A Novel Neural Network Technique for Analysis and Classification of EM Single-Particle Images

Pascual-Montano, Alberto; Donate, Luis-Enrique; Valle, Mikel; Bárcena, Montserrat; Pascual-Marqui, Roberto D.; Carazo, José Marı́a

doi:10.1006/jsbi.2001.4369

Cited by 74 publications

(72 citation statements)

References 27 publications

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“…Peptides p15 ( 50 GNPVCVRPTPKWQKGIGEFFRLSPKDSE 77 ) and p15 [59][60][61][62][63][64][65][66][67][68][69][70] were purchased from Apeptide Co. For NMR, ITC and fluorescence polarization measurements, concentrated peptide stock solutions were prepared dissolving the lyophilized powder in water or in PBS, pH 7.0, and the pH was adjusted with NaOH, if necessary. For crystallization, the buffer was 20 mM Tris, pH 7.5, 0.5 mM TCEP.…”

Section: Methodsmentioning

confidence: 99%

“…To study the role of different p15 regions in the interaction with PCNA, we designed three p15 fragments: the N-terminal deletion mutant p15 (hereafter named p15 DN ) lacking many of the residues experiencing reduced NMR signal intensity and enhanced 15 N R 2 rates on PCNA binding; the p15 fragment comprising the central residues that experience the largest drop in NMR signal intensity on PCNA binding; and p15 [59][60][61][62][63][64][65][66][67][68][69][70] that corresponds to the smallest PIP-box containing fragment of p21 with reported binding to PCNA 19 .…”

Section: P15-pcna Interaction Involves An Extended Pip-box Regionmentioning

confidence: 99%

“…The N-terminal deletion mutant binds PCNA with only slightly lower affinity than p15, implying that any transient interactions of the N-terminal V2-S31 residues stabilize the complex only marginally. The affinity of p15 , however, is reduced by a factor of 5 and the shortest core fragment p15 [59][60][61][62][63][64][65][66][67][68][69][70] even by a factor of 33. These results indicate that residues G50-T58 and/or L71-E77 strongly contribute to PCNA binding, which is further enhanced by residues A32-G49.…”

Section: P15-pcna Interaction Involves An Extended Pip-box Regionmentioning

confidence: 99%

“…The NMR spectra of PCNA in the presence of the different constructs indicate rather similar binding modes for p15, p15 DN and p15 , but less so for p15 [59][60][61][62][63][64][65][66][67][68][69][70] (Supplementary Fig. 2).…”

Section: P15-pcna Interaction Involves An Extended Pip-box Regionmentioning

confidence: 99%

“…5a). The central fragment p15 binds DNA with even lower affinity, and no DNA binding was observed with the core PIP-box fragment p15 [59][60][61][62][63][64][65][66][67][68][69][70] . When DNA was titrated with PCNAbound p15, the increase in fluorescence polarization was larger (Fig.…”

Section: Articlementioning

confidence: 99%

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Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

et al. 2015

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The intrinsically disordered protein p15 PAF regulates DNA replication and repair by binding to the proliferating cell nuclear antigen (PCNA) sliding clamp. We present the structure of the human p15 PAF -PCNA complex. Crystallography and NMR show the central PCNA-interacting protein motif (PIP-box) of p15 PAF tightly bound to the front-face of PCNA. In contrast to other PCNA-interacting proteins, p15 PAF also contacts the inside of, and passes through, the PCNA ring. The disordered p15 PAF termini emerge at opposite faces of the ring, but remain protected from 20S proteasomal degradation. Both free and PCNA-bound p15 PAF binds DNA mainly through its histone-like N-terminal tail, while PCNA does not, and a model of the ternary complex with DNA inside the PCNA ring is consistent with electron micrographs. We propose that p15 PAF acts as a flexible drag that regulates PCNA sliding along the DNA and facilitates the switch from replicative to translesion synthesis polymerase binding.

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Section: Methodsmentioning

confidence: 99%

Section: P15-pcna Interaction Involves An Extended Pip-box Regionmentioning

confidence: 99%

Section: P15-pcna Interaction Involves An Extended Pip-box Regionmentioning

confidence: 99%

Section: P15-pcna Interaction Involves An Extended Pip-box Regionmentioning

confidence: 99%

Section: Articlementioning

confidence: 99%

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Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

et al. 2015

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Characterization of Nano Features in Biopolymers using Small‐angle X‐ray Scattering, Electron Microscopy and Modeling

Krebs

Böttcher

2003

Nanotechnologies for the Life Sciences

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The sections in this article are Introduction Small‐angle X ‐ray Scattering Scattering Technique Scattering Phenomenon Scattering Curve and Pair Distance Distribution Function Determination of Scattering Parameters Experimental Setup Interpretation of Data Direct Methods Indirect Methods Electron Microscopy Image Formation Interference of Electrons with Matter Contrast Transfer Function Sample Preparation Vitrification of Biological Specimens Two‐dimensional Merging of Electron Microscopic Data Cross Correlation Function Identification of the Different Views Merging of EM ‐data in Three Dimensions Sinogram Correlation Reconstruction of the Three‐dimensional Model Merging of Methods Comparison of EM and SAXS Data SAXS Modeling Approaches using EM Information

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Transmission Electron Microscopy (TEM) of Radiation Sensitive Supramolecular Architectures – Strategies for a Comprehensive Structure Characterization

Böttcher¹

2012

Analytical Methods in Supramolecular Chemistry

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A Novel Neural Network Technique for Analysis and Classification of EM Single-Particle Images

Cited by 74 publications

References 27 publications

Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

Characterization of Nano Features in Biopolymers using Small‐angle X‐ray Scattering, Electron Microscopy and Modeling

Transmission Electron Microscopy (TEM) of Radiation Sensitive Supramolecular Architectures – Strategies for a Comprehensive Structure Characterization

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