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Bursch KL, Olp MD, Smith BC. Analysis of continuous enzyme kinetic data using ICEKAT. Methods Enzymol 2023; 690:109-129. [PMID: 37858527 PMCID: PMC10691744 DOI: 10.1016/bs.mie.2023.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
ICEKAT (Interactive Continuous Enzyme Analysis Tool) is an interactive web-based program for calculating initial rates and kinetic parameters (e.g., Vmax, kcat, KM, EC50, IC50) from continuous enzyme kinetic assay data that satisfy Michaelis-Menten and steady-state kinetic assumptions. ICEKAT is valuable in educational and research settings to consistently and accurately calculate initial rates and kinetic parameters, increasing assay veracity and reproducibility. Provided freely online to the scientific community, ICEKAT has been cited in at least 26 publications, and the initial journal article has been accessed nearly 9000 times since its debut in 2020 (Olp et al., 2020). Here, we provide in-depth instructions for software use, offer vital considerations for data analysis, and highlight updated software features for new and existing users. Through ICEKAT, we aim for the analysis of data from continuous enzyme kinetic studies worldwide to become more rapid, reliable, and repeatable. ICEKAT remains free of charge and available to all scientists at https://icekat.herokuapp.com/icekat; the source code for local use is found at https://github.com/SmithLabMCW/icekat.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Michael D Olp
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
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2
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Luzia L, Lao‐Martil D, Savakis P, van Heerden J, van Riel N, Teusink B. pH dependencies of glycolytic enzymes of yeast under in vivo-like assay conditions. FEBS J 2022; 289:6021-6037. [PMID: 35429225 PMCID: PMC9790636 DOI: 10.1111/febs.16459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022]
Abstract
Under carbon source transitions, the intracellular pH of Saccharomyces cerevisiae is subject to change. Dynamics in pH modulate the activity of the glycolytic enzymes, resulting in a change in glycolytic flux and ultimately cell growth. To understand how pH affects the global behavior of glycolysis and ethanol fermentation, we measured the activity of the glycolytic and fermentative enzymes in S. cerevisiae under in vivo-like conditions at different pH. We demonstrate that glycolytic enzymes exhibit differential pH dependencies, and optima, in the pH range observed during carbon source transitions. The forward reaction of GAPDH shows the highest decrease in activity, 83%, during a simulated feast/famine regime upon glucose removal (cytosolic pH drop from 7.1 to 6.4). We complement our biochemical characterization of the glycolytic enzymes by fitting the Vmax to the progression curves of product formation or decay over time. The fitting analysis shows that the observed changes in enzyme activities require changes in Vmax , but changes in Km cannot be excluded. Our study highlights the relevance of pH as a key player in metabolic regulation and provides a large set of quantitative data that can be explored to improve our understanding of metabolism in dynamic environments.
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Affiliation(s)
| | | | | | | | - Natal van Riel
- Department of Biomedical EngineeringTU EindhovenNetherlands
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3
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Kinetic Modeling of Time-Dependent Enzyme Inhibition by Pre-Steady-State Analysis of Progress Curves: The Case Study of the Anti-Alzheimer's Drug Galantamine. Int J Mol Sci 2022; 23:ijms23095072. [PMID: 35563466 PMCID: PMC9105972 DOI: 10.3390/ijms23095072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 01/27/2023] Open
Abstract
The Michaelis–Menten model of enzyme kinetic assumes the free ligand approximation, the steady-state approximation and the rapid equilibrium approximation. Analytical methods to model slow-binding inhibitors by the analysis of initial velocities have been developed but, due to their inherent complexity, they are seldom employed. In order to circumvent the complications that arise from the violation of the rapid equilibrium assumption, inhibition is commonly evaluated by pre-incubating the enzyme and the inhibitors so that, even for slow inhibitors, the binding equilibrium is established before the reaction is started. Here, we show that for long drug-target residence time inhibitors, the conventional analysis of initial velocities by the linear regression of double-reciprocal plots fails to provide a correct description of the inhibition mechanism. As a case study, the inhibition of acetylcholinesterase by galantamine, a drug approved for the symptomatic treatment of Alzheimer’s disease, is reported. For over 50 years, analysis based on the conventional steady-state model has overlooked the time-dependent nature of galantamine inhibition, leading to an erroneous assessment of the drug potency and, hence, to discrepancies between biochemical data and the pharmacological evidence. Re-examination of acetylcholinesterase inhibition by pre-steady state analysis of the reaction progress curves showed that the potency of galantamine has indeed been underestimated by a factor of ~100.
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4
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Monitoring protein conformational changes using fluorescent nanoantennas. Nat Methods 2022; 19:71-80. [PMID: 34969985 DOI: 10.1038/s41592-021-01355-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/10/2021] [Indexed: 01/03/2023]
Abstract
Understanding the relationship between protein structural dynamics and function is crucial for both basic research and biotechnology. However, methods for studying the fast dynamics of structural changes are limited. Here, we introduce fluorescent nanoantennas as a spectroscopic technique to sense and report protein conformational changes through noncovalent dye-protein interactions. Using experiments and molecular simulations, we detect and characterize five distinct conformational states of intestinal alkaline phosphatase, including the transient enzyme-substrate complex. We also explored the universality of the nanoantenna strategy with another model protein, Protein G and its interaction with antibodies, and demonstrated a rapid screening strategy to identify efficient nanoantennas. These versatile nanoantennas can be used with diverse dyes to monitor small and large conformational changes, suggesting that they could be used to characterize diverse protein movements or in high-throughput screening applications.
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5
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Pinto MF, Baici A, Pereira PJB, Macedo-Ribeiro S, Pastore A, Rocha F, Martins PM. interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis. J Mol Biol 2020; 433:166613. [PMID: 32768452 DOI: 10.1016/j.jmb.2020.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 02/01/2023]
Abstract
Enzymatic assays are widely employed to characterize important allosteric and enzyme modulation effects. The high sensitivity of these assays can represent a serious problem if the occurrence of experimental errors surreptitiously affects the reliability of enzyme kinetics results. We have addressed this problem and found that hidden assay interferences can be unveiled by the graphical representation of progress curves in modified reaction coordinates. To render this analysis accessible to users across all levels of expertise, we have developed a webserver, interferENZY, that allows (i) an unprecedented tight quality control of experimental data, (ii) the automated identification of small and major assay interferences, and (iii) the estimation of bias-free kinetic parameters. By eliminating the subjectivity factor in kinetic data reporting, interferENZY will contribute to solving the "reproducibility crisis" that currently challenges experimental molecular biology. The interferENZY webserver is freely available (no login required) at https://interferenzy.i3s.up.pt.
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Affiliation(s)
- Maria Filipa Pinto
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; LEPABE-Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Antonio Baici
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Pedro José Barbosa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Annalisa Pastore
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Rd, Brixton, London SE5 9RT, England, UK
| | - Fernando Rocha
- LEPABE-Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Pedro M Martins
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.
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6
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Olp MD, Kalous KS, Smith BC. ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces. BMC Bioinformatics 2020; 21:186. [PMID: 32410570 PMCID: PMC7222511 DOI: 10.1186/s12859-020-3513-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. However, data analysis is often rate-limiting in high-throughput enzyme assays, as manual inspection and selection of a linear range from individual kinetic traces is cumbersome and prone to user error and bias. Currently available software programs are specialized and designed for the analysis of complex enzymatic models. Despite the widespread use of initial rate determination for processing kinetic data sets, no simple and automated program existed for rapid analysis of initial rates from continuous enzyme kinetic traces. RESULTS An Interactive Continuous Enzyme Kinetics Analysis Tool (ICEKAT) was developed for semi-automated calculation of initial rates from continuous enzyme kinetic traces with particular application to the evaluation of Michaelis-Menten and EC50/IC50 kinetic parameters, as well as the results of high-throughput screening assays. ICEKAT allows users to interactively fit kinetic traces using convenient browser-based selection tools, ameliorating tedious steps involved in defining ranges to fit in general purpose programs like Microsoft Excel and Graphpad Prism, while still maintaining simplicity in determining initial rates. As a test case, we quickly analyzed over 500 continuous enzyme kinetic traces resulting from experimental data on the response of the protein lysine deacetylase SIRT1 to small-molecule activators. CONCLUSIONS ICEKAT allows simultaneous visualization of individual initial rate fits and the resulting Michaelis-Menten or EC50/IC50 kinetic model fits, as well as hits from high-throughput screening assays. In addition to serving as a convenient program for practicing enzymologists, ICEKAT is also a useful teaching aid to visually demonstrate in real-time how incorrect initial rate fits can affect calculated Michaelis-Menten or EC50/IC50 kinetic parameters. For the convenience of the research community, we have made ICEKAT freely available online at https://icekat.herokuapp.com/icekat.
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Affiliation(s)
- Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, 53226, USA
| | - Kelsey S Kalous
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, 53226, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, 53226, USA.
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7
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Oliveira CM, Jesus CDF, Ceneviva LVS, Silva FH, Cruz AJG, Costa CBB, Badino AC. AnaBioPlus: a new package for parameter estimation and simulation of bioprocesses. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2017. [DOI: 10.1590/0104-6632.20170344s20150673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - C. D. F. Jesus
- Brazilian Bioethanol Science and Technology Laboratory, Brazil
| | | | | | - A. J. G. Cruz
- Federal University of São Carlos, Brazil; Federal University of São Carlos, Brazil
| | | | - A. C. Badino
- Federal University of São Carlos, Brazil; Federal University of São Carlos, Brazil
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8
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Kim DH, Kim DK, Zhou K, Park S, Kwon Y, Jeong MG, Lee NK, Ryu SH. Single particle tracking-based reaction progress kinetic analysis reveals a series of molecular mechanisms of cetuximab-induced EGFR processes in a single living cell. Chem Sci 2017; 8:4823-4832. [PMID: 28959404 PMCID: PMC5602156 DOI: 10.1039/c7sc01159h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/21/2017] [Indexed: 01/18/2023] Open
Abstract
Cellular processes occur through the orchestration of multi-step molecular reactions. Reaction progress kinetic analysis (RPKA) can provide the mechanistic details to elucidate the multi-step molecular reactions. However, current tools have limited ability to simultaneously monitor dynamic variations in multiple complex states at the single molecule level to apply RPKA in living cells. In this research, a single particle tracking-based reaction progress kinetic analysis (sptRPKA) was developed to simultaneously determine the kinetics of multiple states of protein complexes in the membrane of a single living cell. The subpopulation ratios of different states were quantitatively (and statistically) reliably extracted from the diffusion coefficient distribution rapidly acquired by single particle tracking at constant and high density over a long period of time using super-resolution microscopy. Using sptRPKA, a series of molecular mechanisms of epidermal growth factor receptor (EGFR) cellular processing induced by cetuximab were investigated. By comprehensively measuring the rate constants and cooperativity of the molecular reactions involving four EGFR complex states, a previously unknown intermediate state was identified that represents the rate limiting step responsible for the selectivity of cetuximab-induced EGFR endocytosis to cancer cells.
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Affiliation(s)
- Do-Hyeon Kim
- Department of Life Sciences , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea .
| | - Dong-Kyun Kim
- School of Interdisciplinary Bioscience and Bioengineering , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea
| | - Kai Zhou
- Department of Life Sciences , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea .
| | - Soyeon Park
- Department of Life Sciences , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea .
| | - Yonghoon Kwon
- Department of Life Sciences , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea .
| | - Min Gyu Jeong
- Integrative Biosciences and Biotechnology , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea
| | - Nam Ki Lee
- School of Interdisciplinary Bioscience and Bioengineering , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea.,Department of Chemistry , Seoul National University , Seoul , 08826 , Republic of Korea .
| | - Sung Ho Ryu
- Department of Life Sciences , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea . .,School of Interdisciplinary Bioscience and Bioengineering , Pohang University of Science and Technology , Pohang , 790-784 , Republic of Korea
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9
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On the estimation errors of KM and V from time-course experiments using the Michaelis–Menten equation. Biophys Chem 2016; 219:17-27. [DOI: 10.1016/j.bpc.2016.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022]
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10
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Penning TM. Single-molecule enzymology of steroid transforming enzymes: Transient kinetic studies and what they tell us. J Steroid Biochem Mol Biol 2016; 161:5-12. [PMID: 26596239 PMCID: PMC4842339 DOI: 10.1016/j.jsbmb.2015.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/02/2015] [Accepted: 10/15/2015] [Indexed: 01/21/2023]
Abstract
Structure-function studies on steroid transforming enzymes often use site-directed mutagenesis to inform mechanisms of catalysis and effects on steroid binding, and data are reported in terms of changes in steady state kinetic parameters kcat, Km and kcat/Km. However, this dissection of function is limited since kcat is governed by the rate-determining step and Km is a complex macroscopic kinetic constant. Often site-directed mutagenesis can lead to a change in the rate-determining step which cannot be revealed by just reporting a decrease in kcat alone. These issues are made more complex when it is considered that many steroid transforming enzymes have more than one substrate and product. We present the case for using transient-kinetics performed with stopped-flow spectrometry to assign rate constants to discrete steps in these multi-substrate reactions and their use to interpret enzyme mechanism and the effects of disease and engineered mutations. We demonstrate that fluorescence kinetic transients can be used to measure ligand binding that may be accompanied by isomerization steps, revealing the existence of new enzyme intermediates. We also demonstrate that single-turnover reactions can provide a klim for the chemical step and Ks for steroid-substrate binding and that when coupled with kinetic isotope effect measurements can provide information on transition state intermediates. We also demonstrate how multiple turnover experiments can provide evidence for either "burst-phase" kinetics, which can reveal a slow product release step, or linear-phase kinetics, in which the chemical step can be rate-determining. With these assignments it becomes more straightforward to analyze the effects of mutations. We use examples from the hydroxysteroid dehydrogenases (AKR1Cs) and human steroid 5β-reductase (AKR1D1) to illustrate the utility of the approach, which are members of the aldo-keto reductase (AKR) superfamily.
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Affiliation(s)
- Trevor M Penning
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, United States.
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11
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Cochran JC. Kinesin Motor Enzymology: Chemistry, Structure, and Physics of Nanoscale Molecular Machines. Biophys Rev 2015; 7:269-299. [PMID: 28510227 DOI: 10.1007/s12551-014-0150-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/16/2014] [Indexed: 11/25/2022] Open
Abstract
Molecular motors are enzymes that convert chemical potential energy into controlled kinetic energy for mechanical work inside cells. Understanding the biophysics of these motors is essential for appreciating life as well as apprehending diseases that arise from motor malfunction. This review focuses on kinesin motor enzymology with special emphasis on the literature that reports the chemistry, structure and physics of several different kinesin superfamily members.
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Affiliation(s)
- J C Cochran
- Department of Molecular & Cellular Biochemistry, Indiana University, Simon Hall Room 405C, 212 S. Hawthorne Dr., Bloomington, IN, 47405, USA.
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12
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Grima R, Walter NG, Schnell S. Single-molecule enzymology à la Michaelis-Menten. FEBS J 2014; 281:518-30. [DOI: 10.1111/febs.12663] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/30/2013] [Accepted: 11/27/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Ramon Grima
- School of Biological Sciences and SynthSys; University of Edinburgh; UK
| | - Nils G. Walter
- Department of Chemistry and Single Molecule Analysis in Real-Time (SMART) Center; University of Michigan; Ann Arbor MI USA
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology; Department of Computational Medicine & Bioinformatics and Brehm Center for Diabetes Research; University of Michigan Medical School; Ann Arbor MI USA
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13
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Chapin JC, Kvasnica M, Purse BW. Molecular Encapsulation in Pyrogallolarene Hexamers Under Nonequilibrium Conditions. J Am Chem Soc 2012; 134:15000-9. [DOI: 10.1021/ja305252t] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer C. Chapin
- Department of Chemistry and
Biochemistry, University of Denver, 2199
S. University Blvd., Denver, Colorado 80208, United States
| | | | - Byron W. Purse
- Department of Chemistry and
Biochemistry, University of Denver, 2199
S. University Blvd., Denver, Colorado 80208, United States
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14
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Bradley MJ, De La Cruz EM. Analyzing ATP utilization by DEAD-Box RNA helicases using kinetic and equilibrium methods. Methods Enzymol 2012; 511:29-63. [PMID: 22713314 PMCID: PMC7768905 DOI: 10.1016/b978-0-12-396546-2.00002-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DEAD-box proteins (DBPs) couple ATP utilization to conformational rearrangement of RNA. In this chapter, we outline a combination of equilibrium and kinetic methods that have been developed and applied to the analysis of ATP utilization and linked RNA remodeling by DBPs, specifically Escherichia coli DbpA and Saccharomyces cerevisiae Mss116. Several important considerations are covered, including solution conditions, DBP assembly/aggregation, and RNA substrate properties. We discuss practical experimental methods for determination of DBP-RNA-nucleotide binding affinities and stoichiometries, steady-state ATPase activity, ATP binding, hydrolysis and product release rate constants, and RNA unwinding. We present general methods to integrate and analyze this combination of experimental data to identify the preferred kinetic pathway of ATP utilization and linked dsRNA unwinding.
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Affiliation(s)
- Michael J Bradley
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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15
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Hanley PS, Hartwig JF. Intermolecular migratory insertion of unactivated olefins into palladium-nitrogen bonds. Steric and electronic effects on the rate of migratory insertion. J Am Chem Soc 2011; 133:15661-73. [PMID: 21815675 DOI: 10.1021/ja205722f] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a detailed examination of the effect of the steric and electronic properties of the ancillary ligand and the alkene reactant on the rate of migratory insertion of unactivated alkenes into the palladium-nitrogen bond of isolated palladium amido complexes. A series of THF-bound and THF-free amidopalladium complexes ligated by cyclometalated benzylphosphine ligands possessing varied steric and electronic properties were synthesized. The THF-free complexes react with ethylene at -50 °C to form olefin-amido complexes that were observed directly and that undergo migratory insertion, followed by β-hydride elimination to generate enamine products. The effect of the steric properties of the ancillary ligand on the binding of the alkene and the rate of migratory insertion were evaluated individually. The relative binding affinity of ethylene vs THF is larger for the less sterically hindered complex than for the more hindered complex, but the less hindered complex undergoes the insertion of ethylene more slowly than does the more hindered complex. These two changes in relative equilibrium and rate constants cause the rates of reaction of ethylene with the two THF-ligated species having different steric properties to be similar to each other. Reactions of the complexes containing electronically varied ancillary ligands showed that the more electron-poor complexes underwent the migratory insertion step faster than the more electron-rich complexes. Reactions of a THF-ligated palladium-amide with substituted vinylarenes showed that electron-poor vinylarenes reacted with the amido complex slightly faster than electron-rich vinylarenes. Separation of the energetics of binding and insertion indicate that the complex of an electron-rich vinylarene is more stable in this system than the complex of a more electron-poor vinylarene but that the insertion step of the bound, electron-rich vinylarene is slower than the insertion step with the bound, electron-poor vinylarene.
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Affiliation(s)
- Patrick S Hanley
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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16
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Ateşin TA, Kundu S, Skugrud K, Lai KA, Swartz BD, Li T, Brennessel WW, Jones WD. Predicting Selectivity in Oxidative Addition of C–S Bonds of Substituted Thiophenes to a Platinum(0) Fragment: An Experimental and Theoretical Study. Organometallics 2011. [DOI: 10.1021/om200352d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tülay A. Ateşin
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sabuj Kundu
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Karlyn Skugrud
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Katherine A. Lai
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Brett D. Swartz
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Ting Li
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - William W. Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - William D. Jones
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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17
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Goličnik M. Exact and approximate solutions for the decades-old Michaelis-Menten equation: Progress-curve analysis through integrated rate equations. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 39:117-25. [PMID: 21445903 DOI: 10.1002/bmb.20479] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The Michaelis-Menten rate equation can be found in most general biochemistry textbooks, where the time derivative of the substrate is a hyperbolic function of two kinetic parameters (the limiting rate V, and the Michaelis constant K(M) ) and the amount of substrate. However, fundamental concepts of enzyme kinetics can be difficult to understand fully, or can even be misunderstood, by students when based only on the differential form of the Michaelis-Menten equation, and the variety of methods available to calculate the kinetic constants from rate versus substrate concentration "textbook data." Consequently, enzyme kinetics can be confusing if an analytical solution of the Michaelis-Menten equation is not available. Therefore, the still rarely known exact solution to the Michaelis-Menten equation is presented here through the explicit closed-form equation in terms of the Lambert W(x) function. Unfortunately, as the W(x) is not available in standard curve-fitting computer programs, the practical use of this direct solution is limited for most life-science students. Thus, the purpose of this article is to provide analytical approximations to the equation for modeling Michaelis-Menten kinetics. The elementary and explicit nature of these approximations can provide students with direct and simple estimations of kinetic parameters from raw experimental time-course data. The Michaelis-Menten kinetics studied in the latter context can provide an ideal alternative to the 100-year-old problems of data transformation, graphical visualization, and data analysis of enzyme-catalyzed reactions. Hence, the content of the course presented here could gradually become an important component of the modern biochemistry curriculum in the 21st century.
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Affiliation(s)
- Marko Goličnik
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia.
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Younker JM. Numerical Integration of the Chemical Rate Equations via a Discretized Adomian Decomposition. Ind Eng Chem Res 2011. [DOI: 10.1021/ie1008647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jarod M. Younker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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19
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Gunther S, Urbanke C, Kindler B, Huchzermeyer B. Nucleotide binding to chloroplast F1-ATPase (CF1) cannot be explained by a two-site model. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19961001216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Kinetic analysis of the inhibition of matrix metalloproteinases: lessons from the study of tissue inhibitors of metalloproteinases. Methods Mol Biol 2010. [PMID: 20135297 DOI: 10.1007/978-1-60327-299-5_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Tissue inhibitors of metalloproteinases (TIMPs) are a group of highly potent inhibitors of matrix metalloproteinases (MMPs) and disintegrin metalloproteinases (ADAMs). The high affinity and "tight-binding" nature of the inhibition of MMPs or ADAMs by TIMPs presents challenges for the determination of both equilibrium and dissociation rate constants of these inhibitory events. Methodologies that enable some of these challenges to be overcome are described in this chapter and represent valuable lessons for the in vitro assessment of MMP or ADAM inhibitors within a drug discovery context.
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Analysis of residuals from enzyme kinetic and protein folding experiments in the presence of correlated experimental noise. Anal Biochem 2009; 395:1-7. [DOI: 10.1016/j.ab.2009.05.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 05/01/2009] [Accepted: 05/04/2009] [Indexed: 11/19/2022]
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22
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Srividhya J, Mourão MA, Crampin EJ, Schnell S. Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction. Comput Biol Chem 2009; 34:11-8. [PMID: 19945917 DOI: 10.1016/j.compbiolchem.2009.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 10/23/2009] [Accepted: 10/23/2009] [Indexed: 11/30/2022]
Abstract
The traditional experimental practice in enzyme kinetics involves the measurement of substrate or product concentrations as a function of time. Advances in computing have produced novel approaches for modeling enzyme catalyzed reactions from time course data. One example of such an approach is the selection of appropriate chemical reactions that best fit the data. A common limitation of this approach resides in the number of chemical species considered. The number of possible chemical reactions grows exponentially with the number of chemical species, which makes difficult to select reactions that uniquely describe the data and diminishes the efficiency of the methods. In addition, a method's performance is also dependent on several quantitative and qualitative properties of the time course data, of which we know very little. This information is important to experimentalists as it could allow them to setup their experiments in ways that optimize the network reconstruction. We have previously described a method for inferring reaction mechanisms and kinetic rate parameters from time course data. Here, we address the limitations in the number of chemical reactions by allowing the introduction of information about chemical interactions. We also address the unknown properties of the input data by determining experimental data properties that maximize our method's performance. We investigate the following properties: initial substrate-enzyme concentration ratios; initial substrate-enzyme concentration variation ranges; number of data points; number of different experiments (time courses); and noise. We test the method using data generated in silico from the Michaelis-Menten and the Hartley-Kilby reaction mechanisms. Our results demonstrate the importance of experimental design for time course assays that has not been considered in experimental protocols. These considerations can have far reaching implications for the computational mechanism reconstruction process.
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Affiliation(s)
- Jeyaraman Srividhya
- Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN 55455, USA
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23
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Brown JA, Suo Z. Elucidating the kinetic mechanism of DNA polymerization catalyzed by Sulfolobus solfataricus P2 DNA polymerase B1. Biochemistry 2009; 48:7502-11. [PMID: 19456143 DOI: 10.1021/bi9005336] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transient-state kinetic techniques were used to resolve the kinetic mechanism of DNA polymerization catalyzed by an exonuclease-deficient mutant of Sulfolobus solfataricus P2 DNA polymerase B1 (PolB1 exo-). Here, we report the kinetic parameters of several elementary steps for the forward polymerization reaction. PolB1 exo- binds tightly to DNA (K(d)(DNA) = 1.8 nM) and a correct incoming nucleotide (apparent K(d)(dTTP) = 11 microM). Moreover, several lines of kinetic evidence suggested that correct nucleotide incorporation catalyzed by PolB1 exo- was limited by a protein conformational change which precedes the chemistry step. The utilization of an "induced fit" mechanism by PolB1 exo- was supported by the following: a small, alpha-thio elemental effect of 1.5, varying DNA dissociation rates for the binary complex (0.043 s(-1)) as well as ternary complexes before (0.18 s(-1)) and after (0.0071 s(-1)) a conformational change, a greater amplitude for the pulse-chase than the pulse-quench reaction, and an activation energy barrier of 38 kcal/mol which is greater than the predicted values of phosphodiester bond formation both in solution and within a polymerase active site. Lastly, PolB1 exo- exhibited a low processivity value of 15, thereby suggesting a protein cofactor confers this replicative DNA polymerase with higher processivity in vivo.
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Affiliation(s)
- Jessica A Brown
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Hsieh J, Walker SC, Fierke CA, Engelke DR. Pre-tRNA turnover catalyzed by the yeast nuclear RNase P holoenzyme is limited by product release. RNA (NEW YORK, N.Y.) 2009; 15:224-234. [PMID: 19095620 PMCID: PMC2648709 DOI: 10.1261/rna.1309409] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 10/24/2008] [Indexed: 05/27/2023]
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein that catalyzes the 5' maturation of precursor transfer RNA in the presence of magnesium ions. The bacterial RNase P holoenzyme consists of one catalytically active RNA component and a single essential but catalytically inactive protein. In contrast, yeast nuclear RNase P is more complex with one RNA subunit and nine protein subunits. We have devised an affinity purification protocol to gently and rapidly purify intact yeast nuclear RNase P holoenzyme for transient kinetic studies. In pre-steady-state kinetic studies under saturating substrate concentrations, we observed an initial burst of tRNA formation followed by a slower, linear, steady-state turnover, with the burst amplitude equal to the concentration of the holoenzyme used in the reaction. These data indicate that the rate-limiting step in turnover occurs after pre-tRNA cleavage, such as mature tRNA release. Additionally, the steady-state rate constants demonstrate a large dependence on temperature that results in nonlinear Arrhenius plots, suggesting that a kinetically important conformational change occurs during catalysis. Finally, deletion of the 3' trailer in pre-tRNA has little or no effect on the steady-state kinetic rate constants. These data suggest that, despite marked differences in subunit composition, the minimal kinetic mechanism for cleavage of pre-tRNA catalyzed by yeast nuclear RNase P holoenzyme is similar to that of the bacterial RNase P holoenzyme.
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Affiliation(s)
- John Hsieh
- Department of Chemistry, University of Michigan, Ann Arbor, 48109-0606, USA
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Johnson KA. Chapter 23 Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer. Methods Enzymol 2009; 467:601-626. [DOI: 10.1016/s0076-6879(09)67023-3] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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26
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Johnson KA, Simpson ZB, Blom T. Global kinetic explorer: a new computer program for dynamic simulation and fitting of kinetic data. Anal Biochem 2008; 387:20-9. [PMID: 19154726 DOI: 10.1016/j.ab.2008.12.024] [Citation(s) in RCA: 437] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Revised: 11/10/2008] [Accepted: 12/15/2008] [Indexed: 11/29/2022]
Abstract
We describe a new dynamic kinetic simulation program that allows multiple data sets to be fit simultaneously to a single model based on numerical integration of the rate equations describing the reaction mechanism. Unlike other programs that allow fitting based on numerical integration of rate equations, in the dynamic simulation rate constants, output factors, and starting concentrations of reactants can be scrolled while observing the change in the shape of the simulated reaction curves. Fast dynamic simulation facilitates the exploration of initial parameters that serve as the starting point for nonlinear regression in fitting data and facilitates exploration of the relationships between individual constants and observable reactions. The exploration of parameter space by dynamic simulation provides a powerful tool for learning kinetics and for evaluating the extent to which parameters are constrained by the data. This feature is critical to avoid overly complex models that are not supported by the data.
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FitSpace explorer: an algorithm to evaluate multidimensional parameter space in fitting kinetic data. Anal Biochem 2008; 387:30-41. [PMID: 19168024 DOI: 10.1016/j.ab.2008.12.025] [Citation(s) in RCA: 261] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Revised: 12/14/2008] [Accepted: 12/15/2008] [Indexed: 11/21/2022]
Abstract
Fitting several sets of kinetic data directly to a model based on numerical integration provides the best method to extract kinetic parameters without relying on the simplifying assumptions required to achieve analytical solutions of rate equations. However, modern computer programs make it too easy to enter an overly complex model, and standard error analysis grossly underestimates errors when a system is underconstrained and fails to reveal the full degree to which multiple parameters are linked through the complex relationships common in kinetic data. Here we describe the application of confidence contour analysis obtained by measuring the dependence of the sum square error on each pair of parameters while allowing all remaining parameters to be adjusted in seeking the best fit. The confidence contours reveal complex relationships between parameters and clearly outline the space over which parameters can vary (the "FitSpace"). The utility of the method is illustrated by examples of well-constrained fits to published data on tryptophan synthase and the kinetics of oligonucleotide binding to a ribozyme. In contrast, analysis of alanine racemase clearly refutes claims that global analysis of progress curves can be used to extract the free energy profiles of enzyme-catalyzed reactions.
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Nikolova N, Tenekedjiev K, Kolev K. Uses and misuses of progress curve analysis in enzyme kinetics. CENTRAL EUROPEAN JOURNAL OF BIOLOGY 2008; 3:345-350. [PMID: 19562082 PMCID: PMC2701647 DOI: 10.2478/s11535-008-0035-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Progress curve analysis is a convenient tool for the characterization of enzyme action: a single reaction mixture provides multiple experimental measured points for continuously varying amounts of substrates and products with exactly the same enzyme and modulator concentrations. The determination of kinetic parameters from the progress curves, however, requires complex mathematical evaluation of the time-course data. Some freely available programs (e.g. FITSIM, DYNAFIT) are widely applied to fit kinetic parameters to user-defined enzymatic mechanisms, but users often overlook the stringent requirements of the analytic procedures for appropriate design of the input experiments. Flaws in the experimental setup result in unreliable parameters with consequent misinterpretation of the biological phenomenon under study. The present commentary suggests some helpful mathematical tools to improve the analytic procedure in order to diagnose major errors in concept and design of kinetic experiments.
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Affiliation(s)
- Natalia Nikolova
- Department of Economics and Management, Technical University - Varna, 9010 Varna, Bulgaria
| | - Kiril Tenekedjiev
- Department of Economics and Management, Technical University - Varna, 9010 Varna, Bulgaria
| | - Krasimir Kolev
- Department of Medical Biochemistry, Semmelweis University, 1088 Budapest, Hungary
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29
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Hanson SM, Schnell S. Reactant Stationary Approximation in Enzyme Kinetics. J Phys Chem A 2008; 112:8654-8. [DOI: 10.1021/jp8026226] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonya M. Hanson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, and Indiana University School of Informatics and Biocomplexity Institute, 901 East Tenth Street, Bloomington, Indiana 47408-3912
| | - Santiago Schnell
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, and Indiana University School of Informatics and Biocomplexity Institute, 901 East Tenth Street, Bloomington, Indiana 47408-3912
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30
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Bevilacqua PC, Turner DH. Use of fluorescence spectroscopy to elucidate RNA folding pathways. ACTA ACUST UNITED AC 2008; Chapter 11:Unit 11.8. [PMID: 18428886 DOI: 10.1002/0471142700.nc1108s09] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This overview unit discusses fluorescence spectroscopy as a tool for studying RNA folding. Ribozymes and oligonucleotides can be labeled with a fluorescent probe and analyzed to give information about both slow and fast kinetic processes with real-time data acquisition. The unit discusses the advantages and disadvantages of various pendant probes and nucleotide analogs, the analytical methods that can be used, instrument setup, control experiments, and a variety of kinetic experiments that can be performed, such as determination of rate constants.
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31
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Ateşin TA, Ateşin AÇ, Skugrud K, Jones WD. Understanding Selectivity in the Oxidative Addition of the Carbon−Sulfur Bonds of 2-Cyanothiophene to Pt(0). Inorg Chem 2008; 47:4596-604. [DOI: 10.1021/ic702273a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tülay A. Ateşin
- Department of Chemistry, University of Rochester, Rochester, New York 14627
| | | | - Karlyn Skugrud
- Department of Chemistry, University of Rochester, Rochester, New York 14627
| | - William D. Jones
- Department of Chemistry, University of Rochester, Rochester, New York 14627
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32
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Affiliation(s)
- Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA.
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Zhang D, Kovach IM, Sheehy JP. Locating the rate-determining step(s) for three-step hydrolase-catalyzed reactions with DYNAFIT. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:827-33. [PMID: 18342021 DOI: 10.1016/j.bbapap.2008.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2007] [Revised: 02/03/2008] [Accepted: 02/11/2008] [Indexed: 10/22/2022]
Abstract
Hydrolytic reactions of oligopeptide 4-nitroanilides catalyzed by human-alpha-thrombin, human activated protein C and human factor Xa were studied at pH 8.0-8.4 and 25.0+/-0.1 degrees C by the progress curve method and individual rate constants were calculated mostly within 10% internal error using DYNAFITV. A systematic strategy has been developed for fitting a three-step consecutive mechanism to eighteen hundred to six thousand time-course data points polled from two to four independent kinetic experiments. Enzyme and substrate concentrations were also calculated. Individual rate constants well reproduce published values obtained under comparable conditions and the Michaelis-Menten kinetic parameters calculated from these elementary rate constants are also within reasonable limits of published values. For comparison, the integrated Michaelis-Menten equation was also fitted to data from twelve sets. Both the k(cat) and k(cat)/K(m) values are within 15% agreement with those calculated using the elementary rate constants obtained with DYNAFITV. Rate constants for the second and third consecutive steps are within 3-4 fold indicating that both determine the overall rate. The Factor Xa-catalyzed hydrolysis of N-alpha-Z-D-Arg-Gly-Arg-pNA.2HCl at pH 8.4 in a series of buffers containing increasing fractions of deuterium at 25.0+/-0.1 degrees C shows a very strong dependence of k(3) and a moderate dependence of k(2) on D content in the buffer: the fractionation factors are: 0.49+/-0.03 for K(1,) 0.70+/-0.05 for k(2), and (0.32+/-0.03)(2) for k(3).
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Affiliation(s)
- Daoning Zhang
- The Catholic University of America, Department of Chemistry, Washington DC 20064, USA
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Hooley RJ, Rebek J. A deep cavitand catalyzes the Diels-Alder reaction of bound maleimides. Org Biomol Chem 2007; 5:3631-6. [PMID: 17971992 DOI: 10.1039/b713104f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A deep cavitand catalyzes Diels-Alder reactions of bound maleimides via activation of the dienophile by interaction with the organized hydrogen bonding network at the cavitand rim. Rapid in-out exchange of reactant and product allows efficient turnover. The increase in steric bulk of the reaction product lessens its binding affinity, reducing (and in some cases completely eliminating) product inhibition.
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Affiliation(s)
- Richard J Hooley
- The Skaggs Institute for Chemical Biology, and the Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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35
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Chen Y, Anderson DE, Rajagopalan M, Erickson HP. Assembly dynamics of Mycobacterium tuberculosis FtsZ. J Biol Chem 2007; 282:27736-43. [PMID: 17644520 PMCID: PMC2630888 DOI: 10.1074/jbc.m703788200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have investigated the assembly of FtsZ from Mycobacterium tuberculosis (MtbFtsZ). Electron microscopy confirmed the previous observation that MtbFtsZ assembled into long, two-stranded filaments at pH 6.5. However, we found that assembly at pH 7.2 or 7.7 produced predominantly short, one-stranded protofilaments, similar to those of Escherichia coli FtsZ (EcFtsZ). Near pH 7, which is close to the pH of M. tuberculosis cytoplasm, MtbFtsZ formed a mixture of single- and two-stranded filaments. We developed a fluorescence resonance energy transfer assay to measure the kinetics of initial assembly and the dynamic properties at steady state. Assembly of MtbFtsZ reached a plateau after 60-100 s, about 10 times slower than EcFtsZ. The initial assembly kinetics were similar at pH 6.5 and 7.7, despite the striking difference in the polymer structures. Both were fit with a cooperative assembly mechanism involving a weak dimer nucleus, similar to EcFtsZ but with slower kinetics. Subunit turnover and GTPase at steady state were also about 10 times slower for MtbFtsZ than for EcFtsZ. Specifically, the half-time for subunit turnover in vitro at pH 7.7 was 42 s for MtbFtsZ compared with 5.5 s for EcFtsZ. Photobleaching studies in vivo showed a range of turnover half-times with an average of 25 s for MtbFtsZ as compared with 9 s for EcFtsZ.
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Affiliation(s)
- Yaodong Chen
- Department of Cell Biology, Duke University, Medical Center, Durham, North Carolina 27710
| | - David E. Anderson
- Department of Cell Biology, Duke University, Medical Center, Durham, North Carolina 27710
| | - Malini Rajagopalan
- Biomedical Research, University of Texas Health Center, Tyler, Texas 75708−3154
| | - Harold P. Erickson
- Department of Cell Biology, Duke University, Medical Center, Durham, North Carolina 27710
- To whom correspondence should be addressed: Dept. of Cell Biology, Duke University Medical Center, Box 3709, Durham, NC 27710. Tel.: 919−684−6385; Fax: 919−684−8090; E-mail:
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Błachut-Okrasińska E, Bojarska E, Stepiński J, Antosiewicz JM. Kinetics of binding the mRNA cap analogues to the translation initiation factor eIF4E under second-order reaction conditions. Biophys Chem 2007; 129:289-97. [PMID: 17651889 DOI: 10.1016/j.bpc.2007.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 06/20/2007] [Accepted: 06/25/2007] [Indexed: 10/23/2022]
Abstract
The kinetics of binding of five analogues of the 5'-mRNA cap, differing in size and electric charge, to the eukaryotic initiation factor eIF4E, at 20 degrees C, pH 7.2, and ionic strength of 150 mM, were measured, after mixing solutions of comparable concentrations of the reagents, in a stopped-flow spectrofluorimeter. The registered stopped-flow signals were fitted using an efficient software package, called Dyna Fit, based on a numerical solution of the kinetic rate equations for assumed reaction mechanisms. One-, two-, and three-step binding models were considered. The quality of fits for these models were compared using two statistical criteria: Akaike's Information Criterion and Bayesian Information Criterion. Based on resulting probabilities of the models, it was concluded that for all investigated ligands a one-step binding model has essentially no support in the experimental observations. Our conclusions were also analysed from the perspective of kinetic transients obtained for cap-eIF4E systems under the so called pseudo-first order reaction condition, which result in the linear correlation of the observed association rate constant with ligand concentration. The existence of such a linear correlation is usually considered as proof of a one-step binding mechanism. The kinetic and optical parameters, derived from fitting a two-step cap-binding model with the DynaFit, were used to simulate kinetic transients under pseudo-first order reaction conditions. It appeared that the observed association rate constants derived from these simulated transients are also linearly correlated with the ligand concentration. This indicated that these linear dependencies are not sufficient to conclude a one-step binding.
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Abstract
Multiple kinetic isotope effects (KIEs) on deoxyadenosine monophosphate (dAMP) hydrolysis in 0.1 M HCl were used to determine the transition state (TS) structure and probe its intrinsic reactivity. The experimental KIEs revealed a stepwise (SN1) mechanism, with a discrete oxacarbenium ion intermediate. This is the first direct evidence for the deoxyribosyl oxacarbenium ion in solution. In 50% methanol/0.1 M HCl the products were deoxyribose 5-phosphate (dRMP) and alpha- and beta-methyl dRMP. The alpha-Me-dRMP/beta-Me-dRMP ratio was 8.5:1. Assuming that a free oxacarbenium ion is equally susceptible to nucleophilic attack on either face, this indicated that approximately 20% proceeded through a solvent-separated ion pair complex, or free oxacarbenium ion, a DN+AN mechanism, while approximately 80% of the reaction proceeded through a contact ion pair complex. The oxacarbenium ion lifetime was estimated at 10(-11)-10(-10) s. Computational transition states were found for ANDN, DN*AN, DN*AN, and DN+AN mechanisms using hybrid density functional theory calculations. After taking into account 20% of DN+AN, there was an excellent match of calculated to experimental KIEs for 80% of the reaction having a DN*AN mechanism. That is, C-N bond cleavage is reversible, with dAMP and the {oxacarbenium ion*adenine} complex in equilibrium. The first irreversible step is water attack on the oxacarbenium ion. The calculated 1'-14C KIE for a stepwise mechanism with irreversible C-N bond cleavage (DN*AN) was 1.052, in the range previously associated only with ANDN transition states, and close to the calculated ANDN value, 1.059. The 1'-14C KIE was strongly dependent on the adenine protonation state.
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Affiliation(s)
- Joe A B McCann
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4M1, Canada
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38
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Yang Q, Fairman ME, Jankowsky E. DEAD-box-protein-assisted RNA structure conversion towards and against thermodynamic equilibrium values. J Mol Biol 2007; 368:1087-100. [PMID: 17391697 PMCID: PMC1913213 DOI: 10.1016/j.jmb.2007.02.071] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 01/30/2007] [Accepted: 02/19/2007] [Indexed: 11/24/2022]
Abstract
RNAs in biological processes often interconvert between defined structures. These RNA structure conversions are assisted by proteins and are frequently coupled to ATP hydrolysis. It is not well understood how proteins coordinate RNA structure conversions and which role ATP hydrolysis has in these processes. Here, we have investigated in vitro how the DEAD-box ATPase Ded1 facilitates RNA structure conversions in a simple model system. We find that Ded1 assists RNA structure conversions via two distinct pathways. One pathway requires ATP hydrolysis and involves the complete disassembly of the RNA strands. This pathway represents a kinetically controlled steady state between the RNA structures, which allows formation of less stable from more stable RNA conformations and thus RNA structure conversion against thermodynamic equilibrium values. The other pathway is ATP-independent and proceeds via multipartite intermediates that are stabilized by Ded1. Our results provide a basic mechanistic framework for protein-assisted RNA structure conversions that illuminates the role of ATP hydrolysis and reveal an unexpected diversity of pathways.
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Affiliation(s)
- Quansheng Yang
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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Abstract
Enolpyruvylshikimate-3-phosphate synthase (AroA, also called EPSP synthase) is a carboxyvinyl transferase involved in aromatic amino acid biosynthesis, forming EPSP from shikimate 3-phosphate and phosphoenolpyruvate. Upon extended incubation, EPSP ketal, a side product, forms by intramolecular nucleophilic addition of O4 to C2' of the enolpyruvyl group. The catalytic significance of this reaction was unclear, as it was initially proposed to arise from nonenzymatic breakdown of tetrahedral intermediate that had dissociated from AroA. This study shows that EPSP ketal formed in AroA's active site, not nonenzymatically, by demonstrating its formation in the presence of excess AroA. It formed both in the normal reaction and during AroA-catalyzed EPSP hydrolysis. In addition, nonenzymatic EPSP hydrolysis was studied to elucidate the catalytic imperative for enolpyruvyl reactions. Hydrolysis was acid-catalyzed, with a rate enhancement of >5 x 10(8)-fold. There was no detectable EPSP breakdown after 16 days at 90 degrees C in 1 M KOH, a solution that is 1000-fold more nucleophilic than neutral aqueous solutions. Thus, an unactivated enolpyruvyl group is not susceptible to nucleophilic attack. Enzymatic EPSP ketal formation therefore requires enolpyruvyl activation through protonation of C3' to form either a cationic intermediate or a highly cation-like transition state. Forming an EPSP cation requires the investment of considerable catalytic power by AroA. Such an intermediate is a potential target motif for inhibitor design.
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Affiliation(s)
- Meghann E Clark
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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Atesin AC, Duckett SB, Flaschenriem C, Brennessel WW, Eisenberg R. Diastereoselective Oxidative Addition of Dihydrogen to IrI(CO)((R)-BINAP) and [Ir(CO)2((R)-BINAP)][SbF6]. Inorg Chem 2007; 46:1196-204. [PMID: 17249655 DOI: 10.1021/ic061471a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two chiral iridium(I) (R)-BINAP complexes, IrI(CO)((R)-BINAP) (1) and [Ir(CO)2((R)-BINAP)][SbF6] (2), have been synthesized and characterized, and their reactivity with dihydrogen has been studied. Complex 1 is formed on the addition of (R)-BINAP to [Bu4N][IrI2(CO)2] in toluene, and 2 is generated by the addition of AgSbF6 to a solution of 1 in dichloromethane under CO. A structure determination of complex 2 confirms a square planar coordination geometry, while that of 1 reveals a significant tetrahedral distortion from the expected planar coordination. Additionally, the structure of 1 shows a disorder between iodide and CO ligands. The reaction of 1 with H2 proceeds under kinetic control and shows a high degree of kinetic and thermodynamic selectivity; the kinetic product is formed by H2 addition across the P-Ir-CO axis of IrI(CO)((R)-BINAP) and yields two diastereomers which then convert over time to two more stable diastereomers which correspond to oxidative addition across the P-Ir-I axis. The kinetically favored diastereomers are formed in an initial ratio of 8.6:1, corresponding to a DeltaDeltaG* of 1.27 kcal/mol. The reaction of H2 with the C2-symmetric complex 2 also leads to the formation of two diastereomers, with one favored over the other kinetically by a 9.9:1 ratio on extrapolation to t = 0. When these reactions are followed using parahydrogen NMR methods, only one of the initially formed diastereomers in each case is found to exhibit substantial parahydrogen-induced polarization in the hydride resonances at room temperature.
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Characterizing Ligand-Microtubule Binding by Competition Methods. METHODS IN MOLECULAR MEDICINE™ 2007; 137:245-60. [DOI: 10.1007/978-1-59745-442-1_17] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Vineyard D, Zhang X, Lee I. Transient kinetic experiments demonstrate the existence of a unique catalytic enzyme form in the peptide-stimulated ATPase mechanism of Escherichia coli Lon protease. Biochemistry 2006; 45:11432-43. [PMID: 16981703 DOI: 10.1021/bi060809+] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lon is an oligomeric serine protease whose proteolytic activity is mediated by ATP hydrolysis. Although each monomeric subunit has an identical sequence, Lon contains two types of ATPase sites that hydrolyze ATP at drastically different rates. The catalytic low-affinity sites display pre-steady-state burst kinetics and hydrolyze ATP prior to peptide cleavage. The high-affinity sites are able to hydrolyze ATP at a very slow rate. By utilizing the differing Kd's, the high-affinity site can be blocked with unlabeled nucleotide while the activity at the low-affinity site is monitored. Little kinetic data are available that describe microscopic events along the reaction pathway of Lon. In this study we utilize MANT-ATP, a fluorescent analogue of ATP, to monitor the rate constants for binding of ATP as well as the release of ADP from Escherichia coli Lon protease. All of the adenine nucleotides tested bound to Lon on the order of 10(5) M(-1) s(-1), and the previously proposed conformational change associated with nucleotide binding was also detected. On the basis of the data obtained in this study we propose that the rate of ADP release is slightly different for the two ATPase sites. As the model peptide substrate [S2; YRGITCSGRQK(Bz)] [Thomas-Wohlever, J., and Lee, I. (2002) Biochemistry 41, 9418-9425] or the protein substrate casein affects only the steady-state ATPase activity of the low-affinity sites, we propose that Lon adopts a different form after its first turnover as an ATP-dependent protease. Based on the obtained rate constants, a revised kinetic model is presented for ATPase activity in Lon protease in both the absence and presence of the model peptide substrate (S2).
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Affiliation(s)
- Diana Vineyard
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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43
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44
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Ghatak A, Julin DA. Kinetics of ATP-stimulated nuclease activity of the Escherichia coli RecBCD enzyme. J Mol Biol 2006; 361:954-68. [PMID: 16887145 DOI: 10.1016/j.jmb.2006.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2006] [Revised: 07/03/2006] [Accepted: 07/07/2006] [Indexed: 11/30/2022]
Abstract
The RecBCD enzyme is an ATP-dependent nuclease on both single-stranded and double-stranded DNA substrates. We have investigated the kinetics of the RecBCD-catalyzed reaction with small, single-stranded oligodeoxyribonucleotide substrates under single-turnover conditions using rapid-quench flow techniques. RecBCD-DNA complexes were allowed to form in pre-incubation mixtures. The nuclease reactions were initiated by mixing with ATP. The reaction time-courses were fit to several possible reaction mechanisms and quantitative estimates were obtained for rate constants for individual reaction steps. The relative rates of forward reaction versus dissociation from the DNA, and the fact that inclusion of excess non-radiolabeled single-stranded DNA to trap free RecBCD has no effect on the nuclease reaction, indicates that the reaction is processive. The reaction products show that the reaction begins near the 3'-end of the [5'-32P]DNA substrates and the major cleavage sites are two to four phosphodiester bonds apart. The product distribution is unchanged as the ATP concentration varies from 10 microM to 100 microM ATP, while the overall reaction rate varies by about tenfold. These observations suggest that DNA cleavage is tightly coordinated with movement of the enzyme along the DNA. The reaction time-courses at low concentrations of ATP (10 microM and 25 microM) have a significant lag before cleavage products appear. We propose that the lag represents ATP-dependent movement of the DNA from an initial binding site in the helicase domain of the RecB subunit to the nuclease active site in a separate domain of RecB. The extent of reaction of the substrate is limited (approximately 50%) under all conditions. This may indicate the formation of a non-productive RecBCD-DNA complex that does not dissociate in the 1-2 s time-scale of our experiments.
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Affiliation(s)
- Archana Ghatak
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
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Gao X, Harris TK. Role of the PH domain in regulating in vitro autophosphorylation events required for reconstitution of PDK1 catalytic activity. Bioorg Chem 2006; 34:200-23. [PMID: 16780920 DOI: 10.1016/j.bioorg.2006.05.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2006] [Accepted: 05/09/2006] [Indexed: 01/17/2023]
Abstract
In addition to its catalytic domain, phosphoinsositide-dependent protein kinase-1 (PDK1) contains a C-terminal pleckstrin homology (PH) domain, which binds the membrane-bound phosphatidylinositol (3,4,5)-triphosphate [PI(3,4,5)P3] second messenger. Here, we report in vitro kinetic, phosphopeptide mapping, and oligomerization studies that address the role of the PH domain in regulating specific autophosphorylation events, which are required for PDK1 catalytic activation. First, 'inactive' unphosphorylated forms of N-terminal His6 tagged full length (His6-PDK1) and catalytic domain constructs [His6-PDK1(Delta PH)] were generated by treatment with Lambda protein phosphatase (lambda PP). Reconstitution of lambda PP-treated His6-PDK1(Delta PH) catalytic activity required activation loop Ser-241 phosphorylation, which occurred only upon trans-addition of 'active' PDK1 with an apparent bimolecular rate constant of (app)k1(S241) = 374+/-29 M(-1) s(-1). In contrast, full length lambda PP-treated His6-PDK1 catalyzed Ser-241 cis-autophosphorylation with an apparent first-order rate constant of (app)k1(S241) = (5.0+/-1.5) x 10(-4) s(-1) but remained 'inactive'. Reconstitution of lambda PP-treated His(6)-PDK1 catalytic activity occurred only when autophosphorylated in the presence of PI(3,4,5)P3 containing vesicles. PI(3,4,5)P3 binding to the PH domain activated apparent first-order Ser-241 autophosphorylation by 20-fold [(app)k1(S241) = (1.1+/-0.1) x 10(-2) s(-1)] and also promoted biphasic Thr-513 trans-autophosphorylation [(app)k2(T513) = (4.9+/-1.1) x 10(2) M(-1) s(-1) and(app)k3(T513) = (1.5+/-0.2) x 10(3) M(-1) s(-1)]. The results of mutagenesis studies suggest that Thr-513 phosphorylation may cause dissociation of autoinhibitory contacts formed between the contiguous regulatory PH and catalytic kinase domains.
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Affiliation(s)
- Xinxin Gao
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, P.O. Box 016129, Miami, FL 33101-6129, USA
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Szepessy E, Sahin-Tóth M. Human mesotrypsin exhibits restricted S1' subsite specificity with a strong preference for small polar side chains. FEBS J 2006; 273:2942-54. [PMID: 16759229 PMCID: PMC1550978 DOI: 10.1111/j.1742-4658.2006.05305.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mesotrypsin, an inhibitor-resistant human trypsin isoform, does not activate or degrade pancreatic protease zymogens at a significant rate. These observations led to the proposal that mesotrypsin is a defective digestive protease on protein substrates. Surprisingly, the studies reported here with alpha1-antitrypsin (alpha1AT) revealed that, even though mesotrypsin was completely resistant to this serpin-type inhibitor, it selectively cleaved the Lys10-Thr11 peptide bond at the N-terminus. Analyzing a library of alpha1AT mutants in which Thr11 was mutated to various amino acids, we found that mesotrypsin hydrolyzed lysyl peptide bonds containing Thr or Ser at the P1' position with relatively high specificity (kcat/KM approximately 10(5) m(-1) x s(-1)). Compared with Thr or Ser, P1' Gly or Met inhibited cleavage 13- and 25-fold, respectively, whereas P1' Asn, Asp, Ile, Phe or Tyr resulted in 100-200-fold diminished rates of proteolysis, and Pro abolished cleavage completely. Consistent with the Ser/Thr P1' preference, mesotrypsin cleaved the Arg358-Ser359 reactive-site peptide bond of alpha1AT Pittsburgh and was rapidly inactivated by the serpin mechanism (ka approximately 10(6) m(-1) s(-1)). Taken together, the results indicate that mesotrypsin is not a defective protease on polypeptide substrates in general, but exhibits a relatively high specificity for Lys/Arg-Ser/Thr peptide bonds. This restricted, thrombin-like subsite specificity explains why mesotrypsin cannot activate pancreatic zymogens, but might activate certain proteinase-activated receptors. The observations also identify alpha1AT Pittsburgh as an effective mesotrypsin inhibitor and the serpin mechanism as a viable stratagem to overcome the inhibitor-resistance of mesotrypsin.
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Affiliation(s)
| | - Miklós Sahin-Tóth
- *Address correspondence to Miklós Sahin-Tóth, 715 Albany Street, Evans-433; Boston, MA 02118; Tel: (617) 414-1070; Fax: (617) 414-1041; E-mail:
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Meadow ND, Savtchenko RS, Remington SJ, Roseman S. Effects of Mutations and Truncations on the Kinetic Behavior of IIAGlc, a Phosphocarrier and Regulatory Protein of the Phosphoenolpyruvate Phosphotransferase System of Escherichia coli. J Biol Chem 2006; 281:11450-5. [PMID: 16439362 DOI: 10.1074/jbc.m507417200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IIAGlc, a component of the glucose-specific phosphoenolpyruvate:phosphotransferase system (PTS) of Escherichia coli, is important in regulating carbohydrate metabolism. In Glc uptake, the phosphotransfer sequence is: phosphoenolpyruvate --> Enzyme I --> HPr --> IIAGlc --> IICBGlc --> Glc. (HPr is the first phosphocarrier protein of the PTS.) We previously reported two classes of IIAGlc mutations that substantially decrease the P-transfer rate constants to/from IIAGlc. A mutant of His75 which adjoins the active site (His90), (H75Q), was 0.5% as active as wild-type IIAGlc in the reversible P-transfer to HPr. Two possible explanations were offered for this result: (a) the imidazole ring of His75 is required for charge delocalization and (b) H75Q disrupts the hydrogen bond network: Thr73, His75, phospho-His90. The present studies directly test the H-bond network hypothesis. Thr73 was replaced by Ser, Ala, or Val to eliminate the network. Because the rate constants for phosphotransfer to/from HPr were largely unaffected, we conclude that the H-bond network hypothesis is not correct. In the second class of mutants, proteolytic truncation of seven residues of the IIAGlc N terminus caused a 20-fold reduction in phosphotransfer to membrane-bound IICBGlc from Salmonella typhimurium. Here, we report the phosphotransfer rates between two genetically constructed N-terminal truncations of IIAGlc (Delta7 and Delta16) and the proteins IICBGlc and IIBGlc (the soluble cytoplasmic domain of IICBGlc). The truncations did not significantly affect reversible P-transfer to IIBGlc but substantially decreased the rate constants to IICBGlc in E. coli and S. typhimurium membranes. The results support the hypothesis (Wang, G., Peterkofsky, A., and Clore, G. M. (2000) J. Biol. Chem. 275, 39811-39814) that the N-terminal 18-residue domain "docks" IIAGlc to the lipid bilayer of membranes containing IICBGlc.
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Affiliation(s)
- Norman D Meadow
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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Huang S, Gao L, Blanchoin L, Staiger CJ. Heterodimeric capping protein from Arabidopsis is regulated by phosphatidic acid. Mol Biol Cell 2006; 17:1946-58. [PMID: 16436516 PMCID: PMC1415281 DOI: 10.1091/mbc.e05-09-0840] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 12/13/2005] [Accepted: 01/17/2006] [Indexed: 11/11/2022] Open
Abstract
The cytoskeleton is a key regulator of morphogenesis, sexual reproduction, and cellular responses to extracellular stimuli. Changes in the cellular architecture are often assumed to require actin-binding proteins as stimulus-response modulators, because many of these proteins are regulated directly by binding to intracellular second messengers or signaling phospholipids. Phosphatidic acid (PA) is gaining widespread acceptance as a major, abundant phospholipid in plants that is required for pollen tube tip growth and mediates responses to osmotic stress, wounding, and phytohormones; however, the number of identified effectors of PA is rather limited. Here we demonstrate that exogenous PA application leads to significant increases in filamentous actin levels in Arabidopsis suspension cells and poppy pollen grains. To investigate further these lipid-induced changes in polymer levels, we analyzed the properties of a key regulator of actin filament polymerization, the heterodimeric capping protein from Arabidopsis thaliana (AtCP). AtCP binds to PA with a K(d) value of 17 muM and stoichiometry of approximately 1:2. It also binds well to PtdIns(4,5)P(2), but not to several other phosphoinositide or acidic phospholipids. The interaction with PA inhibited the actin-binding activity of CP. In the presence of PA, CP is unable to block the barbed or rapidly growing and shrinking end of actin filaments. Precapped filament barbed ends can also be uncapped by addition of PA, allowing rapid filament assembly from an actin monomer pool that is buffered with profilin. The findings support a model in which the inhibition of CP activity in cells by elevated PA results in the stimulation of actin polymerization from a large pool of profilin-actin. Such regulation may be important for the response of plant cells to extracellular stimuli as well as for the normal process of pollen tube tip growth.
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Affiliation(s)
- Shanjin Huang
- Department of Biological Sciences and The Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907-2064, USA
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Nemoda Z, Sahin-Tóth M. Chymotrypsin C (caldecrin) stimulates autoactivation of human cationic trypsinogen. J Biol Chem 2006; 281:11879-86. [PMID: 16505482 PMCID: PMC1586167 DOI: 10.1074/jbc.m600124200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Trypsin-mediated trypsinogen activation (autoactivation) facilitates digestive zymogen activation in the duodenum but may precipitate pancreatitis if it occurs prematurely in the pancreas. Autoactivation of human cationic trypsinogen is inhibited by a repulsive electrostatic interaction between the unique Asp218 on the surface of cationic trypsin and the conserved tetra-aspartate (Asp19-22) motif in the trypsinogen activation peptide (Nemoda, Z., and Sahin-Tóth, M. (2005) J. Biol. Chem. 280, 29645-29652). Here we describe that this interaction is regulated by chymotrypsin C (caldecrin), which can specifically cleave the Phe18-Asp19 peptide bond in the trypsinogen activation peptide and remove the N-terminal tripeptide. In contrast, chymotrypsin B, elastase 2A, or elastase 3A (proteinase E) are ineffective. Autoactivation of N-terminally truncated cationic trypsinogen is stimulated approximately 3-fold, and this effect is dependent on the presence of Asp218. Because chymotrypsinogen C is activated by trypsin, and chymotrypsin C stimulates trypsinogen activation, these reactions establish a positive feedback mechanism in the digestive enzyme cascade of humans. Furthermore, inappropriate activation of chymotrypsinogen C in the pancreas may contribute to the development of pancreatitis. Consistent with this notion, the pancreatitis-associated mutation A16V in cationic trypsinogen increases the rate of chymotrypsin C-mediated processing of the activation peptide 4-fold and causes accelerated trypsinogen activation in vitro.
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Affiliation(s)
| | - Miklós Sahin-Tóth
- Address correspondence to Miklós Sahin-Tóth, 715 Albany Street, Evans-433; Boston, MA 02118; Tel: (617) 414-1070; Fax: (617) 414-1041; E-mail:
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50
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Meadow ND, Savtchenko RS, Nezami A, Roseman S. Transient State Kinetics of Enzyme IICBGlc, a Glucose Transporter of the Phosphoenolpyruvate Phosphotransferase System of Escherichia coli. J Biol Chem 2005; 280:41872-80. [PMID: 16204242 DOI: 10.1074/jbc.m501440200] [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: 11/06/2022] Open
Abstract
During translocation across the cytoplasmic membrane of Escherichia coli, glucose is phosphorylated by phospho-IIA(Glc) and Enzyme IICB(Glc), the last two proteins in the phosphotransfer sequence of the phosphoenolpyruvate:glucose phosphotransferase system. Transient state (rapid quench) methods were used to determine the second order rate constants that describe the phosphotransfer reactions (phospho-IIA(Glc) to IICB(Glc) to Glc) and also the second order rate constants for the transfer from phospho-IIA(Glc) to molecularly cloned IIB(Glc), the soluble, cytoplasmic domain of IICB(Glc). The rate constants for the forward and reverse phosphotransfer reactions between IIA(Glc) and IICB(Glc) were 3.9 x 10(6) and 0.31 x 10(6) m(-1) s(-1), respectively, and the rate constant for the physiologically irreversible reaction between [P]IICB(Glc) and Glc was 3.2 x 10(6) m(-1) s(-1). From the rate constants, the equilibrium constants for the transfer of the phospho-group from His90 of [P]IIA(Glc) to the phosphorylation site Cys of IIB(Glc) or IICB(Glc) were found to be 3.5 and 12, respectively. These equilibrium constants signify that the thiophospho-group in these proteins has a high phosphotransfer potential, similar to that of the phosphohistidinyl phosphotransferase system proteins. In these studies, preparations of IICB(Glc) were invariably found to contain endogenous, firmly bound Glc (estimated K'(D) approximately 10(-7) m). The bound Glc was kinetically competent and was rapidly phosphorylated, indicating that IICB(Glc) has a random order, Bi Bi, substituted enzyme mechanism. The equilibrium constant for the binding of Glc was deduced from differences in the statistical goodness of fit of the phosphotransfer data to the kinetic model.
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Affiliation(s)
- Norman D Meadow
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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