1
|
Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol 2024; 20:751-760. [PMID: 38480980 PMCID: PMC11142920 DOI: 10.1038/s41589-024-01562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/25/2024] [Indexed: 05/30/2024]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has the potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking the binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom-designed topologies.
Collapse
Affiliation(s)
- Marco Mravic
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Li He
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Huong T Kratochvil
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Hailin Hu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Sarah E Nick
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Weiya Bai
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Anne Edwards
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Yale Cancer Center, New Haven, CT, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
| |
Collapse
|
2
|
Dey S, Rout M, Pati S, Singh MK, Dehury B, Subudhi E. All-atoms molecular dynamics study to screen potent efflux pump inhibitors against KpnE protein of Klebsiella pneumoniae. J Biomol Struct Dyn 2024; 42:3492-3506. [PMID: 37218086 DOI: 10.1080/07391102.2023.2214232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
The Small Multidrug Resistance efflux pump protein KpnE, plays a pivotal role in multi-drug resistance in Klebsiella pneumoniae. Despite well-documented study of its close homolog, EmrE, from Escherichia coli, the mechanism of drug binding to KpnE remains obscure due to the absence of a high-resolution experimental structure. Herein, we exclusively elucidate its structure-function mechanism and report some of the potent inhibitors through drug repurposing. We used molecular dynamics simulation to develop a dimeric structure of KpnE and explore its dynamics in lipid-mimetic bilayers. Our study identified both semi-open and open conformations of KpnE, highlighting its importance in transport process. Electrostatic surface potential map suggests a considerable degree of similarity between KpnE and EmrE at the binding cleft, mostly occupied by negatively charged residues. We identify key amino acids Glu14, Trp63 and Tyr44, indispensable for ligand recognition. Molecular docking and binding free energy calculations recognizes potential inhibitors like acarbose, rutin and labetalol. Further validations are needed to confirm the therapeutic role of these compounds. Altogether, our membrane dynamics study uncovers the crucial charged patches, lipid-binding sites and flexible loop that could potentiate substrate recognition, transport mechanism and pave the way for development of novel inhibitors against K. pneumoniae.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Suchanda Dey
- Biomics and Biodiversity lab, Siksha 'O' Anusandhan (deemed to be) University, Bhubaneswar, Odisha, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Enketeswara Subudhi
- Biomics and Biodiversity lab, Siksha 'O' Anusandhan (deemed to be) University, Bhubaneswar, Odisha, India
| |
Collapse
|
3
|
Worm D, Grabe GJ, de Castro GV, Rabinovich S, Warm I, Isherwood K, Helaine S, Barnard A. Stapled Phd Peptides Inhibit Doc Toxin Induced Growth Arrest in Salmonella. ACS Chem Biol 2023; 18:2485-2494. [PMID: 38098459 PMCID: PMC10728895 DOI: 10.1021/acschembio.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 12/18/2023]
Abstract
Bacterial toxin inhibition is a promising approach to overcoming antibiotic failure. InSalmonella, knockout of the toxin Doc has been shown to significantly reduce the formation of antibiotic-tolerant persisters. Doc is a kinase that is inhibited in nontolerant cells by its cognate antitoxin, Phd. In this work, we have developed first-in-class stapled peptide antitoxin mimetics based on the Doc inhibitory sequence of Phd. After making a series of substitutions to improve bacterial uptake, we identified a lead stapled Phd peptide that is able to counteract Doc toxicity in Salmonella. This provides an exciting starting point for the further development of therapeutic peptides capable of reducing antibiotic persistence in pathogenic bacteria.
Collapse
Affiliation(s)
- Dennis
J. Worm
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Grzegorz J. Grabe
- Department
of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Guilherme V. de Castro
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Sofya Rabinovich
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Ian Warm
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Kira Isherwood
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Sophie Helaine
- Department
of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Anna Barnard
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| |
Collapse
|
4
|
Decewicz P, Romaniuk K, Gorecki A, Radlinska M, Dabrowska M, Wyszynska A, Dziewit L. Structure and functions of a multireplicon genome of Antarctic Psychrobacter sp. ANT_H3: characterization of the genetic modules suitable for the construction of the plasmid-vectors for cold-active bacteria. J Appl Genet 2023; 64:545-557. [PMID: 37145222 PMCID: PMC10457243 DOI: 10.1007/s13353-023-00759-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/01/2023] [Accepted: 04/22/2023] [Indexed: 05/06/2023]
Abstract
Among Psychrobacter spp., there are several multireplicon strains, carrying more than two plasmids. Psychrobacter sp. ANT_H3 carries as many as 11 extrachromosomal replicons, which is the highest number in Psychrobacter spp. Plasmids of this strain were subjected to detailed genomic analysis, which enables an insight into the structure and functioning of this multireplicon genome. The replication and conjugal transfer modules of ANT_H3 plasmids were analyzed functionally to discover their potential for being used as building blocks for the construction of novel plasmid-vectors for cold-active bacteria. It was shown that two plasmids have a narrow host range as they were not able to replicate in species other than Psychrobacter, while remaining plasmids had a wider host range and were functional in various Alpha- and Gammaproteobacteria. Moreover, it was confirmed that mobilization modules of seven plasmids were functional, i.e., could be mobilized for conjugal transfer by the RK2 conjugation system. Auxiliary genes were also distinguished in ANT_H3 plasmids, including these encoding putative DNA-protecting protein DprA, multidrug efflux SMR transporter of EmrE family, glycine cleavage system T protein, MscS small-conductance mechanosensitive channel protein, and two type II restriction-modification systems. Finally, all genome-retrieved plasmids of Psychrobacter spp. were subjected to complex genome- and proteome-based comparative analyses showing that Antarctic replicons are significantly different from plasmids from other locations.
Collapse
Affiliation(s)
- Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Krzysztof Romaniuk
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adrian Gorecki
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maria Dabrowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Wyszynska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
5
|
Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.526773. [PMID: 36824741 PMCID: PMC9949092 DOI: 10.1101/2023.02.13.526773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.
Collapse
|
6
|
Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. J Biol Chem 2022; 298:102482. [PMID: 36100040 PMCID: PMC9574504 DOI: 10.1016/j.jbc.2022.102482] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The small multidrug resistance (SMR) family is composed of widespread microbial membrane proteins that fulfill different transport functions. Four functional SMR subtypes have been identified, which variously transport the small, charged metabolite guanidinium, bulky hydrophobic drugs and antiseptics, polyamines, and glycolipids across the membrane bilayer. The transporters possess a minimalist architecture, with ∼100-residue subunits that require assembly into homodimers or heterodimers for transport. In part because of their simple construction, the SMRs are a tractable system for biochemical and biophysical analysis. Studies of SMR transporters over the last 25 years have yielded deep insights for diverse fields, including membrane protein topology and evolution, mechanisms of membrane transport, and bacterial multidrug resistance. Here, we review recent advances in understanding the structures and functions of SMR transporters. New molecular structures of SMRs representing two of the four functional subtypes reveal the conserved structural features that have permitted the emergence of disparate substrate transport functions in the SMR family and illuminate structural similarities with a distantly related membrane transporter family, SLC35/DMT.
Collapse
Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
| |
Collapse
|
7
|
Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
Collapse
Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
8
|
Shuai M, Zhang G, Zeng F, Fu Y, Liang X, Yuan L, Xu F, Gou W, Miao Z, Jiang Z, Wang J, Zhuo L, Chen Y, Ju F, Zheng J. Human Gut Antibiotic Resistome and Progression of Diabetes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104965. [PMID: 35142450 PMCID: PMC9008416 DOI: 10.1002/advs.202104965] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/13/2022] [Indexed: 05/02/2023]
Abstract
The antibiotic resistance crisis underlies globally increasing failures in treating deadly bacterial infections, largely due to the selection of antibiotic resistance genes (ARG) collection, known as the resistome, in human gut microbiota. So far, little is known about the relationship between gut antibiotic resistome and host metabolic disorders such as type 2 diabetes (T2D). Here, metagenomic landscape of gut antibiotic resistome is profiled in a large multiomics human cohort (n = 1210). There is a significant overall shift in gut antibiotic resistome structure among healthy, prediabetes, and T2D groups. It is found that larger ARG diversity is associated with a higher risk of T2D. The novel diabetes ARG score is positively associated with glycemic traits. Longitudinal validation analysis confirms that the ARG score is associated with T2D progression, characterized by the change of insulin resistance. Collectively, the data describe the profiles of gut antibiotic resistome and support its close relationship with T2D progression.
Collapse
Affiliation(s)
- Menglei Shuai
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Guoqing Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhou310030China
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhou310024China
| | - Fang‐fang Zeng
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
- Department of EpidemiologySchool of MedicineJinan UniversityGuangzhou510632China
| | - Yuanqing Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhou310024China
| | - Xinxiu Liang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Ling Yuan
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhou310030China
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhou310024China
| | - Fengzhe Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Wanglong Gou
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Zelei Miao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Zengliang Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhou310024China
| | - Jia‐ting Wang
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
| | - Lai‐bao Zhuo
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
| | - Yu‐ming Chen
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
| | - Feng Ju
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhou310030China
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhou310024China
| | - Ju‐Sheng Zheng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhou310024China
| |
Collapse
|
9
|
Kermani AA, Burata OE, Koff BB, Koide A, Koide S, Stockbridge RB. Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates. eLife 2022; 11:76766. [PMID: 35254261 PMCID: PMC9000954 DOI: 10.7554/elife.76766] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/06/2022] [Indexed: 11/13/2022] Open
Abstract
Proteins from the bacterial small multidrug resistance (SMR) family are proton-coupled exporters of diverse antiseptics and antimicrobials, including polyaromatic cations and quaternary ammonium compounds. The transport mechanism of the Escherichia coli transporter, EmrE, has been studied extensively, but a lack of high-resolution structural information has impeded a structural description of its molecular mechanism. Here, we apply a novel approach, multipurpose crystallization chaperones, to solve several structures of EmrE, including a 2.9 Å structure at low pH without substrate. We report five additional structures in complex with structurally diverse transported substrates, including quaternary phosphonium, quaternary ammonium, and planar polyaromatic compounds. These structures show that binding site tryptophan and glutamate residues adopt different rotamers to conform to disparate structures without requiring major rearrangements of the backbone structure. Structural and functional comparison to Gdx-Clo, an SMR protein that transports a much narrower spectrum of substrates, suggests that in EmrE, a relatively sparse hydrogen bond network among binding site residues permits increased sidechain flexibility.
Collapse
Affiliation(s)
- Ali A Kermani
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Olive E Burata
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - B Ben Koff
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, United States
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, United States
| | - Randy B Stockbridge
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| |
Collapse
|
10
|
Exploring cryo-electron microscopy with molecular dynamics. Biochem Soc Trans 2022; 50:569-581. [PMID: 35212361 DOI: 10.1042/bst20210485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022]
Abstract
Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.
Collapse
|
11
|
High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport. Nat Commun 2022; 13:991. [PMID: 35181664 PMCID: PMC8857205 DOI: 10.1038/s41467-022-28556-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/27/2022] [Indexed: 12/20/2022] Open
Abstract
The homo-dimeric bacterial membrane protein EmrE effluxes polyaromatic cationic substrates in a proton-coupled manner to cause multidrug resistance. We recently determined the structure of substrate-bound EmrE in phospholipid bilayers by measuring hundreds of protein-ligand HN–F distances for a fluorinated substrate, 4-fluoro-tetraphenylphosphonium (F4-TPP+), using solid-state NMR. This structure was solved at low pH where one of the two proton-binding Glu14 residues is protonated. Here, to understand how substrate transport depends on pH, we determine the structure of the EmrE-TPP complex at high pH, where both Glu14 residues are deprotonated. The high-pH complex exhibits an elongated and hydrated binding pocket in which the substrate is similarly exposed to the two sides of the membrane. In contrast, the low-pH complex asymmetrically exposes the substrate to one side of the membrane. These pH-dependent EmrE conformations provide detailed insights into the alternating-access model, and suggest that the high-pH conformation may facilitate proton binding in the presence of the substrate, thus accelerating the conformational change of EmrE to export the substrate. EmrE transporter effluxes cationic substrates across lipid membranes in a pH-coupled manner. Here, the authors solve the structure of ligand-bound EmrE at high pH by NMR, with insights into the transport mechanism.
Collapse
|
12
|
Sommers KJ, Michaud ME, Hogue CE, Scharnow AM, Amoo LE, Petersen AA, Carden RG, Minbiole KPC, Wuest WM. Quaternary Phosphonium Compounds: An Examination of Non-Nitrogenous Cationic Amphiphiles That Evade Disinfectant Resistance. ACS Infect Dis 2022; 8:387-397. [PMID: 35077149 PMCID: PMC8996050 DOI: 10.1021/acsinfecdis.1c00611] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quaternary ammonium compounds (QACs) serve as mainstays in the formulation of disinfectants and antiseptics. However, an over-reliance and misuse of our limited QAC arsenal has driven the development and spread of resistance to these compounds, as well as co-resistance to common antibiotics. Extensive use of these compounds throughout the COVID-19 pandemic thus raises concern for the accelerated proliferation of antimicrobial resistance and demands for next-generation antimicrobials with divergent architectures that may evade resistance. To this end, we endeavored to expand beyond canonical ammonium scaffolds and examine quaternary phosphonium compounds (QPCs). Accordingly, a synthetic and biological investigation into a library of novel QPCs unveiled biscationic QPCs to be effective antimicrobial scaffolds with improved broad-spectrum activities compared to commercial QACs. Notably, a subset of these compounds was found to be less effective against a known QAC-resistant strain of MRSA. Bioinformatic analysis revealed the unique presence of a family of small multiresistant transporter proteins, hypothesized to enable efflux-mediated resistance to QACs and QPCs. Further investigation of this resistance mechanism through efflux-pump inhibition and membrane depolarization assays illustrated the superior ability of P6P-10,10 to perturb the cell membrane and exert the observed broad-spectrum potency compared to its commercial counterparts. Collectively, this work highlights the promise of biscationic phosphonium compounds as next-generation disinfectant molecules with potent bioactivities, thereby laying the foundation for future studies into the synthesis and biological investigation of this nascent antimicrobial class.
Collapse
Affiliation(s)
| | | | - Cody E. Hogue
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Amber M. Scharnow
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Lauren E. Amoo
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Ashley A. Petersen
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Robert G. Carden
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Kevin P. C. Minbiole
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
13
|
Abstract
Constrained peptides represent a relatively new class of biologic therapeutics, which have the potential to overcome several limitations of small-molecule drugs, and of designed antibodies. Because of their modest size, the rational design of such peptides is becoming increasingly amenable to computer simulation; multi-microsecond molecular dynamic (MD) simulations are now routinely possible on consumer-grade graphical processors (GPUs). Here, we describe the procedures for performing and analyzing MD simulations of hydrocarbon-stapled peptides using the CHARMM energy function, in isolation and in complex with a binding partner, to investigate their conformational properties and to compute changes in their binding affinity upon mutation.
Collapse
Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Aravinda Munasinghe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France.
| |
Collapse
|
14
|
Li J, Sae Her A, Traaseth NJ. Asymmetric protonation of glutamate residues drives a preferred transport pathway in EmrE. Proc Natl Acad Sci U S A 2021; 118:e2110790118. [PMID: 34607959 PMCID: PMC8521673 DOI: 10.1073/pnas.2110790118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
EmrE is an Escherichia coli multidrug efflux pump and member of the small multidrug resistance (SMR) family that transports drugs as a homodimer by harnessing energy from the proton motive force. SMR family transporters contain a conserved glutamate residue in transmembrane 1 (Glu14 in EmrE) that is required for binding protons and drugs. Yet the mechanism underlying proton-coupled transport by the two glutamate residues in the dimer remains unresolved. Here, we used NMR spectroscopy to determine acid dissociation constants (pKa ) for wild-type EmrE and heterodimers containing one or two Glu14 residues in the dimer. For wild-type EmrE, we measured chemical shifts of the carboxyl side chain of Glu14 using solid-state NMR in lipid bilayers and obtained unambiguous evidence on the existence of asymmetric protonation states. Subsequent measurements of pKa values for heterodimers with a single Glu14 residue showed no significant differences from heterodimers with two Glu14 residues, supporting a model where the two Glu14 residues have independent pKa values and are not electrostatically coupled. These insights support a transport pathway with well-defined protonation states in each monomer of the dimer, including a preferred cytoplasmic-facing state where Glu14 is deprotonated in monomer A and protonated in monomer B under pH conditions in the cytoplasm of E. coli Our findings also lead to a model, hop-free exchange, which proposes how exchangers with conformation-dependent pKa values reduce proton leakage. This model is relevant to the SMR family and transporters comprised of inverted repeat domains.
Collapse
Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, New York, NY 10003
| | - Ampon Sae Her
- Department of Chemistry, New York University, New York, NY 10003
| | | |
Collapse
|
15
|
Jurasz J, Bagiński M, Czub J, Wieczór M. Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE. PLoS Comput Biol 2021; 17:e1009454. [PMID: 34613958 PMCID: PMC8523053 DOI: 10.1371/journal.pcbi.1009454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/18/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
The current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the smallest known ligand transporters that confers resistance to aromatic cations in a number of clinically relevant species. As an asymmetric homodimer undergoing an “alternating access” protomer-swap conformational change, it serves as a model for the mechanistic understanding of more complex drug transporters. Here, we present a free energy and solvent accessibility analysis that indicates the presence of two complementary ligand translocation pathways that remain operative in a broad range of conditions. Our simulations show a previously undescribed desolvated apo state and anticorrelated accessibility in the ligand-bound state, explaining on a structural level why EmrE does not disrupt the pH gradient through futile proton transfer. By comparing the behavior of a number of model charged and/or aromatic ligands, we also explain the origin of selectivity of EmrE towards a broad class of aromatic cations. Finally, we explore unbiased pathways of ligand entry and exit to identify correlated structural changes implicated in ligand binding and release, as well as characterize key intermediates of occupancy changes. EmrE is a prototypical bacterial multidrug transporter (MDR) that confers resistance to drugs and antiseptics. Due to its structural simplicity, its mechanism of ligand recognition and translocation are relevant for a wide class of transporters. This proton-coupled antiport expels aromatic cations from the cytoplasm using the alternating access mechanism, achieving impressive levels of efficiency and robustness. Our protonation-specific free energy profiles, Grotthuss wire analyses and equilibrium simulations show how a deceivingly simple system can exchange ions with robustness and precision, hopefully inspiring rational efforts to design new MDR inhibitors.
Collapse
Affiliation(s)
- Jakub Jurasz
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, Gdansk, Poland
| | - Maciej Bagiński
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, Gdansk, Poland
- BioTechMed Center, Gdansk University of Technology, Gdansk, Poland
| | - Jacek Czub
- BioTechMed Center, Gdansk University of Technology, Gdansk, Poland
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Miłosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
- Molecular Modeling and Bioinformatics Group, IRB Barcelona, Barcelona, Spain
- * E-mail:
| |
Collapse
|
16
|
Jubair N, Rajagopal M, Chinnappan S, Abdullah NB, Fatima A. Review on the Antibacterial Mechanism of Plant-Derived Compounds against Multidrug-Resistant Bacteria (MDR). EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:3663315. [PMID: 34447454 PMCID: PMC8384518 DOI: 10.1155/2021/3663315] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/27/2021] [Accepted: 07/24/2021] [Indexed: 02/06/2023]
Abstract
Microbial resistance has progressed rapidly and is becoming the leading cause of death globally. The spread of antibiotic-resistant microorganisms has been a significant threat to the successful therapy against microbial infections. Scientists have become more concerned about the possibility of a return to the pre-antibiotic era. Thus, searching for alternatives to fight microorganisms has become a necessity. Some bacteria are naturally resistant to antibiotics, while others acquire resistance mainly by the misuse of antibiotics and the emergence of new resistant variants through mutation. Since ancient times, plants represent the leading source of drugs and alternative medicine for fighting against diseases. Plants are rich sources of valuable secondary metabolites, such as alkaloids, quinones, tannins, terpenoids, flavonoids, and polyphenols. Many studies focus on plant secondary metabolites as a potential source for antibiotic discovery. They have the required structural properties and can act by different mechanisms. This review analyses the antibiotic resistance strategies produced by multidrug-resistant bacteria and explores the phytochemicals from different classes with documented antimicrobial action against resistant bacteria, either alone or in combination with traditional antibiotics.
Collapse
Affiliation(s)
- Najwan Jubair
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | - Mogana Rajagopal
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | - Sasikala Chinnappan
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | | | - Ayesha Fatima
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Turkey
| |
Collapse
|
17
|
Bacterial Resistance to Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10050593. [PMID: 34067579 PMCID: PMC8157006 DOI: 10.3390/antibiotics10050593] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial pathogens as causative agents of infection constitute an alarming concern in the public health sector. In particular, bacteria with resistance to multiple antimicrobial agents can confound chemotherapeutic efficacy towards infectious diseases. Multidrug-resistant bacteria harbor various molecular and cellular mechanisms for antimicrobial resistance. These antimicrobial resistance mechanisms include active antimicrobial efflux, reduced drug entry into cells of pathogens, enzymatic metabolism of antimicrobial agents to inactive products, biofilm formation, altered drug targets, and protection of antimicrobial targets. These microbial systems represent suitable focuses for investigation to establish the means for their circumvention and to reestablish therapeutic effectiveness. This review briefly summarizes the various antimicrobial resistance mechanisms that are harbored within infectious bacteria.
Collapse
|
18
|
Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
Collapse
Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
| |
Collapse
|
19
|
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases. J Mol Biol 2021; 433:167005. [PMID: 33891902 DOI: 10.1016/j.jmb.2021.167005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023]
Abstract
Infectious diseases present a major threat to public health globally. Pathogens can acquire resistance to anti-infectious agents via several means including transporter-mediated efflux. Typically, multidrug transporters feature spacious, dynamic, and chemically malleable binding sites to aid in the recognition and transport of chemically diverse substrates across cell membranes. Here, we discuss recent structural investigations of multidrug transporters involved in resistance to infectious diseases that belong to the ATP-binding cassette (ABC) superfamily, the major facilitator superfamily (MFS), the drug/metabolite transporter (DMT) superfamily, the multidrug and toxic compound extrusion (MATE) family, the small multidrug resistance (SMR) family, and the resistance-nodulation-division (RND) superfamily. These structural insights provide invaluable information for understanding and combatting multidrug resistance.
Collapse
|
20
|
Nierzwicki Ł, Palermo G. Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules. Front Mol Biosci 2021; 8:641208. [PMID: 33884260 PMCID: PMC8053777 DOI: 10.3389/fmolb.2021.641208] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today's cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution density maps obtained for protein flexible domains, as well as the ensemble of coexisting conformational states arising from cryo-EM, poses new challenges and opportunities for Molecular Dynamics (MD) simulations. With the ability to describe the biomolecular dynamics at the atomic level, MD can extend the capabilities of cryo-EM, capturing the conformational variability and predicting biologically relevant short-lived conformational states. Here, we report about the state-of-the-art MD procedures that are currently used to refine, reconstruct and interpret cryo-EM maps. We show the capability of MD to predict short-lived conformational states, finding remarkable confirmation by cryo-EM structures subsequently solved. This has been the case of the CRISPR-Cas9 genome editing machinery, whose catalytically active structure has been predicted through both long-time scale MD and enhanced sampling techniques 2 years earlier than cryo-EM. In summary, this contribution remarks the ability of MD to complement cryo-EM, describing conformational landscapes and relating structural transitions to function, ultimately discerning relevant short-lived conformational states and providing mechanistic knowledge of biological function.
Collapse
Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California, Riverside, CA, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, CA, United States
- Department of Chemistry, University of California, Riverside, CA, United States
| |
Collapse
|
21
|
Reding C, Catalán P, Jansen G, Bergmiller T, Wood E, Rosenstiel P, Schulenburg H, Gudelj I, Beardmore R. The Antibiotic Dosage of Fastest Resistance Evolution: gene amplifications underpinning the inverted-U. Mol Biol Evol 2021; 38:3847-3863. [PMID: 33693929 PMCID: PMC8382913 DOI: 10.1093/molbev/msab025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To determine the dosage at which antibiotic resistance evolution is most rapid, we treated Escherichia coli in vitro, deploying the antibiotic erythromycin at dosages ranging from zero to high. Adaptation was fastest just below erythromycin’s minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis: simultaneous selection for copy number variation in three resistance mechanisms which exhibited an “inverted-U” pattern of dose-dependence, as did several insertion sequences and an integron. Many genes did not conform to this pattern, however, reflecting changes in selection as dose increased: putative media adaptation polymorphisms at zero antibiotic dosage gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux amplifications dominated at the highest dosages. All treatments exhibited E. coli increases in the copy number of efflux operons acrAB and emrE at rates that correlated with increases in population density. For strains where the inverted-U was no longer observed following the genetic manipulation of acrAB, it could be recovered by prolonging the antibiotic treatment at subMIC dosages.
Collapse
Affiliation(s)
- Carlos Reding
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Pablo Catalán
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.,Grupo Interdisciplinar de Sistemas Complejos (GISC), Departamento de Matemáticas, Universidad Carlos III, Madrid, Spain
| | | | | | - Emily Wood
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Phillip Rosenstiel
- Institute of Clinical Molecular Biology (IKMB), CAU Kiel, Kiel 24105, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, CAU Kiel, Kiel 24118, Germany
| | - Ivana Gudelj
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Robert Beardmore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| |
Collapse
|
22
|
Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers. Nat Commun 2021; 12:172. [PMID: 33420032 PMCID: PMC7794478 DOI: 10.1038/s41467-020-20468-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/01/2020] [Indexed: 01/29/2023] Open
Abstract
The dimeric transporter, EmrE, effluxes polyaromatic cationic drugs in a proton-coupled manner to confer multidrug resistance in bacteria. Although the protein is known to adopt an antiparallel asymmetric topology, its high-resolution drug-bound structure is so far unknown, limiting our understanding of the molecular basis of promiscuous transport. Here we report an experimental structure of drug-bound EmrE in phospholipid bilayers, determined using 19F and 1H solid-state NMR and a fluorinated substrate, tetra(4-fluorophenyl) phosphonium (F4-TPP+). The drug-binding site, constrained by 214 protein-substrate distances, is dominated by aromatic residues such as W63 and Y60, but is sufficiently spacious for the tetrahedral drug to reorient at physiological temperature. F4-TPP+ lies closer to the proton-binding residue E14 in subunit A than in subunit B, explaining the asymmetric protonation of the protein. The structure gives insight into the molecular mechanism of multidrug recognition by EmrE and establishes the basis for future design of substrate inhibitors to combat antibiotic resistance.
Collapse
|
23
|
The structural basis of promiscuity in small multidrug resistance transporters. Nat Commun 2020; 11:6064. [PMID: 33247110 PMCID: PMC7695847 DOI: 10.1038/s41467-020-19820-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family’s extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations. Gdx-Clo is a bacterial transporter from the small multidrug resistance (SMR) family. Here, the authors use solid supported membrane electrophysiology to characterize Gdx-Clo functionally and report crystal structures of Gdx-Clo which confirm the dual topology architecture and offer insight into substrate binding and transport mechanism.
Collapse
|
24
|
Abstract
Acinetobacter baumannii has become challenging to treat due to its multidrug resistance mediated by active drug efflux pumps. The prototype member of the proteobacterial antimicrobial compound efflux (PACE) family, AceI of A. baumannii, is implicated in the transport of widely used antiseptic chlorhexidine, while AceR is associated with regulating the expression of the aceI gene. Here we apply native mass spectrometry to show that AceI forms dimers at high pH, and that chlorhexidine binding facilitates the functional form of the protein. Also, we demonstrate how AceR affects the interaction between RNA polymerase and promoter DNA both in the presence and in the absence of chlorhexidine. Overall, these results provide insight into the assembly and regulation of the PACE family. Few antibiotics are effective against Acinetobacter baumannii, one of the most successful pathogens responsible for hospital-acquired infections. Resistance to chlorhexidine, an antiseptic widely used to combat A. baumannii, is effected through the proteobacterial antimicrobial compound efflux (PACE) family. The prototype membrane protein of this family, AceI (Acinetobacter chlorhexidine efflux protein I), is encoded for by the aceI gene and is under the transcriptional control of AceR (Acinetobacter chlorhexidine efflux protein regulator), a LysR-type transcriptional regulator (LTTR) protein. Here we use native mass spectrometry to probe the response of AceI and AceR to chlorhexidine assault. Specifically, we show that AceI forms dimers at high pH, and that binding to chlorhexidine facilitates the functional form of the protein. Changes in the oligomerization of AceR to enable interaction between RNA polymerase and promoter DNA were also observed following chlorhexidine assault. Taken together, these results provide insight into the assembly of PACE family transporters and their regulation via LTTR proteins on drug recognition and suggest potential routes for intervention.
Collapse
|
25
|
Jiang T, Wen PC, Trebesch N, Zhao Z, Pant S, Kapoor K, Shekhar M, Tajkhorshid E. Computational Dissection of Membrane Transport at a Microscopic Level. Trends Biochem Sci 2020; 45:202-216. [PMID: 31813734 PMCID: PMC7024014 DOI: 10.1016/j.tibs.2019.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 01/28/2023]
Abstract
Membrane transporters are key gatekeeper proteins at cellular membranes that closely control the traffic of materials. Their function relies on structural rearrangements of varying degrees that facilitate substrate translocation across the membrane. Characterizing these functionally important molecular events at a microscopic level is key to our understanding of membrane transport, yet challenging to achieve experimentally. Recent advances in simulation technology and computing power have rendered molecular dynamics (MD) simulation a powerful biophysical tool to investigate a wide range of dynamical events spanning multiple spatial and temporal scales. Here, we review recent studies of diverse membrane transporters using computational methods, with an emphasis on highlighting the technical challenges, key lessons learned, and new opportunities to illuminate transporter structure and function.
Collapse
Affiliation(s)
- Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Po-Chao Wen
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Noah Trebesch
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhiyu Zhao
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karan Kapoor
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinal Shekhar
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|
26
|
Leninger M, Sae Her A, Traaseth NJ. Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations. eLife 2019; 8:48909. [PMID: 31637997 PMCID: PMC6805155 DOI: 10.7554/elife.48909] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
Transporters from bacteria to humans contain inverted repeat domains thought to arise evolutionarily from the fusion of smaller membrane protein genes. Association between these domains forms the functional unit that enables transporters to adopt distinct conformations necessary for function. The small multidrug resistance (SMR) family provides an ideal system to explore the role of mutations in altering conformational preference since transporters from this family consist of antiparallel dimers that resemble the inverted repeats present in larger transporters. Here, we show using NMR spectroscopy how a single conservative mutation introduced into an SMR dimer is sufficient to change the resting conformation and function in bacteria. These results underscore the dynamic energy landscape for transporters and demonstrate how conservative mutations can influence structure and function.
Collapse
Affiliation(s)
- Maureen Leninger
- Department of Chemistry, New York University, New York, United States
| | - Ampon Sae Her
- Department of Chemistry, New York University, New York, United States
| | | |
Collapse
|
27
|
Kobylka J, Kuth MS, Müller RT, Geertsma ER, Pos KM. AcrB: a mean, keen, drug efflux machine. Ann N Y Acad Sci 2019; 1459:38-68. [PMID: 31588569 DOI: 10.1111/nyas.14239] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria are intrinsically resistant against cytotoxic substances by means of their outer membrane and a network of multidrug efflux systems, acting in synergy. Efflux pumps from various superfamilies with broad substrate preferences sequester and pump drugs across the inner membrane to supply the highly polyspecific and powerful tripartite resistance-nodulation-cell division (RND) efflux pumps with compounds to be extruded across the outer membrane barrier. In Escherichia coli, the tripartite efflux system AcrAB-TolC is the archetype RND multiple drug efflux pump complex. The homotrimeric inner membrane component acriflavine resistance B (AcrB) is the drug specificity and energy transduction center for the drug/proton antiport process. Drugs are bound and expelled via a cycle of mainly three consecutive states in every protomer, constituting a flexible alternating access channel system. This review recapitulates the molecular basis of drug and inhibitor binding, including mechanistic insights into drug efflux by AcrB. It also summarizes 17 years of mutational analysis of the gene acrB, reporting the effect of every substitution on the ability of E. coli to confer resistance toward antibiotics (http://goethe.link/AcrBsubstitutions). We emphasize the functional robustness of AcrB toward single-site substitutions and highlight regions that are more sensitive to perturbation.
Collapse
Affiliation(s)
- Jessica Kobylka
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Miriam S Kuth
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Reinke T Müller
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
28
|
Peptide-Based Efflux Pump Inhibitors of the Small Multidrug Resistance Protein from Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.00730-19. [PMID: 31209007 DOI: 10.1128/aac.00730-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/09/2019] [Indexed: 01/04/2023] Open
Abstract
Bacteria have acquired multiple mechanisms to evade the lethal effects of current therapeutics, hindering treatment of bacterial infections, such as those caused by the pathogen Pseudomonas aeruginosa, which is responsible for nosocomial and cystic fibrosis lung infections. One resistance mechanism involves membrane-embedded multidrug efflux pumps that can effectively extrude an array of substrates, including common antibiotics, dyes, and biocides. Among these is a small multidrug resistance (SMR) efflux protein, consisting of four transmembrane (TM) helices, that functions as an antiparallel dimer. TM helices 1 to 3 (TM1 to TM3) comprise the substrate binding pocket, while TM4 contains a GG7 heptad sequence motif that mediates the SMR TM4-TM4 dimerization. In the present work, we synthesized a series of peptides containing the residues centered on the TM4-TM4 binding interface found in the P. aeruginosa SMR (PAsmr), typified by Ac-Ala-(Sar)3-LLGIGLIIAGVLV-KKK-NH2 (helix-helix interaction residues are underlined). Here, the acetylated N-terminal sarcosine (N-methyl-Gly) tag [Ac-Ala-(Sar)3] promotes membrane penetration, while the C-terminal Lys tag promotes selectivity for the negatively charged bacterial membranes. This peptide was observed to competitively disrupt PAsmr-mediated efflux, as measured by efflux inhibition of the fluorescent dye ethidium bromide, while having no effect on cell membrane integrity. Alternatively, a corresponding peptide in which the TM4 binding motif is scrambled was inactive in this assay. In addition, when Escherichia coli cells expressing PAsmr were combined with sublethal concentrations of several biocides, growth was significantly inhibited when peptide was added, notably, by up to 95% with the disinfectant benzylalkonium chloride. These results demonstrate promise for an efflux pump inhibitor to address the increasing threat of antibiotic-resistant bacteria.
Collapse
|
29
|
Wu C, Wynne SA, Thomas NE, Uhlemann EM, Tate CG, Henzler-Wildman KA. Identification of an Alternating-Access Dynamics Mutant of EmrE with Impaired Transport. J Mol Biol 2019; 431:2777-2789. [PMID: 31158365 PMCID: PMC6599891 DOI: 10.1016/j.jmb.2019.05.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 11/25/2022]
Abstract
Proteins that perform active transport must alternate the access of a binding site, first to one side of a membrane and then to the other, resulting in the transport of bound substrates across the membrane. To better understand this process, we sought to identify mutants of the small multidrug resistance transporter EmrE with reduced rates of alternating access. We performed extensive scanning mutagenesis by changing every amino acid residue to Val, Ala, or Gly, and then screening the drug resistance phenotypes of the resulting mutants. We identified EmrE mutants that had impaired transport activity but retained the ability to bind substrate and further tested their alternating access rates using NMR. Ultimately, we were able to identify a single mutation, S64V, which significantly reduced the rate of alternating access but did not impair substrate binding. Six other transport-impaired mutants did not have reduced alternating access rates, highlighting the importance of other aspects of the transport cycle to achieve drug resistance activity in vivo. To better understand the transport cycle of EmrE, efforts are now underway to determine a high-resolution structure using the S64V mutant identified here.
Collapse
Affiliation(s)
- Chao Wu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, MO 63110, USA
| | | | - Nathan E Thomas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eva-Maria Uhlemann
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, MO 63110, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|