101
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Fogha J, Diharce J, Obled A, Aci-Sèche S, Bonnet P. Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites. ACS OMEGA 2020; 5:2114-2122. [PMID: 32064372 PMCID: PMC7016913 DOI: 10.1021/acsomega.9b02697] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
Allosteric effect can modulate the biological activity of a protein. Thus, the discovery of new allosteric sites is very attractive for designing new modulators or inhibitors. Here, we propose an innovative way to identify allosteric sites, based on crystallization additives (CA), used to stabilize proteins during the crystallization process. Density and clustering analyses of CA, applied on protein kinase and nuclear receptor families, revealed that CA are not randomly distributed around protein structures, but they tend to aggregate near common sites. All orthosteric and allosteric cavities described in the literature are retrieved from the analysis of CA distribution. In addition, new sites were identified, which could be associated to putative allosteric sites. We proposed an efficient and easy way to use the structural information of CA to identify allosteric sites. This method could assist medicinal chemists for the design of new allosteric compounds targeting cavities of new drug targets.
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102
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Structural Consequences of Multisite Phosphorylation in the BAK1 Kinase Domain. Biophys J 2020; 118:698-707. [PMID: 31962105 DOI: 10.1016/j.bpj.2019.12.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/09/2019] [Accepted: 12/10/2019] [Indexed: 12/26/2022] Open
Abstract
Multisite phosphorylation is an important mechanism of post-translational control of protein kinases. The effects of combinations of possible phosphorylation states on protein kinase activity are difficult to study experimentally because of challenges in isolating a particular phosphorylation state; surprising little effort on this topic has been expended in computational studies. To understand the effects of multisite phosphorylation on the plant protein kinase brassinosteroid insensitive 1-associated kinase 1 (BAK1) conformational ensemble, we performed Gaussian accelerated molecular dynamics simulations on eight BAK1 mod-forms involving phosphorylation of the four activation-loop threonine residues and binding of ATP-Mg2+. We find that unphosphorylated BAK1 transitions into an inactive conformation with a "cracked" activation loop and with the αC helix swung away from the active site. T450 phosphorylation can prevent the activation loop from cracking and keep the αC helix in an active-like conformation, whereas phosphorylation of T455 only slightly stabilizes the activation loop. There is a general trend of reduced flexibility in interlobe motion with increased phosphorylation. Interestingly, the αC helix is destabilized when the activation loop is fully phosphorylated but is again stabilized with ATP-Mg2+ bound. Our results provide insight into the mechanism of phosphorylation-controlled BAK1 activation while at the same time represent the first, to our knowledge, comprehensive, comparative study of the effects of combinatorial phosphorylation states on protein kinase conformational dynamics.
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103
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Lakkaniga NR, Balasubramaniam M, Zhang S, Frett B, Li HY. Structural Characterization of the Aurora Kinase B "DFG-flip" Using Metadynamics. AAPS JOURNAL 2019; 22:14. [PMID: 31853739 DOI: 10.1208/s12248-019-0399-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/13/2019] [Indexed: 11/30/2022]
Abstract
Aurora kinase B (AKB), a Ser/Thr kinase that plays a crucial role in mitosis, is overexpressed in several cancers. Clinical inhibitors targeting AKB bind to the active DFG "in" conformation of the kinase. It would be beneficial, however, to understand if AKB is susceptible to type II kinase inhibitors that bind to the inactive, DFG "out" conformation, since type II inhibitors achieve higher kinome selectivity and higher potency in vivo. The DFG "out" conformation of AKB is not yet experimentally determined which makes the design of type II inhibitors exceedingly difficult. An alternate approach is to simulate the DFG "out" conformation from the experimentally determined DFG "in" conformation using atomistic molecular dynamics (MD) simulation. In this work, we employed metadynamics (MTD) approach to simulate the DFG "out" conformation of AKB by choosing the appropriate collective variables. We examined structural changes during the DFG-flip and determined the interactions crucial to stabilize the kinase in active and inactive states. Interestingly, the MTD approach also identified a unique transition state (DFG "up"), which can be targeted by small molecule inhibitors. Structural insights about these conformations is essential for structure-guided design of next-generation AKB inhibitors. This work also emphasizes the usefulness of MTD simulations in predicting macromolecular conformational changes at reduced computational costs.
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Affiliation(s)
- Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | | | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77225, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA.
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104
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Smith CA, Toth M, Stewart NK, Maltz L, Vakulenko SB. Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2''-phosphotransferases. Acta Crystallogr D Struct Biol 2019; 75:1129-1137. [PMID: 31793906 PMCID: PMC6889913 DOI: 10.1107/s2059798319015079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
Aminoglycoside phosphotransferases (APHs) are one of three families of aminoglycoside-modifying enzymes that confer high-level resistance to the aminoglycoside antibiotics via enzymatic modification. This has now rendered many clinically important drugs almost obsolete. The APHs specifically phosphorylate hydroxyl groups on the aminoglycosides using a nucleotide triphosphate as the phosphate donor. The APH(2'') family comprises four distinct members, isolated primarily from Enterococcus sp., which vary in their substrate specificities and also in their preference for the phosphate donor (ATP or GTP). The structure of the ternary complex of APH(2'')-IIIa with GDP and kanamycin was solved at 1.34 Å resolution and was compared with substrate-bound structures of APH(2'')-Ia, APH(2'')-IIa and APH(2'')-IVa. In contrast to the case for APH(2'')-Ia, where it was proposed that the enzyme-mediated hydrolysis of GTP is regulated by conformational changes in its N-terminal domain upon GTP binding, APH(2'')-IIa, APH(2'')-IIIa and APH(2'')-IVa show no such regulatory mechanism, primarily owing to structural differences in the N-terminal domains of these enzymes.
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Affiliation(s)
- Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Nichole K. Stewart
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Lauren Maltz
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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105
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Bayne AN, Trempe JF. Mechanisms of PINK1, ubiquitin and Parkin interactions in mitochondrial quality control and beyond. Cell Mol Life Sci 2019; 76:4589-4611. [PMID: 31254044 PMCID: PMC11105328 DOI: 10.1007/s00018-019-03203-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) is a degenerative movement disorder resulting from the loss of specific neuron types in the midbrain. Early environmental and pathophysiological studies implicated mitochondrial damage and protein aggregation as the main causes of PD. These findings are now vindicated by the characterization of more than 20 genes implicated in rare familial forms of the disease. In particular, two proteins encoded by the Parkin and PINK1 genes, whose mutations cause early-onset autosomal recessive PD, function together in a mitochondrial quality control pathway. In this review, we will describe recent development in our understanding of their mechanisms of action, structure, and function. We explain how PINK1 acts as a mitochondrial damage sensor via the regulated proteolysis of its N-terminus and the phosphorylation of ubiquitin tethered to outer mitochondrial membrane proteins. In turn, phospho-ubiquitin recruits and activates Parkin via conformational changes that increase its ubiquitin ligase activity. We then describe how the formation of polyubiquitin chains on mitochondria triggers the recruitment of the autophagy machinery or the formation of mitochondria-derived vesicles. Finally, we discuss the evidence for the involvement of these mechanisms in physiological processes such as immunity and inflammation, as well as the links to other PD genes.
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Affiliation(s)
- Andrew N Bayne
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada.
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106
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Joshi MK, Burton RA, Wu H, Lipchik AM, Craddock BP, Mo H, Parker LL, Miller WT, Post CB. Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics. Protein Sci 2019; 29:350-359. [PMID: 31697410 DOI: 10.1002/pro.3777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023]
Abstract
Most signal transduction pathways in humans are regulated by protein kinases through phosphorylation of their protein substrates. Typical eukaryotic protein kinases are of two major types: those that phosphorylate-specific sequences containing tyrosine (~90 kinases) and those that phosphorylate either serine or threonine (~395 kinases). The highly conserved catalytic domain of protein kinases comprises a smaller N lobe and a larger C lobe separated by a cleft region lined by the activation loop. Prior studies find that protein tyrosine kinases recognize peptide substrates by binding the polypeptide chain along the C-lobe on one side of the activation loop, while serine/threonine kinases bind their substrates in the cleft and on the side of the activation loop opposite to that of the tyrosine kinases. Substrate binding structural studies have been limited to four families of the tyrosine kinase group, and did not include Src tyrosine kinases. We examined peptide-substrate binding to Src using paramagnetic-relaxation-enhancement NMR combined with molecular dynamics simulations. The results suggest Src tyrosine kinase can bind substrate positioning residues C-terminal to the phosphoacceptor residue in an orientation similar to serine/threonine kinases, and unlike other tyrosine kinases. Mutagenesis corroborates this new perspective on tyrosine kinase substrate recognition. Rather than an evolutionary split between tyrosine and serine/threonine kinases, a change in substrate recognition may have occurred within the TK group of the human kinome. Protein tyrosine kinases have long been therapeutic targets, but many marketed drugs have deleterious off-target effects. More accurate knowledge of substrate interactions of tyrosine kinases has the potential for improving drug selectivity.
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Affiliation(s)
- Mehul K Joshi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Robert A Burton
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana.,Ancestry, Lehi, Utah
| | - Heng Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Barbara P Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York
| | - Huaping Mo
- Purdue Interdepartmental NMR Facility PINMRF, Purdue University, West Lafayette, Indiana
| | - Laurie L Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York.,Department of Veterans Affairs Medical Center, Northport, New York
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
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107
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Kanev GK, de Graaf C, de Esch IJP, Leurs R, Würdinger T, Westerman BA, Kooistra AJ. The Landscape of Atypical and Eukaryotic Protein Kinases. Trends Pharmacol Sci 2019; 40:818-832. [PMID: 31677919 DOI: 10.1016/j.tips.2019.09.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
Kinases are attractive anticancer targets due to their central role in the growth, survival, and therapy resistance of tumor cells. This review explores the two primary kinase classes, the eukaryotic protein kinases (ePKs) and the atypical protein kinases (aPKs), and provides a structure-centered comparison of their sequences, structures, hydrophobic spines, mutation and SNP hotspots, and inhibitor interaction patterns. Despite the limited sequence similarity between these two classes, atypical kinases commonly share the archetypical kinase fold but lack conserved eukaryotic kinase motifs and possess altered hydrophobic spines. Furthermore, atypical kinase inhibitors explore only a limited number of binding modes both inside and outside the orthosteric binding site. The distribution of genetic variations in both classes shows multiple ways they can interfere with kinase inhibitor binding. This multilayered review provides a research framework bridging the eukaryotic and atypical kinase classes.
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Affiliation(s)
- Georgi K Kanev
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Thomas Würdinger
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
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108
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Hu W, Li Q, Li B, Ma K, Zhang C, Fu X. Optogenetics sheds new light on tissue engineering and regenerative medicine. Biomaterials 2019; 227:119546. [PMID: 31655444 DOI: 10.1016/j.biomaterials.2019.119546] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 01/23/2023]
Abstract
Optogenetics has demonstrated great potential in the fields of tissue engineering and regenerative medicine, from basic research to clinical applications. Spatiotemporal encoding during individual development has been widely identified and is considered a novel strategy for regeneration. A as a noninvasive method with high spatiotemporal resolution, optogenetics are suitable for this strategy. In this review, we discuss roles of dynamic signal coding in cell physiology and embryonic development. Several optogenetic systems are introduced as ideal optogenetic tools, and their features are compared. In addition, potential applications of optogenetics for tissue engineering are discussed, including light-controlled genetic engineering and regulation of signaling pathways. Furthermore, we present how emerging biomaterials and photoelectric technologies have greatly promoted the clinical application of optogenetics and inspired new concepts for optically controlled therapies. Our summation of currently available data conclusively demonstrates that optogenetic tools are a promising method for elucidating and simulating developmental processes, thus providing vast prospects for tissue engineering and regenerative medicine applications.
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Affiliation(s)
- Wenzhi Hu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Qiankun Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Bingmin Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Kui Ma
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Cuiping Zhang
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
| | - Xiaobing Fu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
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109
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Abstract
The crystal structure of SelO, a pseudokinase previously presumed to be inactive, reveals an ATP cofactor sitting in the active site in a flipped orientation compared with canonical kinases, leading to the discovery of an unexpected catalytic activity for this ancient enzyme.
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Affiliation(s)
- Lee Bardwell
- Department of Developmental & Cell Biology, University of California, Irvine, CA 92697, USA.
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110
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Xu P, Ianes C, Gärtner F, Liu C, Burster T, Bakulev V, Rachidi N, Knippschild U, Bischof J. Structure, regulation, and (patho-)physiological functions of the stress-induced protein kinase CK1 delta (CSNK1D). Gene 2019; 715:144005. [PMID: 31376410 PMCID: PMC7939460 DOI: 10.1016/j.gene.2019.144005] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022]
Abstract
Members of the highly conserved pleiotropic CK1 family of serine/threonine-specific kinases are tightly regulated in the cell and play crucial regulatory roles in multiple cellular processes from protozoa to human. Since their dysregulation as well as mutations within their coding regions contribute to the development of various different pathologies, including cancer and neurodegenerative diseases, they have become interesting new drug targets within the last decade. However, to develop optimized CK1 isoform-specific therapeutics in personalized therapy concepts, a detailed knowledge of the regulation and functions of the different CK1 isoforms, their various splice variants and orthologs is mandatory. In this review we will focus on the stress-induced CK1 isoform delta (CK1δ), thereby addressing its regulation, physiological functions, the consequences of its deregulation for the development and progression of diseases, and its potential as therapeutic drug target.
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Affiliation(s)
- Pengfei Xu
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Chiara Ianes
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Fabian Gärtner
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Congxing Liu
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Timo Burster
- Department of Biology, School of Science and Technology, Nazarbayev University, 53 Kabanbay Batyr Ave, Nur-Sultan 020000, Kazakhstan.
| | - Vasiliy Bakulev
- Ural Federal University named after the first President of Russia B. N. Eltsin, Technology for Organic Synthesis Laboratory, 19 Mirastr., 620002 Ekaterinburg, Russia.
| | - Najma Rachidi
- Unité de Parasitologie Moléculaire et Signalisation, Department of Parasites and Insect Vectors, Institut Pasteur and INSERM U1201, 25-28 Rue du Dr Roux, 75015 Paris, France.
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Joachim Bischof
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
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111
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Barbosa ÉDAA, Seraphim TV, Gandin CA, Teixeira LF, da Silva RAG, Righetto GL, Goncalves KDA, Vasconcellos RDS, Almeida MR, Silva Júnior A, Fietto JLR, Kobarg J, Gileadi C, Massirer KB, Borges JC, de Oliveira Neto M, Bressan GC. Insights into the full-length SRPK2 structure and its hydrodynamic behavior. Int J Biol Macromol 2019; 137:205-214. [PMID: 31229549 DOI: 10.1016/j.ijbiomac.2019.06.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/04/2019] [Accepted: 06/19/2019] [Indexed: 11/30/2022]
Abstract
The serine/arginine-rich protein kinase 2 (SRPK2) has been reported as upregulated in several cancer types, with roles in hallmarks such as cell migration, growth, and apoptosis. These findings have indicated that SRPK2 is a promising emerging target in drug discovery initiatives. Although high-resolution models are available for SRPK2 (PDB 2X7G), they have been obtained with a heavily truncated recombinant protein version (~50% of the primary structure), due to the presence of long intrinsically unstructured regions. In the present work, we sought to characterize the structure of a full-length recombinant version of SRPK2 in solution. Low-resolution Small-Angle X-ray Scattering data were obtained for both versions of SRPK2. The truncated ΔNΔS-SRPK2 presented a propensity to dimerize at higher concentrations whereas the full-length SRPK2 was mainly found as dimers. The hydrodynamic behavior of the full-length SRPK2 was further investigated by analytical size exclusion chromatography and sedimentation velocity analytical ultracentrifugation experiments. SRPK2 behaved as a monomer-dimer equilibrium and both forms have an elongated shape in solution, pointing to a stretched-to-closed tendency among the conformational plasticity observed. Taken together, these findings allowed us to define unique structural features of the SRPK2 within SRPK family, characterized by its flexible regions outside the bipartite kinase domain.
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Affiliation(s)
| | | | - César Augusto Gandin
- Departamento de Física e Biofísica, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | | | | | - Germanna L Righetto
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Kaliandra De Almeida Goncalves
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Márcia Rogéria Almeida
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | - Jörg Kobarg
- Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual e Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carina Gileadi
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, Brazil; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Katlin B Massirer
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, Brazil; Center for Molecular Biology and Genetic Engineering, CBMEG, Universidade Estadual de Campinas, Campinas, SPUniversidade Estadual de Campinas, Campinas, Brazil
| | - Julio César Borges
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Gustavo Costa Bressan
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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112
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A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. Cell 2019; 179:205-218.e21. [PMID: 31522888 DOI: 10.1016/j.cell.2019.08.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 01/01/2023]
Abstract
The molecular chaperone HSP90 facilitates the folding of several client proteins, including innate immune receptors and protein kinases. HSP90 is an essential component of plant and animal immunity, yet pathogenic strategies that directly target the chaperone have not been described. Here, we identify the HopBF1 family of bacterial effectors as eukaryotic-specific HSP90 protein kinases. HopBF1 adopts a minimal protein kinase fold that is recognized by HSP90 as a host client. As a result, HopBF1 phosphorylates HSP90 to completely inhibit the chaperone's ATPase activity. We demonstrate that phosphorylation of HSP90 prevents activation of immune receptors that trigger the hypersensitive response in plants. Consequently, HopBF1-dependent phosphorylation of HSP90 is sufficient to induce severe disease symptoms in plants infected with the bacterial pathogen, Pseudomonas syringae. Collectively, our results uncover a family of bacterial effector kinases with toxin-like properties and reveal a previously unrecognized betrayal mechanism by which bacterial pathogens modulate host immunity.
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113
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Ahrari S, Khosravi F, Osouli A, Sakhteman A, Nematollahi A, Ghasemi Y, Savardashtaki A. MARK4 protein can explore the active-like conformations in its non-phosphorylated state. Sci Rep 2019; 9:12967. [PMID: 31506531 PMCID: PMC6737064 DOI: 10.1038/s41598-019-49337-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
Microtubule affinity-regulating kinase 4 (MARK4) is a Ser/Thr protein kinase, best known for its role in phosphorylating microtubule associated proteins, causing their detachment from microtubules. In the current study, the non-phosphorylated conformation of the activation loop was modeled in a structure representing the enzymatically inactive form of this protein, and its dynamics were evaluated through a 100 ns initial all-atom simulation, which was prolonged by another 2 μs. Although the activation loop was folding on itself and was leaning toward ATP site in the initial modeled structure, soon after the initiating the simulation, this loop stretched away from the ATP binding site and stably settled in its new position for the rest of simulation time. A network of hydrogen bonds, mainly between the activation segment residues, αC-helix and the catalytic loop reinforced this conformation. Interestingly, several features of active kinase conformation such as formation of R-spine, Glu106-Lys88 salt-bridge, and DFG-In motif were observed during a considerable number of trajectory frames. However, they were not sustainably established during the simulation time, except for the DFG-In motif. Consequently, this study introduces a stable conformation of the non-phosphorylated form of MARK4 protein with a partially stretched activation loop conformation as well as partial formation of R-spine, closely resembling the active kinase.
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Affiliation(s)
- Sajjad Ahrari
- Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, 71345 15830, Iran
| | - Fatemeh Khosravi
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, 71964 84334, Iran
| | - Ali Osouli
- Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, 71345 15830, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, 71345 15830, Iran
| | - Alireza Nematollahi
- Department of Statistics, College of Sciences, Shiraz University, Shiraz, 71364 84334, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, 71345 15830, Iran
| | - Amir Savardashtaki
- Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, 71345 15830, Iran. .,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 71362 81407, Iran.
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114
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Ahrari S, Mogharrab N, Navapour L. Structure and dynamics of inactive and active MARK4: conformational switching through the activation process. J Biomol Struct Dyn 2019; 38:2468-2481. [DOI: 10.1080/07391102.2019.1655479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sajjad Ahrari
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Navid Mogharrab
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Leila Navapour
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
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115
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Maurice F, Pérébaskine N, Thore S, Fribourg S. In vitro dimerization of human RIO2 kinase. RNA Biol 2019; 16:1633-1642. [PMID: 31390939 DOI: 10.1080/15476286.2019.1653679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
RIO proteins form a conserved family of atypical protein kinases. RIO2 is a serine/threonine protein kinase/ATPase involved in pre-40S ribosomal maturation. Current crystal structures of archaeal and fungal Rio2 proteins report a monomeric form of the protein. Here, we describe three atomic structures of the human RIO2 kinase showing that it forms a homodimer in vitro. Upon self-association, each protomer ATP-binding pocket is partially remodelled and found in an apostate. The homodimerization is mediated by key residues previously shown to be responsible for ATP binding and catalysis. This unusual in vitro protein kinase dimer reveals an intricate mechanism where identical residues are involved in substrate binding and oligomeric state formation. We speculate that such an oligomeric state might be formed also in vivo and might function in maintaining the protein in an inactive state and could be employed during import.
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Affiliation(s)
| | | | - Stéphane Thore
- INSERM U1212, UMR CNRS 5320, Université de Bordeaux , Bordeaux , France
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116
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Bastedo DP, Khan M, Martel A, Seto D, Kireeva I, Zhang J, Masud W, Millar D, Lee JY, Lee AHY, Gong Y, Santos-Severino A, Guttman DS, Desveaux D. Perturbations of the ZED1 pseudokinase activate plant immunity. PLoS Pathog 2019; 15:e1007900. [PMID: 31269090 PMCID: PMC6634424 DOI: 10.1371/journal.ppat.1007900] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/16/2019] [Accepted: 06/08/2019] [Indexed: 11/19/2022] Open
Abstract
The Pseudomonas syringae acetyltransferase HopZ1a is delivered into host cells by the type III secretion system to promote bacterial growth. However, in the model plant host Arabidopsis thaliana, HopZ1a activity results in an effector-triggered immune response (ETI) that limits bacterial proliferation. HopZ1a-triggered immunity requires the nucleotide-binding, leucine-rich repeat domain (NLR) protein, ZAR1, and the pseudokinase, ZED1. Here we demonstrate that HopZ1a can acetylate members of a family of ‘receptor-like cytoplasmic kinases’ (RLCK family VII; also known as PBS1-like kinases, or PBLs) and promote their interaction with ZED1 and ZAR1 to form a ZAR1-ZED1-PBL ternary complex. Interactions between ZED1 and PBL kinases are determined by the pseudokinase features of ZED1, and mutants designed to restore ZED1 kinase motifs can (1) bind to PBLs, (2) recruit ZAR1, and (3) trigger ZAR1-dependent immunity in planta, all independently of HopZ1a. A ZED1 mutant that mimics acetylation by HopZ1a also triggers immunity in planta, providing evidence that effector-induced perturbations of ZED1 also activate ZAR1. Overall, our results suggest that interactions between these two RLCK families are promoted by perturbations of structural features that distinguish active from inactive kinase domain conformations. We propose that effector-induced interactions between ZED1/ZRK pseudokinases (RLCK family XII) and PBL kinases (RLCK family VII) provide a sensitive mechanism for detecting perturbations of either kinase family to activate ZAR1-mediated ETI. All plants must ward off potentially infectious microbes, and those grown in large-scale crop operations are especially vulnerable to the rapid spread of disease by successful pathogens. Although many bacteria and fungi can supress plant immune responses by producing specialized virulence proteins called ‘effectors’, these effectors can also trigger immune responses that render plants resistant to infection. We studied the molecular mechanisms underlying one such effector-triggered immune response elicited by the bacterial effector HopZ1a in the model plant host Arabidopsis thaliana. We have shown that HopZ1a promotes binding between a ZED1, a ‘pseudokinase’ required for HopZ1a-triggered immunity, and several ‘true kinases’ (known as PBLs) that are likely targets of HopZ1a activity in planta. HopZ1a-induced ZED1-PBL interactions also recruit ZAR1, an Arabidopsis ‘resistance protein’ previously implicated in HopZ1a-triggered immunity. Importantly, ZED1 mutants that restore degenerate kinase motifs can bridge interactions between PBLs and ZAR1 (independently of HopZ1a) and trigger immunity in planta. Our results suggest that equilibria between active and inactive kinase domain conformations regulate ZED1-PBL interactions and formation of ternary complexes with ZAR1. Improved models describing molecular interactions between immunity determinants, effectors and effector targets will inform efforts to exploit natural diversity for development of crops with enhanced disease resistance.
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Affiliation(s)
- D. Patrick Bastedo
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Madiha Khan
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Alexandre Martel
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Derek Seto
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Inga Kireeva
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Jianfeng Zhang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Wardah Masud
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - David Millar
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Jee Yeon Lee
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Amy Huei-Yi Lee
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yunchen Gong
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - André Santos-Severino
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (DSG); (DD)
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (DSG); (DD)
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117
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Pisa R, Cupido T, Steinman JB, Jones NH, Kapoor TM. Analyzing Resistance to Design Selective Chemical Inhibitors for AAA Proteins. Cell Chem Biol 2019; 26:1263-1273.e5. [PMID: 31257183 DOI: 10.1016/j.chembiol.2019.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/15/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022]
Abstract
Drug-like inhibitors are often designed by mimicking cofactor or substrate interactions with enzymes. However, as active sites are comprised of conserved residues, it is difficult to identify the critical interactions needed to design selective inhibitors. We are developing an approach, named RADD (resistance analysis during design), which involves engineering point mutations in the target to generate active alleles and testing compounds against them. Mutations that alter compound potency identify residues that make key interactions with the inhibitor and predict target-binding poses. Here, we apply this approach to analyze how diaminotriazole-based inhibitors bind spastin, a microtubule-severing AAA (ATPase associated with diverse cellular activities) protein. The distinct binding poses predicted for two similar inhibitors were confirmed by a series of X-ray structures. Importantly, our approach not only reveals how selective inhibition of the target can be achieved but also identifies resistance-conferring mutations at the early stages of the design process.
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Affiliation(s)
- Rudolf Pisa
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Tommaso Cupido
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan B Steinman
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Natalie H Jones
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
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118
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Haldane A, Flynn WF, He P, Levy RM. Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs. Biophys J 2019; 114:21-31. [PMID: 29320688 DOI: 10.1016/j.bpj.2017.10.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 09/11/2017] [Accepted: 10/17/2017] [Indexed: 01/25/2023] Open
Abstract
The protein kinase catalytic domain is one of the most abundant domains across all branches of life. Although kinases share a common core function of phosphoryl-transfer, they also have wide functional diversity and play varied roles in cell signaling networks, and for this reason are implicated in a number of human diseases. This functional diversity is primarily achieved through sequence variation, and uncovering the sequence-function relationships for the kinase family is a major challenge. In this study we use a statistical inference technique inspired by statistical physics, which builds a coevolutionary "Potts" Hamiltonian model of sequence variation in a protein family. We show how this model has sufficient power to predict the probability of specific subsequences in the highly diverged kinase family, which we verify by comparing the model's predictions with experimental observations in the Uniprot database. We show that the pairwise (residue-residue) interaction terms of the statistical model are necessary and sufficient to capture higher-than-pairwise mutation patterns of natural kinase sequences. We observe that previously identified functional sets of residues have much stronger correlated interaction scores than are typical.
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Affiliation(s)
- Allan Haldane
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania
| | - William F Flynn
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania; Department of Physics and Astronomy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Peng He
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania.
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119
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Ahuja LG, Taylor SS, Kornev AP. Tuning the "violin" of protein kinases: The role of dynamics-based allostery. IUBMB Life 2019; 71:685-696. [PMID: 31063633 PMCID: PMC6690483 DOI: 10.1002/iub.2057] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/12/2019] [Indexed: 12/17/2022]
Abstract
The intricacies of allosteric regulation of protein kinases continue to engage the research community. Allostery, or control from a distance, is seen as a fundamental biomolecular mechanism for proteins. From the traditional methods of conformational selection and induced fit, the field has grown to include the role of protein motions in defining a dynamics-based allosteric approach. Harnessing of these continuous motions in the protein to exert allosteric effects can be defined by a "violin" model that focuses on distributions of protein vibrations as opposed to concerted pathways. According to this model, binding of an allosteric modifier causes global redistribution of dynamics in the protein kinase domain that leads to changes in its catalytic properties. This model is consistent with the "entropy-driven allostery" mechanism proposed by Cooper and Dryden in 1984 and does not require, but does not exclude, any major structural changes. We provide an overview of practical implementation of the violin model and how it stands amidst the other known models of protein allostery. Protein kinases have been described as the biomolecules of interest. © 2019 IUBMB Life, 71(6):685-696, 2019.
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Affiliation(s)
- Lalima G. Ahuja
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
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120
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Bradley D, Beltrao P. Evolution of protein kinase substrate recognition at the active site. PLoS Biol 2019; 17:e3000341. [PMID: 31233486 PMCID: PMC6611643 DOI: 10.1371/journal.pbio.3000341] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023] Open
Abstract
Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase-substrate motif. Kinases have been extensively duplicated throughout evolution, but little is known about when in time new target motifs have arisen. Here, we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity-determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but are not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired around the time of the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
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121
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Hammarén HM, Virtanen AT, Raivola J, Silvennoinen O. The regulation of JAKs in cytokine signaling and its breakdown in disease. Cytokine 2019; 118:48-63. [DOI: 10.1016/j.cyto.2018.03.041] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 01/12/2023]
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122
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Deota S, Rathnachalam S, Namrata K, Boob M, Fulzele A, Radhika S, Ganguli S, Balaji C, Kaypee S, Vishwakarma KK, Kundu TK, Bhandari R, Gonzalez de Peredo A, Mishra M, Venkatramani R, Kolthur-Seetharam U. Allosteric Regulation of Cyclin-B Binding by the Charge State of Catalytic Lysine in CDK1 Is Essential for Cell-Cycle Progression. J Mol Biol 2019; 431:2127-2142. [PMID: 30974121 DOI: 10.1016/j.jmb.2019.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 01/19/2023]
Abstract
Cyclin-dependent kinase 1 (CDK1) is essential for cell-cycle progression. While dependence of CDK activity on cyclin levels is well established, molecular mechanisms that regulate their binding are less understood. Here, we report for the first time that CDK1:cyclin-B binding is not default but rather determined by the evolutionarily conserved catalytic residue, lysine-33 in CDK1. We demonstrate that the charge state of this lysine allosterically remodels the CDK1:cyclin-B interface. Cell cycle-dependent acetylation of lysine-33 or its mutation to glutamine, which mimics acetylation, abrogates cyclin-B binding. Using biochemical approaches and atomistic molecular dynamics simulations, we have uncovered both short-range and long-range effects of perturbing the charged state of the catalytic lysine, which lead to inhibition of kinase activity. Specifically, although loss of the charge state of catalytic lysine did not impact ATP binding significantly, it altered its orientation in the active site. In addition, the catalytic lysine also acts as an intra-molecular electrostatic tether at the active site to orient structural elements interfacing with cyclin-B. Physiologically, opposing activities of SIRT1 and P300 regulate acetylation and thus control the charge state of lysine-33. Importantly, cells expressing acetylation mimic mutant of Cdc2/CDK1 in yeast are arrested in G2 and fail to divide, indicating the requirement of the deacetylated state of the catalytic lysine for cell division. Thus, by illustrating the molecular role of the catalytic lysine and cell cycle-dependent deacetylation as a determinant of CDK1:cyclin-B interaction, our results redefine the current model of CDK1 activation and cell-cycle progression.
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Affiliation(s)
- Shaunak Deota
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Sivasudhan Rathnachalam
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Kanojia Namrata
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Mayank Boob
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Amit Fulzele
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Toulouse 31400, France
| | - S Radhika
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad 500039, India; Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India
| | - Chinthapalli Balaji
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Krishna Kant Vishwakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Tapas Kumar Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad 500039, India
| | | | - Mithilesh Mishra
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India.
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India.
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123
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Suskiewicz MJ, Hajdusits B, Beveridge R, Heuck A, Vu LD, Kurzbauer R, Hauer K, Thoeny V, Rumpel K, Mechtler K, Meinhart A, Clausen T. Structure of McsB, a protein kinase for regulated arginine phosphorylation. Nat Chem Biol 2019; 15:510-518. [PMID: 30962626 DOI: 10.1038/s41589-019-0265-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 03/05/2019] [Indexed: 11/09/2022]
Abstract
Protein phosphorylation regulates key processes in all organisms. In Gram-positive bacteria, protein arginine phosphorylation plays a central role in protein quality control by regulating transcription factors and marking aberrant proteins for degradation. Here, we report structural, biochemical, and in vivo data of the responsible kinase, McsB, the founding member of an arginine-specific class of protein kinases. McsB differs in structure and mechanism from protein kinases that act on serine, threonine, and tyrosine residues and instead has a catalytic domain related to that of phosphagen kinases (PhKs), metabolic enzymes that phosphorylate small guanidino compounds. In McsB, the PhK-like phosphotransferase domain is structurally adapted to target protein substrates and is accompanied by a novel phosphoarginine (pArg)-binding domain that allosterically controls protein kinase activity. The identification of distinct pArg reader domains in this study points to a remarkably complex signaling system, thus challenging simplistic views of bacterial protein phosphorylation.
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Affiliation(s)
- Marcin J Suskiewicz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Bence Hajdusits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Rebecca Beveridge
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Heuck
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Lam Dai Vu
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,VIB/UGent, Ghent, Belgium
| | - Robert Kurzbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Katja Hauer
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria. .,Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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124
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Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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125
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Tian T, Yao Y, Yang B, Zhang K, Liu B. Ultrasensitive amplification-free detection of protein kinase based on catalyzed assembly and enumeration of gold nanoparticles. Chem Commun (Camb) 2019; 55:2505-2508. [PMID: 30741307 DOI: 10.1039/c9cc00131j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A single-particle enumeration method based on phosphorylation-directed in situ assembly of gold nanoparticles is developed for the ultrasensitive sensing of cellular protein kinase A activity. In comparison to existing strategies, the proposed new method demonstrates five orders of linear range and improves the detection limit up to 10-to-1000 fold without the involvement of target amplification.
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Affiliation(s)
- Tongtong Tian
- Department of Chemistry, Shanghai Stomatological Hospital, and State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China.
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Vargas JNS, Wang C, Bunker E, Hao L, Maric D, Schiavo G, Randow F, Youle RJ. Spatiotemporal Control of ULK1 Activation by NDP52 and TBK1 during Selective Autophagy. Mol Cell 2019; 74:347-362.e6. [PMID: 30853401 PMCID: PMC6642318 DOI: 10.1016/j.molcel.2019.02.010] [Citation(s) in RCA: 297] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/26/2018] [Accepted: 02/06/2019] [Indexed: 01/01/2023]
Abstract
Selective autophagy recycles damaged organelles and clears intracellular pathogens to prevent their aberrant accumulation. How ULK1 kinase is targeted and activated during selective autophagic events remains to be elucidated. In this study, we used chemically inducible dimerization (CID) assays in tandem with CRISPR KO lines to systematically analyze the molecular basis of selective autophagosome biogenesis. We demonstrate that ectopic placement of NDP52 on mitochondria or peroxisomes is sufficient to initiate selective autophagy by focally localizing and activating the ULK1 complex. The capability of NDP52 to induce mitophagy is dependent on its interaction with the FIP200/ULK1 complex, which is facilitated by TBK1. Ectopically tethering ULK1 to cargo bypasses the requirement for autophagy receptors and TBK1. Focal activation of ULK1 occurs independently of AMPK and mTOR. Our findings provide a parsimonious model of selective autophagy, which highlights the coordination of ULK1 complex localization by autophagy receptors and TBK1 as principal drivers of targeted autophagosome biogenesis. NDP52 associates with the ULK1 complex through FIP200, facilitated by TBK1 NDP52/TBK1 targets ULK1 to cargo to initiate autophagy in the absence of LC3 ULK1 is activated on cargo independently of AMPK and mTOR activity Ectopic recruitment of FIP200-binding peptide is sufficient to degrade cargo
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Affiliation(s)
- Jose Norberto S Vargas
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Department of Neuromuscular Disorders, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Bunker
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ling Hao
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Diseases and Stroke, Bethesda, MD 20892, USA
| | - Giampietro Schiavo
- Department of Neuromuscular Disorders, UCL Institute of Neurology, University College London, London WC1N 3BG, UK; UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, University College London, London WC1E 6BT, UK; Discoveries Centre for Regenerative and Precision Medicine, UCL Campus, University College London, London WC1E 6BT, UK
| | - Felix Randow
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge CB2 0QH, UK; University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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127
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Arif A, Jia J, Willard B, Li X, Fox PL. Multisite Phosphorylation of S6K1 Directs a Kinase Phospho-code that Determines Substrate Selection. Mol Cell 2019; 73:446-457.e6. [PMID: 30612880 PMCID: PMC6415305 DOI: 10.1016/j.molcel.2018.11.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/16/2018] [Accepted: 11/15/2018] [Indexed: 01/02/2023]
Abstract
Multisite phosphorylation of kinases can induce on-off or graded regulation of catalytic activity; however, its influence on substrate specificity remains unclear. Here, we show that multisite phosphorylation of ribosomal protein S6 kinase 1 (S6K1) alters target selection. Agonist-inducible phosphorylation of glutamyl-prolyl tRNA synthetase (EPRS) by S6K1 in monocytes and adipocytes requires not only canonical phosphorylation at Thr389 by mTORC1 but also phosphorylation at Ser424 and Ser429 in the C terminus by cyclin-dependent kinase 5 (Cdk5). S6K1 phosphorylation at these additional sites induces a conformational switch and is essential for high-affinity binding and phosphorylation of EPRS, but not canonical S6K1 targets, e.g., ribosomal protein S6. Unbiased proteomic analysis identified additional targets phosphorylated by multisite phosphorylated S6K1 in insulin-stimulated adipocytes-namely, coenzyme A synthase, lipocalin 2, and cortactin. Thus, embedded within S6K1 is a target-selective kinase phospho-code that integrates signals from mTORC1 and Cdk5 to direct an insulin-stimulated, post-translational metabolon determining adipocyte lipid metabolism.
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Affiliation(s)
- Abul Arif
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Orthopedics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Jie Jia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Xiaoxia Li
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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128
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Sala L, Cirillo G, Riva G, Romano G, Giussani C, Cialdella A, Todisco A, Virtuoso A, Cerrito MG, Bentivegna A, Grassilli E, Ardizzoia A, Bonoldi E, Giovannoni R, Papa M, Lavitrano M. Specific Expression of a New Bruton Tyrosine Kinase Isoform (p65BTK) in the Glioblastoma Gemistocytic Histotype. Front Mol Neurosci 2019; 12:2. [PMID: 30733667 PMCID: PMC6353843 DOI: 10.3389/fnmol.2019.00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022] Open
Abstract
Bruton's tyrosine-kinase (BTK) is a non-receptor tyrosine kinase recently associated with glioma tumorigenesis and a novel prognostic marker for poor survival in patients with glioma. The p65BTK is a novel BTK isoform involved in different pathways of drug resistance of solid tumors, thus we aimed to investigate the expression and the putative role of p65BTK in tumors of the central nervous system (CNS). We selected a large cohort of patients with glial tumors (n = 71) and analyzed the expression of p65BTK in different histotypes and correlation with clinical parameters. Sections were stained with glial fibrillary acidic protein (GFAP), p53, epidermal growth factor receptor (EGFR), S100, vimentin, and epithelial membrane antigen (EMA) antibodies. Glioma stem cell (GSC) lines, isolated from glioblastoma multiforme (GBM), were treated with different concentrations of ibrutinib, a specific inhibitor of BTK, in order to evaluate their metabolic activity, mitotic index and mortality. Moreover, an orthotopic xenotransplant of GSC from human GBM was used to evaluate the expression of p65BTK in the brain of immunodeficient mice. p65BTK was expressed in GSC and in gemistocytes in human gliomas at different histological grade. We found a significant correlation between BTK expression and low-grade (LG) tumors (p ≤ 0.05) and overall survival (OS) of patients with grade III gliomas (p ≤ 0.05), suggestive of worst prognosis. Interestingly, the expression of p65BTK remained restricted exclusively to gemistocytic cells in the xenograft mouse model. Ibrutinib administration significantly reduced metabolic activity and mitotic index and increased mortality in GSC, highlighting the specific role of p65BTK in cell proliferation and survival. In conclusion, our data demonstrated that p65BTK is expressed in glioma tumors, restricted to gemistocytic cells, has a key role in GSC and has a bad prognostic value, thus highlighting the importance of future research for targeted therapy of human gliomas.
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Affiliation(s)
- Luca Sala
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Giovanni Cirillo
- Laboratory of Neuronal Networks, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Gabriele Riva
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Gabriele Romano
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Carlo Giussani
- Unit of Neurosurgery, School of Medicine and Surgery, Neuroscience Center, University of Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | | | - Antonio Todisco
- Laboratory of Neuronal Networks, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Assunta Virtuoso
- Laboratory of Neuronal Networks, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Emanuela Grassilli
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | | | - Roberto Giovannoni
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Michele Papa
- Laboratory of Neuronal Networks, University of Campania "Luigi Vanvitelli", Naples, Italy
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129
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Wood DJ, Korolchuk S, Tatum NJ, Wang LZ, Endicott JA, Noble MEM, Martin MP. Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition. Cell Chem Biol 2019; 26:121-130.e5. [PMID: 30472117 PMCID: PMC6344228 DOI: 10.1016/j.chembiol.2018.10.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/15/2018] [Accepted: 10/11/2018] [Indexed: 11/23/2022]
Abstract
Dysregulation of the cell cycle characterizes many cancer subtypes, providing a rationale for developing cyclin-dependent kinase (CDK) inhibitors. Potent CDK2 inhibitors might target certain cancers in which CCNE1 is amplified. However, current CDK2 inhibitors also inhibit CDK1, generating a toxicity liability. We have used biophysical measurements and X-ray crystallography to investigate the ATP-competitive inhibitor binding properties of cyclin-free and cyclin-bound CDK1 and CDK2. We show that these kinases can readily be distinguished by such inhibitors when cyclin-free, but not when cyclin-bound. The basis for this discrimination is unclear from either inspection or molecular dynamics simulation of ligand-bound CDKs, but is reflected in the contacts made between the kinase N- and C-lobes. We conclude that there is a subtle but profound difference between the conformational energy landscapes of cyclin-free CDK1 and CDK2. The unusual properties of CDK1 might be exploited to differentiate CDK1 from other CDKs in future cancer therapeutic design.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Svitlana Korolchuk
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Natalie J Tatum
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Lan-Zhen Wang
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martin E M Noble
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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130
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Panicker RC, Chattopadhaya S, Coyne AG, Srinivasan R. Allosteric Small-Molecule Serine/Threonine Kinase Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:253-278. [PMID: 31707707 DOI: 10.1007/978-981-13-8719-7_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deregulation of protein kinase activity has been linked to many diseases ranging from cancer to AIDS and neurodegenerative diseases. Not surprisingly, drugging the human kinome - the complete set of kinases encoded by the human genome - has been one of the major drug discovery pipelines. Majority of the approved clinical kinase inhibitors target the ATP binding site of kinases. However, the remarkable sequence and structural similarity of ATP binding pockets of kinases make selective inhibition of kinases a daunting task. To circumvent these issues, allosteric inhibitors that target sites other than the orthosteric ATP binding pocket have been developed. The structural diversity of the allosteric sites allows these inhibitors to have higher selectivity, lower toxicity and improved physiochemical properties and overcome drug resistance associated with the use of conventional kinase inhibitors. In this chapter, we will focus on the allosteric inhibitors of selected serine/threonine kinases, outline the benefits of using these inhibitors and discuss the challenges and future opportunities.
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Affiliation(s)
- Resmi C Panicker
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | | | - Anthony G Coyne
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China.
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131
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Astl L, Tse A, Verkhivker GM. Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:187-223. [DOI: 10.1007/978-981-13-8719-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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132
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Yu S, Du Z, Dong C, Ren J. In situ study of RSK2 kinase activity in a single living cell by combining single molecule spectroscopy with activity-based probes. Analyst 2019; 144:3756-3764. [DOI: 10.1039/c9an00178f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FCS with the ABP strategy is a very promising method for studying endogenous protein kinases in living cells.
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Affiliation(s)
- Shengrong Yu
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Zhixue Du
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
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133
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Kalaivani R, Narwani TJ, de Brevern AG, Srinivasan N. Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms. Protein Sci 2018; 28:543-560. [PMID: 30468265 DOI: 10.1002/pro.3556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/11/2018] [Accepted: 11/18/2018] [Indexed: 12/24/2022]
Abstract
Many protein kinases are characterized by at least two structural forms corresponding to the highest level of activity (active) and low or no activity, (inactive). Further, protein dynamics is an important consideration in understanding the molecular and mechanistic basis of enzyme function. In this work, we use protein kinase A (PKA) as the model system and perform microsecond range molecular dynamics (MD) simulations on six variants which differ from one another in terms of active and inactive form, with or without bound ligands, C-terminal tail and phosphorylation at the activation loop. We find that the root mean square fluctuations in the MD simulations are generally higher for the inactive forms than the active forms. This difference is statistically significant. The higher dynamics of inactive states has significant contributions from ATP binding loop, catalytic loop, and αG helix. Simulations with and without C-terminal tail show this differential dynamics as well, with lower dynamics both in the active and inactive forms if C-terminal tail is present. Similarly, the dynamics associated with the inactive form is higher irrespective of the phosphorylation status of Thr 197. A relatively stable stature of active kinases may be better suited for binding of substrates and detachment of the product. Also, phosphoryl group transfer from ATP to the phosphosite on the substrate requires precise transient coordination of chemical entities from three different molecules, which may be facilitated by the higher stability of the active state.
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Affiliation(s)
- R Kalaivani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - T J Narwani
- INSERM, U 1134, DSIMB, F-75739, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, F-75739, Paris, France.,Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.,Laboratoire d'Excellence GR-Ex, F-75739, Paris, France
| | - A G de Brevern
- INSERM, U 1134, DSIMB, F-75739, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, F-75739, Paris, France.,Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.,Laboratoire d'Excellence GR-Ex, F-75739, Paris, France
| | - N Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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134
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The Interaction between the Drosophila EAG Potassium Channel and the Protein Kinase CaMKII Involves an Extensive Interface at the Active Site of the Kinase. J Mol Biol 2018; 430:5029-5049. [PMID: 30381148 DOI: 10.1016/j.jmb.2018.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022]
Abstract
The Drosophila EAG (dEAG) potassium channel is the founding member of the superfamily of KNCH channels, which are involved in cardiac repolarization, neuronal excitability and cellular proliferation. In flies, dEAG is involved in regulation of neuron firing and assembles with CaMKII to form a complex implicated in memory formation. We have characterized the interaction between the kinase domain of CaMKII and a 53-residue fragment of the dEAG channel that includes a canonical CaMKII recognition sequence. Crystal structures together with biochemical/biophysical analysis show a substrate-kinase complex with an unusually tight and extensive interface that appears to be strengthened by phosphorylation of the channel fragment. Electrophysiological recordings show that catalytically active CaMKII is required to observe active dEAG channels. A previously identified phosphorylation site in the recognition sequence is not the substrate for this crucial kinase activity, but rather contributes importantly to the tight interaction of the kinase with the channel. The available data suggest that the dEAG channel is a docking platform for the kinase and that phosphorylation of the channel's kinase recognition sequence modulates the strength of the interaction between the channel and the kinase.
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135
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Elkhadragy L, Alsaran H, Morel M, Long W. Activation loop phosphorylation of ERK3 is important for its kinase activity and ability to promote lung cancer cell invasiveness. J Biol Chem 2018; 293:16193-16205. [PMID: 30166347 DOI: 10.1074/jbc.ra118.003699] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/13/2018] [Indexed: 12/23/2022] Open
Abstract
ERK3 is an atypical mitogen-activated protein kinase (MAPK) that has recently gained interest for its role in promoting cancer cell migration and invasion. However, the molecular regulation of ERK3 functions in cancer cells is largely unknown. ERK3 has a single phospho-acceptor site (Ser189) in its activation motif rather than the TXY conserved in conventional MAPKs such as ERK1/2. Although dual phosphorylation of the TXY motif is known to be critical for the activation of conventional MAPKs, the role of Ser189 phosphorylation in ERK3 activity and its function in cancer cells remain elusive. In this study, we revealed that activation loop phosphorylation is important for ERK3 in promoting cancer cell invasiveness, as the S189A mutation greatly decreased the ability of ERK3 to promote migration and invasion of lung cancer cells. Interestingly, a catalytically inactive ERK3 mutant was still capable of increasing migration and invasion, although to a lesser extent compared with WT ERK3, suggesting that ERK3 promotes cancer cell invasiveness by both kinase-dependent and kinase-independent mechanisms. To elucidate how the S189A mutation reduces the invasiveness-promoting ability of ERK3, we tested its effect on the kinase activity of ERK3 toward steroid receptor coactivator 3 (SRC3), a recently identified substrate of ERK3 critical for cancer cell invasiveness. Compared with ERK3, ERK3-S189A exhibited a dramatic decrease in kinase activity toward SRC3 and a concomitantly reduced ability to stimulate matrix metalloproteinase expression. Taken together, our study unravels the importance of Ser189 phosphorylation for intramolecular regulation of ERK3 kinase activity and invasiveness-promoting ability in lung cancer cells.
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Affiliation(s)
- Lobna Elkhadragy
- From the Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Hadel Alsaran
- From the Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Marion Morel
- From the Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Weiwen Long
- From the Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
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136
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Regulation of Herpes Simplex Virus 2 Protein Kinase UL13 by Phosphorylation and Its Role in Viral Pathogenesis. J Virol 2018; 92:JVI.00807-18. [PMID: 29899106 DOI: 10.1128/jvi.00807-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
UL13 proteins are serine/threonine protein kinases encoded by herpes simplex virus 1 (HSV-1) and HSV-2. Although the downstream effects of the HSV protein kinases, mostly those of HSV-1 UL13, have been reported, there is a lack of information on how these viral protein kinases are regulated in HSV-infected cells. In this study, we used a large-scale phosphoproteomic analysis of HSV-2-infected cells to identify a physiological phosphorylation site in HSV-2 UL13 (i.e., Ser-18) and investigated the significance of phosphorylation of this site in HSV-2-infected cell cultures and mice. Our results were as follows. (i) An alanine substitution at UL13 Ser-18 (S18A) significantly reduced HSV-2 replication and cell-to-cell spread in U2OS cells to a level similar to those of the UL13-null and kinase-dead mutations. (ii) The UL13 S18A mutation significantly impaired phosphorylation of a cellular substrate of this viral protein kinase in HSV-2-infected U2OS cells. (iii) Following vaginal infection of mice, the UL13 S18A mutation significantly reduced mortality, HSV-2 replication in the vagina, and development of vaginal disease to levels similar to those of the UL13-null and the kinase-dead mutations. (iv) A phosphomimetic substitution at UL13 Ser-18 significantly restored the phenotype observed with the UL13 S18A mutation in U2OS cells and mice. Collectively, our results suggested that phosphorylation of UL13 Ser-18 regulated UL13 function in HSV-2-infected cells and that this regulation was critical for the functional activity of HSV-2 UL13 in vitro and in vivo and also for HSV-2 replication and pathogenesis.IMPORTANCE Based on studies on cellular protein kinases, it is obvious that the regulatory mechanisms of protein kinases are as crucial as their functional consequences. Herpesviruses each encode at least one protein kinase, but the mechanism by which these kinases are regulated in infected cells remains to be elucidated, with a few exceptions, although information on their functional effects has been accumulating. In this study, we have shown that phosphorylation of the HSV-2 UL13 protein kinase at Ser-18 regulated its function in infected cells, and this regulation was critical for HSV-2 replication and pathogenesis in vivo UL13 is conserved in all members of the family Herpesviridae, and this is the first report clarifying the regulatory mechanism of a conserved herpesvirus protein kinase that is involved in viral replication and pathogenesis in vivo Our study may provide insight into the regulatory mechanisms of the other conserved herpesvirus protein kinases.
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137
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Mukherjee M, Sabir S, O'Regan L, Sampson J, Richards MW, Huguenin-Dezot N, Ault JR, Chin JW, Zhuravleva A, Fry AM, Bayliss R. Mitotic phosphorylation regulates Hsp72 spindle localization by uncoupling ATP binding from substrate release. Sci Signal 2018; 11:11/543/eaao2464. [PMID: 30108182 DOI: 10.1126/scisignal.aao2464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hsp72 is a member of the 70-kDa heat shock family of molecular chaperones (Hsp70s) that comprise a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD) connected by a linker that couples the exchange of adenosine diphosphate (ADP) for adenosine triphosphate (ATP) with the release of the protein substrate. Mitotic phosphorylation of Hsp72 by the kinase NEK6 at Thr66 located in the NBD promotes the localization of Hsp72 to the mitotic spindle and is required for efficient spindle assembly and chromosome congression and segregation. We determined the crystal structure of the Hsp72 NBD containing a genetically encoded phosphoserine at position 66. This revealed structural changes that stabilized interactions between subdomains within the NBD. ATP binding to the NBD of unmodified Hsp72 resulted in the release of substrate from the SBD, but phosphorylated Hsp72 retained substrate in the presence of ATP. Mutations that prevented phosphorylation-dependent subdomain interactions restored the connection between ATP binding and substrate release. Thus, phosphorylation of Thr66 is a reversible mechanism that decouples the allosteric connection between nucleotide binding and substrate release, providing further insight into the regulation of the Hsp70 family. We propose that phosphorylation of Hsp72 on Thr66 by NEK6 during mitosis promotes its localization to the spindle by stabilizing its interactions with components of the mitotic spindle.
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Affiliation(s)
- Manjeet Mukherjee
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah Sabir
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laura O'Regan
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Josephina Sampson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Mark W Richards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nicolas Huguenin-Dezot
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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138
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Xiong S, Lorenzen K, Couzens AL, Templeton CM, Rajendran D, Mao DYL, Juang YC, Chiovitti D, Kurinov I, Guettler S, Gingras AC, Sicheri F. Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment. Structure 2018; 26:1101-1115.e6. [PMID: 29983373 PMCID: PMC6087429 DOI: 10.1016/j.str.2018.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/28/2018] [Accepted: 05/17/2018] [Indexed: 11/27/2022]
Abstract
The human NDR family kinases control diverse aspects of cell growth, and are regulated through phosphorylation and association with scaffolds such as MOB1. Here, we report the crystal structure of the human NDR1 kinase domain in its non-phosphorylated state, revealing a fully resolved atypically long activation segment that blocks substrate binding and stabilizes a non-productive position of helix αC. Consistent with an auto-inhibitory function, mutations within the activation segment of NDR1 dramatically enhance in vitro kinase activity. Interestingly, NDR1 catalytic activity is further potentiated by MOB1 binding, suggesting that regulation through modulation of the activation segment and by MOB1 binding are mechanistically distinct. Lastly, deleting the auto-inhibitory activation segment of NDR1 causes a marked increase in the association with upstream Hippo pathway components and the Furry scaffold. These findings provide a point of departure for future efforts to explore the cellular functions and the mechanism of NDR1.
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MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Binding Sites
- Cell Cycle Proteins
- Cell Line, Tumor
- Cloning, Molecular
- Crystallography, X-Ray
- Epithelial Cells/cytology
- Epithelial Cells/enzymology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Gene Expression Regulation
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HEK293 Cells
- Hepatocyte Growth Factor/chemistry
- Hepatocyte Growth Factor/genetics
- Hepatocyte Growth Factor/metabolism
- Humans
- Kinetics
- Microtubule-Associated Proteins/chemistry
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Serine-Threonine Kinases/chemistry
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/chemistry
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Serine-Threonine Kinase 3
- Signal Transduction
- Substrate Specificity
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Affiliation(s)
- Shawn Xiong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristina Lorenzen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Catherine M Templeton
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Dushyandi Rajendran
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Daniel Y L Mao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Yu-Chi Juang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - David Chiovitti
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Cornell University, Department of Chemistry and Chemical Biology, NE-CAT, Advanced Photon Source, Bldg. 436E, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK.
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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139
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Jia LP, Zhao RN, Wang LJ, Ma RN, Zhang W, Shang L, Wang HS. Aptamer based electrochemical assay for protein kinase activity by coupling hybridization chain reaction. Biosens Bioelectron 2018; 117:690-695. [PMID: 30014942 DOI: 10.1016/j.bios.2018.06.067] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 01/08/2023]
Abstract
The present work reported a simple, lable-free and sensitive electrochemical method for the detection of protein kinase A (PKA) activity. This method was based on the specific recognition of aptamer and the aptamer-induced hybridization chain reaction (HCR) amplification strategy. The aptasensor was constructed by immobilizing capture probe on a gold electrode via an Au-S bond. When adenosine triphosphate (ATP) aptamer was introduced, its one terminus hybridized with capture probe and the other hybridized with the complementary region of an auxiliary probe, which other region triggered HCR between two hairpin DNA (H1 and H2) to form a long DNA concatamer. At last a large number of electroactive methyle blue (MB) molecules were assembled on the dsDNA concatamer, which generated a significantly amplified electrochemical signal. In the presence of ATP, the HCR would not be performed because the aptamer specifically bond to ATP and the electrochemical response would decrease. However, when ATP and PKA coexisted, the electrochemical response would recovery because that ATP had been translated into ADP by PKA. So the activity of PKA could be effectively monitored according to the change of electrochemical signal. Based on the HCR amplification strategy, the aptasensor showed a wide linear range (4 - 4 ×105 U L-1) and a low detection limit (1.5 U L-1) for the detection of PKA. Furthermore, the method was applied to study the inhibitory effect of H-89 on PKA activity. The developed aptasensor was also used to the analysis of drug-induced PKA activity in cell lysates, indicating the potential application of the developed method in the fields of clinical diagnostics and discovery of new targeted drugs.
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Affiliation(s)
- Li-Ping Jia
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252000, China.
| | - Ruo-Nan Zhao
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Li-Juan Wang
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Rong-Na Ma
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Wei Zhang
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Lei Shang
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Huai-Sheng Wang
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252000, China.
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140
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Sultan MM, Kiss G, Pande VS. Towards simple kinetic models of functional dynamics for a kinase subfamily. Nat Chem 2018; 10:903-909. [PMID: 29988151 DOI: 10.1038/s41557-018-0077-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 05/08/2018] [Indexed: 11/09/2022]
Abstract
Kinases are ubiquitous enzymes involved in the regulation of critical cellular pathways. However, in silico modelling of the conformational ensembles of these enzymes is difficult due to inherent limitations and the cost of computational approaches. Recent algorithmic advances combined with homology modelling and parallel simulations have enabled researchers to address this computational sampling bottleneck. Here, we present the results of molecular dynamics studies for seven Src family kinase (SFK) members: Fyn, Lyn, Lck, Hck, Fgr, Yes and Blk. We present a sequence invariant extension to Markov state models, which allows us to quantitatively compare the structural ensembles of the seven kinases. Our findings indicate that in the absence of their regulatory partners, SFK members have similar in silico dynamics with active state populations ranging from 4 to 40% and activation timescales in the hundreds of microseconds. Furthermore, we observe several potentially druggable intermediate states, including a pocket next to the adenosine triphosphate binding site that could potentially be targeted via a small-molecule inhibitor.
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Affiliation(s)
| | - Gert Kiss
- Department of Chemistry, Stanford University, Stanford, CA, USA.,Center for Molecular Analysis and Design, Stanford University, Stanford, CA, USA.,Revolution Medicines, Redwood City, CA, USA
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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141
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Structure activity relationships of anthranilic acid-based compounds on cellular and in vivo mitogen activated protein kinase-5 signaling pathways. Bioorg Med Chem Lett 2018; 28:2294-2301. [DOI: 10.1016/j.bmcl.2018.05.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 11/15/2022]
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142
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Reversible versus irreversible inhibition modes of ERK2: a comparative analysis for ERK2 protein kinase in cancer therapy. Future Med Chem 2018; 10:1003-1015. [DOI: 10.4155/fmc-2017-0275] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Aim: Irreversible covalent drug inhibition is an emerging paradigm; however, critical gaps in unraveling the efficacy of molecular determinants still persist. Methodology: We compare two ERK2 inhibitors with different binding modes. A 5-7-Oxozeaenol is selective inhibitor which irreversibly binds ERK2 by the formation of covalent bond with Cys166 while 5-iodotubercidin binds noncovalently. Result & discussion: Covalent inhibition showed greater protein stability, favorable binding energetics (irreversible inhibition binding free energy [ΔGbind] = -40.4354 kcal/mol and reversible inhibition ΔGbind = -26.2515 kcal/mol); higher correlation in residual movement and multiple van der Waals interactions as evident from residue interaction analysis. Conclusion: This investigation of the different inhibition modes of ERK2 would assist toward the design of more potent and highly site-specific covalent inhibitors in cancer therapy.
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143
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Lučić I, Rathinaswamy MK, Truebestein L, Hamelin DJ, Burke JE, Leonard TA. Conformational sampling of membranes by Akt controls its activation and inactivation. Proc Natl Acad Sci U S A 2018; 115:E3940-E3949. [PMID: 29632185 PMCID: PMC5924885 DOI: 10.1073/pnas.1716109115] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The protein kinase Akt controls myriad signaling processes in cells, ranging from growth and proliferation to differentiation and metabolism. Akt is activated by a combination of binding to the lipid second messenger PI(3,4,5)P3 and its subsequent phosphorylation by phosphoinositide-dependent kinase 1 and mechanistic target of rapamycin complex 2. The relative contributions of these mechanisms to Akt activity and signaling have hitherto not been understood. Here, we show that phosphorylation and activation by membrane binding are mutually interdependent. Moreover, the converse is also true: Akt is more rapidly dephosphorylated in the absence of PIP3, an autoinhibitory process driven by the interaction of its PH and kinase domains. We present biophysical evidence for the conformational changes in Akt that accompany its activation on membranes, show that Akt is robustly autoinhibited in the absence of PIP3 irrespective of its phosphorylation, and map the autoinhibitory PH-kinase interface. Finally, we present a model for the activation and inactivation of Akt by an ordered series of membrane binding, phosphorylation, dissociation, and dephosphorylation events.
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Affiliation(s)
- Iva Lučić
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria;
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
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144
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Khattab M, Wang F, Clayton AHA. Conformational Plasticity in Tyrosine Kinase Inhibitor-Kinase Interactions Revealed with Fluorescence Spectroscopy and Theoretical Calculations. J Phys Chem B 2018; 122:4667-4679. [PMID: 29629773 DOI: 10.1021/acs.jpcb.8b01530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To understand drug-protein dynamics, it is necessary to account for drug molecular flexibility and binding site plasticity. Herein, we exploit fluorescence from a tyrosine kinase inhibitor, AG1478, as a reporter of its conformation and binding site environment when complexed with its cognate kinase. Water-soluble kinases, aminoglycoside phosphotransferase APH(3')-Ia and mitogen-activated protein kinase 14 (MAPK14), were chosen for this study. On the basis of our prior work, the AG1478 conformation (planar or twisted) was inferred from the fluorescence excitation spectrum and the polarity of the AG1478-binding site was deduced from the fluorescence emission spectrum, while red-edge excitation shift (REES) probed the heterogeneity of the binding site (protein conformation and hydration) distributions in the protein conformational ensemble. In the AG1478-APH(3')-Ia complex, both twisted (or partially twisted) and planar AG1478 conformations were evidenced from emission wavelength-dependent excitation spectra. The binding site environment provided by APH(3')-Ia was moderately polar (λmax = 480 nm) with evidence for considerable heterogeneity (REES = 34 nm). In contrast, in the AG1478-MAPK14 complex, AG1478 was in a predominantly planar conformation with a lower degree of conformational heterogeneity. The binding site environment provided by the MAPK14 protein was of relatively low polarity (λmax = 430 nm) with a smaller degree of heterogeneity (REES = 11 nm). The results are compared with the available X-ray data and discussed in the context of our current understanding of tyrosine kinase inhibitor conformation and protein conformational ensembles.
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145
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Leopold AV, Chernov KG, Verkhusha VV. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem Soc Rev 2018; 47:2454-2484. [PMID: 29498733 DOI: 10.1039/c7cs00404d] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.
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Affiliation(s)
- Anna V Leopold
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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146
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García García T, Ventroux M, Derouiche A, Bidnenko V, Correia Santos S, Henry C, Mijakovic I, Noirot-Gros MF, Poncet S. Phosphorylation of the Bacillus subtilis Replication Controller YabA Plays a Role in Regulation of Sporulation and Biofilm Formation. Front Microbiol 2018; 9:486. [PMID: 29619013 PMCID: PMC5871692 DOI: 10.3389/fmicb.2018.00486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/01/2018] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis cells can adopt different life-styles in response to various environmental cues, including planktonic cells during vegetative growth, sessile cells during biofilm formation and sporulation. While switching life-styles, bacteria must coordinate the progression of their cell cycle with their physiological status. Our current understanding of the regulatory pathways controlling the decision-making processes and triggering developmental switches highlights a key role of protein phosphorylation. The regulatory mechanisms that integrate the bacterial chromosome replication status with sporulation involve checkpoint proteins that target the replication initiator DnaA or the kinase phosphorelay controlling the master regulator Spo0A. B. subtilis YabA is known to interact with DnaA to prevent over-initiation of replication during vegetative growth. Here, we report that YabA is phosphorylated by YabT, a Ser/Thr kinase expressed during sporulation and biofilm formation. The phosphorylation of YabA has no effect on replication initiation control but hyper-phosphorylation of YabA leads to an increase in sporulation efficiency and a strong inhibition of biofilm formation. We also provide evidence that YabA phosphorylation affects the level of Spo0A-P in cells. These results indicate that YabA is a multifunctional protein with a dual role in regulating replication initiation and life-style switching, thereby providing a potential mechanism for cross-talk and coordination of cellular processes during adaptation to environmental change.
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Affiliation(s)
| | - Magali Ventroux
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sara Correia Santos
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | | | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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147
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Stroehlein AJ, Young ND, Gasser RB. Advances in kinome research of parasitic worms - implications for fundamental research and applied biotechnological outcomes. Biotechnol Adv 2018; 36:915-934. [PMID: 29477756 DOI: 10.1016/j.biotechadv.2018.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022]
Abstract
Protein kinases are enzymes that play essential roles in the regulation of many cellular processes. Despite expansions in the fields of genomics, transcriptomics and bioinformatics, there is limited information on the kinase complements (kinomes) of most eukaryotic organisms, including parasitic worms that cause serious diseases of humans and animals. The biological uniqueness of these worms and the draft status of their genomes pose challenges for the identification and classification of protein kinases using established tools. In this article, we provide an account of kinase biology, the roles of kinases in diseases and their importance as drug targets, and drug discovery efforts in key socioeconomically important parasitic worms. In this context, we summarise methods and resources commonly used for the curation, identification, classification and functional annotation of protein kinase sequences from draft genomes; review recent advances made in the characterisation of the worm kinomes; and discuss the implications of these advances for investigating kinase signalling and developing small-molecule inhibitors as new anti-parasitic drugs.
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Affiliation(s)
- Andreas J Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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148
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Williams RM, Franke B, Wilkinson M, Fleming JR, Rigden DJ, Benian GM, Eyers PA, Mayans O. Autophosphorylation Is a Mechanism of Inhibition in Twitchin Kinase. J Mol Biol 2018; 430:793-805. [PMID: 29408381 DOI: 10.1016/j.jmb.2018.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 11/17/2022]
Abstract
Titin-like kinases are muscle-specific kinases that regulate mechanical sensing in the sarcomere. Twitchin kinase (TwcK) is the best-characterized member of this family, both structurally and enzymatically. TwcK activity is auto-inhibited by a dual intrasteric mechanism, in which N- and C-terminal tail extensions wrap around the kinase domain, blocking the hinge region, the ATP binding pocket and the peptide substrate binding groove. Physiologically, kinase activation is thought to occur by a stretch-induced displacement of the inhibitory tails from the kinase domain. Here, we now show that TwcK inhibits its catalysis even in the absence of regulatory tails, by undergoing auto-phosphorylation at mechanistically important elements of the kinase fold. Using mass spectrometry, site-directed mutagenesis and catalytic assays on recombinant samples, we identify residues T212, T301, T316 and T401 as primary auto-phosphorylation sites in TwcK in vitro. Taken together, our results suggest that residue T316, located in the peptide substrate binding P+1 loop, is the dominantly regulatory site in TwcK. Based on these findings, we conclude that TwcK is regulated through a triple-inhibitory mechanism consisting of phosphorylation and intrasteric blockage, which is responsive not only to mechanical cues but also to biochemical modulation. This implies that mechanically stretched conformations of TwcK do not necessarily correspond to catalytically active states, as previously postulated. This further suggests a phosphorylation-dependent desensitization of the TwcK-mediated mechanoresponse of the sarcomere in vivo.
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Affiliation(s)
- Rhys M Williams
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Barbara Franke
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Mark Wilkinson
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | | | - Daniel J Rigden
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Guy M Benian
- Department of Pathology, Emory University, Atlanta, GA 30322, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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149
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Abstract
Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research.
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150
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Rasool S, Soya N, Truong L, Croteau N, Lukacs GL, Trempe JF. PINK1 autophosphorylation is required for ubiquitin recognition. EMBO Rep 2018; 19:embr.201744981. [PMID: 29475881 DOI: 10.15252/embr.201744981] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
Mutations in PINK1 cause autosomal recessive Parkinson's disease (PD), a neurodegenerative movement disorder. PINK1 is a kinase that acts as a sensor of mitochondrial damage and initiates Parkin-mediated clearance of the damaged organelle. PINK1 phosphorylates Ser65 in both ubiquitin and the ubiquitin-like (Ubl) domain of Parkin, which stimulates its E3 ligase activity. Autophosphorylation of PINK1 is required for Parkin activation, but how this modulates the ubiquitin kinase activity is unclear. Here, we show that autophosphorylation of Tribolium castaneum PINK1 is required for substrate recognition. Using enzyme kinetics and NMR spectroscopy, we reveal that PINK1 binds the Parkin Ubl with a 10-fold higher affinity than ubiquitin via a conserved interface that is also implicated in RING1 and SH3 binding. The interaction requires phosphorylation at Ser205, an invariant PINK1 residue (Ser228 in human). Using mass spectrometry, we demonstrate that PINK1 rapidly autophosphorylates in trans at Ser205. Small-angle X-ray scattering and hydrogen-deuterium exchange experiments provide insights into the structure of the PINK1 catalytic domain. Our findings suggest that multiple PINK1 molecules autophosphorylate first prior to binding and phosphorylating ubiquitin and Parkin.
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Affiliation(s)
- Shafqat Rasool
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada.,Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Naoto Soya
- Department of Physiology and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Luc Truong
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Gergely L Lukacs
- Department of Biochemistry, McGill University, Montréal, QC, Canada.,Department of Physiology and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
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