Slow folding of cross-linked alpha-helical peptides due to steric hindrance.

The slow folding of cross-linked α-helical peptides is due to steric hindrance SUPPLEMENTARY MATERIAL

Slow Folding of Cross-Linked r-Helical Peptides Due to Steric Hindrance

The folding process of a 16-residue R-helical peptide with an azobenzene cross-linker (covalently bound to residues Cys3 and Cys14) is investigated by 50 molecular dynamics simulations of 4 μs each. The folding kinetics at 281 K show a stretched exponential behavior but become simpler and much faster when a distance restraint is used to emulate a nonbulky cross-linker. The free-energy basin of ...

Bulky side chains and non-native salt bridges slow down the folding of a cross-linked helical peptide: a combined molecular dynamics and time-resolved infrared spectroscopy study.

Multiple 4-micros molecular dynamics (MD) simulations are used to study the folding process of the cross-linked alpha-helical peptide Ac-EACAR(5)EAAAR(10)EAACR(15)Q-NH(2) (EAAAR peptide). The folding kinetics are single exponential at 330 K, while they are complex at 281 K with a clear deviation from single-exponential behavior, in agreement with time-resolved infrared (IR) spectroscopy measure...

Complexity in Protein Folding: Simulation Meets Experiment

We review our joint experimental-theoretical effort on the folding of photo-switchable -helices. The folding kinetics of these peptides is profoundly non-exponential, which is attributed to a partitioning of the unfolded state into several misfolded traps. These traps are connected to the folded state in a hub-like fashion with folding barriers of different heights. Molecular dynamics simulatio...

Effect of Hydration and Macromolecular Crowding on Peptide Conformation, Aggregation and Folding Kinetics

Protein folding/misfolding in vivo takes place in a highly crowded and confined environment. Such crowded environment can possibly lead to fewer water molecules surrounding a protein of interest than that seen under in vitro conditions wherein typically dilute aqueous solutions are used. When considering the aforesaid cellular characteristics, such as water depletion and macromolecular crowding...