101
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Peptide-based targeted therapeutics: Focus on cancer treatment. J Control Release 2018; 292:141-162. [DOI: 10.1016/j.jconrel.2018.11.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/03/2018] [Accepted: 11/03/2018] [Indexed: 12/14/2022]
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102
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Peraro L, Kritzer JA. Emerging Methods and Design Principles for Cell-Penetrant Peptides. Angew Chem Int Ed Engl 2018; 57:11868-11881. [PMID: 29740917 PMCID: PMC7184558 DOI: 10.1002/anie.201801361] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/24/2018] [Indexed: 12/12/2022]
Abstract
Biomolecules such as antibodies, proteins, and peptides are important tools for chemical biology and leads for drug development. They have been used to inhibit a variety of extracellular proteins, but accessing intracellular proteins has been much more challenging. In this review, we discuss diverse chemical approaches that have yielded cell-penetrant peptides and identify three distinct strategies: masking backbone amides, guanidinium group patterning, and amphipathic patterning. We summarize a growing number of large data sets, which are starting to reveal more specific design guidelines for each strategy. We also discuss advantages and disadvantages of current methods for quantifying cell penetration. Finally, we provide an overview of best-odds approaches for applying these new methods and design principles to optimize cytosolic penetration for a given bioactive peptide.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
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103
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Shi Y, Wan M, Fu L, Zhang S, Wang S, Gao L, Fang W. Peptide-Lipid Interaction Sites Affect Vesicles' Responses to Antimicrobial Peptides. Biophys J 2018; 115:1518-1529. [PMID: 30268538 DOI: 10.1016/j.bpj.2018.08.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/22/2018] [Accepted: 08/30/2018] [Indexed: 11/25/2022] Open
Abstract
This article presents coarse-grained molecular dynamics simulations of pore-forming antimicrobial peptide melittin and its interactions with vesicles composed of a mixture of zwitterionic and anionic phospholipids. Besides creating holes in the membrane, the adsorption of melittin also induces vesicle budding, which can develop into vesiculation at high peptide concentrations, as well as vesicle invagination, which can eventually result in a corrugated membrane surface. These rich morphology changes are mediated by the curvature of the vesicles and the peptide concentration. Highly curved vesicles favor the recruitment of melittins with a higher density of binding sites. The peptides mainly penetrate into the membrane surface in monomers via hydrophobic interaction. Lowly curved vesicles recruit melittins with a low density of binding sites. Surplus peptides are prone to form oligomers and shallowly adsorb on the surface of membrane via electrostatic interaction. The penetration of monomers induces membrane pore formation and positive membrane curvature, which promote vesicle budding. The adsorption of oligomers induces negative membrane curvature, which promotes vesicle invagination. This work demonstrates that antimicrobial peptides adopt multiple actions to destroy bacterial membranes.
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Affiliation(s)
- Yu Shi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Mingwei Wan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lei Fu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Shan Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Shiyuan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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104
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 399] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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105
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Avci FG, Akbulut BS, Ozkirimli E. Membrane Active Peptides and Their Biophysical Characterization. Biomolecules 2018; 8:biom8030077. [PMID: 30135402 PMCID: PMC6164437 DOI: 10.3390/biom8030077] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022] Open
Abstract
In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides; AMPs and cell-penetrating peptides (CPPs). Antimicrobial peptides are a group of membrane active peptides that disrupt the membrane integrity or inhibit the cellular functions of bacteria, virus, and fungi. Cell penetrating peptides are another group of membrane active peptides that mainly function as cargo-carriers even though they may also show antimicrobial activity. Biophysical techniques shed light on peptide–membrane interactions at higher resolution due to the advances in optics, image processing, and computational resources. Structural investigation of membrane active peptides in the presence of the membrane provides important clues on the effect of the membrane environment on peptide conformations. Live imaging techniques allow examination of peptide action at a single cell or single molecule level. In addition to these experimental biophysical techniques, molecular dynamics simulations provide clues on the peptide–lipid interactions and dynamics of the cell entry process at atomic detail. In this review, we summarize the recent advances in experimental and computational investigation of membrane active peptides with particular emphasis on two amphipathic membrane active peptides, the AMP melittin and the CPP pVEC.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Marmara University, Kadikoy, 34722 Istanbul, Turkey.
| | | | - Elif Ozkirimli
- Chemical Engineering Department, Bogazici University, Bebek, 34342 Istanbul, Turkey.
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106
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Hazam PK, Goyal R, Ramakrishnan V. Peptide based antimicrobials: Design strategies and therapeutic potential. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 142:10-22. [PMID: 30125585 DOI: 10.1016/j.pbiomolbio.2018.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 12/24/2022]
Abstract
Therapeutic activity of antibiotics is noteworthy, as they are used in the treatment of microbial infections. Regardless of their utility, there has been a steep decrease in the number of drug candidates due to antibiotic resistance, an inevitable consequence of noncompliance with the full therapeutic regimen. A variety of resistant species like MDR (Multi-Drug Resistant), XDR (Extensively Drug-Resistant) and PDR (Pan Drug-Resistant) species have evolved, but discovery pipeline has already shown signs of getting dried up. Therefore, the need for newer antibiotics is of utmost priority to combat the microbial infections of future times. Peptides have some interesting features like minimal side effect, high tolerability and selectivity towards specific targets, which would help them successfully comply with the stringent safety standards set for clinical trials. In this review, we attempt to present the state of the art in the discovery of peptide-based antimicrobials from a design perspective.
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Affiliation(s)
- Prakash Kishore Hazam
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, 781039, India
| | - Ruchika Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, 781039, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, 781039, India.
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107
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Peraro L, Kritzer JA. Neue Methoden und Designprinzipien für zellgängige Peptide. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801361] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Leila Peraro
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
| | - Joshua A. Kritzer
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
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108
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Zhang X, Xu X, Li Y, Hu C, Zhang Z, Gu Z. Virion-Like Membrane-Breaking Nanoparticles with Tumor-Activated Cell-and-Tissue Dual-Penetration Conquer Impermeable Cancer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707240. [PMID: 29774608 DOI: 10.1002/adma.201707240] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/16/2018] [Indexed: 06/08/2023]
Abstract
Poor drug penetration into tumor cells and tissues is a worldwide difficulty in cancer therapy. A strategy is developed for virion-like membrane-breaking nanoparticles (MBNs) to smoothly accomplish tumor-activated cell-and-tissue dual-penetration for surmounting impermeable drug-resistant cancer. Tailor-made dendritic arginine-rich peptide prodrugs are designed to mimic viral protein transduction domains and globular protein architectures. Attractively, these protein mimics self-assemble into virion-like nanoparticles in aqueous solution, having highly ordered secondary structure. Tumor-specific acidity conditions would activate the membrane-breaking ability of these virion-like nanoparticles to perforate artificial and natural membrane systems. As expected, MBNs achieve highly efficient drug penetration into drug-resistant human ovarian (SKOV3/R) cancer cells. Most importantly, the well-organized MBNs can pass through endothelial/tumor cells and spread from one cell to another one. Intravenous injection of MBNs into nude mice bearing impermeable SKOV3/R tumors suggests that the MBNs can recognize the tumor tissue after prolonged blood circulation, evoke the membrane-breaking function for robust transvascular extravasation, and penetrate into the deep tumor tissue. This work provides the first demonstration of sophisticated molecular and supramolecular engineering of virion-like MBNs to realize the long-awaited cell-and-tissue dual-penetration, contributing to the development of a brand-new avenue for dealing with incurable cancers.
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Affiliation(s)
- Xiao Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Xianghui Xu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
- College of Materials Science and Engineering, Nanjing Tech University, Nanjing, Jiangsu, 210009, P. R. China
| | - Yachao Li
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Cheng Hu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Zhijun Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Zhongwei Gu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
- College of Materials Science and Engineering, Nanjing Tech University, Nanjing, Jiangsu, 210009, P. R. China
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109
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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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110
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Abstract
This review summarizes over a decade of investigations into how membrane-binding proteins from the HIV-1 virus interact with lipid membrane mimics various HIV and host T-cell membranes. The goal of the work was to characterize at the molecular level both the elastic and structural changes that occur due to HIV protein/membrane interactions, which could lead to new drugs to thwart the HIV virus. The main technique used to study these interactions is diffuse X-ray scattering, which yields the bending modulus, KC, as well as structural parameters such as membrane thickness, area/lipid and position of HIV peptides (parts of HIV proteins) in the membrane. Our methods also yield information about lipid chain order or disorder caused by the peptides. This review focuses on three stages of the HIV-1 life cycle: 1) infection, 2) Tat membrane transport, and 3) budding. In the infection stage, our lab studied three different parts of HIV-1 gp41 (glycoprotein 41 fusion protein): 1) FP23, the N-terminal 23 amino acids that interact non-specifically with the T-cell host membrane to cause fusion of two membranes, and its trimer version, 2) CRAC (cholesterol recognition amino acid consensus sequence), on the MPER (membrane proximal external region) near the membrane-spanning domain, and 3) LLP2 (lentiviral lytic peptide 2) on the CTT (cytoplasmic C-terminal tail). For Tat transport, we used membrane mimics of the T-cell nuclear membrane as well as simpler models that varied charge and negative curvature. For membrane budding, we varied the myristoylation of the MA31 peptide as well as the negatively charged lipid. These studies show that HIV peptides with different roles in the HIV life cycle affect differently the relevant membrane mimics. In addition, the membrane lipid composition plays an important role in the peptides' effects.
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111
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Alaybeyoglu B, Sariyar Akbulut B, Ozkirimli E. pVEC hydrophobic N-terminus is critical for antibacterial activity. J Pept Sci 2018; 24:e3083. [DOI: 10.1002/psc.3083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Begum Alaybeyoglu
- Chemical Engineering Department; Bogazici University; Bebek 34342 Istanbul Turkey
| | | | - Elif Ozkirimli
- Chemical Engineering Department; Bogazici University; Bebek 34342 Istanbul Turkey
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112
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Mele AR, Marino J, Chen K, Pirrone V, Janetopoulos C, Wigdahl B, Klase Z, Nonnemacher MR. Defining the molecular mechanisms of HIV-1 Tat secretion: PtdIns(4,5)P 2 at the epicenter. Traffic 2018; 19:10.1111/tra.12578. [PMID: 29708629 PMCID: PMC6207469 DOI: 10.1111/tra.12578] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/18/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) transactivator of transcription (Tat) protein functions both intracellularly and extracellularly. Intracellularly, the main function is to enhance transcription of the viral promoter. However, this process only requires a small amount of intracellular Tat. The majority of Tat is secreted through an unconventional mechanism by binding to phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2 ), a phospholipid in the inner leaflet of the plasma membrane that is required for secretion. This interaction is mediated by the basic domain of Tat (residues 48-57) and a conserved tryptophan (residue 11). After binding to PtdIns(4,5)P2 , Tat secretion diverges into multiple pathways, which we categorized as oligomerization-mediated pore formation, spontaneous translocation and incorporation into exosomes. Extracellular Tat has been shown to be neurotoxic and toxic to other cells of the central nervous system (CNS) and periphery, able to recruit immune cells to the CNS and cerebrospinal fluid, and alter the gene expression and morphology of uninfected cells. The effects of extracellular Tat have been examined in HIV-1-associated neurocognitive disorders (HAND); however, only a small number of studies have focused on the mechanisms underlying Tat secretion. In this review, the molecular mechanisms of Tat secretion will be examined in a variety of biologically relevant cell types.
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Affiliation(s)
- Anthony R Mele
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Jamie Marino
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Kenneth Chen
- Department of Biology, University of the Sciences, Philadelphia, Pennsylvania
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Chris Janetopoulos
- Department of Biology, University of the Sciences, Philadelphia, Pennsylvania
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Zachary Klase
- Department of Biology, University of the Sciences, Philadelphia, Pennsylvania
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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113
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Grasso G, Muscat S, Rebella M, Morbiducci U, Audenino A, Danani A, Deriu MA. Cell penetrating peptide modulation of membrane biomechanics by Molecular dynamics. J Biomech 2018; 73:137-144. [PMID: 29631749 DOI: 10.1016/j.jbiomech.2018.03.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/14/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022]
Abstract
The efficacy of a pharmaceutical treatment is often countered by the inadequate membrane permeability, that prevents drugs from reaching their specific intracellular targets. Cell penetrating peptides (CPPs) are able to route across cells' membrane various types of cargo, including drugs and nanoparticles. However, CPPs internalization mechanisms are not yet fully understood and depend on a wide variety of aspects. In this contest, the entry of a CPP into the lipid bilayer might induce molecular conformational changes, including marked variations on membrane's mechanical properties. Understanding how the CPP does influence the mechanical properties of cells membrane is crucial to design, engineer and improve new and existing penetrating peptides. Here, all atom Molecular Dynamics (MD) simulations were used to investigate the interaction between different types of CPPs embedded in a lipid bilayer of dioleoyl phosphatidylcholine (DOPC). In a greater detail, we systematically highlighted how CPP properties are responsible for modulating the membrane bending modulus. Our findings highlighted the CPP hydropathy strongly correlated with penetration of water molecules in the lipid bilayer, thus supporting the hypothesis that the amount of water each CPP can route inside the membrane is modulated by the hydrophobic and hydrophilic character of the peptide. Water penetration promoted by CPPs leads to a local decrease of the lipid order, which emerges macroscopically as a reduction of the membrane bending modulus.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Stefano Muscat
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Martina Rebella
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Alberto Audenino
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland.
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114
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Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630158 DOI: 10.1098/rstb.2016.0219] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Graduate Program in Chemistry, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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115
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Cao Z, Bian Y, Hu G, Zhao L, Kong Z, Yang Y, Wang J, Zhou Y. Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. Int J Mol Sci 2018; 19:E885. [PMID: 29547563 PMCID: PMC5877746 DOI: 10.3390/ijms19030885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 11/16/2022] Open
Abstract
Thermodynamics of the permeation of amino acids from water to lipid bilayers is an important first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and stability. In this work, we employed bias-exchange metadynamics simulations to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) membrane (consists of 256 lipids) by using both directional and torsion angles for conformational sampling. The overall accuracy for the free energy profiles obtained is supported by significant correlation coefficients (correlation coefficient at 0.5-0.6) between our results and previous experimental or computational studies. The free energy profiles indicated that (1) polar amino acids have larger free energy barriers than nonpolar amino acids; (2) negatively charged amino acids are the most difficult to enter into the membrane; and (3) conformational transitions for many amino acids during membrane crossing is the key for reduced free energy barriers. These results represent the first set of simulated free energy profiles of membrane crossing for all 20 amino acids.
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Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Zhenzhen Kong
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Life Science, Shandong Normal University, Jinan 250014, China.
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
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116
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Islam MZ, Sharmin S, Moniruzzaman M, Yamazaki M. Elementary processes for the entry of cell-penetrating peptides into lipid bilayer vesicles and bacterial cells. Appl Microbiol Biotechnol 2018. [DOI: 10.1007/s00253-018-8889-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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117
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Jo E, Heo JS, Lim JY, Lee BR, Yoon CJ, Kim J, Lee J. Peptide ligand-mediated endocytosis of nanoparticles to cancer cells: Cell receptor-binding- versus cell membrane-penetrating peptides. Biotechnol Bioeng 2018; 115:1437-1449. [DOI: 10.1002/bit.26575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/13/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Eunji Jo
- Department of Chemical and Biological Engineering, College of Engineering; Korea University; Seoul Republic of Korea
| | - June Seok Heo
- Department of Integrated Biomedical and Life Sciences, College of Health Science; Korea University; Seoul Republic of Korea
| | - Ja-Yun Lim
- Department of Integrated Biomedical and Life Sciences, College of Health Science; Korea University; Seoul Republic of Korea
| | - Bo-Ram Lee
- Department of Chemical and Biological Engineering, College of Engineering; Korea University; Seoul Republic of Korea
| | - Chul Joo Yoon
- Department of Chemical and Biological Engineering, College of Engineering; Korea University; Seoul Republic of Korea
| | - Jinkwan Kim
- Department of Biomedical Laboratory Science, College of Health Science; Jungwon University; Chung-buk Republic of Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, College of Engineering; Korea University; Seoul Republic of Korea
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Erlich‐Hadad T, Hadad R, Feldman A, Greif H, Lictenstein M, Lorberboum‐Galski H. TAT-MTS-MCM fusion proteins reduce MMA levels and improve mitochondrial activity and liver function in MCM-deficient cells. J Cell Mol Med 2018; 22:1601-1613. [PMID: 29265583 PMCID: PMC5824393 DOI: 10.1111/jcmm.13435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Methylmalonic aciduria (MMA) is a disorder of organic acid metabolism resulting from a functional defect of the mitochondrial enzyme, methylmalonyl-CoA mutase (MCM). The main treatments for MMA patients are dietary restriction of propiogenic amino acids and carnitine supplementation. Liver or combined liver/kidney transplantation has been used to treat those with the most severe clinical manifestations. Thus, therapies are necessary to help improve quality of life and prevent liver, renal and neurological complications. Previously, we successfully used the TAT-MTS-Protein approach for replacing a number of mitochondrial-mutated proteins. In this targeted system, TAT, an 11 a.a peptide, which rapidly and efficiently can cross biological membranes, is fused to a mitochondrial targeting sequence (MTS), followed by the mitochondrial mature protein which sends the protein into the mitochondria. In the mitochondria, the TAT-MTS is cleaved off and the native protein integrates into its natural complexes and is fully functional. In this study, we used heterologous MTSs of human, nuclear-encoded mitochondrial proteins, to target the human MCM protein into the mitochondria. All fusion proteins reached the mitochondria and successfully underwent processing. Treatment of MMA patient fibroblasts with these fusion proteins restored mitochondrial activity such as ATP production, mitochondrial membrane potential and oxygen consumption, indicating the importance of mitochondrial function in this disease. Treatment with the fusion proteins enhanced cell viability and most importantly reduced MMA levels. Treatment also enhanced albumin and urea secretion in a CRISPR/Cas9-engineered HepG2 MUT (-/-) liver cell line. Therefore, we suggest using this TAT-MTS-Protein approach for the treatment of MMA.
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Affiliation(s)
- Tal Erlich‐Hadad
- Department of Biochemistry and Molecular BiologyInstitute for Medical Research Israel‐Canada (IMRIC)Faculty of MedicineHebrew University of JerusalemJerusalemIsrael
| | - Rita Hadad
- Department of Biochemistry and Molecular BiologyInstitute for Medical Research Israel‐Canada (IMRIC)Faculty of MedicineHebrew University of JerusalemJerusalemIsrael
| | | | | | - Michal Lictenstein
- Department of Biochemistry and Molecular BiologyInstitute for Medical Research Israel‐Canada (IMRIC)Faculty of MedicineHebrew University of JerusalemJerusalemIsrael
| | - Haya Lorberboum‐Galski
- Department of Biochemistry and Molecular BiologyInstitute for Medical Research Israel‐Canada (IMRIC)Faculty of MedicineHebrew University of JerusalemJerusalemIsrael
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119
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Pokhrel N, Maibaum L. Free Energy Calculations of Membrane Permeation: Challenges Due to Strong Headgroup-Solute Interactions. J Chem Theory Comput 2018; 14:1762-1771. [PMID: 29406707 DOI: 10.1021/acs.jctc.7b01159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased molecular dynamics computer simulations to calculate and compare the free energy profiles of translocation of several small molecules across 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) lipid bilayers as a first step toward determining the most efficient method for free energy calculations. We study the translocation of arginine, a sodium ion, alanine, and a single water molecule using the metadynamics, umbrella sampling, and replica exchange umbrella sampling techniques. Within the fixed lengths of our simulations, we find that all methods produce similar results for charge-neutral permeants, but not for polar or positively charged molecules. We identify the long relaxation time scale of electrostatic interactions between lipid headgroups and the solute to be the principal cause of this difference and show that this slow process can lead to an erroneous dependence of computed free energy profiles on the initial system configuration. We demonstrate the use of committor analysis to validate the proper sampling of the presumed transition state, which in our simulations is achieved only in replica exchange calculations. On the basis of these results we provide some useful guidance to perform and evaluate free energy calculations of membrane permeation.
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Affiliation(s)
- Nihit Pokhrel
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Lutz Maibaum
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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120
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Castro IH, Ferrari A, Herrera MG, Noguera ME, Maso L, Benini M, Rufini A, Testi R, Costantini P, Santos J. Biophysical characterisation of the recombinant human frataxin precursor. FEBS Open Bio 2018; 8:390-405. [PMID: 29511616 PMCID: PMC5832983 DOI: 10.1002/2211-5463.12376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/25/2017] [Accepted: 12/27/2017] [Indexed: 11/10/2022] Open
Abstract
Friedreich's ataxia is a disease caused by a decrease in the levels of expression or loss of functionality of the mitochondrial protein frataxin (FXN). The development of an active and stable recombinant variant of FXN is important for protein replacement therapy. Although valuable data about the mature form FXN81-210 has been collected, not enough information is available about the conformation of the frataxin precursor (FXN1-210). We investigated the conformation, stability and function of a recombinant precursor variant (His6-TAT-FXN1-210), which includes a TAT peptide in the N-terminal region to assist with transport across cell membranes. His6-TAT-FXN1-210 was expressed in Escherichia coli and conditions were found for purifying folded protein free of aggregation, oxidation or degradation, even after freezing and thawing. The protein was found to be stable and monomeric, with the N-terminal stretch (residues 1-89) mostly unstructured and the C-terminal domain properly folded. The experimental data suggest a complex picture for the folding process of full-length frataxin in vitro: the presence of the N-terminal region increased the tendency of FXN to aggregate at high temperatures but this could be avoided by the addition of low concentrations of GdmCl. The purified precursor was translocated through cell membranes. In addition, immune response against His6-TAT-FXN1-210 was measured, suggesting that the C-terminal fragment was not immunogenic at the assayed protein concentrations. Finally, the recognition of recombinant FXN by cellular proteins was studied to evaluate its functionality. In this regard, cysteine desulfurase NFS1/ISD11/ISCU was activated in vitro by His6-TAT-FXN1-210. Moreover, the results showed that His6-TAT-FXN1-210 can be ubiquitinated in vitro by the recently identified frataxin E3 ligase RNF126, in a similar way as the FXN1-210, suggesting that the His6-TAT extension does not interfere with the ubiquitination machinery.
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Affiliation(s)
- Ignacio Hugo Castro
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Alejandro Ferrari
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - María Georgina Herrera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Martín Ezequiel Noguera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Lorenzo Maso
- Department of Biology University of Padova Italy
| | - Monica Benini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Alessandra Rufini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Roberto Testi
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | | | - Javier Santos
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
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121
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Li M, Mosel S, Knauer SK, Schmuck C. A dipeptide with enhanced anion binding affinity enables cell uptake and protein delivery. Org Biomol Chem 2018. [DOI: 10.1039/c7ob02721d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enhancing the anion binding properties of guanidinium cations through the combination of ion-pairing and H-bonds resulted in a dipeptide that can efficiently penetrate into cells with negligible cytotoxicity and can transport a large model protein into cells.
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Affiliation(s)
- Mao Li
- Institute for Organic Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Stefanie Mosel
- Institute for Biology
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | | | - Carsten Schmuck
- Institute for Organic Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
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122
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Dong N, Li XR, Xu XY, Lv YF, Li ZY, Shan AS, Wang JL. Characterization of bactericidal efficiency, cell selectivity, and mechanism of short interspecific hybrid peptides. Amino Acids 2017; 50:453-468. [PMID: 29282543 DOI: 10.1007/s00726-017-2531-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Facing rising global antibiotics resistance, physical membrane-damaging antimicrobial peptides (AMPs) represent promising antimicrobial agents. Various strategies to design effective hybrid peptides offer many advantages in overcoming the adverse effects of natural AMPs. In this study, hybrid peptides from different species were investigated, and three hybrid antimicrobial peptides, LI, LN, and LC, were designed by combining the typical fragment of human cathelicidin-derived LL37 with either indolicidin, pig nematode cecropin P1 (CP-1) or rat neutrophil peptide-1 (NP-1). In an aqueous solution, all hybrid peptides had an unordered conformation. In simulated membrane conditions, the hybrid peptide LI displayed more β-turn and β-hairpin structures, whereas LN and LC folded into α-helix structures. The three interspecific hybrid peptides LI, LN, and LC exhibited different levels of antimicrobial activity against Gram-positive and Gram-negative bacteria. LI demonstrated the highest antimicrobial activity and cell selectivity. The results of the swimming motility indicated that LI repressed bacterial motility in a concentration-dependent method. Endotoxin binding assay demonstrated that hybrid peptide LI conserved the binding ability to LPS (polyanionic lipopolysaccharides) of its parental peptides. Fluorescence assays, flow cytometry, and SEM further revealed that hybrid peptide LI acted through different bacteriostatic mechanisms than LL37 and indolicidin and that LI killed bacterial cells via membrane damage. In summary, this study demonstrated that hybrid peptide LI produced by interspecific hybrid synthesis possessed strong cell selectivity and is a promising therapeutic candidate for drug-resistant bacteria infection.
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Affiliation(s)
- N Dong
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - X R Li
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - X Y Xu
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Y F Lv
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Z Y Li
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - A S Shan
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China.
| | - J L Wang
- College of Animal Science and Veterinary Medicine, Jinzhou Medical University, Jinzhou, People's Republic of China
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123
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Phan TK, Lay FT, Hulett MD. Importance of phosphoinositide binding by human β-defensin 3 for Akt-dependent cytokine induction. Immunol Cell Biol 2017; 96:54-67. [PMID: 29359392 DOI: 10.1111/imcb.1017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022]
Abstract
Host defense peptides (HDPs) are well-characterized for their antimicrobial activities but also variously display potent immunomodulatory effects. Human β-defensin 3 (HBD-3) belongs to a well-known HDP family known as defensins and is able to induce leukocyte chemotactic recruitment, leukocyte activation/maturation, proinflammatory cytokine release, and co-stimulatory marker expression. HBD-3-stimulated cytokine induction is NF-κB-dependent and was initially suggested to act via G protein-coupled C-C chemokine receptor phospholipase C (PLC) and/or Toll-like receptor signaling. Subsequent pharmacological inhibition, however, revealed that NF-κB activation by HBD-3 is receptor-independent and instead involves the phosphoinositide 3-kinase (PI3K)-protein kinase B (Akt) pathway, the mechanism of which remains undetermined. Recently, we have shown that HBD-3 can enter mammalian cells and bind to inner membrane phosphoinositide 4,5-bisphosphate [PI(4,5)P2], an important second lipid messenger of PLC and PI3K-Akt pathways. In this study, we report that the interaction of HBD-3 with PI(4,5)P2 is important for PI3K-Akt-NF-κΒ-mediated induction of tumor necrosis factor and interleukin-6. These data provide insights into the mechanism of immunomodulation by HBD-3, and more generally, highlight the complex multifaceted signaling roles of HDPs in innate defense. Furthermore, it is suggested that the proposed mode of action may be conserved in other HDPs.
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Affiliation(s)
- Thanh Kha Phan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Fung T Lay
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Mark D Hulett
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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124
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Budagavi DP, Zarin S, Chugh A. Antifungal activity of Latarcin 1 derived cell-penetrating peptides against Fusarium solani. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:250-256. [PMID: 29108892 DOI: 10.1016/j.bbamem.2017.10.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/16/2017] [Accepted: 10/26/2017] [Indexed: 11/19/2022]
Abstract
Cell-penetrating peptides and antimicrobial peptides share physicochemical characteristics and mechanisms of interaction with biological membranes, hence, termed as membrane active peptides. The present study aims at evaluating AMP activity of CPPs. LDP-NLS and LDP are Latarcin 1 derived cell-penetrating peptides and in the current study we have evaluated antifungal and cell-penetrating properties of these CPPs in Fusarium solani. We observed that LDP-NLS and LDP exhibited excellent antifungal activity against the fungus. Cellular uptake experiments with LDP-NLS and LDP showed that LDP-NLS acted as a CPP but LDP uptake into fungal spores and hyphae was negligible. CPP and AMP activity of mutated version of LDP-NLS was also evaluated and it was observed that both the activities of the peptide were compromised, signifying the importance of arginines and lysines present in LDP-NLS for initial interaction of membrane active peptides with biological membranes. Dextrans and Propidium Iodide uptake studies revealed that the mode of entry of LDP-NLS into fungal hyphae is through pore formation. Also, both LDP-NLS and LDP showed no cytotoxicity when infiltered into leaf tissues. Overall, our results suggest that LDP-NLS and LDP are selectively cytotoxic to F. solani and can be a potent peptide based antifungal agents.
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Affiliation(s)
| | - Sheeba Zarin
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India.
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125
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Li Z, Zhang Y, Zhu D, Li S, Yu X, Zhao Y, Ouyang X, Xie Z, Li L. Transporting carriers for intracellular targeting delivery via non-endocytic uptake pathways. Drug Deliv 2017; 24:45-55. [PMID: 29069996 PMCID: PMC8812582 DOI: 10.1080/10717544.2017.1391889] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
To develop novel therapies for clinical treatments, it increasingly depends on sophisticated delivery systems that facilitate the drugs entry into targeting cells. Profound understanding of cellular uptake routes for transporting carriers promotes the optimization of performance in drug delivery systems. Although endocytic pathway is the most important part of cellular uptake routes for many delivery systems, it suffers the trouble of enzymatic degradation of transporting carriers trapped in endosomes/lysosomes. Therefore, it is desirable to develop alternative transporting methods for delivery systems via non-endocytic pathways to achieve more effective intracellular delivery. In this review, we summarize the literature exploring transporting carriers that mediate intracellular delivery via non-endocytic pathways to present the current research status in this field. Cell-penetrating peptides, pH (low) insertion peptides, and nanoparticles are categorized to exhibit their ability to directly transport various cargos into cytoplasm via non-endocytic uptake in different cell lines. It is hoped that this review can spur the interesting on development of drug delivery systems via non-endocytic uptake pathway.
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Affiliation(s)
- Zuhong Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Yanhong Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Shuiqing Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Xiaopeng Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Yalei Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Xiaoxi Ouyang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Zhongyang Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
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126
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Manandhar A, Kang M, Chakraborty K, Tang PK, Loverde SM. Molecular simulations of peptide amphiphiles. Org Biomol Chem 2017; 15:7993-8005. [PMID: 28853474 PMCID: PMC5744600 DOI: 10.1039/c7ob01290j] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review describes recent progress in the area of molecular simulations of peptide assemblies, including peptide-amphiphiles and drug-amphiphiles. The ability to predict the structure and stability of peptide self-assemblies from the molecular level up is vital to the field of nanobiotechnology. Computational methods such as molecular dynamics offer the opportunity to characterize intermolecular forces between peptide-amphiphiles that are critical to the self-assembly process. Furthermore, these computational methods provide the ability to computationally probe the structure of these supramolecular assemblies at the molecular level, which is a challenge experimentally. Herein, we briefly highlight progress in the areas of all-atomistic and coarse-grained simulation studies investigating the self-assembly process of short peptides and peptide amphiphiles. We also discuss recent all-atomistic and coarse-grained simulations of the self-assembly of a drug-amphiphile into elongated filaments. Next, we discuss how these computational methods can provide further insight into the pathway of cylindrical nanofiber formation and predict their biocompatibility by studying the interaction of these peptide-amphiphile nanostructures with model cell membranes.
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Affiliation(s)
- Anjela Manandhar
- Department of Chemistry, College of Staten Island, City University of New York, Staten Island, NY 10314, USA.
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127
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Wang J, Zhang Y, Xu Q, Qiu J, Zheng H, Ye X, Xue Y, Yin Y, Zhang Z, Liu Y, Hao Y, Wei Q, Wang W, Mori K, Izumo S, Kubota R, Shao Y, Xing HQ. Menin mediates Tat-induced neuronal apoptosis in brain frontal cortex of SIV-infected macaques and in Tat-treated cells. Oncotarget 2017; 8:18082-18094. [PMID: 28178646 PMCID: PMC5392309 DOI: 10.18632/oncotarget.14993] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/03/2017] [Indexed: 12/04/2022] Open
Abstract
The molecular mechanisms involved in human immunodeficiency virus (HIV)-associated neurocognitive disorder (HAND) remain poorly understood. It has been recently reported that HIV-1 Tat transactivation requires menin, suggesting that menin may be involved in HAND pathogenesis. But the role of menin is not clear. Here, we found that protein level of menin was increased in simian-human immunodeficiency chimeric virus (SHIV)-SF162.P4 and simian immunodeficiency virus (SIV) sm543-3-infected rhesus macaques compared with the controls by immunohistochemistry (IHC) and western blot. Menin mainly expressed in the frontal cortex neurons of the brain, more importantly, the number of menin-staining cells was positively correlated with cleaved-caspase-3-positive cells while it was negatively correlated with a neuron-specific nuclear protein NeuN-positive cells, suggesting that expression of menin may induce neuronal apoptosis. Further studies showed that menin level was significantly increased during Tat-induced apoptosis, while downregulation of menin by pll3.7-MEN1-shRNA attenuated the Tat-induced cleavage of caspase-3 and caspase-8 in SY5Y cells and primary neuron cultures. Together, our findings reveal a pro-apoptotic role of menin in the brains of the SIV-infected macaques and the cultured neurons, indicating that targeting menin may be potential to block the HIV-1 Tat induced neuronal damage in HAND.
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Affiliation(s)
- Jun Wang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Pathology, Basic Medicine, Medical College, Xiamen University, Xiamen, Fujian 361102, China
| | - Yu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Pathology, Basic Medicine, Medical College, Xiamen University, Xiamen, Fujian 361102, China
| | - Qiping Xu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Pathology, Basic Medicine, Medical College, Xiamen University, Xiamen, Fujian 361102, China
| | - Jinhua Qiu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Pathology, Basic Medicine, Medical College, Xiamen University, Xiamen, Fujian 361102, China
| | - Honghua Zheng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Pathology, Basic Medicine, Medical College, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiang Ye
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Pathology, Basic Medicine, Medical College, Xiamen University, Xiamen, Fujian 361102, China
| | - Yuhua Xue
- School of Pharmaceutical Sciences at Xiamen University, Xiamen, Fujian 361102, China
| | - Yongmei Yin
- The Fifth People's Hospital of Wuxi, Affiliated to Jiangnan University, Wuxi, Jiangsu 214005, China
| | - Zhou Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ying Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanling Hao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qiang Wei
- Institute of Laboratory Animal Sciences of Chinese Academy of Medical Science, Beijing 100021, China
| | - Wei Wang
- Institute of Laboratory Animal Sciences of Chinese Academy of Medical Science, Beijing 100021, China
| | - Kazuyasu Mori
- AIDS Research Center, National Institute of Infectious Disease, Tokyo 862-1640, Japan
| | - Shuji Izumo
- Division of Molecular Pathology, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan
| | - Ryuji Kubota
- Division of Molecular Pathology, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hui Qin Xing
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Pathology, Basic Medicine, Medical College, Xiamen University, Xiamen, Fujian 361102, China
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128
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Ablan FDO, Spaller BL, Abdo KI, Almeida PF. Charge Distribution Fine-Tunes the Translocation of α-Helical Amphipathic Peptides across Membranes. Biophys J 2017; 111:1738-1749. [PMID: 27760360 DOI: 10.1016/j.bpj.2016.08.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/09/2016] [Accepted: 08/30/2016] [Indexed: 11/29/2022] Open
Abstract
Hundreds of cationic antimicrobial and cell-penetrating peptides (CPPs) form amphipathic α-helices when bound to lipid membranes. Here, we test two hypotheses for the differences in the ability of these peptides to translocate across membranes. The first, which we now call the hydrophobicity hypothesis, is that peptide translocation is determined by the Gibbs energy of insertion into the bilayer from the membrane interface. The second, which we call the charge-distribution hypothesis, is that translocation is determined by whether the distribution of cationic residues in the peptide can transiently stabilize a high-energy inserted intermediate by forming salt bridges to the phosphates of lipid headgroups. To test these hypotheses, we measured translocation of two series of peptide variants. The first series was based on TP10W, a peptide derived from the amphipathic CPP transportan 10; the second was based on DL1a, a synthetic peptide derived from staphylococcal δ-lysin. The peptides in those two series had small sequence changes relative to TP10W and DL1a: either single-residue substitutions or two-residue switches, which were designed to increase or decrease translocation differently according to the two hypotheses. We found that with regard to the changes introduced in the sequences, five out of six peptide variants translocated in agreement with the charge-distribution hypothesis, whereas none showed agreement with the hydrophobicity hypothesis. We conclude that large effects on translocation are probably determined by hydrophobicity, but the fine tuning appears to arise from the distribution of cationic residues along the peptide sequence.
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Affiliation(s)
- Francis D O Ablan
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina
| | - B Logan Spaller
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina
| | - Kaitlyn I Abdo
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina
| | - Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina.
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129
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Baar MP, Brandt RMC, Putavet DA, Klein JDD, Derks KWJ, Bourgeois BRM, Stryeck S, Rijksen Y, van Willigenburg H, Feijtel DA, van der Pluijm I, Essers J, van Cappellen WA, van IJcken WF, Houtsmuller AB, Pothof J, de Bruin RWF, Madl T, Hoeijmakers JHJ, Campisi J, de Keizer PLJ. Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging. Cell 2017; 169:132-147.e16. [PMID: 28340339 DOI: 10.1016/j.cell.2017.02.031] [Citation(s) in RCA: 862] [Impact Index Per Article: 123.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 12/29/2016] [Accepted: 02/22/2017] [Indexed: 02/06/2023]
Abstract
The accumulation of irreparable cellular damage restricts healthspan after acute stress or natural aging. Senescent cells are thought to impair tissue function, and their genetic clearance can delay features of aging. Identifying how senescent cells avoid apoptosis allows for the prospective design of anti-senescence compounds to address whether homeostasis can also be restored. Here, we identify FOXO4 as a pivot in senescent cell viability. We designed a FOXO4 peptide that perturbs the FOXO4 interaction with p53. In senescent cells, this selectively causes p53 nuclear exclusion and cell-intrinsic apoptosis. Under conditions where it was well tolerated in vivo, this FOXO4 peptide neutralized doxorubicin-induced chemotoxicity. Moreover, it restored fitness, fur density, and renal function in both fast aging XpdTTD/TTD and naturally aged mice. Thus, therapeutic targeting of senescent cells is feasible under conditions where loss of health has already occurred, and in doing so tissue homeostasis can effectively be restored.
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Affiliation(s)
- Marjolein P Baar
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Diana A Putavet
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Julian D D Klein
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Kasper W J Derks
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Benjamin R M Bourgeois
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Sarah Stryeck
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Yvonne Rijksen
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Hester van Willigenburg
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Danny A Feijtel
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Radiation Oncology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Center and Department of Pathology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Wilfred F van IJcken
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center and Department of Pathology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Ron W F de Bruin
- Department of Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Tobias Madl
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Judith Campisi
- The Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Lawrence Berkeley National Laboratories, Berkeley, CA 94720, USA
| | - Peter L J de Keizer
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; The Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA.
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130
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Wu B, McDonald AJ, Markham K, Rich CB, McHugh KP, Tatzelt J, Colby DW, Millhauser GL, Harris DA. The N-terminus of the prion protein is a toxic effector regulated by the C-terminus. eLife 2017; 6:e23473. [PMID: 28527237 PMCID: PMC5469617 DOI: 10.7554/elife.23473] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/17/2017] [Indexed: 12/23/2022] Open
Abstract
PrPC, the cellular isoform of the prion protein, serves to transduce the neurotoxic effects of PrPSc, the infectious isoform, but how this occurs is mysterious. Here, using a combination of electrophysiological, cellular, and biophysical techniques, we show that the flexible, N-terminal domain of PrPC functions as a powerful toxicity-transducing effector whose activity is tightly regulated in cis by the globular C-terminal domain. Ligands binding to the N-terminal domain abolish the spontaneous ionic currents associated with neurotoxic mutants of PrP, and the isolated N-terminal domain induces currents when expressed in the absence of the C-terminal domain. Anti-PrP antibodies targeting epitopes in the C-terminal domain induce currents, and cause degeneration of dendrites on murine hippocampal neurons, effects that entirely dependent on the effector function of the N-terminus. NMR experiments demonstrate intramolecular docking between N- and C-terminal domains of PrPC, revealing a novel auto-inhibitory mechanism that regulates the functional activity of PrPC.
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Affiliation(s)
- Bei Wu
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
| | - Alex J McDonald
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
| | - Kathleen Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, United States
| | - Celeste B Rich
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
| | - Kyle P McHugh
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, United States
| | - Jörg Tatzelt
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - David W Colby
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, United States
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, United States
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
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131
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Takechi-Haraya Y, Aki K, Tohyama Y, Harano Y, Kawakami T, Saito H, Okamura E. Glycosaminoglycan Binding and Non-Endocytic Membrane Translocation of Cell-Permeable Octaarginine Monitored by Real-Time In-Cell NMR Spectroscopy. Pharmaceuticals (Basel) 2017; 10:ph10020042. [PMID: 28420127 PMCID: PMC5490399 DOI: 10.3390/ph10020042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/13/2022] Open
Abstract
Glycosaminoglycans (GAGs), which are covalently-linked membrane proteins at the cell surface have recently been suggested to involve in not only endocytic cellular uptake but also non-endocytic direct cell membrane translocation of arginine-rich cell-penetrating peptides (CPPs). However, in-situ comprehensive observation and the quantitative analysis of the direct membrane translocation processes are challenging, and the mechanism therefore remains still unresolved. In this work, real-time in-cell NMR spectroscopy was applied to investigate the direct membrane translocation of octaarginine (R8) into living cells. By introducing 4-trifluoromethyl-l-phenylalanine to the N terminus of R8, the non-endocytic membrane translocation of 19F-labeled R8 (19F-R8) into a human myeloid leukemia cell line was observed at 4 °C with a time resolution in the order of minutes. 19F NMR successfully detected real-time R8 translocation: the binding to anionic GAGs at the cell surface, followed by the penetration into the cell membrane, and the entry into cytosol across the membrane. The NMR concentration analysis enabled quantification of how much of R8 was staying in the respective translocation processes with time in situ. Taken together, our in-cell NMR results provide the physicochemical rationale for spontaneous penetration of CPPs in cell membranes.
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Affiliation(s)
- Yuki Takechi-Haraya
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Kenzo Aki
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Yumi Tohyama
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Yuichi Harano
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroyuki Saito
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto 607-8414, Japan.
| | - Emiko Okamura
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
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132
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Lee MW, Han M, Bossa GV, Snell C, Song Z, Tang H, Yin L, Cheng J, May S, Luijten E, Wong GCL. Interactions between Membranes and "Metaphilic" Polypeptide Architectures with Diverse Side-Chain Populations. ACS NANO 2017; 11:2858-2871. [PMID: 28212487 DOI: 10.1021/acsnano.6b07981] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
At physiological conditions, most proteins or peptides can fold into relatively stable structures that present on their molecular surfaces specific chemical patterns partially smeared out by thermal fluctuations. These nanoscopically defined patterns of charge, hydrogen bonding, and/or hydrophobicity, along with their elasticity and shape stability (folded proteins have Young's moduli of ∼1 × 108 Pa), largely determine and limit the interactions of these molecules, such as molecular recognition and allosteric regulation. In this work, we show that the membrane-permeating activity of antimicrobial peptides (AMPs) and cell-penetrating peptides (CPPs) can be significantly enhanced using prototypical peptides with "molten" surfaces: metaphilic peptides with quasi-liquid surfaces and adaptable shapes. These metaphilic peptides have a bottlebrush-like architecture consisting of a rigid helical core decorated with mobile side chains that are terminated by cationic or hydrophobic groups. Computer simulations show that these flexible side chains can undergo significant rearrangement in response to different environments, giving rise to adaptable surface chemistry of the peptide. This quality makes it possible to control their hydrophobicity over a broad range while maintaining water solubility, unlike many AMPs and CPPs. Thus, we are able to show how the activity of these peptides is amplified by hydrophobicity and cationic charge, and rationalize these results using a quantitative mean-field theory. Computer simulations show that the shape-changing properties of the peptides and the resultant adaptive presentation of chemistry play a key enabling role in their interactions with membranes.
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Affiliation(s)
| | | | - Guilherme Volpe Bossa
- Department of Physics, North Dakota State University , Fargo, North Dakota 58108, United States
| | - Carly Snell
- Department of Physics, North Dakota State University , Fargo, North Dakota 58108, United States
| | - Ziyuan Song
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Haoyu Tang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Lichen Yin
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Sylvio May
- Department of Physics, North Dakota State University , Fargo, North Dakota 58108, United States
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133
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Werner M, Bathmann J, Baulin VA, Sommer JU. Thermal Tunneling of Homopolymers through Amphiphilic Membranes. ACS Macro Lett 2017; 6:247-251. [PMID: 35650921 DOI: 10.1021/acsmacrolett.6b00980] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We propose a theory to predict the passive translocation of flexible polymers through amphiphilic membranes. By using a generic model for the potential felt by a monomer across the membrane we calculate the free energy profile for homopolymers as a function of their hydrophobicity. Our model explains the translocation window and the translocation rates as a function of chain hydrophobicity in quantitative agreement with simulation results. The potential model leads to a new adsorption transition where chains switch from a one-sided bound adsorbed state into a bridging state through the membrane core by increasing the hydrophobicity beyond a critical value. We demonstrate that the hydrophobicity leading to the fastest translocation coincides with the solution for the critical point of adsorption in the limit of long chains.
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Affiliation(s)
- Marco Werner
- Universitat Rovira i Virgili, Departament d’Enginyeria Quı́mica, Av. Paisos Catalans 26, 43007 Tarragona, Spain
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße. 6, 01069 Dresden, Germany
| | - Jasper Bathmann
- Technische Universität Dresden, Institute of Theoretical Physics, Zellescher Weg 17, 01069 Dresden, Germany
| | - Vladimir A. Baulin
- Universitat Rovira i Virgili, Departament d’Enginyeria Quı́mica, Av. Paisos Catalans 26, 43007 Tarragona, Spain
| | - Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße. 6, 01069 Dresden, Germany
- Technische Universität Dresden, Institute of Theoretical Physics, Zellescher Weg 17, 01069 Dresden, Germany
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134
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Phan MD, Kim H, Lee S, Yu CJ, Moon B, Shin K. HIV Peptide-Mediated Binding Behaviors of Nanoparticles on a Lipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:2590-2595. [PMID: 28005379 DOI: 10.1021/acs.langmuir.6b04234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The bioinspired design of ligands for nanoparticle coating with remarkable precision in controlling anisotropic connectivity and with universal binding efficiency to the membrane has made a great impact on nanoparticle self-assembly. We utilize the HIV-1-derived trans-activator of transcription peptide (TAT), a member of the cell-penetrating peptides, as a soft shell coating on gold nanoparticles (GNPs) and characterize TAT pepide-mediated binding behaviors of GNPs on the lipid membrane. Whereas the peptides enable GNPs to firmly attach to the membrane, the binding structures are driven by two electrostatic forces: the interparticle peptide repulsion and the peptide-membrane attraction. Although transmission electron microscopy images showed that the densities of membrane-embedded GNPs were almost equal, X-ray reflectivity revealed a significant difference in binding structures of GNPs along the surface normal upon the increase of charge densities (ϕ) of the membrane. In particular, GNPs were densely suspended at ϕ = 70% while they adopted an additional well-defined layer underneath the membrane at ϕ = 100%, in addition to a translocation of the initially bound particles into the membrane. The observed behaviors of GNPs manifest a 3D to 2D transformation of the self-assembled structures from the diffused state to the closely packed state with the increase in the charge density of the membrane. The present study also provides insights on the binding mechanisms of the cell-penetrating peptide-coated nanoparticles to the lipid membranes, which is a common theme of delivery systems in pharmaceutical research.
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Affiliation(s)
- Minh Dinh Phan
- Department of Chemistry, Sogang University , Seoul, Korea
| | - Heesuk Kim
- Department of Chemistry, Sogang University , Seoul, Korea
| | - Songyi Lee
- Department of Chemistry, Sogang University , Seoul, Korea
| | - Chung-Jong Yu
- Beamline Division, Pohang Accelerator Laboratory, Pohang, Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University , Seoul, Korea
| | - Kwanwoo Shin
- Department of Chemistry, Sogang University , Seoul, Korea
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135
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Astrada S, Gomez Y, Barrera E, Obal G, Pritsch O, Pantano S, Vallespí MG, Bollati-Fogolín M. Comparative analysis reveals amino acids critical for anticancer activity of peptide CIGB-552. J Pept Sci 2017; 22:711-722. [PMID: 27933724 DOI: 10.1002/psc.2934] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 12/29/2022]
Abstract
Because of resistance development by cancer cells against current anticancer drugs, there is a considerable interest in developing novel antitumor agents. We have previously demonstrated that CIGB-552, a novel cell-penetrating synthetic peptide, was effective in reducing tumor size and increasing lifespan in tumor-bearing mice. Studies of protein-peptide interactions have shown that COMMD1 protein is a major mediator of CIGB-552 antitumor activity. Furthermore, a typical serine-protease degradation pattern for CIGB-552 in BALB/c mice serum was identified, yielding peptides which differ from CIGB-552 in size and physical properties. In the present study, we show the results obtained from a comparative analysis between CIGB-552 and its main metabolites regarding physicochemical properties, cellular internalization, and their capability to elicit apoptosis in MCF-7 cells. None of the analyzed metabolites proved to be as effective as CIGB-552 in promoting apoptosis in MCF-7. Taking into account these results, it seemed important to examine their cell-penetrating capacity and interaction with COMMD1. We show that internalization, a lipid binding-dependent process, is impaired as well as metabolite-COMMD1 interaction, key component of the apoptotic mechanism. Altogether, our results suggest that features conferred by the amino acid sequence are decisive for CIGB-552 biological activity, turning it into the minimal functional unit. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Soledad Astrada
- Cell Biology Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Yolanda Gomez
- Pharmaceutical Department, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Exequiel Barrera
- Biomolecular Simulations, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Gonzalo Obal
- Protein Biophysics Unit, Institut Pasteur Montevideo, Montevideo, Uruguay.,Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Avenida General Flores 2125, 11800, Montevideo, Uruguay
| | - Otto Pritsch
- Protein Biophysics Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Maribel G Vallespí
- Pharmaceutical Department, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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136
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Zhang Y, Wang H, Xu W, Meng F. Structural effects and translocation of spontaneous membrane-translocating peptides with POPC bilayer. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s021963361750002x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Martini coarse-grained force field simulations have been carried out to estimate the free energy profiles of the spontaneous membrane-translocating peptide TP2 and one negative control peptide ONEG with POPC as the model bilayer. The results show that the free energy minimum of TP2 is [Formula: see text]20[Formula: see text]kJ/mol lower than that of ONEG. In addition, the minimum of TP2 shifts slightly to the bilayer center compared with ONEG. The translocation barrier height for TP2 and ONEG are 119.0[Formula: see text]kJ/mol and 155.7[Formula: see text]kJ/mol, respectively. The lower central energy barrier of TP2 facilitates the transition between two leaflets of POPC. Both translocating peptides induce the formation of funnel-shaped structures at the bilayer center, but TP2 has a more compact structure and brings less perturbation compared with ONEG. Subsequently all atom molecular simulations testify the findings. It is indicated that compared with its negative control ONEG, TP2 binds better with lipid and penetrates deeper into bilayer with less perturbation to the bilayer structure. Our findings may shed light on the design and virtual screening of spontaneous membrane-translocating peptides.
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Affiliation(s)
- Yuan Zhang
- Tianjin University of Traditional Chinese Medicine, Tianjin 300193, P. R. China
| | - Huanjie Wang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical, Research, Tianjin 300193, P. R. China
| | - Weiren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical, Research, Tianjin 300193, P. R. China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical, Research, Tianjin 300193, P. R. China
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137
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Guidotti G, Brambilla L, Rossi D. Cell-Penetrating Peptides: From Basic Research to Clinics. Trends Pharmacol Sci 2017; 38:406-424. [PMID: 28209404 DOI: 10.1016/j.tips.2017.01.003] [Citation(s) in RCA: 734] [Impact Index Per Article: 104.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/04/2017] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
Abstract
The presence of cell and tissue barriers together with the low biomembrane permeability of various therapeutics often hampers systemic drug distribution; thus, most of the available molecules are of limited therapeutic value. Opportunities to increase medicament concentrations in areas that are difficult to access now exist with the advent of cell-penetrating peptides (CPPs), which can transport into the cell a wide variety of biologically active conjugates (cargoes). Numerous preclinical evaluations with CPP-derived therapeutics have provided promising results in various disease models that, in some cases, prompted clinical trials. The outcome of these investigations has thus opened new perspectives for CPP application in the development of unprecedented human therapies that are well tolerated and directed to intracellular targets.
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Affiliation(s)
- Giulia Guidotti
- Laboratory for Research on Neurodegenerative Disorders, IRCCS Maugeri Clinical and Scientific Institutes SpA SB, Via Maugeri 10, 27100 Pavia, Italy
| | - Liliana Brambilla
- Laboratory for Research on Neurodegenerative Disorders, IRCCS Maugeri Clinical and Scientific Institutes SpA SB, Via Maugeri 10, 27100 Pavia, Italy
| | - Daniela Rossi
- Laboratory for Research on Neurodegenerative Disorders, IRCCS Maugeri Clinical and Scientific Institutes SpA SB, Via Maugeri 10, 27100 Pavia, Italy.
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138
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Chen X, Liu S, Deme B, Cristiglio V, Marquardt D, Weller R, Rao P, Wang Y, Bradshaw J. Efficient internalization of TAT peptide in zwitterionic DOPC phospholipid membrane revealed by neutron diffraction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:910-916. [PMID: 28153495 DOI: 10.1016/j.bbamem.2017.01.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/16/2017] [Accepted: 01/28/2017] [Indexed: 11/19/2022]
Abstract
The aim of this study is to investigate the interactions between TAT peptides and a neutral DOPC bilayer by using neutron lamellar diffraction. The distribution of TAT peptides and the perturbation of water distribution across the DOPC bilayer were revealed. When compared to our previous study on an anionic DOPC/DOPS bilayer (X. Chen et al., Biochim Biophys Acta. 2013. 1828 (8), 1982-1988), a much deeper insertion of TAT peptides was found in the hydrophobic core of DOPC bilayer at a depth of 6.0Å from the center of the bilayer, a position close to the double bond of fatty acyl chain. We conclude that the electrostatic attractions between the positively charged TAT peptides and the negatively charged headgroups of phospholipid are not essential for the direct translocation. Furthermore, the interactions of TAT peptides with the DOPC bilayer were found to vary in a concentration-dependent manner. A limited number of peptides first associate with the phosphate moieties on the lipid headgroups by using the guanidinium ions pairing. Then the energetically favorable water defect structures are adopted to maintain the arginine residues hydrated by drawing water molecules and lipid headgroups into the bilayer core. Such bilayer deformations consequently lead to the deep intercalation of TAT peptides into the bilayer core. Once a threshold concentration of TAT peptide in the bilayer is reached, a significant rearrangement of bilayer will happen and steady-state water pores will form.
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Affiliation(s)
- Xiaochao Chen
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China.; The University of Edinburgh, Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, United Kingdom
| | - Shutao Liu
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China
| | - Bruno Deme
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, F-38042 Grenoble Cedex 9, France
| | - Viviana Cristiglio
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, F-38042 Grenoble Cedex 9, France
| | - Drew Marquardt
- Canadian Neutron Beam Centre, National Research Council, Chalk River, ON K0J 1P0, Canada
| | - Richard Weller
- The University of Edinburgh, Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, United Kingdom
| | - Pingfan Rao
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China
| | - Yunqiang Wang
- College of Biological Science and Biotechnology, Fuzhou University, 2 Xue Yuan Road, University Town, 350116 Fuzhou, Fujian, PR China
| | - Jeremy Bradshaw
- The University of Edinburgh, Royal (Dick) School of Veterinary Studies, Easter Bush, Roslin, Midlothian EH25 9RG, United Kingdom.
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139
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de Keizer PL. The Fountain of Youth by Targeting Senescent Cells? Trends Mol Med 2017; 23:6-17. [DOI: 10.1016/j.molmed.2016.11.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022]
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140
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Dobrev P, Donnini S, Groenhof G, Grubmüller H. Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pK(a) Calculations. J Chem Theory Comput 2016; 13:147-160. [PMID: 27966355 DOI: 10.1021/acs.jctc.6b00807] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a "water" molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing "water" molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH.
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Affiliation(s)
- Plamen Dobrev
- Theoretical & Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Helmut Grubmüller
- Theoretical & Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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141
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da Hora GCA, Archilha NL, Lopes JLS, Müller DM, Coutinho K, Itri R, Soares TA. Membrane negative curvature induced by a hybrid peptide from pediocin PA-1 and plantaricin 149 as revealed by atomistic molecular dynamics simulations. SOFT MATTER 2016; 12:8884-8898. [PMID: 27722742 DOI: 10.1039/c6sm01714b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antimicrobial peptides (AMPs) are cationic peptides that kill bacteria with a broad spectrum of action, low toxicity to mammalian cells and exceptionally low rates of bacterial resistance. These features have led to considerable efforts in developing AMPs as an alternative antibacterial therapy. In vitro studies have shown that AMPs interfere with membrane bilayer integrity via several possible mechanisms, which are not entirely understood. We have performed the synthesis, membrane lysis measurements, and biophysical characterization of a novel hybrid peptide. These measurements show that PA-Pln149 does not form nanopores, but instead promotes membrane rupture. It causes fast rupture of the bacterial model membrane (POPG-rich) at concentrations 100-fold lower than that required for the disruption of mammalian model membranes (POPC-rich). Atomistic molecular dynamics (MD) simulations were performed for single and multiple copies of PA-Pln149 in the presence of mixed and pure POPC/POPG bilayers to investigate the concentration-dependent membrane disruption by the hybrid peptide. These simulations reproduced the experimental trend and provided a potential mechanism of action for PA-Pln149. It shows that the PA-Pln149 does not form nanopores, but instead promotes membrane destabilization through peptide aggregation and induction of membrane negative curvature with the collapse of the lamellar arrangement. The sequence of events depicted for PA-Pln149 may offer insights into the mechanism of action of AMPs previously shown to induce negative deformation of membrane curvature and often associated with peptide translocation via non-bilayer intermediate structures.
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Affiliation(s)
- G C A da Hora
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil.
| | - N L Archilha
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo, Brazil.
| | - J L S Lopes
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo, Brazil.
| | - D M Müller
- Departamento de Química Orgánica, Facultad de Bioquímica y Cs. Biológicas, Universidad Nacional del Litoral (U.N.L). Ciudad Universitaria, C.C.242, (C.P:3000) Santa Fe, Argentina
| | - K Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo, Brazil.
| | - R Itri
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo, Brazil.
| | - T A Soares
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil. and Department of Chemistry, Umeå University, 90187 Umeå, Sweden
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142
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King MJ, Bennett AL, Almeida PF, Lee HS. Coarse-grained simulations of hemolytic peptide δ-lysin interacting with a POPC bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3182-3194. [PMID: 27720634 DOI: 10.1016/j.bbamem.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/17/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
δ-lysin, secreted by a Gram-positive bacterium Staphylococcus aureus, is a 26-residue membrane active peptide that shares many common features with antimicrobial peptides (AMPs). However, it possesses a few unique features that differentiate itself from typical AMPs. In particular, δ-lysin has zero net charge, even though it has many charged residues, and it preferentially lyses eukaryotic cells over bacterial cells. Here, we present the results of coarse-grained molecular dynamics simulations of δ-lysin interacting with a zwitterionic membrane over a wide range of peptide concentrations. When the peptides concentration is low, spontaneous dimerization of peptides is observed on the membrane surface, but deep insertion of peptides or pore formation was not observed. However, the calculated free energy of peptide insertion suggests that a small fraction of peptides is likely to be present inside the membrane at the peptide concentrations typically seen in dye efflux experiments. When the simulations with multiple peptides are carried out with a single pre-inserted transmembrane peptide, spontaneous pore formation occurs with a peptide-to-lipid ratio (P/L) as low as P/L=1:42. Inter-peptide salt bridges among the transmembrane peptides seem to play a role in creating compact pores with very low level of hydration. More importantly, the transmembrane peptides making up the pore are constantly pushed to the opposite side of the membrane when the mass imbalance between the two sides of membrane is significant. Thus, the pore is very dynamic, allowing multiple peptides to translocate across the membrane simultaneously.
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Affiliation(s)
- Mariah J King
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Ashley L Bennett
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Hee-Seung Lee
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States.
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143
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He XC, Qu ZG, Xu F. Simulation study of interaction mechanism between peptide and asymmetric membrane. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1228105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- X. C. He
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education, School of Energy and Power Engineering, Xi’an Jiaotong University, Xi’an, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, P.R. China
| | - Z. G. Qu
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education, School of Energy and Power Engineering, Xi’an Jiaotong University, Xi’an, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, P.R. China
| | - F. Xu
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, P.R. China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, P.R. China
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144
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Robison AD, Sun S, Poyton MF, Johnson GA, Pellois JP, Jungwirth P, Vazdar M, Cremer PS. Polyarginine Interacts More Strongly and Cooperatively than Polylysine with Phospholipid Bilayers. J Phys Chem B 2016; 120:9287-96. [PMID: 27571288 PMCID: PMC5912336 DOI: 10.1021/acs.jpcb.6b05604] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The interactions of two highly positively charged short peptide sequences with negatively charged lipid bilayers were explored by fluorescence binding assays and all-atom molecular dynamics simulations. The bilayers consisted of mixtures of phosphatidylglycerol (PG) and phosphatidylcholine (PC) lipids as well as a fluorescence probe that was sensitive to the interfacial potential. The first peptide contained nine arginine repeats (Arg9), and the second one had nine lysine repeats (Lys9). The experimentally determined apparent dissociation constants and Hill cooperativity coefficients demonstrated that the Arg9 peptides exhibited weakly anticooperative binding behavior at the bilayer interface at lower PG concentrations, but this anticooperative effect vanished once the bilayers contained at least 20 mol % PG. By contrast, Lys9 peptides showed strongly anticooperative binding behavior at all PG concentrations, and the dissociation constants with Lys9 were approximately 2 orders of magnitude higher than with Arg9. Moreover, only arginine-rich peptides could bind to the phospholipid bilayers containing just PC lipids. These results along with the corresponding molecular dynamics simulations suggested two important distinctions between the behavior of Arg9 and Lys9 that led to these striking differences in binding and cooperativity. First, the interactions of the guanidinium moieties on the Arg side chains with the phospholipid head groups were stronger than for the amino group. This helped facilitate stronger Arg9 binding at all PG concentrations that were tested. However, at PG concentrations of 20 mol % or greater, the Arg9 peptides came into sufficiently close proximity with each other so that favorable like-charge pairing between the guanidinium moieties could just offset the long-range electrostatic repulsions. This led to Arg9 aggregation at the bilayer surface. By contrast, Lys9 molecules experienced electrostatic repulsion from each other at all PG concentrations. These insights may help explain the propensity for cell penetrating peptides containing arginine to more effectively cross cell membranes in comparison with lysine-rich peptides.
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Affiliation(s)
| | | | | | | | | | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, Prague 6 16610, Czech Republic
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute , P.O.B. 180, HR-10002 Zagreb, Croatia
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
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145
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Bennett WFD, Hong CK, Wang Y, Tieleman DP. Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers. J Chem Theory Comput 2016; 12:4524-33. [DOI: 10.1021/acs.jctc.6b00265] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- W. F. Drew Bennett
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Chun Kit Hong
- Shenzhen
Research Institute, Chinese University of Hong Kong, Nanshan District, Shenzhen 518057, P. R. China
- Department
of Physics, Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Yi Wang
- Shenzhen
Research Institute, Chinese University of Hong Kong, Nanshan District, Shenzhen 518057, P. R. China
- Department
of Physics, Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N1N4, Canada
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146
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Bochicchio D, Panizon E, Ferrando R, Monticelli L, Rossi G. Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling. J Chem Phys 2016; 143:144108. [PMID: 26472364 DOI: 10.1063/1.4932159] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compare the performance of two well-established computational algorithms for the calculation of free-energy landscapes of biomolecular systems, umbrella sampling and metadynamics. We look at benchmark systems composed of polyethylene and polypropylene oligomers interacting with lipid (phosphatidylcholine) membranes, aiming at the calculation of the oligomer water-membrane free energy of transfer. We model our test systems at two different levels of description, united-atom and coarse-grained. We provide optimized parameters for the two methods at both resolutions. We devote special attention to the analysis of statistical errors in the two different methods and propose a general procedure for the error estimation in metadynamics simulations. Metadynamics and umbrella sampling yield the same estimates for the water-membrane free energy profile, but metadynamics can be more efficient, providing lower statistical uncertainties within the same simulation time.
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Affiliation(s)
- Davide Bochicchio
- Physics Department, University of Genoa and CNR-IMEM, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Emanuele Panizon
- Physics Department, University of Genoa and CNR-IMEM, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Riccardo Ferrando
- Physics Department, University of Genoa and CNR-IMEM, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Luca Monticelli
- Bases Moléculaires et Structurales des Systèmes Infectieux (BMSSI), CNRS UMR 5086, 7 Passage du Vercors, 69007 Lyon, France
| | - Giulia Rossi
- Physics Department, University of Genoa and CNR-IMEM, Via Dodecaneso 33, 16146 Genoa, Italy
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147
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Hu Y, Patel S. Thermodynamics of cell-penetrating HIV1 TAT peptide insertion into PC/PS/CHOL model bilayers through transmembrane pores: the roles of cholesterol and anionic lipids. SOFT MATTER 2016; 12:6716-6727. [PMID: 27435187 DOI: 10.1039/c5sm01696g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Efficient delivery of pharmaceutically active molecules across cellular membranes using cell penetrating peptides (CPPs), such as the cationic human immunodeficiency virus-1 trans-acting activator of transcription peptide (HIV-1 TAT), continues to attract scientific attention in drug design and disease treatment. Experimental results show that the TAT peptide is not only capable of directly penetrating the biological membrane in a passive manner, but also forming physical, membrane-spanning pores that may facilitate transport. Experiments further show that anionic lipids accelerate peptide permeation within a range of mole percentage composition. In this work, we explored the structures and translocation thermodynamics of the cationic TAT peptide across a series of DPPC/DPPS model membranes with the presence of 0-30 mol% cholesterol. We computed the potentials of the mean force by using umbrella sampling molecular dynamics simulations coupled to the Martini coarse-grained force field. We systematically investigated the roles of cholesterol and anionic lipids (membrane surface charge) in TAT peptide translocation. In qualitative agreement with experimental findings, the barrier heights were significantly reduced in the presence of anionic lipids. A toroidal hydrophilic pore was strongly suggested by membrane structure analysis. Cholesterol stabilizes the liquid-ordered (Lo) phase of membranes and increases the elastic stiffness of bilayers. Consequently, it hinders transmembrane pore formation and thus modulates solute permeability, since the liquid-ordered phase suppresses reorientation of the lipid molecules on simulation time scales. Though cholesterol contributes marginally to the total free energy associated with peptide permeation, the coordination of cholesterol to the peptide weakens more favorable peptide-lipid interactions. The addition of the anionic lipid DPPS to the neutral DPPC bilayer leads to the emergence and further enhancement of an interfacially stable state of the peptide due to the favorable peptide-anionic lipid interactions. Translocation free energy barriers decrease in lockstep with increasing DPPS composition in the model bilayers simulated. Finally, we investigated the size of hydrophilic pores emerging in our simulations, as well as the qualitative mobility of the peptide on the membrane surface.
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Affiliation(s)
- Yuan Hu
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
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148
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Lin YH, Chen YP, Liu TP, Chien FC, Chou CM, Chen CT, Mou CY. Approach To Deliver Two Antioxidant Enzymes with Mesoporous Silica Nanoparticles into Cells. ACS APPLIED MATERIALS & INTERFACES 2016; 8:17944-17954. [PMID: 27353012 DOI: 10.1021/acsami.6b05834] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Reactive oxygen species (ROS) are important factors in many clinical diseases. However, direct delivery of antioxidant enzymes into cells is difficult due to poor cell uptake. A proper design of delivery of enzymes by nanoparticles is very desirable for therapeutic purposes. To overcome the cell barrier problem, a designed mesoporous silica nanoparticle (MSN) system with attached TAT-fusion denatured enzyme for enhancing cell membrane penetration has been developed. Simultaneous delivery of two up-downstream antioxidant enzymes, superoxide dismutase (SOD) and glutathione peroxidase(GPx), reveals synergistic efficiency of ROS scavenging, compared to single antioxidant enzyme delivery. TAT peptide conjugation provided a facile nonendocytosis cell uptake and escape from endosome while moving and aggregating along the cytoskeleton that would allow them to be close to each other at the same time, resulting in the cellular antioxidation cascade reaction. The two-enzyme delivery shows a significant synergistic effect for protecting cells against ROS-induced cell damage and cell cycle arrest. The nanocarrier strategy for enzyme delivery demonstrates that intracellular anti-ROS cascade reactions could be regulated by multifunctional MSNs carrying image fluorophore and relevant antioxidation enzymes.
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Affiliation(s)
- Yu-Hsuan Lin
- Department of Chemistry, National Taiwan University , Taipei 106, Taiwan
| | | | - Tsang-Pai Liu
- Mackay Junior College of Medicine , Nursing and Management, Taipei 112, Taiwan
- Department of Surgery, Mackay Memorial Hospital , Taipei 104, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University , Taoyuan City 320, Taiwan
| | | | | | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan University , Taipei 106, Taiwan
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149
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Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF. Ion Channels Made from a Single Membrane-Spanning DNA Duplex. NANO LETTERS 2016; 16:4665-9. [PMID: 27324157 PMCID: PMC4948918 DOI: 10.1021/acs.nanolett.6b02039] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/17/2016] [Indexed: 05/21/2023]
Abstract
Because of their hollow interior, transmembrane channels are capable of opening up pathways for ions across lipid membranes of living cells. Here, we demonstrate ion conduction induced by a single DNA duplex that lacks a hollow central channel. Decorated with six porpyrin-tags, our duplex is designed to span lipid membranes. Combining electrophysiology measurements with all-atom molecular dynamics simulations, we elucidate the microscopic conductance pathway. Ions flow at the DNA-lipid interface as the lipid head groups tilt toward the amphiphilic duplex forming a toroidal pore filled with water and ions. Ionic current traces produced by the DNA-lipid channel show well-defined insertion steps, closures, and gating similar to those observed for traditional protein channels or synthetic pores. Ionic conductances obtained through simulations and experiments are in excellent quantitative agreement. The conductance mechanism realized here with the smallest possible DNA-based ion channel offers a route to design a new class of synthetic ion channels with maximum simplicity.
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Affiliation(s)
- Kerstin Göpfrich
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Chen-Yu Li
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Iwona Mames
- School of
Chemistry and Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | | | - Maria Ricci
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jejoong Yoo
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Adam Mames
- School of
Chemistry and Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Alexander Ohmann
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | | | - Eugen Stulz
- School of
Chemistry and Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- E-mail: . Phone: +44(0)238059 9369
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
- E-mail: . Phone: +1(0) 217333 6495
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
- E-mail: . Phone: +44(0)1223
337272
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150
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Lee BL, Kuczera K, Middaugh CR, Jas GS. Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study. J Chem Phys 2016; 144:245103. [DOI: 10.1063/1.4954241] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Brent L. Lee
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, USA
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66045, USA
| | - C. Russell Middaugh
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Gouri S. Jas
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
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