Engineering protein assemblies with allosteric control via monomer fold-switching

[1]  I. Hamley Protein Assemblies: Nature-Inspired and Designed Nanostructures , 2019, Biomacromolecules.

[2]  John Orban,et al.  Structural metamorphism and polymorphism in proteins on the brink of thermodynamic stability , 2018, Protein science : a publication of the Protein Society.

[3]  F. Tezcan,et al.  Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. , 2018, Journal of the American Chemical Society.

[4]  B. Volkman,et al.  Unfolding the Mysteries of Protein Metamorphosis , 2018, ACS chemical biology.

[5]  Loren L Looger,et al.  Extant fold-switching proteins are widespread , 2018, Proceedings of the National Academy of Sciences.

[6]  John A Tainer,et al.  Designing and defining dynamic protein cage nanoassemblies in solution , 2016, Science Advances.

[7]  Neil P. King,et al.  Designed proteins induce the formation of nanocage-containing extracellular vesicles , 2016, Nature.

[8]  J. Brodin,et al.  De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. , 2016, Journal of the American Chemical Society.

[9]  Q. Luo,et al.  Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures. , 2016, Chemical reviews.

[10]  David Baker,et al.  Accurate design of megadalton-scale two-component icosahedral protein complexes , 2016, Science.

[11]  G. Skiniotis,et al.  Flexible, symmetry-directed approach to assembling protein cages , 2016, Proceedings of the National Academy of Sciences.

[12]  C O S Sorzano,et al.  Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy. , 2016, Journal of structural biology.

[13]  E. Lindahl,et al.  Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 , 2016, bioRxiv.

[14]  David Baker,et al.  Design of a hyperstable 60-subunit protein icosahedron , 2016, Nature.

[15]  Q. Luo,et al.  Protein self-assembly via supramolecular strategies. , 2016, Chemical Society reviews.

[16]  P. Zavattieri,et al.  Self-Assembly of Coherently Dynamic, Auxetic Two-Dimensional Protein Crystals , 2016, Nature.

[17]  Victor Muñoz,et al.  Limited cooperativity in protein folding. , 2016, Current opinion in structural biology.

[18]  R. Nolte,et al.  Natural supramolecular protein assemblies. , 2016, Chemical Society reviews.

[19]  N. Grigorieff,et al.  CTFFIND4: Fast and accurate defocus estimation from electron micrographs , 2015, bioRxiv.

[20]  J. Ha,et al.  Engineered Domain Swapping as an On/Off Switch for Protein Function. , 2015, Chemistry & biology.

[21]  Yanzhi Guo,et al.  A structural dissection of large protein-protein crystal packing contacts , 2015, Scientific Reports.

[22]  Sheng Li,et al.  A protein fold switch joins the circadian oscillator to clock output in cyanobacteria , 2015, Science.

[23]  S. Teichmann,et al.  Structure, dynamics, assembly, and evolution of protein complexes. , 2015, Annual review of biochemistry.

[24]  Matthias J. Brunner,et al.  Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement , 2015, Nature Methods.

[25]  David Baker,et al.  Accurate design of co-assembling multi-component protein nanomaterials , 2014, Nature.

[26]  J. Brodin,et al.  Exceptionally stable, redox-active supramolecular protein assemblies with emergent properties , 2014, Proceedings of the National Academy of Sciences.

[27]  Arvind Ramanathan,et al.  Protein conformational populations and functionally relevant substates. , 2014, Accounts of chemical research.

[28]  Wah Chiu,et al.  Reprogramming an ATP-driven protein machine into a light-gated nanocage , 2013, Nature nanotechnology.

[29]  J M Carazo,et al.  Xmipp 3.0: an improved software suite for image processing in electron microscopy. , 2013, Journal of structural biology.

[30]  J. Brodin,et al.  In vitro and cellular self-assembly of a Zn-binding protein cryptand via templated disulfide bonds. , 2013, Journal of the American Chemical Society.

[31]  Hongbin Li,et al.  Highly ordered protein nanorings designed by accurate control of glutathione S-transferase self-assembly. , 2013, Journal of the American Chemical Society.

[32]  D. Agard,et al.  Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM , 2013, Nature Methods.

[33]  Diana M. Mitrea,et al.  Regulated unfolding of proteins in signaling , 2013, FEBS letters.

[34]  F. Tezcan,et al.  Re-engineering protein interfaces yields copper-inducible ferritin cage assembly. , 2013, Nature chemical biology.

[35]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[36]  Jeung-Hoi Ha,et al.  Protein conformational switches: from nature to design. , 2012, Chemistry.

[37]  Duilio Cascio,et al.  Structure of a 16-nm Cage Designed by Using Protein Oligomers , 2012, Science.

[38]  Kristin N. Parent,et al.  Metal-directed, chemically-tunable assembly of one-, two- and three-dimensional crystalline protein arrays , 2012, Nature chemistry.

[39]  Brian Kuhlman,et al.  Computational design of a symmetric homodimer using β-strand assembly , 2011, Proceedings of the National Academy of Sciences.

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

[41]  K. Lindorff-Larsen,et al.  How robust are protein folding simulations with respect to force field parameterization? , 2011, Biophysical journal.

[42]  Owen Johnson,et al.  iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM , 2011, Acta crystallographica. Section D, Biological crystallography.

[43]  Philip R. Evans,et al.  An introduction to data reduction: space-group determination, scaling and intensity statistics , 2011, Acta crystallographica. Section D, Biological crystallography.

[44]  John Orban,et al.  Proteins that switch folds. , 2010, Current opinion in structural biology.

[45]  Brian Kuhlman,et al.  Metal templated design of protein interfaces , 2009, Proceedings of the National Academy of Sciences.

[46]  P. Alexander,et al.  A minimal sequence code for switching protein structure and function , 2009, Proceedings of the National Academy of Sciences.

[47]  Alexey G. Murzin,et al.  Metamorphic Proteins , 2008, Science.

[48]  Brian F. Volkman,et al.  Interconversion between two unrelated protein folds in the lymphotactin native state , 2008, Proceedings of the National Academy of Sciences.

[49]  Oliver F. Lange,et al.  Consistent blind protein structure generation from NMR chemical shift data , 2008, Proceedings of the National Academy of Sciences.

[50]  G. Schulz,et al.  Designed Protein-Protein Association , 2008, Science.

[51]  Min Lu,et al.  A seven-helix coiled coil , 2006, Proceedings of the National Academy of Sciences.

[52]  Sarah A. Teichmann,et al.  3D Complex: A Structural Classification of Protein Complexes , 2006, PLoS Comput. Biol..

[53]  R. Siegel,et al.  Chemically controlled self-assembly of protein nanorings. , 2006, Journal of the American Chemical Society.

[54]  B. Kuhlman,et al.  Computational design of a single amino acid sequence that can switch between two distinct protein folds. , 2006, Journal of the American Chemical Society.

[55]  Gene Kwan,et al.  Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2. , 2005, Biochemistry.

[56]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[57]  Nathan A. Baker,et al.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations , 2004, Nucleic Acids Res..

[58]  S. Petersen,et al.  L-phenylalanine binding and domain organization in human phenylalanine hydroxylase: a differential scanning calorimetry study. , 2002, Biochemistry.

[59]  J. García de la Torre,et al.  HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images , 2001, European Biophysics Journal.

[60]  P. Schuck,et al.  Determination of the sedimentation coefficient distribution by least-squares boundary modeling. , 2000, Biopolymers.

[61]  K Wüthrich,et al.  NMR spectroscopy of large molecules and multimolecular assemblies in solution. , 1999, Current opinion in structural biology.

[62]  E. Freire,et al.  A simple method to measure the absolute heat capacity of proteins. , 1999, Analytical biochemistry.

[63]  K. Williams,et al.  Determination of molecular masses of proteins in solution: Implementation of an HPLC size exclusion chromatography and laser light scattering service in a core laboratory. , 1999, Journal of biomolecular techniques : JBT.

[64]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .

[65]  A. Efimov Structural trees for protein superfamilies , 1997, Proteins.

[66]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

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

[68]  V. Muñoz,et al.  Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales , 1994 .

[69]  A. Fersht,et al.  Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. , 1991, Biochemistry.

[70]  Robert Powers,et al.  A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams , 1991 .

[71]  M. James,et al.  Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. , 1988, Biochemistry.

[72]  Emmanuel D Levy,et al.  Structural, evolutionary, and assembly principles of protein oligomerization. , 2013, Progress in molecular biology and translational science.

[73]  J. Matthews,et al.  Dimers, oligomers, everywhere. , 2012, Advances in experimental medicine and biology.

[74]  D. S. Garrett,et al.  A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams. 1991. , 2011, Journal of magnetic resonance.

[75]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[76]  Vincent B. Chen,et al.  Acta Crystallographica Section D Biological , 2001 .

[77]  Arthur J. Rowe,et al.  Analytical ultracentrifugation in biochemistry and polymer science , 1992 .