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Pitsawong W, Chenprakhon P, Dhammaraj T, Medhanavyn D, Sucharitakul J, Tongsook C, van Berkel WJH, Chaiyen P, Miller AF. Tuning of p Ka values activates substrates in flavin-dependent aromatic hydroxylases. J Biol Chem 2020; 295:3965-3981. [PMID: 32014994 DOI: 10.1074/jbc.ra119.011884] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Hydroxylation of substituted phenols by flavin-dependent monooxygenases is the first step of their biotransformation in various microorganisms. The reaction is thought to proceed via electrophilic aromatic substitution, catalyzed by enzymatic deprotonation of substrate, in single-component hydroxylases that use flavin as a cofactor (group A). However, two-component hydroxylases (group D), which use reduced flavin as a co-substrate, are less amenable to spectroscopic investigation. Herein, we employed 19F NMR in conjunction with fluorinated substrate analogs to directly measure pKa values and to monitor protein events in hydroxylase active sites. We found that the single-component monooxygenase 3-hydroxybenzoate 6-hydroxylase (3HB6H) depresses the pKa of the bound substrate analog 4-fluoro-3-hydroxybenzoate (4F3HB) by 1.6 pH units, consistent with previously proposed mechanisms. 19F NMR was applied anaerobically to the two-component monooxygenase 4-hydroxyphenylacetate 3-hydroxylase (HPAH), revealing depression of the pKa of 3-fluoro-4-hydroxyphenylacetate by 2.5 pH units upon binding to the C2 component of HPAH. 19F NMR also revealed a pKa of 8.7 ± 0.05 that we attributed to an active-site residue involved in deprotonating bound substrate, and assigned to His-120 based on studies of protein variants. Thus, in both types of hydroxylases, we confirmed that binding favors the phenolate form of substrate. The 9 and 14 kJ/mol magnitudes of the effects for 3HB6H and HPAH-C2, respectively, are consistent with pKa tuning by one or more H-bonding interactions. Our implementation of 19F NMR in anaerobic samples is applicable to other two-component flavin-dependent hydroxylases and promises to expand our understanding of their catalytic mechanisms.
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Affiliation(s)
- Warintra Pitsawong
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055
| | - Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Taweesak Dhammaraj
- Faculty of Pharmacy, Mahasarakham University, Maha Sarakham 44150, Thailand
| | - Dheeradhach Medhanavyn
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok 10300, Thailand
| | - Chanakan Tongsook
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan Valley, 555 Moo 1 Payupnai, Wangchan, Rayong 21210, Thailand
| | - Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055
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Hoshino Y, Jibiki T, Nakamoto M, Miura Y. Reversible p K a Modulation of Carboxylic Acids in Temperature-Responsive Nanoparticles through Imprinted Electrostatic Interactions. ACS APPLIED MATERIALS & INTERFACES 2018; 10:31096-31105. [PMID: 30148598 DOI: 10.1021/acsami.8b11397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The acid dissociation constants (p Ka values) of Brønsted acids at the active sites of proteins are reversibly modulated by intramolecular electrostatic interactions with neighboring ions in a reaction cycle. The resulting p Ka shift is crucial for the proteins to capture, transfer, and release target ions. On the other hand, reversible p Ka modulation through electrostatic interactions in synthetic polymer materials has seldom been realized because the interactions are strongly shielded by solvation water molecules in aqueous media. Here, we prepared hydrogel nanoparticles (NPs) bearing carboxylic acid groups whose p Ka values can be reversibly modulated by electrostatic interactions with counterions in the particles. We found that the deprotonated states of the acids were stabilized by electrostatic interactions with countercations only when the acids and cations were both imprinted in hydrophobic microdomains in the NPs during polymerization. Cationic monomers, like primary amine- and guanidium group-containing monomers, which interacted strongly with growing NPs showed greater p Ka modulation than monomers that did not interact with the NPs, such as quaternary ammonium group-containing monomers. Modulation was enhanced when the guanidium moieties were protected with hydrophobic groups during polymerization, so that the guanidium ions were imprinted in the hydrophobic microdomains; the lowest p Ka of ∼4.0 was achieved as a result. The p Ka modulation of the acids could be reversibly removed by inducing a temperature-dependent volume phase transition of the gel NPs. These design principles are applicable to other stimuli-responsive materials and integral to the development of synthetic materials that can be used to capture, transport, and separate target ions.
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Affiliation(s)
- Yu Hoshino
- Department of Chemical Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Toshiki Jibiki
- Department of Chemical Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Masahiko Nakamoto
- Department of Chemical Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Yoshiko Miura
- Department of Chemical Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
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AKUTSU H. Dynamic mechanisms driving conformational conversions of the β and ε subunits involved in rotational catalysis of F 1-ATPase. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:630-647. [PMID: 29021512 PMCID: PMC5743862 DOI: 10.2183/pjab.93.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/16/2017] [Indexed: 05/26/2023]
Abstract
F-type ATPase is a ubiquitous molecular motor. Investigations on thermophilic F1-ATPase and its subunits, β and ε, by NMR were reviewed. Using specific isotope labeling, pKa of the putative catalytic carboxylate in β was estimated. Segmental isotope-labeling enabled us to monitor most residues of β, revealing that the conformational conversion from open to closed form of β on nucleotide binding found in ATPase was an intrinsic property of β and could work as a driving force of the rotational catalysis. A stepwise conformational change was driven by switching of the hydrogen bond networks involving Walker A and B motifs. Segmentally labeled ATPase provided a well resolved NMR spectra, revealing while the open form of β was identical for β monomer and ATPase, its closed form could be different. ATP-binding was also a critical factor in the conformational conversion of ε, an ATP hydrolysis inhibitor. Its structural elucidation was described.
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Affiliation(s)
- Hideo AKUTSU
- Institute for Protein Research, Osaka University, Osaka, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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Martín-García F, Mendieta-Moreno JI, Marcos-Alcalde I, Gómez-Puertas P, Mendieta J. Simulation of catalytic water activation in mitochondrial F1-ATPase using a hybrid quantum mechanics/molecular mechanics approach: an alternative role for β-Glu 188. Biochemistry 2013; 52:959-66. [PMID: 23320924 DOI: 10.1021/bi301109x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The use of quantum mechanics/molecular mechanics simulations to study the free energy landscape of the water activation at the catalytic site of mitochondrial F(1)-ATPase affords us insight into the generation of the nucleophile OH(-) prior to ATP hydrolysis. As a result, the ATP molecule was found to be the final proton acceptor. In the simulated pathway, the transfer of a proton to the nucleotide was not direct but occurred via a second water molecule in a manner similar to the Grotthuss mechanism proposed for proton diffusion. Residue β-Glu 188, previously described as the putative catalytic base, was found to be involved in the stabilization of a transient hydronium ion during water activation. Simulations in the absence of the carboxylate moiety of β-Glu 188 support this role.
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Affiliation(s)
- Fernando Martín-García
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/Nicolás Cabrera 1, Cantoblanco, Madrid, Spain
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Hotze EM, Tweten RK. Membrane assembly of the cholesterol-dependent cytolysin pore complex. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:1028-38. [PMID: 21835159 PMCID: PMC3243806 DOI: 10.1016/j.bbamem.2011.07.036] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 07/24/2011] [Indexed: 12/16/2022]
Abstract
The cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins that are produced, secreted and contribute to the pathogenesis of many species of Gram-positive bacteria. The assembly of the CDC pore-forming complex has been under intense study for the past 20 years. These studies have revealed a molecular mechanism of pore formation that exhibits many novel features. The CDCs form large β-barrel pore complexes that are assembled from 35 to 40 soluble CDC monomers. Pore formation is dependent on the presence of membrane cholesterol, which functions as the receptor for most CDCs. Cholesterol binding initiates significant secondary and tertiary structural changes in the monomers, which lead to the assembly of a large membrane embedded β-barrel pore complex. This review will focus on the molecular mechanism of assembly of the CDC membrane pore complex and how these studies have led to insights into the mechanism of pore formation for other pore-forming proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Eileen M. Hotze
- Department of Microbiology and Immunology, The University of Oklahoma Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Rodney K. Tweten
- Department of Microbiology and Immunology, The University of Oklahoma Sciences Center, Oklahoma City, Oklahoma 73104, USA
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Lukacs A, Haigney A, Brust R, Zhao RK, Stelling AL, Clark IP, Towrie M, Greetham GM, Meech SR, Tonge PJ. Photoexcitation of the blue light using FAD photoreceptor AppA results in ultrafast changes to the protein matrix. J Am Chem Soc 2011; 133:16893-900. [PMID: 21899315 DOI: 10.1021/ja2060098] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoexcitation of the flavin chromophore in the BLUF photosensor AppA results in a conformational change that leads to photosensor activation. This conformational change is mediated by a hydrogen-bonding network that surrounds the flavin, and photoexcitation is known to result in changes in the network that include a strengthening of hydrogen bonding to the flavin C4═O carbonyl group. Q63 is a key residue in the hydrogen-bonding network, and replacement of this residue with a glutamate results in a photoinactive mutant. While the ultrafast time-resolved infrared (TRIR) spectrum of Q63E AppA(BLUF) is characterized by flavin carbonyl modes at 1680 and 1650 cm(-1), which are similar in frequency to the analogous modes from the light activated state of the wild-type protein, a band is also observed in the TRIR spectrum at 1724 cm(-1) that is unambiguously assigned to the Q63E carboxylic acid based on U-(13)C labeling of the protein. Light absorption instantaneously (<100 fs) bleaches the 1724 cm(-1) band leading to a transient absorption at 1707 cm(-1). Because Q63E is not part of the isoalloxazine electronic transition, the shift in frequency must arise from a sub picosecond perturbation to the flavin binding pocket. The light-induced change in the frequency of the Q63E side chain is assigned to an increase in hydrogen-bond strength of 3 kcal mol(-1) caused by electronic reorganization of the isoalloxazine ring in the excited state, providing direct evidence that the protein matrix of AppA responds instantaneously to changes in the electronic structure of the chromophore and supporting a model for photoactivation of the wild-type protein that involves initial tautomerization of the Q63 side chain.
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Affiliation(s)
- Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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Schuerch DW, Wilson-Kubalek EM, Tweten RK. Molecular basis of listeriolysin O pH dependence. Proc Natl Acad Sci U S A 2005; 102:12537-42. [PMID: 16105950 PMCID: PMC1194900 DOI: 10.1073/pnas.0500558102] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Listeriolysin O (LLO) is a cholesterol-dependent cytolysin that is an essential virulence factor of Listeria monocytogenes. LLO pore-forming activity is pH-dependent; it is active at acidic pH (<6), but not at neutral pH. In contrast to other pH-dependent toxins, we have determined that LLO pore-forming activity is controlled by a rapid and irreversible denaturation of its structure at neutral pH at temperatures >30 degrees C. Rapid denaturation is triggered at neutral pH by the premature unfolding of the domain 3 transmembrane beta-hairpins; structures that normally form the transmembrane beta-barrel. A triad of acidic residues within domain 3 function as the pH sensor and initiate the denaturation of LLO by destabilizing the structure of domain 3. These studies provide a view of a molecular mechanism by which the activity of a bacterial toxin is regulated by pH.
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Affiliation(s)
- Daniel W Schuerch
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Baik SH, Michel F, Aghajari N, Haser R, Harayama S. Cooperative effect of two surface amino acid mutations (Q252L and E170K) in glucose dehydrogenase from Bacillus megaterium IWG3 on stabilization of its oligomeric state. Appl Environ Microbiol 2005; 71:3285-93. [PMID: 15933031 PMCID: PMC1151818 DOI: 10.1128/aem.71.6.3285-3293.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A thermostable glucose dehydrogenase (GlcDH) mutant of Bacillus megaterium IWG3 harboring the Q252L substitution (Y. Makino, S. Negoro, I. Urabe, and H. Okada, J. Biol. Chem. 264:6381-6385, 1989) is stable at pH values above 9, but only in the presence of 2 M NaCl. Another GlcDH mutant exhibiting increased stability at an alkaline pH in the absence of NaCl has been isolated previously (S.-H. Baik, T. Ide, H. Yoshida, O. Kagami, and S. Harayama, Appl. Microbiol. Biotechnol. 61:329-335, 2003). This mutant had two amino acid substitutions, Q252L and E170K. In the present study, we characterized three GlcDH mutants harboring the substitutions Q252L, E170K, and Q252L/E170K under low-salt conditions. The GlcDH mutant harboring two substitutions, Q252L/E170K, was stable, but mutants harboring a single substitution, either Q252L or E170K, were unstable at an alkaline pH. Gel filtration chromatography analyses demonstrated that the oligomeric state of the Q252/E170K enzyme was stable, while the tetramers of the enzymes harboring a single substitution (Q252L or E170K) dissociated into dimers at an alkaline pH. These results indicated that the Q252L and E170K substitutions synergistically strengthened the interaction at the dimer-dimer interface. The crystal structure of the E170K/Q252L mutant, determined at 2.0-angstroms resolution, showed that residues 170 and 252 are located in a hydrophobic cavity at the subunit-subunit interface. We concluded that these residues in the wild-type enzyme have thermodynamically unfavorable effects, while the Q252L and E170K substitutions increase the subunit-subunit interactions by stabilizing the hydrophobic cavity.
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Affiliation(s)
- Sang-Ho Baik
- Marine Biotechnology Institute, Heita Kamaishi, Iwate 026-0001, Japan.
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Muneyuki E, Noji H, Amano T, Masaike T, Yoshida M. F(0)F(1)-ATP synthase: general structural features of 'ATP-engine' and a problem on free energy transduction. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:467-81. [PMID: 10838059 DOI: 10.1016/s0005-2728(00)00095-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- E Muneyuki
- Research Laboratory of Resources Utilization, R-1, Tokyo Institute of Technology, Yokohama, Japan
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Abstract
The isolation of ATP synthase (F0F1) (82) and F0 (83) 34 years ago finally revealed that F0F1 is a motor composed of F0 (ion-motor, abc subunits) and F1 (ATP-motor, alpha 3 beta 3 gamma delta epsilon subunits) (Fig. 1). The single molecule videotape (4, 5, 65, 66) revealed that gamma epsilon axis of F1 rotates counterclockwise, proceeds by each 2 pi/3 step, and is driven by torque of 42 pN.nm (12) with nearly 100% efficiency (5) (Fig. 4). The motor is composed of a rotor (gamma epsilon-F0-c) and a stator (alpha 3 beta 3 delta-F0-ab), and the rotor is connected to a shaft (gamma epsilon). Since F0F1 is driven by delta microH+ (9, 10, 84), biophysical studies on stable TF0F1 (1, 7) are essential to elucidate the mechanism. These include nanomechanics (4, 5) (Fig. 4), crystallography (2, 3) (Figs. 2 and 3), NMR (51, 52), ESR (56), synchrotron analysis (3, 28), and electrophysiology (10, 25). The KmATP value of rotation is 0.8 microM, with the Vmax of 3.9 rps (5). This corresponds to the bi-site catalysis in proton transport by F0F1 (10, 70, 84). X-ray crystallography of MF1 (2) and the alpha 3 beta 3 oligomer of TF1 (3) (Fig. 2) together with mutation analyses revealed the role of residues in the rotation. The idea of elastic energy store is proposed in alpha 3 beta 3 gamma during the stepping time (up to a few sec) after the ATP binding. Biological studies have partially clarified the genetic and kinetic regulation of the rotation in MF1. Both theories (6, 7, 62, 64, 85) and the biological significance (17) of the intramolecular rotation of F0F1 await further studies, especially those of F0 and minor subunits.
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Affiliation(s)
- Y Kagawa
- Graduate School, Women's University of Nutrition, Saitama, Japan
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Kagawa Y, Hamamoto T. Intramolecular rotation in ATP synthase: dynamic and crystallographic studies on thermophilic F1. Biochem Biophys Res Commun 1997; 240:247-56. [PMID: 9388462 DOI: 10.1006/bbrc.1997.7574] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A single molecule of ATP synthase (F0F1) is by itself a rotary motor, the smallest ever found, and this biomotor is driven by an electrochemical potential of H+ (delta microH+). F0F1 is composed of an ion-conducting portion (F0) and a catalytic portion (F1). The major breakthroughs in studies on the mechanochemical coupling have been the direct observation of the rotation of a stable alpha 3 beta 3 gamma complex of thermophilic F1 (TF1), and X-ray crystallography of the alpha 3 beta 3 gamma portion of mitochondrial F1 (MF1) and the alpha 3 beta 3 oligomer of TF1. This review focuses on the dynamics of TF1, demonstrated by a crucial experiment. The torque of the rotation was estimated to be 42 pN.nm from the delta microH+ and frictional force. Important unsolved problems are the crystallography of F0, elastic energy conversion, and the stator and rotor of this biomotor.
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Affiliation(s)
- Y Kagawa
- Department of Biochemistry, Jichi Medical School, Tochigi, Japan.
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