Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label

Yang, Yi; Song, Haiping; He, Duofen; Zhang, Shuai; Dai, Shizhong; Lin, Shixian; Meng, Rong; Wang, Chu; Chen, Peng R.

doi:10.1038/ncomms12299

Cited by 78 publications

(69 citation statements)

References 47 publications

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“…This result agrees reasonably with that determined by ITC (K D = 9.4 μM) (20). In addition, this affinity agrees well with that determined using the oriented immobilization strategy [K D = 8.2 ± 0.7 μM, C-terminal biotin labeled H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4me3 peptide] (SI Appendix, Fig. S3).…”

Section: Resultssupporting

confidence: 80%

“…First, we checked the positive controls in this peptide array. The H3K4me3 readers binds to H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4me3 instead of H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4un peptides as expected (Fig. 4B).…”

Section: Resultssupporting

confidence: 51%

“…Empirically, the real positive result should have a RC value less than 10, which means that unregenerable signal contributes less than 10% to the overall signal. We chose H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4me3 and H3 K9crK27cr peptides as examples to analyze their respective signal response to CHD1. The result showed that the regenerable signal of H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4me3 peptide contributes to 99.8% of the overall signal while this value of H3 K9crK27cr peptide is only 53.3% (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The 3D-carbene SPRi platform makes high-throughput kinetic analysis of histone "mark-reader" pairs possible. We analyzed kinetic curves of four peptides [H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4un, H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4ac, H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) K4me1, and H3 (1)(2)(3)(4)(5)(6)(7)…”

Section: Resultsmentioning

confidence: 99%

“…Carbene-based cross-linking strategy, which rapidly immobilizes molecules in random orientation due to its high and diverse chemical reactivity (e.g., carbon insertion, Michael addition, nucleophilic reaction, etc. ), is becoming an optimized immobilization method for microarray fabrications (14)(15)(16). Meanwhile, due to its high loading capacity for biomolecules and antifouling properties, 3D polymer surface with a designed structure often shows high signal-to-noise ratio in SPRi (17)(18)(19).…”

Section: Significancementioning

confidence: 99%

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Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Zhao

Yang

Zhou

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chipbased surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone "reader-mark" pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a mechanism of H3K4me3-mediated DNA damage repair in plant. The mechanisms leading to differential transcriptional and developmental outcomes under the same genetic background are known as epigenetics. Posttranslational modification (PTM) on histones is a major epigenetic regulatory mechanism such that more than 30 types of PTMs occur on histones, with new ones still being discovered (1). The well-studied histone PTMs include methylation, acetylation, phosphorylation, and most recently discovered nonacetyl acylations (2). Histone PTMs regulate transcription either by directly affecting the structure/stability of single nucleosome and the high-order folding of chromatin, or by recruiting specific effector proteins (also called histone readers) recognizing them (3, 4).The ever-expanding repertoire of histone readers are diverse in sequence and structure, and how they engage diversely modified chromatin is complicated, hard to predict, yet important for their functions. Often one type of reader domains can recognize different types of PTMs. For example, PHD finger proteins can recognize unmodified, methylated, or acylated lysine residue on histones (5, 6). Several YEATS domain proteins, originally identified as readers of lysine acetylation (Kac), in fact accommodate a wide range of lysine acylations with lysine crotonylation (Kcr) most preferred (7). These "mark-reader" interactions vary greatly in binding affinity, ranging from submicromolar to millimolar levels. To complicate the matter further, the recognition of marks by reader proteins is often either synergized or antagonized by other marks in close proximity (8). For instance, Spindlin1 recognizes histone H3 trimethylation of Lys-4 (H3K4me3) and asymmetrically dimethylation of Arg-8 (H3R8me2a) in concert, while phosphorylation of Ser-10 on H3 (H3S10ph) completely abrogates the binding of H3 Lys-9 trimethylation (H3K9me3) by HP1 protein (9, 10). BRDT protein binds neither histone H4 Lys-5 acetylation (H4K5ac) nor Lys-8 acetylation (H4K8ac) but engages H4 peptide bearing both marks with decent affinity (K...

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Section: Resultssupporting

confidence: 80%

Section: Resultssupporting

confidence: 51%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

See 3 more Smart Citations

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Zhao

Yang

Zhou

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Selenopeptide Nanomedicine Activates Natural Killer Cells for Enhanced Tumor Chemoimmunotherapy

Wei

Luo

et al. 2022

Advanced Materials

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Stress Dissipation Encoded Silk Fibroin Electrode for the Athlete‐Beneficial Silk Bioelectronics

et al. 2022

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The kinetic body motions have guided the core‐shell fabrics of wearable bioelectronics to be elastoplastic. However, the polymeric electrodes follow the trade‐off relationship between toughness and stretchability. To this end, the stress dissipation encoded silk fibroin electrode is proposed as the core electrode of wearable bioelectronics. Significantly, the high degree of intrinsic stress dissipation is realized via an amino acid crosslink. The canonical phenolic amino acid (i.e., tyrosine) of silk fibroin is engineered to bridge the secondary structures. A sufficient crosslink network is constructed when tyrosine is exposed near the amorphous strand. The stress dissipative tyrosine crosslink affords 12.5‐fold increments of toughness (4.72 to 58.9 MJ m−3) and implements the elastoplastic silk fibroin. The harmony of elastoplastic core electrodes with shell fabrics enables the wearable bioelectronics to employ mechanical performance (elastoplasticity of 750 MJ m−3) and stable electrical response. The proposed wearable is capable of assisting the effective workouts via triboelectricity. In principle, active mobility with suggested wearables potentially relieves muscular fatigues and severe injuries during daily fitness.

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Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label

Cited by 78 publications

References 47 publications

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Selenopeptide Nanomedicine Activates Natural Killer Cells for Enhanced Tumor Chemoimmunotherapy

Stress Dissipation Encoded Silk Fibroin Electrode for the Athlete‐Beneficial Silk Bioelectronics

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