期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2015
卷号：112
期号：27
页码：8302-8307
DOI：10.1073/pnas.1503613112
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceAn outstanding issue in protein science is identifying the relationship between sequence and folding, e.g., do sequences having similar structures have similar folding pathways? The homologs Proteins G & L have been cited as a primary example where sequence variations dramatically affect folding dynamics. However, our new results indicate that the homologs have similar folding behavior. At the highest point on the reaction surface, the pathways converge to similar ensembles. These findings are distinct from descriptions based on the widely used mutational {phi} analysis, partly due to nonnative behavior. Our study emphasizes that significant challenges remain both in characterizing and predicting transition state ensembles even for relatively simple proteins whose folding behavior is believed to be well understood. Experimental and computational folding studies of Proteins L & G and NuG2 typically find that sequence differences determine which of the two hairpins is formed in the transition state ensemble (TSE). However, our recent work on Protein L finds that its TSE contains both hairpins, compelling a reassessment of the influence of sequence on the folding behavior of the other two homologs. We characterize the TSEs for Protein G and NuG2b, a triple mutant of NuG2, using {psi} analysis, a method for identifying contacts in the TSE. All three homologs are found to share a common and near-native TSE topology with interactions between all four strands. However, the helical content varies in the TSE, being largely absent in Proteins G & L but partially present in NuG2b. The variability likely arises from competing propensities for the formation of nonnative {beta} turns in the naturally occurring proteins, as observed in our TerItFix folding algorithm. All-atom folding simulations of NuG2b recapitulate the observed TSEs with four strands for 5 of 27 transition paths [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520]. Our data support the view that homologous proteins have similar folding mechanisms, even when nonnative interactions are present in the transition state. These findings emphasize the ongoing challenge of accurately characterizing and predicting TSEs, even for relatively simple proteins.
