Structural Identification and Systematic Comparison of Phorbol Ester, Dioleoylglycerol, Alcohol and Sevoflurane Binding Sites in PKCδ C1A Domain

Overview

Journal Protein J

Publisher Springer

Specialty Biochemistry

Date 2018 Sep 26

PMID 30251087

Authors

Lijie Shi

Affiliations

Soon will be listed here.

Abstract

Protein kinase C (PKC) is a family of signal transducing enzymes that have been implicated in anesthetic preconditioning signaling cascade. Evidences are emerging that certain exogenous neuromodulators such as n-alkanols and general anesthetics can stimulate PKC activity by binding to regulatory C1A domain of the enzyme. However, the accurate binding sites in C1A domain as well as the molecular mechanism underlying binding-stimulated PKC activation still remain unelucidated. Here, we report a systematic investigation of the intermolecular interaction of human PKCδ C1A domain with its natural activator phorbol ester (PE) and co-activator dioleoylglycerol (DOG) as well as exogenous stimulators butanol, octanol and sevoflurane. The domain is computationally identified to potentially have three spatially vicinal ligand-binding pockets 1, 2 and 3, in which the pockets 1 and 2 have previously been determined as the binding sites of PE and DOG, respectively. Systematic cross-binding analysis reveals that long-chain octanol and DOG are well compatible with the flat, nonpolar pocket 2, where the nonspecific hydrophobic contacts and van der Waals packing are primarily responsible for the binding, while the general anesthetic sevoflurane prefer to interact with the rugged, polar pocket 3 through specific hydrogen bonds and electrostatic forces. Short-chain butanol appears to bind effectively none of the three pockets. In addition, the pocket 1 consists of two angled arms 1 and 2 that are also involved in pockets 2 and 3, respectively. Dynamics characterization imparts that binding of long-chain octanol and DOG to pocket 2 or binding of sevoflurane to pocket 3 can induce a conformational displacement in arm 1 or 2, thus further opening the included angle and enlarging pocket 1, which can improve the pocket 1-PE affinity via an allosteric mechanism, consequently stimulating the PE-induced PKCδ activation.

References

Tian F, Lv Y, Zhou P, Yang L . Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses. J Comput Aided Mol Des. 2011; 25(10):947-58. DOI: 10.1007/s10822-011-9474-5. View

Ananthanarayanan B, Stahelin R, Digman M, Cho W . Activation mechanisms of conventional protein kinase C isoforms are determined by the ligand affinity and conformational flexibility of their C1 domains. J Biol Chem. 2003; 278(47):46886-94. DOI: 10.1074/jbc.M307853200. View

Tian F, Yang C, Wang C, Guo T, Zhou P . Mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A. J Mol Model. 2014; 20(6):2257. DOI: 10.1007/s00894-014-2257-x. View

Duan Y, Wu C, Chowdhury S, Lee M, Xiong G, Zhang W . A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem. 2003; 24(16):1999-2012. DOI: 10.1002/jcc.10349. View

Slater S, Cox K, Lombardi J, Ho C, Kelly M, Rubin E . Inhibition of protein kinase C by alcohols and anaesthetics. Nature. 1993; 364(6432):82-4. DOI: 10.1038/364082a0. View

Gomez R, Guatimosim C, Gomez M . Mechanism of action of volatile anesthetics: role of protein kinase C. Cell Mol Neurobiol. 2004; 23(6):877-85. PMC: 11530178. DOI: 10.1023/b:cemn.0000005316.38838.71. View

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

Das J, Zhou X, Miller K . Identification of an alcohol binding site in the first cysteine-rich domain of protein kinase Cdelta. Protein Sci. 2006; 15(9):2107-19. PMC: 2242605. DOI: 10.1110/ps.062237606. View

Slater S, Kelly M, Larkin J, Ho C, Mazurek A, Taddeo F . Interaction of alcohols and anesthetics with protein kinase Calpha. J Biol Chem. 1997; 272(10):6167-73. DOI: 10.1074/jbc.272.10.6167. View

10.

Ye Z, Huang Y, Wang E, Zuo Z, Guo Q . Sevoflurane-induced delayed neuroprotection involves mitoK(ATP) channel opening and PKC ε activation. Mol Biol Rep. 2012; 39(5):5049-57. DOI: 10.1007/s11033-011-1290-4. View

11.

Morris G, Huey R, Lindstrom W, Sanner M, Belew R, Goodsell D . AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-91. PMC: 2760638. DOI: 10.1002/jcc.21256. View

12.

Rebecchi M, Pentyala S . Anaesthetic actions on other targets: protein kinase C and guanine nucleotide-binding proteins. Br J Anaesth. 2002; 89(1):62-78. DOI: 10.1093/bja/aef160. View

13.

Wang J, Wolf R, Caldwell J, Kollman P, Case D . Development and testing of a general amber force field. J Comput Chem. 2004; 25(9):1157-74. DOI: 10.1002/jcc.20035. View

14.

Saraiva L, Fresco P, Pinto E, Goncalves J . Characterization of phorbol esters activity on individual mammalian protein kinase C isoforms, using the yeast phenotypic assay. Eur J Pharmacol. 2004; 491(2-3):101-10. DOI: 10.1016/j.ejphar.2004.03.035. View

15.

Yu H, Zhou P, Deng M, Shang Z . Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition. J Chem Inf Model. 2014; 54(7):2022-32. DOI: 10.1021/ci5000246. View

16.

Slater S, Ho C, Kelly M, Larkin J, Taddeo F, Yeager M . Protein kinase Calpha contains two activator binding sites that bind phorbol esters and diacylglycerols with opposite affinities. J Biol Chem. 1996; 271(9):4627-31. DOI: 10.1074/jbc.271.9.4627. View

17.

Mellor H, Parker P . The extended protein kinase C superfamily. Biochem J. 1998; 332 ( Pt 2):281-92. PMC: 1219479. DOI: 10.1042/bj3320281. View

18.

Liu C, Liu Y, Shen Z, Miao L, Zhang K, Wang F . Sevoflurane Preconditioning Reduces Intestinal Ischemia-Reperfusion Injury: Role of Protein Kinase C and Mitochondrial ATP-Sensitive Potassium Channel. PLoS One. 2015; 10(10):e0141426. PMC: 4624762. DOI: 10.1371/journal.pone.0141426. View

19.

Luo H, Du T, Zhou P, Yang L, Mei H, Ng H . Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions. Comb Chem High Throughput Screen. 2015; 18(3):296-304. PMC: 4581727. DOI: 10.2174/1386207318666150305144015. View

20.

Hemmings Jr H, Adamo A . Effects of halothane and propofol on purified brain protein kinase C activation. Anesthesiology. 1994; 81(1):147-55. DOI: 10.1097/00000542-199407000-00021. View