Folding simulations of a three-stranded antiparallel β-sheet peptide

Abstract

Protein folding is a grand challenge of the postgenomic era. In this paper, 58 folding events sampled during 47 molecular dynamics trajectories for a total simulation time of more than 4 s provide an atomic detail picture of the folding of a 20-residue synthetic peptide with a stable three-stranded antiparallel ␤-sheet fold. The simulations successfully reproduce the NMR solution conformation, irrespective of the starting structure. The sampling of the conformational space is sufficient to determine the free energy surface and localize the minima and transition states. The statistically predominant folding pathway involves the formation of contacts between strands 2 and 3, starting with the side chains close to the turn, followed by association of the N-terminal strand onto the preformed 2-3 ␤-hairpin. The folding mechanism presented here, formation of a ␤-hairpin followed by consolidation, is in agreement with a computational study of the free energy surface of another synthetic three-stranded antiparallel ␤-sheet by Bursulaya and Brooks [(1999) J. Am. Chem. Soc. 121, 9947-9951]. Hence, it might hold in general for antiparallel ␤-sheets with short turns.protein folding ͉ energy landscape ͉ implicit solvation model T heoretical and experimental studies have provided insights into the protein folding process (1). Yet, a more detailed understanding is required not only to predict the structure of a given amino acid sequence but also for protein engineering purposes, e.g., to design a sequence for a given fold. For the latter, applications relevant to biomedicine are possible. Most proteins contain regular elements of secondary structure, ␣-helices, and͞or ␤-sheets. Therefore, it generally is thought that elucidating the formation of regular secondary structure elements will improve the understanding of the protein folding reaction (2-4). As it is currently not yet feasible to simulate the folding of a protein by using molecular dynamics (MD) simulations with an all-atom model (5), the common approach taken in the past is to unfold starting from the native state (6, 7). Reversible folding simulations have been limited to non-natural oligopeptides in methanol (8) or peptides with an implicit solvation model and adaptive umbrella sampling (9).Beta3s is a designed amino acid sequence (Thr 1 -Trp 2 -Ile 3 -Gln 4 -Asn 5 -Gly 6 -Ser 7 -Thr 8 -Lys 9 -Trp 10 -Tyr 11 -Gln 12 -Asn 13 -Gly 14 -Ser 15 -Thr 16 -Lys 17 -Ile 18 -Tyr 19 -Thr 20 ), and its solution conformation has been studied by NMR (10). Nuclear Overhauser enhancement (NOE) and chemical shift data indicate that at 10°C Beta3s populates a single structured form, the expected three-stranded antiparallel ␤-sheet conformation with turns at Gly-6-Ser-7 and Gly-14-Ser-15, in equilibrium with the random coil. The ␤-sheet population was 13-31% based on NOE intensities and 30-55% based on the chemical shift data (10). Furthermore, Beta3s was shown to be monomeric in aqueous solution by equilibrium sedimentation and NMR dilution experiments (10). In this report, the foldi...

Diffusive reaction dynamics on invariant free energy profiles

“…Folding of the 20-residue Beta3s double-hairpin miniprotein has been studied (31,32), based on a 20-ms equilibrium trajectory calculated with the solventaccessible surface area implicit solvent model (33). Detailed analyses of the folding behavior of this system and its folding network were made.…”

β‐strand interactions at the domain interface critical for the stability of human lens γD‐crystallin

“…The difficulty in deciphering the sequence control of b-sheet folding reflects the importance of interactions between side chains that are distant in the primary amino acid sequence. Although, significant progress has been made in understanding the folding pathways of several b-sheets [21][22][23] and isolated SH3 domain [24][25][26][27][28] using experimental and theoretical/simulation techniques, detailed characterization of the folding/ unfolding landscape of a biologically important b-sheet protein still remains a challenge. 29 For example, even for a small 16-residue b-hairpin (GB1), there are debates over a hydrogen-bond zipping mechanism versus a hydrophobic core collapse mechanism.…”

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

“…In principle, this detailed information is accessible via molecular dynamics (MD) simulations which, when used in concert with experimental evidence, are becoming an increasingly accepted tool to understanding structural details that are not easily accessible via the experimental observables (8). MD simulations with atomistic models of proteins have been used to study the dynamics of small proteins with folding times in the microsecond range (9)(10)(11)(12)(13). However, even though MD simulations make the full spatiotemporal detail accessible to observation, the characterization of the pathway ensemble is computationally difficult: A brute-force approach would start simulations from an equilibrium of unfolded structures, say A, and simulate until they relax into a set of folded state B.…”