Cysteine p<i>K</i><sub>a</sub> Depression by a Protonated Glutamic Acid in Human DJ-1

Witt, Anna C.; Lakshminarasimhan, Mahadevan; Remington, Benjamin C.; Hasim, Sahar; Pozharski, Edwin; Wilson, Mark A.

doi:10.1021/bi801205k

Cited by 24 publications

(57 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While most cysteine residues have pK a values in the 8-9 range, it is likely that a gatekeeper cysteine has an elevated pK a due to the surrounding hydrophobic microenvironment, rendering it especially unreactive. Nature exploits several strategies to depress the pK a values of cysteine including the introduction of electrostatic interactions with nearby positively charged residues (40), hydrogen bonding with polar amino acid side chains/ backbone amides (41), and the use of helix-dipoles (42). Our results suggest that simple modification of the microenvironment around the cysteine gatekeeper by alteration of one nearby residue (i.e., Val323) is sufficient to have a significant impact on inhibitor potency.…”

Section: Discussionmentioning

confidence: 90%

Chemical genetic strategy for targeting protein kinases based on covalent complementarity

Garske

Peters

Cortesi

et al. 2011

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

View full text Add to dashboard Cite

The conserved nature of the ATP-binding site of the >500 human kinases renders the development of specific inhibitors a challenging task. A widely used chemical genetic strategy to overcome the specificity challenge exploits a large-to-small mutation of the gatekeeper residue (a conserved hydrophobic amino acid) and the use of a bulky inhibitor to achieve specificity via shape complementarity. However, in a number of cases, introduction of a glycine or alanine gatekeeper results in diminished kinase activity and ATP affinity. A new chemical genetic approach based on covalent complementarity between an engineered gatekeeper cysteine and an electrophilic inhibitor was developed to address these challenges. This strategy was evaluated with Src, a proto-oncogenic tyrosine kinase known to lose some enzymatic activity using the shape complementarity chemical genetic strategy. We found that Src with a cysteine gatekeeper recapitulates wild type activity and can be irreversibly inhibited both in vitro and in cells. A cocrystal structure of T338C c-Src with a vinylsulfonamide-derivatized pyrazolopyrimidine inhibitor was solved to elucidate the inhibitor binding mode. A panel of electrophilic inhibitors was analyzed against 307 kinases and MOK (MAPK/MAK/MRK overlapping kinase), one of only two human kinases known to have an endogenous cysteine gatekeeper. This analysis revealed remarkably few offtargets, making these compounds the most selective chemical genetic inhibitors reported to date. Protein engineering studies demonstrated that it is possible to increase inhibitor potency through secondary-site mutations. These results suggest that chemical genetic strategies based on covalent complementarity should be widely applicable to the study of protein kinases. chemical genetics | irreversible inhibitor | SgK494

show abstract

Section: Discussionmentioning

confidence: 90%

Chemical genetic strategy for targeting protein kinases based on covalent complementarity

Garske

Peters

Cortesi

et al. 2011

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

View full text Add to dashboard Cite

show abstract

“…The second cysteine is located in the proximity of the novel DAQ species, justifying the reaction between the thiol group and the C2 carbon. Several studies have reported the different reactivity of the carbon ring, and the double conjugation at C2 and C5 is the second major product after the single conjugation on C5 (27,40).…”

Section: Figurementioning

confidence: 99%

“…Molecular Dynamics Simulations and Analysis-The x-ray structure with the highest resolution of the preoxidation complex of human DJ-1 was selected for all of the calculations (PDB code 2OR3) (27). MD simulations were performed using the software GROMACS 3.3 (28 -31) (see supplemental material).…”

mentioning

confidence: 99%

“…MD simulations were performed using the software GROMACS 3.3 (28 -31) (see supplemental material). The models of the covalent complexes of DJ-1 with DA were obtained using the human DJ-1 crystal structure covalently bound to DA (PDB code 2OR3) (27). We selected the best geometries obtained from a docking study using the covalent bond constraint tool part of the GOLD program suite (32).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Dopamine-derived Quinones Affect the Structure of the Redox Sensor DJ-1 through Modifications at Cys-106 and Cys-53

Girotto

Sturlese

Bellanda

et al. 2012

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: DJ-1, a protein involved in PD, protects neurons by acting as an oxidative stress sensor. Results: Through adduct formation on DJ-1 cysteines, DAQs induce both structural perturbations and uncoupling of the sensor function. Conclusion: Cys-53 is the most reactive, but Cys-106 modification induces the most severe effects. Significance: A correlation between DJ-1 DAQ-dependent impairment and the degeneration of dopaminergic neurons observed in PD is suggested.

show abstract

“…Furthermore, its oxidation is believed to be critical to the cytoprotective activity of DJ-1 (Canet- Aviles et al, 2004;Neumann et al, 2004). The glutamate residue (Glu18 in DJ-1) is responsible for the decreased pK a value of Cys106, facilitating its oxidation in DJ-1 (Witt et al, 2008). The majority of the DJ-1 superfamily members are dimers.…”

Section: Resultsmentioning

confidence: 99%

Dissection of the Dimerization Modes in the DJ-1 Superfamily

Jung

Kim

et al. 2012

Molecules and Cells

View full text Add to dashboard Cite

The DJ-1 superfamily (DJ-1/ThiJ/PfpI superfamily) is distributed across all three kingdoms of life. These proteins are involved in a highly diverse range of cellular functions, including chaperone and protease activity. DJ-1 proteins usually form dimers or hexamers in vivo and show at least four different binding orientations via distinct interface patches. Abnormal oligomerization of human DJ-1 is related to neurodegenerative disorders including Parkinson's disease, suggesting important functional roles of quaternary structures. However, the quaternary structures of the DJ-1 superfamily have not been extensively studied. Here, we focus on the diverse oligomerization modes among the DJ-1 superfamily proteins and investigate the functional roles of quaternary structures both computationally and experimentally. The oligomerization modes are classified into 4 types (DJ-1, YhbO, Hsp, and YDR types) depending on the distinct interface patches (I-IV) upon dimerization. A unique, rotated interface via patch I is reported, which may potentially be related to higher order oligomerization. In general, the groups based on sequence similarity are consistent with the quaternary structural classes, but their biochemical functions cannot be directly inferred using sequence information alone. The observed phyletic pattern suggests the dynamic nature of quaternary structures in the course of evolution. The amino acid residues at the interfaces tend to show lower mutation rates than those of non-interfacial surfaces.

show abstract

Cysteine pK_a Depression by a Protonated Glutamic Acid in Human DJ-1

Abstract: Page 7432. Due to a typographical error made in the final typesetting of this article, the third and fourths rows from the bottom of Table 1 should begin "rmsd for angle distances (Å)" and "rmsd for bond lengths (Å)", respectively.

Cited by 24 publications

References 0 publications

Chemical genetic strategy for targeting protein kinases based on covalent complementarity

Chemical genetic strategy for targeting protein kinases based on covalent complementarity

Dopamine-derived Quinones Affect the Structure of the Redox Sensor DJ-1 through Modifications at Cys-106 and Cys-53

Dissection of the Dimerization Modes in the DJ-1 Superfamily

Contact Info

Product

Resources

About

Cysteine pKa Depression by a Protonated Glutamic Acid in Human DJ-1

Abstract: Page 7432. Due to a typographical error made in the final typesetting of this article, the third and fourths rows from the bottom of Table 1 should begin "rmsd for angle distances (Å)" and "rmsd for bond lengths (Å)", respectively.

Cited by 24 publications

References 0 publications

Chemical genetic strategy for targeting protein kinases based on covalent complementarity

Chemical genetic strategy for targeting protein kinases based on covalent complementarity

Dopamine-derived Quinones Affect the Structure of the Redox Sensor DJ-1 through Modifications at Cys-106 and Cys-53

Dissection of the Dimerization Modes in the DJ-1 Superfamily

Contact Info

Product

Resources

About

Cysteine pK_a Depression by a Protonated Glutamic Acid in Human DJ-1