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Velumani K, Arasu A, Issac PK, Kishore Kumar MS, Guru A, Arockiaraj J. Advancements of fish-derived peptides for mucormycosis: a novel strategy to treat diabetic compilation. Mol Biol Rep 2023; 50:10485-10507. [PMID: 37917415 DOI: 10.1007/s11033-023-08882-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
Mucormycosis, an extremely fatal fungal infection, is a major hurdle in the treatment of diabetes consequences. The increasing prevalence and restricted treatment choices urge the investigation of novel therapeutic techniques. Because of their effective antimicrobial characteristics and varied modes of action, fish-derived peptides have lately emerged as viable options in the fight against mucormycosis. This review examines the potential further application of fish-derived peptides in diagnosing and managing mucormycosis in relation to diabetic complications. First, we examine the pathophysiology of mucormycosis and the difficulties in treating it in diabetics. We emphasize the critical need for alternative therapeutic methods for tackling the limitations of currently available antifungal medicines. The possibility of fish-derived peptides as an innovative approach to combat mucormycosis is then investigated. These peptides, derived from several fish species, provide wide antimicrobial properties against a variety of diseases. They also have distinct modes of action, such as rupture of cell membranes, suppression of development, and modification of the host immunological response. Furthermore, we investigate the problems and prospects connected with the clinical application of fish-derived peptides. Ultimately, future advances in fish-derived peptides, offer interesting avenues for the management of mucormycosis in the context of diabetic comorbidities. More research and clinical trials are needed to properly investigate these peptide's therapeutic potential and pave the way for their adoption into future antifungal therapies.
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Affiliation(s)
- Kadhirmathiyan Velumani
- Institute of Biotechnology, Department of Medical Biotechnology and Integrative Physiology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, Tamil Nadu, 602 105, India
| | - Abirami Arasu
- Department of Microbiology, SRM Arts and Science College, Kattankulathur, Chennai, Tamil Nadu, 603 203, India
| | - Praveen Kumar Issac
- Institute of Biotechnology, Department of Medical Biotechnology and Integrative Physiology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, Tamil Nadu, 602 105, India.
| | - Meenakshi Sundaram Kishore Kumar
- Biomedical Research Unit and Laboratory Animal Centre (BRULAC), Department of Anatomy, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600 077, India
| | - Ajay Guru
- Department of Cariology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamil Nadu, 603203, India.
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2
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Jung B, Yun H, Min HJ, Yang S, Shin SY, Lee CW. Discovery of structural and functional transition sites for membrane-penetrating activity of sheep myeloid antimicrobial peptide-18. Sci Rep 2023; 13:1238. [PMID: 36690720 PMCID: PMC9871035 DOI: 10.1038/s41598-023-28386-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Cathelicidin antimicrobial peptides have an extended and/or unstructured conformation in aqueous solutions but fold into ordered conformations, such as the α-helical structure, when interacting with cellular membranes. These structural transitions can be directly correlated to their antimicrobial activity and its underlying mechanisms. SMAP-18, the N-terminal segment (residues 1-18) of sheep cathelicidin (SMAP-29), is known to kill microorganisms by translocating across membranes and interacting with their nucleic acids. The amino acid sequence of SMAP-18 contains three Gly residues (at positions 2, 7, and 13) that significantly affect the flexibility of its peptide structure. This study investigated the role of Gly residues in the structure, membrane interaction, membrane translocation, and antimicrobial mechanisms of SMAP-18. Five analogs were designed and synthesized through Gly → Ala substitution (i.e., G2A, G7A, G13A, G7,13A, and G2,7,13A); these substitutions altered the helical content of SMAP-18 peptides. We found that G7,13A and G2,7,13A changed their mode of action, with circular dichroism and nuclear magnetic resonance studies revealing that these analogs changed the structure of SMAP-18 from a random coil to an α-helical structure. The results of this experiment suggest that the Gly residues at positions 7 and 13 in SMAP-18 are the structural and functional determinants that control its three-dimensional structure, strain-specific activity, and antimicrobial mechanism of action. These results provide valuable information for the design of novel peptide-based antibiotics.
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Affiliation(s)
- Bomi Jung
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hye Jung Min
- Department of Cosmetic Science, Gwangju Women's University, Gwangju, 62396, Republic of Korea
| | - Sungtae Yang
- Department of Microbiology, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea
| | - Song Yub Shin
- Department of Cellular and Molecular Medicine, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
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3
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Bhukta S, Samal SK, Vasudevan S, Sarveswari HB, Shanmugam K, Princy SA, Dandela R. A Prospective Diversity of Antibacterial Small Peptidomimetic and Quorum Sensing Mediated Drug: A Review. ChemistrySelect 2022. [DOI: 10.1002/slct.202102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Swadhapriya Bhukta
- Institute of Chemical Technology-Indian Oil Odisha Campus Department of Industrial and Engineering Chemistry Bhubaneswar 751013 Odisha India
| | - Sangram Keshari Samal
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies Indian Council of Medical Research-Regional Medical Research Center Bhubaneswar 751013 Odisha India
| | - Sahana Vasudevan
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - Hema Bhagavathi Sarveswari
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - Karthi Shanmugam
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - S. Adline Princy
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - Rambabu Dandela
- Institute of Chemical Technology-Indian Oil Odisha Campus Department of Industrial and Engineering Chemistry Bhubaneswar 751013 Odisha India
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4
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Marzuoli I, Cruz CHB, Lorenz CD, Fraternali F. Nanocapsule designs for antimicrobial resistance. NANOSCALE 2021; 13:10342-10355. [PMID: 34137751 DOI: 10.1039/d0nr08146a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The pressing need of new antimicrobial products is growing stronger, particularly because of widespread antimicrobial resistance, endangering our ability to treat common infections. The recent coronavirus pandemic has dramatically highlighted the necessity of effective antibacterial and antiviral protection. This work explores at the molecular level the mechanism of action of antibacterial nanocapsules assembled in virus-like particles, their stability and their interaction with mammal and antimicrobial model membranes. We use Molecular Dynamics with force-fields of different granularity and protein design strategies to study the stability, self-assembly and membrane poration properties of these nanocapsules.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | - Carlos H B Cruz
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | | | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
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5
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Bertrand B, Garduño-Juárez R, Munoz-Garay C. Estimation of pore dimensions in lipid membranes induced by peptides and other biomolecules: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183551. [PMID: 33465367 DOI: 10.1016/j.bbamem.2021.183551] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
The cytoplasmic membrane is one of the most frequent cell targets of antimicrobial peptides (AMPs) and other biomolecules. Understanding the mechanism of action of AMPs at the molecular level is of utmost importance for designing of new membrane-specific molecules. In particular, the formation of pores, the structure and size of these pores are of great interest and require nanoscale resolution approaches, therefore, biophysical strategies are essential to achieve an understanding of these processes at this scale. In the case of membrane active peptides, pore formation or general membrane disruption is usually the last step before cell death, and so, pore size is generally directly associated to pore structure and stability and loss of cellular homeostasis, implicated in overall peptide activity. Up to date, there has not been a critical review discussing the methods that can be used specifically for estimating the pore dimensions induced by membrane active peptides. In this review we discuss the scope, relevance and popularity of the different biophysical techniques such as liposome leakage experiments, advanced microscopy, neutron or X-ray scattering, electrophysiological techniques and molecular dynamics studies, all of them useful for determining pore structure and dimension.
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Affiliation(s)
- Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico.
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6
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Self-assembly of supported lipid multi-bilayers investigated by time-resolved X-ray diffraction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183437. [PMID: 32783887 DOI: 10.1016/j.bbamem.2020.183437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 11/23/2022]
Abstract
Supported lipid multi-bilayers or bilayer stacks are an important model membrane system, particularly suitable for surface-sensitive characterization methods like X-ray and neutron diffraction. Spreading organic solution (sOS) is one of the most widely used protocols for the preparation of lipid multi-bilayers. Despite its great popularity, the self-assembly mechanism of the bilayers is not yet fully elucidated, limiting further improvements of this protocol. In order to solve this problem, we investigated the formation process of lipid bilayers in the sOS protocol, using in-situ time-resolved X-ray diffraction, complemented by X-ray reflectivity and molecular dynamics simulation. Results reveal a simultaneous self-assembly scheme for both cholesterol-free and cholesterol-containing bilayers, with one bilayer phase forming at the surface and the other forming in the solution. The solution phase gradually transforms into the surface phase, yielding clean single phase in the end.
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7
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Bera PK, Kandar AK, Krishnaswamy R, Fontaine P, Impéror-Clerc M, Pansu B, Constantin D, Maiti S, Sanyal MK, Sood AK. Grazing Incidence X-ray Diffraction Studies of Lipid-Peptide Mixed Monolayers during Shear Flow. ACS OMEGA 2020; 5:14555-14563. [PMID: 32596593 PMCID: PMC7315600 DOI: 10.1021/acsomega.0c01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 04/10/2020] [Indexed: 05/20/2023]
Abstract
Grazing incidence X-ray diffraction (GIXD) studies of monolayers of biomolecules at an air-water interface give quantitative information of in-plane packing, coherence length of crystalline domains, etc. Rheo-GIXD measurements can reveal quantitative changes in the nanocrystalline domains of a monolayer under shear. Here, we report GIXD studies of monolayers of alamethicin peptide, DPPC lipid, and their mixtures at an air-water interface under steady shear stress. The alamethicin monolayer and the mixed monolayer show a flow jamming transition. On the other hand, the pure 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) monolayer under constant stress flows steadily with a notable enhancement of the area/molecule and coherence lengths, suggesting the fusion of nanocrystallites during flow. The DPPC-alamethicin mixed monolayer shows no significant change in the area/DPPC molecule, but the coherence lengths of the individual phases (DPPC and alamethicin) increase, suggesting that the crystallites of individual phases grow bigger by merging of domains. More phase separation occurs in the system during flow. Our results show that rheo-GIXD has the potential to explore in situ molecular structural changes under rheological conditions for a diverse range of confined biomolecules at interfaces.
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Affiliation(s)
- Pradip K. Bera
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Ajoy K. Kandar
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
- Soft Condensed Matter,
Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Rema Krishnaswamy
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
- School of Liberal
Studies, Azim Premji University, Bangalore 560100, India
| | - Philippe Fontaine
- SOLEIL Synchrotron, L’Orme des Merisiers, Saint-Aubin, BP48, 91192 Gif-sur-Yvette
Cedex, France
| | - Marianne Impéror-Clerc
- Laboratoire de Physique des
Solides, Unité Mixte de Recherche 8502 Centre National de la
Recherche Scientifique, Université
Paris-Sud 11, 91405 Orsay Cedex, France
| | - Brigitte Pansu
- Laboratoire de Physique des
Solides, Unité Mixte de Recherche 8502 Centre National de la
Recherche Scientifique, Université
Paris-Sud 11, 91405 Orsay Cedex, France
| | - Doru Constantin
- Laboratoire de Physique des
Solides, Unité Mixte de Recherche 8502 Centre National de la
Recherche Scientifique, Université
Paris-Sud 11, 91405 Orsay Cedex, France
| | - Santanu Maiti
- Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
| | - Milan K. Sanyal
- Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
| | - A. K. Sood
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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8
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Dishman AF, Lee MW, de Anda J, Lee EY, He J, Huppler AR, Wong GCL, Volkman BF. Switchable Membrane Remodeling and Antifungal Defense by Metamorphic Chemokine XCL1. ACS Infect Dis 2020; 6:1204-1213. [PMID: 32243126 PMCID: PMC7258946 DOI: 10.1021/acsinfecdis.0c00011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Antimicrobial peptides (AMPs) are
a class of molecules which generally
kill pathogens via preferential cell membrane disruption. Chemokines
are a family of signaling proteins that direct immune cell migration
and share a conserved α–β tertiary structure. Recently,
it was found that a subset of chemokines can also function as AMPs,
including CCL20, CXCL4, and XCL1. It is therefore surprising that
machine learning based analysis predicts that CCL20 and CXCL4’s
α-helices are membrane disruptive, while XCL1’s helix
is not. XCL1, however, is the only chemokine known to be a metamorphic
protein which can interconvert reversibly between two distinct native
structures (a β-sheet dimer and the α–β chemokine
structure). Here, we investigate XCL1’s antimicrobial mechanism
of action with a focus on the role of metamorphic folding. We demonstrate
that XCL1 is a molecular “Swiss army knife” that can
refold into different structures for distinct context-dependent functions:
whereas the α–β chemokine structure controls cell
migration by binding to G-Protein Coupled Receptors (GPCRs), we find
using small angle X-ray scattering (SAXS) that only the β-sheet
and unfolded XCL1 structures can induce negative Gaussian curvature
(NGC) in membranes, the type of curvature topologically required for
membrane permeation. Moreover, the membrane remodeling activity of
XCL1’s β-sheet structure is strongly dependent on membrane
composition: XCL1 selectively remodels bacterial model membranes but
not mammalian model membranes. Interestingly, XCL1 also permeates
fungal model membranes and exhibits anti-Candida activity in vitro, in contrast to the usual mode of antifungal defense
which requires Th17 mediated cell-based responses. These observations
suggest that metamorphic XCL1 is capable of a versatile multimodal
form of antimicrobial defense.
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Affiliation(s)
- Acacia F. Dishman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
| | - Michelle W. Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ernest Y. Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jie He
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
| | - Anna R. Huppler
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
| | - Gerard C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 United States
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9
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Jaksch S, Gutberlet T, Müller-Buschbaum P. Grazing-incidence scattering—status and perspectives in soft matter and biophysics. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2019.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Kuppusamy R, Willcox M, Black DS, Kumar N. Short Cationic Peptidomimetic Antimicrobials. Antibiotics (Basel) 2019; 8:antibiotics8020044. [PMID: 31003540 PMCID: PMC6628222 DOI: 10.3390/antibiotics8020044] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/28/2022] Open
Abstract
The rapid growth of antimicrobial resistance against several frontline antibiotics has encouraged scientists worldwide to develop new alternatives with unique mechanisms of action. Antimicrobial peptides (AMPs) have attracted considerable interest due to their rapid killing and broad-spectrum activity. Peptidomimetics overcome some of the obstacles of AMPs such as high cost of synthesis, short half-life in vivo due to their susceptibility to proteolytic degradation, and issues with toxicity. This review will examine the development of short cationic peptidomimetics as antimicrobials.
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Affiliation(s)
- Rajesh Kuppusamy
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia.
| | - David StC Black
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Naresh Kumar
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
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11
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Lee MW, Lee EY, Wong GCL. What Can Pleiotropic Proteins in Innate Immunity Teach Us about Bioconjugation and Molecular Design? Bioconjug Chem 2018; 29:2127-2139. [PMID: 29771496 DOI: 10.1021/acs.bioconjchem.8b00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A common bioengineering strategy to add function to a given molecule is by conjugation of a new moiety onto that molecule. Adding multiple functions in this way becomes increasingly challenging and leads to composite molecules with larger molecular weights. In this review, we attempt to gain a new perspective by looking at this problem in reverse, by examining nature's strategies of multiplexing different functions into the same pleiotropic molecule using emerging analysis techniques such as machine learning. We concentrate on examples from the innate immune system, which employs a finite repertoire of molecules for a broad range of tasks. An improved understanding of how diverse functions are multiplexed into a single molecule can inspire new approaches for the deterministic design of multifunctional molecules.
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12
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Azar E, Constantin D, Warschawski DE. The effect of gramicidin inclusions on the local order of membrane components. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:44. [PMID: 29582214 PMCID: PMC7088371 DOI: 10.1140/epje/i2018-11644-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
We study the local effect of the antimicrobial peptide Gramicidin A on bilayers composed of lipids or surfactants using nuclear magnetic resonance spectroscopy and wide-angle X-ray scattering, techniques that probe the orientational and positional order of the alkyl chains, respectively. The two types of order vary with temperature and peptide concentration in complex ways which depend on the membrane composition, highlighting the subtlety of the interaction between inclusions and the host bilayer. The amplitude of the variation is relatively low, indicating that the macroscopic constants used to describe the elasticity of the bilayer are unlikely to change with the addition of peptide.
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Affiliation(s)
- Elise Azar
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Doru Constantin
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France.
| | - Dror E Warschawski
- UMR 7099, CNRS-Université Paris Diderot, Institut de Biologie Physico-Chimique, Paris, France
- Département de Chimie, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, H3C 3P8, Montreal, Canada
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13
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Lee EY, Lee MW, Fulan BM, Ferguson AL, Wong GCL. What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning? Interface Focus 2017; 7:20160153. [PMID: 29147555 DOI: 10.1098/rsfs.2016.0153] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Antimicrobial peptides (AMPs) are a diverse class of well-studied membrane-permeating peptides with important functions in innate host defense. In this short review, we provide a historical overview of AMPs, summarize previous applications of machine learning to AMPs, and discuss the results of our studies in the context of the latest AMP literature. Much work has been recently done in leveraging computational tools to design new AMP candidates with high therapeutic efficacies for drug-resistant infections. We show that machine learning on AMPs can be used to identify essential physico-chemical determinants of AMP functionality, and identify and design peptide sequences to generate membrane curvature. In a broader scope, we discuss the implications of our findings for the discovery of membrane-active peptides in general, and uncovering membrane activity in new and existing peptide taxonomies.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Michelle W Lee
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Benjamin M Fulan
- Department of Mathematics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew L Ferguson
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
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14
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Alvares DS, Viegas TG, Ruggiero Neto J. Lipid-packing perturbation of model membranes by pH-responsive antimicrobial peptides. Biophys Rev 2017; 9:669-682. [PMID: 28853007 PMCID: PMC5662038 DOI: 10.1007/s12551-017-0296-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022] Open
Abstract
The indiscriminate use of conventional antibiotics is leading to an increase in the number of resistant bacterial strains, motivating the search for new compounds to overcome this challenging problem. Antimicrobial peptides, acting only in the lipid phase of membranes without requiring specific membrane receptors as do conventional antibiotics, have shown great potential as possible substituents of these drugs. These peptides are in general rich in basic and hydrophobic residues forming an amphipathic structure when in contact with membranes. The outer leaflet of the prokaryotic cell membrane is rich in anionic lipids, while the surface of the eukaryotic cell is zwitterionic. Due to their positive net charge, many of these peptides are selective to the prokaryotic membrane. Notwithstanding this preference for anionic membranes, some of them can also act on neutral ones, hampering their therapeutic use. In addition to the electrostatic interaction driving peptide adsorption by the membrane, the ability of the peptide to perturb lipid packing is of paramount importance in their capacity to induce cell lysis, which is strongly dependent on electrostatic and hydrophobic interactions. In the present research, we revised the adsorption of antimicrobial peptides by model membranes as well as the perturbation that they induce in lipid packing. In particular, we focused on some peptides that have simultaneously acidic and basic residues. The net charges of these peptides are modulated by pH changes and the lipid composition of model membranes. We discuss the experimental approaches used to explore these aspects of lipid membranes using lipid vesicles and lipid monolayer as model membranes.
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Affiliation(s)
- Dayane S Alvares
- Department of Physics, UNESP - São Paulo State University, IBILCE, R. Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP 15054-000, Brazil
| | - Taisa Giordano Viegas
- Department of Physics, UNESP - São Paulo State University, IBILCE, R. Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP 15054-000, Brazil
| | - João Ruggiero Neto
- Department of Physics, UNESP - São Paulo State University, IBILCE, R. Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP 15054-000, Brazil.
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15
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Chung PY, Khanum R. Antimicrobial peptides as potential anti-biofilm agents against multidrug-resistant bacteria. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 50:405-410. [DOI: 10.1016/j.jmii.2016.12.005] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/20/2016] [Accepted: 12/03/2016] [Indexed: 10/19/2022]
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16
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Ponnappan N, Budagavi DP, Yadav BK, Chugh A. Membrane-active peptides from marine organisms--antimicrobials, cell-penetrating peptides and peptide toxins: applications and prospects. Probiotics Antimicrob Proteins 2016; 7:75-89. [PMID: 25559972 DOI: 10.1007/s12602-014-9182-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Marine organisms are known to be a rich and unique source of bioactive compounds as they are exposed to extreme conditions in the oceans. The present study is an attempt to briefly describe some of the important membrane-active peptides (MAPs) such as antimicrobial peptides (AMPs), cell-penetrating peptides (CPPs) and peptide toxins from marine organisms. Since both AMPs and CPPs play a role in membrane perturbation and exhibit interchangeable role, they can speculatively fall under the broad umbrella of MAPs. The study focuses on the structural and functional characteristics of different classes of marine MAPs. Further, AMPs are considered as a potential remedy to antibiotic resistance acquired by several pathogens. Peptides from marine organisms show novel post-translational modifications such as cysteine knots, halogenation and histidino-alanine bridge that enable these peptides to withstand harsh marine environmental conditions. These unusual modifications of AMPs from marine organisms are expected to increase their half-life in living systems, contributing to their increased bioavailability and stability when administered as drug in in vivo systems. Apart from AMPs, marine toxins with membrane-perturbing properties could be essentially investigated for their cytotoxic effect on various pathogens and their cell-penetrating activity across various mammalian cells. The current review will help in identifying the MAPs from marine organisms with crucial post-translational modifications that can be used as template for designing novel therapeutic agents and drug-delivery vehicles for treatment of human diseases.
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Affiliation(s)
- Nisha Ponnappan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
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17
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Rost U, Xu Y, Salditt T, Diederichsen U. Heavy-Atom Labeled Transmembrane β-Peptides: Synthesis, CD-Spectroscopy, and X-ray Diffraction Studies in Model Lipid Multilayer. Chemphyschem 2016; 17:2525-34. [DOI: 10.1002/cphc.201600289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Ulrike Rost
- Institute for Organic and Biomolecular Chemistry; Georg-August-University Göttingen; Tammannstr. 2 37077 Göttingen Germany
| | - Yihui Xu
- Institute for X-ray Physics; Georg-August-University Göttingen; Friedrich-Hund-Platz 1 37077 Göttingen Germany
| | - Tim Salditt
- Institute for X-ray Physics; Georg-August-University Göttingen; Friedrich-Hund-Platz 1 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry; Georg-August-University Göttingen; Tammannstr. 2 37077 Göttingen Germany
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18
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Milov AD, Tsvetkov YD, Raap J, De Zotti M, Formaggio F, Toniolo C. Review conformation, self-aggregation, and membrane interaction of peptaibols as studied by pulsed electron double resonance spectroscopy. Biopolymers 2016; 106:6-24. [DOI: 10.1002/bip.22713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/29/2015] [Accepted: 08/09/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Alexander D. Milov
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Yuri D. Tsvetkov
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University; 2300 RA Leiden The Netherlands
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova 35131 Italy
| | | | - Claudio Toniolo
- Department of Chemistry; University of Padova; Padova 35131 Italy
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19
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Strategies for Exploring Electrostatic and Nonelectrostatic Contributions to the Interaction of Helical Antimicrobial Peptides with Model Membranes. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2016. [DOI: 10.1016/bs.abl.2016.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Bobone S, De Zotti M, Bortolotti A, Biondi B, Ballano G, Palleschi A, Toniolo C, Formaggio F, Stella L. The fluorescence and infrared absorption probepara-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides. Biopolymers 2015; 104:521-32. [DOI: 10.1002/bip.22674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Sara Bobone
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Annalisa Bortolotti
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Gema Ballano
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
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21
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Yang FC, Peters RD, Dies H, Rheinstädter MC. Hierarchical, self-similar structure in native squid pen. SOFT MATTER 2014; 10:5541-5549. [PMID: 24957525 DOI: 10.1039/c4sm00301b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The structure of native squid pen (gladius) was investigated in two different species on different length scales. By combining microscopy, atomic force microscopy (AFM), and X-ray diffraction, the experiments probed length scales from millimetres down to nanometres. The gladii showed a hierarchical, self-similar structure in the optical experiments with fibres of different size oriented along the long axis of the gladius. The fibre-like structure was reproduced at the nanoscale in AFM measurements and fibres with diameters of 500 μm, 100 μm, 10 μm, 2 μm and 0.2 μm were observed. Their molecular structure was determined using X-ray diffraction. In the squid gladius, the chitin molecules are known to form nano-crystallites of monoclinic lattice symmetry wrapped in a protein layer, resulting in β-chitin nano-fibrils. Signals corresponding to the α-coil protein phase and β-chitin crystallites were observed in the X-ray experiments and their orientation with respect to the fibre-axis was determined. The size of a nano-fibril was estimated from the X-ray experiments to be about 150 × 300 Å. About 100 of these nano-fibrils are needed to form a 0.2 μm thick micro-fibre. We found that the molecular structure is highly anisotropic with ∼90% of the α-coils and β-chitin crystallites oriented along the fibre-axis, indicating a strong correlation between the macroscale structure and molecular orientation.
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Affiliation(s)
- Fei-Chi Yang
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada.
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22
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2014.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Watkins EB, Miller CE, Liao WP, Kuhl TL. Equilibrium or quenched: fundamental differences between lipid monolayers, supported bilayers, and membranes. ACS NANO 2014; 8:3181-91. [PMID: 24601564 DOI: 10.1021/nn4052953] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this work, we establish fundamental differences between the structure and packing of lipids in monolayers, supported bilayers, and multilayer films. High resolution grazing incidence X-ray diffraction reveals that monolayer structure is largely retained upon deposition onto substrates with the area per molecule controlled by deposition pressure. Such structural changes are consistent with a quenched rather than equilibrated supported membrane structure. Supported bilayers formed by vesicle fusion exhibit structural similarity to bilayers deposited at 38 mN/m, whereas packing in lipid multilayers more closely resembled bilayers deposited below 30 mN/m. At the molecular level, coupling between opposing lipid acyl chains is observed for all deposition pressures with the outer leaflet templating on the inner leaflet. Leaflet coupling induces a small condensation in the area per lipid molecule and a surprising increase in acyl chain tilt. Moreover, supported lipid bilayers exhibit preferential acyl chain alignment: the system cannot be modeled with freely rotating acyl chains as in free-standing lipid monolayers. Such acyl chain alignment is consistent with orientational texture of lipid tilt directors at larger length scales. These findings clearly demonstrate that supported, gel-phase bilayer membrane structure can be controlled and maintained by deposition onto solid supports and that increasing surface pressure induces preferential alignment of the acyl chains both within and between membrane leaflets.
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Affiliation(s)
- Erik B Watkins
- Biophysics Graduate Group, University of California , Davis, California 95616, United States
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Lu S, Walters G, Parg R, Dutcher JR. Nanomechanical response of bacterial cells to cationic antimicrobial peptides. SOFT MATTER 2014; 10:1806-1815. [PMID: 24652481 DOI: 10.1039/c3sm52801d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The effectiveness of antimicrobial compounds can be easily screened, however their mechanism of action is much more difficult to determine. Many compounds act by compromising the mechanical integrity of the bacterial cell envelope, and our study introduces an AFM-based creep deformation technique to evaluate changes in the time-dependent mechanical properties of Pseudomonas aeruginosa PAO1 bacterial cells upon exposure to two different but structurally related antimicrobial peptides. We observed a distinctive signature for the loss of integrity of the bacterial cell envelope following exposure to the peptides. Measurements performed before and after exposure, as well as time-resolved measurements and those performed at different concentrations, revealed large changes to the viscoelastic parameters that are consistent with differences in the membrane permeabilizing effects of the peptides. The AFM creep deformation measurement provides new, unique insight into the kinetics and mechanism of action of antimicrobial peptides on bacteria.
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Affiliation(s)
- Shun Lu
- Department of Physics, University of Guelph, Guelph, N1G 2W1, Ontario, Canada.
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25
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Bortolus M, De Zotti M, Formaggio F, Maniero AL. Alamethicin in bicelles: Orientation, aggregation, and bilayer modification as a function of peptide concentration. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2620-7. [DOI: 10.1016/j.bbamem.2013.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/24/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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26
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:98-105. [PMID: 24071593 DOI: 10.1016/j.bbamem.2013.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 12/15/2022]
Abstract
The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself.
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Affiliation(s)
- Asif Rahaman
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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27
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Schmidt NW, Wong GCL. Antimicrobial peptides and induced membrane curvature: geometry, coordination chemistry, and molecular engineering. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2013; 17:151-163. [PMID: 24778573 PMCID: PMC4000235 DOI: 10.1016/j.cossms.2013.09.004] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Short cationic, amphipathic antimicrobial peptides are multi-functional molecules that have roles in host defense as direct microbicides and modulators of the immune response. While a general mechanism of microbicidal activity involves the selective disruption and permeabilization of cell membranes, the relationships between peptide sequence and membrane activity are still under investigation. Here, we review the diverse functions that AMPs collectively have in host defense, and show that these functions can be multiplexed with a membrane mechanism of activity derived from the generation of negative Gaussian membrane curvature. As AMPs preferentially generate this curvature in model bacterial cell membranes, the selective generation of negative Gaussian curvature provides AMPs with a broad mechanism to target microbial membranes. The amino acid constraints placed on AMPs by the geometric requirement to induce negative Gaussian curvature are consistent with known AMP sequences. This 'saddle-splay curvature selection rule' is not strongly restrictive so AMPs have significant compositional freedom to multiplex membrane activity with other useful functions. The observation that certain proteins involved in cellular processes which require negative Gaussian curvature contain domains with similar motifs as AMPs, suggests this rule may be applicable to other curvature-generating proteins. Since our saddle-splay curvature design rule is based upon both a mechanism of activity and the existing motifs of natural AMPs, we believe it will assist the development of synthetic antimicrobials.
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Affiliation(s)
- Nathan W. Schmidt
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Gerard C. L. Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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28
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Ghosh SK, Salgin B, Pontoni D, Reusch T, Keil P, Vogel D, Rohwerder M, Reichert H, Salditt T. Structure and Volta potential of lipid multilayers: effect of X-ray irradiation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:815-824. [PMID: 23231362 DOI: 10.1021/la304139w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The effect of hard X-ray radiation on the structure and electrostatics of solid-supported lipid multilayer membranes is investigated using a scanning Kelvin probe (SKP) integrated with a high-energy synchrotron beamline to enable in situ measurements of the membranes' local Volta potential (V(p)) during X-ray structural characterization. The undulator radiation employed does not induce any detectable structural damage, but the V(p) of both bare and lipid-modified substrates is found to undergo strong radiation-induced shifts, almost immediately after X-ray exposure. Sample regions that are macroscopically distant (~cm) from the irradiated region experience an exponential V(p) growth with a characteristic time constant of several minutes. The V(p) variations occurring upon periodic on/off X-ray beam switching are fully or partially reversible depending on the location and time-scale of the SKP measurement. The general relevance of these findings for synchrotron-based characterization of biomolecular thin films is critically reviewed.
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Affiliation(s)
- S K Ghosh
- Institute for X-ray Physics, University of Göttingen, Göttingen, Germany.
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29
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Okorochenkov SA, Zheltukhina GA, Nebol'sin VE. [Antimicrobial peptides: mode of action and perspectives of practical application]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2012; 58:131-43. [PMID: 22724354 DOI: 10.18097/pbmc20125802131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review is devoted to antimicrobial peptides (AMP's) that demonstrate activity against bacteria, viruses and fungi. It considers structure and mechanism of AMP interaction with lipid membrane and intracellular targets of pathogens. Special attention is paid to modem state and perspectives of AMP practical application and also to approaches that increase efficacy and reduce toxicity of AMP by chemical modification of their structure.
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30
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Ye S, Li H, Wei F, Jasensky J, Boughton AP, Yang P, Chen Z. Observing a model ion channel gating action in model cell membranes in real time in situ: membrane potential change induced alamethicin orientation change. J Am Chem Soc 2012; 134:6237-43. [PMID: 22420296 PMCID: PMC3328217 DOI: 10.1021/ja2110784] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ion channels play crucial roles in transport and regulatory functions of living cells. Understanding the gating mechanisms of these channels is important to understanding and treating diseases that have been linked to ion channels. One potential model peptide for studying the mechanism of ion channel gating is alamethicin, which adopts a split α/3(10)-helix structure and responds to changes in electric potential. In this study, sum frequency generation vibrational spectroscopy (SFG-VS), supplemented by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), has been applied to characterize interactions between alamethicin (a model for larger channel proteins) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayers in the presence of an electric potential across the membrane. The membrane potential difference was controlled by changing the pH of the solution in contact with the bilayer and was measured using fluorescence spectroscopy. The orientation angle of alamethicin in POPC lipid bilayers was then determined at different pH values using polarized SFG amide I spectra. Assuming that all molecules adopt the same orientation (a δ distribution), at pH = 6.7 the α-helix at the N-terminus and the 3(10)-helix at the C-terminus tilt at about 72° (θ(1)) and 50° (θ(2)) versus the surface normal, respectively. When pH increases to 11.9, θ(1) and θ(2) decrease to 56.5° and 45°, respectively. The δ distribution assumption was verified using a combination of SFG and ATR-FTIR measurements, which showed a quite narrow distribution in the angle of θ(1) for both pH conditions. This indicates that all alamethicin molecules at the surface adopt a nearly identical orientation in POPC lipid bilayers. The localized pH change in proximity to the bilayer modulates the membrane potential and thus induces a decrease in both the tilt and the bend angles of the two helices in alamethicin. This is the first reported application of SFG to the study of model ion channel gating mechanisms in model cell membranes.
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Affiliation(s)
- Shuji Ye
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, P.R.China 230026
| | - Hongchun Li
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, P.R.China 230026
| | - Feng Wei
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, P.R.China 230026
| | - Joshua Jasensky
- Department of Biophysics, University of Michigan, AnnArbor, MI 48109, USA
| | - Andrew P. Boughton
- Department of Chemistry, University of Michigan, AnnArbor, MI 48109, USA
| | - Pei Yang
- Department of Chemistry, University of Michigan, AnnArbor, MI 48109, USA
| | - Zhan Chen
- Department of Biophysics, University of Michigan, AnnArbor, MI 48109, USA
- Department of Chemistry, University of Michigan, AnnArbor, MI 48109, USA
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31
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Affiliation(s)
- Francisco Zaera
- Department of Chemistry, University of California, Riverside, California 92521, United States
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32
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Ghosh SK, Aeffner S, Salditt T. Effect of PIP2 on Bilayer Structure and Phase Behavior of DOPC: An X-ray Scattering Study. Chemphyschem 2011; 12:2633-40. [DOI: 10.1002/cphc.201100154] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 06/16/2011] [Indexed: 01/16/2023]
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33
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Okorochenkov SA, Zheltukhina GA, Nebol’sin VE. Antimicrobial peptides: the mode of action and perspectives of practical application. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2011. [DOI: 10.1134/s1990750811020120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Schneggenburger PE, Beerlink A, Weinhausen B, Salditt T, Diederichsen U. Peptide model helices in lipid membranes: insertion, positioning, and lipid response on aggregation studied by X-ray scattering. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2011; 40:417-36. [PMID: 21181143 PMCID: PMC3070074 DOI: 10.1007/s00249-010-0645-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 11/08/2010] [Accepted: 11/12/2010] [Indexed: 11/18/2022]
Abstract
Studying membrane active peptides or protein fragments within the lipid bilayer environment is particularly challenging in the case of synthetically modified, labeled, artificial, or recently discovered native structures. For such samples the localization and orientation of the molecular species or probe within the lipid bilayer environment is the focus of research prior to an evaluation of their dynamic or mechanistic behavior. X-ray scattering is a powerful method to study peptide/lipid interactions in the fluid, fully hydrated state of a lipid bilayer. For one, the lipid response can be revealed by observing membrane thickening and thinning as well as packing in the membrane plane; at the same time, the distinct positions of peptide moieties within lipid membranes can be elucidated at resolutions of up to several angstroms by applying heavy-atom labeling techniques. In this study, we describe a generally applicable X-ray scattering approach that provides robust and quantitative information about peptide insertion and localization as well as peptide/lipid interaction within highly oriented, hydrated multilamellar membrane stacks. To this end, we have studied an artificial, designed β-helical peptide motif in its homodimeric and hairpin variants adopting different states of oligomerization. These peptide lipid complexes were analyzed by grazing incidence diffraction (GID) to monitor changes in the lateral lipid packing and ordering. In addition, we have applied anomalous reflectivity using synchrotron radiation as well as in-house X-ray reflectivity in combination with iodine-labeling in order to determine the electron density distribution ρ(z) along the membrane normal (z axis), and thereby reveal the hydrophobic mismatch situation as well as the position of certain amino acid side chains within the lipid bilayer. In the case of multiple labeling, the latter technique is not only applicable to demonstrate the peptide's reconstitution but also to generate evidence about the relative peptide orientation with respect to the lipid bilayer.
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Affiliation(s)
- Philipp E. Schneggenburger
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - André Beerlink
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Britta Weinhausen
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
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Abstract
AbstractIncreased prevalence of multi-drug resistance in pathogens has encouraged researchers to focus on finding novel forms of anti-infective agents. Antimicrobial peptides (AMPs) found in animal secretions are components of host innate immune response and have survived eons of pathogen evolution. Thus, they are likely to be active against pathogens and even those that are resistant to conventional drugs. Many peptides have been isolated and shown to be effective against multi-drug resistant pathogens. More than 500 AMPs have been identified from amphibians. The abundance of AMPs in frog skin is remarkable and constitutes a rich source for design of novel pharmaceutical molecules. Expression and post-translational modifications, discovery, activities and probable therapeutic application prospects of amphibian AMPs will be discussed in this article.
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Affiliation(s)
- Yao Xiao
- 1Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Cunbao Liu
- 1Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Ren Lai
- 1Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
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36
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Gebhardt R, Pechkova E, Riekel C, Nicolini C. In situ muGISAXS: II. Thaumatin crystal growth kinetic. Biophys J 2010; 99:1262-7. [PMID: 20713011 DOI: 10.1016/j.bpj.2010.03.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 03/15/2010] [Accepted: 03/22/2010] [Indexed: 10/19/2022] Open
Abstract
The formation of thaumatin crystals by Langmuir-Blodgett (LB) film nanotemplates was studied by the hanging-drop technique in a flow-through cell by synchrotron radiation micrograzing-incidence small-angle x-ray scattering. The kinetics of crystallization was measured directly on the interface of the LB film crystallization nanotemplate. The evolution of the micrograzing-incidence small-angle x-ray scattering patterns suggests that the increase in intensity in the Yoneda region is due to protein incorporation into the LB film. The intensity variation suggests several steps, which were modeled by system dynamics based on first-order differential equations. The kinetic data can be described by two processes that take place on the LB film, a first, fast, process, attributed to the crystal growth and its detachment from the LB film, and a second, slower process, attributed to an unordered association and conversion of protein on the LB film.
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Affiliation(s)
- Ronald Gebhardt
- European Synchrotron Radiation Facility, B.P. 220, F-38043 Grenoble Cedex, France
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Ye S, Nguyen KT, Chen Z. Interactions of alamethicin with model cell membranes investigated using sum frequency generation vibrational spectroscopy in real time in situ. J Phys Chem B 2010; 114:3334-40. [PMID: 20163089 PMCID: PMC2844632 DOI: 10.1021/jp911174d] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Structures of membrane-associated peptides and molecular interactions between peptides and cell membrane bilayers govern biological functions of these peptides. Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study such structures and interactions at the molecular level. In this research, SFG has been applied, supplemented by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), to characterize the interactions between alamethicin (a model for larger channel proteins) and different lipid bilayers in the absence of membrane potential. The orientation of alamethicin in lipid bilayers has been determined using SFG amide I spectra detected with different polarization combinations. It was found that alamethicin adopts a mixed alpha-helical and 3(10)-helical structure in fluid-phase lipid bilayers. The helix (mainly alpha-helix) at the N-terminus tilts at about 63 degrees versus the surface normal in a fluid-phase 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine-1,1,2,2-d4-N,N,N-trimethyl-d9 (d-DMPC)/1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer. The 3(10)-helix at the C-terminus (beyond the Pro14 residue) tilts at about 43 degrees versus the surface normal. This is the first time to apply SFG to study a 3(10)-helix experimentally. When interacting with a gel-phase lipid bilayer, alamethicin lies down on the gel-phase bilayer surface or aggregates or both, which does not have significant insertion into the lipid bilayer.
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Affiliation(s)
- Shuji Ye
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, P.R. China 230026
| | - Khoi Tan Nguyen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Bertelsen K, Paaske B, Thøgersen L, Tajkhorshid E, Schiøtt B, Skrydstrup T, Nielsen NC, Vosegaard T. Residue-specific information about the dynamics of antimicrobial peptides from (1)H-(15)N and (2)H solid-state NMR spectroscopy. J Am Chem Soc 2010; 131:18335-42. [PMID: 19929000 DOI: 10.1021/ja908604u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a new method to obtain information about the conformational dynamics of membrane-proteins using solid-state NMR experiments of oriented samples. By measuring the orientation-dependent (1)H-(15)N dipole-dipole coupling, (15)N anisotropic chemical shift, and (2)H quadrupole coupling parameters for a single residue, it is possible to obtain information about the local dynamics of each residue in the protein. This may be interpreted on an individual basis or through models extended to study conformational motion of membrane-protein segments. The method is demonstrated for the antimicrobial peptaibol alamethicin for which combined analysis of anisotropic interactions for the Aib(8) residue provides detailed information about helix-tilt angle, wobbling, and oscillatory rotation around the helix axis in the membrane bound state. This information is in very good agreement with coarse-grained MD simulations of the peptide in lipid bilayers.
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Affiliation(s)
- Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Bioinformatics Research Center, University of Aarhus, DK-8000 Aarhus C, Denmark
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Structure and alignment of the membrane-associated peptaibols ampullosporin A and alamethicin by oriented 15N and 31P solid-state NMR spectroscopy. Biophys J 2010; 96:86-100. [PMID: 18835909 DOI: 10.1529/biophysj.108.136242] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 09/03/2008] [Indexed: 11/18/2022] Open
Abstract
Ampullosporin A and alamethicin are two members of the peptaibol family of antimicrobial peptides. These compounds are produced by fungi and are characterized by a high content of hydrophobic amino acids, and in particular the alpha-tetrasubstituted amino acid residue ?-aminoisobutyric acid. Here ampullosporin A and alamethicin were uniformly labeled with (15)N, purified and reconstituted into oriented phophatidylcholine lipid bilayers and investigated by proton-decoupled (15)N and (31)P solid-state NMR spectroscopy. Whereas alamethicin (20 amino acid residues) adopts transmembrane alignments in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes the much shorter ampullosporin A (15 residues) exhibits comparable configurations only in thin membranes. In contrast the latter compound is oriented parallel to the membrane surface in 1,2-dimyristoleoyl-sn-glycero-3-phosphocholine and POPC bilayers indicating that hydrophobic mismatch has a decisive effect on the membrane topology of these peptides. Two-dimensional (15)N chemical shift -(1)H-(15)N dipolar coupling solid-state NMR correlation spectroscopy suggests that in their transmembrane configuration both peptides adopt mixed alpha-/3(10)-helical structures which can be explained by the restraints imposed by the membranes and the bulky alpha-aminoisobutyric acid residues. The (15)N solid-state NMR spectra also provide detailed information on the helical tilt angles. The results are discussed with regard to the antimicrobial activities of the peptides.
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Diamond G, Beckloff N, Weinberg A, Kisich KO. The roles of antimicrobial peptides in innate host defense. Curr Pharm Des 2009; 15:2377-92. [PMID: 19601838 DOI: 10.2174/138161209788682325] [Citation(s) in RCA: 415] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Antimicrobial peptides (AMPs) are multi-functional peptides whose fundamental biological role in vivo has been proposed to be the elimination of pathogenic microorganisms, including Gram-positive and -negative bacteria, fungi, and viruses. Genes encoding these peptides are expressed in a variety of cells in the host, including circulating phagocytic cells and mucosal epithelial cells, demonstrating a wide range of utility in the innate immune system. Expression of these genes is tightly regulated; they are induced by pathogens and cytokines as part of the host defense response, and they can be suppressed by bacterial virulence factors and environmental factors which can lead to increased susceptibility to infection. New research has also cast light on alternative functionalities, including immunomodulatory activities, which are related to their unique structural characteristics. These peptides represent not only an important component of innate host defense against microbial colonization and a link between innate and adaptive immunity, but also form a foundation for the development of new therapeutic agents.
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Affiliation(s)
- Gill Diamond
- Department of Oral Biology, UMDNJ-New Jersey Dental School, Newark, NJ 07101, USA.
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41
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Ye S, Nguyen KT, Le Clair SV, Chen Z. In situ molecular level studies on membrane related peptides and proteins in real time using sum frequency generation vibrational spectroscopy. J Struct Biol 2009; 168:61-77. [PMID: 19306928 PMCID: PMC2753614 DOI: 10.1016/j.jsb.2009.03.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 03/11/2009] [Accepted: 03/13/2009] [Indexed: 12/11/2022]
Abstract
Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study the molecular structures of surfaces and interfaces in different chemical environments. This review summarizes recent SFG studies on hybrid bilayer membranes and substrate-supported lipid monolayers and bilayers, the interaction between peptides/proteins and lipid monolayers/bilayers, and bilayer perturbation induced by peptides/proteins. To demonstrate the ability of SFG to determine the orientations of various secondary structures, studies on the interactions between different peptides/proteins (melittin, G proteins, alamethicin, and tachyplesin I) and lipid bilayers are discussed. Molecular level details revealed by SFG in these studies show that SFG can provide a unique understanding on the interactions between a lipid monolayer/bilayer and peptides/proteins in real time, in situ and without any exogenous labeling.
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Affiliation(s)
- Shuji Ye
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Khoi Tan Nguyen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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Miller CE, Majewski J, Gog T, Kuhl TL. Grazing incidence diffraction of cadmium arachidate multilayers at the solid-liquid interface. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.2005.220.12.987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Using complementary X-ray reflectivity (XR) and grazing incidence X-ray diffraction (GIXD), we report structural studies of supported thin-organic layers in contact with water and air. Using a monochromatic synchrotron beam to penetrate 10 mm of liquid, we have characterized buried films composed of 12.5 repeating bilayers of arachidic acid (C20H40O2) complexed with cadmium ions (cadmium arachidate, CdAr2). We found that the layered structure of the CdAr2 multilayers do not exhibit rearrangement after exposure to water with negligible water penetration into the inner layers when compared to their dry state. These findings are consistent with the formation of extremely robust CdAr2 multilayers that can withstand multiple rinses in strong organic solvents, acid, and mechanical wear. The second goal was to demonstrate the feasibility of similar experiments to study much thinner single bilayer bio-membranes. These studies are the first successful GIXD experiments of ultra thin-organic film composed of a few layers at the solid-liquid interface.
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Affiliation(s)
- Chad E. Miller
- University of California, Biophysics Graduate Group, Davis, California, U.S.A
| | - Jaroslaw Majewski
- Los Alamos National Laboratory, Manuel Lujan Neutron Scattering Center, Los Alamos, New Mexiko, U.S.A
| | - Thomas Gog
- Argonne National Laboratory, Advanced Photon Source, Argonne, U.S.A
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Schneggenburger PE, Beerlink A, Worbs B, Salditt T, Diederichsen U. A Novel Heavy-Atom Label for Side-Specific Peptide Iodination: Synthesis, Membrane Incorporation and X-ray Reflectivity. Chemphyschem 2009; 10:1567-76. [DOI: 10.1002/cphc.200900241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Milov AD, Samoilova RI, Tsvetkov YD, De Zotti M, Formaggio F, Toniolo C, Handgraaf JW, Raap J. Structure of self-aggregated alamethicin in ePC membranes detected by pulsed electron-electron double resonance and electron spin echo envelope modulation spectroscopies. Biophys J 2009; 96:3197-209. [PMID: 19383464 DOI: 10.1016/j.bpj.2009.01.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 01/14/2009] [Accepted: 01/15/2009] [Indexed: 11/17/2022] Open
Abstract
PELDOR spectroscopy was exploited to study the self-assembled super-structure of the [Glu(OMe)(7,18,19)]alamethicin molecules in vesicular membranes at peptide to lipid molar ratios in the range of 1:70-1:200. The peptide molecules were site-specifically labeled with TOAC electron spins. From the magnetic dipole-dipole interaction between the nitroxides of the monolabeled constituents and the PELDOR decay patterns measured at 77 K, intermolecular-distance distribution functions were obtained and the number of aggregated molecules (n approximately 4) was estimated. The distance distribution functions exhibit a similar maximum at 2.3 nm. In contrast to Alm16, for Alm1 and Alm8 additional maxima were recorded at 3.2 and approximately 5.2 nm. From ESEEM experiments and based on the membrane polarity profiles, the penetration depths of the different spin-labeled positions into the membrane were qualitatively estimated. It was found that the water accessibility of the spin-labels follows the order TOAC-1 > TOAC-8 approximately TOAC-16. The geometric data obtained are discussed in terms of a penknife molecular model. At least two peptide chains are aligned parallel and eight ester groups of the polar Glu(OMe)(18,19) residues are suggested to stabilize the self-aggregate superstructure.
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Affiliation(s)
- Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Novosibirsk, 630090 Russian Federation
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45
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Watkins EB, Miller CE, Mulder DJ, Kuhl TL, Majewski J. Structure and orientational texture of self-organizing lipid bilayers. PHYSICAL REVIEW LETTERS 2009; 102:238101. [PMID: 19658974 DOI: 10.1103/physrevlett.102.238101] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Indexed: 05/28/2023]
Abstract
The structure of single supported dipalmitoyl-phosphatidylcholine bilayers prepared by vesicle fusion or Langmuir-Blodgett-Schaeffer (LBS) deposition techniques was characterized by x-ray reflectivity and grazing incidence diffraction in bulk water. LBS bilayers display symmetric leaflets similar to monolayer structures, while vesicle fusion yields more inhomogeneous bilayers. Diffraction establishes that lipids are always coupled across the bilayer even when leaflets are deposited independently and suggests the existence of orientational texture.
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Affiliation(s)
- E B Watkins
- Biophysics Graduate Group, University of California, Davis, CA 95616, USA
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46
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Alamethicin in lipid bilayers: combined use of X-ray scattering and MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1387-97. [PMID: 19248763 DOI: 10.1016/j.bbamem.2009.02.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 01/29/2009] [Accepted: 02/19/2009] [Indexed: 10/21/2022]
Abstract
We study fully hydrated bilayers of two di-monounsaturated phospholipids diC18:1PC (DOPC) and diC22:1PC with varying amounts of alamethicin (Alm). We combine the use of X-ray diffuse scattering and molecular dynamics simulations to determine the orientation of alamethicin in model lipids. Comparison of the experimental and simulated form factors shows that Alm helices are inserted transmembrane at high humidity and high concentrations, in agreement with earlier results. The X-ray scattering data and the MD simulations agree that membrane thickness changes very little up to 1/10 Alm/DOPC. In contrast, the X-ray data indicate that the thicker diC22:1PC membrane thins with added Alm, a total decrease in thickness of 4 A at 1/10 Alm/diC22:1PC. The different effect of Alm on the thickness changes of the two bilayers is consistent with Alm having a hydrophobic thickness close to the hydrophobic thickness of 27 A for DOPC; Alm is then mismatched with the 7 A thicker diC22:1PC bilayer. The X-ray data indicate that Alm decreases the bending modulus (K(C)) by a factor of approximately 2 in DOPC and a factor of approximately 10 in diC22:1PC membranes (P/L approximately 1/10). The van der Waals and fluctuational interactions between bilayers are also evaluated through determination of the anisotropic B compressibility modulus.
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47
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Salnikov ES, Zotti MD, Formaggio F, Li X, Toniolo C, OʼNeil JDJ, Raap J, Dzuba SA, Bechinger B. Alamethicin Topology in Phospholipid Membranes by Oriented Solid-state NMR and EPR Spectroscopies: a Comparison. J Phys Chem B 2009; 113:3034-42. [DOI: 10.1021/jp8101805] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evgeniy S. Salnikov
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Marta De Zotti
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Fernando Formaggio
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Xing Li
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Claudio Toniolo
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Joe D. J. OʼNeil
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jan Raap
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Burkhard Bechinger
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation, University of Strasbourg/CNRS, UMR7177, Institut de Chimie, 67070 Strasbourg, France, Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy, Department of Chemistry, University of Manitoba, Winnipeg, Canada R3T 2N2, and Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
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Integration of ganglioside GT1b receptor into DPPE and DPPC phospholipid monolayers: an X-ray reflectivity and grazing-incidence diffraction study. Biophys J 2008; 95:3278-86. [PMID: 18599631 DOI: 10.1529/biophysj.107.128538] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using synchrotron grazing-incidence x-ray diffraction (GIXD) and reflectivity, the in-plane and out-of-plane structures of mixed-ganglioside GT(1b)-phospholipid monolayers were investigated at the air-liquid interface and compared with monolayers of the pure components. The receptor GT(1b) is involved in the binding of lectins and toxins, including botulinum neurotoxin, to cell membranes. Monolayers composed of 20 mol % ganglioside GT(1b), the phospholipid dipalmitoyl phosphatidylethanolamine (DPPE), and the phospholipid dipalmitoyl phosphatidylcholine (DPPC) were studied in the gel phase at 23 degrees C and at surface pressures of 20 and 40 mN/m, and at pH 7.4 and 5. Under these conditions, the two components did not phase-separate, and no evidence of domain formation was observed. The x-ray scattering measurements revealed that GT(1b) was intercalated within the host DPPE/DPPC monolayers, and slightly expanded DPPE but condensed the DPPC matrix. The oligosaccharide headgroups extended normally from the monolayer surfaces into the subphase. This study demonstrated that these monolayers can serve as platforms for investigating toxin membrane binding and penetration.
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49
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Miller CE, Majewski J, Watkins EB, Mulder DJ, Gog T, Kuhl TL. Probing the local order of single phospholipid membranes using grazing incidence x-ray diffraction. PHYSICAL REVIEW LETTERS 2008; 100:058103. [PMID: 18352436 DOI: 10.1103/physrevlett.100.058103] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Indexed: 05/26/2023]
Abstract
We report the first grazing incidence x-ray diffraction measurements of a single phospholipid bilayer at the solid-liquid interface. Our grazing incidence x-ray diffraction and reflectivity measurements reveal that the lateral ordering in a supported DPPE (1, 2-Dipalmitoyl-sn-Glycero-3-Phosphoethanolamine) bilayer is significantly less than that of an equivalent monolayer at the air-liquid interface. Our findings also indicate that the leaflets of the bilayer are uncoupled in contrast to the scattering from free standing phosphatidylcholine bilayers. The methodology presented can be readily implemented to study more complicated biomembranes and their interaction with proteins.
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Affiliation(s)
- C E Miller
- Manuel Lujan Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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50
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Küsel A, Khattari Z, Schneggenburger PE, Banerjee A, Salditt T, Diederichsen U. Conformation and Interaction of ad,l-Alternating Peptide with a Bilayer Membrane: X-ray Reflectivity, CD, and FTIR Spectroscopy. Chemphyschem 2007; 8:2336-43. [DOI: 10.1002/cphc.200700477] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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