Programmable design of orthogonal protein heterodimers

[1]  E. Goldman,et al.  Orthogonal Synthetic Zippers as Protein Scaffolds , 2018, ACS omega.

[2]  Albert J R Heck,et al.  Parsimonious Charge Deconvolution for Native Mass Spectrometry , 2018, Journal of proteome research.

[3]  D. Baker,et al.  Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS , 2018, Proceedings of the National Academy of Sciences.

[4]  D. Baker,et al.  Global analysis of protein folding using massively parallel design, synthesis, and testing , 2017, Science.

[5]  Robert A. Langan,et al.  De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity , 2016, Science.

[6]  A. Lubben,et al.  Deriving Heterospecific Self-Assembling Protein–Protein Interactions Using a Computational Interactome Screen , 2016, Journal of molecular biology.

[7]  M. Laub,et al.  Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates , 2015, Cell.

[8]  P. Parren,et al.  Tandem Native Mass-Spectrometry on Antibody-Drug Conjugates and Submillion Da Antibody-Antigen Protein Assemblies on an Orbitrap EMR Equipped with a High-Mass Quadrupole Mass Selector. , 2015, Analytical chemistry.

[9]  Erik G Marklund,et al.  Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. , 2015, Analytical chemistry.

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

[11]  Jukka Westermarck,et al.  ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays , 2014, PloS one.

[12]  V. Wysocki,et al.  Surface induced dissociation: dissecting noncovalent protein complexes in the gas phase. , 2014, Accounts of chemical research.

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

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

[15]  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.

[16]  V. Wysocki,et al.  Surface-induced dissociation of ion mobility-separated noncovalent complexes in a quadrupole/time-of-flight mass spectrometer. , 2012, Analytical chemistry.

[17]  Kenneth Evan Thompson,et al.  SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains , 2012, ACS synthetic biology.

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

[19]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[20]  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.

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

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

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

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

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

[26]  W. Kabsch.  XDS , 2010, Acta crystallographica. Section D, Biological crystallography.

[27]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[28]  Michael T. Laub,et al.  Rewiring the Specificity of Two-Component Signal Transduction Systems , 2008, Cell.

[29]  G. B. Wisely,et al.  Automated in-line gel filtration for native state mass spectrometry , 2008, Journal of the American Society for Mass Spectrometry.

[30]  A. J. Kennan,et al.  Orthogonal recognition in dimeric coiled coils via buried polar-group modulation. , 2008, Journal of the American Chemical Society.

[31]  Randy J. Read,et al.  Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard , 2007 .

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

[33]  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 .

[34]  C. Robinson,et al.  Aspects of native proteins are retained in vacuum. , 2006, Current opinion in chemical biology.

[35]  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.

[36]  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.

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

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

[39]  Gevorg Grigoryan,et al.  Structure-based prediction of bZIP partnering specificity. , 2006, Journal of molecular biology.

[40]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

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

[42]  R. Schiestl,et al.  High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier , 1989, Current Genetics.

[43]  Wendell A. Lim,et al.  Optimization of specificity in a cellular protein interaction network by negative selection , 2003, Nature.

[44]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

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

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

[47]  S. Jones,et al.  Principles of protein-protein interactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

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

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

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

[51]  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.

[52]  C. Chien.  A novel genetic system to detect protein-protein interactions , 1991 .

[53]  Francis Crick,et al.  The Fourier transform of a coiled-coil , 1953 .