1
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Machin JM, Kalli AC, Ranson NA, Radford SE. Protein-lipid charge interactions control the folding of outer membrane proteins into asymmetric membranes. Nat Chem 2023; 15:1754-1764. [PMID: 37710048 PMCID: PMC10695831 DOI: 10.1038/s41557-023-01319-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Biological membranes consist of two leaflets of phospholipid molecules that form a bilayer, each leaflet comprising a distinct lipid composition. This asymmetry is created and maintained in vivo by dedicated biochemical pathways, but difficulties in creating stable asymmetric membranes in vitro have restricted our understanding of how bilayer asymmetry modulates the folding, stability and function of membrane proteins. In this study, we used cyclodextrin-mediated lipid exchange to generate liposomes with asymmetric bilayers and characterize the stability and folding kinetics of two bacterial outer membrane proteins (OMPs), OmpA and BamA. We found that excess negative charge in the outer leaflet of a liposome impedes their insertion and folding, while excess negative charge in the inner leaflet accelerates their folding relative to symmetric liposomes with the same membrane composition. Using molecular dynamics, mutational analysis and bioinformatics, we identified a positively charged patch critical for folding and stability. These results rationalize the well-known 'positive-outside' rule of OMPs and suggest insights into the mechanisms that drive OMP folding and assembly in vitro and in vivo.
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Affiliation(s)
- Jonathan M Machin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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2
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Montezano D, Bernstein R, Copeland MM, Slusky JSG. General features of transmembrane beta barrels from a large database. Proc Natl Acad Sci U S A 2023; 120:e2220762120. [PMID: 37432995 PMCID: PMC10629564 DOI: 10.1073/pnas.2220762120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 06/03/2023] [Indexed: 07/13/2023] Open
Abstract
Large datasets contribute new insights to subjects formerly investigated by exemplars. We used coevolution data to create a large, high-quality database of transmembrane β-barrels (TMBB). By applying simple feature detection on generated evolutionary contact maps, our method (IsItABarrel) achieves 95.88% balanced accuracy when discriminating among protein classes. Moreover, comparison with IsItABarrel revealed a high rate of false positives in previous TMBB algorithms. In addition to being more accurate than previous datasets, our database (available online) contains 1,938,936 bacterial TMBB proteins from 38 phyla, respectively, 17 and 2.2 times larger than the previous sets TMBB-DB and OMPdb. We anticipate that due to its quality and size, the database will serve as a useful resource where high-quality TMBB sequence data are required. We found that TMBBs can be divided into 11 types, three of which have not been previously reported. We find tremendous variance in proteome percentage among TMBB-containing organisms with some using 6.79% of their proteome for TMBBs and others using as little as 0.27% of their proteome. The distribution of the lengths of the TMBBs is suggestive of previously hypothesized duplication events. In addition, we find that the C-terminal β-signal varies among different classes of bacteria though its consensus sequence is LGLGYRF. However, this β-signal is only characteristic of prototypical TMBBs. The ten non-prototypical barrel types have other C-terminal motifs, and it remains to be determined if these alternative motifs facilitate TMBB insertion or perform any other signaling function.
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Affiliation(s)
- Daniel Montezano
- Computational Biology Program, University of Kansas, Lawrence, KS66045
| | - Rebecca Bernstein
- Computational Biology Program, University of Kansas, Lawrence, KS66045
| | | | - Joanna S. G. Slusky
- Computational Biology Program, University of Kansas, Lawrence, KS66045
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66045
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3
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Gardea-Gutiérrez D, Núñez-García E, Oseguera-Guerra BE, Román-Aguirre M, Montes-Fonseca SL. Asymmetric Lipid Vesicles: Techniques, Applications, and Future Perspectives as an Innovative Drug Delivery System. Pharmaceuticals (Basel) 2023; 16:777. [PMID: 37375725 DOI: 10.3390/ph16060777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/12/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
Novel lipid-based nanosystems have been of interest in improving conventional drug release methods. Liposomes are the most studied nanostructures, consisting of lipid bilayers ideal for drug delivery, thanks to their resemblance to the cell plasma membrane. Asymmetric liposomes are vesicles with different lipids in their inner and outer layers; because of this, they can be configured to be compatible with the therapeutic drug while achieving biocompatibility and stability. Throughout this review, topics such as the applications, advantages, and synthesis techniques of asymmetric liposomes will be discussed. Further, an in silico analysis by computational tools will be examined as a helpful tool for designing and understanding asymmetric liposome mechanisms in pharmaceutical applications. The dual-engineered design of asymmetric liposomes makes them an ideal alternative for transdermal drug delivery because of the improved protection of pharmaceuticals without lowering adsorption rates and system biocompatibility.
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Affiliation(s)
- Denisse Gardea-Gutiérrez
- Tecnologico de Monterrey, School of Engineering and Sciences, Av. H. Colegio Militar 4700, Nombre de Dios, Chihuahua 31300, Chih, Mexico
| | - Eduardo Núñez-García
- Tecnologico de Monterrey, School of Engineering and Sciences, Av. H. Colegio Militar 4700, Nombre de Dios, Chihuahua 31300, Chih, Mexico
| | - Berenice E Oseguera-Guerra
- Tecnologico de Monterrey, School of Engineering and Sciences, Av. H. Colegio Militar 4700, Nombre de Dios, Chihuahua 31300, Chih, Mexico
| | - Manuel Román-Aguirre
- Centro de Investigación en Materiales Avanzados CIMAV, Av. Miguel de Cervantes 120, Complejo Industrial Chihuahua, Chihuahua 31136, Chih, Mexico
| | - Silvia L Montes-Fonseca
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Av. H. Colegio Militar 4700, Nombre de Dios, Chihuahua 31300, Chih, Mexico
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4
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Wu HJ, Xiao ZG, Lv XJ, Huang HT, Liao C, Hui CY, Xu Y, Li HF. Drug‑resistant Acinetobacter baumannii: From molecular mechanisms to potential therapeutics (Review). Exp Ther Med 2023; 25:209. [PMID: 37090073 PMCID: PMC10119666 DOI: 10.3892/etm.2023.11908] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/24/2023] [Indexed: 04/25/2023] Open
Abstract
Bacterial drug resistance is increasingly becoming an important problem that needs to be solved urgently in modern clinical practices. Infection caused by Acinetobacter baumannii is a serious threat to the life and health of patients. The drug resistance rate of Acinetobacter baumannii strains is increasing, thus research on the drug resistance of Acinetobacter baumannii has also seen an increase. When patients are infected with drug-resistant Acinetobacter baumannii, the availability of suitable antibiotics commonly used in clinical practices is becoming increasingly limited and the prognosis of patients is worsening. Studying the molecular mechanism of the drug resistance of Acinetobacter baumannii is fundamental to solving the problem of drug-resistant Acinetobacter baumannii and potentially other 'super bacteria'. Drug resistance mechanisms primarily include enzymes, membrane proteins, efflux pumps and beneficial mutations. Research on the underlying mechanisms provides a theoretical basis for the use and development of antibiotics and the development of novel treatment methods.
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Affiliation(s)
- Hao-Jia Wu
- Clinical College of Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, P.R. China
| | - Zhi-Gang Xiao
- Department of Orthopedics, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, P.R. China
| | - Xiao-Juan Lv
- Department of Hepatology, Hubei Key Laboratory of The Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, Hubei 430074, P.R. China
| | - Hai-Tang Huang
- Department of Hepatology, Hubei Key Laboratory of The Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, Hubei 430074, P.R. China
| | - Chu Liao
- Department of Hepatology, Hubei Key Laboratory of The Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, Hubei 430074, P.R. China
| | - Chen-Yang Hui
- Department of Hepatology, Hubei Key Laboratory of The Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, Hubei 430074, P.R. China
| | - Yue Xu
- Clinical College of Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, P.R. China
| | - Heng-Fei Li
- Department of Hepatology, Hubei Key Laboratory of The Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei 430061, P.R. China
- Department of Infection, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, Hubei 430074, P.R. China
- Correspondence to: Professor Heng-Fei Li, Department of Hepatology, Hubei Key Laboratory of The Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Room 4, Garden Hill, Wuchang, Wuhan, Hubei 430061, P.R. China
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5
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Gao Q, Lu S, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Sun D, Tian B, Cheng A. Putative Riemerella anatipestifer Outer Membrane Protein H Affects Virulence. Front Microbiol 2021; 12:708225. [PMID: 34616377 PMCID: PMC8488386 DOI: 10.3389/fmicb.2021.708225] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
Riemerella anatipestifer causes serious contagious disease in ducks, geese, and other fowl. However, as a harmful pathogen causing significant economic losses in the poultry industry, R. anatipestifer is still poorly understood for its pathogenesis mechanisms. In a previous study, we developed an indirect ELISA method for detecting R. anatipestifer infection using B739_0832 protein, a putative outer membrane protein H (OmpH) that is conserved among different serotypes of R. anatipestifer. Although OmpH in some pathogenic bacteria, such as Pasteurella, has been reported as a virulence factor, it is still not clear whether B739_0832 protein contributes to the virulence of R. anatipestifer. In this study, we confirmed that B739_0832 protein in R. anatipestifer localizes to the outer membrane. We constructed a B739_0832 deletion mutant strain (ΔB739_0832) and assayed various effects from the deletion of B739_0832. ΔB739_0832 strain had a similar growth rate to wild-type R. anatipestifer CH-1. However, the survival rate of ducklings in 10 days after infection from ΔB739_0832 strain was 50%, whereas no ducklings survived from wild-type R. anatipestifer infection. Furthermore, the median lethal dose (LD50) of the ΔB739_0832 strain was approximately 150 times higher than that of the wild-type strain. Pathology examinations on infected ducklings found that, at 36 h after infection, bacterial loads in blood, liver, and brain tissues from ΔB739_0832-infected ducklings were considerably lower than those from wild-type infected ducklings. These results demonstrate that the B739_0832 protein contributes to the virulence of R. anatipestifer CH-1.
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Affiliation(s)
- Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shuwei Lu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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6
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Principles and Methods in Computational Membrane Protein Design. J Mol Biol 2021; 433:167154. [PMID: 34271008 DOI: 10.1016/j.jmb.2021.167154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 01/13/2023]
Abstract
After decades of progress in computational protein design, the design of proteins folding and functioning in lipid membranes appears today as the next frontier. Some notable successes in the de novo design of simplified model membrane protein systems have helped articulate fundamental principles of protein folding, architecture and interaction in the hydrophobic lipid environment. These principles are reviewed here, together with the computational methods and approaches that were used to identify them. We provide an overview of the methodological innovations in the generation of new protein structures and functions and in the development of membrane-specific energy functions. We highlight the opportunities offered by new machine learning approaches applied to protein design, and by new experimental characterization techniques applied to membrane proteins. Although membrane protein design is in its infancy, it appears more reachable than previously thought.
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7
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Lee J, Song WJ. Folding of Circularly Permuted and Split Outer Membrane Protein F via Electrostatic Interactions with Terminal Residues. Biochemistry 2021; 60:1787-1796. [PMID: 34060805 DOI: 10.1021/acs.biochem.1c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are essential targets in drug design, biosensing, and catalysis. In this study, we explored the folding of engineered outer membrane protein F (OmpF), an abundant and functional β-barrel protein expressed in Gram-negative bacteria. We carried out circular permutation, splitting and self-complementation, and point mutation. The folding efficiency and kinetic analyses demonstrated that the N- and C-terminal residues of OmpF played critical roles in folding via electrostatic interactions with lipid headgroups. Our results indicate that native porins without charged terminal residues may be tightly downregulated to retain the integrity of the outer membrane, and this modification may facilitate the insertion and folding of modified membrane proteins under in vitro and in vivo conditions for various applications.
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Affiliation(s)
- Jaewon Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
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8
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Dhar R, Feehan R, Slusky JSG. Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels. J Phys Chem B 2021; 125:3622-3628. [PMID: 33797916 DOI: 10.1021/acs.jpcb.1c00878] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Up-and-down β-barrel topology exists in both the membrane and soluble environment. By comparing features of these structurally similar proteins, we can determine what features are particular to the environment rather than the fold. Here we compare structures of membrane β-barrels to soluble β-barrels and evaluate their relative size, shape, amino acid composition, hydrophobicity, and periodicity. We find that membrane β-barrels are generally larger than soluble β-barrels, with more strands per barrel and more amino acids per strand, making them wider and taller. We also find that membrane β-barrels are inside-out soluble β-barrels. The inward region of membrane β-barrels has similar hydrophobicity to the outward region of soluble β-barrels, and the outward region of membrane β-barrels has similar hydrophobicity to the inward region of the soluble β-barrels. Moreover, even though both types of β-barrel have been assumed to have strands with amino acids that alternate in direction and hydrophobicity, we find that the membrane β-barrels have more regular alternation than soluble β-barrels. These features give insight into how membrane barrels maintain their fold and function in the membrane.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Ryan Feehan
- Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States
| | - Joanna S G Slusky
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States.,Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States
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9
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Uppalapati SR, Sett A, Pathania R. The Outer Membrane Proteins OmpA, CarO, and OprD of Acinetobacter baumannii Confer a Two-Pronged Defense in Facilitating Its Success as a Potent Human Pathogen. Front Microbiol 2020; 11:589234. [PMID: 33123117 PMCID: PMC7573547 DOI: 10.3389/fmicb.2020.589234] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
Of all the ESKAPE pathogens, carbapenem-resistant and multidrug-resistant Acinetobacter baumannii is the leading cause of hospital-acquired and ventilator-associated pneumonia. A. baumannii infections are notoriously hard to eradicate due to its propensity to rapidly acquire multitude of resistance determinants and the virulence factor cornucopia elucidated by the bacterium that help it fend off a wide range of adverse conditions imposed upon by host and environment. One such weapon in the arsenal of A. baumannii is the outer membrane protein (OMP) compendium. OMPs in A. baumannii play distinctive roles in facilitating the bacterial acclimatization to antibiotic- and host-induced stresses, albeit following entirely different mechanisms. OMPs are major immunogenic proteins in bacteria conferring bacteria host-fitness advantages including immune evasion, stress tolerance, and resistance to antibiotics and antibacterials. In this review, we summarize the current knowledge of major A. baumannii OMPs and discuss their versatile role in antibiotic resistance and virulence. Specifically, we explore how OmpA, CarO, and OprD-like porins mediate antibiotic and amino acid shuttle and host virulence.
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Affiliation(s)
- Siva R Uppalapati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Abhiroop Sett
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ranjana Pathania
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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10
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Mbaye MN, Hou Q, Basu S, Teheux F, Pucci F, Rooman M. A comprehensive computational study of amino acid interactions in membrane proteins. Sci Rep 2019; 9:12043. [PMID: 31427701 PMCID: PMC6700154 DOI: 10.1038/s41598-019-48541-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/07/2019] [Indexed: 01/26/2023] Open
Abstract
Transmembrane proteins play a fundamental role in a wide series of biological processes but, despite their importance, they are less studied than globular proteins, essentially because their embedding in lipid membranes hampers their experimental characterization. In this paper, we improved our understanding of their structural stability through the development of new knowledge-based energy functions describing amino acid pair interactions that prevail in the transmembrane and extramembrane regions of membrane proteins. The comparison of these potentials and those derived from globular proteins yields an objective view of the relative strength of amino acid interactions in the different protein environments, and their role in protein stabilization. Separate potentials were also derived from α-helical and β-barrel transmembrane regions to investigate possible dissimilarities. We found that, in extramembrane regions, hydrophobic residues are less frequent but interactions between aromatic and aliphatic amino acids as well as aromatic-sulfur interactions contribute more to stability. In transmembrane regions, polar residues are less abundant but interactions between residues of equal or opposite charges or non-charged polar residues as well as anion-π interactions appear stronger. This shows indirectly the preference of the water and lipid molecules to interact with polar and hydrophobic residues, respectively. We applied these new energy functions to predict whether a residue is located in the trans- or extramembrane region, and obtained an AUC score of 83% in cross validation, which demonstrates their accuracy. As their application is, moreover, extremely fast, they are optimal instruments for membrane protein design and large-scale investigations of membrane protein stability.
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Affiliation(s)
- Mame Ndew Mbaye
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Mathematics and Informatics, Cheikh Anta Diop University, Dakar-Fann, Senegal
| | - Qingzhen Hou
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sankar Basu
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabian Teheux
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
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11
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Andreev K, Martynowycz MW, Gidalevitz D. Peptoid drug discovery and optimization via surface X-ray scattering. Biopolymers 2019; 110:e23274. [PMID: 30892696 PMCID: PMC6661014 DOI: 10.1002/bip.23274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022]
Abstract
Synthetic polymers mimicking antimicrobial peptides have drawn considerable interest as potential therapeutics. N-substituted glycines, or peptoids, are recognized by their in vivo stability and ease of synthesis. Peptoids are thought to act primarily on the negatively charged lipids that are abundant in bacterial cell membranes. A mechanistic understanding of lipid-peptoid interaction at the molecular level will provide insights for rational design and optimization of peptoids. Here, we highlight recent studies that utilize synchrotron liquid surface X-ray scattering to characterize the underlying peptoid interactions with bacterial and eukaryotic membranes. Cellular membranes are highly complex, and difficult to characterize at the molecular level. Model systems including Langmuir monolayers, are used in these studies to reduce system complexity. The general workflow of these systems and the corresponding data analysis techniques are presented alongside recent findings. These studies investigate the role of peptoid physicochemical characteristics on membrane activity. Specifically, the roles of cationic charge, conformational constraint via macrocyclization, and hydrophobicity are shown to correlate their membrane interactions to biological activities in vitro. These structure-activity relationships have led to new insights into the mechanism of action by peptoid antimicrobials, and suggest optimization strategies for future therapeutics based on peptoids.
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Affiliation(s)
- Konstantin Andreev
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois
| | | | - David Gidalevitz
- Center for the Molecular Study of Condensed Soft Matter and Department of Physics, Illinois Institute of Technology, Chicago, Illinois
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12
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Franklin MW, Nepomnyachyi S, Feehan R, Ben-Tal N, Kolodny R, Slusky JS. Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins. eLife 2018; 7:40308. [PMID: 30489257 PMCID: PMC6340704 DOI: 10.7554/elife.40308] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022] Open
Abstract
Outer membrane proteins (OMPs) are the proteins in the surface of Gram-negative bacteria. These proteins have diverse functions but a single topology: the β-barrel. Sequence analysis has suggested that this common fold is a β-hairpin repeat protein, and that amplification of the β-hairpin has resulted in 8-26-stranded barrels. Using an integrated approach that combines sequence and structural analyses, we find events in which non-amplification diversification also increases barrel strand number. Our network-based analysis reveals strand-number-based evolutionary pathways, including one that progresses from a primordial 8-stranded barrel to 16-strands and further, to 18-strands. Among these pathways are mechanisms of strand number accretion without domain duplication, like a loop-to-hairpin transition. These mechanisms illustrate perpetuation of repeat protein topology without genetic duplication, likely induced by the hydrophobic membrane. Finally, we find that the evolutionary trace is particularly prominent in the C-terminal half of OMPs, implicating this region in the nucleation of OMP folding.
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Affiliation(s)
| | - Sergey Nepomnyachyi
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.,Department of Computer Science, University of Haifa, Haifa, Israel
| | - Ryan Feehan
- Center for Computational Biology, University of Kansas, Kansas, United States
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Joanna Sg Slusky
- Center for Computational Biology, University of Kansas, Kansas, United States.,Department of Molecular Biosciences, University of Kansas, Kansas, United States
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13
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Peterson JH, Hussain S, Bernstein HD. Identification of a novel post-insertion step in the assembly of a bacterial outer membrane protein. Mol Microbiol 2018; 110:143-159. [PMID: 30107065 DOI: 10.1111/mmi.14102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2018] [Indexed: 01/09/2023]
Abstract
Although the barrel assembly machinery (Bam) complex has been shown to facilitate the insertion of β barrel proteins into the bacterial outer membrane (OM), the stage at which β barrels fold is unknown. Here, we describe insights into β barrel assembly that emerged from an analysis of a member of the autotransporter family of OM proteins (EspP) in Escherichia coli. EspP contains an extracellular 'passenger' domain that is translocated across the OM and then released from the covalently linked β barrel domain in an intra-barrel cleavage reaction. We found that the mutation of an unusual lipid-exposed lysine residue impairs a previously unidentified late folding step that follows both the membrane insertion of the β barrel domain and the secretion of the passenger domain but that precedes proteolytic maturation. Our results demonstrate that β barrel assembly can be completed at a post-insertion stage and raise the possibility that interactions with membrane lipids can promote folding in vivo. Furthermore, by showing that the passenger domain is secreted before the β barrel domain is fully assembled, our results also provide evidence against the long-standing hypothesis that autotransporters are autonomous protein secretion systems.
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Affiliation(s)
- Janine H Peterson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0538, USA
| | - Sunyia Hussain
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0538, USA
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0538, USA
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14
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Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG. Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. Structure 2018; 26:1266-1274.e2. [PMID: 30057025 PMCID: PMC6125174 DOI: 10.1016/j.str.2018.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/17/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
There are around 100 varieties of outer membrane proteins in each Gram-negative bacteria. All of these proteins have the same fold-an up-down β-barrel. It has been suggested that all membrane β-barrels excluding lysins are homologous. Here we suggest that β-barrels of efflux pumps have converged on this fold as well. By grouping structurally solved outer membrane β-barrels (OMBBs) by sequence we find that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that the outer membrane factor of efflux pumps evolutionarily converged on the barrel. Rather than being related to other OMBBs, sequence and structural similarity in the periplasmic region of the outer membrane factor of efflux pumps suggests an evolutionary link to the periplasmic subunit of the same pump complex.
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Affiliation(s)
| | - Sergey Nepomnyachiy
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; Department of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Ryan Feehan
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Joanna S G Slusky
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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15
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Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding. J Mol Biol 2018; 430:3251-3265. [PMID: 29944853 DOI: 10.1016/j.jmb.2018.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/29/2018] [Accepted: 06/04/2018] [Indexed: 11/21/2022]
Abstract
As a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4 to 6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands, they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the side chain and backbone 2 to 4 residues away from that side chain plays an important role. These bonds preferentially use an Asp, Asn, Ser, or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.
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16
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Peyret A, Zhao H, Lecommandoux S. Preparation and Properties of Asymmetric Synthetic Membranes Based on Lipid and Polymer Self-Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:3376-3385. [PMID: 29486556 DOI: 10.1021/acs.langmuir.7b04233] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cell membrane asymmetry is a common structural feature of all biological cells. Researchers have tried for decades to better study its formation and its function in membrane-regulated phenomena. In particular, there has been increasing interest in developing synthetic asymmetric membrane models in the laboratory, with the aim of studying basic physical chemistry properties that may be correlated to a relevant biological function. The present article aims to summarize the main presented approaches to prepare asymmetric membranes, which are most often made from lipids, polymers, or a combination of both.
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Affiliation(s)
- Ariane Peyret
- Laboratoire de Chimie des Polymères Organiques, LCPO, Université de Bordeaux, CNRS, Bordeaux INP, UMR 5629 , 16 Avenue Pey Berland F-33600 Pessac , France
| | - Hang Zhao
- Laboratoire de Chimie des Polymères Organiques, LCPO, Université de Bordeaux, CNRS, Bordeaux INP, UMR 5629 , 16 Avenue Pey Berland F-33600 Pessac , France
| | - Sébastien Lecommandoux
- Laboratoire de Chimie des Polymères Organiques, LCPO, Université de Bordeaux, CNRS, Bordeaux INP, UMR 5629 , 16 Avenue Pey Berland F-33600 Pessac , France
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17
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Koehler Leman J, Bonneau R, Ulmschneider MB. Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins. Sci Rep 2018. [PMID: 29535329 PMCID: PMC5849751 DOI: 10.1038/s41598-018-22476-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Modeling membrane protein (MP) folding, insertion, association and their interactions with other proteins, lipids, and drugs requires accurate transfer free energies (TFEs). Various TFE scales have been derived to quantify the energy required or released to insert an amino acid or protein into the membrane. Experimental measurement of TFEs is challenging, and only few scales were extended to depth-dependent energetic profiles. Statistical approaches can be used to derive such potentials; however, this requires a sufficient number of MP structures. Furthermore, MPs are tightly coupled to bilayers that are heterogeneous in terms of lipid composition, asymmetry, and protein content between organisms and organelles. Here we derived asymmetric implicit membrane potentials from β-barrel and α-helical MPs and use them to predict topology, depth and orientation of proteins in the membrane. Our data confirm the ‘charge-outside’ and ‘positive-inside’ rules for β-barrels and α-helical proteins, respectively. We find that the β-barrel profiles have greater asymmetry than the ones from α-helical proteins, as a result of the different membrane architecture of gram-negative bacterial outer membranes and the existence of lipopolysaccharide in the outer leaflet. Our data further suggest that pore-facing residues in β-barrels have a larger contribution to membrane insertion and stability than previously suggested.
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, 10010 NY, USA. .,Department of Biology, Center for Genomics and Systems Biology, New York University, New York, 10003 NY, USA.
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, 10010 NY, USA.,Department of Biology, Center for Genomics and Systems Biology, New York University, New York, 10003 NY, USA.,Department of Computer Science, New York University, New York, 10012 NY, USA
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18
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Tian W, Lin M, Naveed H, Liang J. Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins. Bioinformatics 2018; 33:1664-1671. [PMID: 28158457 DOI: 10.1093/bioinformatics/btx053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/25/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure-function relationship. However, experimental measurement of TFEs of TMBs is challenging. Although a recent computational method can be used to calculate TFEs, the results of which are in excellent agreement with experimentally measured values, this method does not scale up, and is limited to small TMBs. Results We have developed an approximation method that calculates TFEs of TM residues in TMBs accurately, with which depth-dependent transfer free energy profiles can be derived. Our results are in excellent agreement with experimental measurements. This method is efficient and applicable to all bacterial TMBs regardless of the size of the protein. Availability and Implementation An online webserver is available at http://tanto.bioe.uic.edu/tmb-tfe . Contact : jliang@uic.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wei Tian
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Meishan Lin
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Hammad Naveed
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | - Jie Liang
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
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19
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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20
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Wanag A, Rokicka P, Kusiak-Nejman E, Kapica-Kozar J, Wrobel RJ, Markowska-Szczupak A, Morawski AW. Antibacterial properties of TiO 2 modified with reduced graphene oxide. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:788-793. [PMID: 28946119 DOI: 10.1016/j.ecoenv.2017.09.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/09/2017] [Accepted: 09/14/2017] [Indexed: 05/19/2023]
Abstract
In this paper, the antibacterial activity of titanium dioxide modified with reduced graphene oxide (rGO) was presented. TiO2/rGO photocatalysts were prepared by the hydrothermal method under elevated pressure at 180°C and heated at 100°C in Ar flow. The obtained photocatalysts were characterized by means of XRD, FTIR/DRS, UV-vis/DR, Raman spectroscopy and scanning electron microscopy (SEM). The carbon content was also examined. FTIR/DRS and Raman analysis confirmed the presence of rGO in the TiO2 structure, suggesting a successful modification. The antimicrobial photoactivity of photocatalysts was conducted against E. coli under an artificial solar light. The results show that all TiO2/rGO photocatalysts exhibited an antibacterial activity higher than unmodified TiO2. The best result was found for sample with 1.5wt% additive of reduced graphene oxide. In this case, total inactivation of E. coli was noticed after 75min of irradiation. It was found that the presence of rGO in sample improves the antimicrobial activity.
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Affiliation(s)
- Agnieszka Wanag
- West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering, Institute of Inorganic Technology and Environment Engineering, Pułaskiego 10, 70-322 Szczecin, Poland.
| | - Paulina Rokicka
- West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering, Institute of Inorganic Technology and Environment Engineering, Pułaskiego 10, 70-322 Szczecin, Poland
| | - Ewelina Kusiak-Nejman
- West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering, Institute of Inorganic Technology and Environment Engineering, Pułaskiego 10, 70-322 Szczecin, Poland
| | - Joanna Kapica-Kozar
- West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering, Institute of Inorganic Technology and Environment Engineering, Pułaskiego 10, 70-322 Szczecin, Poland
| | - Rafał J Wrobel
- West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering, Institute of Inorganic Technology and Environment Engineering, Pułaskiego 10, 70-322 Szczecin, Poland
| | - Agata Markowska-Szczupak
- West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering, Institute of Inorganic Technology and Environment Engineering, Pułaskiego 10, 70-322 Szczecin, Poland
| | - Antoni W Morawski
- West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering, Institute of Inorganic Technology and Environment Engineering, Pułaskiego 10, 70-322 Szczecin, Poland
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21
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Peterson JH, Plummer AM, Fleming KG, Bernstein HD. Selective pressure for rapid membrane integration constrains the sequence of bacterial outer membrane proteins. Mol Microbiol 2017; 106:777-792. [PMID: 28941249 DOI: 10.1111/mmi.13845] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2017] [Indexed: 12/11/2022]
Abstract
Almost all bacterial outer membrane proteins (OMPs) contain a β barrel domain that serves as a membrane anchor, but the assembly and quality control of these proteins are poorly understood. Here, we show that the introduction of a single lipid-facing arginine residue near the middle of the β barrel of the Escherichia coli OMPs OmpLA and EspP creates an energy barrier that impedes membrane insertion. Although several unintegrated OmpLA mutants remained insertion-competent, they were slowly degraded by the periplasmic protease DegP. Two EspP mutants were also gradually degraded by DegP but were toxic because they first bound to the Bam complex, an essential heteroligomer that catalyzes the membrane insertion of OMPs. Interestingly, another EspP mutant likewise formed a prolonged, deleterious interaction with the Bam complex but was protected from degradation and eventually inserted into the membrane in a native conformation. The different types of interactions between the EspP mutants and the Bam complex that we observed may correspond to distinct stages in OMP assembly. Our results show that sequences that significantly delay assembly are disfavored not only because unintegrated OMPs are subjected to degradation, but also because OMPs that assemble slowly can form dominant-negative interactions with the Bam complex.
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Affiliation(s)
- Janine H Peterson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health, Bethesda, MD 20892, USA
| | - Ashlee M Plummer
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health, Bethesda, MD 20892, USA
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22
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Balusek C, Gumbart JC. Role of the Native Outer-Membrane Environment on the Transporter BtuB. Biophys J 2017; 111:1409-1417. [PMID: 27705764 DOI: 10.1016/j.bpj.2016.08.033] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 11/19/2022] Open
Abstract
BtuB is a TonB-dependent transporter that permits the high-affinity binding and transport of cobalamin (CBL), or vitamin B12, across the asymmetric outer membrane (OM) of Gram-negative bacteria. It has been shown that Ca2+ binding is necessary for high-affinity binding of CBL to BtuB, and earlier simulations suggested that calcium ions serve to stabilize key substrate-binding extracellular loops. However, those simulations did not account for the lipopolysaccharides in the OM. To illuminate the roles of both Ca2+ and lipopolysaccharides in protein functionality, we performed simulations of apo and Ca2+-loaded BtuB in symmetric and asymmetric bilayers. The simulations reveal that the oligosaccharides of LPS stabilize the extracellular loops to some degree, apparently obviating the need for Ca2+. However, it is shown that Ca2+ ions stabilize a key substrate-binding loop to an even greater degree, as well as reposition specific CBL-binding residues, bringing them closer to the organization found in the CBL-bound structure. These results indicate the importance of including realistic membrane models when simulating outer-membrane proteins.
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Affiliation(s)
- Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
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23
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Geng Z, Han Y, Jiang W. Structural transformation of vesicles formed by a polystyrene-b-poly(acrylic acid)/polystyrene-b-poly(4-vinyl pyridine) mixture: from symmetric to asymmetric membranes. SOFT MATTER 2017; 13:2634-2642. [PMID: 28327712 DOI: 10.1039/c7sm00255f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Asymmetric vesicles with different inner and outer corona compositions are applicable in microreactors, drug delivery, and biomimics because of their unique functions in membrane permeability and protein localization. In this study, we develop a novel approach to construct asymmetric vesicles and demonstrate the first structural transformation of polymeric vesicles from symmetric to asymmetric membranes. Experimental results and Monte Carlo simulation results clearly reveal that increased intercorona repulsion and enhanced hydrophobic chain mobility are essential to realize this transformation. Moreover, similar transformation processes are observed where either HCl or NaOH is added to change the intercorona interaction. This finding indicates that the observed structural transformation is dominated by physical interactions rather than chemical environment. The constructed asymmetric vesicles can be selectively decorated with gold nanoparticles on the outer corona. This study introduces a novel approach to prepare asymmetric vesicles and provides insights into the mechanism underlying the structural transformation of polymeric vesicles from symmetric to asymmetric membranes.
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Affiliation(s)
- Zhen Geng
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China. and University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Han
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China.
| | - Wei Jiang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China.
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24
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Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1180-1189. [PMID: 28341438 DOI: 10.1016/j.bbamem.2017.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/20/2017] [Accepted: 03/18/2017] [Indexed: 12/12/2022]
Abstract
β-Barrelmembrane proteins (βMPs) form barrel-shaped pores in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Because of the robustness of their barrel structures, βMPs have great potential as nanosensors for single-molecule detection. However, natural βMPs currently employed have inflexible biophysical properties and are limited in their pore geometry, hindering their applications in sensing molecules of different sizes and properties. Computational engineering has the promise to generate βMPs with desired properties. Here we report a method for engineering novel βMPs based on the discovery of sequence motifs that predominantly interact with the cell membrane and appear in more than 75% of transmembrane strands. By replacing β1-β6 strands of the protein OmpF that lack these motifs with β1-β6 strands of OmpG enriched with these motifs and computational verification of increased stability of its transmembrane section, we engineered a novel βMP called OmpGF. OmpGF is predicted to form a monomer with a stable transmembrane region. Experimental validations showed that OmpGF could refold in vitro with a predominant β-sheet structure, as confirmed by circular dichroism. Evidence of OmpGF membrane insertion was provided by intrinsic tryptophan fluorescence spectroscopy, and its pore-forming property was determined by a dye-leakage assay. Furthermore, single-channel conductance measurements confirmed that OmpGF function as a monomer and exhibits increased conductance than OmpG and OmpF. These results demonstrated that a novel and functional βMP can be successfully engineered through strand replacement based on sequence motif analysis and stability calculation.
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25
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Koehler Leman J, Lyskov S, Bonneau R. Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. BMC Bioinformatics 2017; 18:115. [PMID: 28219343 PMCID: PMC5319049 DOI: 10.1186/s12859-017-1541-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/08/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Although programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins. RESULTS Here we present mp_lipid_acc, the first method to identify lipid accessible residues from the protein structure, implemented in the RosettaMP framework and available as a webserver. Our method uses protein structures transformed in membrane coordinates, for instance from PDBTM or OPM databases, and a defined membrane thickness to classify lipid accessibility of residues. mp_lipid_acc is applicable to both α-helical and β-barrel membrane proteins of diverse architectures with or without water-filled pores and uses a concave hull algorithm for surface-residue classification. We further provide a manually curated benchmark dataset that can be used for further method development. CONCLUSIONS We present a novel tool to classify lipid accessibility from the protein structure, which is applicable to proteins of diverse architectures and achieves prediction accuracies of 90% on a manually curated database. mp_lipid_acc is part of the Rosetta software suite, available at www.rosettacommons.org . The webserver is available at http://rosie.graylab.jhu.edu/mp_lipid_acc/submit and the benchmark dataset is available at http://tinyurl.com/mp-lipid-acc-dataset .
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY 10010 USA
- Departments of Biology and Computer Science, Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY 10010 USA
- Departments of Biology and Computer Science, Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
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26
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St. Clair JR, Wang Q, Li G, London E. Preparation and Physical Properties of Asymmetric Model Membrane Vesicles. SPRINGER SERIES IN BIOPHYSICS 2017. [DOI: 10.1007/978-981-10-6244-5_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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27
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Abstract
Transmembrane beta-barrels (TMBBs) constitute an important structural class of membrane proteins located in the outer membrane of gram-negative bacteria, and in the outer membrane of chloroplasts and mitochondria. They are involved in a wide variety of cellular functions and the prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes is of great importance as they are promising targets for antimicrobial drugs and vaccines. Several methods have been applied for the prediction of the transmembrane segments and the topology of beta barrel transmembrane proteins utilizing different algorithmic techniques. Hidden Markov Models (HMMs) have been efficiently used in the development of several computational methods used for this task. In this chapter we give a brief review of different available prediction methods for beta barrel transmembrane proteins pointing out sequence and structural features that should be incorporated in a prediction method. We then describe the procedure of the design and development of a Hidden Markov Model capable of predicting the transmembrane beta strands of TMBBs and discriminating them from globular proteins.
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Affiliation(s)
- Georgios N Tsaousis
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, 15701, Greece
| | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, 15701, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, Lamia, 35100, Greece.
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28
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Slusky JS. Outer membrane protein design. Curr Opin Struct Biol 2016; 45:45-52. [PMID: 27894013 DOI: 10.1016/j.sbi.2016.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/02/2016] [Indexed: 01/23/2023]
Abstract
Membrane proteins are the gateway to the cell. These proteins are also a control center of the cell, as information from the outside is passed through membrane proteins as signals to the cellular machinery. The design of membrane proteins seeks to harness the power of these gateways and signal carriers. This review will focus on the design of the membrane proteins that are in the outer membrane, a membrane which only exists for gram negative bacteria, mitochondria, and chloroplasts. Unlike other membrane proteins, outer membrane proteins are uniquely shaped as β-barrels. Herein, I describe most known examples of membrane β-barrel design to date, focusing particularly on categorizing designs as: Firstly, structural deconstruction; secondly, structural changes; thirdly, chemical function design; and finally, the creation of new folds.
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Affiliation(s)
- Joanna Sg Slusky
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 4010 Haworth Hall, 1200 Sunnyside Ave., Lawrence, KS 66045, United States.
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29
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McDonald SK, Fleming KG. Negative Charge Neutralization in the Loops and Turns of Outer Membrane Phospholipase A Impacts Folding Hysteresis at Neutral pH. Biochemistry 2016; 55:6133-6137. [PMID: 27731977 DOI: 10.1021/acs.biochem.6b00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hysteresis in equilibrium protein folding titrations is an experimental barrier that must be overcome to extract meaningful thermodynamic quantities. Traditional approaches to solving this problem involve testing a spectrum of solution conditions to find ones that achieve path independence. Through this procedure, a specific pH of 3.8 was required to achieve path independence for the water-to-bilayer equilibrium folding of outer membrane protein OmpLA. We hypothesized that the neutralization of negatively charged side chains (Asp and Glu) at pH 3.8 could be the physical basis for path-independent folding at this pH. To test this idea, we engineered variants of OmpLA with Asp → Asn and Glu → Gln mutations to neutralize the negative charges within various regions of the protein and tested for reversible folding at neutral pH. Although not fully resolved, our results show that these mutations in the periplasmic turns and extracellular loops are responsible for 60% of the hysteresis in wild-type folding. Overall, our study suggests that negative charges impact the folding hysteresis in outer membrane proteins and their neutralization may aid in protein engineering applications.
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Affiliation(s)
- Sarah K McDonald
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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30
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Tsirigos KD, Elofsson A, Bagos PG. PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. Bioinformatics 2016; 32:i665-i671. [DOI: 10.1093/bioinformatics/btw444] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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31
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McDonald SK, Fleming KG. Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal. J Am Chem Soc 2016; 138:7946-50. [PMID: 27254476 DOI: 10.1021/jacs.6b03460] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitating and understanding the physical forces responsible for the interactions of biomolecules are fundamental to the biological sciences. This is especially challenging for membrane proteins because they are embedded within cellular bilayers that provide a unique medium in which hydrophobic sequences must fold. Knowledge of the energetics of protein-lipid interactions is thus vital to understand cellular processes involving membrane proteins. Here we used a host-guest mutational strategy to calculate the Gibbs free energy changes of water-to-lipid transfer for the aromatic side chains Trp, Tyr, and Phe as a function of depth in the membrane. This work reveals an energetic gradient in the transfer free energies for Trp and Tyr, where transfer was most favorable to the membrane interfacial region and comparatively less favorable into the bilayer center. The transfer energetics follows the concentration gradient of polar atoms across the bilayer normal that naturally occurs in biological membranes. Additional measurements revealed nearest-neighbor coupling in the data set are influenced by a network of aromatic side chains in the host protein. Taken together, these results show that aromatic side chains contribute significantly to membrane protein stability through either aromatic-aromatic interactions or placement at the membrane interface.
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Affiliation(s)
- Sarah K McDonald
- T.C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Karen G Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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32
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Lin M, Gessmann D, Naveed H, Liang J. Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale. J Am Chem Soc 2016; 138:2592-601. [PMID: 26860422 DOI: 10.1021/jacs.5b10307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Knowledge of the transfer free energy of amino acids from aqueous solution to a lipid bilayer is essential for understanding membrane protein folding and for predicting membrane protein structure. Here we report a computational approach that can calculate the folding free energy of the transmembrane region of outer membrane β-barrel proteins (OMPs) by combining an empirical energy function with a reduced discrete state space model. We quantitatively analyzed the transfer free energies of 20 amino acid residues at the center of the lipid bilayer of OmpLA. Our results are in excellent agreement with the experimentally derived hydrophobicity scales. We further exhaustively calculated the transfer free energies of 20 amino acids at all positions in the TM region of OmpLA. We found that the asymmetry of the Gram-negative bacterial outer membrane as well as the TM residues of an OMP determine its functional fold in vivo. Our results suggest that the folding process of an OMP is driven by the lipid-facing residues in its hydrophobic core, and its NC-IN topology is determined by the differential stabilities of OMPs in the asymmetrical outer membrane. The folding free energy is further reduced by lipid A and assisted by general depth-dependent cooperativities that exist between polar and ionizable residues. Moreover, context-dependency of transfer free energies at specific positions in OmpLA predict regions important for protein function as well as structural anomalies. Our computational approach is fast, efficient and applicable to any OMP.
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Affiliation(s)
- Meishan Lin
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Dennis Gessmann
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Hammad Naveed
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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33
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Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Living on the edge: Simulations of bacterial outer-membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1753-9. [PMID: 26826270 DOI: 10.1016/j.bbamem.2016.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 01/06/2023]
Abstract
Gram-negative bacteria are distinguished in part by a second, outer membrane surrounding them. This membrane is distinct from others, possessing an outer leaflet composed not of typical phospholipids but rather large, highly charged molecules known as lipopolysaccharides. Therefore, modeling the structure and dynamics of proteins embedded in the outer membrane requires careful consideration of their native environment. In this review, we examine how simulations of such outer-membrane proteins have evolved over the last two decades, culminating most recently in detailed, highly accurate atomistic models of the outer membrane. We also draw attention to how the simulations have coupled with experiments to produce novel insights unattainable through a single approach. 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)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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34
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Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley DC, Elazar A, Gray JJ. An Integrated Framework Advancing Membrane Protein Modeling and Design. PLoS Comput Biol 2015; 11:e1004398. [PMID: 26325167 PMCID: PMC4556676 DOI: 10.1371/journal.pcbi.1004398] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/09/2015] [Indexed: 11/19/2022] Open
Abstract
Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design.
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Affiliation(s)
- Rebecca F. Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Brian D. Weitzner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Amanda M. Duran
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Drew C. Tilley
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, California, United States of America
| | - Assaf Elazar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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35
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An empirical energy function for structural assessment of protein transmembrane domains. Biochimie 2015; 115:155-61. [DOI: 10.1016/j.biochi.2015.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022]
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36
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Computational redesign of the lipid-facing surface of the outer membrane protein OmpA. Proc Natl Acad Sci U S A 2015. [PMID: 26199411 DOI: 10.1073/pnas.1501836112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Advances in computational design methods have made possible extensive engineering of soluble proteins, but designed β-barrel membrane proteins await improvements in our understanding of the sequence determinants of folding and stability. A subset of the amino acid residues of membrane proteins interact with the cell membrane, and the design rules that govern this lipid-facing surface are poorly understood. We applied a residue-level depth potential for β-barrel membrane proteins to the complete redesign of the lipid-facing surface of Escherichia coli OmpA. Initial designs failed to fold correctly, but reversion of a small number of mutations indicated by backcross experiments yielded designs with substitutions to up to 60% of the surface that did support folding and membrane insertion.
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37
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Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
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Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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38
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Sánchez-Díaz LE, Shew CY, Li X, Wu B, Smith GS, Chen WR. Phase behavior under a noncentrosymmetric interaction: shifted-charge colloids investigated by Monte Carlo simulation. J Phys Chem B 2014; 118:6963-71. [PMID: 24849261 DOI: 10.1021/jp504049r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using Monte Carlo simulations, we investigate the structural characteristics of an interacting hard-sphere system with shifted charge to elucidate the effect of the noncentrosymmetric interaction on its phase behavior. Two different phase transitions are identified for this model system. With increasing volume fraction, an abrupt liquid-to-crystal transition first occurs at a significantly lower volume fraction than in centrosymmetrically charged systems. This is due to the stronger effective interparticle repulsion caused by the additional charge anisotropy. Moreover, within the crystal state at higher volume fraction, the system further undergoes a continuous disorder-to-order transition with respect to charge orientation. Detailed analyses in this work disclose the nature of these transitions, and orientation fluctuation can cause noncentrosymmetric unit cells. The dependence of crystal formation and orientational ordering on temperature was also examined. These findings indicate that the noncentrosymmetric interaction in this work results in additional freedoms to fine-tune the phase diagram and increase the functionalities of materials. Moreover, these model studies are essential to advance the future understanding regarding the fundamental physiochemical properties of novel Janus colloidal particles and protein crystallization conditions.
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Affiliation(s)
- Luis E Sánchez-Díaz
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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39
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Wu EL, Fleming PJ, Yeom MS, Widmalm G, Klauda JB, Fleming KG, Im W. E. coli outer membrane and interactions with OmpLA. Biophys J 2014; 106:2493-502. [PMID: 24896129 PMCID: PMC4052237 DOI: 10.1016/j.bpj.2014.04.024] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/17/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022] Open
Abstract
The outer membrane of Gram-negative bacteria is a unique asymmetric lipid bilayer composed of phospholipids (PLs) in the inner leaflet and lipopolysaccharides (LPSs) in the outer leaflet. Its function as a selective barrier is crucial for the survival of bacteria in many distinct environments, and it also renders Gram-negative bacteria more resistant to antibiotics than their Gram-positive counterparts. Here, we report the structural properties of a model of the Escherichia coli outer membrane and its interaction with outer membrane phospholipase A (OmpLA) utilizing molecular dynamics simulations. Our results reveal that given the lipid composition used here, the hydrophobic thickness of the outer membrane is ∼3 Å thinner than the corresponding PL bilayer, mainly because of the thinner LPS leaflet. Further thinning in the vicinity of OmpLA is observed due to hydrophobic matching. The particular shape of the OmpLA barrel induces various interactions between LPS and PL leaflets, resulting in asymmetric thinning around the protein. The interaction between OmpLA extracellular loops and LPS (headgroups and core oligosaccharides) stabilizes the loop conformation with reduced dynamics, which leads to secondary structure variation and loop displacement compared to that in a DLPC bilayer. In addition, we demonstrate that the LPS/PL ratios in asymmetric bilayers can be reliably estimated by the per-lipid surface area of each lipid type, and there is no statistical difference in the overall membrane structure for the outer membranes with one more or less LPS in the outer leaflet, although individual lipid properties vary slightly.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Patrick J Fleming
- T. C. Jenkins Department of Biophysics, John Hopkins University, Baltimore, Maryland
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information, Daejeon, Korea
| | - Göran Widmalm
- Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, The University of Maryland, College Park, Maryland
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, John Hopkins University, Baltimore, Maryland.
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas.
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