A docking model based on mass spectrometric and biochemical data describes phage packaging motor incorporation.

PubWeight™: 0.95‹?› | Rank: Top 15%

🔗 View Article (PMC 2938058)

Published in Mol Cell Proteomics on February 02, 2010

Authors

Chi-yu Fu1, Charlotte Uetrecht, Sebyung Kang, Marc C Morais, Albert J R Heck, Mark R Walter, Peter E Prevelige

Author Affiliations

1: Deptartment of Microbiology, University of Alabama, Birmingham, Alabama 35294-2170, USA.

Articles cited by this

UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) 112.47

Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19

Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77

The bacteriophage straight phi29 portal motor can package DNA against a large internal force. Nature (2001) 8.99

Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature (2005) 8.19

ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) 7.52

In-gel digestion of proteins for internal sequence analysis after one- or two-dimensional gel electrophoresis. Anal Biochem (1992) 6.44

The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell (1998) 5.91

Structure of the bacteriophage phi29 DNA packaging motor. Nature (2000) 5.25

A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal Chem (2002) 3.83

Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom Rev (2006) 3.67

Native mass spectrometry: a bridge between interactomics and structural biology. Nat Methods (2008) 3.11

Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol (2005) 2.98

Assembly of a tailed bacterial virus and its genome release studied in three dimensions. Cell (1998) 2.91

Fitting atomic models into electron-microscopy maps. Acta Crystallogr D Biol Crystallogr (2000) 2.87

Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29. Mol Cell (2005) 2.80

Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle. J Mol Biol (2002) 2.75

Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem Rev (2007) 2.57

MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J Am Soc Mass Spectrom (2003) 2.56

The DNA translocating vertex of dsDNA bacteriophage. Annu Rev Microbiol (1985) 2.55

P22 morphogenesis. I: Catalytic scaffolding protein in capsid assembly. J Supramol Struct (1974) 2.44

Chemical cross-linking and mass spectrometry for protein structural modeling. J Mol Biol (2003) 2.29

Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal Chem (2006) 2.06

Structure of phage P22 coat protein aggregates formed in the absence of the scaffolding protein. J Mol Biol (1978) 1.79

Bacteriophage phi29 scaffolding protein gp7 before and after prohead assembly. Nat Struct Biol (2003) 1.74

Regulation of the phage phi 29 prohead shape and size by the portal vertex. Virology (1991) 1.70

Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage phi29. Biophys J (2007) 1.68

High-resolution mass spectrometry of viral assemblies: molecular composition and stability of dimorphic hepatitis B virus capsids. Proc Natl Acad Sci U S A (2008) 1.64

Native protein mass spectrometry: from intact oligomers to functional machineries. Curr Opin Chem Biol (2004) 1.61

Model for DNA packaging into bacteriophage T4 heads. J Virol (1978) 1.45

Macromolecular electron microscopy in the era of structural genomics. Trends Biochem Sci (2000) 1.41

Data-driven docking for the study of biomolecular complexes. FEBS J (2005) 1.37

Initiation of P22 procapsid assembly in vivo. J Mol Biol (1988) 1.35

Scaffolding mutants identifying domains required for P22 procapsid assembly and maturation. Virology (1996) 1.21

Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture. Structure (2007) 1.19

Molecular dissection of ø29 scaffolding protein function in an in vitro assembly system. J Mol Biol (2006) 1.14

Bacteriophage p22 portal vertex formation in vivo. J Mol Biol (2002) 1.09

Macromolecular mass spectrometry and electron microscopy as complementary tools for investigation of the heterogeneity of bacteriophage portal assemblies. J Struct Biol (2006) 1.00

Determinants of bacteriophage phi29 head morphology. Structure (2006) 0.99

Formation of the prohead core of bacteriophage T4 in vivo. J Virol (1984) 0.98

In vitro incorporation of the phage Phi29 connector complex. Virology (2009) 0.95

Articles by these authors

The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24

Interferons, interferon-like cytokines, and their receptors. Immunol Rev (2004) 6.21

Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature (2011) 6.09

Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol (2011) 6.02

Interleukin-10 and related cytokines and receptors. Annu Rev Immunol (2004) 5.41

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc (2009) 4.61

RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A (2011) 4.58

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34

Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem (2004) 4.06

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J (2012) 3.70

A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 3.34

Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol Cell Proteomics (2007) 3.33

Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell (2009) 3.03

Wnt signaling through inhibition of β-catenin degradation in an intact Axin1 complex. Cell (2012) 3.03

Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat Struct Biol (2003) 2.76

Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors. Nature (2012) 2.76

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics (2010) 2.64

Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7. J Cell Biol (2008) 2.56

GATA-1 forms distinct activating and repressive complexes in erythroid cells. EMBO J (2005) 2.56

MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res (2010) 2.40

Sequential waves of functionally related proteins are expressed when B cells prepare for antibody secretion. Immunity (2003) 2.40

Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet (2012) 2.39

Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol (2003) 2.37

The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Natl Acad Sci U S A (2007) 2.36

Key interactions in HIV-1 maturation identified by hydrogen-deuterium exchange. Nat Struct Mol Biol (2004) 2.34

Identification of novel interactions in HIV-1 capsid protein assembly by high-resolution mass spectrometry. J Mol Biol (2003) 2.32

Lipid II is an intrinsic component of the pore induced by nisin in bacterial membranes. J Biol Chem (2003) 2.26

GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7. Mol Cell (2005) 2.21

Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol Cell Biol (2004) 2.18

Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal Chem (2009) 2.10

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics (2012) 2.10

Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal Chem (2006) 2.06

Phosphopeptide fragmentation and analysis by mass spectrometry. J Mass Spectrom (2009) 2.04

A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics (2006) 2.04

Mass spectrometry-based proteomics and network biology. Annu Rev Biochem (2012) 2.02

A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat Biotechnol (2013) 1.93

Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res (2011) 1.93

Structural changes of bacteriophage phi29 upon DNA packaging and release. EMBO J (2006) 1.90

Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides. Proc Natl Acad Sci U S A (2004) 1.89

Combining X-ray crystallography and electron microscopy. Structure (2005) 1.88

Mechanism of scaffolding-assisted viral assembly. Adv Protein Chem (2003) 1.87

Munc13-4 is an effector of rab27a and controls secretion of lysosomes in hematopoietic cells. Mol Biol Cell (2004) 1.85

A central role for TFIID in the pluripotent transcription circuitry. Nature (2013) 1.82

The leukemia-associated Mllt10/Af10-Dot1l are Tcf4/β-catenin coactivators essential for intestinal homeostasis. PLoS Biol (2010) 1.81

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J Proteome Res (2007) 1.80

Monitoring macromolecular complexes involved in the chaperonin-assisted protein folding cycle by mass spectrometry. Nat Methods (2005) 1.79

Ion mobility mass spectrometry of proteins and protein assemblies. Chem Soc Rev (2009) 1.77

Three-dimensional structure of a viral genome-delivery portal vertex. Nat Struct Mol Biol (2011) 1.71

Activation of FoxM1 during G2 requires cyclin A/Cdk-dependent relief of autorepression by the FoxM1 N-terminal domain. Mol Cell Biol (2008) 1.67

High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nat Methods (2012) 1.67

High-resolution mass spectrometry of viral assemblies: molecular composition and stability of dimorphic hepatitis B virus capsids. Proc Natl Acad Sci U S A (2008) 1.64

Structure and mechanism of receptor sharing by the IL-10R2 common chain. Structure (2010) 1.63

Human Ccr4-Not complexes contain variable deadenylase subunits. Biochem J (2009) 1.61

Native protein mass spectrometry: from intact oligomers to functional machineries. Curr Opin Chem Biol (2004) 1.61

An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics. Nat Methods (2007) 1.59

BiP/GRP78 is an intracellular target for MDA-7/IL-24 induction of cancer-specific apoptosis. Cancer Res (2006) 1.58

Dis3-like 1: a novel exoribonuclease associated with the human exosome. EMBO J (2010) 1.57

Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography. J Virol (2008) 1.56

Kinetic analysis of the role of intersubunit interactions in human immunodeficiency virus type 1 capsid protein assembly in vitro. J Virol (2002) 1.55

Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Proteomics (2008) 1.54

Complement is activated by IgG hexamers assembled at the cell surface. Science (2014) 1.52

Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses. Proc Natl Acad Sci U S A (2008) 1.51

Unique aspects of mda-7/IL-24 antitumor bystander activity: establishing a role for secretion of MDA-7/IL-24 protein by normal cells. Oncogene (2005) 1.49

Interrogating viral capsid assembly with ion mobility-mass spectrometry. Nat Chem (2010) 1.47

Engineering nanocages with polyglutamate domains for coupling to hydroxyapatite biomaterials and allograft bone. Biomaterials (2013) 1.47

Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol (2006) 1.47

Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase. Nat Methods (2008) 1.46

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol (2011) 1.44

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44

Quantitative proteomics by metabolic labeling of model organisms. Mol Cell Proteomics (2009) 1.42

Structure of the yeast vacuolar ATPase. J Biol Chem (2008) 1.41

Comprehensive analysis of the secreted proteins of the parasite Haemonchus contortus reveals extensive sequence variation and differential immune recognition. J Biol Chem (2003) 1.41

Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Mol Cell Proteomics (2012) 1.40

Isolation of flagellated bacteria implicated in Crohn's disease. Inflamm Bowel Dis (2007) 1.40

RNA polymerase I contains a TFIIF-related DNA-binding subcomplex. Mol Cell (2010) 1.40

Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes Dev (2008) 1.38

Toward a comprehensive characterization of a human cancer cell phosphoproteome. J Proteome Res (2012) 1.37

MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosome biogenesis. Immunol Cell Biol (2010) 1.37

Species-specific determinants in the IgG CH3 domain enable Fab-arm exchange by affecting the noncovalent CH3-CH3 interaction strength. J Immunol (2011) 1.34

Chaperonin complexes monitored by ion mobility mass spectrometry. J Am Chem Soc (2009) 1.33

Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. Anal Chem (2012) 1.32

On terminal alkynes that can react with active-site cysteine nucleophiles in proteases. J Am Chem Soc (2013) 1.32

Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J Proteome Res (2012) 1.32

Crystal structure of human cytomegalovirus IL-10 bound to soluble human IL-10R1. Proc Natl Acad Sci U S A (2002) 1.32

Conformational changes mediate interleukin-10 receptor 2 (IL-10R2) binding to IL-10 and assembly of the signaling complex. J Biol Chem (2006) 1.31

The phosphoproteomics data explosion. Curr Opin Chem Biol (2009) 1.30

Asymmetric binding of transferrin receptor to parvovirus capsids. Proc Natl Acad Sci U S A (2007) 1.30

Targeted analysis of protein termini. J Proteome Res (2007) 1.28

Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. Mol Cell Proteomics (2010) 1.28

The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit. Structure (2009) 1.27

Determination of stoichiometry and conformational changes in the first step of the P22 tail assembly. J Mol Biol (2008) 1.27

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics (2009) 1.27

cGMP-binding prepares PKG for substrate binding by disclosing the C-terminal domain. J Mol Biol (2007) 1.27

Norwalk virus assembly and stability monitored by mass spectrometry. Mol Cell Proteomics (2010) 1.26

Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain. Structure (2005) 1.26

Stoichiometry of the peripheral stalk subunits E and G of yeast V1-ATPase determined by mass spectrometry. J Biol Chem (2007) 1.26

Endogenous phosphatidylcholine and a long spacer ligand stabilize the lipid-binding groove of CD1b. EMBO J (2006) 1.26