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Evolutionary information for specifying a protein fold

Abstract

Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures. The artificial proteins show thermodynamic stabilities similar to natural WW domains, and structure determination of one artificial protein shows excellent agreement with the WW fold at atomic resolution. The relative simplicity of the information used for creating sequences suggests a marked reduction to the potential complexity of the protein-folding problem.

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Figure 1: SCA-based protein design.
Figure 2: Experimental evaluation of artificial proteins (part 1).
Figure 3: Experimental evaluation of artificial proteins (part 2).
Figure 4: Summary of experiments on all natural and artificial WW sequences.
Figure 5: NMR structure determination of CC45, an artificial WW domain.

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Acknowledgements

We thank A. G. Gilman, M. Rosen, and members of the Ranganathan laboratory for advice and critical review of the manuscript, and E. Olson for contributing to this project. R.R. and S.W.L. thank the students of the 2001 Woods Hole physiology course for participating in an initial phase of this work. This study was supported by the Robert A. Welch foundation (R.R. and K.H.G.), the Mallinckrodt Foundation Scholar Award (R.R.), and the NIH (K.H.G.). W.P.R. is an associate and R.R. is an investigator of the Howard Hughes Medical Institute.

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Correspondence to Rama Ranganathan.

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Competing interests

Atomic coordinates for CC45 have been deposited in the Protein Data Bank under accession code 1YMZ. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

Supplementary Table S1, Supplementary Table S2, Supplementary Methods and Supplementary Figure Legends. (DOC 156 kb)

Supplementary Figure S1

Statistical coupling analysis for one site in the WW domain family. (PDF 578 kb)

Supplementary Figure S2

Summary of all sequences constructed and experimentally tested. (PDF 2191 kb)

Supplementary Figure S3

Assessment of expression and solubility of all sequences constructed. (PDF 12056 kb)

Supplementary Figure S4

Thermal denaturation and renaturation studies. (PDF 5249 kb)

Supplementary Figure S5

One-dimensional proton NMR spectra for natural WW domains (a), CC sequences (b), and IC sequences (c). (PDF 6444 kb)

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Socolich, M., Lockless, S., Russ, W. et al. Evolutionary information for specifying a protein fold. Nature 437, 512–518 (2005). https://doi.org/10.1038/nature03991

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