' elastic constants, simulations were performed by mimicking experiments carried out with atomic force microscopy. A different approach was used to determine the interaction force between the alpha- and beta-monomers by using 16 different monomer configurations based on different intermonomer distances. The obtained results show an elastic constant value for alpha-tubulin of 3.8-3.9 Nm, while for the beta-tubulin, the elastic constant was measured to be 3.3-3.6 Nm. The maximum interaction force between the monomers was estimated to be 11.9 nN. A mechanical model of the tubulin dimer was then constructed and, using the results from MD simulations, Young's modulus was estimated to be 0.6 GPa. A fine agreement with Young's modulus values from literature (0.1-2.5 GPa) is found, thus validating this approach for obtaining molecular scale mechanical characteristics. In perspective, these outcomes will allow exchanging atomic level description with key mechanical features enabling microtubule characterization by continuum mechanics approach.

In this work, a helical spring made from a pseudoelastic shape memory alloy was embedded in a dynamic system also composed of a mass, a linear spring and an excitation system. The mechanical behaviour of shape memory alloys is highly complex, involving hysteresis, which leads to damping capabilities and varying stiffness. Besides, these properties depend on the temperature and pretension conditions. Because of these capabilities, shape memory alloys are interesting in relation to engineering design of dynamic systems. A theoretical model based on a modification of the 1D Brinson model was established. Basically, the hardening and the sub-loop behaviour were altered. The model parameters were extracted from force–displacement tests of the spring at different constant temperatures as well as from differential scanning calorimetry. Model predictions were compared with experimental results of free and forced vibrations of the system setup under different temperature conditions. The experiments give a thorough insight into dynamic systems involving pseudoelastic shape memory alloys. Comparison between experimental results and the proposed model shows that the model is able to explain and predict the overall nonlinear behaviour of the system.

That protein folding is a non-random, guided process has been known even prior to Levinthal's paradox; yet, guided searches, attendant mechanisms and their relation to primary sequence remain obscure. Using extensive molecular dynamics simulations of a β-hairpin with key sequence features similar to those of >13,000 β-hairpins in full proteins, we provide significant insights on the entire pre-folding dynamics at single-residue levels and describe a single, highly coordinated roll-up folding mechanism, with clearly identifiable stages, directing structural progression toward native state. Additional simulations of single-site mutants illustrate the role of three key residues in facilitating this roll-up mechanism. Given the many β-hairpins in full proteins with similar residue arrangements and since β-hairpins are believed to act as nucleation sites in early-stage folding dynamics of full proteins, the topologically guided mechanism seen here may represent one of Nature's strategies for reducing early-stage folding complexity.