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Wang H, Liu X, Yan X, Du Y, Pu F, Ren J, Qu X. An ATPase-Mimicking MXene nanozyme pharmacologically breaks the ironclad defense system for ferroptosis cancer therapy. Biomaterials 2024; 307:122523. [PMID: 38432004 DOI: 10.1016/j.biomaterials.2024.122523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/04/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Anticancer nanomedicines used for ferroptosis therapy generally rely on the direct delivery of Fenton catalysts to drive lipid peroxidation in cancer cells. However, the therapeutic efficacy is limited by the ferroptosis resistance caused by the intracellular anti-ferroptotic signals. Herein, we report the intrinsic ATPase-mimicking activity of a vanadium carbide MXene nanozyme (PVCMs) to pharmacologically modulate the nuclear factor erythroid 2-related factor 2 (Nrf2) program, which is the master anti-ferroptotic mediator in the ironclad defense system in triple-negative breast cancer (TNBC) cells. The PVCMs perform high ATPase-like activity that can effectively and selectively catalyze the dephosphorylation of ATP to generate ADP. Through a cascade mechanism initiated by falling energy status, PVCMs can powerfully hinder the Nrf2 program to selectively drive ferroptosis in TNBC cells in response to PVCMs-induced glutathione depletion. This study provides a paradigm for the use of pharmacologically active nanozymes to moderate specific cellular signals and elicit desirable pharmacological activities for therapeutic applications.
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Affiliation(s)
- Huan Wang
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China
| | - Xinchen Liu
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School of Stomatology, Jilin University, Changchun 130021, PR China
| | - Xiangyu Yan
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083, PR China
| | - Yong Du
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083, PR China
| | - Fang Pu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China.
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China.
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2
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Ogrizek M, Janežič M, Valjavec K, Perdih A. Catalytic Mechanism of ATP Hydrolysis in the ATPase Domain of Human DNA Topoisomerase IIα. J Chem Inf Model 2022; 62:3896-3909. [PMID: 35948041 PMCID: PMC9400105 DOI: 10.1021/acs.jcim.2c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Human DNA topoisomerase IIα is a biological nanomachine
that
regulates the topological changes of the DNA molecule and is considered
a prime target for anticancer drugs. Despite intensive research, many
atomic details about its mechanism of action remain unknown. We investigated
the ATPase domain, a segment of the human DNA topoisomerase IIα,
using all-atom molecular simulations, multiscale quantum mechanics/molecular
mechanics (QM/MM) calculations, and a point mutation study. The results
suggested that the binding of ATP affects the overall dynamics of
the ATPase dimer. Reaction modeling revealed that ATP hydrolysis favors
the dissociative substrate-assisted reaction mechanism with the catalytic
Glu87 serving to properly position and polarize the lytic water molecule.
The point mutation study complemented our computational results, demonstrating
that Lys378, part of the important QTK loop, acts as a stabilizing
residue. The work aims to pave the way to a deeper understanding of
these important molecular motors and to advance the development of
new therapeutics.
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Affiliation(s)
- Mitja Ogrizek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Katja Valjavec
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI 1000 Ljubljana, Slovenia
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3
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Abreu B, Cruz C, Oliveira ASF, Soares CM. ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK 2E importer. Sci Rep 2021; 11:10591. [PMID: 34012037 PMCID: PMC8134467 DOI: 10.1038/s41598-021-89556-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/27/2021] [Indexed: 02/03/2023] Open
Abstract
ATP binding cassette (ABC) transporters employ ATP hydrolysis to harness substrate translocation across membranes. The Escherichia coli MalFGK2E maltose importer is an example of a type I ABC importer and a model system for this class of ABC transporters. The MalFGK2E importer is responsible for the intake of malto-oligossacharides in E.coli. Despite being extensively studied, little is known about the effect of ATP hydrolysis and nucleotide exit on substrate transport. In this work, we studied this phenomenon using extensive molecular dynamics simulations (MD) along with potential of mean force calculations of maltose transport across the pore, in the pre-hydrolysis, post-hydrolysis and nucleotide-free states. We concluded that ATP hydrolysis and nucleotide exit trigger conformational changes that result in the decrease of energetic barriers to maltose translocation towards the cytoplasm, with a concomitant increase of the energy barrier in the periplasmic side of the pore, contributing for the irreversibility of the process. We also identified key residues that aid in positioning and orientation of maltose, as well as a novel binding pocket for maltose in MalG. Additionally, ATP hydrolysis leads to conformations similar to the nucleotide-free state. This study shows the contribution of ATP hydrolysis and nucleotide exit in the transport cycle, shedding light on ABC type I importer mechanisms.
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Affiliation(s)
- Bárbara Abreu
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Carlos Cruz
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - A. Sofia F. Oliveira
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal ,grid.5337.20000 0004 1936 7603School of Biochemistry and Centre for Computational Chemistry, University of Bristol, Bristol, UK
| | - Cláudio M. Soares
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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4
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Structural dynamics of ABC transporters: molecular simulation studies. Biochem Soc Trans 2021; 49:405-414. [PMID: 33634827 DOI: 10.1042/bst20200710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/31/2022]
Abstract
The biological activities of living organisms involve various inputs and outputs. The ATP-driven substances (biomolecules) responsible for these kinds of activities through membrane (i.e. uptake and efflux of substrates) include ATP-binding cassette (ABC) transporters, some of which play important roles in multidrug resistance. The basic architecture of ABC transporters comprises transmembrane domains (TMDs) and nucleotide-binding domains (NBDs). The functional dynamics (substrate transport) of ABC transporters are realized by concerted motions, such as NBD dimerization, mechanical transmission via coupling helices (CHs), and the translocation of substrates through TMDs, which are induced by the binding and/or hydrolysis of ATP molecules and substrates. In this mini-review, we briefly discuss recent progresses in the structural dynamics as revealed by molecular simulation studies at all-atom (AA), coarse-grained (CG), and quantum mechanics/molecular mechanics (QM/MM) levels.
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5
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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6
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Abreu B, Lopes EF, Oliveira ASF, Soares CM. F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis. Proteins 2019; 88:113-126. [PMID: 31298435 DOI: 10.1002/prot.25776] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/17/2019] [Accepted: 07/06/2019] [Indexed: 12/20/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) channel is an ion channel responsible for chloride transport in epithelia and it belongs to the class of ABC transporters. The deletion of phenylalanine 508 (F508del) in CFTR is the most common mutation responsible for cystic fibrosis. Little is known about the effect of the mutation in the isolated nucleotide binding domains (NBDs), on dimer dynamics, ATP hydrolysis and even on nucleotide binding. Using molecular dynamics simulations of the human CFTR NBD dimer, we showed that F508del increases, in the prehydrolysis state, the inter-motif distance in both ATP binding sites (ABP) when ATP is bound. Additionally, a decrease in the number of catalytically competent conformations was observed in the presence of F508del. We used the subtraction technique to study the first 300 ps after ATP hydrolysis in the catalytic competent site and found that the F508del dimer evidences lower conformational changes than the wild type. Using longer simulation times, the magnitude of the conformational changes in both forms increases. Nonetheless, the F508del dimer shows lower C-α RMS values in comparison to the wild-type, on the F508del loop, on the residues surrounding the catalytic site and the portion of NBD2 adjacent to ABP1. These results provide evidence that F508del interferes with the NBD dynamics before and after ATP hydrolysis. These findings shed a new light on the effect of F508del on NBD dynamics and reveal a novel mechanism for the influence of F508del on CFTR.
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Affiliation(s)
- Bárbara Abreu
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Emanuel F Lopes
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - A S F Oliveira
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal.,School of Biochemistry & Center for Computational Chemistry, University of Bristol, Bristol, UK
| | - Cláudio M Soares
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
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7
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Arana MR, Altenberg GA. ATP-binding Cassette Exporters: Structure and Mechanism with a Focus on P-glycoprotein and MRP1. Curr Med Chem 2019; 26:1062-1078. [PMID: 29022498 DOI: 10.2174/0929867324666171012105143] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Proteins that belong to the ATP-binding cassette superfamily include transporters that mediate the efflux of substrates from cells. Among these exporters, P-glycoprotein and MRP1 are involved in cancer multidrug resistance, protection from endo and xenobiotics, determination of drug pharmacokinetics, and the pathophysiology of a variety of disorders. OBJECTIVE To review the information available on ATP-binding cassette exporters, with a focus on Pglycoprotein, MRP1 and related proteins. We describe tissue localization and function of these transporters in health and disease, and discuss the mechanisms of substrate transport. We also correlate recent structural information with the function of the exporters, and discuss details of their molecular mechanism with a focus on the nucleotide-binding domains. METHODS Evaluation of selected publications on the structure and function of ATP-binding cassette proteins. CONCLUSIONS Conformational changes on the nucleotide-binding domains side of the exporters switch the accessibility of the substrate-binding pocket between the inside and outside, which is coupled to substrate efflux. However, there is no agreement on the magnitude and nature of the changes at the nucleotide- binding domains side that drive the alternate-accessibility. Comparison of the structures of Pglycoprotein and MRP1 helps explain differences in substrate selectivity and the bases for polyspecificity. P-glycoprotein substrates are hydrophobic and/or weak bases, and polyspecificity is explained by a flexible hydrophobic multi-binding site that has a few acidic patches. MRP1 substrates are mostly organic acids, and its polyspecificity is due to a single bipartite binding site that is flexible and displays positive charge.
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Affiliation(s)
- Maite Rocío Arana
- Instituto de Fisiología Experimental, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 570, 2000 Rosario, Argentina
| | - Guillermo Alejandro Altenberg
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-6551, United States
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8
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Huang W, Huang Y, Xu J, Liao JL. How Does the Spliceosome Catalyze Intron Lariat Formation? Insights from Quantum Mechanics/Molecular Mechanics Free-Energy Simulations. J Phys Chem B 2019; 123:6049-6055. [DOI: 10.1021/acs.jpcb.9b04377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Wenting Huang
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
| | - Yan Huang
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China
| | - Jie-Lou Liao
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
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9
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Prieß M, Göddeke H, Groenhof G, Schäfer LV. Molecular Mechanism of ATP Hydrolysis in an ABC Transporter. ACS CENTRAL SCIENCE 2018; 4:1334-1343. [PMID: 30410971 PMCID: PMC6202651 DOI: 10.1021/acscentsci.8b00369] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Indexed: 05/28/2023]
Abstract
Hydrolysis of nucleoside triphosphate (NTP) plays a key role for the function of many biomolecular systems. However, the chemistry of the catalytic reaction in terms of an atomic-level understanding of the structural, dynamic, and free energy changes associated with it often remains unknown. Here, we report the molecular mechanism of adenosine triphosphate (ATP) hydrolysis in the ATP-binding cassette (ABC) transporter BtuCD-F. Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. First, nucleophilic attack of an activated lytic water molecule at the ATP γ-phosphate yields ADP + HPO4 2- as intermediate product. A conserved glutamate that is located very close to the γ-phosphate transiently accepts a proton and thus acts as catalytic base. In the second step, the proton is transferred back from the catalytic base to the γ-phosphate, yielding ADP + H2PO4 -. These two chemical reaction steps are followed by rearrangements of the hydrogen bond network and the coordination of the Mg2+ ion. The rate constant estimated from the computed free energy barriers is in very good agreement with experiments. The overall free energy change of the reaction is close to zero, suggesting that phosphate bond cleavage itself does not provide a power stroke for conformational changes. Instead, ATP binding is essential for tight dimerization of the nucleotide-binding domains and the transition of the transmembrane domains from inward- to outward-facing, whereas ATP hydrolysis resets the conformational cycle. The mechanism is likely relevant for all ABC transporters and might have implications also for other NTPases, as many residues involved in nucleotide binding and hydrolysis are strictly conserved.
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Affiliation(s)
- Marten Prieß
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Hendrik Göddeke
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Gerrit Groenhof
- Department
of Chemistry and Nanoscience Center, University
of Jyväskylä, P.O. Box
35, FI-40014 Jyväskylä, Finland
| | - Lars V. Schäfer
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
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10
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Zhou Y, Ojeda-May P, Nagaraju M, Kim B, Pu J. Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method. Molecules 2018; 23:molecules23102652. [PMID: 30332773 PMCID: PMC6222333 DOI: 10.3390/molecules23102652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/16/2022] Open
Abstract
HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.
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Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Mulpuri Nagaraju
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Bryant Kim
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
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11
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Zoghbi ME, Altenberg GA. Luminescence resonance energy transfer spectroscopy of ATP-binding cassette proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:854-867. [PMID: 28801111 DOI: 10.1016/j.bbamem.2017.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
Abstract
The ATP-binding cassette (ABC) superfamily includes regulatory and transport proteins. Most human ABC exporters pump substrates out of cells using energy from ATP hydrolysis. Although major advances have been made toward understanding the molecular mechanism of ABC exporters, there are still many issues unresolved. During the last few years, luminescence resonance energy transfer has been used to detect conformational changes in real time, with atomic resolution, in isolated ABC nucleotide binding domains (NBDs) and full-length ABC exporters. NBDs are particularly interesting because they provide the power stroke for substrate transport. Luminescence resonance energy transfer (LRET) is a spectroscopic technique that can provide dynamic information with atomic-resolution of protein conformational changes under physiological conditions. Using LRET, it has been shown that NBD dimerization, a critical step in ABC proteins catalytic cycle, requires binding of ATP to two nucleotide binding sites. However, hydrolysis at just one of the sites can drive dissociation of the NBD dimer. It was also found that the NBDs of the bacterial ABC exporter MsbA reconstituted in a lipid bilayer membrane and studied at 37°C never separate as much as suggested by crystal structures. This observation stresses the importance of performing structural/functional studies of ABC exporters under physiologic conditions. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Maria E Zoghbi
- School of Natural Sciences, University of California, Merced, 4225 N. Hospital Road, Atwater, CA, USA
| | - Guillermo A Altenberg
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79423-6551, USA.
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Hsu WL, Furuta T, Sakurai M. ATP Hydrolysis Mechanism in a Maltose Transporter Explored by QM/MM Metadynamics Simulation. J Phys Chem B 2016; 120:11102-11112. [PMID: 27712074 DOI: 10.1021/acs.jpcb.6b07332] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Translocation of substrates across the cell membrane by adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporters depends on the energy provided by ATP hydrolysis within the nucleotide-binding domains (NBDs). However, the detailed mechanism remains unclear. In this study, we focused on maltose transporter NBDs (MalK2) and performed a quantum mechanical/molecular mechanical (QM/MM) well-tempered metadynamics simulation to address this issue. We explored the free-energy profile along an assigned collective variable. As a result, it was determined that the activation free energy is approximately 10.5 kcal/mol, and the reaction released approximately 3.8 kcal/mol of free energy, indicating that the reaction of interest is a one-step exothermic reaction. The dissociation of the ATP γ-phosphate seems to be the rate-limiting step, which supports the so-called dissociative model. Moreover, Glu159, located in the Walker B motif, acts as a base to abstract the proton from the lytic water, but is not the catalytic base, which corresponds to an atypical general base catalysis model. We also observed two interesting proton transfers: transfer from the His192 ε-position nitrogen to the dissociated inorganic phosphate, Pi, and transfer from the Lys42 side chain to adenosine 5'-diphosphate β-phosphate. These proton transfers would stabilize the posthydrolysis state. Our study provides significant insight into the ATP hydrolysis mechanism in MalK2 from a dynamical viewpoint, and this insight would be applicable to other ABC transporters.
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Affiliation(s)
- Wei-Lin Hsu
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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