Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein

Abstract

The effects of a single-point mutation on folding thermodynamics and kinetics are usually interpreted by focusing on the native structure and the transition state. Here, the entire conformational spaces of a 20-residue three-stranded antiparallel beta-sheet peptide (double hairpin) and of its single-point mutant W10V are sampled close to the melting temperature by equilibrium folding-unfolding molecular dynamics simulations for a total of 40 micros. The folded state as well as the most populated free energy basins in the denatured state are isolated by grouping conformations according to fast relaxation at equilibrium. Such kinetic analysis provides more detailed and useful information than a simple projection of the free energy. The W10V mutant has the same native structure as the wild type peptide, and similar folding rate and stability. In the denatured state, the N-terminal hairpin is about 20% more structured in W10V than the wild type mainly because of van der Waals interactions. Notably, the W10V mutation influences also the van der Waals energy at the transition state ensemble causing a shift in the ratio of fluxes between two different transition state regions on parallel folding pathways corresponding to nucleation at either of the two beta-hairpins. Previous experimental studies have focused on the effects of denaturant-dependent or temperature-dependent changes in the structure of the denatured state. The atomistic simulations show that a single-point mutation in the central strand of a beta-sheet peptide results in remarkable changes in the topography of the denatured state ensemble. These changes modulate the relative accessibility of parallel folding pathways because of kinetic partitioning of the denatured state. Therefore, the observed dependence of the folding process on the starting ensemble raises questions on the biological significance of in vitro folding studies under strongly denaturing conditions.

The OH stretch vibration of liquid water reveals hydrogen-bond clusters

“…Network approaches have pointed out the presence of multiple stable structures in the unfolded state of a protein, which is a somewhat surprising result, giving the fact that folding often appears to be a two-state process [13,16]. Complex network analysis methods, which initially have been inspired by social and computer sciences (e.g.…”

“…In turn, the dynamics of the simulation is represented as a kinetic network -the conformation-space-networkwhere the microstates and the transitions between them observed during the simulation represent the nodes (vertices) and the links (edges), respectively. Conformationspace-networks represent a high resolution mapping of the underlying free-energy surface where highly interconnected groups of nodes indicate kinetically homogeneous free-energy valleys [16,20].…”

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

“…DS2: Data are derived from recently published simulations on the intrinsically disordered peptide Aβ [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28] . 39 The trajectory contained 7.5x10 5 snapshots saved at an interval of 20 ps, and the same 144, partially redundant internal distances that DS1 was originally derived from were extracted at each frame (D = 144).…”

“…The literature offers similar, kinetic (re)grouping techniques that operate on fine-grained mesostate networks obtained from structural clustering. 16,19,28 In clustering, the issue of dimensionality deserves particular attention since very frequently molecular simulation data are represented in fairly high-dimensional spaces (D ≈ 100 -1000). The so-called "curse of dimensionality" 29 is a colloquialism for the fact that high-dimensional spaces generally lead to low data density (sparsity) due to exponential growth of the available space.…”

“…37 Note again that the aforementioned algorithms are general data processing tools with a modular definition of similarity, and that dedicated grouping schemes as discussed may be available. 19,27,28 In this contribution, we propose a tree-based algorithm that relies on partitioning according to a preset schedule of threshold criteria operating at each level of the tree. Clusters or mesostates at coarser resolution serve as parent nodes to a set of mesostates at the next finest level.…”