151
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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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152
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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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153
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Takechi-Haraya Y, Nadai R, Kimura H, Nishitsuji K, Uchimura K, Sakai-Kato K, Kawakami K, Shigenaga A, Kawakami T, Otaka A, Hojo H, Sakashita N, Saito H. Enthalpy-driven interactions with sulfated glycosaminoglycans promote cell membrane penetration of arginine peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1339-49. [DOI: 10.1016/j.bbamem.2016.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/12/2016] [Accepted: 03/17/2016] [Indexed: 12/16/2022]
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154
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Sugawara K, Shinohara H, Kadoya T, Kuramitz H. Sensing lymphoma cells based on a cell-penetrating/apoptosis-inducing/electron-transfer peptide probe. Anal Chim Acta 2016; 924:106-113. [DOI: 10.1016/j.aca.2016.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 04/09/2016] [Accepted: 04/16/2016] [Indexed: 10/21/2022]
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155
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Yoo B, Zhu Y, Maginn EJ. Molecular Mechanism of Ionic-Liquid-Induced Membrane Disruption: Morphological Changes to Bilayers, Multilayers, and Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5403-5411. [PMID: 27159842 DOI: 10.1021/acs.langmuir.6b00768] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The application of ionic liquids (ILs) in many industrially relevant processes provides an urgent need to better understand their molecular interactions with biological systems. A detailed understanding of the cytotoxicity mechanism of ILs can be helpful in facilitating the molecular design of nontoxic ILs. Using coarse-grained molecular dynamics (MD) simulations, we investigate the effects of imidazolium-based ILs on several lipid bilayer morphologies. Our results demonstrate that the asymmetric insertion of IL cations into one side of a lipid bilayer leaflet enhances the leaflet strain, which upon reaching a critical value triggers a morphological disruption in the bilayer. Consistently, the bending modulus of the bilayer is reduced by 1 to 2 orders of magnitude relative to that of an IL-free planar bilayer prior to the disruption event. Our results suggest that ILs that can easily insert into the lipid bilayer without diffusing across or inducing lipid flip-flop can be more disruptive to a lipid biomembrane.
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Affiliation(s)
- Brian Yoo
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , 182 Fitzpatrick Hall, Notre Dame, Indiana 46556-5637, United States
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University , 5050 Anthony Wayne Drive, Detroit, Michigan 48202, United States
| | - Edward J Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , 182 Fitzpatrick Hall, Notre Dame, Indiana 46556-5637, United States
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156
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GUO ZHENGRONG, PENG HUANYAN, KANG JIWEN, SUN DIANXING. Cell-penetrating peptides: Possible transduction mechanisms and therapeutic applications. Biomed Rep 2016; 4:528-534. [PMID: 27123243 PMCID: PMC4840506 DOI: 10.3892/br.2016.639] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/09/2016] [Indexed: 01/09/2023] Open
Abstract
Cell-penetrating peptides (CPPs), also known as protein transduction domains, are a class of diverse peptides with 5-30 amino acids. CPPs are divided into cationic, amphipathic and hydrophobic CPPs. They are able to carry small molecules, plasmid DNA, small interfering RNA, proteins, viruses, imaging agents and other various nanoparticles across the cellular membrane, resulting in internalization of the intact cargos. However, the mechanisms of CPP internalization remain to be elucidated. Recently, CPPs have received considerable attention due to their high transduction efficiency and low cytotoxicity. These peptides have a significant potential for diagnostic and therapeutic applications, such as delivery of fluorescent or radioactive compounds for imaging, delivery of peptides and proteins for therapeutic application, and delivery of molecules into induced pluripotent stem cells for directing differentiation. The present study reviews the classifications and transduction mechanisms of CPPs, as well as their potential applications.
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Affiliation(s)
- ZHENGRONG GUO
- The Liver Diseases Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei 050082, P.R. China
- Department of Gastroenterology, The First Hospital of Shijiazhuang City, Shijiazhuang, Hebei 050011, P.R. China
| | - HUANYAN PENG
- The Liver Diseases Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei 050082, P.R. China
- Hebei Medical University Graduate School, Shijiazhuang, Hebei 050017, P.R. China
| | - JIWEN KANG
- The Liver Diseases Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei 050082, P.R. China
| | - DIANXING SUN
- The Liver Diseases Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei 050082, P.R. China
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157
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Riduan SN, Yuan Y, Zhou F, Leong J, Su H, Zhang Y. Ultrafast Killing and Self-Gelling Antimicrobial Imidazolium Oligomers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:1928-1934. [PMID: 26891016 DOI: 10.1002/smll.201600006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Infectious diseases and the increasing threat of worldwide pandemics have underscored the importance of antibiotics and hygiene. Intensive efforts have been devoted to developing new antibiotics to meet the rapidly growing demand. In particular, advancing the knowledge of the structure-property-activity relationship is critical to expedite the design and development of novel antimicrobial with the needed potential and efficacy. Herein, a series of new antimicrobial imidazolium oligomers are developed with the rational manipulation of terminal group's hydrophobicity. These materials exhibit superior activity, excellent selectivity, ultrafast killing (>99.7% killing within 30 s), and desirable self-gelling properties. Molecular dynamic simulations reveal the delicate effect of structural changes on the translocation motion across the microbial cell membrane. The energy barrier of the translocation process analyzed by free energy calculations provides clear kinetic information to suggest that the spontaneous penetration requires a very short timescale of seconds to minutes for the new imidazolium oligomers.
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Affiliation(s)
- Siti Nurhanna Riduan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way The Nanos, Singapore, 138669, Singapore
| | - Yuan Yuan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way The Nanos, Singapore, 138669, Singapore
| | - Feng Zhou
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Jiayu Leong
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way The Nanos, Singapore, 138669, Singapore
| | - Haibin Su
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yugen Zhang
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way The Nanos, Singapore, 138669, Singapore
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158
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Alaybeyoglu B, Sariyar Akbulut B, Ozkirimli E. Insights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations. J Biomol Struct Dyn 2016; 34:2387-98. [DOI: 10.1080/07391102.2015.1117396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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159
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Li ZL, Ding HM, Ma YQ. Interaction of peptides with cell membranes: insights from molecular modeling. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:083001. [PMID: 26828575 DOI: 10.1088/0953-8984/28/8/083001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.
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Affiliation(s)
- Zhen-lu Li
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
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160
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Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface. Chem Phys Lipids 2016; 196:33-51. [PMID: 26827904 DOI: 10.1016/j.chemphyslip.2016.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/23/2022]
Abstract
We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein-lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein-protein but weaker protein-lipid interactions for a dimeric protein on membrane surfaces.
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161
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Masuda R, Yamamoto K, Koide T. Cellular Uptake of IgG Using Collagen-Like Cell-Penetrating Peptides. Biol Pharm Bull 2016; 39:130-4. [DOI: 10.1248/bpb.b15-00548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ryo Masuda
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University
- Research Institute for Science and Engineering, Waseda University
| | - Kazuhiro Yamamoto
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University
| | - Takaki Koide
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University
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162
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Yue T, Sun M, Zhang S, Ren H, Ge B, Huang F. How transmembrane peptides insert and orientate in biomembranes: a combined experimental and simulation study. Phys Chem Chem Phys 2016; 18:17483-94. [DOI: 10.1039/c6cp01133k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
After the synthesis of transmembrane peptides/proteins (TMPs), their insertion into a lipid bilayer is a fundamental biophysical process.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Mingbin Sun
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Shuai Zhang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
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163
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Ganesan SJ, Xu H, Matysiak S. Effect of lipid head group interactions on membrane properties and membrane-induced cationic β-hairpin folding. Phys Chem Chem Phys 2016; 18:17836-50. [DOI: 10.1039/c5cp07669b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Stages in membrane induced SVS-1 folding.
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Affiliation(s)
- Sai J. Ganesan
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
| | - Hongcheng Xu
- Biophysics Program
- University of Maryland
- College Park
- USA
| | - Silvina Matysiak
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
- Biophysics Program
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164
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Computer Simulation and Modeling Techniques in the Study of Nanoparticle-Membrane Interactions. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/bs.arcc.2016.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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165
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Allolio C, Baxova K, Vazdar M, Jungwirth P. Guanidinium Pairing Facilitates Membrane Translocation. J Phys Chem B 2015; 120:143-53. [DOI: 10.1021/acs.jpcb.5b10404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christoph Allolio
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
- Institut
für Physikalische and Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Katarina Baxova
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Mario Vazdar
- Institut
Rudjer
Bošković, Bijenička
cesta 54, 10000 Zagreb, Croatia
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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166
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Cell-penetrating compounds preferentially bind glycosaminoglycans over plasma membrane lipids in a charge density- and stereochemistry-dependent manner. Biophys Chem 2015; 207:40-50. [DOI: 10.1016/j.bpc.2015.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022]
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167
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Neale C, Huang K, García AE, Tristram-Nagle S. Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-ray Scattering. MEMBRANES 2015; 5:473-94. [PMID: 26402709 PMCID: PMC4584291 DOI: 10.3390/membranes5030473] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/09/2015] [Indexed: 01/07/2023]
Abstract
The interactions of the basic, cell-penetrating region (Y47GRKKRRQRRR57) of the HIV-1 Tat protein with dioleoylphosphatidylcholine (DOPC) bilayers were previously assessed by comparing experimental X-ray diffuse scattering with atomistic molecular dynamics simulations. Here, we extend this investigation by evaluating the influence of phosphatidylethanolamine (PE) lipids. Using experimental bilayer form factors derivedfrom X-ray diffuse scattering data as a guide, our simulations indicate that Tat peptides localize close to the carbonyl-glycerol group in the headgroup region of bilayers composed of either DOPC or DOPC:DOPE (1:1) lipid. Our results also suggest that Tat peptides may more frequently insert into the hydrophobic core of bilayers composed of PC:PE (1:1) lipids than into bilayers composed entirely of PC lipids. PE lipids may facilitate peptide translocation across a lipid bilayer by stabilizing intermediate states in which hydrated peptides span the bilayer.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Kun Huang
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Angel E García
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180-3590, USA.
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
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168
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Look J, Wilhelm N, von Briesen H, Noske N, Günther C, Langer K, Gorjup E. Ligand-Modified Human Serum Albumin Nanoparticles for Enhanced Gene Delivery. Mol Pharm 2015. [PMID: 26218774 DOI: 10.1021/acs.molpharmaceut.5b00153] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development of nonviral gene delivery systems is a great challenge to enable safe gene therapy. In this study, ligand-modified nanoparticles based on human serum albumin (HSA) were developed and optimized for an efficient gene therapy. Different glutaraldehyde cross-linking degrees were investigated to optimize the HSA nanoparticles for gene delivery. The peptide sequence arginine-glycine-aspartate (RGD) and the HIV-1 transactivator of transduction sequence (Tat) are well-known as promising targeting ligands. Plasmid DNA loaded HSA nanoparticles were covalently modified on their surface with these different ligands. The transfection potential of the obtained plasmid DNA loaded RGD- and Tat-modified nanoparticles was investigated in vitro, and optimal incubation conditions for these preparations were studied. It turned out that Tat-modified HSA nanoparticles with the lowest cross-linking degree of 20% showed the highest transfection potential. Taken together, ligand-functionalized HSA nanoparticles represent promising tools for efficient and safe gene therapy.
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Affiliation(s)
- Jennifer Look
- Institute of Pharmaceutical Technology and Biopharmacy, University of Muenster , Corrensstraße 48, Muenster 48149, Germany
| | - Nadine Wilhelm
- Fraunhofer Institute for Biomedical Engineering , Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
| | - Hagen von Briesen
- Fraunhofer Institute for Biomedical Engineering , Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
| | - Nadja Noske
- apceth GmbH & Co. KG , Max-Lebsche-Platz 30, 81377 Munich, Germany
| | | | - Klaus Langer
- Institute of Pharmaceutical Technology and Biopharmacy, University of Muenster , Corrensstraße 48, Muenster 48149, Germany
| | - Erwin Gorjup
- Fraunhofer Institute for Biomedical Engineering , Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
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169
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Abstract
Nearly 30years ago, certain small, relatively nontoxic peptides were discovered to be capable of traversing the cell membrane. These cell-penetrating peptides, as they are now called, have been shown to not only be capable of crossing the cell membrane themselves but can also carry many different therapeutic agents into cells, including small molecules, plasmid DNA, siRNA, therapeutic proteins, viruses, imaging agents, and other various nanoparticles. Many cell-penetrating peptides have been derived from natural proteins, but several other cell-penetrating peptides have been developed that are either chimeric or completely synthetic. How cell-penetrating peptides are internalized into cells has been a topic of debate, with some peptides seemingly entering cells through an endocytic mechanism and others by directly penetrating the cell membrane. Although the entry mechanism is still not entirely understood, it seems to be dependent on the peptide type, the peptide concentration, the cargo the peptide transports, and the cell type tested. With new intracellular disease targets being discovered, cell-penetrating peptides offer an exciting approach for delivering drugs to these intracellular targets. There are hundreds of cell-penetrating peptides being studied for drug delivery, and ongoing studies are demonstrating their success both in vitro and in vivo.
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Affiliation(s)
- Joshua D Ramsey
- School of Chemical Engineering, Oklahoma State University, Stillwater, OK 74078, United States.
| | - Nicholas H Flynn
- School of Chemical Engineering, Oklahoma State University, Stillwater, OK 74078, United States
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170
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Computational Investigations of Arginine-Rich Peptides Interacting with Lipid Membranes. MACROMOL THEOR SIMUL 2015. [DOI: 10.1002/mats.201500023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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171
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Cardenas AE, Shrestha R, Webb LJ, Elber R. Membrane permeation of a peptide: it is better to be positive. J Phys Chem B 2015; 119:6412-20. [PMID: 25941740 DOI: 10.1021/acs.jpcb.5b02122] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A joint experimental and computational study investigates the translocation of a tryptophan molecule through a phospholipid membrane. Time dependent spectroscopy of the tryptophan side chain determines the rate of permeation into 150 nm phospholipid vesicles. Atomically detailed simulations are conducted to calculate the free energy profiles and the permeation coefficient. Different charging conditions of the peptide (positive, negative, or zwitterion) are considered. Both experiment and simulation reproduce the qualitative trend and suggest that the fastest permeation is when the tryptophan is positively charged. The permeation mechanism, which is revealed by molecular dynamics simulations, is of a translocation assisted by a local defect. The influence of long-range electrostatic interactions, such as the membrane dipole potential on the permeation process, is not significant.
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Affiliation(s)
- Alfredo E Cardenas
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Rebika Shrestha
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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172
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Cardenas AE, Elber R. Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation. J Chem Phys 2015; 141:054101. [PMID: 25106564 DOI: 10.1063/1.4891305] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Coarse graining of membrane simulations by translating atomistic dynamics to densities and fields with Milestoning is discussed. The space of the membrane system is divided into cells and the different cells are characterized by order parameters presenting the number densities. The dynamics of the order parameters are probed with Milestoning. The methodology is illustrated here for a phospholipid membrane system (a hydrated bilayer of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) lipid molecules). Significant inhomogeneity in membrane internal number density leads to complex free energy landscape and local maps of transition times. Dynamics and distributions of cavities within the membrane assist the permeation of nonpolar solutes such as xenon atoms. It is illustrated that quantitative and detailed dynamics of water transport through DOPC membrane can be analyzed using Milestoning with fields. The reaction space for water transport includes at least two slow variables: the normal to the membrane plane, and the water density.
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Affiliation(s)
- Alfredo E Cardenas
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ron Elber
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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173
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Durzyńska J, Przysiecka Ł, Nawrot R, Barylski J, Nowicki G, Warowicka A, Musidlak O, Goździcka-Józefiak A. Viral and Other Cell-Penetrating Peptides as Vectors of Therapeutic Agents in Medicine. J Pharmacol Exp Ther 2015; 354:32-42. [DOI: 10.1124/jpet.115.223305] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/27/2015] [Indexed: 12/20/2022] Open
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174
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NKCS, a Mutant of the NK-2 Peptide, Causes Severe Distortions and Perforations in Bacterial, But Not Human Model Lipid Membranes. Molecules 2015; 20:6941-58. [PMID: 25913932 PMCID: PMC6272639 DOI: 10.3390/molecules20046941] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 01/05/2023] Open
Abstract
NKCS is an improved mutant of the bioactive peptide NK-2, which shows strong activity against Escherichia coli and low toxicity towards human cells. The different activity demonstrates the relevance of the physico-chemical nature of the target membrane for the biological effect of this peptide. We studied the effect of this potent antimicrobial peptide on model membranes by activity studies, differential scanning calorimetry, single molecule tracking and tracer efflux experiments. We found that NKCS severely distorted, penetrated and perforated model lipid membranes that resembled bacterial membranes, but not those that were similar to human cell membranes. The interactions of NKCS with phosphatidylethanolamine, which is abundant in bacterial membranes, were especially strong and are probably responsible for its antimicrobial activity.
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175
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Lane LA, Qian X, Smith AM, Nie S. Physical chemistry of nanomedicine: understanding the complex behaviors of nanoparticles in vivo. Annu Rev Phys Chem 2015; 66:521-47. [PMID: 25622189 PMCID: PMC8590374 DOI: 10.1146/annurev-physchem-040513-103718] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Nanomedicine is an interdisciplinary field of research at the interface of science, engineering, and medicine, with broad clinical applications ranging from molecular imaging to medical diagnostics, targeted therapy, and image-guided surgery. Despite major advances during the past 20 years, there are still major fundamental and technical barriers that need to be understood and overcome. In particular, the complex behaviors of nanoparticles under physiological conditions are poorly understood, and detailed kinetic and thermodynamic principles are still not available to guide the rational design and development of nanoparticle agents. Here we discuss the interactions of nanoparticles with proteins, cells, tissues, and organs from a quantitative physical chemistry point of view. We also discuss insights and strategies on how to minimize nonspecific protein binding, how to design multistage and activatable nanostructures for improved drug delivery, and how to use the enhanced permeability and retention effect to deliver imaging agents for image-guided cancer surgery.
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Affiliation(s)
- Lucas A Lane
- Departments of Biomedical Engineering and Chemistry, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322;
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176
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Sun D, Forsman J, Woodward CE. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol. J Chem Theory Comput 2015; 11:1775-91. [PMID: 26574387 DOI: 10.1021/ct501063a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.
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Affiliation(s)
- Delin Sun
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
| | - Jan Forsman
- Theoretical Chemistry, Chemical Centre, Lund University , P.O. Box 124, S-221 00 Lund, Sweden
| | - Clifford E Woodward
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
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177
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Abstract
This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described. The reliability of current simulation methods is analyzed by comparison of computational predictions obtained using different models with each other and with experimental data. A brief discussion of coarse-grained modeling and future directions is also presented.
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Affiliation(s)
- Krzysztof Kuczera
- Departments of Chemistry and Molecular Biosciences, University of Kansas, 1251 Wescoe Hall Drive, Room 5090, Lawrence, KS, 66045, USA,
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178
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Song J, Zhang Y, Zhang W, Chen J, Yang X, Ma P, Zhang B, Liu B, Ni J, Wang R. Cell penetrating peptide TAT can kill cancer cells via membrane disruption after attachment of camptothecin. Peptides 2015; 63:143-9. [PMID: 25496911 DOI: 10.1016/j.peptides.2014.12.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
Abstract
Attachment of traditional anticancer drugs to cell penetrating peptides is an effective strategy to improve their application in cancer treatment. In this study, we designed and synthesized the conjugates TAT-CPT and TAT-2CPT by attaching camptothecin (CPT) to the N-terminus of the cell penetrating peptide TAT. Interestingly, we found that TAT-CPT and especially TAT-2CPT could kill cancer cells via membrane disruption, which is similar to antimicrobial peptides. This might be because that CPT could perform as a hydrophobic residue to increase the extent of membrane insertion of TAT and the stability of the pores. In addition, TAT-CPT and TAT-2CPT could also kill cancer cells by the released CPT after they entered cells. Taken together, attachment of CPT could turn cell penetrating peptide TAT into an antimicrobial peptide with a dual mechanism of anticancer action, which presents a new strategy to develop anticancer peptides based on cell penetrating peptides.
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Affiliation(s)
- Jingjing Song
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yun Zhang
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Wei Zhang
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jianbo Chen
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaoli Yang
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Panpan Ma
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Bangzhi Zhang
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Beijun Liu
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jingman Ni
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
| | - Rui Wang
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
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179
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Di Pisa M, Chassaing G, Swiecicki JM. Translocation Mechanism(s) of Cell-Penetrating Peptides: Biophysical Studies Using Artificial Membrane Bilayers. Biochemistry 2014; 54:194-207. [DOI: 10.1021/bi501392n] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Margherita Di Pisa
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- ENS, UMR 7203, Laboratoire des Biomolécules,
Département de Chimie, Ecole Normale Supérieure, 24 Rue Lhomond, F-75005 Paris, France
| | - Gérard Chassaing
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- ENS, UMR 7203, Laboratoire des Biomolécules,
Département de Chimie, Ecole Normale Supérieure, 24 Rue Lhomond, F-75005 Paris, France
| | - Jean-Marie Swiecicki
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- ENS, UMR 7203, Laboratoire des Biomolécules,
Département de Chimie, Ecole Normale Supérieure, 24 Rue Lhomond, F-75005 Paris, France
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180
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Yamada T, Signorelli S, Cannistraro S, Beattie CW, Bizzarri AR. Chirality switching within an anionic cell-penetrating peptide inhibits translocation without affecting preferential entry. Mol Pharm 2014; 12:140-9. [PMID: 25478723 DOI: 10.1021/mp500495u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Multiple substitution of d- for l-amino acids decreases the intracellular uptake of cationic cell penetrating peptides (CPP) in a cell line-dependent manner. We show here that a single d-amino acid substitution can decrease the overall uptake of the anionic, amphipathic CPP, p28, into cancer and histologically matched normal cell lines, while not altering the preferential uptake of p28 into cancer cells. The decrease appears dependent on the position of the d-substitution within the peptide and the ability of the substituted d-amino acid to alter chirality. We also suggest that when d-substitution alters the ratio of α-helix to β-sheet content of an anionic CPP, its translocation across the cell membrane is altered, reducing overall entry. These observations may have a significant effect on the design of future d-substituted analogues of cell penetrating peptides.
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Affiliation(s)
- Tohru Yamada
- Division of Surgical Oncology, Department of Surgery, University of Illinois College of Medicine , Chicago, Illinois 60612, United States
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181
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Herce HD, Garcia AE, Cardoso MC. Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules. J Am Chem Soc 2014; 136:17459-67. [PMID: 25405895 PMCID: PMC4277769 DOI: 10.1021/ja507790z] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Guanidinium-rich
molecules, such as cell-penetrating peptides,
efficiently enter living cells in a non-endocytic energy-independent
manner and transport a wide range of cargos, including drugs and biomarkers.
The mechanism by which these highly cationic molecules efficiently
cross the hydrophobic barrier imposed by the plasma membrane remains
a fundamental open question. Here, a combination of computational
results and in vitro and live-cell experimental evidence reveals an
efficient energy-independent translocation mechanism for arginine-rich
molecules. This mechanism unveils the essential role of guanidinium
groups and two universal cell components: fatty acids and the cell
membrane pH gradient. Deprotonated fatty acids in contact with the
cell exterior interact with guanidinium groups, leading to a transient
membrane channel that facilitates the transport of arginine-rich peptides
toward the cell interior. On the cytosolic side, the fatty acids become
protonated, releasing the peptides and resealing the channel. This
fundamental mechanism appears to be universal across cells from different
species and kingdoms.
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Affiliation(s)
- Henry D Herce
- Department of Physics, Applied Physics and Astronomy and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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182
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Piantavigna S, Abdelhamid ME, Zhao C, Qu X, McCubbin GA, Graham B, Spiccia L, O'Mullane AP, Martin LL. Mechanistic Details of the Membrane Perforation and Passive Translocation of TAT Peptides. Chempluschem 2014. [DOI: 10.1002/cplu.201402209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stefania Piantavigna
- School of Chemistry, Monash University, Clayton, VIC 3800 (Australia), Fax: (+61) 3‐9905‐4597
| | - Muhammad E. Abdelhamid
- School of Chemistry, Monash University, Clayton, VIC 3800 (Australia), Fax: (+61) 3‐9905‐4597
- School of Applied Sciences, RMIT University, Melbourne VIC 3001 (Australia)
| | - Chuan Zhao
- School of Chemistry, Monash University, Clayton, VIC 3800 (Australia), Fax: (+61) 3‐9905‐4597
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052 (Australia)
| | - Xiaohu Qu
- School of Chemistry, Monash University, Clayton, VIC 3800 (Australia), Fax: (+61) 3‐9905‐4597
| | - George A. McCubbin
- School of Chemistry, Monash University, Clayton, VIC 3800 (Australia), Fax: (+61) 3‐9905‐4597
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052 (Australia)
| | - Leone Spiccia
- School of Chemistry, Monash University, Clayton, VIC 3800 (Australia), Fax: (+61) 3‐9905‐4597
| | - Anthony P. O'Mullane
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, QLD 4001 (Australia)
| | - Lisandra L. Martin
- School of Chemistry, Monash University, Clayton, VIC 3800 (Australia), Fax: (+61) 3‐9905‐4597
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183
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Hong C, Tieleman DP, Wang Y. Microsecond molecular dynamics simulations of lipid mixing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:11993-2001. [PMID: 25237736 PMCID: PMC4196744 DOI: 10.1021/la502363b] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/11/2014] [Indexed: 05/19/2023]
Abstract
Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na(+) ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes.
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Affiliation(s)
- Chunkit Hong
- Department of Physics, Chinese University
of Hong Kong, Shatin, N.T., Hong Kong
| | - D. Peter Tieleman
- Department of Biological
Sciences and Center for Molecular Simulation, University of Calgary, Calgary, Alberta Canada
| | - Yi Wang
- Department of Physics, Chinese University
of Hong Kong, Shatin, N.T., Hong Kong
- E-mail: (Y.W.)
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184
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Hu Y, Sinha SK, Patel S. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers. J Phys Chem B 2014; 118:11973-92. [PMID: 25290376 PMCID: PMC4199542 DOI: 10.1021/jp504853t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations.
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Affiliation(s)
- Yuan Hu
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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185
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Kang M, Loverde SM. Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes. J Phys Chem B 2014; 118:11965-72. [DOI: 10.1021/jp5047613] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Myungshim Kang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
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186
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Chu NK, Shabbir W, Bove-Fenderson E, Araman C, Lemmens-Gruber R, Harris DA, Becker CFW. A C-terminal membrane anchor affects the interactions of prion proteins with lipid membranes. J Biol Chem 2014; 289:30144-60. [PMID: 25217642 DOI: 10.1074/jbc.m114.587345] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Membrane attachment via a C-terminal glycosylphosphatidylinositol anchor is critical for conversion of PrP(C) into pathogenic PrP(Sc). Therefore the effects of the anchor on PrP structure and function need to be deciphered. Three PrP variants, including full-length PrP (residues 23-231, FL_PrP), N-terminally truncated PrP (residues 90-231, T_PrP), and PrP missing its central hydrophobic region (Δ105-125, ΔCR_PrP), were equipped with a C-terminal membrane anchor via a semisynthesis strategy. Analyses of the interactions of lipidated PrPs with phospholipid membranes demonstrated that C-terminal membrane attachment induces a different binding mode of PrP to membranes, distinct from that of non-lipidated PrPs, and influences the biochemical and conformational properties of PrPs. Additionally, fluorescence-based assays indicated pore formation by lipidated ΔCR_PrP, a variant that is known to be highly neurotoxic in transgenic mice. This finding was supported by using patch clamp electrophysiological measurements of cultured cells. These results provide new evidence for the role of the membrane anchor in PrP-lipid interactions, highlighting the importance of the N-terminal and the central hydrophobic domain in these interactions.
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Affiliation(s)
- Nam K Chu
- From the Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
| | - Waheed Shabbir
- the Department of Pharmacology and Toxicology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria, and
| | - Erin Bove-Fenderson
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Can Araman
- From the Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
| | - Rosa Lemmens-Gruber
- the Department of Pharmacology and Toxicology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria, and
| | - David A Harris
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Christian F W Becker
- From the Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria,
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187
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Bennett WFD, Sapay N, Tieleman DP. Atomistic simulations of pore formation and closure in lipid bilayers. Biophys J 2014; 106:210-9. [PMID: 24411253 DOI: 10.1016/j.bpj.2013.11.4486] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/13/2013] [Accepted: 11/25/2013] [Indexed: 10/25/2022] Open
Abstract
Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes.
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Affiliation(s)
- W F Drew Bennett
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada
| | - Nicolas Sapay
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada
| | - D Peter Tieleman
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada.
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188
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HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3078-87. [PMID: 25148702 DOI: 10.1016/j.bbamem.2014.08.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 07/08/2014] [Accepted: 08/05/2014] [Indexed: 11/21/2022]
Abstract
We report the effect on lipid bilayers of the Tat peptide Y47GRKKRRQRRR57 from the HIV-1 virus transactivator of translation (Tat) protein. Synergistic use of low-angle X-ray scattering (LAXS) and atomistic molecular dynamic simulations (MD) indicate Tat peptide binding to neutral dioleoylphosphocholine (DOPC) lipid headgroups. This binding induced the local lipid phosphate groups to move 3Å closer to the center of the bilayer. Many of the positively charged guanidinium components of the arginines were as close to the center of the bilayer as the locally thinned lipid phosphate groups. LAXS data for DOPC, DOPC/dioleoylphosphoethanolamine (DOPE), DOPC/dioleoylphosphoserine (DOPS), and a mimic of the nuclear membrane gave similar results. Generally, the Tat peptide decreased the bilayer bending modulus KC and increased the area/lipid. Further indications that Tat softens a membrane, thereby facilitating translocation, were provided by wide-angle X-ray scattering (WAXS) and neutron scattering. CD spectroscopy was also applied to further characterize Tat/membrane interactions. Although a mechanism for translation remains obscure, this study suggests that the peptide/lipid interaction makes the Tat peptide poised to translocate from the headgroup region.
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189
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Bennett WFD, Tieleman DP. The importance of membrane defects-lessons from simulations. Acc Chem Res 2014; 47:2244-51. [PMID: 24892900 DOI: 10.1021/ar4002729] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The defects and pores within lipid membranes are scientifically interesting and have a number of biological applications. Although lipid bilayers are extremely thin hydrophobic barriers, just ∼3 nm thick, they include diverse chemistry and have complex structures. Bilayers are soft and dynamic, and as a result, they can bend and deform in response to different stimuli by means of structural changes in their component lipids. Though defects occur within these structures, their transience and small size have made it difficult to characterize them. However, with recent advances in computer power and computational modeling techniques, researchers can now use simulations as a powerful tool to probe the mechanism and energies of defect and pore formation in a number of situations. In this Account, we present results from our detailed molecular dynamics computer simulations of hydrophilic pores and related defects in lipid bilayers at an atomistic level. Electroporation can be used to increase the permeability of cellular membranes, with potential therapeutic applications. Atomistic simulations of electroporation have illustrated the molecular details of this process, including the importance of water dipole interactions at the water-membrane interface. Characterization of the lipid-protein interactions provides an important tool for understanding transmembrane protein structure and thermodynamic stability. Atomistic simulations give a detailed picture of the free energies of model peptides and side chains in lipid membranes; the energetic cost of defect formation strongly influences the energies of interactions between lipids and polar and charged residues. Many antimicrobial peptides form hydrophilic pores in lipid membranes, killing bacteria or cancer cells. On the basis of simulation data, at least some of these peptides form defects and pores near the center of the bilayer, with a common disordered structure where hydrated headgroups form an approximately toroidal shape. The localization and trafficking of lipids supports general membrane structure and a number of important signaling cascades, such as those involving ceramide, diacylglycerol, and cholesterol. Atomistic simulations have determined the rates and free energies of lipid flip-flop. During the flip-flop of most phosphatidylcholine lipids, a hydrophilic pore forms when the headgroup moves near the center of the bilayer. Simulations have provided novel insight into many features of defects and pores in lipid membranes. Simulation data from very different systems and models show how water penetration and defect formation can determine the free energies of many membrane processes. Bilayers can deform and allow transient defects and pores when exposed to a diverse range of stimuli. Future work will explore many aspects of membrane defects with increased resolution and scope, including the study of more complex lipid mixtures, membrane domains, and large-scale membrane remodeling. Such studies will examine processes including vesicle budding and fusion, non-bilayer lipid phases, and interactions between lipid bilayers and other biomolecules. Simulations provide information that complements experimental studies, allowing microscopic insight into experimental observations and suggesting novel hypotheses and experiments. These studies should enable a deeper understanding of the role of lipid bilayers in cellular biology and support the development of future lipid-based biotechnology.
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Affiliation(s)
- W. F. Drew Bennett
- Department of Biological
Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - D. Peter Tieleman
- Department of Biological
Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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190
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Chen L, Li X, Gao L, Fang W. Theoretical insight into the relationship between the structures of antimicrobial peptides and their actions on bacterial membranes. J Phys Chem B 2014; 119:850-60. [PMID: 25062757 DOI: 10.1021/jp505497k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antimicrobial peptides with diverse cationic charges, amphiphathicities, and secondary structures possess a variety of antimicrobial activities against bacteria, fungi, and other generalized targets. To illustrate the relationship between the structures of these peptide and their actions at microscopic level, we present systematic coarse-grained dissipative particle dynamics simulations of eight types of antimicrobial peptides with different secondary structures interacting with a lipid bilayer membrane. We find that the peptides use multiple mechanisms to exert their membrane-disruptive activities: A cationic charge is essential for the peptides to selectively target negatively charged bacterial membranes. This cationic charge is also responsible for promoting electroporation. A significant hydrophobic portion is necessary to disrupt the membrane through formation of a permeable pore or translocation. Alternatively, the secondary structure and the corresponding rigidity of the peptides determine the pore structure and the translocation pathway.
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Affiliation(s)
- Licui Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Xin-wai-da-jie 19#, Beijing 100875, China
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191
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García-Sosa AT, Tulp I, Langel K, Langel Ü. Peptide-ligand binding modeling of siRNA with cell-penetrating peptides. BIOMED RESEARCH INTERNATIONAL 2014; 2014:257040. [PMID: 25147791 PMCID: PMC4131515 DOI: 10.1155/2014/257040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/15/2014] [Indexed: 12/04/2022]
Abstract
The binding affinity of a series of cell-penetrating peptides (CPP) was modeled through docking and making use of the number of intermolecular hydrogen bonds, lipophilic contacts, and the number of sp3 molecular orbital hybridization carbons. The new ranking of the peptides is consistent with the experimentally determined efficiency in the downregulation of luciferase activity, which includes the peptides' ability to bind and deliver the siRNA into the cell. The predicted structures of the complexes of peptides to siRNA were stable throughout 10 ns long, explicit water molecular dynamics simulations. The stability and binding affinity of peptide-siRNA complexes was related to the sidechains and modifications of the CPPs, with the stearyl and quinoline groups improving affinity and stability. The reranking of the peptides docked to siRNA, together with explicit water molecular dynamics simulations, appears to be well suited to describe and predict the interaction of CPPs with siRNA.
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Affiliation(s)
| | - Indrek Tulp
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Kent Langel
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Ülo Langel
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
- Department of Neurochemistry, Stockholm University, 106 91 Stockholm, Sweden
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192
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Jang S, Hyun S, Kim S, Lee S, Lee IS, Baba M, Lee Y, Yu J. Cell-Penetrating, Dimeric α-Helical Peptides: Nanomolar Inhibitors of HIV-1 Transcription. Angew Chem Int Ed Engl 2014; 53:10086-9. [DOI: 10.1002/anie.201404684] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 11/10/2022]
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193
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Jang S, Hyun S, Kim S, Lee S, Lee IS, Baba M, Lee Y, Yu J. Cell-Penetrating, Dimeric α-Helical Peptides: Nanomolar Inhibitors of HIV-1 Transcription. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404684] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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194
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Van Lehn RC, Ricci M, Silva PH, Andreozzi P, Reguera J, Voïtchovsky K, Stellacci F, Alexander-Katz A. Lipid tail protrusions mediate the insertion of nanoparticles into model cell membranes. Nat Commun 2014; 5:4482. [DOI: 10.1038/ncomms5482] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 06/23/2014] [Indexed: 12/30/2022] Open
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195
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Qian Z, LaRochelle J, Jiang B, Lian W, Hard RL, Selner NG, Luechapanichkul R, Barrios AM, Pei D. Early endosomal escape of a cyclic cell-penetrating peptide allows effective cytosolic cargo delivery. Biochemistry 2014; 53:4034-46. [PMID: 24896852 PMCID: PMC4075989 DOI: 10.1021/bi5004102] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 05/27/2014] [Indexed: 12/29/2022]
Abstract
Cyclic heptapeptide cyclo(FΦRRRRQ) (cFΦR4, where Φ is l-2-naphthylalanine) was recently found to be efficiently internalized by mammalian cells. In this study, its mechanism of internalization was investigated by perturbing various endocytic events through the introduction of pharmacologic agents and genetic mutations. The results show that cFΦR4 binds directly to membrane phospholipids, is internalized into human cancer cells through endocytosis, and escapes from early endosomes into the cytoplasm. Its cargo capacity was examined with a wide variety of molecules, including small-molecule dyes, linear and cyclic peptides of various charged states, and proteins. Depending on the nature of the cargos, they may be delivered by endocyclic (insertion of cargo into the cFΦR4 ring), exocyclic (attachment of cargo to the Gln side chain), or bicyclic approaches (fusion of cFΦR4 and cyclic cargo rings). The overall delivery efficiency (i.e., delivery of cargo into the cytoplasm and nucleus) of cFΦR4 was 4-12-fold higher than those of nonaarginine, HIV Tat-derived peptide, or penetratin. The higher delivery efficiency, coupled with superior serum stability, minimal toxicity, and synthetic accessibility, renders cFΦR4 a useful transporter for intracellular cargo delivery and a suitable system for investigating the mechanism of endosomal escape.
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Affiliation(s)
- Ziqing Qian
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Jonathan
R. LaRochelle
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Bisheng Jiang
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Wenlong Lian
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Ryan L. Hard
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Nicholas G. Selner
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Rinrada Luechapanichkul
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Amy M. Barrios
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Dehua Pei
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
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196
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Dong N, Zhu X, Chou S, Shan A, Li W, Jiang J. Antimicrobial potency and selectivity of simplified symmetric-end peptides. Biomaterials 2014; 35:8028-39. [PMID: 24952979 DOI: 10.1016/j.biomaterials.2014.06.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/01/2014] [Indexed: 11/19/2022]
Abstract
Because antimicrobial peptides (AMPs) are potentially useful for the treatment of multidrug-resistant infections, more attention is being paid to the structural modification and structure-function relationship of both naturally occurring and synthetic AMPs. Previous studies indicated that Protegrin-1 (PG-1), isolated from porcine leukocytes, exhibited considerable antimicrobial activity and cytotoxicity. The β-turn of PG-1 floated on the surface of bacterial membrane, while its β-strand inserted into the bacterial membrane and formed pores that were dedicated to producing cytotoxicity. For reducing cytotoxicity and improving cells selectivity, we designed a series of simplified symmetric-end peptides by combining the β-turn of PG-1 with simple amino acid repeat sequences. The sequence of designed symmetric-end peptides is (XR)nH(RX)n, (n = 1,2; X represents I, F, W and P; H represents CRRRFC). The symmetric-end peptides displayed antimicrobial activity against both gram-positive and gram-negative bacteria. In particular, (XR)2H(RX)2 (X here is I, F and W) showed greater antimicrobial potency than PG-1. Hemolysis activity and cytotoxicity, detected by using human red blood cells (RBCs) and human embryonic lung fibroblasts MRC-5 cells, were observably lower than the native peptide PG-1. (IR)2H(RI)2 (IR2), folded into β-sheet structures, displayed the highest therapeutic index, suggesting its great cell selectivity. The fluorescence spectroscopy, flow cytometry, and electron microscopy observation indicated that IR2 exhibited great membrane penetration potential by inducing membrane blebbing, disruption and lysis. Collectively, generating symmetric-end β-sheet peptides is a promising strategy for designing effective AMPs with great antimicrobial activities and cell selectivity.
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Affiliation(s)
- Na Dong
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, PR China
| | - Xin Zhu
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, PR China
| | - Shuli Chou
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, PR China
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, PR China.
| | - Weizhong Li
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, PR China
| | - Junguang Jiang
- The State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, PR China
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197
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Salomone F, Breton M, Leray I, Cardarelli F, Boccardi C, Bonhenry D, Tarek M, Mir LM, Beltram F. High-Yield Nontoxic Gene Transfer through Conjugation of the CM18-Tat11 Chimeric Peptide with Nanosecond Electric Pulses. Mol Pharm 2014; 11:2466-74. [DOI: 10.1021/mp500223t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabrizio Salomone
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
- Center
for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Marie Breton
- CNRS, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses,
UMR 8203, Orsay F-91405, France
| | - Isabelle Leray
- CNRS, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Université Paris-Sud, Laboratoire de Vectorologie et
Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- Institute Gustave-Roussy, Laboratoire de
Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Francesco Cardarelli
- Center
for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Claudia Boccardi
- Center
for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Daniel Bonhenry
- Université de Lorraine, UMR 7565, Structure et Réactivité
des
Systèmes Moléculaires Complexes, CNRS, Nancy F-54003, France
| | - Mounir Tarek
- Université de Lorraine, UMR 7565, Structure et Réactivité
des
Systèmes Moléculaires Complexes, CNRS, Nancy F-54003, France
| | - Lluis M. Mir
- CNRS, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Université Paris-Sud, Laboratoire de Vectorologie et
Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- Institute Gustave-Roussy, Laboratoire de
Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Fabio Beltram
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
- Center
for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
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198
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Cohen-Avrahami M, Shames AI, Ottaviani MF, Aserin A, Garti N. HIV-TAT Enhances the Transdermal Delivery of NSAID Drugs from Liquid Crystalline Mesophases. J Phys Chem B 2014; 118:6277-87. [DOI: 10.1021/jp412739p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Marganit Cohen-Avrahami
- Casali
Institute of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Alexander I. Shames
- Department
of Physics, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - M. Francesca Ottaviani
- Department
of Earth, Life and Environment Sciences, University of Urbino, Località
Crocicchia, Urbino 61029, Italy
| | - Abraham Aserin
- Casali
Institute of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Nissim Garti
- Casali
Institute of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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199
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Water-mediated ion-ion interactions are enhanced at the water vapor-liquid interface. Proc Natl Acad Sci U S A 2014; 111:8729-34. [PMID: 24889634 DOI: 10.1073/pnas.1403294111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is overwhelming evidence that ions are present near the vapor-liquid interface of aqueous salt solutions. Charged groups can also be driven to interfaces by attaching them to hydrophobic moieties. Despite their importance in many self-assembly phenomena, how ion-ion interactions are affected by interfaces is not understood. We use molecular simulations to show that the effective forces between small ions change character dramatically near the water vapor-liquid interface. Specifically, the water-mediated attraction between oppositely charged ions is enhanced relative to that in bulk water. Further, the repulsion between like-charged ions is weaker than that expected from a continuum dielectric description and can even become attractive as the ions are drawn to the vapor side. We show that thermodynamics of ion association are governed by a delicate balance of ion hydration, interfacial tension, and restriction of capillary fluctuations at the interface, leading to nonintuitive phenomena, such as water-mediated like charge attraction. "Sticky" electrostatic interactions may have important consequences on biomolecular structure, assembly, and aggregation at soft liquid interfaces. We demonstrate this by studying an interfacially active model peptide that changes its structure from α-helical to a hairpin-turn-like one in response to charging of its ends.
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200
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Loverde SM. Molecular Simulation of the Transport of Drugs across Model Membranes. J Phys Chem Lett 2014; 5:1659-1665. [PMID: 26270362 DOI: 10.1021/jz500321d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This Perspective describes recent progress in the area of the molecular simulation of the interactions of hydrophobic and hydrophilic solutes with membranes. The ability to predict drug solubility prior to synthesis is an extremely desirable goal for pharmaceutical research. A major advantage of molecular dynamics is the ability to computationally probe both the drug solubility as well as the pathway for the transport of drugs across membranes. Computational methods to predict the interaction free energy of solutes with membranes have advanced significantly in recent years and can characterize the intra- and intermolecular state of the drug as well as perturbations of the drug to the membrane environment itself. In addition to a brief review on computational methods to characterize the transport of drugs across membranes, we will highlight recent discoveries and discuss the challenges and opportunities in the field.
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Affiliation(s)
- Sharon M Loverde
- Department of Chemistry, City University of New York, College of Staten Island, 2800 Victory Boulevard, Staten Island, New York 10314, United States
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