Comparison of surface and hydrogel-based protein microchips

Zubtsov, D.A.; Savvateeva, Elena; Rubina, A. Yu.; Pan’kov, S. V.; Коновалова, Е. В.; Moiseeva, O. V.; Chechetkin, V. R.; Заседателев, А. С.

doi:10.1016/j.ab.2007.04.040

Cited by 72 publications

(86 citation statements)

References 19 publications

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“…A longer cellulose chain may attach more robustly to the slide, thereby increasing CPC density and assay sensitivity, consistent with previous reports of increased sensitivity for protein and peptide microarrays employing three-dimensional polymer scaffolds for surface attachment (56,57). However, this advantage must be balanced against the general insolubility of cellulose, which may lead to precipitation and printing anomalies.…”

Section: Cpcma Production and Optimization-frank And Colleagues Recensupporting

confidence: 65%

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

Engelmann

Kim

Wang

et al. 2014

Molecular & Cellular Proteomics

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Protein interaction domain (PID) linear peptide motif interactions direct diverse cellular processes in a specific and coordinated fashion. PID specificity, or the interaction selectivity derived from affinity preferences between possible PID-peptide pairs is the basis of this ability. Here, we develop an integrated experimental and computational cellulose peptide conjugate microarray (CPCMA) based approach for the high throughput analysis of PID specificity that provides unprecedented quantitative resolution and reproducibility. As a test system, we quantify the specificity preferences of four Src Homology 2 domains and 124 physiological phosphopeptides to produce a novel quantitative interactome. The quantitative data set covers a broad affinity range, is highly precise, and agrees well with orthogonal biophysical validation, in vivo interactions, and peptide library trained algorithm predictions. In contrast to preceding approaches, the CPCMAs proved capable of confidently assigning interactions into affinity categories, resolving the subtle affinity contributions of residue correlations, and yielded predictive peptide motif affinity matrices. Unique CPCMA enabled modes of systems level analysis reveal a physiological interactome with expected node degree value decreasing as a function of affinity, resulting in minimal high affinity binding overlap between domains; uncover that Src Homology 2 domains bind ligands with a similar average affinity yet strikingly different levels of promiscuity and binding dynamic range; and parse with unprecedented quantitative resolution contextual factors directing specificity. The CPCMA platform promises broad application within the fields of PID specificity, synthetic biology, specificity focused drug design, and network biology. Molecular & Cellular Proteomics 13: 10.1074/mcp.O114.038695, 3647-3662, 2014. Protein interaction domains (PIDs)1 often compete for the same linear motif binding sites across a range of affinities, resulting in many potential interactions that may enable the rapid assembly and disassembly of signaling proteins in response to external and internal cues (1, 2). PID-peptide interactions have small binding interfaces, resulting in moderate affinity interactions mediated primarily by a few amino acid "hot-spots" within motifs specific for a particular PID family (3-5). The power of individual residues to direct interactions, the absence of structural constraint for linear motifs, and the modularity of PIDs has enabled the rapid evolution of these networks resulting in many large multimember PID families in higher eukaryotes (6 -9). For these large families dedicated to the recognition of similar ligands, PID specificity-or the interaction selectivity derived from affinity preferences between possible PID-peptide pairs-underpins the effective conveyance of specific cell signals. High throughput interaction mapping efforts are used to decipher how this PID "specificity space" is populated, thereby providing insight into protein function and the principles ...

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Section: Cpcma Production and Optimization-frank And Colleagues Recensupporting

confidence: 65%

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

Engelmann

Kim

Wang

et al. 2014

Molecular & Cellular Proteomics

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“…Размеры чипа: 7,5´15´0,25 мм; площадь активированной зоны S=0,4 мм 2 ; полная площадь чипа S п =112,5 мм 2 . III Инкубация АСМ-чипа в растворе аналита (белка) (4). IV АСМ-чип с выловленными молекулами белка (5) в рабочей активированной зоне.…”

Section: рисунокunclassified

Irreversible chemical afm-fishing for the detection of low-copied proteins

IuD

et al. 2014

BIOMED KHIM

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The atomic-force microscopy-based method of irreversible chemical AFM-fishing (AFM-IF ) has been developed for the detection of proteins at ultra-low concentrations in solution. Using this method, a very low concentration of horseradish peroxidase (HRP) protein (10 17 M) was detected in solution. A theoretical model that allows the description of obtained experimental data, is proposed. This model takes into consideration both the transport of the protein from the bulk solution onto the AFM-chip surface and its irreversible binding to the activated area.

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“…Drobyshev et al [24] showed that prolonged incubation times at each stage of solid-phase amplification (and especially at the denaturation step) along with a reduction in reaction volume covering the microarray gel element led to more efficient solid-phase amplification. Further to overcome the limited diffusion issues, and low loading capacity of two dimensional array elements [47], the use of micrometre-sized beads (microbeads) and nanoparticles possessing high surfaceto-volume ratios and more efficient surface diffusion has been reported [11,[48][49][50][51].…”

Section: Solid-phase Amplification Within Threedimensional Microarraymentioning

confidence: 99%

Recent developments in nucleic acid identification using solid-phase enzymatic assays

Khodakov

Ellis

2014

Microchim Acta

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Comparison of surface and hydrogel-based protein microchips

Cited by 72 publications

References 19 publications

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

Irreversible chemical afm-fishing for the detection of low-copied proteins

Recent developments in nucleic acid identification using solid-phase enzymatic assays

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