1
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Shaw AL, Parson MAH, Truebestein L, Jenkins ML, Leonard TA, Burke JE. ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1. Structure 2023; 31:343-354.e3. [PMID: 36758543 DOI: 10.1016/j.str.2023.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023]
Abstract
Akt is a master regulator of pro-growth signaling in the cell. Akt is activated by phosphoinositides that disrupt the autoinhibitory interface between the kinase and pleckstrin homology (PH) domains and then is phosphorylated at T308 and S473. Akt hyperactivation is oncogenic, which has spurred development of potent and selective inhibitors as therapeutics. Using hydrogen deuterium exchange mass spectrometry (HDX-MS), we interrogated the conformational changes upon binding Akt ATP-competitive and allosteric inhibitors. We compared inhibitors against three different states of Akt1. The allosteric inhibitor caused substantive conformational changes and restricts membrane binding. ATP-competitive inhibitors caused extensive allosteric conformational changes, altering the autoinhibitory interface and leading to increased membrane binding, suggesting that the PH domain is more accessible for membrane binding. This work provides unique insight into the autoinhibitory conformation of the PH and kinase domain and conformational changes induced by Akt inhibitors and has important implications for the design of Akt targeted therapeutics.
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Affiliation(s)
- Alexandria L Shaw
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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2
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Pauk JN, Raju Palanisamy J, Kager J, Koczka K, Berghammer G, Herwig C, Veiter L. Advances in monitoring and control of refolding kinetics combining PAT and modeling. Appl Microbiol Biotechnol 2021; 105:2243-2260. [PMID: 33598720 PMCID: PMC7954745 DOI: 10.1007/s00253-021-11151-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 12/21/2022]
Abstract
Overexpression of recombinant proteins in Escherichia coli results in misfolded and non-active protein aggregates in the cytoplasm, so-called inclusion bodies (IB). In recent years, a change in the mindset regarding IBs could be observed: IBs are no longer considered an unwanted waste product, but a valid alternative to produce a product with high yield, purity, and stability in short process times. However, solubilization of IBs and subsequent refolding is necessary to obtain a correctly folded and active product. This protein refolding process is a crucial downstream unit operation-commonly done as a dilution in batch or fed-batch mode. Drawbacks of the state-of-the-art include the following: the large volume of buffers and capacities of refolding tanks, issues with uniform mixing, challenging analytics at low protein concentrations, reaction kinetics in non-usable aggregates, and generally low re-folding yields. There is no generic platform procedure available and a lack of robust control strategies. The introduction of Quality by Design (QbD) is the method-of-choice to provide a controlled and reproducible refolding environment. However, reliable online monitoring techniques to describe the refolding kinetics in real-time are scarce. In our view, only monitoring and control of re-folding kinetics can ensure a productive, scalable, and versatile platform technology for re-folding processes. For this review, we screened the current literature for a combination of online process analytical technology (PAT) and modeling techniques to ensure a controlled refolding process. Based on our research, we propose an integrated approach based on the idea that all aspects that cannot be monitored directly are estimated via digital twins and used in real-time for process control. KEY POINTS: • Monitoring and a thorough understanding of refolding kinetics are essential for model-based control of refolding processes. • The introduction of Quality by Design combining Process Analytical Technology and modeling ensures a robust platform for inclusion body refolding.
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Affiliation(s)
- Jan Niklas Pauk
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
- Competence Center CHASE GmbH, Altenbergerstraße 69, 4040, Linz, Austria
| | - Janani Raju Palanisamy
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
| | - Julian Kager
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
| | - Krisztina Koczka
- Bilfinger Industrietechnik Salzburg GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Gerald Berghammer
- Bilfinger Industrietechnik Salzburg GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Christoph Herwig
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria.
| | - Lukas Veiter
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
- Competence Center CHASE GmbH, Altenbergerstraße 69, 4040, Linz, Austria
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3
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Bayer KU, Schulman H. CaM Kinase: Still Inspiring at 40. Neuron 2019; 103:380-394. [PMID: 31394063 DOI: 10.1016/j.neuron.2019.05.033] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/12/2019] [Accepted: 05/21/2019] [Indexed: 01/07/2023]
Abstract
The Ca2+/calmodulin (CaM)-dependent protein kinase II (CaMKII) was touted as a memory molecule, even before its involvement in long-term potentiation (LTP) was shown. The enzyme has not disappointed, with subsequent demonstrations of remarkable structural and regulatory properties. Its neuronal functions now extend to long-term depression (LTD), and last year saw the first direct evidence for memory storage by CaMKII. Although CaMKII may have taken the spotlight, it is a member of a large family of diverse and interesting CaM kinases. Our aim is to place CaMKII in context of the other CaM kinases and then review certain aspects of this kinase that are of current interest.
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Affiliation(s)
- K Ulrich Bayer
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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4
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Harrington L, Alexander LT, Knapp S, Bayley H. Single-Molecule Protein Phosphorylation and Dephosphorylation by Nanopore Enzymology. ACS NANO 2019; 13:633-641. [PMID: 30588793 DOI: 10.1021/acsnano.8b07697] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Reversible protein phosphorylation plays a crucial and ubiquitous role in the control of almost all cellular processes. The interplay of protein kinases and phosphatases acting in opposition ensures tight dynamic control of protein phosphorylation states within the cell. Previously, engineered α-hemolysin pores bearing kinase substrate peptides have been developed as single-molecule stochastic sensors for protein kinases. Here, we have used these pores to observe, label-free, the phosphorylation and dephosphorylation of a single substrate molecule. Further, we investigated the effect of Mg2+ and Mn2+ upon substrate and product binding and found that Mn2+ relaxes active-site specificity toward nucleotides and enhances product binding. In doing so, we demonstrate the power and versatility of nanopore enzymology to scrutinize a critical post-translational modification.
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Affiliation(s)
- Leon Harrington
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Leila T Alexander
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute , University of Oxford , Oxford OX3 7DQ , United Kingdom
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute , University of Oxford , Oxford OX3 7DQ , United Kingdom
| | - Hagan Bayley
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
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5
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Singh I, Singh S, Verma V, Uversky VN, Chandra R. In silico evaluation of the resistance of the T790M variant of epidermal growth factor receptor kinase to cancer drug Erlotinib. J Biomol Struct Dyn 2017; 36:4209-4219. [PMID: 29183267 DOI: 10.1080/07391102.2017.1411293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epidermal growth factor receptor kinase is implicated in cancer development due to either overexpression or activation variants in its functional intracellular kinase domain. Threonine to methionine (Thr 790 Met) is one such variant observed commonly in patients showing resistance to kinase inhibitor drug Erlotinib. Two mechanisms for resistance have been proposed (1) steric hindrance and (2) enhanced binding to ATP. In this study, we employed molecular dynamics simulations and studied both the mechanisms. Extensive simulations and free energy of binding analyses has shown that steric hindrance does not explain appropriately the mechanism for resistance against Erlotinib therapy for this variant. It has been observed that conformational switching from an intermediate intrinsically disordered C-helix conformation is required for completion of the kinase's catalytic cycle. Our study substantiates that T790M variant has greater tendency for early transition to this intrinsically disordered C-helix intermediate state. We propose that enhanced catalytic efficiency in addition to enhanced ATP binding explains mechanism of T790M resistance to drug Erlotinib.
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Affiliation(s)
- Inderpal Singh
- a Department of Biotechnology , Shri Mata Vaishno Devi University (SMVDU) , Kakryal , Katra 182320 , Jammu and Kashmir , India.,b Bioinformatics Infrastructure Facility, Department of Biotechnology , Shri Mata Vaishno Devi University (SMVDU) , Kakryal , Katra 182320 , Jammu and Kashmir , India
| | - Shashank Singh
- c Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR-IIIM) , Canal Road, Jammu 180001 , Jammu and Kashmir , India
| | - Vijeshwar Verma
- a Department of Biotechnology , Shri Mata Vaishno Devi University (SMVDU) , Kakryal , Katra 182320 , Jammu and Kashmir , India.,b Bioinformatics Infrastructure Facility, Department of Biotechnology , Shri Mata Vaishno Devi University (SMVDU) , Kakryal , Katra 182320 , Jammu and Kashmir , India
| | - Vladimir N Uversky
- d Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine, University of South Florida, University of South Florida , Tampa , FL , USA.,e Laboratory of New Methods in Biology, Institute for Biological Instrumentation , Russian Academy of Sciences , 142290 Pushchino , Moscow Region , Russia
| | - Ratna Chandra
- a Department of Biotechnology , Shri Mata Vaishno Devi University (SMVDU) , Kakryal , Katra 182320 , Jammu and Kashmir , India
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6
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Sorrenti A, Leira-Iglesias J, Sato A, Hermans TM. Non-equilibrium steady states in supramolecular polymerization. Nat Commun 2017. [PMID: 28627512 PMCID: PMC5481825 DOI: 10.1038/ncomms15899] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Living systems use fuel-driven supramolecular polymers such as actin to control important cell functions. Fuel molecules like ATP are used to control when and where such polymers should assemble and disassemble. The cell supplies fresh ATP to the cytosol and removes waste products to sustain steady states. Artificial fuel-driven polymers have been developed recently, but keeping them in sustained non-equilibrium steady states (NESS) has proven challenging. Here we show a supramolecular polymer that can be kept in NESS, inside a membrane reactor where ATP is added and waste removed continuously. Assembly and disassembly of our polymer is regulated by phosphorylation and dephosphorylation, respectively. Waste products lead to inhibition, causing the reaction cycle to stop. Inside the membrane reactor, however, waste can be removed leading to long-lived NESS conditions. We anticipate that our approach to obtain NESS can be applied to other stimuli-responsive materials to achieve more life-like behaviour. Several cell functions are based on the fuel-driven assembly and disassembly of supramolecular polymers under non-equilibrium conditions. Here, the authors show controlled formation and breaking of a supramolecular polymer by enzymatic phosphorylation and dephosphorylation of a building block by continuously adding ATP fuel and removing waste products.
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Affiliation(s)
| | | | - Akihiro Sato
- University of Strasbourg, CNRS, ISIS UMR 7006, F-67000 Strasbourg, France
| | - Thomas M Hermans
- University of Strasbourg, CNRS, ISIS UMR 7006, F-67000 Strasbourg, France
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7
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. Understanding how cAMP-dependent protein kinase can catalyze phosphoryl transfer in the presence of Ca2+and Sr2+: a QM/MM study. Phys Chem Chem Phys 2017; 19:10377-10394. [DOI: 10.1039/c7cp00666g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Theoretical results demonstrate for the first time at the molecular level that the overall PKAc-catalyzed phosphoryl-transfer reaction is plausible with Ca2+and Sr2+, alkaline earth metal ions other than Mg2+, which is in good agreement with experiments.
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Affiliation(s)
- Ayax Pérez-Gallegos
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - Mireia Garcia-Viloca
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
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8
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Das A, Gerlits O, Parks JM, Langan P, Kovalevsky A, Heller WT. Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation. Structure 2015; 23:2331-2340. [PMID: 26585512 DOI: 10.1016/j.str.2015.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/31/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
Abstract
The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg(2+) binds first to the M1 site as a complex with ATP and is followed by Mg(2+) binding to the M2 site. Concurrently, the target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. Lastly, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.
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Affiliation(s)
- Amit Das
- Biology & Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Oksana Gerlits
- Biology & Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul Langan
- Biology & Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Biology & Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - William T Heller
- Biology & Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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9
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Rowland MA, Harrison B, Deeds EJ. Phosphatase specificity and pathway insulation in signaling networks. Biophys J 2015; 108:986-996. [PMID: 25692603 DOI: 10.1016/j.bpj.2014.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/13/2014] [Accepted: 12/05/2014] [Indexed: 12/31/2022] Open
Abstract
Phosphatases play an important role in cellular signaling networks by regulating the phosphorylation state of proteins. Phosphatases are classically considered to be promiscuous, acting on tens to hundreds of different substrates. We recently demonstrated that a shared phosphatase can couple the responses of two proteins to incoming signals, even if those two substrates are from otherwise isolated areas of the network. This finding raises a potential paradox: if phosphatases are indeed highly promiscuous, how do cells insulate themselves against unwanted crosstalk? Here, we use mathematical models to explore three possible insulation mechanisms. One approach involves evolving phosphatase KM values that are large enough to prevent saturation by the phosphatase's substrates. Although this is an effective method for generating isolation, the phosphatase becomes a highly inefficient enzyme, which prevents the system from achieving switch-like responses and can result in slow response kinetics. We also explore the idea that substrate degradation can serve as an effective phosphatase. Assuming that degradation is unsaturatable, this mechanism could insulate substrates from crosstalk, but it would also preclude ultrasensitive responses and would require very high substrate turnover to achieve rapid dephosphorylation kinetics. Finally, we show that adaptor subunits, such as those found on phosphatases like PP2A, can provide effective insulation against phosphatase crosstalk, but only if their binding to substrates is uncoupled from their binding to the catalytic core. Analysis of the interaction network of PP2A's adaptor domains reveals that although its adaptors may isolate subsets of targets from one another, there is still a strong potential for phosphatase crosstalk within those subsets. Understanding how phosphatase crosstalk and the insulation mechanisms described here impact the function and evolution of signaling networks represents a major challenge for experimental and computational systems biology.
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Affiliation(s)
- Michael A Rowland
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Brian Harrison
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Eric J Deeds
- Center for Computational Biology, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas; Santa Fe Institute, Santa Fe, New Mexico.
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10
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. SP20 Phosphorylation Reaction Catalyzed by Protein Kinase A: QM/MM Calculations Based on Recently Determined Crystallographic Structures. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01064] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ayax Pérez-Gallegos
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Mireia Garcia-Viloca
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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11
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. A QM/MM study of Kemptide phosphorylation catalyzed by protein kinase A. The role of Asp166 as a general acid/base catalyst. Phys Chem Chem Phys 2014; 17:3497-511. [PMID: 25535906 DOI: 10.1039/c4cp03579h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this work a theoretical study of the γ-phosphoryl group transfer from ATP to Ser17 of the synthetic substrate Kemptide (LRRASLG) in protein kinase A (PKA) has been carried out with a solvated model of the PKA-Mg2ATP-Kemptide system based on the X-ray crystallographic structure. We have used high levels (B3LYP/MM and MP2/MM) of theory to determine the overall reaction paths of the so-called concerted loose mechanism trying to clarify some aspects of that mechanism still under debate. Our calculations demonstrate for the first time in a complete model of the ternary system the viability of the final step of the catalytic mechanism in which the protonation of the phosphokemptide product by Asp166 takes place. Asp166 is a base catalyst that abstracts the HγSer17 of Kemptide thus facilitating the phosphoryl transfer, but it also acts as an acid catalyst by donating the proton just accepted from Ser17 to the O2γATP atom of the phosphoryl group.
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Affiliation(s)
- Ayax Pérez-Gallegos
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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12
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Srivastava AK, McDonald LR, Cembran A, Kim J, Masterson LR, McClendon CL, Taylor SS, Veglia G. Synchronous opening and closing motions are essential for cAMP-dependent protein kinase A signaling. Structure 2014; 22:1735-1743. [PMID: 25458836 DOI: 10.1016/j.str.2014.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 02/07/2023]
Abstract
Conformational fluctuations play a central role in enzymatic catalysis. However, it is not clear how the rates and the coordination of the motions affect the different catalytic steps. Here, we used NMR spectroscopy to analyze the conformational fluctuations of the catalytic subunit of the cAMP-dependent protein kinase (PKA-C), a ubiquitous enzyme involved in a myriad of cell signaling events. We found that the wild-type enzyme undergoes synchronous motions involving several structural elements located in the small lobe of the kinase, which is responsible for nucleotide binding and release. In contrast, a mutation (Y204A) located far from the active site desynchronizes the opening and closing of the active cleft without changing the enzyme's structure, rendering it catalytically inefficient. Since the opening and closing motions govern the rate-determining product release, we conclude that optimal and coherent conformational fluctuations are necessary for efficient turnover of protein kinases.
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Affiliation(s)
- Atul K Srivastava
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Leanna R McDonald
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alessandro Cembran
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Larry R Masterson
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher L McClendon
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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13
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Abstract
![]()
Although ADP release is the rate
limiting step in product turnover
by protein kinase A, the steps and motions involved in this process
are not well resolved. Here we report the apo and ADP bound structures
of the myristylated catalytic subunit of PKA at 2.9 and 3.5 Å
resolution, respectively. The ADP bound structure adopts a conformation
that does not conform to the previously characterized open, closed,
or intermediate states. In the ADP bound structure, the C-terminal
tail and Gly-rich loop are more closed than in the open state adopted
in the apo structure but are also much more open than the intermediate
or closed conformations. Furthermore, ADP binds at the active site
with only one magnesium ion, termed Mg2 from previous structures.
These structures thus support a model where ADP release proceeds through
release of the substrate and Mg1 followed by lifting of the Gly-rich
loop and disengagement of the C-terminal tail. Coupling of these two
structural elements with the release of the first metal ion fills
in a key step in the catalytic cycle that has been missing and supports
an ensemble of correlated conformational states that mediate the full
catalytic cycle for a protein kinase.
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Affiliation(s)
- Adam C Bastidas
- Department of Pharmacology, University of California, San Diego , San Diego, California 92093, United States
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14
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Gerlits O, Das A, Keshwani MM, Taylor S, Waltman MJ, Langan P, Heller WT, Kovalevsky A. Metal-free cAMP-dependent protein kinase can catalyze phosphoryl transfer. Biochemistry 2014; 53:3179-86. [PMID: 24786636 PMCID: PMC4030786 DOI: 10.1021/bi5000965] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray structures of several ternary product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with no bound metal ions and with Na(+) or K(+) coordinated at two metal-binding sites. The metal-free PKAc and the enzyme with alkali metals were able to facilitate the phosphoryl transfer reaction. In all studied complexes, the ATP and the substrate peptide (SP20) were modified into the products ADP and the phosphorylated peptide. The products of the phosphotransfer reaction were also found when ATP-γS, a nonhydrolyzable ATP analogue, reacted with SP20 in the PKAc active site containing no metals. Single turnover enzyme kinetics measurements utilizing (32)P-labeled ATP confirmed the phosphotransferase activity of the enzyme in the absence of metal ions and in the presence of alkali metals. In addition, the structure of the apo-PKAc binary complex with SP20 suggests that the sequence of binding events may become ordered in a metal-free environment, with SP20 binding first to prime the enzyme for subsequent ATP binding. Comparison of these structures reveals conformational and hydrogen bonding changes that might be important for the mechanism of catalysis.
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Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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15
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A quantitative model of ERK MAP kinase phosphorylation in crowded media. Sci Rep 2013; 3:1541. [PMID: 23528948 PMCID: PMC3607838 DOI: 10.1038/srep01541] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/08/2013] [Indexed: 11/23/2022] Open
Abstract
Cytoplasm contains a large number of macromolecules at extremely high densities. How this striking nature of intracellular milieu called macromolecular crowding affects intracellular signaling remains uncharacterized. Here, we examined the effect of macromolecular crowding on ERK MAPK phosphorylation by MEK MAPKK. Addition of polyethylene glycol-6000 (PEG-6000) as a crowder to mimic intracellular environments, elicited a biphasic response to the overall ERK phosphorylation rate. Furthermore, probability of processive phosphorylation (processivity) of tyrosine and threonine residues within the activation loop on ERK increased non-linearly for increasing PEG-6000 concentration. Based on the experimental data, we developed for the first time a mathematical model integrating all of the effects of thermodynamic activity, viscosity, and processivity in crowded media, and found that ERK phosphorylation is transition-state-limited reaction. The mathematical model allows accurate estimation of the effects of macromolecular crowding on a wide range of reaction kinetics, from transition-state-limited to diffusion-limited reactions.
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16
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Veglia G, Cembran A. Role of conformational entropy in the activity and regulation of the catalytic subunit of protein kinase A. FEBS J 2013; 280:5608-15. [PMID: 23902454 DOI: 10.1111/febs.12462] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 12/01/2022]
Abstract
Protein kinase A (PKA) is the archetypical phosphokinase, sharing a catalytic core with the entire protein kinase superfamily. In eukaryotes, the ubiquitous location of PKA makes it one of the most important cellular signaling molecules, involved in a myriad of events. The catalytic subunit of PKA (PKA-C) is one of the most studied enzymes and was the first kinase to be crystallized; however, the effects of ligand binding, post-translational modifications and mutations on the activity of the kinase have been difficult to understand with only structural data. Here, we review our latest NMR studies on PKA-C, the results of which underscore the role of fast and slow conformational dynamics in the activation and inhibition of the kinase.
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Affiliation(s)
- Gianluigi Veglia
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Jackson Hall, MN, USA; Department of Chemistry, University of Minnesota, Smith Hall, MN, USA
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17
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Gerlits O, Waltman MJ, Taylor S, Langan P, Kovalevsky A. Insights into the phosphoryl transfer catalyzed by cAMP-dependent protein kinase: an X-ray crystallographic study of complexes with various metals and peptide substrate SP20. Biochemistry 2013; 52:3721-7. [PMID: 23672593 PMCID: PMC3666212 DOI: 10.1021/bi400066a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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X-ray
structures of several ternary substrate and product complexes
of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have
been determined with different bound metal ions. In the PKAc complexes,
Mg2+, Ca2+, Sr2+, and Ba2+ metal ions could bind to the active site and facilitate the phosphoryl
transfer reaction. ATP and a substrate peptide (SP20) were modified,
and the reaction products ADP and the phosphorylated peptide were
found trapped in the enzyme active site. Finally, we determined the
structure of a pseudo-Michaelis complex containing Mg2+, nonhydrolyzable AMP-PCP (β,γ-methyleneadenosine 5′-triphosphate)
and SP20. The product structures together with the pseudo-Michaelis
complex provide snapshots of different stages of the phosphorylation
reaction. Comparison of these structures reveals conformational, coordination,
and hydrogen bonding changes that might occur during the reaction
and shed new light on its mechanism, roles of metals, and active site
residues.
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Affiliation(s)
- Oksana Gerlits
- Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87544, United States
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18
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Sims PC, Moody IS, Choi Y, Dong C, Iftikhar M, Corso BL, Gul OT, Collins PG, Weiss GA. Electronic measurements of single-molecule catalysis by cAMP-dependent protein kinase A. J Am Chem Soc 2013; 135:7861-8. [PMID: 23631749 DOI: 10.1021/ja311604j] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-molecule studies of enzymes open a window into their dynamics and kinetics. A single molecule of the catalytic domain of cAMP-dependent protein kinase A (PKA) was attached to a single-walled carbon nanotube device for long-duration monitoring. The electronic recording clearly resolves substrate binding, ATP binding, and cooperative formation of PKA's catalytically functional, ternary complex. Using recordings of a single PKA molecule extending over 10 min and tens of thousands of binding events, we determine the full transition probability matrix and conversion rates governing formation of the apo, intermediate, and closed enzyme configurations. We also observe kinetic rates varying over 2 orders of magnitude from one second to another. Anti-correlation of the on and off rates for PKA binding to the peptide substrate, but not ATP, demonstrates that regulation of enzyme activity results from altering the stability of the PKA-substrate complex, not its binding to ATP. The results depict a highly dynamic enzyme offering dramatic possibilities for regulated activity, an attribute useful for an enzyme with crucial roles in cell signaling.
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Affiliation(s)
- Patrick C Sims
- Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
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19
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Jacobsen D, Bao ZQ, O’Brien P, Brooks CL, Young MA. Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase. J Am Chem Soc 2012; 134:15357-70. [PMID: 22891849 PMCID: PMC3446636 DOI: 10.1021/ja304419t] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Indexed: 11/28/2022]
Abstract
Incorporation of divalent metal ions into an active site is a fundamental catalytic tool used by diverse enzymes. Divalent cations are used by protein kinases to both stabilize ATP binding and accelerate chemistry. Kinetic analysis establishes that Cyclin-dependent kinase 2 (CDK2) requires simultaneous binding of two Mg(2+) ions for catalysis of phosphoryl transfer. This tool, however, comes with a price: the rate-acceleration effects are opposed by an unavoidable rate-limiting consequence of the use of two Mg(2+) ions by CDK2. The essential metal ions stabilize ADP product binding and limit the overall rate of the reaction. We demonstrate that product release is rate limiting for activated CDK2 and evaluate the effects of the two catalytically essential Mg(2+) ions on the stability of the ADP product within the active site. We present two new crystal structures of CDK2 bound to ADP showing how the phosphate groups can be coordinated by either one or two Mg(2+) ions, with the occupancy of one site in a weaker equilibrium. Molecular dynamics simulations indicate that ADP phosphate mobility is more restricted when ADP is coordinated by two Mg(2+) ions compared to one. The structural similarity between the rigid ADP·2Mg product and the cooperatively assembled transition state provides a mechanistic rational for the rate-limiting ADP release that is observed. We demonstrate that although the simultaneous binding of two Mg(2+) ions is essential for efficient phosphoryl transfer, the presence of both Mg(2+) ions in the active site also cooperatively increases ADP affinity and opposes its release. Evolution of protein kinases must have involved careful tuning of the affinity for the second Mg(2+) ion in order to balance the needs to stabilize the chemical transition state and allow timely product release. The link between Mg(2+) site affinity and activity presents a chemical handle that may be used by regulatory factors as well as explain some mutational effects.
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Affiliation(s)
- Douglas
M. Jacobsen
- Department of Computational Medicine and Bioinformatics, Department of Pharmacology, Department of Biological
Chemistry, Department of Chemistry, Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Zhao-Qin Bao
- Department of Computational Medicine and Bioinformatics, Department of Pharmacology, Department of Biological
Chemistry, Department of Chemistry, Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Patrick O’Brien
- Department of Computational Medicine and Bioinformatics, Department of Pharmacology, Department of Biological
Chemistry, Department of Chemistry, Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Charles L. Brooks
- Department of Computational Medicine and Bioinformatics, Department of Pharmacology, Department of Biological
Chemistry, Department of Chemistry, Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Matthew A. Young
- Department of Computational Medicine and Bioinformatics, Department of Pharmacology, Department of Biological
Chemistry, Department of Chemistry, Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109,
United States
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20
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Kovalevsky AY, Johnson H, Hanson BL, Waltman MJ, Fisher SZ, Taylor S, Langan P. Low- and room-temperature X-ray structures of protein kinase A ternary complexes shed new light on its activity. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:854-60. [PMID: 22751671 DOI: 10.1107/s0907444912014886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/04/2012] [Indexed: 11/10/2022]
Abstract
Post-translational protein phosphorylation by protein kinase A (PKA) is a ubiquitous signalling mechanism which regulates many cellular processes. A low-temperature X-ray structure of the ternary complex of the PKA catalytic subunit (PKAc) with ATP and a 20-residue peptidic inhibitor (IP20) at the physiological Mg(2+) concentration of ∼0.5 mM (LT PKA-MgATP-IP20) revealed a single metal ion in the active site. The lack of a second metal in LT PKA-MgATP-IP20 renders the β- and γ-phosphoryl groups of ATP very flexible, with high thermal B factors. Thus, the second metal is crucial for tight positioning of the terminal phosphoryl group for transfer to a substrate, as demonstrated by comparison of the former structure with that of the LT PKA-Mg(2)ATP-IP20 complex obtained at high Mg(2+) concentration. In addition to its kinase activity, PKAc is also able to slowly catalyze the hydrolysis of ATP using a water molecule as a substrate. It was found that ATP can be readily and completely hydrolyzed to ADP and a free phosphate ion in the crystals of the ternary complex PKA-Mg(2)ATP-IP20 by X-ray irradiation at room temperature. The cleavage of ATP may be aided by X-ray-generated free hydroxyl radicals, a very reactive chemical species, which move rapidly through the crystal at room temperature. The phosphate anion is clearly visible in the electron-density maps; it remains in the active site but slides about 2 Å from its position in ATP towards Ala21 of IP20, which mimics the phosphorylation site. The phosphate thus pushes the peptidic inhibitor away from the product ADP, while resulting in dramatic conformational changes of the terminal residues 24 and 25 of IP20. X-ray structures of PKAc in complex with the nonhydrolysable ATP analogue AMP-PNP at both room and low temperature demonstrated no temperature effects on the conformation and position of IP20.
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Affiliation(s)
- Andrey Y Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, MS M888, Los Alamos, NM 87545, USA.
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21
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Masterson LR, Cembran A, Shi L, Veglia G. Allostery and binding cooperativity of the catalytic subunit of protein kinase A by NMR spectroscopy and molecular dynamics simulations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 87:363-89. [PMID: 22607761 DOI: 10.1016/b978-0-12-398312-1.00012-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The catalytic subunit of cAMP-dependent protein kinase A (PKA-C) is an exquisite example of a single molecule allosteric enzyme, where classical and modern views of allosteric signaling merge. In this chapter, we describe the mapping of PKA-C conformational dynamics and allosteric signaling in the free and bound states using a combination of NMR spectroscopy and molecular dynamics simulations. We show that ligand binding affects the enzyme's conformational dynamics, shaping the free-energy landscape toward the next stage of the catalytic cycle. While nucleotide and substrate binding enhance the enzyme's conformational entropy and define dynamically committed states, inhibitor binding attenuates the internal dynamics in favor of enthalpic interactions and delineates dynamically quenched states. These studies support a central role of conformational dynamics in many aspects of enzymatic turnover and suggest future avenues for controlling enzymatic function.
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Affiliation(s)
- Larry R Masterson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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22
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Bao J, Krylova SM, Wilson DJ, Reinstein O, Johnson PE, Krylov SN. Kinetic Capillary Electrophoresis with Mass-Spectrometry Detection (KCE-MS) Facilitates Label-Free Solution-Based Kinetic Analysis of Protein-Small Molecule Binding. Chembiochem 2011; 12:2551-4. [DOI: 10.1002/cbic.201100617] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Indexed: 01/22/2023]
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23
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O'Leary H, Liu WH, Rorabaugh JM, Coultrap SJ, Bayer KU. Nucleotides and phosphorylation bi-directionally modulate Ca2+/calmodulin-dependent protein kinase II (CaMKII) binding to the N-methyl-D-aspartate (NMDA) receptor subunit GluN2B. J Biol Chem 2011; 286:31272-81. [PMID: 21768120 DOI: 10.1074/jbc.m111.233668] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Ca(2+)/calmodulin (CaM)-dependent protein kinase II (CaMKII) and the NMDA-type glutamate receptor are key regulators of synaptic plasticity underlying learning and memory. Direct binding of CaMKII to the NMDA receptor subunit GluN2B (formerly known as NR2B) (i) is induced by Ca(2+)/CaM but outlasts this initial Ca(2+)-stimulus, (ii) mediates CaMKII translocation to synapses, and (iii) regulates synaptic strength. CaMKII binds to GluN2B around S1303, the major CaMKII phosphorylation site on GluN2B. We show here that a phospho-mimetic S1303D mutation inhibited CaM-induced CaMKII binding to GluN2B in vitro, presenting a conundrum how binding can occur within cells, where high ATP concentration should promote S1303 phosphorylation. Surprisingly, addition of ATP actually enhanced the binding. Mutational analysis revealed that this positive net effect was caused by four modulatory effects of ATP, two positive (direct nucleotide binding and CaMKII T286 autophosphorylation) and two negative (GluN2B S1303 phosphorylation and CaMKII T305/6 autophosphorylation). Imaging showed positive regulation by nucleotide binding also within transfected HEK cells and neurons. In fact, nucleotide binding was a requirement for efficient CaMKII interaction with GluN2B in cells, while T286 autophosphorylation was not. Kinetic considerations support a model in which positive regulation by nucleotide binding and T286 autophosphorylation occurs faster than negative modulation by GluN2B S1303 and CaMKII T305/6 phosphorylation, allowing efficient CaMKII binding to GluN2B despite the inhibitory effects of the two slower reactions.
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Affiliation(s)
- Heather O'Leary
- Department of Pharmacology, School of Medicine, University of Colorado Denver, Aurora, Colorado 80045, USA
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24
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Jura N, Zhang X, Endres NF, Seeliger MA, Schindler T, Kuriyan J. Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms. Mol Cell 2011; 42:9-22. [PMID: 21474065 DOI: 10.1016/j.molcel.2011.03.004] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 12/23/2022]
Abstract
In contrast to the active conformations of protein kinases, which are essentially the same for all kinases, inactive kinase conformations are structurally diverse. Some inactive conformations are, however, observed repeatedly in different kinases, perhaps reflecting an important role in catalysis. In this review, we analyze one of these recurring conformations, first identified in CDK and Src kinases, which turned out to be central to understanding of how kinase domain of the EGF receptor is activated. This mechanism, which involves the stabilization of the active conformation of an α helix, has features in common with mechanisms operative in several other kinases.
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Affiliation(s)
- Natalia Jura
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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25
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Masterson LR, Cheng C, Yu T, Tonelli M, Kornev A, Taylor SS, Veglia G. Dynamics connect substrate recognition to catalysis in protein kinase A. Nat Chem Biol 2010; 6:821-8. [PMID: 20890288 PMCID: PMC3487389 DOI: 10.1038/nchembio.452] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 09/03/2010] [Indexed: 12/12/2022]
Abstract
Atomic resolution studies of protein kinases have traditionally been carried out in the inhibitory state, limiting our current knowledge on the mechanisms of substrate recognition and catalysis. Using NMR, X-ray crystallography and thermodynamic measurements, we analyzed the substrate recognition process of cAMP-dependent protein kinase (PKA), finding that entropy and protein dynamics play a prominent role. The nucleotide acts as a dynamic and allosteric activator by coupling the two lobes of apo PKA, enhancing the enzyme dynamics synchronously and priming it for catalysis. The formation of the ternary complex is entropically driven, and NMR spin relaxation data reveal that both substrate and PKA are dynamic in the closed state. Our results show that the enzyme toggles between open and closed states, which indicates that a conformational selection rather than an induced-fit mechanism governs substrate recognition.
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Affiliation(s)
- Larry R. Masterson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455-0431
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Cecilia Cheng
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA 92093-0654
| | - Tao Yu
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544
| | - Alexandr Kornev
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA 92093-0654
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA 92093-0654
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455-0431
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431
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26
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Khavrutskii IV, Grant B, Taylor SS, McCammon JA. A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A. Biochemistry 2009; 48:11532-45. [PMID: 19886670 PMCID: PMC2789581 DOI: 10.1021/bi901475g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
Protein kinases are key regulators of diverse signaling networks
critical for growth and development. Protein kinase A (PKA) is an
important kinase prototype that phosphorylates protein targets at
Ser and Thr residues by converting ATP to ADP. Mg2+ ions
play a crucial role in regulating phosphoryl transfer and can limit
overall enzyme turnover by affecting ADP release. However, the mechanism
by which Mg2+ participates in ADP release is poorly understood.
Here we use a novel transition path ensemble technique, the harmonic
Fourier beads method, to explore the atomic and energetic details
of the Mg2+-dependent ADP binding and release. Our studies
demonstrate that adenine-driven ADP binding to PKA creates three ion-binding
sites at the ADP/PKA interface that are absent otherwise. Two of these
sites bind the previously characterized Mg2+ ions, whereas
the third site binds a monovalent cation with high affinity. This
third site can bind the P-3 residue of substrate proteins and may
serve as a reporter of the active site occupation. Binding of Mg2+ ions restricts mobility of the Gly-rich loop that closes
over the active site. We find that simultaneous release of ADP with
Mg2+ ions from the active site is unfeasible. Thus, we
conclude that Mg2+ ions act as a linchpin and that at least
one ion must be removed prior to pyrophosphate-driven ADP release.
The results of the present study enhance understanding of Mg2+-dependent association of nucleotides with protein kinases.
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Affiliation(s)
- Ilja V Khavrutskii
- Howard Hughes Medical Institute, University of California San Diego,La Jolla, California 92093-0365, USA.
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27
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A conserved protonation-dependent switch controls drug binding in the Abl kinase. Proc Natl Acad Sci U S A 2008; 106:139-44. [PMID: 19109437 DOI: 10.1073/pnas.0811223106] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many protein kinases, a characteristic conformational change (the "DFG flip") connects catalytically active and inactive conformations. Many kinase inhibitors--including the cancer drug imatinib--selectively target a specific DFG conformation, but the function and mechanism of the flip remain unclear. Using long molecular dynamics simulations of the Abl kinase, we visualized the DFG flip in atomic-level detail and formulated an energetic model predicting that protonation of the DFG aspartate controls the flip. Consistent with our model's predictions, we demonstrated experimentally that the kinetics of imatinib binding to Abl kinase have a pH dependence that disappears when the DFG aspartate is mutated. Our model suggests a possible explanation for the high degree of conservation of the DFG motif: that the flip, modulated by electrostatic changes inherent to the catalytic cycle, allows the kinase to access flexible conformations facilitating nucleotide binding and release.
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Abstract
Biological responses to mechanical stress require strain-sensing molecules, whose mechanically induced conformational changes are relayed to signaling cascades mediating changes in cell and tissue properties. In vertebrate muscle, the giant elastic protein titin is involved in strain sensing via its C-terminal kinase domain (TK) at the sarcomeric M-band and contributes to the adaptation of muscle in response to changes in mechanical strain. TK is regulated in a unique dual autoinhibition mechanism by a C-terminal regulatory tail, blocking the ATP binding site, and tyrosine autoinhibition of the catalytic base. For access to the ATP binding site and phosphorylation of the autoinhibitory tyrosine, the C-terminal autoinhibitory tail needs to be removed. Here, we use AFM-based single-molecule force spectroscopy, molecular dynamics simulations, and enzymatics to study the conformational changes during strain-induced activation of human TK. We show that mechanical strain activates ATP binding before unfolding of the structural titin domains, and that TK can thus act as a biological force sensor. Furthermore, we identify the steps in which the autoinhibition of TK is mechanically relieved at low forces, leading to binding of the cosubstrate ATP and priming the enzyme for subsequent autophosphorylation and substrate turnover.
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29
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Abstract
Allosteric signaling in proteins requires long-range communication mediated by highly conserved residues, often triggered by ligand binding. In this article, we map the allosteric network in the catalytic subunit of protein kinase A using NMR spectroscopy. We show that positive allosteric cooperativity is generated by nucleotide and substrate binding during the transitions through the major conformational states: apo, intermediate, and closed. The allosteric network is disrupted by a single site mutation (Y204A), which also decouples the cooperativity of ligand binding. Because protein kinase A is the prototype for the entire kinome, these findings may serve as a paradigm for describing long-range coupling in other protein kinases.
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30
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Rominger CM, Schaber MD, Yang J, Gontarek RR, Weaver KL, Broderick T, Carter L, Copeland RA, May EW. An intrinsic ATPase activity of phospho-MEK-1 uncoupled from downstream ERK phosphorylation. Arch Biochem Biophys 2007; 464:130-7. [PMID: 17490600 DOI: 10.1016/j.abb.2007.04.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 03/30/2007] [Accepted: 04/02/2007] [Indexed: 11/25/2022]
Abstract
We have developed a highly sensitive assay of MEK-mediated ATP hydrolysis by coupling the formation of ADP to NADH oxidation through the enzymes pyruvate kinase and lactate dehydrogenase. Robust ATP hydrolysis is catalyzed by phosphorylated MEK in the absence of the protein substrate ERK. This ERK-uncoupled ATPase activity is dependent on the phosphorylation status of MEK and is abrogated by the selective MEK kinase inhibitor U0126. ADP production is concomitant with Raf-mediated phosphorylation of MEK. Based on this finding, a coupled Raf/MEK assay is developed for measuring the Raf activity. A kinetic treatment derived under steady-state assumptions is presented for the analysis of the reaction progress curve generated by this coupled assay. We have shown that inhibitory potency of selective Raf inhibitors can be determined accurately by this assay.
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Affiliation(s)
- Cynthia M Rominger
- Department of Enzymology and Mechanistic Pharmacology, GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, Collegeville, PA 19426, USA
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31
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Schauble S, King CC, Darshi M, Koller A, Shah K, Taylor SS. Identification of ChChd3 as a novel substrate of the cAMP-dependent protein kinase (PKA) using an analog-sensitive catalytic subunit. J Biol Chem 2007; 282:14952-9. [PMID: 17242405 DOI: 10.1074/jbc.m609221200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Due to the numerous kinases in the cell, many with overlapping substrates, it is difficult to find novel substrates for a specific kinase. To identify novel substrates of cAMP-dependent protein kinase (PKA), the PKA catalytic subunit was engineered to accept bulky N(6)-substituted ATP analogs, using a chemical genetics approach initially pioneered with v-Src (1). Methionine 120 was mutated to glycine in the ATP-binding pocket of the catalytic subunit. To express the stable mutant C-subunit in Escherichia coli required co-expression with PDK1. This mutant protein was active and fully phosphorylated on Thr(197) and Ser(338). Based on its kinetic properties, the engineered C-subunit preferred N(6)(benzyl)-ATP and N(6)(phenethyl)-ATP over other ATP analogs, but still retained a 30 microm K(m) for ATP. This mutant recombinant C-subunit was used to identify three novel PKA substrates. One protein, a novel mitochondrial ChChd protein, ChChd3, was identified, suggesting that PKA may regulate mitochondria proteins.
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Affiliation(s)
- Sharmin Schauble
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0654, USA
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32
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Jones PP, Bazzazi H, Kargacin GJ, Colyer J. Inhibition of cAMP-dependent protein kinase under conditions occurring in the cardiac dyad during a Ca2+ transient. Biophys J 2006; 91:433-43. [PMID: 16632511 PMCID: PMC1483070 DOI: 10.1529/biophysj.106.083931] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The space between the t-tubule invagination and the sarcoplasmic reticulum (SR) membrane, the dyad, in ventricular myocytes has been predicted to experience very high [Ca2+] for short periods of time during a Ca2+ transient. The dyadic space accommodates many protein kinases responsible for the regulation of Ca2+ handling proteins of the cell. We show in vitro that cAMP-dependent protein kinase (PKA) is inhibited by high [Ca2+] through a shift in the ratio of CaATP/MgATP toward CaATP. We further generate a three-dimensional mathematical model of Ca2+ and ATP diffusion within dyad. We use this model to predict the extent to which PKA would be inhibited by an increased CaATP/MgATP ratio during a Ca2+ transient in the dyad in vivo. Our results suggest that under normal physiological conditions a myocyte paced at 1 Hz would experience up to 55% inhibition of PKA within the cardiac dyad, with inhibition averaging 5% throughout the transient, an effect which becomes more pronounced as the myocyte contractile frequency increases (at 7 Hz, PKA inhibition averages 28% across the dyad throughout the duration of a Ca2+ transient).
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Affiliation(s)
- Peter P Jones
- Institute of Membrane and Systems Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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Taylor SS, Kim C, Vigil D, Haste NM, Yang J, Wu J, Anand GS. Dynamics of signaling by PKA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1754:25-37. [PMID: 16214430 DOI: 10.1016/j.bbapap.2005.08.024] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2005] [Revised: 08/11/2005] [Accepted: 08/12/2005] [Indexed: 11/16/2022]
Abstract
The catalytic and regulatory subunits of cAMP-dependent protein kinase (PKA) are highly dynamic signaling proteins. In its dissociated state the catalytic subunit opens and closes as it moves through its catalytic cycle. In this subunit, the core that is shared by all members of the protein kinase family is flanked by N- and C-terminal segments. Each are anchored firmly to the core by well-defined motifs and serve to stabilize the core. Protein kinases are not only catalysts, they are also scaffolds. One of their major functions is to bind to other proteins. In addition to its interactions with the N- and C- termini, the catalytic subunit interacts with its inhibitor proteins, PKI and the regulatory subunits. Both bind with subnanomolar affinity. To achieve this tight binding requires docking of a substrate mimetic to the active site cleft as well as a peripheral docking site. The peripheral site used by PKI is distinct from that used by RIalpha as revealed by a recent structure of a C:RIalpha complex. Upon binding to the catalytic subunit, the linker region of RIalpha becomes ordered. In addition, cAMP-binding domain A undergoes major conformational changes. RIalpha is a highly malleable protein. Using small angle X-ray scattering, the overall shape of the regulatory subunits and corresponding holoenzymes have been elucidated. These studies reveal striking and surprising isoform differences.
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Affiliation(s)
- Susan S Taylor
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA.
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34
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Yang S, Rogers KM, Johnson DA. MgATP-induced conformational change of the catalytic subunit of cAMP-dependent protein kinase. Biophys Chem 2005; 113:193-9. [PMID: 15617827 DOI: 10.1016/j.bpc.2004.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/31/2004] [Accepted: 08/31/2004] [Indexed: 11/24/2022]
Abstract
Conformational changes of the cAMP-dependent protein kinase (PKA) catalytic (C) subunit are critical for the catalysis of gamma-phosphate transfer from adenosine 5'-triphosphate (ATP) to target proteins. Time-resolved fluorescence anisotropy (TRFA) was used to investigate the respective roles of Mg(2+), ATP, MgATP, and the inhibitor peptide (IP20) in the conformational changes of a 5,6-carboxyfluorescein succinimidyl ester (CF) labeled C subunit ((CF)C). TRFA decays were fit to a biexponential equation incorporating the fast and slow rotational correlation times phi(F) and phi(S). The (CF)C apoenzyme exhibited the rotational correlation times phi(F)=1.8+/-0.3 ns and phi(S)=20.1+/-0.6 ns which were reduced to phi(F)=1.1+/-0.2 ns and phi(S)=13.3+/-0.9 ns in the presence of MgATP. The reduction in rotational correlation times indicated that the (CF)C subunit adopted a more compact shape upon formation of a (CF)C.MgATP binary complex. Neither Mg(2+) (1-3 mM) nor ATP (0.4 mM) alone induced changes in the (CF)C subunit conformation equivalent to those induced by MgATP. The effect of MgATP was removed in the presence of ethylenediaminetetraacetic acid (EDTA). The addition of IP20 and MgATP to form the (CF)C x MgATP x IP20 ternary complex produced rotational correlation times similar to those of the (CF)C x MgATP binary complex. However, IP20 alone did not elicit an equivalent reduction in rotational correlation times. The results indicate that binding of MgATP to the C subunit may induce conformation changes in the C subunit necessary for the proper stereochemical alignment of substrates in the subsequent phosphorylation.
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Affiliation(s)
- Shumei Yang
- Department of Chemistry, California State University, San Bernardino, CA 92407, USA.
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35
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Lu B, Wong CF, McCammon JA. Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study. Protein Sci 2005; 14:159-68. [PMID: 15608120 PMCID: PMC2253316 DOI: 10.1110/ps.04894605] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Substrate phosphorylation by cAMP-dependent-protein kinase A (protein kinase A, PKA) has been studied extensively. Phosphoryl transfer was found to be fast, whereas ADP release was found to be the slow, rate-limiting step. There is also evidence that ADP release may be preceded by a partially rate-limiting conformational change. However, the atomic details of the conformational change and the mode of ADP release are difficult to obtain experimentally. In this work, we studied ADP release from PKA by carrying out molecular dynamics simulations with different pulling forces applied to the ligand. The detailed ADP release pathway and the associated conformational changes were analyzed. The ADP release process was found to involve a swinging motion with the phosphate of ADP anchored to the Gly-rich loop, so that the more buried adenine base and ribose ring came out before the phosphate. In contrast to the common belief that a hinge-bending motion was responsible for the opening of the ligand-binding cleft, our simulations showed that the small lobe exhibited a large amplitude "rocking" motion when the ligand came out. The largest conformational change of the protein was observed at about the first quarter time point along the release pathway. Two prominent intermediate states were observed in the release process.
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Affiliation(s)
- Benzhuo Lu
- Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0365, USA
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36
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Busenlehner LS, Armstrong RN. Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Arch Biochem Biophys 2005; 433:34-46. [PMID: 15581564 DOI: 10.1016/j.abb.2004.09.002] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 09/02/2004] [Indexed: 11/25/2022]
Abstract
Conformational changes and protein dynamics play an important role in the catalytic efficiency of enzymes. Amide H/D exchange mass spectrometry (H/D exchange MS) is emerging as an efficient technique to study the local and global changes in protein structure and dynamics due to ligand binding, protein activation-inactivation by modification, and protein-protein interactions. By monitoring the selective exchange of hydrogen for deuterium along a peptide backbone, this sensitive technique probes protein motions and structural elements that may be relevant to allostery and function. In this report, several applications of H/D exchange MS are presented which demonstrate the unique capability of amide hydrogen/deuterium exchange mass spectrometry for examining dynamic and structural changes associated with enzyme catalysis.
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Affiliation(s)
- Laura S Busenlehner
- Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0416, USA.
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37
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Characterization of a mixing device adapted to the kinetics of a specific enzyme: the horse liver alcohol dehydrogenase model. Biochem Eng J 2003. [DOI: 10.1016/s1369-703x(02)00189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Akamine P, Wu J, Xuong NH, Ten Eyck LF, Taylor SS. Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure. J Mol Biol 2003; 327:159-71. [PMID: 12614615 DOI: 10.1016/s0022-2836(02)01446-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To better understand the mechanism of ligand binding and ligand-induced conformational change, the crystal structure of apoenzyme catalytic (C) subunit of adenosine-3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) was solved. The apoenzyme structure (Apo) provides a snapshot of the enzyme in the first step of the catalytic cycle, and in this unliganded form the PKA C subunit adopts an open conformation. A hydrophobic junction is formed by residues from the small and large lobes that come into close contact. This "greasy" patch may lubricate the shearing motion associated with domain rotation, and the opening and closing of the active-site cleft. Although Apo appears to be quite dynamic, many important residues for MgATP binding and phosphoryl transfer in the active site are preformed. Residues around the adenine ring of ATP and residues involved in phosphoryl transfer from the large lobe are mostly preformed, whereas residues involved in ribose binding and in the Gly-rich loop are not. Prior to ligand binding, Lys72 and the C-terminal tail, two important ATP-binding elements are also disordered. The surface created in the active site is contoured to bind ATP, but not GTP, and appears to be held in place by a stable hydrophobic core, which includes helices C, E, and F, and beta strand 6. This core seems to provide a network for communicating from the active site, where nucleotide binds, to the peripheral peptide-binding F-to-G helix loop, exemplified by Phe239. Two potential lines of communication are the D helix and the F helix. The conserved Trp222-Phe238 network, which lies adjacent to the F-to-G helix loop, suggests that this network would exist in other protein kinases and may be a conserved means of communicating ATP binding from the active site to the distal peptide-binding ledge.
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Affiliation(s)
- Pearl Akamine
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA
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39
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Hirano Y, Hata M, Hoshino T, Tsuda M. Quantum Chemical Study on the Catalytic Mechanism of the C-Subunit of cAMP-Dependent Protein Kinase. J Phys Chem B 2002. [DOI: 10.1021/jp014538i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yoshinori Hirano
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Masayuki Hata
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Minoru Tsuda
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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40
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Waas WF, Dalby KN. Transient protein-protein interactions and a random-ordered kinetic mechanism for the phosphorylation of a transcription factor by extracellular-regulated protein kinase 2. J Biol Chem 2002; 277:12532-40. [PMID: 11812784 DOI: 10.1074/jbc.m110523200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
No thorough mechanistic study of extracellular signal-regulated protein kinase 2 (ERK2) has appeared in the literature. A recombinant protein termed EtsDelta138, which comprises of residues 1-138 of the transcription factor Ets-1 is an excellent substrate of ERK2 (Waas W. F., and Dalby, K. N. (2001) Protein Exp. Purif. 23, 191-197). The kinetic mechanism of ERK2 was examined, with excess magnesium, by initial velocity measurements, both in the absence and presence of products at 27 degrees C, pH 7.5, and ionic strength 0.1 m (KCl). The velocity data are consistent with a steady-state random-ordered ternary complex mechanism, where both substrates have unhindered access to binding sites on the enzyme. The mechanism and magnitude of product inhibition by monophosphorylated EtsDelta138 is consistent with, but does not prove, the notion that ERK2 forms a discrete interaction with EtsDelta138 in the absence of active site interactions, and that this "docking complex" facilitates intramolecular phosphorylation of the substrate. The approximation of the steady-state data to a rapid equilibrium model strongly suggests that the formation of ERK2.Ets138 complexes are transient in nature with dissociation constants of greater magnitude than the catalytic constant, of k(cat) = 17 s(-1).
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Affiliation(s)
- William F Waas
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
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41
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Engh RA, Bossemeyer D. Structural aspects of protein kinase control-role of conformational flexibility. Pharmacol Ther 2002; 93:99-111. [PMID: 12191603 DOI: 10.1016/s0163-7258(02)00180-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein kinases catalyze the phosphotransfer reaction fundamental to most signaling and regulatory processes in the eukaryotic cell. Absolute control of individual protein kinase activity is, therefore, of utmost importance to signaling fidelity in the cell. Mechanisms for activity modulation, including complete and reversible inactivation, have been shown by crystal structures of many active and inactive protein kinases. The structures of inactivated kinases, compared with those of active and catalytically competent kinases such as the protein kinase A catalytic subunit, highlight recurring structural alterations among a set of elements of the catalytic kinase core. These 'activity modulation sites' apparently comprise the principal evolved mechanisms for control of enzyme activity in the catalytic domain. In combination, they enable diverse physiological regulatory mechanisms operative for most protein kinases. Identification and characterization of these sites should impact strategies for discovery and design of target-specific therapeutic drugs as the range of structural variations for specific kinases becomes known. The principle site, the ATP-binding pocket, is the target of many physiological regulators and also most experimental or therapeutic inhibitors, which typically block it in a competitive or allosteric fashion. Co-crystallization studies with protein kinase A and other kinases have revealed binding features of several classes of protein kinase inhibitors. Ligand-induced structural changes are common and tend to optimize buried surface areas. The ability to optimize binding energies arising from the hydrophobic effect creates a logarithmic dependence of binding energy on buried surface areas. Exceptions to this rule arise for specific inhibitor classes, and possibly also as artifacts of structure determination.
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Affiliation(s)
- Richard A Engh
- Roche Diagnostics GmbH, Penzberg and MPI Biochemistry, Martinsried, Germany
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42
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Affiliation(s)
- J A Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0506, USA.
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43
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Johnson DA, Akamine P, Radzio-Andzelm E, Madhusudan M, Taylor SS. Dynamics of cAMP-dependent protein kinase. Chem Rev 2001; 101:2243-70. [PMID: 11749372 DOI: 10.1021/cr000226k] [Citation(s) in RCA: 317] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D A Johnson
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0654, USA
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44
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Andersen MD, Shaffer J, Jennings PA, Adams JA. Structural characterization of protein kinase A as a function of nucleotide binding. Hydrogen-deuterium exchange studies using matrix-assisted laser desorption ionization-time of flight mass spectrometry detection. J Biol Chem 2001; 276:14204-11. [PMID: 11278927 DOI: 10.1074/jbc.m011543200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transient state kinetic studies indicate that substrate phosphorylation in protein kinase A is partially rate-limited by conformational changes, some of which may be associated with nucleotide binding (Shaffer, J., and Adams, J. A. (1999) Biochemistry 38, 12072-12079). To assess whether specific structural changes are associated with the binding of nucleotides, hydrogen-deuterium exchange experiments were performed on the enzyme in the absence and presence of ADP. Four regions of the protein are protected from exchange in the presence of ADP. Two regions encompass the catalytic and glycine-rich loops and are integral parts of the active site. Conversely, protection of probes in the C terminus is consistent with nucleotide-induced domain closure. One protected probe encompasses a portion of helix C, a secondary structural element that does not make any direct contacts with the nucleotide but has been reported to undergo segmental motion upon the activation of some protein kinases. The combined data suggest that binding of the nucleotide has distal structural effects that may include stabilizing the closed state of the enzyme and altering the position of a critical helix outside the active site. The latter represents the first evidence that the nucleotide alone can induce changes in helix C in solution.
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Affiliation(s)
- M D Andersen
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0506, USA
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45
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Enke DA, Kaldis P, Solomon MJ. Kinetic analysis of the cyclin-dependent kinase-activating kinase (Cak1p) from budding yeast. J Biol Chem 2000; 275:33267-71. [PMID: 10934199 DOI: 10.1074/jbc.m004748200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cak1p, the Cyclin-dependent kinase-activating kinase from budding yeast, is an unusual protein kinase that lacks many of the highly conserved motifs observed among members of the protein kinase superfamily. Cak1p phosphorylates and activates Cdc28p, the major cyclin-dependent kinase (CDK) in yeast, and is thereby required for passage through the yeast cell cycle. In this paper, we explore the kinetics of CDK phosphorylation by Cak1p, and we examine the role of the catalytic step in the reaction mechanism. Cak1p proceeds by a sequential reaction mechanism, binding to both ATP and CDK2 with reasonable affinities, exhibiting K(d) values of 7.2 and 0.6 microm, respectively. Interestingly, these values are approximately the same as the K(M) values, indicating that the binding of substrates is fast with respect to catalysis and that the most likely reaction mechanism is rapid equilibrium random. Cak1p is a slow enzyme, with a catalytic rate of only 4.3 min(-)(1). The absence of a burst phase indicates that product release is not rate-limiting. This result, and a solvent isotope effect, suggests that a catalytic step is rate-limiting.
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Affiliation(s)
- D A Enke
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8114, USA
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46
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Ni Q, Shaffer J, Adams JA. Insights into nucleotide binding in protein kinase A using fluorescent adenosine derivatives. Protein Sci 2000; 9:1818-27. [PMID: 11045627 PMCID: PMC2144695 DOI: 10.1110/ps.9.9.1818] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The binding of the methylanthraniloyl derivatives of ATP (mant-ATP), ADP (mant-ADP), 2'deoxyATP (mant-2'deoxyATP), and 3'deoxyATP (mant-3'deoxyATP) to the catalytic subunit of protein kinase A was studied to gain insights into the mechanism of nucleotide binding. The binding of the mant nucleotides leads to a large increase in fluorescence energy transfer at 440 nm, allowing direct measurements of nucleotide affinity. The dissociation constant of mant-ADP is identical to that for ADP, while that for mant-ATP is approximately threefold higher than that for ATP. The dissociation constant for mant-3'deoxyATP is approximately fivefold higher than that for 3'deoxyATP while derivatization of 2'deoxyATP does not affect affinity. The time-dependent binding of mant-ATP, mant-2'deoxyATP, and mant-ADP, measured using stopped-flow fluorescence spectroscopy, is best fit to three exponentials. The fast phase is ligand dependent, while the two slower phases are ligand independent. The slower phases are similar but not identical in rate, and have opposite fluorescence amplitudes. Both isomers of mant-ATP are equivalent substrates, as judged by reversed-phase chromatography, although the rate of phosphorylation is approximately 20-fold lower than the natural nucleotide. The kinetic data are consistent with a three-step binding mechanism in which initial association of the nucleotide derivatives produces a highly fluorescent complex. Either one or two conformational changes can occur after the formation of this binary species, but one of the isomerized forms must have low fluorescence compared to the initial binary complex. These data soundly attest to the structural plasticity within the kinase core that may be essential for catalysis. Overall, the mant nucleotides present a useful reporter system for gauging these conformational changes in light of the prevailing three-dimensional models for the enzyme.
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Affiliation(s)
- Q Ni
- Department of Pharmacology, University of California, San Diego, La Jolla 92093-0506, USA
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47
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Aimes RT, Hemmer W, Taylor SS. Serine-53 at the tip of the glycine-rich loop of cAMP-dependent protein kinase: role in catalysis, P-site specificity, and interaction with inhibitors. Biochemistry 2000; 39:8325-32. [PMID: 10889042 DOI: 10.1021/bi992800w] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The glycine-rich loop, one of the most important motifs in the conserved protein kinase catalytic core, embraces the entire nucleotide, is very mobile, and is exquisitely sensitive to what occupies the active site cleft. Of the three conserved glycines [G(50)TG(52)SFG(55) in cAMP-dependent protein kinase (cAPK)], Gly(52) is the most important for catalysis because it allows the backbone amide of Ser(53) at the tip of the loop to hydrogen bond to the gamma-phosphate of ATP [Grant, B. D. et al. (1998) Biochemistry 37, 7708]. The structural model of the catalytic subunit:ATP:PKI((5)(-)(24)) (heat-stable protein kinase inhibitor) ternary complex in the closed conformation suggests that Ser(53) also might be essential for stabilization of the peptide substrate-enzyme complex via a hydrogen bond between the P-site carbonyl in PKI and the Ser(53) side-chain hydroxyl [Bossemeyer, D. et al. (1993) EMBO J. 12, 849]. To address the importance of the Ser(53) side chain in catalysis, inhibition, and P-site specificity, Ser(53) was replaced with threonine, glycine, and proline. Removal of the side chain (i.e., mutation to glycine) had no effect on the steady-state phosphorylation of a peptide substrate (LRRASLG) or on the interaction with physiological inhibitors, including the type-I and -II regulatory subunits and PKI. However, this mutation did affect the P-site specificity; the glycine mutant can more readily phosphorylate a P-site threonine in a peptide substrate (5-6-fold better than wild-type). The proline mutant is compromised catalytically with altered k(cat) and K(m) for both peptide and ATP and with altered sensitivity to both regulatory subunits and PKI. Steric constraints as well as restricted flexibility could account for these effects. These combined results demonstrate that while the backbone amide of Ser(53) may be required for efficient catalysis, the side chain is not.
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Affiliation(s)
- R T Aimes
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093-0654, USA
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48
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Smith CM, Radzio-Andzelm E, Akamine P, Taylor SS. The catalytic subunit of cAMP-dependent protein kinase: prototype for an extended network of communication. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1999; 71:313-41. [PMID: 10354702 DOI: 10.1016/s0079-6107(98)00059-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The protein kinase catalytic core in essence comprises an extended network of interactions that link distal parts of the molecule to the active site where they facilitate phosphoryl transfer from ATP to protein substrate. This review defines key sequence and structural elements, describes what is currently known about the molecular interactions, and how they are involved in catalysis.
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Affiliation(s)
- C M Smith
- San Diego Supercomputer Center, University of California, La Jolla 92093-0505, USA.
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49
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Taylor SS, Radzio-Andzelm E, Cheng X, Ten Eyck L, Narayana N. Catalytic subunit of cyclic AMP-dependent protein kinase: structure and dynamics of the active site cleft. Pharmacol Ther 1999; 82:133-41. [PMID: 10454192 DOI: 10.1016/s0163-7258(99)00007-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The catalytic subunit of cyclic AMP-dependent protein kinase serves as a structural template for the entire family of Ser, Thr, and Tyr specific protein kinases. We review here the dynamics of the active catalytic subunit. These dynamics correlate with an opening and closing of the active site cleft, and are considered to be a requirement for catalysis. The motions, described by a set of several crystal structures, reveal a very fluid active site cleft. This active site cleft with its dynamic opening and closing is a prime target for protein kinase inhibitors.
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Affiliation(s)
- S S Taylor
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0654, USA
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50
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Mattei P, Kast P, Hilvert D. Bacillus subtilis chorismate mutase is partially diffusion-controlled. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:25-32. [PMID: 10103029 DOI: 10.1046/j.1432-1327.1999.00169.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The effect of viscosogens on the enzyme-catalyzed rearrangement of chorismate to prephenate has been studied. The steady-state parameters kcat and kcat/Km for the monofunctional chorismate mutase from Bacillus subtilis (BsCM) decreased significantly with increasing concentrations of glycerol, whereas the 'sluggish' BsCM mutants C75A and C75S were insensitive to changes in microviscosity. The latter results rule out extraneous interactions of the viscosogen as an explanation for the effects observed with the wild-type enzyme. Additional control experiments show that neither viscosogen-induced shifts in the pH-dependence of the enzyme-catalyzed reaction nor small perturbations of the conformational equilibrium of chorismate can account for the observed effects. Instead, BsCM appears to be limited by substrate binding and product release at low and high substrate concentrations, respectively. Analysis of the kinetic data indicates that diffusive transition states are between 30 and 40% rate-determining in these concentration regimes; the chemical step must contribute to the remaining kinetic barrier. The relatively low value of the 'on' rates for chorismate and prephenate (approximately 2 x 106 m-1.s-1) probably reflects the need for a rare conformation of the enzyme, the ligand, or both for successful binding. Interestingly, the chorismate mutase domain of the bifunctional chorismate mutase-prephenate dehydratase from Escherichia coli, which has steady-state kinetic parameters comparable to those of BsCM but has a much less accessible active site, is insensitive to changes in viscosity and the reaction it catalyses is not diffusion-controlled.
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Affiliation(s)
- P Mattei
- Laboratorium für Organische Chemie, Swiss Federal Institute of Technology, Zürich, Switzerland
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