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Register a new userOptimizations of force-field parameters for protein systems with the secondary-structure stability and instability
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We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $psi$ (N-C$^{alpha}$-C-N) and $zeta$ (C$^{beta}$-C$^{alpha}$-C-N) of the backbone dihedral angles. We then performed folding simulations of $alpha$-helical and $beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.
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Thermal shift assays (TSAs) have been extensively used to study thermodynamics of proteins and provide an efficient means to assess protein-ligand binding or protein-protein interaction. However, existing TSAs have limitations such as time consuming, labor intensive, or low sensitivity. Here we introduce a novel acousto thermal shift assay (ATSA), the first ultrasound enabled TSA, for real-time analysis of protein thermodynamic stability. It capitalizes the novel coupling of unique acoustic mechanisms to achieve protein unfolding, concentration, and measurement on a single microfluidic chip within minutes. Compared to conventional TSA methods, our ATSA technique enabled ultra-fast (at least 30 times faster), highly sensitive (7-34 folds higher), and label-free monitoring of protein-ligand interactions and protein stability. ATSA paves new avenues for protein analysis in biology, medicine and fast diagnosis.
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Here we investigate tigh peptide knot (TPK) characteristics in detail by pulling selected 3_1 and 4_1-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3_1 and 4_1-TPK lengths are typically Delta l~4.7 nm and 6.9 nm, respectively, for a wide range of tensions (F < 1.5 nN), pointing to a pore diameter of ~2 nm below which a translocated knotted protein might get stuck. The 4_1-knot length is in agreement with recent AFM pulling experiments. Detailed TPK characteristics however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water molecule trapping capability of hydrophobic TPKs due to side chain shielding of the polar TPK core. Water capturing and release is found to be controlla ble by the tightening force in a few cases. These mechanisms result into a sequence-specific locking and metastability of TPKs what might lead to a blocking of knotted peptide transport at designated sequence-positions. Intriguingly, macroscopic tight 4_1-knot structures are reproduced microscopically (figure-of-eight vs. the pretzel) and can be tuned by sequence in contrast to mathematical predictions. Our findings may explain a function of knots in native proteins, challenge previous studies on macromolecular knots, and may find use in bio- and nanotechnology.
A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially assumed to be nonlinear and represented by the Sine-Gordon equation, while the nonlinear external bosonic sources is represented by $phi^4$ interaction. It is argued that the nonlinear source induces the folding pathway in a different way than the previous work with initially linear backbone. Also, the nonlinearity of protein backbone decreases the folding speed.
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible folding/unfolding transitions and the experimental methods that are available for extracting thermodynamic parameters. We highlight the importance of modelling both how the folding equilibrium depends on a perturbing variable such as temperature or denaturant concentration, and the importance of modelling the baselines in the experimental observables.
The statistical properties of protein folding within the {phi}^4 model are investigated. The calculation is performed using statistical mechanics and path integral method. In particular, the evolution of heat capacity in term of temperature is given for various levels of the nonlinearity of source and the strength of interaction between protein backbone and nonlinear source. It is found that the nonlinear source contributes constructively to the specific heat especially at higher temperature when it is weakly interacting with the protein backbone. This indicates increasing energy absorption as the intensity of nonlinear sources are getting greater. The simulation of protein folding dynamics within the model is also refined.
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