1
|
Zhao Y, Min H, Luo K, Chen H, Chen Q, Sun W. Insight into sulfamethoxazole effects on aerobic denitrification by strain Pseudomonas aeruginosa PCN-2: From simultaneous degradation performance to transcriptome analysis. CHEMOSPHERE 2023; 313:137471. [PMID: 36493888 DOI: 10.1016/j.chemosphere.2022.137471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/26/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
It is a well-established fact that aerobic denitrifying strains are profoundly affected by antibiotics, but bacterium performing simultaneous aerobic denitrification and antibiotic degradation is hardly reported. Here, a typical aerobic denitrifying bacterium Pseudomonas aeruginosa PCN-2 was discovered to be capable of sulfamethoxazole (SMX) degradation. The results showed that nitrate removal efficiency was decreased from 100% to 88.12%, but the resistance of strain PCN-2 to SMX stress was enhanced with the increment of SMX concentration from 0 to 100 mg/L. Transcriptome analysis revealed that the down-regulation of energy metabolism pathways rather than the denitrifying functional genes was responsible for the suppressed nitrogen removal, while the up-regulation of antibiotic resistance pathways (e.g., biofilm formation, multi-drug efflux system, and quorum sensing) ensured the survival of bacterium and the carrying out of aerobic denitrification. Intriguingly, strain PCN-2 could degrade SMX during aerobic denitrification. Seven metabolites were identified by the UHPLC-MS, and three degradation pathways (which includes a new pathway that has never been reported) was proposed combined with the expressions of drug metabolic genes (e.g., cytP450, FMN, ALDH and NAT). This work provides a mechanistic understanding of the metabolic adaption of strain PCN-2 under SMX stress, which provided a broader idea for the treatment of SMX-containing wastewater.
Collapse
Affiliation(s)
- Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China
| | - Hongchao Min
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China
| | - Huan Chen
- Department of Environmental Engineering and Earth Sciences, Clemson University, South Carolina, 29634, United States
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China.
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China
| |
Collapse
|
2
|
Cacciotto P, Basciu A, Oliva F, Malloci G, Zacharias M, Ruggerone P, Vargiu AV. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA. Comput Struct Biotechnol J 2022; 20:252-260. [PMID: 35024097 PMCID: PMC8717590 DOI: 10.1016/j.csbj.2021.11.042] [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: 09/02/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Efflux pumps of the Resistance-Nodulation-cell Division (RND) superfamily contribute to intrinsic and acquired resistance in Gram-negative pathogens by expelling chemically unrelated antibiotics with high efficiency. They are tripartite systems constituted by an inner-membrane-anchored transporter, an outer membrane factor protein, and a membrane fusion protein. Multimerization of the membrane fusion protein is an essential prerequisite for full functionality of these efflux pumps. In this work, we employed complementary computational techniques to investigate the stability of a dimeric unit of MexA (the membrane fusion protein of the MexAB-OprM RND efflux pump of Pseudomonas aeruginosa), and to provide a molecular rationale for the effect of the G72S substitution, which affects MexAB-OprM functionality by impairing the assembly of MexA. Our findings indicate that: i) dimers of this protein are stable in multiple µs-long molecular dynamics simulations; ii) the mutation drastically alters the conformational equilibrium of MexA, favouring a collapsed conformation that is unlikely to form dimers or higher order assemblies. Unveiling the mechanistic aspects underlying large conformational distortions induced by minor sequence changes is informative to efforts at interfering with the activity of this elusive bacterial weapon. In this respect, our work further confirms how molecular simulations can give important contribution and useful insights to characterize the mechanism of highly complex biological systems.
Collapse
Affiliation(s)
- Pierpaolo Cacciotto
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Andrea Basciu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesco Oliva
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Martin Zacharias
- Physics Department, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| |
Collapse
|
3
|
Liu WS, Li HG, Ding CH, Zhang HX, Wang RR, Li JQ. Screening potential FDA-approved inhibitors of the SARS-CoV-2 major protease 3CL pro through high-throughput virtual screening and molecular dynamics simulation. Aging (Albany NY) 2021; 13:6258-6272. [PMID: 33678621 PMCID: PMC7993695 DOI: 10.18632/aging.202703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/03/2021] [Indexed: 04/16/2023]
Abstract
It has been confirmed that the new coronavirus SARS-CoV-2 caused the global pandemic of coronavirus disease 2019 (COVID-19). Studies have found that 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for virus replication, and could be used as a potential target to inhibit SARS-CoV-2. In this work, 3CLpro was used as the target to complete the high-throughput virtual screening of the FDA-approved drugs, and Indinavir and other 10 drugs with high docking scores for 3CLpro were obtained. Studies on the binding pattern of 3CLpro and Indinavir found that Indinavir could form the stable hydrogen bond (H-bond) interactions with the catalytic dyad residues His41-Cys145. Binding free energy study found that Indinavir had high binding affinity with 3CLpro. Subsequently, molecular dynamics simulations were performed on the 3CLpro and 3CLpro-Indinavir systems, respectively. The post-dynamic analyses showed that the conformational state of the 3CLpro-Indinavir system transformed significantly and the system tended to be more stable. Moreover, analyses of the residue interaction network (RIN) and H-bond occupancy revealed that the residue-residue interaction at the catalytic site of 3CLpro was significantly enhanced after binding with Indinavir, which in turn inactivated the protein. In short, through this research, we hope to provide more valuable clues against COVID-19.
Collapse
Affiliation(s)
- Wen-Shan Liu
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Han-Gao Li
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Hai-Xia Zhang
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Jia-Qiu Li
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| |
Collapse
|
4
|
Design and synthesis of novel 4-substituted quinazoline-2-carboxamide derivatives targeting AcrB to reverse the bacterial multidrug resistance. Bioorg Chem 2020; 105:104394. [DOI: 10.1016/j.bioorg.2020.104394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/28/2020] [Accepted: 10/17/2020] [Indexed: 12/30/2022]
|
5
|
Antibiotic export by MexB multidrug efflux transporter is allosterically controlled by a MexA-OprM chaperone-like complex. Nat Commun 2020; 11:4948. [PMID: 33009415 PMCID: PMC7532149 DOI: 10.1038/s41467-020-18770-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
The tripartite multidrug efflux system MexAB-OprM is a major actor in Pseudomonas aeruginosa antibiotic resistance by exporting a large variety of antimicrobial compounds. Crystal structures of MexB and of its Escherichia coli homolog AcrB had revealed asymmetric trimers depicting a directional drug pathway by a conformational interconversion (from Loose and Tight binding pockets to Open gate (LTO) for drug exit). It remains unclear how MexB acquires its LTO form. Here by performing functional and cryo-EM structural investigations of MexB at various stages of the assembly process, we unveil that MexB inserted in lipid membrane is not set for active transport because it displays an inactive LTC form with a Closed exit gate. In the tripartite complex, OprM and MexA form a corset-like platform that converts MexB into the active form. Our findings shed new light on the resistance nodulation cell division (RND) cognate partners which act as allosteric factors eliciting the functional drug extrusion.
Collapse
|
6
|
Ancy I, Sivanandam M, Kalaivani R, Kumaradhas P. Insights of inhibition mechanism of sifuvirtide and MT-sifuvirtide against wild and mutant HIV-1 envelope glycoprotein41: a molecular dynamics simulation and binding free energy study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1716978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Iruthayaraj Ancy
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Raju Kalaivani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| |
Collapse
|
7
|
Saranya V, Radhika R, Shankar R, Vijayakumar S. In silico studies of the inhibition mechanism of dengue with papain. J Biomol Struct Dyn 2020; 39:1912-1927. [PMID: 32249700 DOI: 10.1080/07391102.2020.1742205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of -352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue.
Collapse
|
8
|
Travers T, Wang KJ, López CA, Gnanakaran S. Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes. Res Microbiol 2018; 169:414-424. [DOI: 10.1016/j.resmic.2018.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/21/2018] [Indexed: 01/12/2023]
|
9
|
Vargiu AV, Ramaswamy VK, Malloci G, Malvacio I, Atzori A, Ruggerone P. Computer simulations of the activity of RND efflux pumps. Res Microbiol 2018; 169:384-392. [PMID: 29407044 DOI: 10.1016/j.resmic.2017.12.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/01/2017] [Accepted: 12/05/2017] [Indexed: 12/25/2022]
Abstract
The putative mechanism by which bacterial RND-type multidrug efflux pumps recognize and transport their substrates is a complex and fascinating enigma of structural biology. How a single protein can recognize a huge number of unrelated compounds and transport them through one or just a few mechanisms is an amazing feature not yet completely unveiled. The appearance of cooperativity further complicates the understanding of structure-dynamics-activity relationships in these complex machineries. Experimental techniques may have limited access to the molecular determinants and to the energetics of key processes regulating the activity of these pumps. Computer simulations are a complementary approach that can help unveil these features and inspire new experiments. Here we review recent computational studies that addressed the various molecular processes regulating the activity of RND efflux pumps.
Collapse
Affiliation(s)
- Attilio Vittorio Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy.
| | - Venkata Krishnan Ramaswamy
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Ivana Malvacio
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Alessio Atzori
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy.
| |
Collapse
|
10
|
Cacciotto P, Ramaswamy VK, Malloci G, Ruggerone P, Vargiu AV. Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters. Methods Mol Biol 2018; 1700:179-219. [PMID: 29177832 DOI: 10.1007/978-1-4939-7454-2_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Efflux pumps of the resistance nodulation division (RND) superfamily are among the major contributors to intrinsic and acquired multidrug resistance in Gram-negative bacteria. Structural information on AcrAB-TolC and MexAB-OprM, major efflux pumps of Escherichia coli and Pseudomonas aeruginosa respectively, boosted intensive research aimed at understanding the molecular mechanisms ruling the active extrusion processes. In particular, several studies were devoted to the understanding of the determinants behind the extraordinary broad specificity of the RND transporters AcrB and MexB. In this chapter, we discuss the ever-growing role computational methods have been playing in deciphering key structural and dynamical features of these transporters and of their interaction with substrates and inhibitors. We further discuss and illustrate examples from our lab of how molecular docking, homology modeling, all-atom molecular dynamics simulations and in silico free energy estimations can all together give precious insights into the processes of recognition and extrusion of substrates, as well as on the possible inhibition strategies.
Collapse
Affiliation(s)
- Pierpaolo Cacciotto
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Venkata K Ramaswamy
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy.
| |
Collapse
|
11
|
López CA, Travers T, Pos KM, Zgurskaya HI, Gnanakaran S. Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface. Sci Rep 2017; 7:16521. [PMID: 29184094 PMCID: PMC5705723 DOI: 10.1038/s41598-017-16497-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/30/2017] [Indexed: 11/30/2022] Open
Abstract
Antibiotic efflux is one of the most critical mechanisms leading to bacterial multidrug resistance. Antibiotics are effluxed out of the bacterial cell by a tripartite efflux pump, a complex machinery comprised of outer membrane, periplasmic adaptor, and inner membrane protein components. Understanding the mechanism of efflux pump assembly and its dynamics could facilitate discovery of novel approaches to counteract antibiotic resistance in bacteria. We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM pump in a Gram-negative membrane model that contained both inner and outer membranes separated by a periplasmic space. All-atom molecular dynamics (MD) simulations confirm that the fully assembled pump is stable in the microsecond timescale. Using a combination of all-atom and coarse-grained MD simulations and sequence covariation analysis, we characterized the interface between MexA and OprM in the context of the entire efflux pump. These analyses suggest a plausible mechanism by which OprM is activated via opening of its periplasmic aperture through a concerted interaction with MexA.
Collapse
Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.,Center for Nonlinear Sciences, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University, Frankfurt am Main, Germany.,Cluster of Excellence Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
| |
Collapse
|
12
|
Murata D, Okano H, Angkawidjaja C, Akutsu M, Tanaka SI, Kitahara K, Yoshizawa T, Matsumura H, Kado Y, Mizohata E, Inoue T, Sano S, Koga Y, Kanaya S, Takano K. Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain. Biochemistry 2017; 56:6281-6291. [PMID: 29094929 DOI: 10.1021/acs.biochem.7b00985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Serratia marcescens secretes a lipase, LipA, through a type I secretion system (T1SS). The T1SS for LipA, the Lip system, is composed of an inner membrane ABC transporter with its nucleotide-binding domains (NBD), LipB, a membrane fusion protein, LipC, and an outer membrane channel protein, LipD. Passenger protein secreted by this system has been functionally and structurally characterized well, but relatively little information about the transporter complex is available. Here, we report the crystallographic studies of LipC without the membrane anchor region, LipC-, and the NBD of LipB (LipB-NBD). LipC- crystallographic analysis has led to the determination of the structure of the long α-helical and lipoyl domains, but not the area where it interacts with LipB, suggesting that the region is flexible without LipB. The long α-helical domain has three α-helices, which interacts with LipD in the periplasm. LipB-NBD has the common overall architecture and ATP hydrolysis activity of ABC transporter NBDs. Using the predicted models of full-length LipB and LipD, the overall structural insight into the Lip system is discussed.
Collapse
Affiliation(s)
- Daichi Murata
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hiroyuki Okano
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Clement Angkawidjaja
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt , Max-von-Laue-Straße, 60438 Frankfurt am Main, Germany
| | - Shun-Ichi Tanaka
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Kenyu Kitahara
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Takuya Yoshizawa
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Hiroyoshi Matsumura
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Yuji Kado
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Eiichi Mizohata
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Tsuyoshi Inoue
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Satoshi Sano
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Yuichi Koga
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Shigenori Kanaya
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| |
Collapse
|
13
|
Scorciapino MA, Acosta-Gutierrez S, Benkerrou D, D'Agostino T, Malloci G, Samanta S, Bodrenko I, Ceccarelli M. Rationalizing the permeation of polar antibiotics into Gram-negative bacteria. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:113001. [PMID: 28155846 DOI: 10.1088/1361-648x/aa543b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.
Collapse
Affiliation(s)
- Mariano Andrea Scorciapino
- Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700-09042 Monserrato (CA), Italy
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Abdali N, Parks JM, Haynes KM, Chaney JL, Green AT, Wolloscheck D, Walker JK, Rybenkov VV, Baudry J, Smith JC, Zgurskaya HI. Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump. ACS Infect Dis 2017; 3:89-98. [PMID: 27768847 DOI: 10.1021/acsinfecdis.6b00167] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Antibiotic resistance is a major threat to human welfare. Inhibitors of multidrug efflux pumps (EPIs) are promising alternative therapeutics that could revive activities of antibiotics and reduce bacterial virulence. Identification of new druggable sites for inhibition is critical for the development of effective EPIs, especially in light of constantly emerging resistance. Here, we describe EPIs that interact with periplasmic membrane fusion proteins, critical components of efflux pumps that are responsible for the activation of the transporter and the recruitment of the outer-membrane channel. The discovered EPIs bind to AcrA, a component of the prototypical AcrAB-TolC pump, change its structure in vivo, inhibit efflux of fluorescent probes, and potentiate the activities of antibiotics in Escherichia coli and other Gram-negative bacteria. Our findings expand the chemical and mechanistic diversity of EPIs, suggest the mechanism for regulation of the efflux pump assembly and activity, and provide a promising path for reviving the activities of antibiotics in resistant bacteria.
Collapse
Affiliation(s)
- Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jerry M. Parks
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Keith M. Haynes
- Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Julie L. Chaney
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Adam T. Green
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - David Wolloscheck
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - John K. Walker
- Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jerome Baudry
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- UT/ORNL Center
for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| |
Collapse
|
15
|
Molecular Epidemiology of Mutations in Antimicrobial Resistance Loci of Pseudomonas aeruginosa Isolates from Airways of Cystic Fibrosis Patients. Antimicrob Agents Chemother 2016; 60:6726-6734. [PMID: 27572404 DOI: 10.1128/aac.00724-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/23/2016] [Indexed: 01/30/2023] Open
Abstract
The chronic airway infections with Pseudomonas aeruginosa in people with cystic fibrosis (CF) are treated with aerosolized antibiotics, oral fluoroquinolones, and/or intravenous combination therapy with aminoglycosides and β-lactam antibiotics. An international strain collection of 361 P. aeruginosa isolates from 258 CF patients seen at 30 CF clinics was examined for mutations in 17 antimicrobial susceptibility and resistance loci that had been identified as hot spots of mutation by genome sequencing of serial isolates from a single CF clinic. Combinatorial amplicon sequencing of pooled PCR products identified 1,112 sequence variants that were not present in the genomes of representative strains of the 20 most common clones of the global P. aeruginosa population. A high frequency of singular coding variants was seen in spuE, mexA, gyrA, rpoB, fusA1, mexZ, mexY, oprD, ampD, parR, parS, and envZ (amgS), reflecting the pressure upon P. aeruginosa in lungs of CF patients to generate novel protein variants. The proportion of nonneutral amino acid exchanges was high. Of the 17 loci, mexA, mexZ, and pagL were most frequently affected by independent stop mutations. Private and de novo mutations seem to play a pivotal role in the response of P. aeruginosa populations to the antimicrobial load and the individual CF host.
Collapse
|
16
|
Urbina P, Bersch B, De Angelis F, Derfoufi KM, Prévost M, Goormaghtigh E, Vandenbussche G. Structural and Functional Investigation of the Ag+/Cu+ Binding Domains of the Periplasmic Adaptor Protein SilB from Cupriavidus metallidurans CH34. Biochemistry 2016; 55:2883-97. [DOI: 10.1021/acs.biochem.6b00022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patricia Urbina
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Beate Bersch
- Institut
de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Fabien De Angelis
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Kheiro-Mouna Derfoufi
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Martine Prévost
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Erik Goormaghtigh
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Guy Vandenbussche
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| |
Collapse
|
17
|
Kan W, Fang F, Chen L, Wang R, Deng Q. Influence of the R823W mutation on the interaction of the ANKS6-ANKS3: insights from molecular dynamics simulation and free energy analysis. J Biomol Struct Dyn 2016; 34:1113-22. [PMID: 26295479 DOI: 10.1080/07391102.2015.1071281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The sterile alpha motif (SAM) domain of the protein ANKS6, a protein-protein interaction domain, is responsible for autosomal dominant polycystic kidney disease. Although the disease is the result of the R823W point mutation in the SAM domain of the protein ANKS6, the molecular details are still unclear. We applied molecular dynamics simulations, the principal component analysis, and the molecular mechanics Poisson-Boltzmann surface area binding free energy calculation to explore the structural and dynamic effects of the R823W point mutation on the complex ANKS6-ANKS3 (PDB ID: 4NL9) in comparison to the wild proteins. The energetic analysis presents that the wild type has a more stable structure than the mutant. The R823W point mutation not only disrupts the structure of the ANKS6 SAM domain but also negatively affects the interaction of the ANKS6-ANKS3. These results further clarify the previous experiments to understand the ANKS6-ANKS3 interaction comprehensively. In summary, this study would provide useful suggestions to understand the interaction of these proteins and their fatal action on mediating kidney function.
Collapse
Affiliation(s)
- Wei Kan
- a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China
| | - Fengqin Fang
- a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China
| | - Lin Chen
- a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China
| | - Ruige Wang
- a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China
| | - Qigang Deng
- a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China
| |
Collapse
|
18
|
Daury L, Orange F, Taveau JC, Verchère A, Monlezun L, Gounou C, Marreddy RKR, Picard M, Broutin I, Pos KM, Lambert O. Tripartite assembly of RND multidrug efflux pumps. Nat Commun 2016; 7:10731. [PMID: 26867482 PMCID: PMC4754349 DOI: 10.1038/ncomms10731] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/15/2016] [Indexed: 12/18/2022] Open
Abstract
Tripartite multidrug efflux systems of Gram-negative bacteria are composed of an inner membrane transporter, an outer membrane channel and a periplasmic adaptor protein. They are assumed to form ducts inside the periplasm facilitating drug exit across the outer membrane. Here we present the reconstitution of native Pseudomonas aeruginosa MexAB–OprM and Escherichia coli AcrAB–TolC tripartite Resistance Nodulation and cell Division (RND) efflux systems in a lipid nanodisc system. Single-particle analysis by electron microscopy reveals the inner and outer membrane protein components linked together via the periplasmic adaptor protein. This intrinsic ability of the native components to self-assemble also leads to the formation of a stable interspecies AcrA–MexB–TolC complex suggesting a common mechanism of tripartite assembly. Projection structures of all three complexes emphasize the role of the periplasmic adaptor protein as part of the exit duct with no physical interaction between the inner and outer membrane components. Tripartite efflux systems consist of inner membrane, outer membrane and periplasmic components. Here, Daury et al. reconstitute native versions of RND transporters in nanodiscs and present projection structures emphasizing the role of the periplasmic adaptor in linking the inner and outer membrane proteins.
Collapse
Affiliation(s)
- Laetitia Daury
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - François Orange
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - Jean-Christophe Taveau
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - Alice Verchère
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Laura Monlezun
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Céline Gounou
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - Ravi K R Marreddy
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Martin Picard
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Isabelle Broutin
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Olivier Lambert
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| |
Collapse
|
19
|
An overview of bacterial efflux pumps and computational approaches to study efflux pump inhibitors. Future Med Chem 2016; 8:195-210. [DOI: 10.4155/fmc.15.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Micro-organisms express a wide range of transmembrane pumps known as multidrug efflux pumps that improve the micro-organism's ability to survive in severe environments and contribute to resistance against antibiotic and antimicrobial agents. There is significant interest in developing efflux inhibitors as an adjunct to treatment with current and next generation of antibiotics. A greater understanding of drug recognition and transport by multidrug efflux pumps is needed to develop clinically useful inhibitors, given the breadth of molecules that can be effluxed by these systems. We summarize some structural and functional data that could provide insights into the inhibition of transport mechanisms of these intricate molecular nanomachines with a focus on the advances in computational approaches.
Collapse
|
20
|
Focus on the Outer Membrane Factor OprM, the Forgotten Player from Efflux Pumps Assemblies. Antibiotics (Basel) 2015; 4:544-66. [PMID: 27025640 PMCID: PMC4790312 DOI: 10.3390/antibiotics4040544] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/26/2015] [Accepted: 11/02/2015] [Indexed: 12/14/2022] Open
Abstract
Antibiotics have been used extensively during several decades and we are now facing the emergence of multidrug resistant strains. It has become a major public concern, urging the need to discover new strategies to combat them. Among the different ways used by bacteria to resist antibiotics, the active efflux is one of the main mechanisms. In Gram-negative bacteria the efflux pumps are comprised of three components forming a long edifice crossing the complete cell wall from the inside to the outside of the cell. Blocking these pumps would permit the restoration of the effectiveness of the current antibiotherapy which is why it is important to increase our knowledge on the different proteins involved in these complexes. A tremendous number of experiments have been performed on the inner membrane protein AcrB from Escherichia coli and, to a lesser extent, the protein partners forming the AcrAB-TolC pump, but less information is available concerning the efflux pumps from other virulent Gram-negative bacteria. The present review will focus on the OprM outer membrane protein from the MexAB-OprM pump of Pseudomonas aeruginosa, highlighting similarities and differences compare to the archetypal AcrAB-TolC in terms of structure, function, and assembly properties.
Collapse
|
21
|
Dreier J, Ruggerone P. Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa. Front Microbiol 2015; 6:660. [PMID: 26217310 PMCID: PMC4495556 DOI: 10.3389/fmicb.2015.00660] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/16/2015] [Indexed: 01/14/2023] Open
Abstract
Pseudomonas aeruginosa infections are becoming increasingly difficult to treat due to intrinsic antibiotic resistance and the propensity of this pathogen to accumulate diverse resistance mechanisms. Hyperexpression of efflux pumps of the Resistance-Nodulation-Cell Division (RND)-type multidrug efflux pumps (e.g., MexAB-OprM), chromosomally encoded by mexAB-oprM, mexCD-oprJ, mexEF-oprN, and mexXY (-oprA) is often detected in clinical isolates and contributes to worrying multi-drug resistance phenotypes. Not all antibiotics are affected to the same extent by the aforementioned RND efflux pumps. The impact of efflux on antibiotic activity varies not only between different classes of antibiotics but also between members of the same family of antibiotics. Subtle differences in physicochemical features of compound-pump and compound-solvent interactions largely determine how compounds are affected by efflux activity. The combination of different high-resolution techniques helps to gain insight into the functioning of these molecular machineries. This review discusses substrate recognition patterns based on experimental evidence and computer simulations with a focus on MexB, the pump subunit of the main RND transporter in P. aeruginosa.
Collapse
Affiliation(s)
- Jürg Dreier
- Basilea Pharmaceutica International Ltd.,Basel, Switzerland
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università di Cagliari – Cittadella UniversitariaMonserrato, Italy
| |
Collapse
|
22
|
Symmons MF, Marshall RL, Bavro VN. Architecture and roles of periplasmic adaptor proteins in tripartite efflux assemblies. Front Microbiol 2015; 6:513. [PMID: 26074901 PMCID: PMC4446572 DOI: 10.3389/fmicb.2015.00513] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022] Open
Abstract
Recent years have seen major advances in the structural understanding of the different components of tripartite efflux assemblies, which encompass the multidrug efflux (MDR) pumps and type I secretion systems. The majority of these investigations have focused on the role played by the inner membrane transporters and the outer membrane factor (OMF), leaving the third component of the system – the Periplasmic Adaptor Proteins (PAPs) – relatively understudied. Here we review the current state of knowledge of these versatile proteins which, far from being passive linkers between the OMF and the transporter, emerge as active architects of tripartite assemblies, and play diverse roles in the transport process. Recognition between the PAPs and OMFs is essential for pump assembly and function, and targeting this interaction may provide a novel avenue for combating multidrug resistance. With the recent advances elucidating the drug efflux and energetics of the tripartite assemblies, the understanding of the interaction between the OMFs and PAPs is the last piece remaining in the complete structure of the tripartite pump assembly puzzle.
Collapse
Affiliation(s)
- Martyn F Symmons
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Robert L Marshall
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
| |
Collapse
|
23
|
Yamaguchi A, Nakashima R, Sakurai K. Structural basis of RND-type multidrug exporters. Front Microbiol 2015; 6:327. [PMID: 25941524 PMCID: PMC4403515 DOI: 10.3389/fmicb.2015.00327] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/01/2015] [Indexed: 12/29/2022] Open
Abstract
Bacterial multidrug exporters are intrinsic membrane transporters that act as cellular self-defense mechanism. The most notable characteristics of multidrug exporters is that they export a wide range of drugs and toxic compounds. The overexpression of these exporters causes multidrug resistance. Multidrug-resistant pathogens have become a serious problem in modern chemotherapy. Over the past decade, investigations into the structure of bacterial multidrug exporters have revealed the multidrug recognition and export mechanisms. In this review, we primarily discuss RND-type multidrug exporters particularly AcrAB-TolC, major drug exporter in Gram-negative bacteria. RND-type drug exporters are tripartite complexes comprising a cell membrane transporter, an outer membrane channel and an adaptor protein. Cell membrane transporters and outer membrane channels are homo-trimers; however, there is no consensus on the number of adaptor proteins in these tripartite complexes. The three monomers of a cell membrane transporter have varying conformations (access, binding, and extrusion) during transport. Drugs are exported following an ordered conformational change in these three monomers, through a functional rotation mechanism coupled with the proton relay cycle in ion pairs, which is driven by proton translocation. Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules. The voluminous multidrug-binding pocket may have numerous binding sites even for a single substrate, suggesting that substrates may move between binding sites during transport, an idea named as multisite-drug-oscillation hypothesis. This hypothesis is consistent with the apparently broad substrate specificity of cell membrane exporters and their highly efficient ejection of drugs from the cell. Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel. Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.
Collapse
Affiliation(s)
- Akihito Yamaguchi
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan
| | - Ryosuke Nakashima
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan
| | - Keisuke Sakurai
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan
| |
Collapse
|
24
|
Zgurskaya HI, Weeks JW, Ntreh AT, Nickels LM, Wolloscheck D. Mechanism of coupling drug transport reactions located in two different membranes. Front Microbiol 2015; 6:100. [PMID: 25759685 PMCID: PMC4338810 DOI: 10.3389/fmicb.2015.00100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/26/2015] [Indexed: 01/01/2023] Open
Abstract
Gram- negative bacteria utilize a diverse array of multidrug transporters to pump toxic compounds out of the cell. Some transporters, together with periplasmic membrane fusion proteins (MFPs) and outer membrane channels, assemble trans-envelope complexes that expel multiple antibiotics across outer membranes of Gram-negative bacteria and into the external medium. Others further potentiate this efflux by pumping drugs across the inner membrane into the periplasm. Together these transporters create a powerful network of efflux that protects bacteria against a broad range of antimicrobial agents. This review is focused on the mechanism of coupling transport reactions located in two different membranes of Gram-negative bacteria. Using a combination of biochemical, genetic and biophysical approaches we have reconstructed the sequence of events leading to the assembly of trans-envelope drug efflux complexes and characterized the roles of periplasmic and outer membrane proteins in this process. Our recent data suggest a critical step in the activation of intermembrane efflux pumps, which is controlled by MFPs. We propose that the reaction cycles of transporters are tightly coupled to the assembly of the trans-envelope complexes. Transporters and MFPs exist in the inner membrane as dormant complexes. The activation of complexes is triggered by MFP binding to the outer membrane channel, which leads to a conformational change in the membrane proximal domain of MFP needed for stimulation of transporters. The activated MFP-transporter complex engages the outer membrane channel to expel substrates across the outer membrane. The recruitment of the channel is likely triggered by binding of effectors (substrates) to MFP or MFP-transporter complexes. This model together with recent structural and functional advances in the field of drug efflux provides a fairly detailed understanding of the mechanism of drug efflux across the two membranes.
Collapse
Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Abigail T Ntreh
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Logan M Nickels
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - David Wolloscheck
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| |
Collapse
|
25
|
Computational study of correlated domain motions in the AcrB efflux transporter. BIOMED RESEARCH INTERNATIONAL 2015; 2015:487298. [PMID: 25685792 PMCID: PMC4313061 DOI: 10.1155/2015/487298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/09/2014] [Accepted: 10/23/2014] [Indexed: 12/14/2022]
Abstract
As active part of the major efflux system in E. coli bacteria, AcrB is responsible for the uptake and pumping of toxic substrates from the periplasm toward the extracellular space. In combination with the channel protein TolC and membrane fusion protein AcrA, this efflux pump is able to help the bacterium to survive different kinds of noxious compounds. With the present study we intend to enhance the understanding of the interactions between the domains and monomers, for example, the transduction of mechanical energy from the transmembrane domain into the porter domain, correlated motions of different subdomains within monomers, and cooperative effects between monomers. To this end, targeted molecular dynamics simulations have been employed either steering the whole protein complex or specific parts thereof. By forcing only parts of the complex towards specific conformational states, the risk for transient artificial conformations during the simulations is reduced. Distinct cooperative effects between the monomers in AcrB have been observed. Possible allosteric couplings have been identified providing microscopic insights that might be exploited to design more efficient inhibitors of efflux systems.
Collapse
|
26
|
Hinchliffe P, Greene NP, Paterson NG, Crow A, Hughes C, Koronakis V. Structure of the periplasmic adaptor protein from a major facilitator superfamily (MFS) multidrug efflux pump. FEBS Lett 2014; 588:3147-53. [PMID: 24996185 PMCID: PMC4158417 DOI: 10.1016/j.febslet.2014.06.055] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 10/28/2022]
Abstract
Periplasmic adaptor proteins are key components of bacterial tripartite efflux pumps. The 2.85 Å resolution structure of an MFS (major facilitator superfamily) pump adaptor, Aquifex aeolicus EmrA, shows linearly arranged α-helical coiled-coil, lipoyl, and β-barrel domains, but lacks the fourth membrane-proximal domain shown in other pumps to interact with the inner membrane transporter. The adaptor α-hairpin, which binds outer membrane TolC, is exceptionally long at 127 Å, and the β-barrel contains a conserved disordered loop. The structure extends the view of adaptors as flexible, modular components that mediate diverse pump assembly, and suggests that in MFS tripartite pumps a hexamer of adaptors could provide a periplasmic seal.
Collapse
Affiliation(s)
- Philip Hinchliffe
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Nicholas P Greene
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Neil G Paterson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Allister Crow
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Colin Hughes
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Vassilis Koronakis
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| |
Collapse
|
27
|
Fischer N, Raunest M, Schmidt TH, Koch DC, Kandt C. Efflux pump-mediated antibiotics resistance: Insights from computational structural biology. Interdiscip Sci 2014; 6:1-12. [DOI: 10.1007/s12539-014-0191-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 09/03/2013] [Accepted: 11/18/2013] [Indexed: 01/08/2023]
|
28
|
Greene NP, Hinchliffe P, Crow A, Ababou A, Hughes C, Koronakis V. Structure of an atypical periplasmic adaptor from a multidrug efflux pump of the spirochete Borrelia burgdorferi. FEBS Lett 2013; 587:2984-8. [PMID: 23851070 PMCID: PMC3807786 DOI: 10.1016/j.febslet.2013.06.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/26/2013] [Accepted: 06/28/2013] [Indexed: 11/30/2022]
Abstract
Periplasmic adaptors are essential to tripartite drug efflux pump assembly. We present the structure of the periplasmic adaptor BesA from Borrelia burgdorferi. BesA lacks the α-hairpin shown to underpin exit duct recruitment and pump assembly. Recruitment of the TolC exit duct must be different in this pump. The BesA structure has implications for proposed models of pump assembly.
Periplasmic adaptor proteins are essential components of bacterial tripartite multidrug efflux pumps. Here we report the 2.35 Å resolution crystal structure of the BesA adaptor from the spirochete Borrelia burgdorferi solved using selenomethionine derivatized protein. BesA shows the archetypal linear, flexible, multi-domain architecture evident among proteobacteria and retains the lipoyl, β-barrel and membrane-proximal domains that interact with the periplasmic domains of the inner membrane transporter. However, it lacks the α-hairpin domain shown to establish extensive coiled-coil interactions with the periplasmic entrance helices of the outer membrane-anchored TolC exit duct. This has implications for the modelling of assembled tripartite efflux pumps.
Collapse
|
29
|
Hinchliffe P, Symmons MF, Hughes C, Koronakis V. Structure and operation of bacterial tripartite pumps. Annu Rev Microbiol 2013; 67:221-42. [PMID: 23808339 DOI: 10.1146/annurev-micro-092412-155718] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In bacteria such as Pseudomonas aeruginosa and Escherichia coli, tripartite membrane machineries, or pumps, determine the efflux of small noxious molecules, such as detergents, heavy metals, and antibiotics, and the export of large proteins including toxins. They are therefore influential in bacterial survival, particularly during infections caused by multidrug-resistant pathogens. In these tripartite pumps an inner membrane transporter, typically an ATPase or proton antiporter, binds and translocates export or efflux substrates. In cooperation with a periplasmic adaptor protein it recruits and opens a TolC family cell exit duct, which is anchored in the outer membrane and projects across the periplasmic space between inner and outer membranes. Assembled tripartite pumps thus span the entire bacterial cell envelope. We review the atomic structures of each of the three pump components and discuss how these have allowed high-resolution views of tripartite pump assembly, operation, and possible inhibition.
Collapse
Affiliation(s)
- Philip Hinchliffe
- Department of Pathology, Cambridge University, Cambridge CB2 1QP, United Kingdom; , , ,
| | | | | | | |
Collapse
|
30
|
Ruggerone P, Vargiu AV, Collu F, Fischer N, Kandt C. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps. Comput Struct Biotechnol J 2013; 5:e201302008. [PMID: 24688701 PMCID: PMC3962194 DOI: 10.5936/csbj.201302008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 01/13/2023] Open
Abstract
Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Collapse
Affiliation(s)
- Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700, 09042 Monserrato (CA), Cagliari, Italy ; CNR-IOM, Unità SLACS, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700, 09042 Monserrato (CA), Cagliari, Italy ; CNR-IOM, Unità SLACS, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesca Collu
- Departement fu r Chemie und Biochemie, Universita t Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Nadine Fischer
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
| | - Christian Kandt
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
| |
Collapse
|
31
|
Wang B, Weng J, Fan K, Wang W. Interdomain flexibility and pH-induced conformational changes of AcrA revealed by molecular dynamics simulations. J Phys Chem B 2012; 116:3411-20. [PMID: 22339851 DOI: 10.1021/jp212221v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The membrane fusion protein (MFP) AcrA is proposed to link the inner membrane transporter AcrB and outer membrane protein TolC, forming the tripartite AcrAB-TolC efflux pump, and was shown to be functionally indispensible. Structural and EPR studies showed that AcrA has high conformational flexibility and exhibited pH-induced conformational change. In this study, we built the complete structure of AcrA through homology modeling and performed atomistic simulations of AcrA at different pH values. It was shown that the conformational flexibility of AcrA originates from the motions of α-hairpin and MP domains. The conformational dynamics of AcrA is sensitive to specific point mutations and pH values. In agreement with the EPR experiments, the interdomain motions were restrained upon lowering pH from 7.0 to 5.0 in the simulations. It was found that the protonation/deprotonation of His285 underlies the pH-regulated conformational dynamics of AcrA by disturbing the local hydrogen bond interactions, suggesting that the changes of pH in the periplasm accompanying the drug efflux could act as a signal to trigger the action of AcrA, which undergoes reversible conformational rearrangement.
Collapse
Affiliation(s)
- Beibei Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, PR China
| | | | | | | |
Collapse
|
32
|
Raunest M, Kandt C. Locked on one side only: ground state dynamics of the outer membrane efflux duct TolC. Biochemistry 2012; 51:1719-29. [PMID: 22313049 DOI: 10.1021/bi201814s] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Playing a major role in the expulsion of antibiotics and the secretion of cell toxins in conjunction with inner membrane transporters of three protein superfamilies, the outer membrane channel TolC occurs in at least two states blocking or permitting the passage of substrates. The details of the underlying gating mechanism are not fully understood. Addressing the questions of extracellular access control and periplasmic gating mechanism, we conducted a series of independent, unbiased 150-300 ns molecular dynamics simulations of wild-type TolC in a phospholipid membrane/150 mM NaCl water environment. We find that TolC opens and closes freely on the extracellular side, suggesting the absence of a gating mechanism on this side in the isolated protein. On the periplasmic side, we observe the outer periplasmic bottleneck region adopting in all simulations a conformation more open than the TolC wild-type crystal structures until in one run the successive binding of two sodium ions induces the transition to a conformation more closed than any of the available TolC X-ray structures. Concurrent with a heightened sodium residence probability near Asp374, the inner periplasmic bottleneck region at Asp374 remains closed throughout the simulations unless all NaCl is removed from the system, inducing a reopening of the outer and inner bottleneck. Our findings suggest that TolC is locked only on the periplasmic side in a sodium-dependent manner.
Collapse
Affiliation(s)
- Martin Raunest
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life and Medical Sciences Center, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany
| | | |
Collapse
|
33
|
McIntosh EDG. Efflux: how bacteria use pumps to control their microenvironment. Handb Exp Pharmacol 2012:153-166. [PMID: 23090601 DOI: 10.1007/978-3-642-28951-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Efflux pumps are a potent and clinically important cause of antibiotic resistance. The particular focus of this chapter is on the efflux pump as a target for antimicrobial therapy and the development of new antibacterials to address the efflux problem.Tigecycline is an example of how old antibiotics, in this case tetracyclines, which have become substrates for efflux pumps, can be extensively modified to restore antimicrobial activity and clinical efficacy.
Collapse
|
34
|
Mealman TD, Blackburn NJ, McEvoy MM. Metal export by CusCFBA, the periplasmic Cu(I)/Ag(I) transport system of Escherichia coli. CURRENT TOPICS IN MEMBRANES 2012; 69:163-96. [PMID: 23046651 DOI: 10.1016/b978-0-12-394390-3.00007-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High levels of metal ions have the potential to cause cellular toxicity through a variety of mechanisms; therefore, cells have developed numerous systems that regulate their intracellular concentrations. The Cus resistance system aids in protection of Escherichia coli from high levels of Cu(I) and Ag(I) by actively transporting these metal ions to the extracellular environment. The Cus system forms a continuous complex, CusCBA, that spans the inner membrane, periplasm, and outer membrane of Gram-negative bacteria, together with a novel fourth component, the periplasmic metallochaperone, CusF. The metal-binding sites of CusA, CusB, and CusF are exquisitely tuned for Cu(I) and Ag(I), and thus effectively discriminate these ions for transport from other metals that may be required in the cell. Furthermore, direct transfer of metal from protein to protein within the Cus system during the transport process is likely to reduce the potential toxicity posed by the free metal ions. Here we review the wealth of structural, biochemical, and genetic information on the Cus system, which demonstrates the many intriguing aspects of function for metal-transporting efflux systems.
Collapse
Affiliation(s)
- Tiffany D Mealman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | | | | |
Collapse
|
35
|
Gyimesi G, Ramachandran S, Kota P, Dokholyan NV, Sarkadi B, Hegedus T. ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2954-64. [PMID: 21840296 DOI: 10.1016/j.bbamem.2011.07.038] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 06/23/2011] [Accepted: 07/25/2011] [Indexed: 12/23/2022]
Abstract
ABC transporters play important roles in all types of organisms by participating in physiological and pathological processes. In order to modulate the function of ABC transporters, detailed knowledge regarding their structure and dynamics is necessary. Available structures of ABC proteins indicate three major conformations, a nucleotide-bound "bottom-closed" state with the two nucleotide binding domains (NBDs) tightly closed, and two nucleotide-free conformations, the "bottom-closed" and the "bottom-open", which differ in the extent of separation of the NBDs. However, it remains a question how the widely open conformation should be interpreted, and whether hydrolysis at one of the sites can drive conformational transitions while the NBDs remain in contact. To extend our knowledge, we have investigated the dynamic properties of the Sav1866 transporter using molecular dynamics (MD) simulations. We demonstrate that the replacement of one ATP by ADP alters the correlated motion patterns of the NBDs and the transmembrane domains (TMD). The results suggest that the hydrolysis of a single nucleotide could lead to extracellular closure, driving the transport cycle. Essential dynamics analysis of simulations suggests that single nucleotide hydrolysis can drive the system toward a "bottom-closed" apo conformation similar to that observed in the structure of the MsbA transporter. We also found significant structural instability of the "bottom-open" form of the transporters in simulations. Our results suggest that ATP hydrolysis at one of the sites promotes transport related conformational changes leading to the "bottom-closed" apo conformation, which could thus be physiologically more relevant for describing the structure of the apo state.
Collapse
Affiliation(s)
- Gergely Gyimesi
- Membrane Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | | | | | | | | | | |
Collapse
|
36
|
Bersch B, Derfoufi KM, De Angelis F, Auquier V, Ekendé EN, Mergeay M, Ruysschaert JM, Vandenbussche G. Structural and metal binding characterization of the C-terminal metallochaperone domain of membrane fusion protein SilB from Cupriavidus metallidurans CH34. Biochemistry 2011; 50:2194-204. [PMID: 21299248 DOI: 10.1021/bi200005k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Detoxification of heavy metal ions in Proteobacteria is tightly controlled by various systems regulating their sequestration and transport. In Cupriavidus metallidurans CH34, a model organism for heavy metal resistance studies, the sil determinant is potentially involved in the efflux of silver and copper ions. Proteins SilA, SilB, and SilC form a resistance nodulation cell division (RND)-based transport system in which SilB is the periplasmic adaptor protein belonging to the membrane fusion protein (MFP) family. In addition to the four domains typical of known MFPs, SilB has a fifth additional C-terminal domain, called SilB(440-521), which is characterized here. Structure and backbone dynamics of SilB(440-521) have been investigated using nuclear magnetic resonance, and the residues of the metal site were identified from (15)N- and (13)C-edited HSQC spectra. The solution structure and additional metal binding experiments demonstrated that this C-terminal domain folds independently of the rest of the protein and has a conformation and a Ag(+) and Cu(+) binding specificity similar to those determined for CusF from Escherichia coli. The small protein CusF plays a role in metal trafficking in the periplasm. The similarity with CusF suggests a potential metallochaperone role for SilB(440-521) that is discussed in the context of simultaneous expression of different determinants involved in copper resistance in C. metallidurans CH34.
Collapse
Affiliation(s)
- Beate Bersch
- CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Trépout S, Taveau JC, Benabdelhak H, Granier T, Ducruix A, Frangakis AS, Lambert O. Structure of reconstituted bacterial membrane efflux pump by cryo-electron tomography. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1953-60. [PMID: 20599691 DOI: 10.1016/j.bbamem.2010.06.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/07/2010] [Accepted: 06/18/2010] [Indexed: 11/19/2022]
Abstract
Complexes of OprM and MexA, two proteins of the MexA-MexB-OprM multidrug efflux pump from Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, were reconstituted into proteoliposomes by detergent removal. Stacks of protein layers with a constant height of 21nm, separated by lipid bilayers, were obtained at stoichiometry of 1:1 (w/w). Using cryo-electron microscopy and tomography, we showed that these protein layers were composed of MexA-OprM complexes self-assembled into regular arrays. Image processing of extracted sub-tomograms depicted the architecture of the bipartite complex sandwiched between two lipid bilayers, representing an environment close to that of the native whole pump (i.e. anchored between outer and inner membranes of P. aeruginosa). The MexA-OprM complex appeared as a cylindrical structure in which we were able to identify the OprM molecule and the MexA moiety. MexA molecules have a cylindrical shape prolonging the periplasmic helices of OprM, and widening near the lipid bilayer. The flared part is likely composed of two MexA domains adjacent to the lipid bilayer, although their precise organization was not reachable mainly due to their flexibility. Moreover, the intermembrane distance of 21nm indicated that the height of the bipartite complex is larger than that of the tripartite AcrA-AcrB-TolC built-up model in which TolC and AcrB are docked into contact. We proposed a model of MexA-OprM taking into account features of previous models based on AcrA-AcrB-TolC and our structural results providing clues to a possible mechanism of tripartite system assembly.
Collapse
Affiliation(s)
- Sylvain Trépout
- CBMN UMR 5248 CNRS-Université Bordeaux-ENITAB, IECB, Avenue des Facultés, F-33405 Talence, France
| | | | | | | | | | | | | |
Collapse
|
38
|
Schulz R, Vargiu AV, Collu F, Kleinekathöfer U, Ruggerone P. Functional rotation of the transporter AcrB: insights into drug extrusion from simulations. PLoS Comput Biol 2010; 6:e1000806. [PMID: 20548943 PMCID: PMC2883587 DOI: 10.1371/journal.pcbi.1000806] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 05/05/2010] [Indexed: 01/16/2023] Open
Abstract
The tripartite complex AcrAB-TolC is the major efflux system in Escherichia coli. It extrudes a wide spectrum of noxious compounds out of the bacterium, including many antibiotics. Its active part, the homotrimeric transporter AcrB, is responsible for the selective binding of substrates and energy transduction. Based on available crystal structures and biochemical data, the transport of substrates by AcrB has been proposed to take place via a functional rotation, in which each monomer assumes a particular conformation. However, there is no molecular-level description of the conformational changes associated with the rotation and their connection to drug extrusion. To obtain insights thereon, we have performed extensive targeted molecular dynamics simulations mimicking the functional rotation of AcrB containing doxorubicin, one of the two substrates that were co-crystallized so far. The simulations, including almost half a million atoms, have been used to test several hypotheses concerning the structure-dynamics-function relationship of this transporter. Our results indicate that, upon induction of conformational changes, the substrate detaches from the binding pocket and approaches the gate to the central funnel. Furthermore, we provide strong evidence for the proposed peristaltic transport involving a zipper-like closure of the binding pocket, responsible for the displacement of the drug. A concerted opening of the channel between the binding pocket and the gate further favors the displacement of the drug. This microscopically well-funded information allows one to identify the role of specific amino acids during the transitions and to shed light on the functioning of AcrB. In nature, bacteria have to resist several toxic threats to be able to survive, from bile acids in intestines up to antibiotics. The Escherichia coli bacterium, which usually is a commensal inhabitant of human intestines, can also acquire pathogenic properties which would harm the human body. To dispose of toxic compounds, E. coli has developed a protein machinery which is called “efflux pump”. Here, we studied the dynamics of the transporter protein AcrB, a component of the E. coli major efflux system, in complex with an antibiotic (doxorubicin). We used computer simulations to complement the existing experimental data. Our purpose was to gain more detailed insights into the pumping mechanism at the molecular level. In our simulations the drug leaves the binding pocket upon induction of functional rotation in the protein, although a complete extrusion was never observed. A peristaltic motion, which starts with a zipper-like closure of the interior of the protein, is an important step for the extrusion of the drug. Interestingly, such a peristaltic mechanism of pumping has been suggested before on the basis of structural data. The molecular details obtained in this study shall deepen the understanding of the functioning of the efflux pump.
Collapse
Affiliation(s)
- Robert Schulz
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
| | - Attilio V. Vargiu
- Istituto Officina dei Materiali del CNR, UOS SLACS and Dipartimento di Fisica, Universita' degli Studi di Cagliari, Monserrato, Italy
- * E-mail:
| | - Francesca Collu
- Istituto Officina dei Materiali del CNR, UOS SLACS and Dipartimento di Fisica, Universita' degli Studi di Cagliari, Monserrato, Italy
| | | | - Paolo Ruggerone
- Istituto Officina dei Materiali del CNR, UOS SLACS and Dipartimento di Fisica, Universita' degli Studi di Cagliari, Monserrato, Italy
| |
Collapse
|
39
|
Blair JMA, Piddock LJV. Structure, function and inhibition of RND efflux pumps in Gram-negative bacteria: an update. Curr Opin Microbiol 2009; 12:512-9. [DOI: 10.1016/j.mib.2009.07.003] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/02/2009] [Accepted: 07/08/2009] [Indexed: 01/07/2023]
|
40
|
Blair JMA, La Ragione RM, Woodward MJ, Piddock LJV. Periplasmic adaptor protein AcrA has a distinct role in the antibiotic resistance and virulence of Salmonella enterica serovar Typhimurium. J Antimicrob Chemother 2009; 64:965-72. [PMID: 19744979 DOI: 10.1093/jac/dkp311] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES AcrA can function as the periplasmic adaptor protein (PAP) in several RND tripartite efflux pumps, of which AcrAB-TolC is considered the most important. This system confers innate multiple antibiotic resistance. Disruption of acrB or tolC impairs the ability of Salmonella Typhimurium to colonize and persist in the host. The aim of this study was to investigate the role of AcrA alone in multidrug resistance and pathogenicity. METHODS The acrA gene was inactivated in Salmonella Typhimurium SL1344 by insertion of the aph gene and this mutant complemented with pWKS30acrA. The antimicrobial susceptibility of the mutant to six antibiotics as well as various dyes and detergents was determined. In addition, efflux activity was quantified. The ability of the mutant to adhere to, and invade, tissue culture cells in vitro was measured. RESULTS Following disruption of acrA, RT-PCR and western blotting confirmed that acrB/AcrB was still expressed when acrA was disrupted. The acrA mutant was hypersusceptible to antibiotics, dyes and detergents. In some cases, lower MICs were seen than for the acrB or tolC mutants. Efflux of the fluorescent dye Hoechst H33342 was less than in wild-type following disruption of acrA. acrA was also required for adherence to, and invasion of, tissue culture cells. CONCLUSIONS Inactivation of acrA conferred a phenotype distinct to that of acrB::aph and tolC::aph. These data indicate a role for AcrA distinct to that of other protein partners in both efflux of substrates and virulence.
Collapse
Affiliation(s)
- Jessica M A Blair
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | | | | |
Collapse
|
41
|
Reddy AS, Izmitli A, de Pablo JJ. Effect of trehalose on amyloid β (29–40)-membrane interaction. J Chem Phys 2009; 131:085101. [DOI: 10.1063/1.3193726] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
42
|
Abstract
Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.
Collapse
Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario K1A OK9, Canada
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202, USA
| |
Collapse
|
43
|
Abstract
Abstract
The tripartite efflux system AcrA/AcrB/TolC is the main pump in Escherichia coli for the efflux of multiple antibiotics, dyes, bile salts and detergents. The inner membrane component AcrB is central to substrate recognition and energy transduction and acts as a proton/drug antiporter. Recent structural studies show that homotrimeric AcrB can adopt different monomer conformations representing consecutive states in an allosteric functional rotation transport cycle. The conformational changes create an alternate access drug transport tunnel including a hydrophobic substrate binding pocket in one of the cycle intermediates.
Collapse
|
44
|
The assembled structure of a complete tripartite bacterial multidrug efflux pump. Proc Natl Acad Sci U S A 2009; 106:7173-8. [PMID: 19342493 DOI: 10.1073/pnas.0900693106] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria like Escherichia coli and Pseudomonas aeruginosa expel drugs via tripartite multidrug efflux pumps spanning both inner and outer membranes and the intervening periplasm. In these pumps a periplasmic adaptor protein connects a substrate-binding inner membrane transporter to an outer membrane-anchored TolC-type exit duct. High-resolution structures of all 3 components are available, but a pump model has been precluded by the incomplete adaptor structure, because of the apparent disorder of its N and C termini. We reveal that the adaptor termini assemble a beta-roll structure forming the final domain adjacent to the inner membrane. The completed structure enabled in vivo cross-linking to map intermolecular contacts between the adaptor AcrA and the transporter AcrB, defining a periplasmic interface between several transporter subdomains and the contiguous beta-roll, beta-barrel, and lipoyl domains of the adaptor. With short and long cross-links expressed as distance restraints, the flexible linear topology of the adaptor allowed a multidomain docking approach to model the transporter-adaptor complex, revealing that the adaptor docks to a transporter region of comparative stability distinct from those key to the proposed rotatory pump mechanism, putative drug-binding pockets, and the binding site of inhibitory DARPins. Finally, we combined this docking with our previous resolution of the AcrA hairpin-TolC interaction to develop a model of the assembled tripartite complex, satisfying all of the experimentally-derived distance constraints. This AcrA(3)-AcrB(3)-TolC(3) model presents a 610,000-Da, 270-A-long efflux pump crossing the entire bacterial cell envelope.
Collapse
|
45
|
Zgurskaya HI, Yamada Y, Tikhonova EB, Ge Q, Krishnamoorthy G. Structural and functional diversity of bacterial membrane fusion proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:794-807. [PMID: 19041958 DOI: 10.1016/j.bbapap.2008.10.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 10/21/2008] [Accepted: 10/22/2008] [Indexed: 10/21/2022]
Abstract
Membrane Fusion Proteins (MFPs) are functional subunits of multi-component transporters that perform diverse physiological functions in both Gram-positive and Gram-negative bacteria. MFPs associate with transporters belonging to Resistance-Nodulation-cell Division (RND), ATP-Binding Cassette (ABC) and Major Facilitator (MF) superfamilies of proteins. Recent studies suggested that MFPs interact with substrates and play an active role in transport reactions. In addition, the MFP-dependent transporters from Gram-negative bacteria recruit the outer membrane channels to expel various substrates across the outer membrane into external medium. This review is focused on the diversity, structure and molecular mechanism of MFPs that function in multidrug efflux. Using phylogenetic approaches we analyzed diversity and representation of multidrug MFPs in sequenced bacterial genomes. In addition to previously characterized MFPs from Gram-negative bacteria, we identified MFPs that associate with RND-, MF- and ABC-type transporters in Gram-positive bacteria. Sequence analyses showed that MFPs vary significantly in size (200-650 amino acid residues) with some of them lacking the signature alpha-helical domain of multidrug MFPs. Furthermore, many transport operons contain two- or three genes encoding distinct MFPs. We further discuss the diversity of MFPs in the context of current views on the mechanism and structure of MFP-dependent transporters.
Collapse
Affiliation(s)
- Helen I Zgurskaya
- University of Oklahoma Department of Chemistry and Biochemistry 620 Parrington Oval, Room 208 Norman, OK 73019, USA.
| | | | | | | | | |
Collapse
|
46
|
Abstract
Drug extrusion via efflux through a tripartite complex (an inner membrane pump, an outer membrane protein, and a periplasmic protein) is a widely used mechanism in Gram-negative bacteria. The outer membrane protein (TolC in Escherichia coli; OprM in Pseudomonas aeruginosa) forms a tunnel-like pore through the periplasmic space and the outer membrane. Molecular dynamics simulations of TolC have been performed, and are compared to simulations of Y362F/R367S mutant, and to simulations of its homolog OprM. The results reveal a complex pattern of conformation dynamics in the TolC protein. Two putative gate regions, located at either end of the protein, can be distinguished. These regions are the extracellular loops and the mouth of the periplasmic domain, respectively. The periplasmic gate has been implicated in the conformational changes leading from the closed x-ray structure to a proposed open state of TolC. Between the two gates, a peristaltic motion of the periplasmic domain is observed, which may facilitate transport of the solutes from one end of the tunnel to the other. The motions observed in the atomistic simulations are also seen in coarse-grained simulations in which the protein tertiary structure is represented by an elastic network model.
Collapse
|
47
|
Gristwood T, Fineran PC, Everson L, Salmond GPC. PigZ, a TetR/AcrR family repressor, modulates secondary metabolism via the expression of a putative four-component resistance-nodulation-cell-division efflux pump, ZrpADBC, in Serratia sp. ATCC 39006. Mol Microbiol 2008; 69:418-35. [PMID: 18485072 DOI: 10.1111/j.1365-2958.2008.06291.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Gram-negative enterobacterium, Serratia sp. ATCC 39006 synthesizes several secondary metabolites, including prodigiosin (Pig) and a carbapenem antibiotic (Car). A complex hierarchical network of regulatory proteins control Pig and Car production. In this study we characterize a TetR family regulator, PigZ, which represses transcription of a divergently transcribed putative resistance-nodulation-cell-division (RND) efflux pump, encoded by zrp (PigZ repressed pump) ADBC, via direct binding to the zrpA-pigZ intergenic region. Unusually, this putative RND pump contains two predicted membrane fusion proteins (MFPs), ZrpA and ZrpD. A mutation in pigZ resulted in multiple phenotypic changes, including exoenzyme production, motility and differential regulation of Pig and Car production. A polar suppressor mutation, within zrpA, restored all tested phenotypes to parental strain levels, indicating that the changes observed are due to the increase in expression of ZrpADBC in the absence of the repressor, PigZ. Genomic deletions of zrpA and zrpD indicate that the MFP ZrpD, but not ZrpA, is essential for activity of the putative pump. Bioinformatic analysis revealed that putative RND efflux pumps encoding two MFP components are not uncommon, particularly among plant-associated, Gram-negative bacteria. In addition, based on phylogenetic analysis, we propose that these pairs of MFPs consist of two distinct subtypes.
Collapse
Affiliation(s)
- Tamzin Gristwood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | | | | | | |
Collapse
|
48
|
Ortmans I, Prévost M. Analysis of the structural and dynamic properties of human N-terminal domain of apolipoprotein E by molecular dynamics simulations. J Phys Chem B 2008; 112:8730-6. [PMID: 18582019 DOI: 10.1021/jp8002678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Whereas the lipid-free N-terminal domain of apolipoprotein E (apoE-NT) adopts a four-helix bundle, the lipid-bound form is believed to undergo a large conformational change likely to be characterized by the opening of the bundle. ApoE-NT in a water/alcohol mixture was also shown to experience conformational changes exhibiting similarities with those induced upon lipid binding. The structure and dynamics of apoE-NT have been here investigated by analyzing 40 ns and 60 ns molecular dynamics simulations performed in water and in a water/propanol mixture, respectively. The overall structural properties show alterations of the tertiary structure of apoE-NT in the water/alcohol system in agreement with those observed experimentally. In contrast, in the water simulation, the sampled conformations remain closer to the crystal structure that served as a starting point for both simulations. Interestingly, several propanol molecules are seen to penetrate two hydrophobic regions of the bundle interior. One of these regions is enclosed in part by the short helix (H1') connecting helices 1 and 2 of the bundle which has been experimentally shown to be important for modulating lipid binding activity of apoE-NT. Principal component analysis of the water/propanol trajectory confirms that the region including H1' is the locus of the largest motion. Another region involves the loop connecting helix 2 and helix 3 which has been hypothesized to play the role of a hinge in the opening of the bundle.
Collapse
Affiliation(s)
- Isabelle Ortmans
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, CP 206/2, Bld du Triomphe, B-1050 Bruxelles, Belgium
| | | |
Collapse
|
49
|
Bagai I, Liu W, Rensing C, Blackburn NJ, McEvoy MM. Substrate-linked conformational change in the periplasmic component of a Cu(I)/Ag(I) efflux system. J Biol Chem 2007; 282:35695-702. [PMID: 17893146 DOI: 10.1074/jbc.m703937200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gram-negative bacteria utilize dual membrane resistance nodulation division-type efflux systems to export a variety of substrates. These systems contain an essential periplasmic component that is important for assembly of the protein complex. We show here that the periplasmic protein CusB from the Cus copper/silver efflux system has a critical role in Cu(I) and Ag(I) binding. Isothermal titration calorimetry experiments demonstrate that one Ag(I) ion is bound per CusB molecule with high affinity. X-ray absorption spectroscopy data indicate that the metal environment is an all-sulfur 3-coordinate environment. Candidates for the metal-coordinating residues were identified from sequence analysis, which showed four conserved methionine residues. Mutations of three of these methionine residues to isoleucine resulted in significant effects on CusB metal binding in vitro. Cells containing these CusB variants also show a decrease in their ability to grow on copper-containing plates, indicating an important functional role for metal binding by CusB. Gel filtration chromatography demonstrates that upon binding metal, CusB undergoes a conformational change to a more compact structure. Based on these structural and functional effects of metal binding, we propose that the periplasmic component of resistance nodulation division-type efflux systems plays an active role in export through substrate-linked conformational changes.
Collapse
Affiliation(s)
- Ireena Bagai
- Department of Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | | | |
Collapse
|
50
|
Lobedanz S, Bokma E, Symmons MF, Koronakis E, Hughes C, Koronakis V. A periplasmic coiled-coil interface underlying TolC recruitment and the assembly of bacterial drug efflux pumps. Proc Natl Acad Sci U S A 2007; 104:4612-7. [PMID: 17360572 PMCID: PMC1838649 DOI: 10.1073/pnas.0610160104] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacteria such as Escherichia coli and Pseudomonas aeruginosa expel antibiotics and other inhibitors via tripartite multidrug efflux pumps spanning the inner and outer membranes and the intervening periplasmic space. A key event in pump assembly is the recruitment of an outer membrane-anchored TolC exit duct by the adaptor protein of a cognate inner membrane translocase, establishing a contiguous transenvelope efflux pore. We describe the underlying interaction of juxtaposed periplasmic exit duct and adaptor coiled-coils in the widespread RND-type pump TolC/AcrAB of E. coli, using in vivo cross-linking to map the extent of intermolecular contacts. Cross-linking of site-specific TolC cysteine variants to wild-type AcrA adaptor identified residues on the lower alpha-helical barrel domain of TolC, defining a contiguous cluster close to the entrance aperture of the exit duct. Reciprocally, site-specific cross-linking of AcrA cysteine variants to wild-type TolC identified the interaction surface on the adaptor within the N-terminal alpha-helix of the AcrA coiled-coil. The experimental data allowed a data-driven docking approach to model the interaction surface central to pump assembly. The lowest energy docked model satisfying all of the cross-link distance constraints places the adaptor at the intramolecular groove formed by the TolC entrance helices, aligning the adaptor coiled-coil with the exposed TolC outer helix. A key feature of this positioning is that it allows space for the proposed movement of the inner coil of TolC during transition to its open state.
Collapse
Affiliation(s)
- Sune Lobedanz
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | - Evert Bokma
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | - Martyn F. Symmons
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | - Eva Koronakis
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | - Colin Hughes
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
- To whom correspondence should be addressed. E-mail:
| | - Vassilis Koronakis
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| |
Collapse
|