1
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Piselli C, Golla VK, Benz R, Kleinekathöfer U. Importance of the lysine cluster in the translocation of anions through the pyrophosphate specific channel OprO. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184086. [PMID: 36370909 DOI: 10.1016/j.bbamem.2022.184086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium with an intrinsic resistance towards antibiotics due to the lack of a large diffusion pores. Exchange of substances with the environment is done mainly through a set of narrow and substrate-specific porins in its outer membrane that filter molecules according to their size and chemical composition. Among these proteins are OprP and OprO involved in the selective uptake of mono- and pyrophosphates, respectively. Both proteins are homotrimers and each monomer features an hourglass-shaped channel structure including a periplasmic cavity with a lysine cluster. In this study, we focus on the characterization of this lysine cluster in OprO. The importance of these lysine residues was shown with alanine substitutions in single channel conductance experiments, by titration of mono- and pyrophosphate in multi-channel analysis and by molecular dynamics simulations. All obtained data demonstrated that the closer the mutated lysine residues are to arginine 133, the lower gets the single channel conductance. It was found that the ion flow through each monomer can follow two different lysine paths indicating that phosphate ions have a larger freedom on the periplasmic side of the constriction region. Our results emphasize the important role of the lysine residue 121 in the binding site together with arginine 133 and aspartic acid 94. An improved understanding of the ion mobility across these channels can potentially lead to an optimized permeation of (phosphonic acid containing) antibiotics through the outer membrane of P. aeruginosa and the development of new drug molecules.
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Affiliation(s)
- Claudio Piselli
- School of Science, Jacobs University Bremen, Campusring 1, 28759 Bremen, Germany
| | - Vinaya Kumar Golla
- School of Science, Jacobs University Bremen, Campusring 1, 28759 Bremen, Germany
| | - Roland Benz
- School of Science, Jacobs University Bremen, Campusring 1, 28759 Bremen, Germany
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2
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Sowlati-Hashjin S, Gandhi A, Garton M. Dawn of a New Era for Membrane Protein Design. BIODESIGN RESEARCH 2022; 2022:9791435. [PMID: 37850134 PMCID: PMC10521746 DOI: 10.34133/2022/9791435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/20/2022] [Indexed: 10/19/2023] Open
Abstract
A major advancement has recently occurred in the ability to predict protein secondary structure from sequence using artificial neural networks. This new accessibility to high-quality predicted structures provides a big opportunity for the protein design community. It is particularly welcome for membrane protein design, where the scarcity of solved structures has been a major limitation of the field for decades. Here, we review the work done to date on the membrane protein design and set out established and emerging tools that can be used to most effectively exploit this new access to structures.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Aanshi Gandhi
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
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3
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Khalid S, Schroeder C, Bond PJ, Duncan AL. What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35294337 PMCID: PMC9558347 DOI: 10.1099/mic.0.001165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial cell envelopes are compositionally complex and crowded and while highly dynamic in some areas, their molecular motion is very limited, to the point of being almost static in others. Therefore, it is no real surprise that studying them at high resolution across a range of temporal and spatial scales requires a number of different techniques. Details at atomistic to molecular scales for up to tens of microseconds are now within range for molecular dynamics simulations. Here we review how such simulations have contributed to our current understanding of the cell envelopes of Gram-negative bacteria.
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Affiliation(s)
- Syma Khalid
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Cyril Schroeder
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), Singapore 138671, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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4
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Golla VK, Piselli C, Kleinekathöfer U, Benz R. Permeation of Fosfomycin through the Phosphate-Specific Channels OprP and OprO of Pseudomonas aeruginosa. J Phys Chem B 2022; 126:1388-1403. [PMID: 35138863 DOI: 10.1021/acs.jpcb.1c08696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen responsible for many nosocomial infections. It is quite resistant to various antibiotics, caused by the absence of general diffusion pores in the outer membrane. Instead, it contains many substrate-specific channels. Among them are the two phosphate- and pyrophosphate-specific porins OprP and OprO. Phosphonic acid antibiotics such as fosfomycin and fosmidomycin seem to be good candidates for using these channels to enter P. aeruginosa bacteria. Here, we investigated the permeation of fosfomycin through OprP and OprO using electrophysiology and molecular dynamics (MD) simulations. The results were compared to those of the fosmidomycin translocation, for which additional MD simulations were performed. In the electrophysiological approach, we noticed a higher binding affinity of fosfomycin than of fosmidomycin to OprP and OprO. In MD simulations, the ladder of arginine residues and the cluster of lysine residues play an important role in the permeation of fosfomycin through the OprP and OprO channels. Molecular details on the permeation of fosfomycin through OprP and OprO channels were derived from MD simulations and compared to those of fosmidomycin translocation. In summary, this study demonstrates that the selectivity of membrane channels can be employed to improve the permeation of antibiotics into Gram-negative bacteria and especially into resistant P. aeruginosa strains.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Claudio Piselli
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
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5
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Awang T, Pongprayoon P. The penetration of human defensin 5 (HD5) through bacterial outer membrane: simulation studies. J Mol Model 2021; 27:291. [PMID: 34546425 DOI: 10.1007/s00894-021-04915-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022]
Abstract
Human α-defensin 5 (HD5) is one of cationic antimicrobial peptides which plays a crucial role in an innate immune system in human body. HD5 shows the killing activity against a broad spectrum of pathogenic bacteria by making a pore in a bacterial membrane and penetrating into a cytosol. Nonetheless, its pore-forming mechanisms remain unclear. Thus, in this work, the constant-velocity steered molecular dynamics (SMD) simulation was used to simulate the permeation of a dimeric HD5 into a gram-negative lipopolysaccharide (LPS) membrane model. Arginine-rich HD5 is found to strongly interact with a LPS surface. Upon arrival, arginines on HD5 interact with lipid A head groups (a top part of LPS) and then drag these charged moieties down into a hydrophobic core resulting in the formation of water-filled pore. Although all arginines are found to interact with a membrane, Arg13 and Arg32 appear to play a dominant role in the HD5 adsorption on a gram-negative membrane. Furthermore, one chain of a dimeric HD5 is required for HD5 adhesion. The interactions of arginine-lipid A head groups play a major role in adhering a cationic HD5 on a membrane surface and retarding a HD5 passage in the meantime.
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Affiliation(s)
- Tadsanee Awang
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. .,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand.
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6
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Acharya A, Prajapati JD, Kleinekathöfer U. Improved Sampling and Free Energy Estimates for Antibiotic Permeation through Bacterial Porins. J Chem Theory Comput 2021; 17:4564-4577. [PMID: 34138557 DOI: 10.1021/acs.jctc.1c00369] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Antibiotics enter into bacterial cells via protein channels that serve as low-energy pathways through the outer membrane, which is otherwise impenetrable. Insights into the molecular mechanisms underlying the transport processes are vital for the development of effective antibacterials. A much-desired prerequisite is an accurate and reproducible determination of free energy surfaces for antibiotic translocation, enabling quantitative and meaningful comparisons of permeation mechanisms for different classes of antibiotics. Inefficient sampling along the orthogonal degrees of freedom, for example, in umbrella sampling and metadynamics approaches, is however a key limitation affecting the accuracy and the convergence of free energy estimates. To overcome this limitation, two sampling methods have been employed in the present study that, respectively, combine umbrella sampling and metadynamics-style biasing schemes with temperature acceleration for improved sampling along orthogonal degrees of freedom. As a model for the transport of bulky solutes, the ciprofloxacin-OmpF system has been selected. The well-tempered metadynamics approach with multiple walkers is compared with its "temperature-accelerated" variant in terms of improvements in sampling and convergence of free energy estimates. We find that the inclusion of collective variables governing solute degrees of freedom and solute-water interactions within the sampling scheme largely alleviates sampling issues. Concerning improved sampling and convergence of free energy estimates from independent simulations, the temperature-accelerated sliced sampling approach that combines umbrella sampling with temperature-accelerated molecular dynamics performs even better as shown for the ciprofloxacin-OmpF system.
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Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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7
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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8
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Golla VK, Prajapati JD, Kleinekathöfer U. Millisecond-Long Simulations of Antibiotics Transport through Outer Membrane Channels. J Chem Theory Comput 2021; 17:549-559. [PMID: 33378186 DOI: 10.1021/acs.jctc.0c01088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To reach their target site inside Gram-negative bacteria, almost all antibiotics need to cross the outer membrane. Computational modeling of such processes can be numerically demanding due to the size of the systems and especially due to the timescales involved. Recently, a hybrid Brownian and molecular dynamics approach, i.e., Brownian dynamics including explicit atoms (BRODEA), has been developed and evaluated for studying the transport of monoatomic ions through membrane channels. Later on, this numerically efficient scheme has been applied to determine the free energy surfaces of the ciprofloxacin and enrofloxacin translocation through the porin OmpC using temperature-accelerated simulations. To improve the usability and accuracy of the approach, schemes to approximate the position-dependent diffusion constant of the molecule while traversing the pore had to be established. To this end, we have studied the translocation of the charged phosphonic acid antibiotic fosfomycin through the porin OmpF from Escherichia coli devising and benchmarking several diffusion models. To test the efficiency and sensitivity of these models, the effect of OmpF mutations on the permeation of fosfomycin was analyzed. Permeation events have been recorded over millisecond-long biased and unbiased simulations, from which thermodynamics and kinetics quantities of the translocation processes were determined. As a result, the use of the BRODEA approach, together with the appropriate diffusion model, was seen to accurately reproduce the findings observed in electrophysiology experiments and all-atom molecular dynamics simulations. These results suggest that the BRODEA approach can become a valuable tool for screening numerous compounds to evaluate their outer membrane permeability, a property important in the development of new antibiotics.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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9
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Prajapati JD, Kleinekathöfer U. Voltage-Dependent Transport of Neutral Solutes through Nanopores: A Molecular View. J Phys Chem B 2020; 124:10718-10731. [PMID: 33175522 DOI: 10.1021/acs.jpcb.0c08401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The permeation of (neutral) molecules through nanopores in the presence of external voltages depends on several factors including pore electrostatics, electrophoretic force, and electro-osmotic drag. In earlier single-channel electrophysiology experiments, voltage-dependent asymmetric transport of neutral α-cyclodextrin (α-CD) molecules through the biological nanopore ΔCymA was observed. The voltage-dependent ion-associated flow of water, the so-called electro-osmotic flow, has been suggested to be the key factor behind the observed asymmetric behavior. The influence of pore electrostatics and electrophoretic force and their interplay with the electro-osmotic drag with varying buffers and voltages has not yet been analyzed at the molecular level. Hence, the detailed physical mechanism behind this intriguing permeation process is in part still unclear. In the present study, we have performed 36 μs all-atom free energy calculations by combining applied-field molecular dynamics simulations with metadynamics techniques. The influence of several ionic conditions as well as external voltages on the permeation of α-CD molecules across the ΔCymA pore has been investigated. To decipher the thermodynamic and kinetic details, the lowest energy paths and the permeation times for α-CD translocation have been estimated. In the presence of KCl or MgCl2 salts, the charge of the cations is found to control the direction and magnitude of the electro-osmotic flow, which in turn strongly affects α-CD permeation. Overall, the present findings significantly improve the fundamental understanding of the voltage-dependent transport of neutral solutes across nanopores.
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Affiliation(s)
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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10
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Physicochemical Evidence that Francisella FupA and FupB Proteins Are Porins. Int J Mol Sci 2020; 21:ijms21155496. [PMID: 32752076 PMCID: PMC7432831 DOI: 10.3390/ijms21155496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022] Open
Abstract
Responsible for tularemia, Francisella tularensis bacteria are highly infectious Gram-negative, category A bioterrorism agents. The molecular mechanisms for their virulence and resistance to antibiotics remain largely unknown. FupA (Fer Utilization Protein), a protein mediating high-affinity transport of ferrous iron across the outer membrane, is associated with both. Recent studies demonstrated that fupA deletion contributed to lower F. tularensis susceptibility towards fluoroquinolones, by increasing the production of outer membrane vesicles. Although the paralogous FupB protein lacks such activity, iron transport capacity and a role in membrane stability were reported for the FupA/B chimera, a protein found in some F. tularensis strains, including the live vaccine strain (LVS). To investigate the mode of action of these proteins, we purified recombinant FupA, FupB and FupA/B proteins expressed in Escherichia coli and incorporated them into mixed lipid bilayers. We examined the porin-forming activity of the FupA/B proteoliposomes using a fluorescent 8-aminonaphthalene-1,3,6-trisulfonic acid, disodium salt (ANTS) probe. Using electrophysiology on tethered bilayer lipid membranes, we confirmed that the FupA/B fusion protein exhibits pore-forming activity with large ionic conductance, a property shared with both FupA and FupB. This demonstration opens up new avenues for identifying functional genes, and novel therapeutic strategies against F. tularensis infections.
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11
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Accumulation of ambient phosphate into the periplasm of marine bacteria is proton motive force dependent. Nat Commun 2020; 11:2642. [PMID: 32457313 PMCID: PMC7250820 DOI: 10.1038/s41467-020-16428-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteria acquire phosphate (Pi) by maintaining a periplasmic concentration below environmental levels. We recently described an extracellular Pi buffer which appears to counteract the gradient required for Pi diffusion. Here, we demonstrate that various treatments to outer membrane (OM) constituents do not affect the buffered Pi because bacteria accumulate Pi in the periplasm, from which it can be removed hypo-osmotically. The periplasmic Pi can be gradually imported into the cytoplasm by ATP-powered transport, however, the proton motive force (PMF) is not required to keep Pi in the periplasm. In contrast, the accumulation of Pi into the periplasm across the OM is PMF-dependent and can be enhanced by light energy. Because the conventional mechanism of Pi-specific transport cannot explain Pi accumulation in the periplasm we propose that periplasmic Pi anions pair with chemiosmotic cations of the PMF and millions of accumulated Pi pairs could influence the periplasmic osmolarity of marine bacteria. The ubiquitous oceanic bacteria harbour an external phosphate buffer for modulating phosphate (Pi) uptake. Here, using both oceanic SAR11, Prochlorococcus and Synechococcus strains as a model, the authors show that the Pi buffer accumulation in the periplasm is proton motive force-dependent and can be enhanced by light energy.
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12
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Golla VK, Prajapati JD, Joshi M, Kleinekathöfer U. Exploration of Free Energy Surfaces Across a Membrane Channel Using Metadynamics and Umbrella Sampling. J Chem Theory Comput 2020; 16:2751-2765. [PMID: 32167296 DOI: 10.1021/acs.jctc.9b00992] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To reach their site of action, it is essential for antibiotic molecules to cross the bacterial outer membrane. The progress of enhanced sampling techniques in molecular dynamics simulations enables us to understand these translocations at an atomic level. To this end, calculations of free energy surfaces for these permeation processes are of key importance. Herein, we investigate the translocation of a variety of anionic solutes through the outer membrane pore OprO of the Gram-negative bacterium Pseudomonas aeruginosa using the metadynamics and umbrella sampling techniques at the all-atom level. Free energy calculations have been performed employing these two distinct methods in order to illustrate the difference in computed free energies, if any. The investigated solutes range from a single atomic chloride ion over a multiatomic monophosphate ion to a more bulky fosmidomycin antibiotic. The role of complexity of the permeating solutes in estimating accurate free energy profiles is demonstrated by performing extensive convergence analysis. For simple monatomic ions, good agreement between the well-tempered metadynamics and the umbrella sampling approaches is achieved, while for the permeation of the monophosphate ion differences start to appear. In the case of larger molecules such as fosmidomycin it is a tough challenge to achieve converged free energy profiles. This issue is mainly due to neglecting orthogonal degrees of freedom during the free energy calculations. Nevertheless, the freely driven metadynamics approach leads to clearly advantageous results. Additionally, atomistic insights of the translocation mechanisms of all three solutes are discussed.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Manas Joshi
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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13
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Samsudin F, Khalid S. Movement of Arginine through OprD: The Energetics of Permeation and the Role of Lipopolysaccharide in Directing Arginine to the Protein. J Phys Chem B 2019; 123:2824-2832. [DOI: 10.1021/acs.jpcb.9b00063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Firdaus Samsudin
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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14
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Santos RS, Figueiredo C, Azevedo NF, Braeckmans K, De Smedt SC. Nanomaterials and molecular transporters to overcome the bacterial envelope barrier: Towards advanced delivery of antibiotics. Adv Drug Deliv Rev 2018; 136-137:28-48. [PMID: 29248479 DOI: 10.1016/j.addr.2017.12.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 01/13/2023]
Abstract
With the dramatic consequences of bacterial resistance to antibiotics, nanomaterials and molecular transporters have started to be investigated as alternative antibacterials or anti-infective carrier systems to improve the internalization of bactericidal drugs. However, the capability of nanomaterials/molecular transporters to overcome the bacterial cell envelope is poorly understood. It is critical to consider the sophisticated architecture of bacterial envelopes and reflect how nanomaterials/molecular transporters can interact with these envelopes, being the major aim of this review. The first part of this manuscript overviews the permeability of bacterial envelopes and how it limits the internalization of common antibiotic and novel oligonucleotide drugs. Subsequently we critically discuss the mechanisms that allow nanomaterials/molecular transporters to overcome the bacterial envelopes, focusing on the most promising ones to this end - siderophores, cyclodextrins, metal nanoparticles, antimicrobial/cell-penetrating peptides and fusogenic liposomes. This review may stimulate drug delivery and microbiology scientists in designing effective nanomaterials/molecular transporters against bacterial infections.
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15
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Dubey V, Han M, Kopec W, Solov'yov IA, Abe K, Khandelia H. K + binding and proton redistribution in the E 2P state of the H +, K +-ATPase. Sci Rep 2018; 8:12732. [PMID: 30143663 PMCID: PMC6109069 DOI: 10.1038/s41598-018-30885-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
The H+, K+-ATPase (HKA) uses ATP to pump protons into the gastric lumen against a million-fold proton concentration gradient while counter-transporting K+ from the lumen. The mechanism of release of a proton into a highly acidic stomach environment, and the subsequent binding of a K+ ion necessitates a network of protonable residues and dynamically changing protonation states in the cation binding pocket dominated by five acidic amino acid residues E343, E795, E820, D824, and D942. We perform molecular dynamics simulations of spontaneous K+ binding to all possible protonation combinations of the acidic amino acids and carry out free energy calculations to determine the optimal protonation state of the luminal-open E2P state of the pump which is ready to bind luminal K+. A dynamic pKa correlation analysis reveals the likelihood of proton transfer events within the cation binding pocket. In agreement with in-vitro measurements, we find that E795 is likely to be protonated, and that E820 is at the center of the proton transfer network in the luminal-open E2P state. The acidic residues D942 and D824 are likely to remain protonated, and the proton redistribution occurs predominantly amongst the glutamate residues exposed to the lumen. The analysis also shows that a lower number of K+ ions bind at lower pH, modeled by a higher number of protons in the cation binding pocket, in agreement with the 'transport stoichiometry variation' hypothesis.
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Affiliation(s)
- Vikas Dubey
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark
- MEMPHYS-Center for Biomembrane Physics, Odense, Denmark
| | - Minwoo Han
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark
- MEMPHYS-Center for Biomembrane Physics, Odense, Denmark
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute and Department of Medicinal Science, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Himanshu Khandelia
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, 5230 M, Denmark.
- MEMPHYS-Center for Biomembrane Physics, Odense, Denmark.
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16
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Peng J, Miao L, Chen X, Liu P. Comparative Transcriptome Analysis of Pseudomonas putida KT2440 Revealed Its Response Mechanisms to Elevated Levels of Zinc Stress. Front Microbiol 2018; 9:1669. [PMID: 30087671 PMCID: PMC6066579 DOI: 10.3389/fmicb.2018.01669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/04/2018] [Indexed: 01/03/2023] Open
Abstract
The whole-genome transcriptional response of Pseudomonas putida KT2440 to stress-inducing concentrations of zinc was analyzed in this study by RNA sequencing to thoroughly investigate the bacterial cell response to zinc toxicity. The data revealed that different levels of zinc stress strongly affected the transcription of genes from the following categories: metal transport genes, genes involved in membrane homeostasis, oxidative-stress-responding genes, and genes associated with basic cellular metabolism. At the lowest zinc dose, only several genes associated with metal transport and membrane homeostasis were strongly influenced. At the intermediate zinc dose, transcriptional changes of genes belonging to these two categories were highly pronounced. In addition, the intermediate zinc stress produced high levels of oxidative stress, and influenced amino acid metabolism and respiratory chains of P. putida. At the highest zinc dose, the induction of genes responsible for Fe–S cluster biogenesis was the most remarkable feature. Moreover, upregulation of glyoxylate cycle was observed. In summary, the adaptation of the cell envelope, the maintenance of metal homeostasis and intracellular redox status, and the transcriptional control of metabolism are the main elements of stress response, which facilitates the survival of P. putida KT2440 in zinc-polluted environments.
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Affiliation(s)
- Jun Peng
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Lihong Miao
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Xi Chen
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Pulin Liu
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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17
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Heinz LP, Kopec W, de Groot BL, Fink RHA. In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways. Sci Rep 2018; 8:6886. [PMID: 29720700 PMCID: PMC5932038 DOI: 10.1038/s41598-018-25061-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/13/2018] [Indexed: 12/18/2022] Open
Abstract
The ryanodine receptor 1 is a large calcium ion channel found in mammalian skeletal muscle. The ion channel gained a lot of attention recently, after multiple independent authors published near-atomic cryo electron microscopy data. Taking advantage of the unprecedented quality of structural data, we performed molecular dynamics simulations on the entire ion channel as well as on a reduced model. We calculated potentials of mean force for Ba2+, Ca2+, Mg2+, K+, Na+ and Cl- ions using umbrella sampling to identify the key residues involved in ion permeation. We found two main binding sites for the cations, whereas the channel is strongly repulsive for chloride ions. Furthermore, the data is consistent with the model that the receptor achieves its ion selectivity by over-affinity for divalent cations in a calcium-block-like fashion. We reproduced the experimental conductance for potassium ions in permeation simulations with applied voltage. The analysis of the permeation paths shows that ions exit the pore via multiple pathways, which we suggest to be related to the experimental observation of different subconducting states.
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Affiliation(s)
- Leonard P Heinz
- Medical Biophysics Unit, Medical Faculty, Institute of Physiology and Pathophysiology, Heidelberg University, 69120, Heidelberg, Germany.
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Rainer H A Fink
- Medical Biophysics Unit, Medical Faculty, Institute of Physiology and Pathophysiology, Heidelberg University, 69120, Heidelberg, Germany
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18
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Abstract
Collective antibiotic drug resistance is a global threat, especially with respect to Gram-negative bacteria. The low permeability of the bacterial outer cell wall has been identified as a challenging barrier that prevents a sufficient antibiotic effect to be attained at low doses of the antibiotic. The Gram-negative bacterial cell envelope comprises an outer membrane that delimits the periplasm from the exterior milieu. The crucial mechanisms of antibiotic entry via outer membrane includes general diffusion porins (Omps) responsible for hydrophilic antibiotics and lipid-mediated pathway for hydrophobic antibiotics. The protein and lipid arrangements of the outer membrane have had a strong impact on the understanding of bacteria and their resistance to many types of antibiotics. Thus, one of the current challenges is effective interpretation at the molecular basis of the outer membrane permeability. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in solute influx. Moreover, it aims toward further understanding and exploration of prospects to improve our knowledge of physicochemical limitations that direct the translocation of antibiotics via bacterial outer membrane.
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Affiliation(s)
- Ishan Ghai
- School of Engineering and Life Sciences, Jacobs University, Bremen, Germany.,Consultation Division, RSGBIOGEN, New Delhi, India
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19
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Prajapati JD, Solano CJF, Winterhalter M, Kleinekathöfer U. Enrofloxacin Permeation Pathways across the Porin OmpC. J Phys Chem B 2018; 122:1417-1426. [PMID: 29307192 DOI: 10.1021/acs.jpcb.7b12568] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In Gram-negative bacteria, the lack or quenching of antibiotic translocation across the outer membrane is one of the main factors for acquiring antibiotic resistance. An atomic-level comprehension of the key features governing the transport of drugs by outer-membrane protein channels would be very helpful in developing the next generation of antibiotics. In a previous study [ J. D. Prajapati et al. J. Chem. Theory Comput. 2017 , 13 , 4553 ], we characterized the diffusion pathway of a ciprofloxacin molecule through the outer membrane porin OmpC of Escherichia coli by combining metadynamics and a zero-temperature string method. Here, we evaluate the diffusion route through the OmpC porin for a similar fluoroquinolone, that is, the enrofloxacin molecule, using the previously developed protocol. As a result, it was found that the lowest-energy pathway was similar to that for ciprofloxacin; namely, a reorientation was required on the extracellular side with the carboxyl group ahead before enrofloxacin reached the constriction region. In turn, the free-energy basins for both antibiotics are located at similar positions in the space defined by selected reaction coordinates, and their affinity sites share a wide number of porin residues. However, there are some important deviations due to the chemical differences of these two drugs. On the one hand, a slower diffusion process is expected for enrofloxacin, as the permeation pathway exhibits higher overall energy barriers, mainly in the constriction region. On the other hand, enrofloxacin needs to replace some polar interactions in its affinity sites with nonpolar ones. This study demonstrates how minor chemical modifications can qualitatively affect the translocation mechanism of an antibiotic molecule.
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Affiliation(s)
- Jigneshkumar Dahyabhai Prajapati
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Carlos José Fernández Solano
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Mathias Winterhalter
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
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20
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Chevalier S, Bouffartigues E, Bodilis J, Maillot O, Lesouhaitier O, Feuilloley MGJ, Orange N, Dufour A, Cornelis P. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiol Rev 2017; 41:698-722. [PMID: 28981745 DOI: 10.1093/femsre/fux020] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/24/2017] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium belonging to the γ-proteobacteria. Like other members of the Pseudomonas genus, it is known for its metabolic versatility and its ability to colonize a wide range of ecological niches, such as rhizosphere, water environments and animal hosts, including humans where it can cause severe infections. Another particularity of P. aeruginosa is its high intrinsic resistance to antiseptics and antibiotics, which is partly due to its low outer membrane permeability. In contrast to Enterobacteria, pseudomonads do not possess general diffusion porins in their outer membrane, but rather express specific channel proteins for the uptake of different nutrients. The major outer membrane 'porin', OprF, has been extensively investigated, and displays structural, adhesion and signaling functions while its role in the diffusion of nutrients is still under discussion. Other porins include OprB and OprB2 for the diffusion of glucose, the two small outer membrane proteins OprG and OprH, and the two porins involved in phosphate/pyrophosphate uptake, OprP and OprO. The remaining nineteen porins belong to the so-called OprD (Occ) family, which is further split into two subfamilies termed OccD (8 members) and OccK (11 members). In the past years, a large amount of information concerning the structure, function and regulation of these porins has been published, justifying why an updated review is timely.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Josselin Bodilis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Laboratoire de Biotechnologie et Chimie Marines EA 3884, Université de Bretagne-Sud (UEB), 56321 Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
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21
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Ganguly S, Kesireddy A, Bárcena-Uribarri I, Kleinekathöfer U, Benz R. Conversion of OprO into an OprP-like Channel by Exchanging Key Residues in the Channel Constriction. Biophys J 2017; 113:829-834. [PMID: 28834719 DOI: 10.1016/j.bpj.2017.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 06/23/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022] Open
Abstract
Under phosphate-limiting conditions, the channels OprP and OprO are induced and expressed in the outer membrane of Pseudomonas aeruginosa. Despite their large homology, the phosphate-specific OprP and the diphosphate-specific OprO pores show structural differences in their binding sites situated in the constriction region. Previously, it was shown that the mutation of amino acids in OprP (Y62F and Y114D) led to an exchange in substrate specificity similar to OprO. To support the role of these key amino acids in the substrate sorting of these specific channels, the reverse mutants for OprO (F62Y, D114Y, and F62Y/D114Y) were created in this study. The phosphate and diphosphate binding of the generated channels was studied in planar lipid bilayers. Our results show that mutations of key residues indeed reverse the substrate specificity of OprO to OprP and support the view that just a few strategically positioned amino acids are mainly responsible for its substrate specificity.
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Affiliation(s)
- Sonalli Ganguly
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany.
| | - Anusha Kesireddy
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | - Iván Bárcena-Uribarri
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | | | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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22
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Abstract
One of the main fundamental mechanisms of antibiotic resistance in Gram-negative bacteria comprises an effective change in the membrane permeability to antibiotics. The Gram-negative bacterial complex cell envelope comprises an outer membrane that delimits the periplasm from the exterior environment. The outer membrane contains numerous protein channels, termed as porins or nanopores, which are mainly involved in the influx of hydrophilic compounds, including antibiotics. Bacterial adaptation to reduce influx through these outer membrane proteins (Omps) is one of the crucial mechanisms behind antibiotic resistance. Thus to interpret the molecular basis of the outer membrane permeability is the current challenge. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in antibiotic influx. Further, it aims to study the bacterial response to antibiotic membrane permeability and hopefully provoke a discussion toward understanding and further exploration of prospects to improve our knowledge on physicochemical parameters that direct the translocation of antibiotics through the bacterial membrane protein channels.
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Affiliation(s)
- Ishan Ghai
- School of Engineering and Life Sciences, Jacobs University, Bremen
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23
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Ariz-Extreme I, Hub JS. Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B 2017; 121:1506-1519. [PMID: 28128570 DOI: 10.1021/acs.jpcb.6b11279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
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24
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Modi N, Ganguly S, Bárcena-Uribarri I, Benz R, van den Berg B, Kleinekathöfer U. Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa. Biophys J 2016; 109:1429-38. [PMID: 26445443 DOI: 10.1016/j.bpj.2015.07.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/26/2015] [Accepted: 07/28/2015] [Indexed: 01/09/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria functions as a selective permeability barrier between cell and environment. For nutrient acquisition, the OM contains a number of channels that mediate uptake of small molecules by diffusion. Many of these channels are specific, i.e., they prefer certain substrates over others. In electrophysiological experiments, the OM channels OprP and OprO from Pseudomonas aeruginosa show a specificity for phosphate and diphosphate, respectively. In this study we use x-ray crystallography, free-energy molecular dynamics (MD) simulations, and electrophysiology to uncover the atomic basis for the different substrate specificity of these highly similar channels. A structural analysis of OprP and OprO revealed two crucial differences in the central constriction region. In OprP there are two tyrosine residues, Y62 and Y114, whereas the corresponding residues in OprO are phenylalanine F62 and aspartate D114. To probe the importance of these two residues in generating the different substrate specificities, the double mutants were generated in silico and in vitro. Applied-field MD simulations and electrophysiological experiments demonstrated that the double mutations interchange the phosphate and diphosphate specificities of OprP and OprO. Our findings outline a possible strategy to rationally design channel specificity by modification of a small number of residues that may be applicable to other pores as well.
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Affiliation(s)
- Niraj Modi
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | - Sonalli Ganguly
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Iván Bárcena-Uribarri
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, UK.
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany.
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25
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Manara RMA, Guy AT, Wallace EJ, Khalid S. Free-energy calculations reveal the subtle differences in the interactions of DNA bases with α-hemolysin. J Chem Theory Comput 2016; 11:810-6. [PMID: 26579606 DOI: 10.1021/ct501081h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Next generation DNA sequencing methods that utilize protein nanopores have the potential to revolutionize this area of biotechnology. While the technique is underpinned by simple physics, the wild-type protein pores do not have all of the desired properties for efficient and accurate DNA sequencing. Much of the research efforts have focused on protein nanopores, such as α-hemolysin from Staphylococcus aureus. However, the speed of DNA translocation has historically been an issue, hampered in part by incomplete knowledge of the energetics of translocation. Here we have utilized atomistic molecular dynamics simulations of nucleotide fragments in order to calculate the potential of mean force (PMF) through α-hemolysin. Our results reveal specific regions within the pore that play a key role in the interaction with DNA. In particular, charged residues such as D127 and K131 provide stabilizing interactions with the anionic DNA and therefore are likely to reduce the speed of translocation. These regions provide rational targets for pore optimization. Furthermore, we show that the energetic contributions to the protein-DNA interactions are a complex combination of electrostatics and short-range interactions, often mediated by water molecules.
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Affiliation(s)
- Richard M A Manara
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Andrew T Guy
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - E Jayne Wallace
- Oxford Nanopore Technologies Ltd., Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, United Kingdom
| | - Syma Khalid
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
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26
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Parkin J, Chavent M, Khalid S. Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes. Biophys J 2016; 109:461-8. [PMID: 26244728 DOI: 10.1016/j.bpj.2015.06.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/09/2015] [Accepted: 06/24/2015] [Indexed: 01/05/2023] Open
Abstract
In the following review we use recent examples from the literature to discuss progress in the area of atomistic and coarse-grained molecular dynamics simulations of selected bacterial membranes and proteins, with a particular focus on Gram-negative bacteria. As structural biology continues to provide increasingly high-resolution data on the proteins that reside within these membranes, simulations have an important role to play in linking these data with the dynamical behavior and function of these proteins. In particular, in the last few years there has been significant progress in addressing the issue of biochemical complexity of bacterial membranes such that the heterogeneity of the lipid and protein components of these membranes are now being incorporated into molecular-level models. Thus, in future we can look forward to complementary data from structural biology and molecular simulations combining to provide key details of structure-dynamics-function relationships in bacterial membranes.
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Affiliation(s)
- Jamie Parkin
- School of Chemistry, University of Southampton, Southampton, UK
| | | | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK.
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27
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In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality. Int J Mol Sci 2016; 17:ijms17040599. [PMID: 27110766 PMCID: PMC4849052 DOI: 10.3390/ijms17040599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 12/18/2022] Open
Abstract
Diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (OMP) family in Gram-negative bacteria. Differences in pore size and amino acid composition contribute to the specificity. Structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. Entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, specificity and biological niche adaptation. The high mutation rate in their surface-exposed loops is likely an important mechanism for host immune system evasion. Multiple sequence alignments for each subclass revealed conserved residue positions that are involved in substrate recognition and specificity. An analysis of monomeric protein channels revealed particular sequence patterns of amino acids that were observed in other classes at multimeric interfaces. This adds to the emerging evidence that all members of the family exist in a multimeric state. Our findings are important for understanding the role of members of this family in a wide range of bacterial processes, including bacterial food uptake, survival and adaptation mechanisms.
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28
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Why do the outer membrane proteins OmpF from E. coli and OprP from P. aeruginosa prefer trimers? Simulation studies. J Mol Graph Model 2016; 65:1-7. [DOI: 10.1016/j.jmgm.2016.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/18/2015] [Accepted: 02/06/2016] [Indexed: 01/27/2023]
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29
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Molecular Modeling and Its Applications in Protein Engineering. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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30
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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31
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Wee CL, Ulmschneider MB, Sansom MSP. Membrane/Toxin Interaction Energetics via Serial Multiscale Molecular Dynamics Simulations. J Chem Theory Comput 2015; 6:966-76. [PMID: 26613320 DOI: 10.1021/ct900652s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Computing free energies of complex biomolecular systems via atomistic (AT) molecular dynamics (MD) simulations remains a challenge due to the need for adequate sampling and convergence. Recent coarse-grained (CG) methodology allows simulations of significantly larger systems (∼10(6) to 10(8) atoms) over longer (μs/ms) time scales. Such CG models appear to be capable of making semiquantitative predictions. However, their ability to reproduce accurate thermodynamic quantities remains uncertain. We have recently used CG MD simulations to compute the potential of mean force (PMF) or free energy profile of a small peptide toxin interacting with a lipid bilayer along a 1D reaction coordinate. The toxin studied was VSTx1 (Voltage Sensor Toxin 1) from spider venom which inhibits the archeabacterial voltage-gated potassium (Kv) channel KvAP by binding to the voltage-sensor (VS) domains. Here, we re-estimate this PMF profile using (i) AT MD simulations with explicit membrane and solvent and (ii) an implicit membrane and solvent (generalized Born; GBIM) model where only the peptide was explicit. We used the CG MD free energy simulations to guide the setup of the corresponding AT MD simulations. The aim was to avoid local minima in the AT simulations which would be difficult over shorter AT time scales. A cross-comparison of the PMF profiles revealed a conserved topology, although there were differences in the magnitude of the free energies. The CG and AT simulations predicted a membrane/water interface free energy well of -27 and -23 kcal/mol, respectively (with respect to water). The GBIM model, however, gave a reduced interfacial free energy well (-12 kcal/mol). In addition, the CG and GBIM models predicted a free energy barrier of +61 and +96 kcal/mol, respectively, for positioning the toxin at the center of the bilayer, which was considerably smaller in the AT simulations (+26 kcal/mol). Thus, we present a framework for serially combining CG and AT simulations to estimate the free energy of peptide/membrane interactions. Such approaches for combining simulations at different levels of granularity will become increasingly important in future studies of complex membrane/protein systems.
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Affiliation(s)
- Chze Ling Wee
- Department of Biochemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Martin B Ulmschneider
- Department of Biochemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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32
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Parkin J, Khalid S. Atomistic molecular-dynamics simulations enable prediction of the arginine permeation pathway through OccD1/OprD from Pseudomonas aeruginosa. Biophys J 2015; 107:1853-1861. [PMID: 25418166 DOI: 10.1016/j.bpj.2014.08.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 01/11/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that does not contain large, nonspecific porins in its outer membrane. Consequently, the outer membrane is highly impermeable to polar solutes and serves as a barrier against the penetration of antimicrobial agents. This is one of the reasons why such bacteria are intrinsically resistant to antibiotics. Polar molecules that permeate across the outer membrane do so through substrate-specific channels proteins. To design antibiotics that target substrate-channel proteins, it is essential to first identify the permeation pathways of their natural substrates. In P. aeruginosa, the largest family of substrate-specific proteins is the OccD (previously reported under the name OprD) family. Here, we employ equilibrium and steered molecular-dynamics simulations to study OccD1/OprD, the archetypical member of the OccD family. We study the permeation of arginine, one of the natural substrates of OccD1, through the protein. The combination of simulation methods allows us to predict the pathway taken by the amino acid, which is enabled by conformational rearrangements of the extracellular loops of the protein. Furthermore, we show that arginine adopts a specific orientation to form the molecular interactions that facilitate its passage through part of the protein. We predict a three-stage permeation process for arginine.
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Affiliation(s)
- Jamie Parkin
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, United Kingdom.
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33
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Krammer EM, Vu GT, Homblé F, Prévost M. Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites. PLoS One 2015; 10:e0121746. [PMID: 25860993 PMCID: PMC4393092 DOI: 10.1371/journal.pone.0121746] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022] Open
Abstract
In the exchange of metabolites and ions between the mitochondrion and the cytosol, the voltage-dependent anion channel (VDAC) is a key element, as it forms the major transport pathway for these compounds through the mitochondrial outer membrane. Numerous experimental studies have promoted the idea that VDAC acts as a regulator of essential mitochondrial functions. In this study, using a combination of molecular dynamics simulations, free-energy calculations, and electrophysiological measurements, we investigated the transport of ions through VDAC, with a focus on phosphate ions and metabolites. We showed that selectivity of VDAC towards small anions including monovalent phosphates arises from short-lived interactions with positively charged residues scattered throughout the pore. In dramatic contrast, permeation of divalent phosphate ions and phosphate metabolites (AMP and ATP) involves binding sites along a specific translocation pathway. This permeation mechanism offers an explanation for the decrease in VDAC conductance measured in the presence of ATP or AMP at physiological salt concentration. The binding sites occur at similar locations for the divalent phosphate ions, AMP and ATP, and contain identical basic residues. ATP features a marked affinity for a central region of the pore lined by two lysines and one arginine of the N-terminal helix. This cluster of residues together with a few other basic amino acids forms a "charged brush" which facilitates the passage of the anionic metabolites through the pore. All of this reveals that VDAC controls the transport of the inorganic phosphates and phosphate metabolites studied here through two different mechanisms.
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Affiliation(s)
- Eva-Maria Krammer
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Giang Thi Vu
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Fabrice Homblé
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
- * E-mail: (MP)
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34
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Modi N, Bárcena-Uribarri I, Bains M, Benz R, Hancock REW, Kleinekathöfer U. Tuning the affinity of anion binding sites in porin channels with negatively charged residues: molecular details for OprP. ACS Chem Biol 2015; 10:441-51. [PMID: 25333751 DOI: 10.1021/cb500399j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The cell envelope of the Gram negative opportunistic pathogen Pseudomonas aeruginosa is poorly permeable to many classes of hydrophilic molecules including antibiotics due to the presence of the narrow and selective porins. Here we focused on one of the narrow-channel porins, that is, OprP, which is responsible for the high-affinity uptake of phosphate ions. Its two central binding sites for phosphate contain a number of positively charged amino acids together with a single negatively charged residue (D94). The presence of this negatively charged residue in a binding site for negatively charged phosphate ions is highly surprising due to the potentially reduced binding affinity. The goal of this study was to better understand the role of D94 in phosphate binding, selectivity, and transport using a combination of mutagenesis, electrophysiology, and free-energy calculations. The presence of a negatively charged residue in the binding site is critical for this specific porin OprP as emphasized by the evolutionary conservation of such negatively charged residue in the binding site of several anion-selective porins. Mutations of D94 in OprP to any positively charged or neutral residue increased the binding affinity of phosphate for OprP. Detailed analysis indicated that this anionic residue in the phosphate binding site of OprP, despite its negative charge, maintained energetically favorable phosphate binding sites in the central region of the channel and at the same time decreased residence time thus preventing excessively strong binding of phosphate that would oppose phosphate flux through the channel. Intriguingly mutations of D94 to positively charged residues, lysine and arginine, resulted in very different binding affinities and free energy profiles, indicating the importance of side chain conformations of these positively charged residues in phosphate binding to OprP.
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Affiliation(s)
- Niraj Modi
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Iván Bárcena-Uribarri
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Manjeet Bains
- Centre for Microbial Diseases and Immunity Research,
Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Roland Benz
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research,
Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Kleinekathöfer
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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35
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The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations. NANOMATERIALS 2015; 5:144-153. [PMID: 28347003 PMCID: PMC5312860 DOI: 10.3390/nano5010144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 12/31/2022]
Abstract
Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.
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36
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Trick JL, Wallace EJ, Bayley H, Sansom MSP. Designing a hydrophobic barrier within biomimetic nanopores. ACS NANO 2014; 8:11268-11279. [PMID: 25317664 DOI: 10.1021/nn503930p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nanopores in membranes have a range of potential applications. Biomimetic design of nanopores aims to mimic key functions of biological pores within a stable template structure. Molecular dynamics simulations have been used to test whether a simple β-barrel protein nanopore can be modified to incorporate a hydrophobic barrier to permeation. Simulations have been used to evaluate functional properties of such nanopores, using water flux as a proxy for ionic conductance. The behavior of these model pores has been characterized as a function of pore size and of the hydrophobicity of the amino acid side chains lining the narrow central constriction of the pore. Potential of mean force calculations have been used to calculate free energy landscapes for water and for ion permeation in selected models. These studies demonstrate that a hydrophobic barrier can indeed be designed into a β-barrel protein nanopore, and that the height of the barrier can be adjusted by modifying the number of consecutive rings of hydrophobic side chains. A hydrophobic barrier prevents both water and ion permeation even though the pore is sterically unoccluded. These results both provide insights into the nature of hydrophobic gating in biological pores and channels, and furthermore demonstrate that simple design features may be computationally transplanted into β-barrel membrane proteins to generate functionally complex nanopores.
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Affiliation(s)
- Jemma L Trick
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, Oxford, United Kingdom
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37
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Structural dynamics of the cell wall precursor lipid II in the presence and absence of the lantibiotic nisin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3061-8. [PMID: 25128154 DOI: 10.1016/j.bbamem.2014.07.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 01/06/2023]
Abstract
Representing a physiological "Achilles' heel", the cell wall precursor lipid II (LII) is a prime target for various classes of antibiotics. Over the years LII-binding agents have been recognized as promising candidates and templates in the search for new antibacterial compounds to complement or replace existing drugs. To elucidate the molecular structural basis underlying LII functional mechanism and to better understand if and how lantibiotic binding alters the molecular behavior of LII, we performed molecular dynamics (MD) simulations of phospholipid membrane-embedded LII in the absence and presence of the LII-binding lantibiotic nisin. In a series of 2×4 independent, unbiased 100ns MD simulations we sampled the conformational dynamics of nine LII as well as nine LII-nisin complexes embedded in an aqueous 150mM NaCl/POPC phospholipid membrane environment. We found that nisin binding to LII induces a reduction of LII mobility and flexibility, an outward shift of the LII pentapeptide, an inward movement of the LII disaccharide section, and an overall deeper insertion of the LII tail group into the membrane. The latter effect might indicate an initial step in adopting a stabilizing, scaffold-like structure in the process of nisin-induced membrane leakage. At the same time nisin conformation and LII interaction remain similar to the 1WCO LII-nisin NMR solution structure.
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38
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Villinger S, Giller K, Bayrhuber M, Lange A, Griesinger C, Becker S, Zweckstetter M. Nucleotide interactions of the human voltage-dependent anion channel. J Biol Chem 2014; 289:13397-406. [PMID: 24668813 DOI: 10.1074/jbc.m113.524173] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) mediates and gates the flux of metabolites and ions across the outer mitochondrial membrane and is a key player in cellular metabolism and apoptosis. Here we characterized the binding of nucleotides to human VDAC1 (hVDAC1) on a single-residue level using NMR spectroscopy and site-directed mutagenesis. We find that hVDAC1 possesses one major binding region for ATP, UTP, and GTP that partially overlaps with a previously determined NADH binding site. This nucleotide binding region is formed by the N-terminal α-helix, the linker connecting the helix to the first β-strand and adjacent barrel residues. hVDAC1 preferentially binds the charged forms of ATP, providing support for a mechanism of metabolite transport in which direct binding to the charged form exerts selectivity while at the same time permeation of the Mg(2+)-complexed ATP form is possible.
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Affiliation(s)
- Saskia Villinger
- From the Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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39
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Fowler P, Abad E, Beckstein O, Sansom MSP. Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels. J Chem Theory Comput 2013; 9:5176-5189. [PMID: 24353479 PMCID: PMC3864263 DOI: 10.1021/ct4005933] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Indexed: 12/18/2022]
Abstract
Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF). These can be used, in conjunction with the electro-diffusion theory, to predict the conductance of a specific ion channel. Here, we calculate seven independent PMFs, thereby studying the differences between two potassium ion channels, the effect of the CHARMM CMAP forcefield correction, and the sensitivity and reproducibility of the method. Thermodynamically stable ion-water configurations of the selectivity filter can be identified from all the free energy landscapes, but the heights of the kinetic barriers for potassium ions to move through the selectivity filter are, in nearly all cases, too high to predict conductances in line with experiment. This implies it is not currently feasible to predict the conductance of potassium ion channels, but other simpler channels may be more tractable.
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Affiliation(s)
- Philip
W. Fowler
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Enrique Abad
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Oliver Beckstein
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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40
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Dreyer J, Strodel P, Ippoliti E, Finnerty J, Eisenberg B, Carloni P. Ion permeation in the NanC porin from Escherichia coli: free energy calculations along pathways identified by coarse-grain simulations. J Phys Chem B 2013; 117:13534-42. [PMID: 24147565 DOI: 10.1021/jp4081838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using the X-ray structure of a recently discovered bacterial protein, the N-acetylneuraminic acid-inducible channel (NanC), we investigate computationally K(+) and Cl(-) ions' permeation. We identify ion permeation pathways that are likely to be populated using coarse-grain Monte Carlo simulations. Next, we use these pathways as reaction coordinates for umbrella sampling-based free energy simulations. We find distinct tubelike pathways connecting specific binding sites for K(+) and, more pronounced, for Cl(-) ions. Both ions permeate the porin preserving almost all of their first hydration shell. The calculated free energy barriers are G(#) ≈ 4 kJ/mol and G(#) ≈ 8 kJ/mol for Cl(-) and K(+), respectively. Within the approximations associated with these values, discussed in detail in this work, we suggest that the porin is slightly selective for Cl(-) versus K(+). Our suggestion is consistent with the experimentally observed weak Cl(-) over K(+) selectivity. A rationale for the latter is suggested by a comparison with previous calculations on strongly anion selective porins.
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Affiliation(s)
- Jens Dreyer
- Computational Biophysics, German Research School for Simulation Sciences , D-52425 Jülich, Germany
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41
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Modi N, Bárcena-Uribarri I, Bains M, Benz R, Hancock REW, Kleinekathöfer U. Role of the central arginine R133 toward the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation. Biochemistry 2013; 52:5522-32. [PMID: 23875754 DOI: 10.1021/bi400522b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The outer membrane porin OprP of Pseudomonas aeruginosa forms a highly specific phosphate selective channel. This channel is responsible for the high-affinity uptake of phosphate ions into the periplasmic space of the bacteria. A detailed investigation of the structure-function relationship of OprP is inevitable to decipher the anion and phosphate selectivity of this porin in particular and to broaden the present understanding of the ion selectivity of different channels. To this end we investigated the role of the central arginine of OprP, R133, in terms of its effects in selectivity and ion transport properties of the pore. Electrophysiological bilayer measurements and free-energy molecular dynamics simulations were carried out to probe the transport of different ions through various R133 mutants. For these mutants, the change in phosphate binding specificity, ion conduction, and anion selectivity was determined and compared to previous molecular dynamic calculations and electrophysiological measurements with wild-type OprP. Molecular analysis revealed a rather particular role of arginine 133 and its charge, while at the same time this residue together with the network of other residues, namely, D94 and Y114, has the ability to dehydrate the permeating ion. These very specific features govern the ion selectivity of OprP.
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Affiliation(s)
- Niraj Modi
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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42
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Eren E, Parkin J, Adelanwa A, Cheneke B, Movileanu L, Khalid S, van den Berg B. Toward understanding the outer membrane uptake of small molecules by Pseudomonas aeruginosa. J Biol Chem 2013; 288:12042-53. [PMID: 23467408 DOI: 10.1074/jbc.m113.463570] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Because small molecules enter Gram-negative bacteria via outer membrane (OM) channels, understanding OM transport is essential for the rational design of improved and new antibiotics. In the human pathogen Pseudomonas aeruginosa, most small molecules are taken up by outer membrane carboxylate channel (Occ) proteins, which can be divided into two distinct subfamilies, OccD and OccK. Here we characterize substrate transport mediated by Occ proteins belonging to both subfamilies. Based on the determination of the OccK2-glucuronate co-crystal structure, we identify the channel residues that are essential for substrate transport. We further show that the pore regions of the channels are rigid in the OccK subfamily and highly dynamic in the OccD subfamily. We also demonstrate that the substrate carboxylate group interacts with central residues of the basic ladder, a row of arginine and lysine residues that leads to and away from the binding site at the channel constriction. Moreover, the importance of the basic ladder residues corresponds to their degree of conservation. Finally, we apply the generated insights by converting the archetype of the entire family, OccD1, from a basic amino acid-specific channel into a channel with a preference for negatively charged amino acids.
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Affiliation(s)
- Elif Eren
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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43
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Kattner C, Zaucha J, Jaenecke F, Zachariae U, Tanabe M. Identification of a cation transport pathway in Neisseria meningitidis PorB. Proteins 2013; 81:830-40. [PMID: 23255122 DOI: 10.1002/prot.24241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/06/2012] [Accepted: 12/08/2012] [Indexed: 11/10/2022]
Abstract
Neisseria meningitidis is the main causative agent of bacterial meningitis. In its outer membrane, the trimeric Neisserial porin PorB is responsible for the diffusive transport of essential hydrophilic solutes across the bilayer. Previous molecular dynamics simulations based on the recent crystal structure of PorB have suggested the presence of distinct solute translocation pathways through this channel. Although PorB has been electrophysiologically characterized as anion-selective, cation translocation through nucleotide-bound PorB during pathogenesis is thought to be instrumental for host cell death. As a result, we were particularly interested in further characterizing cation transport through the pore. We combined a structural approach with additional computational analysis. Here, we present two crystal structures of PorB at 2.1 and 2.65 Å resolution. The new structures display additional electron densities around the protruding loop 3 (L3) inside the pore. We show that these electron densities can be identified as monovalent cations, in our case Cs(+), which are tightly bound to the inner channel. Molecular dynamics simulations reveal further ion interactions and the free energy landscape for ions inside PorB. Our results suggest that the crystallographically identified locations of Cs(+) form a cation transport pathway inside the pore. This finding suggests how positively charged ions are translocated through PorB when the channel is inserted into mitochondrial membranes during Neisserial infection, a process which is considered to dissipate the mitochondrial transmembrane potential gradient and thereby induce apoptosis.
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Affiliation(s)
- Christof Kattner
- HALOmem, Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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44
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Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. Protein Eng Des Sel 2013; 26:325-33. [DOI: 10.1093/protein/gzt004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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45
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Mortuza SM, Banerjee S. Molecular modeling study of agglomeration of [6,6]-phenyl-C61-butyric acid methyl ester in solvents. J Chem Phys 2012; 137:244308. [DOI: 10.1063/1.4772759] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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47
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Modi N, Benz R, Hancock REW, Kleinekathöfer U. Modeling the Ion Selectivity of the Phosphate Specific Channel OprP. J Phys Chem Lett 2012; 3:3639-3645. [PMID: 26290999 DOI: 10.1021/jz301637d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ion selectivity of transport systems is an essential property of membranes from living organisms. These entities are used to regulate multifarious biological processes by virtue of selective participation of specific ions in transport processes. To understand this process, we studied the phosphate selectivity of the OprP porin from Pseudomonas aeruginosa using all-atom free-energy molecular dynamics simulations. These calculations were performed to define the energetics of phosphate, sulfate, chloride, and potassium ion transport through OprP. Atomic-level analysis revealed that the overall electrostatic environment of the channel was responsible for the anion selectivity of the channel, whereas the particular balance of interactions between the permeating ions and water as well as channel residues drove the selectivity between different anions. The selectivity of OprP is discussed in light of well-studied ion channels that are highly selective for potassium or chloride.
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Affiliation(s)
- Niraj Modi
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany and
| | - Roland Benz
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany and
| | - Robert E W Hancock
- ‡Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Ulrich Kleinekathöfer
- †School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany and
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48
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Zachariae U, Schneider R, Briones R, Gattin Z, Demers JP, Giller K, Maier E, Zweckstetter M, Griesinger C, Becker S, Benz R, de Groot BL, Lange A. β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure 2012; 20:1540-9. [PMID: 22841291 PMCID: PMC5650048 DOI: 10.1016/j.str.2012.06.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 05/30/2012] [Accepted: 06/04/2012] [Indexed: 11/27/2022]
Abstract
The voltage-dependent anion channel (VDAC) is the major protein in the outer mitochondrial membrane, where it mediates transport of ATP and ADP. Changes in its permeability, induced by voltage or apoptosis-related proteins, have been implicated in apoptotic pathways. The three-dimensional structure of VDAC has recently been determined as a 19-stranded β-barrel with an in-lying N-terminal helix. However, its gating mechanism is still unclear. Using solid-state NMR spectroscopy, molecular dynamics simulations, and electrophysiology, we show that deletion of the rigid N-terminal helix sharply increases overall motion in VDAC's β-barrel, resulting in elliptic, semicollapsed barrel shapes. These states quantitatively reproduce conductance and selectivity of the closed VDAC conformation. Mutation of the N-terminal helix leads to a phenotype intermediate to the open and closed states. These data suggest that the N-terminal helix controls entry into elliptic β-barrel states which underlie VDAC closure. Our results also indicate that β-barrel channels are intrinsically flexible.
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Affiliation(s)
- Ulrich Zachariae
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- SUPA, School of Physics and Astronomy, The University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK
| | - Robert Schneider
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Protein Dynamics and Flexibility by NMR, Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Zrinka Gattin
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jean-Philippe Demers
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Elke Maier
- Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Markus Zweckstetter
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Roland Benz
- Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
- School of Engineering and Science, Jacobs University Bremen, Campusring 1, 28759 Bremen, Germany
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Lange
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Type II-dependent secretion of a Pseudomonas aeruginosa DING protein. Res Microbiol 2012; 163:457-69. [PMID: 22835944 DOI: 10.1016/j.resmic.2012.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/16/2012] [Indexed: 11/24/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that uses a wide range of protein secretion systems to interact with its host. Genes encoding the PAO1 Hxc type II secretion system are linked to genes encoding phosphatases (LapA/LapB). Microarray genotyping suggested that Pseudomonas aeruginosa clinical isolates, including urinary tract (JJ692) and blood (X13273) isolates, lacked the lapA/lapB genes. Instead, we show that they carry a gene encoding a protein of the PstS family. This protein, which we call LapC, also has significant similarities with LapA/LapB. LapC belongs to the family of DING proteins and displays the canonical DINGGG motif within its N terminus. DING proteins are members of a prokaryotic phosphate binding protein superfamily. We show that LapC is secreted in an Hxc-dependent manner and is under the control of the PhoB response regulator. The genetic organization hxc-lapC found in JJ692 and X13273 is similar to PA14, which is the most frequent P. aeruginosa genotype. While the role of LapA, LapB and LapC proteins remains unclear in P. aeruginosa pathogenesis, they are likely to be part of a phosphate scavenging or sensing system needed to survive and thrive when low phosphate environments are encountered within the host.
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Pongprayoon P, Beckstein O, Sansom MSP. Biomimetic design of a brush-like nanopore: simulation studies. J Phys Chem B 2011; 116:462-8. [PMID: 22129038 DOI: 10.1021/jp206754w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combining a high degree of selectivity and nanoscale dimensions, biological pores are attractive potential components for nanotechnology devices and applications. Biomimetic design will facilitate production of stable synthetic nanopores with defined functionality. Bacterial porins offer a good source of possible templates for such nanopores as they form stable, selective pores in lipid bilayers. Molecular dynamics simulations have been used to design simple model nanopores with permeation free energy profiles that can be made to mimic a template protein, the OprP porin, which forms pores selective for anions. In particular, we explored the effects of varying the nature of pore-lining groups on free energy profiles for phosphate and chloride ions along the pore axis and the total charge of the permeation pathway of the pore. Cationic side chains lining the model nanopore are required to model the local detail of the OprP permeation landscape, whereas the total charge contributes to its magnitude. These studies indicate that a locally accurate biomimetic design has captured the essentials of the structure/function relationship of the parent protein.
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