title: Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.
abstract: 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 ψ 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 β 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637;
authors.forename: Michael C
authors.initials: MC
authors.lastname: Baxa
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637; Center for Proteome Biophysics, Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 711-873, Korea;
authors.forename: Wookyung
authors.initials: W
authors.lastname: Yu
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637; Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, IL 60637;
authors.forename: Aashish N
authors.initials: AN
authors.lastname: Adhikari
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637;
authors.forename: Liang
authors.initials: L
authors.lastname: Ge
authors.affiliation: Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598; Institute of Quantitative Biology and Medicine, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China;
authors.forename: Zhen
authors.initials: Z
authors.lastname: Xia
authors.affiliation: Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598; Institute of Quantitative Biology and Medicine, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China;
authors.forename: Ruhong
authors.initials: R
authors.lastname: Zhou
authors.affiliation: Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, IL 60637; Computation Institute, The University of Chicago, Chicago, IL 60637 freed@uchicago.edu trsosnic@uchicago.edu.
authors.forename: Karl F
authors.initials: KF
authors.lastname: Freed
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637; Computation Institute, The University of Chicago, Chicago, IL 60637 freed@uchicago.edu trsosnic@uchicago.edu.
authors.forename: Tobin R
authors.initials: TR
authors.lastname: Sosnick
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: bi-histidine; protein folding; transition state ensemble; ψ analysis; ϕ analysis