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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Sosnick, Tobin R. Baxa, Michael C. Ge, Liang Freed, Karl F. Adhikari, Aashish N. Xia, Zhen Yu, Wookyung Zhou, Ruhong |
| Description | Author Affiliation: Baxa MC ( Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637); Yu W ( Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637); Adhikari AN ( Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637); Ge L ( Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637); Xia Z ( Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598); Zhou R ( Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598); Freed KF ( Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, IL 60637); Sosnick TR ( Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637); |
| 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 ß 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. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 27 |
| Volume Number | 112 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2015-07-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Molecular Dynamics Simulation Protein Folding Protein Structure, Secondary Proteins Chemistry Algorithms Amino Acid Sequence Kinetics Molecular Sequence Data Mutation Genetics Thermodynamics Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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