Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

Abstract

Many experimental and theoretical studies have suggested a significant role for nonnative interactions in protein folding pathways, but the energetic contributions of these interactions are not well understood. We have addressed the energetics and the position specificity of nonnative hydrophobic interactions by developing a continuum coarse-grained chain model with a nativecentric potential augmented by sequence-dependent hydrophobic interactions. By modeling the effect of different hydrophobicity values at various positions in the Fyn SH3 domain, we predicted energetically significant nonnative interactions that led to acceleration or deceleration of the folding rate depending on whether they were more populated in the transition state or unfolded state. These nonnative contacts were centered on position 53 in the Fyn SH3 domain, which lies in an exposed position in a 310-helix. The energetic importance of the predicted nonnative interactions was confirmed experimentally by folding kinetics studies combined with double mutant thermodynamic cycles. By attaining agreement of theoretical and experimental investigations, this study provides a compelling demonstration that specific nonnative interactions can significantly influence folding energetics. Moreover, we show that a coarse-grained model with a simple consideration of hydrophobicity is sufficient for the accurate prediction of kinetically important nonnative interactions. double mutant cycles ͉ Fyn SH3 domain ͉ Gō models ͉ HP model ͉ Langevin dynamics

Biophysics of protein evolution and evolutionary protein biophysics

“…[71]. Mutations can affect folding speeds of both two-state-like and non-two-state proteins by modulating the interactions that favour the native state [72][73][74][75] or through strengthening certain non-native interactions not present in the folded structure [76,77]. Folding kinetics can be subject to natural selection.…”

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

“…1 Such a favorable role of non-native interaction in the formation of protein folding nucleus is in line with previous experimental and theoretical studies, suggesting that specific non-native interactions may accelerate folding by reducing conformational search to the native state. [53][54][55][56][57][58][59][60][61][62][63] The identification of a critical salt-bridge in a crystallin folding/unfolding intermediate is another example of non-native interactions crucial for protein folding. Similarly, Presta and Rose 59 described helix stop signals that were not necessarily retained in the native state of the folded proteins.…”

Hydrophobic interactions in the formation of secondary structures in small peptides

“…They are a major driving force for protein tertiary structure [5][6][7]; they can lead to non-native interactions during folding [8]; and they can affect the formation of α helices and β sheets [9] in proteins through packing [10] and local sterics [11]. The importance of hydrophobic interactions in the formation of secondary structures in globular proteins is highlighted by an experimental study of the mutations at the helical segments of T4 lysozyme.…”