Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.

PubWeight™: 1.03‹?› | Rank: Top 15%

🔗 View Article (PMC 3093456)

Published in Proc Natl Acad Sci U S A on April 25, 2011

Authors

Ryan N Gilbreth1, Khue Truong, Ikenna Madu, Akiko Koide, John B Wojcik, Nan-Sheng Li, Joseph A Piccirilli, Yuan Chen, Shohei Koide

Author Affiliations

1: Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

Articles citing this

Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. J Mol Biol (2011) 1.29

Structural insights for engineering binding proteins based on non-antibody scaffolds. Curr Opin Struct Biol (2012) 1.18

Computational design of a symmetric homodimer using β-strand assembly. Proc Natl Acad Sci U S A (2011) 1.12

Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications. Protein Eng Des Sel (2014) 0.89

Monobody-mediated alteration of enzyme specificity. Nat Chem Biol (2015) 0.84

Isolation of monobodies that bind specifically to the SH3 domain of the Fyn tyrosine protein kinase. N Biotechnol (2011) 0.83

Potent and specific inhibition of glycosidases by small artificial binding proteins (affitins). PLoS One (2014) 0.82

Characterization of monobody scaffold interactions with ligand via force spectroscopy and steered molecular dynamics. Sci Rep (2015) 0.82

Inhibition of RAS function through targeting an allosteric regulatory site. Nat Chem Biol (2016) 0.81

Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment. BMC Biochem (2013) 0.79

A strategy for phage display selection of functional domain-exchanged immunoglobulin scaffolds with high affinity for glycan targets. J Immunol Methods (2011) 0.79

Binding properties of SUMO-interacting motifs (SIMs) in yeast. J Mol Model (2015) 0.76

Directed Evolution of a Highly Specific FN3 Monobody to the SH3 Domain of Human Lyn Tyrosine Kinase. PLoS One (2016) 0.75

High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains. PLoS One (2015) 0.75

sNASP and ASF1A function through both competitive and compatible modes of histone binding. Nucleic Acids Res (2016) 0.75

Epitope-guided engineering of monobody binders for in vivo inhibition of Erk-2 signaling. ACS Chem Biol (2012) 0.75

Crystallization and preliminary X-ray analysis of the C-type lectin domain of the spicule matrix protein SM50 from Strongylocentrotus purpuratus. Acta Crystallogr F Struct Biol Commun (2014) 0.75

Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci (2017) 0.75

Articles cited by this

WebLogo: a sequence logo generator. Genome Res (2004) 59.58

Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74

Protein modification by SUMO. Annu Rev Biochem (2004) 10.59

Shape complementarity at protein/protein interfaces. J Mol Biol (1993) 10.40

Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci (1993) 9.38

A small ubiquitin-related polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2. Cell (1997) 9.01

A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex. J Cell Biol (1996) 7.64

Functional heterogeneity of small ubiquitin-related protein modifiers SUMO-1 versus SUMO-2/3. J Biol Chem (2000) 5.30

The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Mol Cell Biol (2010) 4.72

Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Nature (2005) 4.63

Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc Natl Acad Sci U S A (2004) 4.19

Specification of SUMO1- and SUMO2-interacting motifs. J Biol Chem (2006) 3.59

Covalent modification of p73alpha by SUMO-1. Two-hybrid screening with p73 identifies novel SUMO-1-interacting proteins and a SUMO-1 interaction motif. J Biol Chem (2000) 3.01

The fibronectin type III domain as a scaffold for novel binding proteins. J Mol Biol (1998) 2.65

Distinct and overlapping sets of SUMO-1 and SUMO-2 target proteins revealed by quantitative proteomics. Mol Cell Proteomics (2006) 2.64

SUMO junction-what's your function? New insights through SUMO-interacting motifs. EMBO Rep (2007) 2.58

Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation. J Biol Chem (2005) 2.44

Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature (2010) 2.41

High-affinity single-domain binding proteins with a binary-code interface. Proc Natl Acad Sci U S A (2007) 2.18

SUMO protease SENP1 induces isomerization of the scissile peptide bond. Nat Struct Mol Biol (2006) 1.89

A proline-90 residue unique to SUMO-4 prevents maturation and sumoylation. Biochem Biophys Res Commun (2005) 1.68

Small ubiquitin-related modifier (SUMO) binding determines substrate recognition and paralog-selective SUMO modification. J Biol Chem (2008) 1.65

Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library. Proteins (1992) 1.63

Engineering of recombinant crystallization chaperones. Curr Opin Struct Biol (2009) 1.53

A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nat Struct Mol Biol (2010) 1.47

A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J Mol Biol (2008) 1.45

Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. Methods Mol Biol (2007) 1.41

A small conserved surface in SUMO is the critical structural determinant of its transcriptional inhibitory properties. Mol Cell Biol (2005) 1.40

Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor. Proc Natl Acad Sci U S A (2002) 1.40

Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a SUMO E3 ligase that is SIM-dependent and SUMO-2/3-specific. J Biol Chem (2009) 1.23

Structure of the small ubiquitin-like modifier (SUMO)-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3. J Biol Chem (2008) 1.23

Design of cyclic peptides that bind protein surfaces with antibody-like affinity. ACS Chem Biol (2007) 1.23

Conformationally constrained peptide analogues of pTyr-Glu-Glu-Ile as inhibitors of the Src SH2 domain binding. J Med Chem (2004) 1.12

FRET-based in vitro assays for the analysis of SUMO protease activities. Methods Mol Biol (2009) 0.99

Affinity chromatography of native SUMO proteins using His-tagged recombinant UBC9 bound to Co2+-charged talon resin. Protein Expr Purif (2007) 0.97

Role of SUMO:SIM-mediated protein-protein interaction in non-homologous end joining. Oncogene (2010) 0.95

Articles by these authors

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics (2010) 15.90

Ensembl 2011. Nucleic Acids Res (2010) 14.68

Ensembl's 10th year. Nucleic Acids Res (2009) 10.82

An overview of Ensembl. Genome Res (2004) 10.35

A first-generation linkage disequilibrium map of human chromosome 22. Nature (2002) 7.03

The DNA sequence of the human X chromosome. Nature (2005) 6.97

Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet (2012) 5.28

A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics (2010) 4.68

The functional spectrum of low-frequency coding variation. Genome Biol (2011) 4.42

Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc Natl Acad Sci U S A (2004) 4.19

Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med (2010) 4.19

Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12

Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83

Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet (2012) 3.30

Spread of an inactive form of caspase-12 in humans is due to recent positive selection. Am J Hum Genet (2006) 3.00

SNP and haplotype mapping for genetic analysis in the rat. Nat Genet (2008) 2.96

General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol (2005) 2.88

High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol (2007) 2.88

Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am J Hum Genet (2008) 2.65

Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation. J Biol Chem (2005) 2.44

Crystal structure of full-length KcsA in its closed conformation. Proc Natl Acad Sci U S A (2009) 2.35

Molecular mechanism of Thioflavin-T binding to amyloid fibrils. Biochim Biophys Acta (2010) 2.22

How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta Biochim Biophys Sin (Shanghai) (2008) 2.19

Repair of methylation damage in DNA and RNA by mammalian AlkB homologues. J Biol Chem (2005) 2.19

High-affinity single-domain binding proteins with a binary-code interface. Proc Natl Acad Sci U S A (2007) 2.18

Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide. Nature (2013) 2.14

Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis. Cell (2011) 2.11

The intrinsic affinity between E2 and the Cys domain of E1 in ubiquitin-like modifications. Mol Cell (2007) 2.05

The 2.5 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. Immunity (2010) 2.02

Orally bioavailable small-molecule inhibitor of transcription factor Stat3 regresses human breast and lung cancer xenografts. Proc Natl Acad Sci U S A (2012) 1.94

Elevated expression of CUEDC2 protein confers endocrine resistance in breast cancer. Nat Med (2011) 1.93

Mice lacking sodium channel beta1 subunits display defects in neuronal excitability, sodium channel expression, and nodal architecture. J Neurosci (2004) 1.92

Unique binding interactions among Ubc9, SUMO and RanBP2 reveal a mechanism for SUMO paralog selection. Nat Struct Mol Biol (2004) 1.90

Curve analysis of the aging orbital aperture. Plast Reconstr Surg (2002) 1.87

RNA catalyses nuclear pre-mRNA splicing. Nature (2013) 1.86

A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res (2012) 1.83

Phage display for engineering and analyzing protein interaction interfaces. Curr Opin Struct Biol (2007) 1.81

Impact of the bag exchange procedure on risk of peritonitis. Perit Dial Int (2010) 1.80

Solution structure of the C-terminal domain of Ku80 suggests important sites for protein-protein interactions. Structure (2004) 1.78

Botulinum toxin type A for the treatment of trigeminal neuralgia: results from a randomized, double-blind, placebo-controlled trial. Cephalalgia (2012) 1.78

Antibacterial activity of graphite, graphite oxide, graphene oxide, and reduced graphene oxide: membrane and oxidative stress. ACS Nano (2011) 1.78

Sequential posttranslational modifications program FEN1 degradation during cell-cycle progression. Mol Cell (2012) 1.76

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry (2005) 1.73

Identification of a substrate recognition site on Ubc9. J Biol Chem (2002) 1.71

Role of an N-terminal site of Ubc9 in SUMO-1, -2, and -3 binding and conjugation. Biochemistry (2003) 1.70

Stabilization of G-quadruplex DNA and down-regulation of oncogene c-myc by quindoline derivatives. J Med Chem (2007) 1.70

Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies. J Mol Biol (2008) 1.70

Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res (2007) 1.66

Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci U S A (2008) 1.54

New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis. Chem Biol (2004) 1.53

Reduced sodium channel density, altered voltage dependence of inactivation, and increased susceptibility to seizures in mice lacking sodium channel beta 2-subunits. Proc Natl Acad Sci U S A (2002) 1.52

Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A (2007) 1.51

Transcriptional dynamics of bile salt export pump during pregnancy: mechanisms and implications in intrahepatic cholestasis of pregnancy. Hepatology (2014) 1.48

A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nat Struct Mol Biol (2010) 1.47

EGFR mutation detection in NSCLC--assessment of diagnostic application and recommendations of the German Panel for Mutation Testing in NSCLC. Virchows Arch (2010) 1.45

A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J Mol Biol (2008) 1.45

Genetic basis of Y-linked hearing impairment. Am J Hum Genet (2013) 1.42

Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. Methods Mol Biol (2007) 1.41

Genome-wide association study identifies ALDH7A1 as a novel susceptibility gene for osteoporosis. PLoS Genet (2010) 1.41

Genome-wide association study suggested copy number variation may be associated with body mass index in the Chinese population. J Hum Genet (2009) 1.40

Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor. Proc Natl Acad Sci U S A (2002) 1.40

Design of protein function leaps by directed domain interface evolution. Proc Natl Acad Sci U S A (2008) 1.39

Mesenchymal stem cells induce mature dendritic cells into a novel Jagged-2-dependent regulatory dendritic cell population. Blood (2008) 1.39

A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS Genet (2010) 1.35

Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. J Mol Biol (2011) 1.29

Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3). Methods Enzymol (2012) 1.29

Sharper and faster "nano darts" kill more bacteria: a study of antibacterial activity of individually dispersed pristine single-walled carbon nanotube. ACS Nano (2009) 1.29

A second divalent metal ion in the group II intron reaction center. Chem Biol (2007) 1.29

Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science (2009) 1.27

CDR-H3 diversity is not required for antigen recognition by synthetic antibodies. J Mol Biol (2012) 1.27

The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nat Struct Mol Biol (2006) 1.26

Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. Proc Natl Acad Sci U S A (2013) 1.25

Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange. J Mol Biol (2002) 1.25

Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin. J Mol Biol (2003) 1.24

The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing. Mol Cell (2010) 1.23

The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes. Nucleic Acids Res (2004) 1.21

Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein Sci (2008) 1.20

Associations of HLA-DP variants with hepatitis B virus infection in southern and northern Han Chinese populations: a multicenter case-control study. PLoS One (2011) 1.19

A new permutation strategy of pathway-based approach for genome-wide association study. BMC Bioinformatics (2009) 1.19

A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol (2010) 1.18

Structural insights for engineering binding proteins based on non-antibody scaffolds. Curr Opin Struct Biol (2012) 1.18