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Published online on March 14, 2006, 10.1073/pnas.0600433103
PNAS | March 21, 2006 | vol. 103 | no. 12 | 4433-4438


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BIOLOGICAL SCIENCES / BIOPHYSICS
Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state

George Stan*, Bernard R. Brooks*, George H. Lorimer{dagger},{ddagger}, and D. Thirumalai{dagger},{ddagger}

*Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and {dagger}Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742

Contributed by George H. Lorimer, January 19, 2006

We have used a bioinformatic approach to predict the natural substrate proteins for the Escherichia coli chaperonin GroEL based on two simple criteria. Natural substrate proteins should contain binding motifs similar in sequence to the mobile loop peptide of GroES that displaces the binding motif during the chaperonin cycle. Secondly, each substrate protein should contain multiple copies of the binding motif so that the chaperonin can perform "work" on the substrate protein. To validate these criteria, we have used a database of 252 proteins that have been experimentally shown to interact with the chaperonin machinery in vivo. More than 80% are identified by these criteria. The binding motifs of all 79 proteins in the database with a known three-dimensional structure are buried (<50% solvent-accessible surface area) in the native state. Our results show that the binding motifs are inaccessible in the native state but become solvent-exposed in unfolded state, thus enabling GroEL to distinguish between unfolded and native states. The structures of the binding motif in the native states of the substrate proteins include {alpha}-helices, beta-strands, and random coils. The diversity of secondary structures implies that there are large and varied conformational transitions in the recognition motifs after their displacement by the mobile loops of GroES.

chaperonin | E. coli | natural substrates | recognition motif

Author contributions: G.S., B.R.B., G.H.L., and D.T. designed research; G.S. performed research; B.R.B. contributed new reagents/analytic tools; G.S., B.R.B., G.H.L., and D.T. analyzed data; and G.S., G.H.L., and D.T. wrote the paper.

Conflict of interest statement: No conflicts declared.

{ddagger}To whom correspondence may be addressed. E-mail: glorimer{at}umd.eduor thirum{at}glue.umd.edu

© 2006 by The National Academy of Sciences of the USA


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