1
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Glockzin K, Kostomiris D, Minnow YVT, Suthagar K, Clinch K, Gai S, Buckler JN, Schramm VL, Tyler PC, Meek TD, Katzfuss A. Kinetic Characterization and Inhibition of Trypanosoma cruzi Hypoxanthine–Guanine Phosphoribosyltransferases. Biochemistry 2022; 61:2088-2105. [PMID: 36193631 PMCID: PMC9536471 DOI: 10.1021/acs.biochem.2c00312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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Chagas disease, caused by the parasitic protozoan Trypanosoma cruzi, affects over 8 million people
worldwide. Current antiparasitic treatments for Chagas disease are
ineffective in treating advanced, chronic stages of the disease, and
are noted for their toxicity. Like most parasitic protozoa, T. cruzi is unable to synthesize purines de novo, and relies on the salvage of preformed purines
from the host. Hypoxanthine–guanine phosphoribosyltransferases
(HGPRTs) are enzymes that are critical for the salvage of preformed
purines, catalyzing the formation of inosine monophosphate (IMP) and
guanosine monophosphate (GMP) from the nucleobases hypoxanthine and
guanine, respectively. Due to the central role of HGPRTs in purine
salvage, these enzymes are promising targets for the development of
new treatment methods for Chagas disease. In this study, we characterized
two gene products in the T. cruzi CL
Brener strain that encodes enzymes with functionally identical HGPRT
activities in vitro: TcA (TcCLB.509693.70) and TcC
(TcCLB.506457.30). The TcC isozyme was kinetically characterized to
reveal mechanistic details on catalysis, including identification
of the rate-limiting step(s) of catalysis. Furthermore, we identified
and characterized inhibitors of T. cruzi HGPRTs originally developed as transition-state analogue inhibitors
(TSAIs) of Plasmodium falciparum hypoxanthine–guanine–xanthine
phosphoribosyltransferase (PfHGXPRT), where the most
potent compound bound to T. cruzi HGPRT
with low nanomolar affinity. Our results validated the repurposing
of TSAIs to serve as selective inhibitors for orthologous molecular
targets, where primary and secondary structures as well as putatively
common chemical mechanisms are conserved.
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Affiliation(s)
- Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Demetrios Kostomiris
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Yacoba V. T. Minnow
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1602, United States
| | - Kajitha Suthagar
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Keith Clinch
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Sinan Gai
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Joshua N. Buckler
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1602, United States
| | - Peter C. Tyler
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Thomas D. Meek
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
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2
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Shajhutdinova Z, Pashirova T, Masson P. Kinetic Processes in Enzymatic Nanoreactors for In Vivo Detoxification. Biomedicines 2022; 10:biomedicines10040784. [PMID: 35453533 PMCID: PMC9025091 DOI: 10.3390/biomedicines10040784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/20/2022] Open
Abstract
Enzymatic nanoreactors are enzyme-encapsulated nanobodies that are capable of performing biosynthetic or catabolic reactions. For this paper, we focused on therapeutic enzyme nanoreactors for the neutralization of toxicants, paying special attention to the inactivation of organophosphorus compounds (OP). Therapeutic enzymes that are capable of detoxifying OPs are known as bioscavengers. The encapsulation of injectable bioscavengers by nanoparticles was first used to prevent fast clearance and the immune response to heterologous enzymes. The aim of enzyme nanoreactors is also to provide a high concentration of the reactive enzyme in stable nanocontainers. Under these conditions, the detoxification reaction takes place inside the compartment, where the enzyme concentration is much higher than in the toxicant diffusing across the nanoreactor membrane. Thus, the determination of the concentration of the encapsulated enzyme is an important issue in nanoreactor biotechnology. The implications of second-order reaction conditions, the nanoreactor’s permeability in terms of substrates, and the reaction products and their possible osmotic, viscosity, and crowding effects are also examined.
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Affiliation(s)
- Zukhra Shajhutdinova
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, Kremlevskaya Str. 18, 420111 Kazan, Russia;
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia;
| | - Tatiana Pashirova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia;
| | - Patrick Masson
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, Kremlevskaya Str. 18, 420111 Kazan, Russia;
- Correspondence:
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3
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Lisitsa AE, Sukovatyi LA, Bartsev SI, Deeva AA, Kratasyuk VA, Nemtseva EV. Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction. Int J Mol Sci 2021; 22:8827. [PMID: 34445534 PMCID: PMC8396235 DOI: 10.3390/ijms22168827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important αGlu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.
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Affiliation(s)
- Albert E Lisitsa
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Lev A Sukovatyi
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Sergey I Bartsev
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Anna A Deeva
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Valentina A Kratasyuk
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
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4
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Merten H, Brandl F, Zimmermann M, Schaefer JV, Irpinio L, Sand KMK, Nilsen J, Andersen JT, Zangemeister-Wittke U, Plückthun A. Half-life extension of efficiently produced DARPin serum albumin fusions as a function of FcRn affinity and recycling. Eur J Pharm Biopharm 2021; 167:104-113. [PMID: 34303832 DOI: 10.1016/j.ejpb.2021.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022]
Abstract
Serum albumin shows slow clearance from circulation due to neonatal Fc receptor (FcRn)-mediated recycling and has been used for half-life extension. We report here fusions to a high-affinity DARPin, binding to Epithelial Cell Adhesion Molecule (EpCAM). We developed a novel, efficient expression system for such fusion proteins in Pichia pastoris with titers above 300 mg/L of lab-scale shake-flask culture. Since human serum albumin (HSA) does not bind to the murine FcRn, half-lives of therapeutic candidates are frequently measured in human FcRn transgenic mice, limiting useable tumor models. Additionally, serum albumins with extended half-life have been designed. We tested HSA7, motivated by its previously claimed extraordinarily long half-life in mice, which we could not confirm. Instead, we determined a half-life of only 29 h for HSA7, comparable to MSA. The fusion of HSA7 to a DARPin showed a similar half-life. To rationalize these findings, we measured binding kinetics and affinities to murine and human FcRn. Briefly, HSA7 showed affinity to murine FcRn only in the micromolar range, comparable to MSA to its cognate murine FcRn, and an affinity in the nanomolar range only to the human FcRn. This explains the comparable half-life of MSA and HSA7 in mice, while wild-type-HSA has a half-life of only 21 h, as it does not bind the murine FcRn and is not recycled. Thus, HSA-fusions with improved FcRn-affinity, such as HSA7, can be used for preclinical experiments in mice when FcRn transgenes cannot be used, as they reflect better the complex FcRn-mediated recycling and distribution mechanisms.
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Affiliation(s)
- Hannes Merten
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Fabian Brandl
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland; Institute of Pharmacology, University of Bern, Inselspital INO-F, 3010 Bern, Switzerland
| | - Martina Zimmermann
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Linda Irpinio
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Kine M K Sand
- Department of Immunology, University of Oslo and Oslo University Hospital Rikshospitalet, N-0372 Oslo, Norway; Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, N-0318 Oslo, Norway
| | - Jeannette Nilsen
- Department of Immunology, University of Oslo and Oslo University Hospital Rikshospitalet, N-0372 Oslo, Norway; Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, N-0318 Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, University of Oslo and Oslo University Hospital Rikshospitalet, N-0372 Oslo, Norway; Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, N-0318 Oslo, Norway
| | - Uwe Zangemeister-Wittke
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland; Institute of Pharmacology, University of Bern, Inselspital INO-F, 3010 Bern, Switzerland.
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
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5
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Ferreira C, Pinto MF, Macedo-Ribeiro S, Pereira PJB, Rocha FA, Martins PM. Protein crystals as a key for deciphering macromolecular crowding effects on biological reactions. Phys Chem Chem Phys 2020; 22:16143-16149. [PMID: 32638771 DOI: 10.1039/d0cp02469d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When placed in the same environment, biochemically unrelated macromolecules influence each other's biological function through macromolecular crowding (MC) effects. This has been illustrated in vitro by the effects of inert polymers on protein stability, protein structure, enzyme kinetics and protein aggregation kinetics. While a unified way to quantitatively characterize MC is still lacking, we show that the crystal solubility of lysozyme can be used to predict the influence of crowding agents on the catalytic efficiency of this enzyme. In order to capture general enthalpic effects, as well as hard entropic effects that are specific of large molecules, we tested sucrose and its cross-linked polymer Ficoll-70 as additives. Despite the different conditions of pH and ionic strength adopted, both the crystallization and the enzymatic assays point to an entropic contribution of approximately -1 kcal mol-1 caused by MC. Our results demonstrate that the thermodynamic activity of proteins is markedly increased by the reduction of accessible volume caused by the presence of macromolecular cosolutes. Unlike what is observed in protein folding studies, this MC effect cannot be reproduced using equivalent concentrations of monomeric crowding units. Applicable to any crystallizable protein, the thermodynamic interpretation of MC based on crystal solubility is expected to help in elucidating the full extent and importance of hard-type interactions in the crowded environment of the cell.
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Affiliation(s)
- Cecília Ferreira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria Filipa Pinto
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal and ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal and IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Fernando Alberto Rocha
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Pedro Miguel Martins
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal and IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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6
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Lang X, Hong X, Baker CA, Otto TC, Wheeldon I. Molecular binding scaffolds increase local substrate concentration enhancing the enzymatic hydrolysis of VX nerve agent. Biotechnol Bioeng 2020; 117:1970-1978. [PMID: 32239488 DOI: 10.1002/bit.27346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/25/2022]
Abstract
Kinetic enhancement of organophosphate hydrolysis is a long-standing challenge in catalysis. For prophylactic treatment against organophosphate exposure, enzymatic hydrolysis needs to occur at high rates in the presence of low substrate concentrations and enzymatic activity should persist over days and weeks. Here, the conjugation of small DNA scaffolds was used to introduce substrate binding sites with micromolar affinity to VX, paraoxon, and methyl-parathion in close proximity to the enzyme phosphotriesterase (PTE). The result was a decrease in KM and increase in the rate at low substrate concentrations. An optimized system for paraoxon hydrolysis decreased KM by 11-fold, with a corresponding increase in second-order rate constant. The initial rates of VX and methyl-parathion hydrolysis were also increased by 3.1- and 6.7-fold, respectively. The designed scaffolds not only increased the local substrate concentration, but they also resulted in increased stability and PTE-DNA particle size tuning between 25 and ~150 nm. The scaffold engineering approach taken here is focused on altering the local chemical and physical microenvironment around the enzyme and is therefore compatible with active site engineering via combinatorial and computational approaches.
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Affiliation(s)
- Xuye Lang
- Chemical and Environmental Engineering Department, University of California, Riverside, California
| | - Xiao Hong
- Biochemistry Department, University of California, Riverside, California
| | - Cetara A Baker
- U.S. Army Medical Research Institute of Chemical Defense, Aberdeen Proving Ground, Aberdeen, Maryland
| | - Tamara C Otto
- U.S. Army Medical Research Institute of Chemical Defense, Aberdeen Proving Ground, Aberdeen, Maryland
| | - Ian Wheeldon
- Chemical and Environmental Engineering Department, University of California, Riverside, California.,Center for Industrial Biotechnology, University of California, Riverside, California
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7
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Subedi BP, Fitzpatrick PF. Mutagenesis of an Active-Site Loop in Tryptophan Hydroxylase Dramatically Slows the Formation of an Early Intermediate in Catalysis. J Am Chem Soc 2018; 140:5185-5192. [PMID: 29589922 DOI: 10.1021/jacs.8b00936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solution studies of the aromatic amino acid hydroxylases are consistent with the FeIVO intermediate not forming until both the amino acid and tetrahydropterin substrates have bound. Structural studies have shown that the positions of active-site loops differs significantly between the free enzyme and the enzyme-amino acid-tetrahydropterin complex. In tryptophan hydroxylase (TrpH) these mobile loops contain residues 124-134 and 365-371, with a key interaction involving Ile366. The I366N mutation in TrpH results in decreases of 1-2 orders of magnitude in the kcat and kcat/ Km values. Single turnover analyses establish that the limiting rate constant for turnover is product release for the wild-type enzyme but is formation of the first detectable intermediate I in catalysis in the mutant enzyme. The mutation does not alter the kinetics of NO binding to the ternary complex nor does it uncouple FeIVO formation from amino acid hydroxylation. The effects on the kcat value of wild-type TrpH of changing viscosity are consistent with rate-limiting product release. While the effect of viscosity on the kcat/ KO2 value is small, consistent with reversible oxygen binding, the effects on the kcat/ Km values for tryptophan and the tetrahydropterin are large, with the latter value exceeding the expected limit and varying with the identity of the viscogen. In contrast, the kinetic parameters of I366N TrpH show small changes with viscosity. The results are consistent with binding of the amino acid and pterin substrate to form the ternary complex being directly coupled to closure of loops over the active site and formation of the reactive complex. The mutation destabilizes this initial event.
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Affiliation(s)
- Bishnu P Subedi
- Department of Biochemistry and Structural Biology , University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology , University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
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8
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Oppenheimer N, Stone HA. Effect of Hydrodynamic Interactions on Reaction Rates in Membranes. Biophys J 2017; 113:440-447. [PMID: 28746854 DOI: 10.1016/j.bpj.2017.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/04/2017] [Accepted: 06/07/2017] [Indexed: 11/18/2022] Open
Abstract
The Brownian motion of two particles in three dimensions serves as a model for predicting the diffusion-limited reaction rate, as first discussed by von Smoluchowski. Deutch and Felderhof extended the calculation to account for hydrodynamic interactions between the particles and the target, which results in a reduction of the rate coefficient by about half. Many chemical reactions take place in quasi-two-dimensional systems, such as on the membrane or surface of a cell. We perform a Smoluchowski-like calculation in a quasi-two-dimensional geometry, i.e., a membrane surrounded by fluid, and account for hydrodynamic interactions between the particles. We show that rate coefficients are reduced relative to the case of no interactions. The reduction is more pronounced than the three-dimensional case due to the long-range nature of two-dimensional flows.
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Affiliation(s)
- Naomi Oppenheimer
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey.
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey.
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9
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Gao Y, Roberts CC, Toop A, Chang CEA, Wheeldon I. Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis. Chembiochem 2016; 17:1430-6. [PMID: 27173175 DOI: 10.1002/cbic.201600224] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 12/12/2022]
Abstract
Understanding and controlling the molecular interactions between enzyme substrates and DNA nanostructures has important implications in the advancement of enzyme-DNA technologies as solutions in biocatalysis. Such hybrid nanostructures can be used to create enzyme systems with enhanced catalysis by controlling the local chemical and physical environments and the spatial organization of enzymes. Here we have used molecular simulations with corresponding experiments to describe a mechanism of enhanced catalysis due to locally increased substrate concentrations. With a series of DNA nanostructures conjugated to horseradish peroxidase, we show that binding interactions between substrates and the DNA structures can increase local substrate concentrations. Increased local substrate concentrations in HRP(DNA) nanostructures resulted in 2.9- and 2.4-fold decreases in the apparent Michaelis constants of tetramethylbenzidine and 4-aminophenol, substrates of HRP with tunable binding interactions to DNA nanostructures with dissociation constants in the micromolar range. Molecular simulations and kinetic analysis also revealed that increased local substrate concentrations enhanced the rates of substrate association. Identification of the mechanism of increased local concentration of substrates in close proximity to enzymes and their active sites adds to our understanding of nanostructured biocatalysis from which we can develop guidelines for enhancing catalysis in rationally designed systems.
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Affiliation(s)
- Yingning Gao
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Christopher C Roberts
- The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Aaron Toop
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ian Wheeldon
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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10
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Murakawa T, Hamaguchi A, Nakanishi S, Kataoka M, Nakai T, Kawano Y, Yamaguchi H, Hayashi H, Tanizawa K, Okajima T. Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions. J Biol Chem 2015; 290:23094-109. [PMID: 26269595 DOI: 10.1074/jbc.m115.662726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 11/06/2022] Open
Abstract
The catalytic reaction of copper amine oxidase proceeds through a ping-pong mechanism comprising two half-reactions. In the initial half-reaction, the substrate amine reduces the Tyr-derived cofactor, topa quinone (TPQ), to an aminoresorcinol form (TPQamr) that is in equilibrium with a semiquinone radical (TPQsq) via an intramolecular electron transfer to the active-site copper. We have analyzed this reductive half-reaction in crystals of the copper amine oxidase from Arthrobacter globiformis. Anerobic soaking of the crystals with an amine substrate shifted the equilibrium toward TPQsq in an "on-copper" conformation, in which the 4-OH group ligated axially to the copper center, which was probably reduced to Cu(I). When the crystals were soaked with substrate in the presence of halide ions, which act as uncompetitive and noncompetitive inhibitors with respect to the amine substrate and dioxygen, respectively, the equilibrium in the crystals shifted toward the "off-copper" conformation of TPQamr. The halide ion was bound to the axial position of the copper center, thereby preventing TPQamr from adopting the on-copper conformation. Furthermore, transient kinetic analyses in the presence of viscogen (glycerol) revealed that only the rate constant in the step of TPQamr/TPQsq interconversion is markedly affected by the viscogen, which probably perturbs the conformational change. These findings unequivocally demonstrate that TPQ undergoes large conformational changes during the reductive half-reaction.
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Affiliation(s)
- Takeshi Murakawa
- From the Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Akio Hamaguchi
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Shota Nakanishi
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Misumi Kataoka
- the School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan, the Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan
| | - Tadashi Nakai
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Yoshiaki Kawano
- the Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroshi Yamaguchi
- the School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan, the Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideyuki Hayashi
- the Department of Chemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan, and
| | - Katsuyuki Tanizawa
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, the Center of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Toshihide Okajima
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, the Department of Chemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan, and
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11
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Shoup DE. Diffusion-controlled reaction rates for two active sites on a sphere. BMC BIOPHYSICS 2014; 7:3. [PMID: 24982756 PMCID: PMC4058695 DOI: 10.1186/2046-1682-7-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/27/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND The diffusion-limited reaction rate of a uniform spherical reactant is generalized to anisotropic reactivity. Previous work has shown that the protein model of a uniform sphere is unsatisfactory in many cases. Competition of ligands binding to two active sites, on a spherical enzyme or cell is studied analytically. RESULTS The reaction rate constant is given for two sites at opposite ends of the species of interest. This is compared with twice the reaction rate for a single site. It is found that the competition between sites lowers the reaction rate over what is expected for two sites individually. Competition between sites does not show up, until the site half angle is greater than 30 degrees. CONCLUSIONS Competition between sites is negligible until the site size becomes large. The competitive effect grows as theta becomes large. The maximum effect is given for theta = pi/2.
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Affiliation(s)
- David E Shoup
- Mathematics and Science Department, Lincoln Land Community College, 5250 Shepherd Rd, P.O. Box 19256, Springfield, IL 62794, USA
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12
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Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies. Biochem J 2013; 454:387-99. [DOI: 10.1042/bj20130389] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.
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13
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Liu L, Wang N, Guo L. Convertible electron transfer pathways of cytochrome c at TiO2 quantum electrode. RSC Adv 2012. [DOI: 10.1039/c2ra01049f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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14
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Huff GS, Doncheva IS, Brinkley DW, Angeles-Boza AM, Mukherjee A, Cramer CJ, Roth JP. Experimental and Computational Investigations of Oxygen Reactivity in a Heme and Tyrosyl Radical-Containing Fatty Acid α-(Di)oxygenase. Biochemistry 2011; 50:7375-89. [DOI: 10.1021/bi201016h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Gregory S. Huff
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Irina S. Doncheva
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis,
Minnesota 55455, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
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15
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Thibodeaux CJ, Liu HW. Mechanistic studies of 1-aminocyclopropane-1-carboxylate deaminase: characterization of an unusual pyridoxal 5'-phosphate-dependent reaction. Biochemistry 2011; 50:1950-62. [PMID: 21244019 DOI: 10.1021/bi101927s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that cleaves the cyclopropane ring of ACC, to give α-ketobutyric acid and ammonia as products. The cleavage of the C(α)-C(β) bond of an amino acid substrate is a rare event in PLP-dependent enzyme catalysis. Potential chemical mechanisms involving nucleophile- or acid-catalyzed cyclopropane ring opening have been proposed for the unusual transformation catalyzed by ACCD, but the actual mode of cyclopropane ring cleavage remains obscure. In this report, we aim to elucidate the mechanistic features of ACCD catalysis by investigating the kinetic properties of ACCD from Pseudomonas sp. ACP and several of its mutant enzymes. Our studies suggest that the pK(a) of the conserved active site residue, Tyr294, is lowered by a hydrogen bonding interaction with a second conserved residue, Tyr268. This allows Tyr294 to deprotonate the incoming amino group of ACC to initiate the aldimine exchange reaction between ACC and the PLP coenzyme and also likely helps to activate Tyr294 for a role as a nucleophile to attack and cleave the cyclopropane ring of the substrate. In addition, solvent kinetic isotope effect (KIE), proton inventory, and (13)C KIE studies of the wild type enzyme suggest that the C(α)-C(β) bond cleavage step in the chemical mechanism is at least partially rate-limiting under k(cat)/K(m) conditions and is likely preceded in the mechanism by a partially rate-limiting step involving the conversion of a stable gem-diamine intermediate into a reactive external aldimine intermediate that is poised for cyclopropane ring cleavage. When viewed within the context of previous mechanistic and structural studies of ACCD enzymes, our studies are most consistent with a mode of cyclopropane ring cleavage involving nucleophilic catalysis by Tyr294.
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Affiliation(s)
- Christopher J Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy, Department of Chemistry and Biochemistry, and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, United States
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16
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Streit TM, Borazjani A, Lentz SE, Wierdl M, Potter PM, Gwaltney SR, Ross MK. Evaluation of the ‘side door’ in carboxylesterase-mediated catalysis and inhibition. Biol Chem 2008; 389:149-62. [DOI: 10.1515/bc.2008.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Structures of mammalian carboxylesterases (CEs) reveal the presence of a ‘side door’ that is proposed to act as an alternative pore for the trafficking of substrates and products. p-Nitrobenzyl esterase (pnb CE) from Bacillus subtilis exhibits close structural homology and a similar side-door domain as mammalian CEs. We investigated the role of a specific ‘gate’ residue at the side door (i.e., Leu 362) during pnb CE-catalyzed hydrolysis of model esters, pesticides, and lipids. Recombinant pnb CE proteins containing mutations at position 362 demonstrated markedly lower k
cat and k
cat/K
m values. The mutation with the most significant impact on catalysis was the L362R mutant (k
cat/K
m was 22-fold lower). Moreover, the ability of the L362R mutant to be inhibited by organophosphates (OP) was also lower. Investigation into the altered catalytic proficiency using pH-activity studies indicated that the catalytic triad of the mutant enzyme was preserved. Furthermore, viscosity variation and carbamate inhibition experiments indicated that rates of substrate association and acylation/deacylation were lower. Finally, recombinant CEs were found to possess lipolytic activity toward cholesteryl oleate and 2-arachidonylglycerol. In summary, the L362R mutant CE markedly slowed the rate of ester hydrolysis and was less sensitive to OP inhibition. The apparent causes of the diminished catalysis are discussed.
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17
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Tworowski D, Feldman AV, Safro MG. Electrostatic potential of aminoacyl-tRNA synthetase navigates tRNA on its pathway to the binding site. J Mol Biol 2005; 350:866-82. [PMID: 15964014 DOI: 10.1016/j.jmb.2005.05.051] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Revised: 05/17/2005] [Accepted: 05/19/2005] [Indexed: 10/25/2022]
Abstract
In the first stage of a diffusion-controlled enzymatic reaction, aminoacyl-tRNA synthetases (aaRSs) interact with cognate tRNAs forming non-specific encounters. The aaRSs catalyzing the same overall aminoacylation reaction vary greatly in subunit organization, structural domain composition and amino acid sequence. The diffusional association of aaRS and tRNA was found to be governed by long-range electrostatic interactions when the homogeneous negative potential of tRNA fits to the patches of positive potential produced by aaRS; one patch for each tRNA substrate molecule. Considering aaRS as a molecule with anisotropic reactivity and on the basis of continuum electrostatics and Smoluchowski's theory, the reaction conditions for tRNA-aaRS diffusional encounters were formulated. The domains, categorized as enzymatically relevant, appeared to be non-essential for field sculpturing at long distances. On the other hand, a set of complementary domains exerts primary control on the aaRS isopotential surface formation. Subdividing the aaRS charged residues into native, conservative and non-conservative subsets, we evaluated the contribution of each group to long-range electrostatic potential. Surprisingly, the electrostatic potential landscapes generated by native and non-conservative subsets are fairly similar, thus suggesting the non-conservative subset is developed specifically for efficient tRNA attraction.
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Affiliation(s)
- Dmitry Tworowski
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
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18
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Peschke M, Verkerk UH, Kebarle P. Features of the ESI mechanism that affect the observation of multiply charged noncovalent protein complexes and the determination of the association constant by the titration method. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1424-1434. [PMID: 15465355 DOI: 10.1016/j.jasms.2004.05.005] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Revised: 04/30/2004] [Accepted: 05/04/2004] [Indexed: 05/24/2023]
Abstract
Several factors, attributable to the ESIMS mechanism, that can affect the assumptions of the titration method are examined: (1) The assumption that the concentrations in solution of the protein P, the ligand L, and the complex PL are proportional to the respective ion intensities observed with ESIMS, is examined with experiments in which ion intensities of two non-interacting proteins are compared with the respective concentrations. The intensities are found to be approximately proportional to the concentrations. The proportionality factors are found to increase as the mass of the protein is decreased. Very small proteins have much higher intensities. The results suggest that it is preferable to use only the intensity ratio of PL and P, whose masses are very close to each other when L is small, to determine the association constant KA in solution. (2) From the charge residue model (CRM) one expects that the solution will experience a very large increase of concentration due to evaporation of the precursor droplets, before the proteins P and PL are produced in the gas phase. This can shift the equilibrium in the droplets: P + L = PL, towards PL. Analysis of the droplet evaporation history shows that such a shift is not likely, because the time of droplet evolution is very short, only several micros, and the equilibrium relaxation time is much longer. (3) The droplet history shows that unreacted P and L can be often present together in the same droplet. On complete evaporation of such droplets L will land on P leading to PL and this effect will lead to values of KA that are too high. However, it is argued that mostly accidental, weakly bonded, complexes will form and these will dissociate in the clean up stages (heated transfer capillary and CAD region). Thus only very small errors are expected due to this cause. (4) Some PL complexes may have bonding that is too weak in the gas phase even though they have KA values in solution that predict high solution PL yields. In this case the PL complexes may decompose in the clean up stages and not be observed with sufficient intensity in the mass spectrum. This will lead to KA values that are too low. The effect is expected for complexes that involve significant hydrophobic interaction that leads to high stability of the complex in solution but low stability in the gas phase. The titration method is not suited for such systems.
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Affiliation(s)
- Michael Peschke
- Department of Chemistry, E3-44, University of Alberta, T6G 2G2, Edmonton, Alberta, Canada
| | - Udo H Verkerk
- Department of Chemistry, E3-44, University of Alberta, T6G 2G2, Edmonton, Alberta, Canada
| | - Paul Kebarle
- Department of Chemistry, E3-44, University of Alberta, T6G 2G2, Edmonton, Alberta, Canada.
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19
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Jia H, Zhu G, Wang P. Catalytic behaviors of enzymes attached to nanoparticles: the effect of particle mobility. Biotechnol Bioeng 2004; 84:406-14. [PMID: 14574697 DOI: 10.1002/bit.10781] [Citation(s) in RCA: 273] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nanoparticles provide an ideal remedy to the usually contradictory issues encountered in the optimization of immobilized enzymes: minimum diffusional limitation, maximum surface area per unit mass, and high effective enzyme loading. In addition to the promising performance features, the unique solution behaviors of the nanoparticles also point to a transitional region between the heterogeneous (with immobilized enzymes) and homogeneous (with soluble free enzymes) catalysis. The particle mobility, which is related to particle size and solution viscosity through Stokes-Einstein equation, may impact the reaction kinetics according to the collision theory. The mobility-activity relationship was examined through experimental studies and theoretical modeling in the present work. Polystyrene particles with diameters ranging from 110-1000 nm were prepared. A model enzyme, alpha-chymotrypsin, was covalently attached to the nanoparticles up to 6.6 wt%. The collision theory model was found feasible in correlating the catalytic activities of particles to particle size and solution viscosity. Changes in the size of particles and the viscosity of reaction media, which all affect the mobility of the enzyme catalyst, evidently altered the intrinsic activity of the particle-attached enzyme. Compared to K(M), k(cat) appeared to be less sensitive to particle size and viscosity.
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Affiliation(s)
- Hongfei Jia
- Department of Chemical Engineering, The University of Akron, Akron, Ohio 44325-3906, USA
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20
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Lonhienne TGA, Reilly PEB, Winzor DJ. Further evidence for the reliance of catalysis by rabbit muscle pyruvate kinase upon isomerization of the ternary complex between enzyme and products. Biophys Chem 2003; 104:189-98. [PMID: 12834837 DOI: 10.1016/s0301-4622(02)00366-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Isothermal calorimetry has been used to examine the effect of thermodynamic non-ideality on the kinetics of catalysis by rabbit muscle pyruvate kinase as the result of molecular crowding by inert cosolutes. The investigation, designed to detect substrate-mediated isomerization of pyruvate kinase, has revealed a 15% enhancement of maximal velocity by supplementation of reaction mixtures with 0.1 M proline, glycine or sorbitol. This effect of thermodynamic non-ideality implicates the existence of a substrate-induced conformational change that is governed by a minor volume decrease and a very small isomerization constant; and hence, substantiates earlier inferences that the rate-determining step in pyruvate kinase kinetics is isomerization of the ternary enzyme product complex rather than the release of products.
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Affiliation(s)
- Thierry G A Lonhienne
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Qld 4072, Australia
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21
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Park C, Raines RT. Catalysis by ribonuclease A is limited by the rate of substrate association. Biochemistry 2003; 42:3509-18. [PMID: 12653555 DOI: 10.1021/bi026076k] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The value of k(cat)/K(M) for catalysis of RNA cleavage by ribonuclease (RNase) A can exceed 10(9) M(-1) s(-1) in a solution of low salt concentration. This value approaches that expected for the diffusional encounter of the enzyme and its substrate. To reveal the physicochemical constraints upon catalysis by RNase A, the effects of salt concentration, pH, solvent isotope, and solvent viscosity on catalysis were determined with synthetic substrates that bind to all of the enzymic subsites and thereby enable a meaningful analysis. The pK(a) values determined from pH-k(cat)/K(M) profiles at 0.010, 0.20, and 1.0 M NaCl are inconsistent with the known macroscopic pK(a) values of RNase A. This incongruity indicates that catalysis of RNA cleavage by RNase A is limited by the rate of substrate association, even at 1.0 M NaCl. The effect of solvent isotope and solvent viscosity on catalysis support this conclusion. The data are consistent with a mechanism in which RNase A associates with RNA in an intermediate complex, which is stabilized by Coulombic interactions, prior to the formation of a Michaelis complex. Thus, RNase A has evolved to become an enzyme limited by physics rather than chemistry, a requisite attribute of a perfect catalyst.
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Affiliation(s)
- Chiwook Park
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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22
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Lonhienne TGA, Jackson CM, Winzor DJ. Thermodynamic non-ideality as an alternative source of the effect of sucrose on the thrombin-catalyzed hydrolysis of peptide p-nitroanilide substrates. Biophys Chem 2003; 103:259-69. [PMID: 12727288 DOI: 10.1016/s0301-4622(02)00322-8] [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: 12/01/2022]
Abstract
The inhibitory effect of sucrose on the kinetics of thrombin-catalyzed hydrolysis of the chromogenic substrate S-2238 (D-phenylalanyl-pipecolyl-arginoyl-p-nitroanilide) is re-examined as a possible consequence of thermodynamic non-ideality-an inhibition originally attributed to the increased viscosity of reaction mixtures. However, those published results may also be rationalized in terms of the suppression of a substrate-induced isomerization of thrombin to a slightly more expanded (or more asymmetric) transition state prior to the irreversible kinetic steps that lead to substrate hydrolysis. This reinterpretation of the kinetic results solely in terms of molecular crowding does not signify the lack of an effect of viscosity on any reaction step(s) subject to diffusion control. Instead, it highlights the need for development of analytical procedures that can accommodate the concomitant operation of thermodynamic non-ideality and viscosity effects.
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Affiliation(s)
- Thierry G A Lonhienne
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
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23
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Wu H, Zheng Y, Wang ZX. Evaluation of the catalytic mechanism of the p21-activated protein kinase PAK2. Biochemistry 2003; 42:1129-39. [PMID: 12549935 DOI: 10.1021/bi026857l] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The p21-activated kinases (PAKs) play important roles in diverse cellular processes. In the present study, we provide an in-depth kinetic analysis of one of the PAK family members, PAK2, in phosphorylation of a protein substrate, myelin basic protein (MBP), and a synthetic peptide substrate derived from LIM kinase, LIMKtide. Steady-state kinetic analysis of the initial reaction velocity of PAK2 phosphorylation of MBP is consistent with both randomly and compulsorily ordered mechanisms. Further kinetic studies carried out in various concentrations of sucrose revealed that solvent viscosities had no effect on k(cat)/K(m) for either ATP or MBP while k(cat) was highly sensitive to solvent viscosity, indicating that the enzymatic phosphorylation by PAK2 can be best interpreted by a rapid-equilibrium random bi-bi reaction model, and k(cat) is partially limited by both phosphoryl group transfer (31 s(-)(1)) and the product release (19 s(-)(1)). In the phosphorylation of LIMKtide, both k(cat) and k(cat)/K(m) were insensitive to solvent viscosity, and the product release (86 s(-)(1)) was much faster than the phosphoryl group transfer step (19 s(-)(1)). These studies suggest that the release of phospho-MBP product is likely partially rate determining for the PAK2-catalyzed reaction since the dissociation rate of products from the PAK2 active site for LIMKtide phosphorylation differs from that of MBP significantly. Such a mechanism is in contrast to the previously established kinetics for the phosphorylation of peptide substrates by cAMP-dependent kinase, in which this process is limited by the release of ADP but not the phospho-peptide product. These results complement previous structure-function studies of PAKs and provide important insight for mechanistic interpretation of the kinase functions.
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Affiliation(s)
- Hao Wu
- National Laboratory of Biomacromolecules, Center for Molecular Biology, Institute of Biophysics, Academia Sinica, Beijing 100101, People's Republic of China
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24
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Abstract
A simple assumption allows the prediction of the numerical value for a 'universal' limiting kinetic rate for wholly diffusion-limited reactions between small neutral molecules and macromolecules. This prediction is compared with appropriate experimental data for binding of ligands to myoglobin and to enzymes. It is shown that in the absence of electrostatic effects, this limit is approached but not exceeded. The model also makes very specific predictions concerning the viscosity and temperature dependence of such reactions.
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Affiliation(s)
- K E van Holde
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA.
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25
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Khandelwal P, Keliikuli K, Smith CL, Saper MA, Zuiderweg ERP. Solution structure and phosphopeptide binding to the N-terminal domain of Yersinia YopH: comparison with a crystal structure. Biochemistry 2002; 41:11425-37. [PMID: 12234185 DOI: 10.1021/bi026333l] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Virulence of pathogenic bacteria of the genus Yersinia requires the injection of six effector proteins into the cytoplasm of host cells. The amino-terminal domain of one of these effectors, the tyrosine phosphatase YopH, is essential for translocation of YopH, as well as for targeting it to phosphotyrosine-containing substrates of the type pYxxP. We report the high-resolution solution structure of the N-terminal domain (residues 1-129) from the Yersinia pseudotuberculosis YopH (YopH-NT) in complex with N-acetyl-DEpYDDPF-NH(2), a peptide derived from an in vivo protein substrate. In contrast to the domain-swapped dimer observed in a crystal structure of the same protein (Smith, C. L., Khandelwal, P., Keliikuli, K., Zuiderweg, E. R. P., and Saper, M. A. (2001) Mol. Microbiol. 42, 967-979), YopH-NT is monomeric in solution. The peptide binding site is located on a beta-hairpin that becomes the crossover point in the dimer structure. The binding site has several characteristics that are reminiscent of SH2 domains, which also bind to pYxxP sequences.
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Affiliation(s)
- Purnima Khandelwal
- Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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26
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Stevenson LM, Deal MS, Hagopian JC, Lew J. Activation mechanism of CDK2: role of cyclin binding versus phosphorylation. Biochemistry 2002; 41:8528-34. [PMID: 12081504 DOI: 10.1021/bi025812h] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation of the cyclin-dependent kinases is a two-step process involving cyclin binding followed by phosphorylation at a conserved threonine residue within the kinase activation loop. In this study, we describe the separate roles of cyclin A binding versus phosphorylation in the overall activation mechanism of CDK2. Interaction of CDK2 with cyclin A results in a partially active complex that is moderately defective in the binding of the protein substrate, but not ATP, and severely defective in both phosphoryl group transfer and turnover. Alternatively, phosphorylation of the CDK2 monomer also results in a partially activated species, but one that is severely (> or = 480-fold) defective in substrate binding exclusively. Catalytic turnover in the phosphorylated CDK2 monomer is largely unimpaired (approximately 8-fold lower). Our data support a model for the activation of CDK2 in vivo, in which interaction of unphosphorylated CDK2 with cyclin A serves to configure the active site for ground-state binding of both ATP and the protein substrate, and further aligns ATP in the transition state for phosphoryl transfer. Optimizing the alignment of protein substrates in the phosphoryl transfer reaction is the principal role of phosphorylation at Thr(160).
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Affiliation(s)
- Lisa M Stevenson
- Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, California 93106, USA
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27
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Shih MJ, Edinger JW, Creighton DJ. Diffusion-dependent kinetic properties of glyoxalase I and estimates of the steady-state concentrations of glyoxalase-pathway intermediates in glycolyzing erythrocytes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:852-7. [PMID: 9108256 DOI: 10.1111/j.1432-1033.1997.00852.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The diffusion-dependent kinetic properties of the yeast glyoxalase I reaction have been measured by means of viscosometric methods. For the glyoxalase-I-catalyzed isomerization of glutathione (GSH)-methylglyoxal thiohemiacetal to S-D-lactoylglutathione, the k(cat)/Km (3.5 x 10(6) M(-1) s(-1), pH 7, 25 degrees C) undergoes a progressive decrease in magnitude with increasing solution viscosity, using sucrose as a viscogenic agent. The viscosity effect is unlikely to be due to a sucrose-induced change in the intrinsic kinetic properties of the enzyme, as the magnitude of k(cat)/Km for the slow substrate GSH-t-butylglyoxal thiohemiacetal (3.5 x 10(3) M(-1) s(-1), pH 7, 25 degrees C) is independent of solution viscosity. Quantitative treatment of the data by means of the Stokes-Einstein diffusion law suggests that catalysis will be about 50% diffusion limited under conditions where [substrate] << Km; the encounter complex between enzyme and substrate partitions nearly equally between product formation and dissociation to form free enzyme and substrate. In a related study, the steady-state concentrations of glyoxalase-pathway intermediates in glycolyzing human erythrocytes are estimated to be in the nanomolar concentration range, on the basis of published values for the activities of glyoxalase I and glyoxalase II in lysed erythrocytes and the steady-state rate of formation of D-lactate in intact erythrocytes. This is consistent with a model of the glyoxalase pathway in which the enzyme-catalyzed steps are significantly diffusion limited under physiological conditions.
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Affiliation(s)
- M J Shih
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore 21228, USA
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28
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29
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Wang C, Lee TR, Lawrence DS, Adams JA. Rate-determining steps for tyrosine phosphorylation by the kinase domain of v-fps. Biochemistry 1996; 35:1533-9. [PMID: 8634284 DOI: 10.1021/bi952435i] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The rate-determining steps in the phosphorylation of four tyrosine-containing peptides by the kinase domain of the nonreceptor tyrosine protein kinase v-fps were measured using viscosometric methods. The peptides were phosphorylated by a fusion protein of glutathione-S-transferase and the kinase domain of v-fps (GST-kin) and the initial velocities were determined by a coupled enzyme assay. Peptides I (EEEIYEEIE), II (EAEIYEAIE), and III (DADIYDAID) were phosphorylated by GST-kin with similar kinetic constants. The viscosogens, glycerol and sucrose, were found to have intermediate effects on kcat and no effect on kcat/Kpeptide for the phosphorylation of these three peptides. The data are interpreted according to the Stokes-Einstein equation and a simple three-step mechanism involving substrate binding, phosphoryl group transfer, and net product release. Two competitive inhibitors (EAEIFEAIE and DADIFDAID) exhibited K1 values that are 6-10-fold higher than the Kpeptide values for their analogous peptide substrates. The data imply that peptides I-III are in rapid equilibrium with the enzyme and that kcat is partially limited by both phosphoryl group transfer (40-100 s-1) and product release (17-22 s-1). GST-kin phosphorylates peptide IV (R5AENLEYamide) with a low Km (100 microM) and a kcat that is 40-fold lower than that for peptide I. No effect of solvent viscosity was observed for the phosphorylation of this peptide on either kcat or kcat/Kpeptide. This suggests that highly viscous solutions do not perturb structure and that the rate-determining step for this poor substrate is phosphoryl group transfer. The data indicate that the kinase domain of v-fps phosphorylates its best substrate with a chemical rate constant that is at least 5-fold lower than that for the serine-specific cAMP-dependent protein kinase and its best substrate LRRASLG (Adams & Taylor, 1992). Interestingly, both enzymes exhibit a similar affinity for their substrates and both enzymes release their products at a similar rate. This implies that the differences in catalytic efficiency between serine- and tyrosine-specific protein kinases lie exclusively in the rate constants for phosphoryl group transfer and not in substrate absorption or product desorption.
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Affiliation(s)
- C Wang
- Department of Chemistry, San Diego State University, California 92182-1030, USA
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Bakovic M, Dunford HB. pH and temperature dependence of the rate of compound I formation from the reaction of prostaglandin endoperoxide synthase with hydrogen peroxide. Biochem Cell Biol 1996; 74:117-24. [PMID: 9035685 DOI: 10.1139/o96-013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The formation of primary oxidized compound of prostaglandin endoperoxide synthase, compound I, was studied as a function of pH and temperature using hydrogen peroxide as a substrate. Analysis of the results indicates that compound I formation is influenced by an ionizable group with a pKa of 4.06 +/- 0.04. The protonated form of hydrogen peroxide preferentially reacts with the unprotonated form of the enzyme over the pH range of 3.5 to 9.1, suggesting the importance of acid-base catalysis for compound I formation. The second-order rate constant for the reaction of the enzyme with hydrogen peroxide in the pH-independent region is (4.6 +/- 0.2) x 10(5) M-1 S-1 at an ionic strength of 0.1 M and temperature of 4.0 +/- 0.2 degrees C. The effect of temperature on the rate of compound I formation was studied from 3.4 to 24.1 degrees C in the pH-independent region (pH 6.98) and at a constant ionic strength of 0.1 M. The kinetic parameters obtained from the temperature dependence are the following: Arrhenius activation energy, Ea = 102 +/- 5 kJ/mol; free energy of activation, delta G++, 36 +/- 3 kJ/mol; enthalpy of activation, delta H++, 100 +/- 5 kJ/mol; entropy of activation, delta S++, 215 +/- 9 J/mol K. These activation values are very different from those obtained for the reactions of other peroxidases and catalases with hydrogen peroxide, indicating profound differences in active site structure.
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Affiliation(s)
- M Bakovic
- Department of Chemistry, University of Alberta, Edmonton, Canada
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Stone SR, Morrison JF. Dihydrofolate reductase from Escherichia coli: the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates. Biochemistry 1988; 27:5493-9. [PMID: 3052577 DOI: 10.1021/bi00415a016] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Kinetic studies on the reaction catalyzed by dihydrofolate reductase from Escherichia coli have been undertaken with the aim of characterizing further the kinetic mechanism of the reaction. For this purpose, the kinetic properties of substrates were determined by measurement of (a) initial velocities over a wide range of substrate concentrations and (b) the stickiness of substrates in ternary enzyme complexes. Stickiness is defined as the rate at which a substrate reacts to give products relative to the rate at which that substrate dissociates. Stickiness was determined by varying the viscosity of reaction mixtures and the concentration of one substrate in the presence of a saturating concentration of the other substrate. The results indicate that NADPH is sticky in the enzyme-NADPH-dihydrofolate complex, while dihydrofolate is much less sticky in this complex. At higher concentrations, NADPH functions as an activator through the formation of an enzyme-NADPH-tetrahydrofolate from which tetrahydrofolate is released more rapidly than from an enzyme-tetrahydrofolate complex. Higher concentrations of dihydrofolate also cause enzyme activation, and it appears that this effect is due to the ability of dihydrofolate to displace tetrahydrofolate from a binary enzyme complex through the formation of a transitory enzyme-tetrahydrofolate-dihydrofolate complex. As NADPH and dihydrofolate function as activators and as NADPH behaves as a sticky substrate, the kinetic mechanism of the dihydrofolate reductase reaction with the natural substrates is steady-state random. By contrast with NADPH, reduced 3-acetylpyridine adenine dinucleotide phosphate exhibits only slight stickiness and does not function as an activator.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S R Stone
- Department of Biochemistry, John Curtin School of Medical Research, Australian National University, Canberra City
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Dunford HB, Hasinoff BB. On the rates of enzymatic, protein and model compound reactions: the importance of diffusion control. J Inorg Biochem 1986; 28:263-9. [PMID: 3027256 DOI: 10.1016/0162-0134(86)80090-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A meaningful method of comparison is suggested for saturation kinetics, typical of enzyme-catalyzed reactions, and nonsaturation kinetics, often typical of model compound reactions. True diffusion-controlled reactions do not give saturation behavior; but enzymes may need saturation behavior to attain selectivity and stereospecificity for complicated substrates or for reactions beyond the complexity of electron transfer. However, the diffusion controlled limit provides a better reference point for rate comparisons than does the rate of uncatalyzed reaction. The failure of the Stokes-Einstein equation for small substrates is documented, as are ways of circumventing the problem. Advantages and pitfalls in the use of viscosogens to test for diffusion control are delineated. Finally, the possible advantages of surface diffusion for an enzyme, but lack of experimental evidence, is discussed.
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Hess S, Monchick L. A simple analytic model of the diffusion controlled reaction rates of asymmetric molecules. J Chem Phys 1986. [DOI: 10.1063/1.450479] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bazelyansky M, Robey E, Kirsch JF. Fractional diffusion-limited component of reactions catalyzed by acetylcholinesterase. Biochemistry 1986; 25:125-30. [PMID: 3954986 DOI: 10.1021/bi00349a019] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The values of kcat/Km for the reactions of four substrates, p-nitrophenyl acetate (PNPA), propionyl-beta-methylthiocholine (PrMSCh), 3,3-dimethylbutyl thioacetate (DBTA), and acetylthiocholine (AcSCh), with acetylcholinesterase were determined as a function of increasing viscosity (eta rel) in sucrose-containing and in glycerol-containing buffers. Glycerol, or possibly some contaminant of it, was found to be a nonspecific inhibitor and sucrose a nonspecific activator of the enzyme as reflected in the dependence of kcat/Km values measured for PNPA and PrMSCh upon the concentration of these reagents. The rates of reactions of these two substrates, the first neutral and the second cationic, are chemically limited rather than diffusion limited, and they thus serve as quantitative controls or internal standards to monitor the effects of the viscosogens on the enzyme, which are not related to diffusion. The additional effect on kcat/Km over the controls observed for the rapidly reacting substrates AcSCh (cationic) and DBTA (neutral) serves as a measure of the extent to which these values of kcat/Km measure diffusion-controlled processes. The reaction rate of DBTA with the enzyme is 24% diffusion controlled as measured in glycerol-containing buffers and 16-20% as determined in sucrose-containing buffers, while that for AcSCh is 100% (in glycerol) and 24-40% (in sucrose) diffusion controlled.
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Interfacial electrochemistry of cytochrome c at tin oxide, indium oxide, gold, and platinum electrodes. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/s0022-0728(84)80193-x] [Citation(s) in RCA: 173] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Adediran SA, Dunford HB. Structure of horseradish peroxidase compound I. Kinetic evidence for the incorporation of one oxygen atom from the oxidizing substrate into the enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 132:147-50. [PMID: 6840076 DOI: 10.1111/j.1432-1033.1983.tb07339.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The kinetics of the reaction between horseradish peroxidase and p-nitroperbenzoic acid to form compound I have been studied at 25 degrees C in phosphate buffer pH 7.2 and ionic strength of 0.11 M by transient-state and steady-state methods. The second-order rate constant for compound I formation obtained by stopped-flow measurements at 403 nm is (3.7 +/- 0.2) x 10(7) M-1 s-1. For the disappearance of p-nitroperbenzoic acid and appearance of p-nitrobenzoic acid using steady-state kinetics measured at 265 nm the rate constant is (3.0 +/- 0.6) x 10(7) M-1 s-1. The results provide an independent confirmation that one and only one oxygen atom is incorporated from the oxidizing substrate into compound I.
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Sommer J, Jonah C, Fukuda R, Bersohn R. Production and subsequent second-order decomposition of protein disulfide anions lengthy collisions between proteins. J Mol Biol 1982; 159:721-44. [PMID: 6815333 DOI: 10.1016/0022-2836(82)90110-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Van De Waterbeemd JTM, Van Boekel CCAA, De Sévaux RLFM, Jansen ACA, Gerritsma KW. Transport in QSAR IV. ACTA ACUST UNITED AC 1981. [DOI: 10.1007/bf02193157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zuiderweg ER, Hamers LF, Rollema HS, de Bruin SH, Hilbers CW. 31P NMR study of the kinetics of binding of myo-inositol hexakisphosphate to human hemoglobin. Observation of fast-exchange kinetics in high-affinity systems. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 118:95-104. [PMID: 7285916 DOI: 10.1111/j.1432-1033.1981.tb05490.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The association and dissociation kinetics of the complexes of myo-inositol hexakisphosphate (P6-inositol) with deoxyhemoglobin (Hb) and carboxyhemoglobin (HbCO) have been investigated by 31P NMR between pH 6.8 and pH 5.5. These complexes represent high-affinity systems with binding constants varying between 10(5) M-1 and 2 X 10(9) M-1. 31P NMR spectra of P6-inositol were recorded in the presence of hemoglobin as a function of the P6-inositol/hemoglobin molar ratio. It appeared that the exchange of the polyphosphate molecule between the solution and the central cavity binding site is fast on the NMR time scale. This observation cannot be reconciled with a single-step binding mechanism of P6-inositol to hemoglobin. Analysis of the spectra revealed the occurrence of additional binding of P6-inositol to both Hb and HbCO. This binding was also observed in pH-state experiments performed at low ionic strength. 31P NMR experiments carried out with hemoglobin of which the alpha-chain N termini were carbamylated, strongly suggest that these termini constitute the additional binding site for P6-inositol. A model is proposed which accounts for the enhancement of exchange kinetics in these high-affinity systems. In this model a rapid migration is assumed for P6-inositol between the central cavity binding site and an entry/leaving site on the hemoglobin molecule. Based on this model 31P NMR linewidths and chemical shift patterns for this three-site exchange problem were calculated.
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