1
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Alpízar-Pedraza D, Roque-Diaz Y, Garay-Pérez H, Rosenau F, Ständker L, Montero-Alejo V. Insights into the Adsorption Mechanisms of the Antimicrobial Peptide CIDEM-501 on Membrane Models. Antibiotics (Basel) 2024; 13:167. [PMID: 38391553 PMCID: PMC10886324 DOI: 10.3390/antibiotics13020167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
CIDEM-501 is a hybrid antimicrobial peptide rationally designed based on the structure of panusin and panulirin template peptides. The new peptide exhibits significant antibacterial activity against multidrug-resistant pathogens (MIC = 2-4 μM) while conserving no toxicity in human cell lines. We conducted molecular dynamics (MD) simulations using the CHARMM-36 force field to explore the CIDEM-501 adsorption mechanism with different membrane compositions. Several parameters that characterize these interactions were analyzed to elucidate individual residues' structural and thermodynamic contributions. The membrane models were constructed using CHARMM-GUI, mimicking the bacterial and eukaryotic phospholipid compositions. Molecular dynamics simulations were conducted over 500 ns, showing rapid and highly stable peptide adsorption to bacterial lipids components rather than the zwitterionic eucaryotic model membrane. A predominant peptide orientation was observed in all models dominated by an electric dipole. The peptide remained parallel to the membrane surface with the center loop oriented to the lipids. Our findings shed light on the antibacterial activity of CIDEM-501 on bacterial membranes and yield insights valuable for designing potent antimicrobial peptides targeting multi- and extreme drug-resistant bacteria.
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Affiliation(s)
- Daniel Alpízar-Pedraza
- Biochemistry and Molecular Biology Department, Center for Pharmaceutical Research and Development, Ave. 26 # 1605, Nuevo Vedado, Ciudad de La Habana 10400, Cuba
| | - Yessica Roque-Diaz
- Biochemistry and Molecular Biology Department, Center for Pharmaceutical Research and Development, Ave. 26 # 1605, Nuevo Vedado, Ciudad de La Habana 10400, Cuba
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Hilda Garay-Pérez
- Peptide Synthesis Group, Center for Genetic Engineering and Biotechnology, Ave. 31 e/158 y 190, Playa, Habana 11600, Cuba
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Ludger Ständker
- Core Facility for Functional Peptidomics, Ulm Peptide Pharmaceuticals (U-PEP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany
| | - Vivian Montero-Alejo
- Biochemistry and Molecular Biology Department, Center for Pharmaceutical Research and Development, Ave. 26 # 1605, Nuevo Vedado, Ciudad de La Habana 10400, Cuba
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2
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Maurer M, Lazaridis T. Transmembrane β-Barrel Models of α-Synuclein Oligomers. J Chem Inf Model 2023; 63:7171-7179. [PMID: 37963823 DOI: 10.1021/acs.jcim.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The aggregation of α-synuclein is implicated in a number of neurodegenerative diseases, such as Parkinson's and Multiple System Atrophy, but the role of these aggregates in disease development is not clear. One possible mechanism of cytotoxicity is the disturbance or permeabilization of cell membranes by certain types of oligomers. However, no high-resolution structure of such membrane-embedded complexes has ever been determined. Here we construct and evaluate putative transmembrane β-barrels formed by this protein. Examination of the α-synuclein sequence reveals two regions that could form membrane-embedded β-hairpins: 64-92 (the NAC), and 35-56, which harbors many familial Parkinson's mutations. The stability of β-barrels formed by these hairpins is examined first in implicit membrane pores and then by multimicrosecond all-atom simulations. We find that a NAC region barrel remains stably inserted and hydrated for at least 10 μs. A 35-56 barrel remains stably inserted in the membrane but dehydrates and collapses if all His50 are neutral or if His50 is replaced by Q. If half of the His50 are doubly protonated, the barrel takes an oval shape but remains hydrated for at least 10 μs. Possible implications of these findings for α-synuclein pathology are discussed.
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Affiliation(s)
- Manuela Maurer
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
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3
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Dutta A, Sepehri A, Lazaridis T. Putative Pore Structures of Amyloid β 25-35 in Lipid Bilayers. Biochemistry 2023; 62:2549-2558. [PMID: 37582191 DOI: 10.1021/acs.biochem.3c00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
The amyloid β peptide aggregates to form extracellular plaques in the brains of Alzheimer's disease patients. Certain of its fragments have been found to have similar properties to those of the full-length peptide. The best-studied of these is 25-35, which aggregates into fibrils, is toxic to neurons, and forms ion channels in synthetic lipid bilayers. Here, we investigate possible pore-forming structures of oligomers of this peptide in a POPC/POPG membrane. We consider octameric and decameric β-barrels of different topology, strand orientation, and shear, evaluate their stability in an implicit membrane model, and subject the best models to multimicrosecond all-atom molecular dynamics simulations. We find two decameric structures that are kinetically stable in membranes on this time scale: an imperfectly closed antiparallel β-barrel with K28 in the pore lumen and a short parallel β-barrel with K28 toward the membrane interface. Both structures exhibit dehydrated gaps in the pore lumen, which are larger for the antiparallel barrel. Based on these results, the experimental cation selectivity, the dependence of ion channel activity on voltage direction, and certain mutation data, the parallel model seems more compatible with experimental data.
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Affiliation(s)
- Ankita Dutta
- Department of Chemistry, City College of New York/CUNY, 160 Convent Avenue, New York, New York 10031, United States
- Graduate Program in Biochemistry, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Aliasghar Sepehri
- Department of Chemistry, City College of New York/CUNY, 160 Convent Avenue, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, 160 Convent Avenue, New York, New York 10031, United States
- Graduate Programs in Chemistry, Biochemistry, and Physics The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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4
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Almeida PF. In Search of a Molecular View of Peptide-Lipid Interactions in Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37478368 DOI: 10.1021/acs.langmuir.3c00538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Lipid bilayer membranes are often represented as a continuous nonpolar slab with a certain thickness bounded by two more polar interfaces. Phenomena such as peptide binding to the membrane surface, folding, insertion, translocation, and diffusion are typically interpreted on the basis of this view. In this Perspective, I argue that this membrane representation as a hydrophobic continuum solvent is not adequate to understand peptide-lipid interactions. Lipids are not small compared to membrane-active peptides: their sizes are similar. Therefore, peptide diffusion needs to be understood in terms of free volume, not classical continuum mechanics; peptide solubility or partitioning in membranes cannot be interpreted in terms of hydrophobic mismatch between membrane thickness and peptide length; peptide folding and translocation, often involving cationic peptides, can only be understood if realizing that lipids adapt to the presence of peptides and the membrane may undergo considerable lipid redistribution in the process. In all of those instances, the detailed molecular interactions between the peptide residues and the lipid components are essential to understand the mechanisms involved.
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Affiliation(s)
- Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
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5
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Abstract
Perturbation of cell membranes by amyloid β (Ab) peptide oligomers is one possible mechanism of cytotoxicity in Alzheimer's disease, but the structure of such Ab-membrane complexes is unknown. Here we examine the stability of several putative structures by implicit membrane and all-atom molecular dynamics simulations. The structures include (a) a variety of models proposed by other researchers in the past, (b) a heptameric β barrel determined by grafting the Ab sequence onto α-hemolysin, (c) a similar structure with modified strand orientation and turn location based on an experimental β-hairpin structure, (d) oligomers inserting C-terminal β hairpins into one leaflet of the bilayer, (e) oligomers forming parallel C-terminal β barrels, and (f) a helical hexamer made of C-terminal fragments. The α-hemolysin-grafted structure and its alternately oriented variant are stable in the membrane and form an aqueous pore. In contrast, the C-terminal parallel barrels are not stable, presumably due to excessive hydrophobicity of their inner surface. The helical hexamer also failed to stabilize an aqueous pore for the same reason. The C-terminal hairpin-inserting structures remain stably inserted but, again, do not form an aqueous pore. Our results suggest that only β-barrels inserting a combination of C-terminal and other residues can form stable aqueous pores.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York10016, United States
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6
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Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci 2022; 13:2766-2777. [PMID: 36095304 DOI: 10.1021/acschemneuro.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amphipathic peptides can cause biological membranes to leak either by dissolving their lipid content via a detergent-like mechanism or by forming pores on the membrane surface. These modes of membrane damage have been related to the toxicity of amyloid peptides and to the activity of antimicrobial peptides. Here, we perform the first all-atom simulations in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tail of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. These strong interactions enable lipids to be dragged out of the bilayer by oligomeric structures accounting for detergent-like damage. They also disturb the orientation of lipid tails in the vicinity of peptides. These distortions are minimized around pore structures. We also show that membrane-bound β-sheets become twisted with one of their extremities partially penetrating the lipid bilayer. This allows peptides on opposite leaflets to interact and form a long transmembrane β-sheet, which initiates poration. In simulations, where peptides are deposited on a single leaflet, the twist in β-sheets allows them to penetrate the membrane and form pores. In addition, our simulations show that fibril-like structures produce little damage to lipid membranes, as non-polar side chains in these structures are unavailable to interact with the acyl tail of lipids.
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Hannah Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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7
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Sepehri A, Nepal B, Lazaridis T. Distinct Modes of Action of IAPP Oligomers on Membranes. J Chem Inf Model 2021; 61:4645-4655. [PMID: 34499498 DOI: 10.1021/acs.jcim.1c00767] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Islet amyloid polypeptide (IAPP, also known as amylin) is a peptide hormone that is co-secreted with insulin by pancreatic β-cells and forms amyloid aggregates in type II diabetes. Various lines of evidence indicate that oligomers of this peptide may induce toxicity by disrupting or forming pores in cell membranes, but the structure of these pores is unknown. Here, we create models of pores for both helical and β-structured peptides using implicit membrane modeling and test their stability using multimicrosecond all-atom simulations. We find that the helical peptides behave similarly to antimicrobial peptides; they remain stably inserted in a highly tilted or partially unfolded configuration creating a narrow water channel. Parallel helix orientation creates a somewhat larger pore. An octameric β barrel of parallel β-hairpins is highly stable in the membrane, whereas the corresponding barrel made of antiparallel hairpins is not. We propose that certain experiments probe the helical pore state while others probe the β-structured pore state; this provides a possible explanation for lack of correlation that is sometimes observed between in vivo toxicity and in vitro liposome permeabilization experiments.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Binod Nepal
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York 10031, United States.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York, New York 10016, United States
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8
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Aronica PGA, Reid LM, Desai N, Li J, Fox SJ, Yadahalli S, Essex JW, Verma CS. Computational Methods and Tools in Antimicrobial Peptide Research. J Chem Inf Model 2021; 61:3172-3196. [PMID: 34165973 DOI: 10.1021/acs.jcim.1c00175] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The evolution of antibiotic-resistant bacteria is an ongoing and troubling development that has increased the number of diseases and infections that risk going untreated. There is an urgent need to develop alternative strategies and treatments to address this issue. One class of molecules that is attracting significant interest is that of antimicrobial peptides (AMPs). Their design and development has been aided considerably by the applications of molecular models, and we review these here. These methods include the use of tools to explore the relationships between their structures, dynamics, and functions and the increasing application of machine learning and molecular dynamics simulations. This review compiles resources such as AMP databases, AMP-related web servers, and commonly used techniques, together aimed at aiding researchers in the area toward complementing experimental studies with computational approaches.
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Affiliation(s)
- Pietro G A Aronica
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Lauren M Reid
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Chemistry, University of Southampton, Highfield Southampton, Hampshire, U.K. SO17 1BJ.,MedChemica Ltd, Alderley Park, Macclesfield, Cheshire, U.K. SK10 4TG
| | - Nirali Desai
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Division of Biological and Life Sciences, Ahmedabad University, Central Campus, Ahmedabad, Gujarat, India 380009
| | - Jianguo Li
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Singapore Eye Research Institute, 20 College Road Discovery Tower, Singapore 169856
| | - Stephen J Fox
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Shilpa Yadahalli
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield Southampton, Hampshire, U.K. SO17 1BJ
| | - Chandra S Verma
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore.,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, 637551 Singapore
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9
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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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10
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Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes. Methods Mol Biol 2021. [PMID: 32856257 DOI: 10.1007/978-1-0716-0928-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In studying biological processes and focusing on the molecular mechanisms at the basis of these, molecular dynamics (MD) simulations have demonstrated to be a very useful tool for the past 50 years. This suite of computational methods calculates the time-dependent evolution of a molecular system using physics-based first principles. In this chapter, we give a brief introduction to the theory and practical use of molecular dynamics simulations, highlighting the different models and algorithms that have been developed to tackle specific problems, with a special focus on classical force fields. Some examples of how simulations have been used in the past will help the reader in discerning their power, limitations, and significance.
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11
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Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition. J Membr Biol 2021; 254:75-96. [PMID: 33564914 DOI: 10.1007/s00232-021-00174-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 12/16/2022]
Abstract
The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore-forming peptide into a selective pore-former for different lipid types. A library of 2916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.
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12
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Outer membrane protein evolution. Curr Opin Struct Biol 2021; 68:122-128. [PMID: 33493965 DOI: 10.1016/j.sbi.2021.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 01/02/2021] [Indexed: 01/31/2023]
Abstract
Outer membrane proteins have remarkably homogeneous structure. They are all up down β-barrels. Up down barrels themselves are composed of repeated sets of β-hairpins. The consistency of the usage of the β-hairpin throughout the outer membrane milieu allows for interrogation of the evolution of these repetitive structures. Here we describe recent investigations of outer membrane protein evolution and how evolutionary precepts have been used for novel outer membrane protein design.
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13
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Chakraborty A, Kobzev E, Chan J, de Zoysa GH, Sarojini V, Piggot TJ, Allison JR. Molecular Dynamics Simulation of the Interaction of Two Linear Battacin Analogs with Model Gram-Positive and Gram-Negative Bacterial Cell Membranes. ACS OMEGA 2021; 6:388-400. [PMID: 33458490 PMCID: PMC7807746 DOI: 10.1021/acsomega.0c04752] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Antimicrobial peptides (AMPs) are a potential solution to the increasing threat of antibiotic resistance, but successful design of active but nontoxic AMPs requires understanding their mechanism of action. Molecular dynamics (MD) simulations can provide atomic-level information regarding how AMPs interact with the cell membrane. Here, we have used MD simulations to study two linear analogs of battacin, a naturally occurring cyclic, lipidated, nonribosomal AMP. Like battacin, these analogs are active against Gram-negative multidrug resistant and Gram-positive bacteria, but they are less toxic than battacin. Our simulations show that this activity depends upon a combination of positively charged and hydrophobic moieties. Favorable interactions with negatively charged membrane lipid head groups drive association with the membrane and insertion of hydrophobic residues, and the N-terminal lipid anchors the peptides to the membrane surface. Both effects are required for stable membrane binding.
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Affiliation(s)
- Aparajita Chakraborty
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
| | - Elisey Kobzev
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
- School
of Computational and Natural Sciences, Massey
University Auckland, Auckland 0632, New Zealand
| | - Jonathan Chan
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Department
of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, United
Kingdom
| | | | - Vijayalekshmi Sarojini
- School of
Chemical Sciences, University of Auckland, Auckland 1010, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Thomas J. Piggot
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Chemical
Biological and Radiological Sciences, Defence
Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Jane R Allison
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
- Biomolecular
Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand
- Digital
Life Institute, University of Auckland, Auckland 1010, New Zealand
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14
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Men WQ, Xu SG, Mou R. Hepatic transcriptome study of Taenia asiatica infection in suckling pigs. Microb Pathog 2020; 152:104598. [PMID: 33157217 DOI: 10.1016/j.micpath.2020.104598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 01/05/2023]
Abstract
Taenia asiatica is a crucial Taenia that is prevalent in East and Southeast Asia. Domestic pigs and wild boars are essential intermediate hosts for Taenia. Cysticercus larvae are mainly parasitic in the liver of domestic pigs. The Taenia asiatica was collected from Liangmu Township, Duyun City, Guizhou Province. Twelve Yorkshire Suckling pigs of 20 days of age were randomly divided into an experimental and control group of 6 pigs each. RNA sequencing (RNA-seq) technology was used to detect the expression differences of the mRNA transcriptomes in the liver of the experimental and control group at different infection times. Differential genes were analyzed by bioinformatics and verified by Real Time-PCR(RT-PCR). On the 15th and 75th days after infection, 152 and 558 differentially expressed genes were detected in the liver of the experimental group, respectively, accounting for 0.85% and 3.12% of all identified transcribed RNA genes, respectively. Through GO and KEGG related bioinformatics analysis, it was found that these differentially expressed genes are involved in the immune response, material metabolism, fibrosis, and tissue proliferation and repair of suckling pig liver, and related to MHC antigen processing and presentation, cytochrome P450, transforming growth factor-beta (TGF-β) signaling pathway and so on. Cysticercus asiatica parasites cause significant differential gene expression in the liver of suckling pigs. Specific differentially expressed genes are involved in biological processes such as liver metabolism, immune response, and tissue repair or regeneration in suckling pigs. The immune evasion is related to the immuno-suppressive response of the intermediate host.
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Affiliation(s)
- Wan-Qi Men
- Department of Parasitology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, China; Characteristic and Key Laboratory of Modern Pathogenic Biology, Guizhou Medical University, Guiyang, 550025, China
| | - Shi-Gang Xu
- Department of Parasitology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, China; Characteristic and Key Laboratory of Modern Pathogenic Biology, Guizhou Medical University, Guiyang, 550025, China
| | - Rong Mou
- Department of Parasitology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, China; Characteristic and Key Laboratory of Modern Pathogenic Biology, Guizhou Medical University, Guiyang, 550025, China.
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15
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Abstract
Invasive fungal infections in humans are generally associated with high mortality, making the choice of antifungal drug crucial for the outcome of the patient. The limited spectrum of antifungals available and the development of drug resistance represent the main concerns for the current antifungal treatments, requiring alternative strategies. Antimicrobial peptides (AMPs), expressed in several organisms and used as first-line defenses against microbial infections, have emerged as potential candidates for developing new antifungal therapies, characterized by negligible host toxicity and low resistance rates. Most of the current literature focuses on peptides with antibacterial activity, but there are fewer studies of their antifungal properties. This review focuses on AMPs with antifungal effects, including their in vitro and in vivo activities, with the biological repercussions on the fungal cells, when known. The classification of the peptides is based on their mode of action: although the majority of AMPs exert their activity through the interaction with membranes, other mechanisms have been identified, including cell wall inhibition and nucleic acid binding. In addition, antifungal compounds with unknown modes of action are also described. The elucidation of such mechanisms can be useful to identify novel drug targets and, possibly, to serve as the templates for the synthesis of new antimicrobial compounds with increased activity and reduced host toxicity.
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16
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Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol 2020; 253:287-298. [PMID: 32500172 DOI: 10.1007/s00232-020-00124-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/23/2020] [Indexed: 12/16/2022]
Abstract
Protegrin-1 (PG-1), an 18-residue β-hairpin stabilized by two disulfide bonds, is a member of a family of powerful antimicrobial peptides which are believed to act through membrane permeabilization. Here we used a combination of experimental and computational approaches to characterize possible structural arrangements of PG-1 in lipid bilayers mimicking bacterial membranes. We have measured the dose-response function of the PG-1-induced leakage of markers of various sizes from vesicles and found it to be consistent with the formation of pores of two different sizes. The first one allows the release of small dyes and occurs at peptide:lipid ratios < 0.006. Above this ratio, larger pores are observed through which the smallest of dextrans FD4 can be released. In parallel with pore formation, we observe a general large-scale destabilization of vesicles which is probably related to complete rupture of some vesicles. The population of vesicles that are completely ruptured depends linearly on PG-1:lipid ratio. Neither pore size, nor vesicle rupture are influenced by the formation of disulfide bonds. Previous computational work on oxidized protegrin is complemented here by all-atom MD simulations of PG-1 with reduced disulfide bonds both in solution (monomer) and in a bilayer (dimer and octamer). The simulations provide molecular insights into the influence of disulfide bonds on peptide conformation, aggregation, and oligomeric structure.
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Affiliation(s)
- Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Binod Nepal
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Themis Lazaridis
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. .,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, NY, 10016, USA.
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17
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Sepehri A, PeBenito L, Pino-Angeles A, Lazaridis T. What Makes a Good Pore Former: A Study of Synthetic Melittin Derivatives. Biophys J 2020; 118:1901-1913. [PMID: 32183940 DOI: 10.1016/j.bpj.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/25/2020] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Pore formation by membrane-active peptides, naturally encountered in innate immunity and infection, could have important medical and technological applications. Recently, the well-studied lytic peptide melittin has formed the basis for the development of combinatorial libraries from which potent pore-forming peptides have been derived, optimized to work under different conditions. We investigate three such peptides, macrolittin70, which is most active at neutral pH; pHD15, which is active only at low pH; and MelP5_Δ6, which was rationally designed to be active at low pH but formed only small pores. There are three, six, and six acidic residues in macrolittin70, pHD15, and MelP5_Δ6, respectively. We perform multi-microsecond simulations in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) of hexamers of these peptides starting from transmembrane orientations at neutral pH (all residues at standard protonation), low pH (acidic residues and His protonated), and highly acidic environments in which C-termini are also protonated. Previous simulations of the parent peptides melittin and MelP5 in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) are repeated in POPC. We find that the most potent pore-forming peptides exhibit strong interpeptide interactions, including salt bridges, H-bonds, and polar interactions. Protonation of the C-terminus promotes helicity and pore size. The proximity of the peptides allows fewer lipid headgroups to line the pores than in previous simulations, making the pores intermediate between barrel stave and toroidal. Based on these structures and geometrical arguments, we attempt to rationalize the factors that under different conditions can increase or decrease pore stability and propose mutations that could be tested experimentally.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York
| | - Leo PeBenito
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York; Graduate Program in Chemistry, The Graduate Center, City University of New York, New York, New York
| | - Almudena Pino-Angeles
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York
| | - Themis Lazaridis
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York; Graduate Program in Chemistry, The Graduate Center, City University of New York, New York, New York.
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18
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Deplazes E, Chin YKY, King GF, Mancera RL. The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides. Proteins 2019; 88:485-502. [PMID: 31589791 DOI: 10.1002/prot.25828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/04/2023]
Abstract
The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.
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Affiliation(s)
- Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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Marzuoli I, Margreitter C, Fraternali F. Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput 2019; 15:5175-5193. [PMID: 31433640 PMCID: PMC7377650 DOI: 10.1021/acs.jctc.9b00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Christian Margreitter
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
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Ermakova E, Kurbanov R, Zuev Y. Coarse-grained molecular dynamics of membrane semitoroidal pore formation in model lipid-peptide systems. J Mol Graph Model 2019; 87:1-10. [DOI: 10.1016/j.jmgm.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022]
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Lai PK, Kaznessis YN. Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations. ACS OMEGA 2018; 3:6056-6065. [PMID: 29978143 PMCID: PMC6026836 DOI: 10.1021/acsomega.8b00483] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Protegrin-1 (PG-1) is a cationic arginine-rich antimicrobial peptide. It is widely accepted that PG-1 induces membrane disruption by forming pores that lead to cell death. However, the insertion mechanism for these highly cationic peptides into the hydrophobic membrane environment is still poorly understood at the molecular scale. It has previously been determined that the association of arginine guanidinium and lipid phosphate groups results in strong bidentate bonds that stabilize peptide-lipid complexes. It has also been suggested that arginine residues are able to drag phosphate groups as they insert inside the membrane to form a toroidal pore. However, whether bidentate bonds play a significant role in inducing a pore formation remains unclear. To investigate the role of bidentate complexes in PG-1 translocation, we conducted molecular dynamics simulations. Two computational electroporation methods were implemented to examine the translocation process. We found that PG-1 could insert into the membrane, provided the external electric potential is large enough to first induce a water column or a pore within the lipid bilayer membrane. We also found that the highly charged PG-1 is capable in itself of inducing molecular electroporation. Substitution of arginines with charge-equivalent lysines showed a markedly reduced tendency for insertion. This indicates that the guanidinium group likely facilitates PG-1 translocation. Potential of mean force calculations suggests that peptide insertion inside the hydrophobic environment of the membrane core is not favored. We found that formation of a water column or a pore might be a prerequisite for PG-1 translocation. We also found that PG-1 can stabilize the pore after insertion. We suggest that PG-1 could be a pore inducer and stabilizer. This work sheds some light on PG-1 translocation mechanisms at the molecular level. Methods presented in this study may be extended to other arginine-rich antimicrobial and cell-penetrating peptides.
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