Atomic molecular dynamics simulation advances of -designed proteins.

Proteins are vital biological macromolecules that execute biological functions and form the core of synthetic biological systems. The history of protein has evolved from initial successes in subordinate structural design to more intricate protein creation, challenging the complexities of natural proteins. Recent strides in protein design have leveraged computational methods to craft proteins for functions beyond their natural capabilities.

[Collagen peptide partially restores immune function in mice under the condition of X-ray irradiation combined with simulated weightlessness].

Objective To investigate the effects of collagen peptides on the immune function of mice under the condition of X-ray irradiation combined with simulated weightlessness. Methods Mice were randomly divided into control group, modelling group and collagen peptide group. Mice in collagen peptide group were intraperitoneally injected with collagen peptide (600 mg/kg) once a day from the first day of the experiment, while mice in the other two groups were intraperitoneally injected with normal saline.

Correction: A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

Correction for 'A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding' by Jie Hu et al., Phys. Chem.

A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119.