Principles for designing ideal protein structures

Abstract

Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features—for example kinked α-helices, bulged β-strands, strained loops and buried polar groups—that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of α-helices, β-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.

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Figure 1: Fundamental rules.
Figure 2: Derivation of secondary structure lengths from the rules for five protein topologies.
Figure 3: Characterization of design for each of the five folds.
Figure 4: Comparison of computational models with experimentally determined structures.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

TheNMR structures of the five designs have been deposited in the RCSB Protein Data Bank under the accession numbers 2KL8 (Di-I_5), 2LV8 (Di-II_10), 2LN3 (Di-III_14), 2LVB (Di-IV_5) and 2LTA (Di-V_7). NMR data have been deposited in the Biological Magnetic Resonance Data Bank under the accession numbers 16387 (Di-I_5), 18558 (Di-II_10), 18145 (Di-III_14), 18561 (Di-IV_5) and 18465 (Di-V_7).

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Acknowledgements

We thank N. Grishin for suggesting target folds for design, P. Rajagopal for one-dimensional NMR measurements of Folds-I and -II, and J. Siegel for measurements by mass spectrometer. We also thank P.-S. Huang and Y.-E. A. Ban for computational tools; J. L. Gallaher for experimental assistance; J. Castellanos for the help with designing Fold-IV; H.-W. Lee, K. Pederson and J. Prestegard for measurements of residual dipolar couplings; and S. Khare, F. DiMaio, I. Andre, S. Fleishman, J. Mills, S. Takada, S. Fuchigami and G. Chikenji for comments on the manuscript. This work was supported by HHMI, DOE, DARPA, DTRA and the National Institutes of General Medical Science Protein Structure Initiative (PSI:Biology) programme, grant U54 GM094597. N.K. was also supported by Japan Society for the Promotion of Science (JSPS) Postdoctoral Fellowships for Research Abroad.

Author information

N.K., R.T.-K., G.L., G.T.M. and D.B. designed the research. N.K. performed folding simulations and analysed natural proteins. N.K. wrote program code. N.K. and R.T.-K. performed computational design work: Di-I_5 and Di-IV_5 were designed by N.K., and Di-II_10, Di-III_14 and Di-V_7 were designed by R.T.-K. R.T.-K. expressed, purified and characterized the designed proteins by biochemical assay. R.X. and T.B.A. prepared isotope-enriched protein samples for NMR structure determination. G.L. collected NMR data and determined the solution NMR structures. N.K., R.T.-K., G.L., G.T.M. and D.B. wrote the manuscript.

Correspondence to Gaetano T. Montelione or David Baker.

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Supplementary Information

This file contains Supplementary Figures 1-14, Supplementary Tables 1-8, Supplementary Discussions 1-2, Supplementary Methods 1-5 and Supplementary references (see contents for further details). (PDF 4484 kb)

Supplementary Data

This file contains Supplementary Data for Rosetta command lines to perform the design protocol. (ZIP 6 kb)

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Koga, N., Tatsumi-Koga, R., Liu, G. et al. Principles for designing ideal protein structures. Nature 491, 222–227 (2012). https://doi.org/10.1038/nature11600

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