Chaperone-assisted crystallography with DARPins.

The structure of proteins that are difficult to crystallize can often be solved by forming a noncovalent complex with a helper protein--a crystallization "chaperone." Although several such applications have been described to date, their handling usually is still very laborious. A valuable addition to the present repertoire of binding proteins is the recently developed designed ankyrin repeat protein (DARPin) technology. DARPins are built based on the natural ankyrin repeat protein fold with randomized surface residue positions allowing specific binding to virtually any target protein. The broad potential of these binding proteins for X-ray crystallography is illustrated by five cocrystal structures that have been determined recently comprising target proteins from distinct families, namely a sugar binding protein, two kinases, a caspase, and a membrane protein. This article reviews the opportunities of this technology for structural biology and the structural aspects of the DARPin-protein complexes.

[1]  Cynthia Wolberger,et al.  The Structure of GABPα/β: An ETS Domain- Ankyrin Repeat Heterodimer Bound to DNA , 1998 .

[2]  G. P. Smith,et al.  Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. , 1985, Science.

[3]  Christophe Briand,et al.  Crystal Structure of Caspase-2, Apical Initiator of the Intrinsic Apoptotic Pathway* , 2003, Journal of Biological Chemistry.

[4]  G. Cohen,et al.  Interactions of protein antigens with antibodies. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Andreas Plückthun,et al.  Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. , 2003, Journal of molecular biology.

[6]  M. A. Carrondo,et al.  Structure of wild-type Plk-1 kinase domain in complex with a selective DARPin. , 2008, Acta crystallographica. Section D, Biological crystallography.

[7]  Sachdev S Sidhu,et al.  Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[8]  M. Stumpp,et al.  DARPins: a true alternative to antibodies. , 2007, Current opinion in drug discovery & development.

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

[10]  S. Smerdon,et al.  The ankyrin repeat: a diversity of interactions on a common structural framework. , 1999, Trends in biochemical sciences.

[11]  Shohei Koide,et al.  High-affinity single-domain binding proteins with a binary-code interface , 2007, Proceedings of the National Academy of Sciences.

[12]  H. Michel,et al.  Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase , 1995, Nature Structural Biology.

[13]  Andreas Plückthun,et al.  Intracellular Kinase Inhibitors Selected from Combinatorial Libraries of Designed Ankyrin Repeat Proteins* , 2005, Journal of Biological Chemistry.

[14]  S. Harrison,et al.  Structure of an IκBα/NF-κB Complex , 1998, Cell.

[15]  S. Harrison,et al.  Cocrystals of the DNA-binding domain of phage 434 repressor and a synthetic phage 434 operator. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[16]  G. Air,et al.  Epitopes on protein antigens: Misconceptions and realities , 1990, Cell.

[17]  Frederic A. Fellouse,et al.  Synthetic antibodies for specific recognition and crystallization of structured RNA , 2008, Proceedings of the National Academy of Sciences.

[18]  Philip D. Jeffrey,et al.  Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a , 1998, Nature.

[19]  S. Ghosh,et al.  X-ray Crystal Structure of an IκBβ·NF-κB p65 Homodimer Complex* , 2003, Journal of Biological Chemistry.

[20]  K. Diederichs,et al.  Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism , 2006, Science.

[21]  A. Plückthun,et al.  High-affinity binders selected from designed ankyrin repeat protein libraries , 2004, Nature Biotechnology.

[22]  H. Berglund,et al.  An affibody in complex with a target protein: Structure and coupled folding , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Andreas Plückthun,et al.  Allosteric inhibition of aminoglycoside phosphotransferase by a designed ankyrin repeat protein. , 2005, Structure.

[24]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[25]  Roderick MacKinnon,et al.  Gating the Selectivity Filter in ClC Chloride Channels , 2003, Science.

[26]  Satoshi Murakami,et al.  Crystal structure of bacterial multidrug efflux transporter AcrB , 2002, Nature.

[27]  C. Briand,et al.  Drug Export Pathway of Multidrug Exporter AcrB Revealed by DARPin Inhibitors , 2006, PLoS biology.

[28]  Robert M. Sweet,et al.  Structure of an Enzyme Required for Aminoglycoside Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases , 1997, Cell.

[29]  Satoshi Murakami,et al.  Crystal structures of a multidrug transporter reveal a functionally rotating mechanism , 2006, Nature.

[30]  J Koepke,et al.  Structure at 2.3 A resolution of the cytochrome bc(1) complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment. , 2000, Structure.

[31]  Bentley Ga The crystal structures of complexes formed between lysozyme and antibody fragments. , 1996 .

[32]  Manuel Serrano,et al.  Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d , 1998, Nature.

[33]  Rhett A. Kovall,et al.  Crystal Structure of the CSL-Notch-Mastermind Ternary Complex Bound to DNA , 2006, Cell.

[34]  A. Plückthun,et al.  In vitro selection and evolution of functional proteins by using ribosome display. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Frederic A. Fellouse,et al.  High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. , 2007, Journal of molecular biology.

[36]  R. Poljak,et al.  Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution , 1986, Science.

[37]  N. Damle,et al.  Biopharmaceutical drug discovery using novel protein scaffolds. , 2006, Current opinion in biotechnology.

[38]  R. Webster,et al.  Recombinant anti-sialidase single-chain variable fragment antibody. Characterization, formation of dimer and higher-molecular-mass multimers and the solution of the crystal structure of the single-chain variable fragment/sialidase complex. , 1994, European journal of biochemistry.

[39]  Yoshihide Hayashizaki,et al.  Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome. , 2007, Structure.

[40]  Seok-Yong Lee,et al.  Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy. , 2002, Journal of molecular biology.

[41]  P. Vekilov,et al.  Entropy and surface engineering in protein crystallization. , 2006, Acta crystallographica. Section D, Biological crystallography.

[42]  N. Pavletich,et al.  Structural basis of inhibition of CDK-cyclin complexes by INK4 inhibitors. , 2000, Genes & development.

[43]  Sachdev S Sidhu,et al.  Molecular recognition by a binary code. , 2005, Journal of molecular biology.

[44]  A. Honegger,et al.  The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. , 2008, Journal of molecular biology.

[45]  A. Plückthun,et al.  Designed to be stable: Crystal structure of a consensus ankyrin repeat protein , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Zygmunt S Derewenda,et al.  The use of recombinant methods and molecular engineering in protein crystallization. , 2004, Methods.

[47]  Andreas Plückthun,et al.  Inhibition of caspase-2 by a designed ankyrin repeat protein: specificity, structure, and inhibition mechanism. , 2007, Structure.

[48]  W. V. Shaw,et al.  Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts , 1991, Nature.

[49]  A. Cheng,et al.  Structure of the catalytic domain of human polo-like kinase 1. , 2007, Biochemistry.

[50]  R. MacKinnon,et al.  Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution , 2001, Nature.

[51]  P. Nordlund,et al.  Structural basis for recognition by an in vitro evolved affibody , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[52]  E. Padlan On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands , 1990, Proteins.

[53]  G. Ghosh,et al.  The Crystal Structure of the IκBα/NF-κB Complex Reveals Mechanisms of NF-κB Inactivation , 1998, Cell.

[54]  Hartmut Michel,et al.  Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans , 1995, Nature.

[55]  Lode Wyns,et al.  Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme , 1996, Nature Structural Biology.

[56]  H. Michel,et al.  Crystallisation of membrane proteins mediated by antibody fragments. , 2002, Current opinion in structural biology.

[57]  P. Bork Hundreds of ankyrin‐like repeats in functionally diverse proteins: Mobile modules that cross phyla horizontally? , 1993, Proteins.

[58]  Masami Horikoshi,et al.  Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. , 2007, Biochemical and biophysical research communications.