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Ermakova EA, Kurbanov RK. Interaction of Uperin Peptides with Model Membranes: Molecular Dynamics Study. MEMBRANES 2023; 13:370. [PMID: 37103797 PMCID: PMC10146956 DOI: 10.3390/membranes13040370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
The interaction of antimicrobial and amyloid peptides with cell membranes is a critical step in their activities. Peptides of the uperin family obtained from the skin secretion of Australian amphibians demonstrate antimicrobial and amyloidogenic properties. All-atomic molecular dynamics and an umbrella sampling approach were used to study the interaction of uperins with model bacterial membrane. Two stable configurations of peptides were found. In the bound state, the peptides in helical form were located right under the head group region in parallel orientation with respect to the bilayer surface. Stable transmembrane configuration was observed for wild-type uperin and its alanine mutant in both alpha-helical and extended unstructured forms. The potential of mean force characterized the process of peptide binding from water to the lipid bilayer and its insertion into the membrane, and revealed that the transition of uperins from the bound state to the transmembrane position was accompanied by the rotation of peptides and passes through the energy barrier of 4-5 kcal/mol. Uperins have a weak effect on membrane properties.
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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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Martins IBS, Viegas TG, Dos Santos Alvares D, de Souza BM, Palma MS, Ruggiero Neto J, de Araujo AS. The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy. Amino Acids 2021; 53:753-767. [PMID: 33890127 DOI: 10.1007/s00726-021-02982-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/12/2021] [Indexed: 01/09/2023]
Abstract
Antimicrobial peptides (AMPs) are part of the innate immune system of many species. AMPs are short sequences rich in charged and non-polar residues. They act on the lipid phase of the plasma membrane without requiring membrane receptors. Polybia-MP1 (MP1), extracted from a native wasp, is a broad-spectrum bactericide, an inhibitor of cancer cell proliferation being non-hemolytic and non-cytotoxic. MP1 mechanism of action and its adsorption mode is not yet completely known. Its adsorption to lipid bilayer and lytic activity is most likely dependent on the ionization state of its two acidic and three basic residues and consequently on the bulk pH. Here we investigated the effect of bulk acidic (pH 5.5) and neutral pH (7.4) solution on the adsorption, insertion, and lytic activity of MP1 and its analog H-MP1 to anionic (7POPC:3POPG) model membrane. H-MP1 is a synthetic analog of MP1 with lysines replaced by histidines. Bulk pH changes could modulate this peptide efficiency. The combination of different experimental techniques and molecular dynamics (MD) simulations showed that the adsorption, insertion, and lytic activity of H-MP1 are highly sensitive to bulk pH in opposition to MP1. The atomistic details, provided by MD simulations, showed peptides contact their N-termini to the bilayer before the insertion and then lay parallel to the bilayer. Their hydrophobic faces inserted into the acyl chain phase disturb the lipid-packing.
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Affiliation(s)
- Ingrid Bernardes Santana Martins
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil
| | - Taisa Giordano Viegas
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil
| | - Dayane Dos Santos Alvares
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil
| | - Bibiana Monson de Souza
- Department of Basic and Applied Biology, Institute of Biosciences, UNESP-São Paulo State University, Rio Claro, SP, Brazil
| | - Mário Sérgio Palma
- Department of Basic and Applied Biology, Institute of Biosciences, UNESP-São Paulo State University, Rio Claro, SP, Brazil
| | - João Ruggiero Neto
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil.
| | - Alexandre Suman de Araujo
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil.
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Alvares DDS, Martins IBS, Viegas TG, Palma MS, de Araujo AS, de Carvalho SJ, Ruggiero Neto J. Modulatory Effects of Acidic pH and Membrane Potential on the Adsorption of pH-Sensitive Peptides to Anionic Lipid Membrane. MEMBRANES 2021; 11:membranes11050307. [PMID: 33922150 PMCID: PMC8143466 DOI: 10.3390/membranes11050307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 11/16/2022]
Abstract
Anionic lipid membrane electrostatic potential and solution pH can influence cationic peptide adsorption to these bilayers, especially those containing simultaneously acid and basic residues. Here, we investigate the effects of the pH solution on MP1 (IDWKKLLDAAKQIL-NH2) adsorption to anionic (7POPC:3POPG) lipid vesicles in comparison to its analog H-MP1, with histidines substituting lysines. We used the association of adsorption isotherms and constant pH molecular dynamic simulations (CpHMD) to explore the effects of membrane potential and pH on peptides' adsorption on this lipid membrane. We analyzed the fluorescence and zeta potential adsorption isotherms using the Gouy-Chapman theory. In CpHMD simulations for the peptides in solution and adsorbed on the lipid bilayer, we used the conformations obtained by conventional MD simulations at a μs timescale. Non-equilibrium Monte Carlo simulations provided the protonation states of acidic and basic residues. CpHMD showed average pKa shifts of two to three units, resulting in a higher net charge for the analog than for MP1, strongly modulating the peptide adsorption. The fractions of the protonation of acidic and basic residues and the peptides' net charges obtained from the analysis of the adsorption isotherms were in reasonable agreement with those from CpHMD. MP1 adsorption was almost insensitive to solution pH. H-MP1 was much more sensitive to partitioning, at acidic pH, with an affinity ten times higher than in neutral ones.
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Affiliation(s)
- Dayane dos Santos Alvares
- IBILCE, Department of Physics, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (D.d.S.A.); (I.B.S.M.); (T.G.V.); (A.S.d.A.); (S.J.d.C.)
| | - Ingrid Bernardes Santana Martins
- IBILCE, Department of Physics, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (D.d.S.A.); (I.B.S.M.); (T.G.V.); (A.S.d.A.); (S.J.d.C.)
| | - Taisa Giordano Viegas
- IBILCE, Department of Physics, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (D.d.S.A.); (I.B.S.M.); (T.G.V.); (A.S.d.A.); (S.J.d.C.)
| | - Mario Sergio Palma
- Institute of Biosciences, Department of Basic and Applied Biology, UNESP—São Paulo State University, Rio Claro 13506-752, SP, Brazil;
| | - Alexandre Suman de Araujo
- IBILCE, Department of Physics, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (D.d.S.A.); (I.B.S.M.); (T.G.V.); (A.S.d.A.); (S.J.d.C.)
| | - Sidney Jurado de Carvalho
- IBILCE, Department of Physics, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (D.d.S.A.); (I.B.S.M.); (T.G.V.); (A.S.d.A.); (S.J.d.C.)
| | - João Ruggiero Neto
- IBILCE, Department of Physics, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (D.d.S.A.); (I.B.S.M.); (T.G.V.); (A.S.d.A.); (S.J.d.C.)
- Correspondence:
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Pore-forming proteins: From defense factors to endogenous executors of cell death. Chem Phys Lipids 2020; 234:105026. [PMID: 33309552 DOI: 10.1016/j.chemphyslip.2020.105026] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Pore-forming proteins (PFPs) and small antimicrobial peptides (AMPs) represent a large family of molecules with the common ability to punch holes in cell membranes to alter their permeability. They play a fundamental role as infectious bacteria's defensive tools against host's immune system and as executors of endogenous machineries of regulated cell death in eukaryotic cells. Despite being highly divergent in primary sequence and 3D structure, specific folds of pore-forming domains have been conserved. In fact, pore formation is considered an ancient mechanism that takes place through a general multistep process involving: membrane partitioning and insertion, oligomerization and pore formation. However, different PFPs and AMPs assemble and form pores following different mechanisms that could end up either in the formation of protein-lined or protein-lipid pores. In this review, we analyze the current findings in the mechanism of action of different PFPs and AMPs that support a wide role of membrane pore formation in nature. We also provide the newest insights into the development of state-of-art techniques that have facilitated the characterization of membrane pores. To understand the physiological role of these peptides/proteins or develop clinical applications, it is essential to uncover the molecular mechanism of how they perforate membranes.
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Yurkova MS, Zenin VA, Sadykhov EG, Fedorov AN. Dimerization of Antimicrobial Peptide Polyphemusin I into One Polypeptide Chain: Theoretical and Practical Consequences. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820090100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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