De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity

Building with designed proteins General design principles for protein interaction specificity are challenging to extract. DNA nanotechnology, on the other hand, has harnessed the limited set of hydrogen-bonding interactions from Watson-Crick base-pairing to design and build a wide range of shapes. Protein-based materials have the potential for even greater geometric and chemical diversity, including additional functionality. Boyken et al. designed a class of protein oligomers that have interaction specificity determined by modular arrays of extensive hydrogen bond networks (see the Perspective by Netzer and Fleishman). They use the approach, which could one day become programmable, to build novel topologies with two concentric rings of helices. Science, this issue p. 680; see also p. 657 Protein oligomers with designed arrays of hydrogen bond networks enable programming of interaction specificity. In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.

[1]  F. Crick,et al.  The packing of α‐helices: simple coiled‐coils , 1953 .

[2]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[3]  S. Fields,et al.  The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[4]  P. S. Kim,et al.  A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. , 1993, Science.

[5]  David J. States,et al.  Identification of protein coding regions by database similarity search , 1993, Nature Genetics.

[6]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[7]  P. S. Kim,et al.  A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. , 1995, Biochemistry.

[8]  D. Woolfson,et al.  Predicting oligomerization states of coiled coils , 1995, Protein science : a publication of the Protein Society.

[9]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[10]  D. Woolfson,et al.  Buried polar residues and structural specificity in the GCN4 leucine zipper , 1996, Nature Structural Biology.

[11]  S. L. Mayo,et al.  Protein design automation , 1996, Protein science : a publication of the Protein Society.

[12]  Stanley Fields,et al.  A protein linkage map of Escherichia coli bacteriophage T7 , 1996, Nature Genetics.

[13]  D. Eisenberg,et al.  The crystal structure of the designed trimeric coiled coil coil‐VaLd: Implications for engineering crystals and supramolecular assemblies , 1997, Protein science : a publication of the Protein Society.

[14]  R. Nussinov,et al.  Hydrogen bonds and salt bridges across protein-protein interfaces. , 1997, Protein engineering.

[15]  W. DeGrado,et al.  De novo design of native proteins: characterization of proteins intended to fold into antiparallel, rop-like, four-helix bundles. , 1997, Biochemistry.

[16]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[17]  P. S. Kim,et al.  High-resolution protein design with backbone freedom. , 1998, Science.

[18]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[19]  P. S. Kim,et al.  Crystal structure of GCN4-pIQI, a trimeric coiled coil with buried polar residues. , 1998, Journal of molecular biology.

[20]  S. L. Mayo,et al.  Computational protein design. , 1999, Structure.

[21]  D. Baker,et al.  Native protein sequences are close to optimal for their structures. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Liam J. McGuffin,et al.  The PSIPRED protein structure prediction server , 2000, Bioinform..

[23]  P S Kim,et al.  Buried polar residues in coiled-coil interfaces. , 2001, Biochemistry.

[24]  P. Burkhard,et al.  Coiled coils: a highly versatile protein folding motif. , 2001, Trends in cell biology.

[25]  C. Vinson,et al.  A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K. , 2002, Biochemistry.

[26]  Barry Honig,et al.  On the role of electrostatic interactions in the design of protein-protein interfaces. , 2002, Journal of molecular biology.

[27]  D. Baker,et al.  Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.

[28]  Markus Gruber,et al.  Historical review: another 50th anniversary--new periodicities in coiled coils. , 2003, Trends in biochemical sciences.

[29]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[30]  D. Baker,et al.  Computational redesign of protein-protein interaction specificity , 2004, Nature Structural &Molecular Biology.

[31]  Richard A Friesner,et al.  Sequence optimization and designability of enzyme active sites. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[32]  G. Rose,et al.  Do all backbone polar groups in proteins form hydrogen bonds? , 2005, Protein science : a publication of the Protein Society.

[33]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[34]  W. DeGrado,et al.  Polar networks control oligomeric assembly in membranes. , 2006, Journal of the American Chemical Society.

[35]  D. Baker,et al.  Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. , 2006, Journal of molecular biology.

[36]  C. Vinson,et al.  Stability of 100 homo and heterotypic coiled-coil a-a' pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R). , 2006, Biochemistry.

[37]  William Stafford Noble,et al.  Semi-supervised learning for peptide identification from shotgun proteomics datasets , 2007, Nature Methods.

[38]  D. Tabb,et al.  Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. , 2007, Journal of proteome research.

[39]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[40]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[41]  Stephen L Mayo,et al.  A de novo designed protein–protein interface , 2007, Protein science : a publication of the Protein Society.

[42]  A. Keating,et al.  Structural specificity in coiled-coil interactions. , 2008, Current opinion in structural biology.

[43]  Gevorg Grigoryan,et al.  Design of protein-interaction specificity affords selective bZIP-binding peptides , 2009, Nature.

[44]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[45]  D. Baker,et al.  Simultaneous prediction of protein folding and docking at high resolution , 2009, Proceedings of the National Academy of Sciences.

[46]  W. Bras,et al.  Scatter: software for the analysis of nano‐ and mesoscale small‐angle scattering , 2010 .

[47]  Pu Liu,et al.  Fast determination of the optimal rotational matrix for macromolecular superpositions , 2009, J. Comput. Chem..

[48]  Amy E Keating,et al.  A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering. , 2010, Journal of the American Chemical Society.

[49]  Paul D Adams,et al.  Joint X-ray and neutron refinement with phenix.refine. , 2010, Acta crystallographica. Section D, Biological crystallography.

[50]  Andrej Sali,et al.  FoXS: a web server for rapid computation and fitting of SAXS profiles , 2010, Nucleic Acids Res..

[51]  Gevorg Grigoryan,et al.  Probing designability via a generalized model of helical bundle geometry. , 2011, Journal of molecular biology.

[52]  Aimee L Boyle,et al.  De novo designed peptides for biological applications. , 2011, Chemical Society reviews.

[53]  Timothy A. Whitehead,et al.  Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin , 2011, Science.

[54]  Jens Meiler,et al.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.

[55]  R. Jerala,et al.  De novo design of orthogonal peptide pairs forming parallel coiled‐coil heterodimers , 2011, Journal of peptide science : an official publication of the European Peptide Society.

[56]  John A Tainer,et al.  Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. , 2011, Biopolymers.

[57]  Jens Meiler,et al.  RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite , 2011, PloS one.

[58]  David Baker,et al.  Modeling Symmetric Macromolecular Structures in Rosetta3 , 2011, PloS one.

[59]  D. Baker,et al.  RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design , 2011, PloS one.

[60]  David Baker,et al.  A de novo protein binding pair by computational design and directed evolution. , 2011, Molecular cell.

[61]  Aimee L. Boyle,et al.  A basis set of de novo coiled-coil peptide oligomers for rational protein design and synthetic biology. , 2012, ACS synthetic biology.

[62]  B. Kuhlman,et al.  Computational protein design with explicit consideration of surface hydrophobic patches , 2012, Proteins.

[63]  P. Yin,et al.  Complex shapes self-assembled from single-stranded DNA tiles , 2012, Nature.

[64]  D. Baker,et al.  Principles for designing ideal protein structures , 2012, Nature.

[65]  Randy J. Read,et al.  Phenix - a comprehensive python-based system for macromolecular structure solution , 2012 .

[66]  D. Baker,et al.  Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy , 2012, Science.

[67]  Shintaro Minami,et al.  MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments , 2012, BMC Bioinformatics.

[68]  John A Tainer,et al.  Accurate SAXS profile computation and its assessment by contrast variation experiments. , 2013, Biophysical journal.

[69]  D. Baker,et al.  Computational design of a protein-based enzyme inhibitor. , 2013, Journal of molecular biology.

[70]  Orr Ashenberg,et al.  Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution , 2013, Science.

[71]  B. Kuhlman,et al.  A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds , 2013, Protein science : a publication of the Protein Society.

[72]  Aimee L Boyle,et al.  A set of de novo designed parallel heterodimeric coiled coils with quantified dissociation constants in the micromolar to sub-nanomolar regime. , 2013, Journal of the American Chemical Society.

[73]  Gevorg Grigoryan,et al.  De novo design of a transmembrane Zn2+-transporting four-helix bundle , 2014, Science.

[74]  John A Tainer,et al.  High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. , 2014, Methods in molecular biology.

[75]  Richard B. Sessions,et al.  Computational design of water-soluble α-helical barrels , 2014, Science.

[76]  B. Herguedas,et al.  A hydrogen bond network in the active site of Anabaena ferredoxin-NADP(+) reductase modulates its catalytic efficiency. , 2014, Biochimica et biophysica acta.

[77]  Jenifer B. Kaplan,et al.  Increasing the affinity of selective bZIP‐binding peptides through surface residue redesign , 2014, Protein science : a publication of the Protein Society.

[78]  Hao Yan,et al.  Structural DNA Nanotechnology: State of the Art and Future Perspective , 2014, Journal of the American Chemical Society.

[79]  S. Elliott,et al.  Hydrogen Bonding Networks Tune Proton-Coupled Redox Steps during the Enzymatic Six-Electron Conversion of Nitrite to Ammonia , 2014, Biochemistry.

[80]  D. Baker,et al.  High thermodynamic stability of parametrically designed helical bundles , 2014, Science.

[81]  Matthew J. O’Meara,et al.  Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. , 2015, Journal of chemical theory and computation.

[82]  N. Linden,et al.  Local and macroscopic electrostatic interactions in single α-helices. , 2015, Nature chemical biology.

[83]  Richard A. Muscat,et al.  DNA nanotechnology from the test tube to the cell. , 2015, Nature nanotechnology.