Photo-lysine captures proteins that bind lysine post-translational modifications

Yang, Tangpo; Bao, Xiucong; Fung, YS; Li, Xiang

doi:10.1038/nchembio.1990

Cited by 82 publications

(76 citation statements)

References 25 publications

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“…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%

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: Significancementioning

confidence: 99%

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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“…It therefore appeared desirable to introduce the diazirine tag into positions that would allow probing the vicinity of polar groups that are engaged in non‐covalent bonding in peptide complexes. Recently, a lysine residue called photolysine, containing the diazirine ring in the side chain, has been reported that addressed this need . However, photolysine is obtained by a multistep synthesis and is not readily available for studies of peptide complexes.…”

Section: Methodsmentioning

confidence: 99%

Position‐tunable diazirine tags for peptide–peptide ion cross‐linking in the gas phase

2017

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“…Fortunately, other photoreactive UAAs are available. These include a diazirine-containing analogue of lysine, termed photolysine, 49 which generates a reactive carbene species upon UV irradiation. This photoreactive amino acid can be nonspecifically incorporated into cellular proteins by simply including the UAA in the cell culture medium—the high lysine content of histones makes them well suited to this approach.…”

Section: Chemical Approaches For Modifying Chromatin In Cellsmentioning

confidence: 99%

Emerging Chemistry Strategies for Engineering Native Chromatin

David

Muir

2017

J. Am. Chem. Soc.

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Chromosomes present one of most challenging of all substrates for biochemical study. This is because genomic DNA is physically associated with an astonishing collection of nuclear factors, which serve to not only store the nucleic acid in a stable form, but also grant access to the information it encodes when needed. Understanding this complex molecular choreography is central to the field of epigenetics. One of the great challenges in this area is to move beyond correlative type information, which is now in abundant supply, to the point where we can truly connect the dots at the molecular level. Establishing such causal relationships requires precise manipulation of the covalent structure of chromatin. Tools for this purpose are currently in short supply, creating an opportunity that, as we will argue in this Perspective, is well suited to the sensibilities of the chemist.

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Photo-lysine captures proteins that bind lysine post-translational modifications

Cited by 82 publications

References 25 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

Position‐tunable diazirine tags for peptide–peptide ion cross‐linking in the gas phase

Emerging Chemistry Strategies for Engineering Native Chromatin

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