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

Abstract

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 measurements. Network analysis of the conformation space sampled by the MD simulations reveals four main folding channels which start from conformations with partially formed helical structure and non-native salt-bridges in a kinetically partitioned unfolded state. The independent folding pathways explain the comparable quality of models based on stretched exponential and multiexponential fitting of the kinetic traces at low temperature. The rearrangement of bulky side chains, and in particular their reorientation with respect to the cross-linker, makes the EAAAR peptide a slower folder at 281 K than a similar peptide devoid of the three glutamate side chains. On the basis of this simulation result, extracted from a total MD sampling of 1.0 ms, a mutant with additional bulky side chains (three methionines replacing alanines at positions 2, 7, and 12) is suggested to fold slower than the EAAAR peptide. This prediction is confirmed by time-resolved IR spectroscopy.

The Free Energy Landscape of Small Molecule Unbinding

“…These methods have been used successfully to analyze MD simulations thereby revealing multiple pathways and unmasking the complexity of the folding free energy surface of -sheet [11], [13], [20], [21], [22] and -helical [23], [24], [25] peptides, as well as small and fast-folding proteins [26], [27], [28], [29]. Yet, no network analysis of the free energy surface of ligand (un)binding has been reported as of today.…”

Optical Modulation of Azobenzene‐Modified Peptide for Gold Surface Binding

“…The mixture of GolP and parameters for proteins in CHARMM and NAMD format were kindly provided by Bellucci . The parameters for the Azo‐liner were taken from Paoli et al . The Azo‐linker was initially tilted relative to the gold surface to avoid biasing its interaction with either the gold surface or water.…”

“…The mixture of GolP and parameters for proteins in CHARMM and NAMD format were kindly provided by Bellucci. [35][36][37][38] The parameters for the Azo-liner were taken from Paoli et al [39] The Azo-linker was initially tilted relative to the gold surface to avoid biasing its interaction with either the gold surface or water.T he system was solvated in aT IP3 water box of 6.0 nm height to avoid image interaction. One of the initial configurations is shown in Figure 3a.U sing replica-exchange molecular dynamics simulations, the adsorbed peptide structures were prepared.…”

Wordom: A user‐friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

“…Both RMSD-based and coarse-grained clustering have proven to be good discretization methods of MD trajectory snapshots into a set of microstates that describe large conformational changes (see Ref 40, 48,. and53–56 for examples in protein folding). Application to large proteins requires more sophisticated clustering procedures like principal component space 57…”