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Berscheid A, Straetener J, Schilling NA, Ruppelt D, Konnerth MC, Schittek B, Krismer B, Peschel A, Steinem C, Grond S, Brötz-Oesterhelt H. The microbiome-derived antibacterial lugdunin acts as a cation ionophore in synergy with host peptides. mBio 2024:e0057824. [PMID: 39133006 DOI: 10.1128/mbio.00578-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/02/2024] [Indexed: 08/13/2024] Open
Abstract
Lugdunin is a microbiome-derived antibacterial agent with good activity against Gram-positive pathogens in vitro and in animal models of nose colonization and skin infection. We have previously shown that lugdunin depletes bacterial energy resources by dissipating the membrane potential of Staphylococcus aureus. Here, we explored the mechanism of action of lugdunin in more detail and show that lugdunin quickly depolarizes cytoplasmic membranes of different bacterial species and acidifies the cytoplasm of S. aureus within minutes due to protonophore activity. Varying the salt species and concentrations in buffers revealed that not only protons are transported, and we demonstrate the binding of the monovalent cations K+, Na+, and Li+ to lugdunin. By comparing known ionophores with various ion transport mechanisms, we conclude that the ion selectivity of lugdunin largely resembles that of 15-mer linear peptide gramicidin A. Direct interference with the main bacterial metabolic pathways including DNA, RNA, protein, and cell wall biosyntheses can be excluded. The previously observed synergism of lugdunin with dermcidin-derived peptides such as DCD-1 in killing S. aureus is mechanistically based on potentiated membrane depolarization. We also found that lugdunin was active against certain eukaryotic cells, however strongly depending on the cell line and growth conditions. While adherent lung epithelial cell lines were almost unaffected, more sensitive cells showed dissipation of the mitochondrial membrane potential. Lugdunin seems specifically adapted to its natural environment in the respiratory tract. The ionophore mechanism is refractory to resistance development and benefits from synergy with host-derived antimicrobial peptides. IMPORTANCE The vast majority of antimicrobial peptides produced by members of the microbiome target the bacterial cell envelope by many different mechanisms. These compounds and their producers have evolved side-by-side with their host and were constantly challenged by the host's immune system. These molecules are optimized to be well tolerated at their physiological site of production, and their modes of action have proven efficient in vivo. Imbalancing the cellular ion homeostasis is a prominent mechanism among antibacterial natural products. For instance, over 120 naturally occurring polyether ionophores are known to date, and antimicrobial peptides with ionophore activity have also been detected in microbiomes. In this study, we elucidated the mechanism underlying the membrane potential-dissipating activity of the thiazolidine-containing cycloheptapeptide lugdunin, the first member of the fibupeptides discovered in a commensal bacterium from the human nose, which is a promising future probiotic candidate that is not prone to resistance development.
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Affiliation(s)
- Anne Berscheid
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jan Straetener
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Dominik Ruppelt
- Georg-August-Universität Göttingen, Institute of Organic and Biomolecular Chemistry, Göttingen, Germany
| | - Martin C Konnerth
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Birgit Schittek
- Department of Dermatology, Division of Dermatooncology, University of Tübingen, Tübingen, Germany
| | - Bernhard Krismer
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
| | - Andreas Peschel
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
| | - Claudia Steinem
- Georg-August-Universität Göttingen, Institute of Organic and Biomolecular Chemistry, Göttingen, Germany
- Max-Planck-Institute for Dynamics and Self Organization, Göttingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
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Asada Y, Tanaka S, Nagano H, Noguchi H, Yoshino A, Taga K, Yamamoto Y, Shervani Z. Morphology Observation of Two-Dimensional Monolayers of Model Proteins on Water Surface as Revealed by Dropping Method. Bioengineering (Basel) 2024; 11:366. [PMID: 38671787 PMCID: PMC11048086 DOI: 10.3390/bioengineering11040366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
We have investigated the morphology of two-dimensional monolayers of gramicidin-D (GD) and alamethicin (Al) formed on the water surface by the dropping method (DM) using surface tension measurement (STm), Brewster angle microscopy (BAM), and atomic force microscopy (AFM). Dynamic light scattering (DLS) revealed that GD in alcoholic solutions formed a dimeric helical structure. According to the CD and NMR spectroscopies, GD molecules existed in dimer form in methanol and lipid membrane environments. The STm results and BAM images revealed that the GD dimer monolayer was in a liquid expanded (LE) state, whereas the Al monolayer was in a liquid condensed (LC) state. The limiting molecular area (A0) was 6.2 ± 0.5 nm2 for the GD-dimer and 3.6 ± 0.5 nm2 for the Al molecule. The AFM images also showed that the molecular long axes of both the GD-dimer and Al were horizontal to the water surface. The stability of each monolayer was confirmed by the time dependence of the surface pressure (π) observed using the STm method. The DM monolayer preparation method for GD-dimer and Al peptide molecules is a useful technique for revealing how the model biological membrane's components assemble in two dimensions on the water surface.
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Affiliation(s)
- Yukie Asada
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Shinya Tanaka
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Hirotaka Nagano
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Hiroki Noguchi
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Akihiro Yoshino
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Keijiro Taga
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Yasushi Yamamoto
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Zameer Shervani
- Food & Energy Security Research & Product Centre, Sendai 980-0871, Japan
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3
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Špaček J, Benner SA. Agnostic Life Finder (ALF) for Large-Scale Screening of Martian Life During In Situ Refueling. ASTROBIOLOGY 2022; 22:1255-1263. [PMID: 35796703 DOI: 10.1089/ast.2021.0070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Before the first humans depart for Mars in the next decade, hundreds of tons of martian water-ice must be harvested to produce propellant for the return vehicle, a process known as in situ resource utilization (ISRU). We describe here an instrument, the Agnostic Life Finder (ALF), that is an inexpensive life-detection add-on to ISRU. ALF exploits a well-supported view that informational genetic biopolymers in life in water must have two structural features: (1) Informational biopolymers must carry a repeating charge; they must be polyelectrolytes. (2) Their building blocks must fit into an aperiodic crystal structure; the building blocks must be size-shape regular. ALF exploits the first structural feature to extract polyelectrolytes from ∼10 cubic meters of mined martian water by applying a voltage gradient perpendicularly to the water's flow. This gradient diverts polyelectrolytes from the flow toward their respective electrodes (polyanions to the anode, polycations to the cathode), where they are captured in cartridges before they encounter the electrodes. There, they can later be released to analyze their building blocks, for example, by mass spectrometry or nanopore. Upstream, martian cells holding martian informational polyelectrolytes are disrupted by ultrasound. To manage the (unknown) conductivity of the water due to the presence of salts, the mined water is preconditioned by electrodialysis using porous membranes. ALF uses only resources and technology that must already be available for ISRU. Thus, life detection is easily and inexpensively integrated into SpaceX or NASA ISRU missions.
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Affiliation(s)
- Jan Špaček
- Firebird Biomolecular Sciences, LLC, Alachua, Florida, USA
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4
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Jerath G, Darvin P, Christian Y, Trivedi V, Kumar TRS, Ramakrishnan V. Delivery of Small Molecules by Syndiotactic Peptides for Breast Cancer Therapy. Mol Pharm 2022; 19:2877-2887. [PMID: 35839086 DOI: 10.1021/acs.molpharmaceut.2c00238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The utilization of peptide-based drug delivery systems has been suboptimal due to their poor proteolytic susceptibility, poor cell permeability, and limited tumor homing capabilities. Earlier attempts in using d-enantiomers in peptide sequences increased proteolytic stability but have compromised the overall penetration capability. We designed a series of peptides (STRAPs) with a syndiotactic polypeptide backbone that can potentially form a spatial array of cationic groups, an important feature that facilitates cellular uptake. The peptides penetrate cell membranes through a combination of active and passive modes. Furthermore, the cellular uptake of the peptides was unaffected by the presence of or treatment with bovine serum and human plasma. The designed peptides successfully delivered methotrexate, an anticancer drug, to the in vitro and in vivo models of breast cancer, with the best performing peptide STRAP-4-MTX conjugate having an EC50 value of 1.34 μM. Peptide drug delivery in mouse xenograft models showed a greater reduction of primary tumor and metastasis of breast cancer, in comparison to methotrexate of the same dose. The in vivo biodistribution assay of the STRAP-4 peptide suggests that the peptide accumulates at the tumor site after 2 h of treatment, and in the absence of tumors, the peptide gets metabolized and excreted from the system.
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Affiliation(s)
- Gaurav Jerath
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Pramod Darvin
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Yvonne Christian
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Vishal Trivedi
- Malaria Research Group, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - T R Santhosh Kumar
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Vibin Ramakrishnan
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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5
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Krüger P, Both JH, Linne U, Chirot F, Weitzel KM. Photoelectron Circular Dichroism of Electrosprayed Gramicidin Anions. J Phys Chem Lett 2022; 13:6110-6116. [PMID: 35759344 DOI: 10.1021/acs.jpclett.2c01437] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many sophisticated approaches for analyzing properties of chiral matter have been developed in recent years. But in general, the available chiroptical methods are limited to either solvated or small gaseous molecules. Studying the chirality of large biopolymers in the gas phase, including aspects of the secondary structure, becomes accessible by combining the electrospray ionization technique with chiroptical detection protocols. Here, laser-induced photodetachment from gramicidin anions, a peptide consisting of 15 amino acids has been investigated. The angular distribution of photoelectrons is demonstrated to be sensitive to the substitution of protons by cesium ions, which is accompanied by a conformational change. The photoelectron circular dichroism (PECD) is -0.5% for bare gramicidin, whereas gramicidin with several Cs+ ions attached exhibits a PECD of +0.5%. The results are complemented and supported by ion mobility studies. The presented approach offers the prospect of studying chirality and the secondary structure of various biopolymers.
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Affiliation(s)
- Peter Krüger
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Jon Henrik Both
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Fabien Chirot
- Institut Lumière Matière, UMR5306 Université de Lyon, Université Lyon 1, CNRS, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Karl-Michael Weitzel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
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6
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SUSI HEINO, MICHAEL BYLER D. Fourier Transform Infrared Study of Proteins with Parallel β-Chains. Arch Biochem Biophys 2022; 726:109235. [DOI: 10.1016/j.abb.2022.109235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Kelley EG, Butler PD, Nagao M. Collective dynamics in lipid membranes containing transmembrane peptides. SOFT MATTER 2021; 17:5671-5681. [PMID: 33942045 PMCID: PMC10466476 DOI: 10.1039/d1sm00314c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biological membranes are composed of complex mixtures of lipids and proteins that influence each other's structure and function. The biological activities of many channel-forming peptides and proteins are known to depend on the material properties of the surrounding lipid bilayer. However, less is known about how membrane-spanning channels affect the lipid bilayer properties, and in particular, their collective fluctuation dynamics. Here we use neutron spin echo spectroscopy (NSE) to measure the collective bending and thickness fluctuation dynamics in dimyristoylphosphatidylcholine (di 14 : 0 PC, DMPC) lipid membranes containing two different antimicrobial peptides, alamethicin (Ala) and gramicidin (gD). Ala and gD are both well-studied antimicrobial peptides that form oligomeric membrane-spanning channels with different structures. At low concentrations, the peptides did not have a measurable effect on the average bilayer structure, yet significantly changed the collective membrane dynamics. Despite both peptides forming transmembrane channels, they had opposite effects on the relaxation time of the collective bending fluctuations and associated effective bending modulus, where gD addition stiffened the membrane while Ala addition softened the membrane. Meanwhile, the lowest gD concentrations enhanced the collective thickness fluctuation dynamics, while the higher gD concentrations and all studied Ala concentrations dampened these dynamics. The results highlight the synergy between lipids and proteins in determining the collective membrane dynamics and that not all peptides can be universally treated as rigid bodies when considering their effects on the lipid bilayer fluctuations.
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Affiliation(s)
- Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, USA.
| | - Paul D Butler
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, USA. and Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA and Department of Chemistry, The University of Tennessee Knoxville, TN 37996, USA
| | - Michihiro Nagao
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, USA. and Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA and Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
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8
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Dyett BP, Yu H, Lakic B, De Silva N, Dahdah A, Bao L, Blanch EW, Drummond CJ, Conn CE. Delivery of antimicrobial peptides to model membranes by cubosome nanocarriers. J Colloid Interface Sci 2021; 600:14-22. [PMID: 34000474 DOI: 10.1016/j.jcis.2021.03.161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/21/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022]
Abstract
Antimicrobial peptides (AMPs), which typically disrupt the bacterial wall prompting leakage or lysis of the cell, form a growing contingent in the arsenal against antibiotic resistant bacteria. The effectiveness of AMPs is, however, hampered by their low solubility, general chemical and physical instability, and short half-life in vivo. Lipid nanocarriers such as cubosomes are effective at encapsulating and protecting proteins while simultaneously showing promise in delivery applications. Here, the efficacy of cubosome mediated delivery of AMPs is evaluated by the in-situ surface characterization of model membranes with varying composition. The cubosomes were observed to initially fuse with the membranes, with subsequent membrane disruption observed after approximately 20 - 60 min. The time for the disruption was sensitive to the charge of the cubosome as well as the composition of the bilayer. More physiologically relevant bilayers including lipids with phospho-(1'-rac-glycerol) (PG) or phosphoethanolamine (PE) headgroups were more vulnerable than those of neat phosphocholine (PC). Notably, disruption to the bilayer occurred an order of magnitude faster for encapsulated AMP compared to free AMP.
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Affiliation(s)
- Brendan P Dyett
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Haitao Yu
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Biserka Lakic
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Nilamuni De Silva
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Anthony Dahdah
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Lei Bao
- School of Engineering, STEM College, RMIT University, Victoria, Australia
| | - Ewan W Blanch
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Victoria, Australia.
| | - Charlotte E Conn
- School of Science, STEM College, RMIT University, Victoria, Australia.
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Foreman-Ortiz IU, Liang D, Laudadio ED, Calderin JD, Wu M, Keshri P, Zhang X, Schwartz MP, Hamers RJ, Rotello VM, Murphy CJ, Cui Q, Pedersen JA. Anionic nanoparticle-induced perturbation to phospholipid membranes affects ion channel function. Proc Natl Acad Sci U S A 2020; 117:27854-27861. [PMID: 33106430 PMCID: PMC7668003 DOI: 10.1073/pnas.2004736117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the mechanisms of nanoparticle interaction with cell membranes is essential for designing materials for applications such as bioimaging and drug delivery, as well as for assessing engineered nanomaterial safety. Much attention has focused on nanoparticles that bind strongly to biological membranes or induce membrane damage, leading to adverse impacts on cells. More subtle effects on membrane function mediated via changes in biophysical properties of the phospholipid bilayer have received little study. Here, we combine electrophysiology measurements, infrared spectroscopy, and molecular dynamics simulations to obtain insight into a mode of nanoparticle-mediated modulation of membrane protein function that was previously only hinted at in prior work. Electrophysiology measurements on gramicidin A (gA) ion channels embedded in planar suspended lipid bilayers demonstrate that anionic gold nanoparticles (AuNPs) reduce channel activity and extend channel lifetimes without disrupting membrane integrity, in a manner consistent with changes in membrane mechanical properties. Vibrational spectroscopy indicates that AuNP interaction with the bilayer does not perturb the conformation of membrane-embedded gA. Molecular dynamics simulations reinforce the experimental findings, showing that anionic AuNPs do not directly interact with embedded gA channels but perturb the local properties of lipid bilayers. Our results are most consistent with a mechanism in which anionic AuNPs disrupt ion channel function in an indirect manner by altering the mechanical properties of the surrounding bilayer. Alteration of membrane mechanical properties represents a potentially important mechanism by which nanoparticles induce biological effects, as the function of many embedded membrane proteins depends on phospholipid bilayer biophysical properties.
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Affiliation(s)
| | - Dongyue Liang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, Boston University, Boston, MA 02215
| | | | - Jorge D Calderin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Meng Wu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Xianzhi Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Michael P Schwartz
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Robert J Hamers
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215
- Department of Physics, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Joel A Pedersen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706;
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI 53706
- Department of Civil & Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706
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10
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Xin P, Zhao L, Mao L, Xu L, Hou S, Kong H, Fang H, Zhu H, Jiang T, Chen CP. Effect of charge status on the ion transport and antimicrobial activity of synthetic channels. Chem Commun (Camb) 2020; 56:13796-13799. [DOI: 10.1039/d0cc05730d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge status of channels formed by pillararene–gramicidin hybrid molecules has a significant impact on their trans-membrane transport properties, membrane-association abilities and antimicrobial activities.
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11
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Kuncha SK, Kruparani SP, Sankaranarayanan R. Chiral checkpoints during protein biosynthesis. J Biol Chem 2019; 294:16535-16548. [PMID: 31591268 DOI: 10.1074/jbc.rev119.008166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein chains contain only l-amino acids, with the exception of the achiral glycine, making the chains homochiral. This homochirality is a prerequisite for proper protein folding and, hence, normal cellular function. The importance of d-amino acids as a component of the bacterial cell wall and their roles in neurotransmission in higher eukaryotes are well-established. However, the wider presence and the corresponding physiological roles of these specific amino acid stereoisomers have been appreciated only recently. Therefore, it is expected that enantiomeric fidelity has to be a key component of all of the steps in translation. Cells employ various molecular mechanisms for keeping d-amino acids away from the synthesis of nascent polypeptide chains. The major factors involved in this exclusion are aminoacyl-tRNA synthetases (aaRSs), elongation factor thermo-unstable (EF-Tu), the ribosome, and d-aminoacyl-tRNA deacylase (DTD). aaRS, EF-Tu, and the ribosome act as "chiral checkpoints" by preferentially binding to l-amino acids or l-aminoacyl-tRNAs, thereby excluding d-amino acids. Interestingly, DTD, which is conserved across all life forms, performs "chiral proofreading," as it removes d-amino acids erroneously added to tRNA. Here, we comprehensively review d-amino acids with respect to their occurrence and physiological roles, implications for chiral checkpoints required for translation fidelity, and potential use in synthetic biology.
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Affiliation(s)
- Santosh Kumar Kuncha
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India.,Academy of Scientific and Innovative Research, CSIR-CCMB Campus, Hyderabad, Telangana 500007, India
| | - Shobha P Kruparani
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
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12
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Hazam PK, Akhil R, Jerath G, Saikia J, Ramakrishnan V. Topological effects on the designability and bactericidal potency of antimicrobial peptides. Biophys Chem 2019; 248:1-8. [DOI: 10.1016/j.bpc.2019.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
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13
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14
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Sugár IP, Bonanno AP, Chong PLG. Gramicidin Lateral Distribution in Phospholipid Membranes: Fluorescence Phasor Plots and Statistical Mechanical Model. Int J Mol Sci 2018; 19:E3690. [PMID: 30469389 PMCID: PMC6274966 DOI: 10.3390/ijms19113690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 11/16/2022] Open
Abstract
When using small mole fraction increments to study gramicidins in phospholipid membranes, we found that the phasor dots of intrinsic fluorescence of gramicidin D and gramicidin A in dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar and multilamellar vesicles exhibit a biphasic change with peptide content at 0.143 gramicidin mole fraction. To understand this phenomenon, we developed a statistical mechanical model of gramicidin/DMPC mixtures. Our model assumes a sludge-like mixture of fluid phase and aggregates of rigid clusters. In the fluid phase, gramicidin monomers are randomly distributed. A rigid cluster is formed by a gramicidin dimer and DMPC molecules that are condensed to the dimer, following particular stoichiometries (critical gramicidin mole fractions, Xcr including 0.143). Rigid clusters form aggregates in which gramicidin dimers are regularly distributed, in some cases, even to superlattices. At Xcr, the size of cluster aggregates and regular distributions reach a local maximum. Before a similar model was developed for cholesterol/DMPC mixtures (Sugar and Chong (2012) J. Am. Chem. Soc. 134, 1164⁻1171) and here the similarities and differences are discussed between these two models.
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Affiliation(s)
- István P Sugár
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Alexander P Bonanno
- Department of Medical Genetics and Molecular Biochemistry, The Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
| | - Parkson Lee-Gau Chong
- Department of Medical Genetics and Molecular Biochemistry, The Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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15
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Wu HC, Yoshioka T, Nakagawa K, Shintani T, Tsuru T, Saeki D, Shaikh AR, Matsuyama H. Preparation of Amphotericin B-Ergosterol structures and molecular simulation of water adsorption and diffusion. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2017.09.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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16
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Xin P, Sun Y, Kong H, Wang Y, Tan S, Guo J, Jiang T, Dong W, Chen CP. A unimolecular channel formed by dual helical peptide modified pillar[5]arene: correlating transmembrane transport properties with antimicrobial activity and haemolytic toxicity. Chem Commun (Camb) 2017; 53:11492-11495. [DOI: 10.1039/c7cc06697j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Five unimolecular channels with different lengths are presented. The varying length of these channels has significant impact on their transport properties.
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Affiliation(s)
- Pengyang Xin
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Yonghui Sun
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Huiyuan Kong
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Yaodong Wang
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Si Tan
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Jingjing Guo
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Tao Jiang
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Wenpei Dong
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
| | - Chang-Po Chen
- Henan Engineering Laboratory of Chemical Pharmaceuticals & Biomedical Materials
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
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17
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Patrick JW, Zerfas B, Gao J, Russell DH. Rapid capillary mixing experiments for the analysis of hydrophobic membrane complexes directly from aqueous lipid bilayer solutions. Analyst 2017; 142:310-315. [DOI: 10.1039/c6an02290a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mixing tee-electrospray ionization coupled to ion mobility-mass spectrometry reveals gramicidin A dimer conformer preferences.
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Affiliation(s)
- John W. Patrick
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | | | - Jianmin Gao
- Department of Chemistry
- Boston College
- Chestnut Hill
- USA
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18
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Qiao Y, Tu B, Lu B. Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified PNP equations. J Chem Phys 2014; 140:174102. [DOI: 10.1063/1.4872330] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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19
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Jiang Z, Yang J, Purpura LA, Liu Y, Ripps H, Shen W. Glycinergic feedback enhances synaptic gain in the distal retina. J Physiol 2014; 592:1479-92. [PMID: 24421349 DOI: 10.1113/jphysiol.2013.265785] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Glycine input originates with interplexiform cells, a group of neurons situated within the inner retina that transmit signals centrifugally to the distal retina. The effect on visual function of this novel mechanism is largely unknown. Using gramicidin-perforated patch whole cell recordings, intracellular recordings and specific antibody labelling techniques, we examined the effects of the synaptic connections between glycinergic interplexiform cells, photoreceptors and bipolar cells. To confirm that interplexiform cells make centrifugal feedback on bipolar cell dendrites, we recorded the postsynaptic glycine currents from axon-detached bipolar cells while stimulating presynaptic interplexiform cells. The results show that glycinergic interplexiform cells activate bipolar cell dendrites that express the α3 subunit of the glycine receptor, as well as a subclass of unidentified receptors on photoreceptors. By virtue of their synaptic contacts, glycine centrifugal feedback increases glutamate release from photoreceptors and suppresses the uptake of glutamate by the type 2A excitatory amino acid transporter on photoreceptors. The net effect is a significant increase in synaptic gain between photoreceptors and their second-order neurons.
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Affiliation(s)
- Zheng Jiang
- Department of Biomedical Science, Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA.
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20
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Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2014. [DOI: 10.2478/mlbmb-2014-0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract Gramicidin A is a small and well characterized peptide that forms an ion channel in lipid membranes. An important feature of gramicidin A (gA) pore is that its conductance is affected by the electric charges near the its entrance. This property has led to the application of gramicidin A as a biochemical sensor for monitoring and quantifying a number of chemical and enzymatic reactions. Here, a mathematical model of conductance changes of gramicidin A pores in response to the presence of electrical charges near its entrance, either on membrane surface or attached to gramicidin A itself, is presented. In this numerical simulation, a two dimensional computational domain is set to mimic the structure of a gramicidin A channel in the bilayer surrounded by electrolyte. The transport of ions through the channel is modeled by the Poisson-Nernst-Planck (PNP) equations that are solved by Finite Element Method (FEM). Preliminary numerical simulations of this mathematical model are in qualitative agreement with the experimental results in the literature. In addition to the model and simulations, we also present the analysis of the stability of the solution to the boundary conditions and the convergence of FEM method for the two dimensional PNP equations in our model.
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21
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de Bruyn Ouboter D, Schuster TB, Sigg SJ, Meier WP. Self-assembled peptide beads used as a template for ordered gold nanoparticle superstructures. Colloids Surf B Biointerfaces 2013; 112:542-7. [DOI: 10.1016/j.colsurfb.2013.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 11/25/2022]
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22
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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Glinel K, Thebault P, Humblot V, Pradier CM, Jouenne T. Antibacterial surfaces developed from bio-inspired approaches. Acta Biomater 2012; 8:1670-84. [PMID: 22289644 DOI: 10.1016/j.actbio.2012.01.011] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/20/2011] [Accepted: 01/10/2012] [Indexed: 11/16/2022]
Abstract
Prevention of bacterial adhesion and biofilm formation on the surfaces of materials is a topic of major medical and societal importance. Various synthetic approaches based on immobilization or release of bactericidal substances such as metal derivatives, polyammonium salts and antibiotics were extensively explored to produce antibacterial coatings. Although providing encouraging results, these approaches suffer from the use of active agents which may be associated with side-effects such as cytotoxicity, hypersensibility, inflammatory responses or the progressive alarming phenomenon of antibiotic resistance. In addition to these synthetic approaches, living organisms, e.g. animals and plants, have developed fascinating strategies over millions of years to prevent efficiently the colonization of their surfaces by pathogens. These strategies have been recently mimicked to create a new generation of bio-inspired biofilm-resistant surfaces. In this review, we discuss some of these bio-inspired methods devoted to the development of antibiofilm surfaces. We describe the elaboration of antibacterial coatings based on natural bactericidal substances produced by living organisms such as antimicrobial peptides, bacteriolytic enzymes and essential oils. We discuss also the development of layers mimicking algae surfaces and based on anti-quorum-sensing molecules which affect cell-to-cell communication. Finally, we report on very recent strategies directly inspired from marine animal life and based on surface microstructuring.
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Affiliation(s)
- K Glinel
- Institute of Condensed Matter and Nanosciences (Bio- and Soft Matter), Université catholique de Louvain, Louvain-la-Neuve, Belgium.
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24
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Schuster TB, de Bruyn Ouboter D, Bruns N, Meier W. Exploiting dimerization of purely peptidic amphiphiles to form vesicles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2158-2162. [PMID: 21626692 DOI: 10.1002/smll.201100701] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Thomas B Schuster
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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25
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Schuster TB, Ouboter DDB, Palivan CG, Meier W. From fibers to micelles using point-mutated amphiphilic peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:4578-4584. [PMID: 21413731 DOI: 10.1021/la200443p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biocompatible, self-assembled nanostructures are attracting ever more attention, in particular in aqueous media for biomedical applications. Here, we present the successful, solid-phase peptide synthesis (SPPS) and characterization of short amino acid sequences with amphiphilic character with the aim of gaining insight into their self-assembled, supramolecular structures. The peptide design includes three parts: (a) a charged lysine part, (b) an acetylated lysine part, and (c) a constant hydrophobic rodlike helix, based on gramicidin A (gA). By stepwise replacement of free lysine (K) with acetylated lysine (X) we generated a library of a total of 10 peptides, Ac-X(8)-gA and K(m)X(8-m)-gA (m ranging from 0 to 8). By using point mutations, we adjusted the degree of acetylation (DA) and thus the overall amphiphilicity of the peptides, which led to a change in the secondary structure in the aqueous environment from a β-sheet to an α-helix. This transition generated a significant change in the morphology of the self-assembled structures from fibers to micelles. Two different regions were observed for the conformation of the hydrophilic part of the peptide: one region, a β-sheet-like secondary structure, inducing fiber formation (high DA), the other an α-helical-like secondary structure, generating micelle formation (moderate and low DA). The micellar structures depended on the degree of acetylation, which influenced their critical micelle concentration (cmc). These morphology regions were determined by a combination of circular dichroism, dynamic light scattering, surface tension, and transmission electron microscopy, which allowed us to correlate the generated supramolecular architectures with the fine changes obtained by means of the point mutation strategy.
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Affiliation(s)
- Thomas B Schuster
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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26
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Gill P, Moghadam TT, Ranjbar B. Differential scanning calorimetry techniques: applications in biology and nanoscience. J Biomol Tech 2010; 21:167-93. [PMID: 21119929 PMCID: PMC2977967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This paper reviews the best-known differential scanning calorimetries (DSCs), such as conventional DSC, microelectromechanical systems-DSC, infrared-heated DSC, modulated-temperature DSC, gas flow-modulated DSC, parallel-nano DSC, pressure perturbation calorimetry, self-reference DSC, and high-performance DSC. Also, we describe here the most extensive applications of DSC in biology and nanoscience.
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Affiliation(s)
| | | | - Bijan Ranjbar
- Departments of Nanobiotechnology and
- Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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27
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Proposed Mechanism for H(II) Phase Induction by Gramicidin in Model Membranes and Its Relation to Channel Formation. Biophys J 2010; 53:111-7. [PMID: 19431714 DOI: 10.1016/s0006-3495(88)83072-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A model is proposed for the molecular mechanism of H(II) phase induction by gramicidin in model membranes. The model describes the sequence of events that occurs upon hydration of a mixed lipid/gramicidin film, relating them to gramicidin channel formation and to relevant literature on gramicidin and lipid structure.
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28
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Cornell BA, Separovic F, Baldassi AJ, Smith R. Conformation and orientation of gramicidin a in oriented phospholipid bilayers measured by solid state carbon-13 NMR. Biophys J 2010; 53:67-76. [PMID: 19431717 DOI: 10.1016/s0006-3495(88)83066-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Three analogues of the helical ionophore gramicidin A have been synthesized with (13)C-labeled carbonyls ((13)C=O) incorporated at either Gly(2), Ala(3), or Val(7). A fourth compound incorporated (13)C at both the carbonyl and alpha-carbon of Gly(2) within the same molecule. These labels were studied using solid-state, proton-enhanced, (13)C nuclear magnetic resonance (NMR) in hydrated dispersions of dimyristoylphosphatidylcholine (DMPC)-gramicidin A. The dispersions were aligned on glass coverslips whose orientation to the magnetic field could be varied through 180 degrees . The orientation dependence of the NMR spectrum was used to obtain an accurate measurement of the (13)C chemical shift anisotropy (CSA), and in the case of the fourth compound, the (13)C-(13)C dipolar coupling constant. From the measured CSA and estimates of the orientation of the (13)C shielding tensor, we are able to determine the direction of the (13)C=O bonds and to compare these with the predictions of the various reported models for the configuration of gramicidin A in phospholipid bilayers. Our results are consistent with the left-handed pipi(6.3) (LD) single-stranded helix (Urry, D. W., J. T. Walker, and T. L. Trapane. 1982. J. Membr. Biol. 69:225-231). The right-handed pipi(6.3) (LD) single-stranded helix observed for gramicidin A in sodium dodecyl sulfate micelles (Arseniev, A. S., I. L. Barsukov, V. F. Bystrov, A. L. Loize, and Yu A. Ovchinnikov. 1985. FEBS (Fed. Eur. Biochem. Soc.) Lett. 186:168-174) yields a poorer fit to the data. However, the width of the carbonyl resonances suggests a distribution of molecular geometries possibly resulting from a spread in the helix pitch and handedness. Double-stranded helices and beta sheet structures are excluded. In dispersions in which the lipid is in the L(alpha) phase, the gramicidin A undergoes rapid reorientation about an axis which is centered on the normal to the plane of the coverslips. When the supporting lipid is in the L(beta') phase the helices are rigid on the timescale of (13)C-NMR. The configuration of gramicidin A is unaltered by L(alpha)-L(beta') phase transition of the bilayer lipid.
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29
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Schneggenburger PE, Beerlink A, Worbs B, Salditt T, Diederichsen U. A Novel Heavy-Atom Label for Side-Specific Peptide Iodination: Synthesis, Membrane Incorporation and X-ray Reflectivity. Chemphyschem 2009; 10:1567-76. [DOI: 10.1002/cphc.200900241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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30
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Schwartz E, Koepf M, Kitto HJ, Espelt M, Nebot-Carda VJ, De Gelder R, Nolte RJM, Cornelissen JJLM, Rowan AE. Water soluble azido polyisocyanopeptides as functional β-sheet mimics. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/pola.23477] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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LELIEVRE D, TRUDELLE Y, HEITZ F, SPACH G. Synthesis and characterization of retro gramicidin A-dAla-gramicidin A, a 31-residue-long gramicidin analogue. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1989.tb00698.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Forney MW, Janosi L, Kosztin I. Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:051913. [PMID: 19113161 DOI: 10.1103/physreve.78.051913] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Indexed: 05/27/2023]
Abstract
Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin, J. Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by different methods. Our approach appears to be about one order of magnitude faster than the other PMF calculation methods and, in addition, it also provides the position-dependent diffusion coefficient along the RC. Thus, the obtained PMF and diffusion coefficient can be used in an overdamped Brownian model to estimate important characteristics of the studied systems, e.g., the mean folding time of the stretched deca-alanine and the mean diffusion time of the potassium ion through gramicidin A.
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Affiliation(s)
- Michael W Forney
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, USA
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33
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Mehnert T, Routh A, Judge PJ, Lam YH, Fischer D, Watts A, Fischer WB. Biophysical characterization of Vpu from HIV-1 suggests a channel-pore dualism. Proteins 2008; 70:1488-97. [PMID: 17910056 PMCID: PMC7167847 DOI: 10.1002/prot.21642] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Vpu from HIV‐1 is an 81 amino acid type I integral membrane protein which consists of a cytoplasmic and a transmembrane (TM) domain. The TM domain is known to alter membrane permeability for ions and substrates when inserted into artificial membranes. Peptides corresponding to the TM domain of Vpu (Vpu1‐32) and mutant peptides (Vpu1‐32‐W23L, Vpu1‐32‐R31V, Vpu1‐32‐S24L) have been synthesized and reconstituted into artificial lipid bilayers. All peptides show channel activity with a main conductance level of around 20 pS. Vpu1‐32‐W23L has a considerable flickering pattern in the recordings and longer open times than Vpu1‐32. Whilst recordings for Vpu1‐32‐R31V are almost indistinguishable from those of the WT peptide, recordings for Vpu1‐32‐S24L do not exhibit any noticeable channel activity. Recordings of WT peptide and Vpu1‐32‐W23L indicate Michaelis–Menten behavior when the salt concentration is increased. Both peptide channels follow the Eisenman series I, indicative for a weak ion channel with almost pore like characteristics. Proteins 2008. © 2007 Wiley‐Liss, Inc.
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Affiliation(s)
- T. Mehnert
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - A. Routh
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - P. J. Judge
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - Y. H. Lam
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - D. Fischer
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - A. Watts
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - W. B. Fischer
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
- Bionanotechnology Interdisciplinary Research Collaboration, Clarendon Laboratory, Department of Physics, Oxford University, Oxford OX1 3PU, United Kingdom
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Mayer M, Semetey V, Gitlin I, Yang J, Whitesides GM. Using ion channel-forming peptides to quantify protein-ligand interactions. J Am Chem Soc 2008; 130:1453-65. [PMID: 18179217 DOI: 10.1021/ja077555f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper proposes a method for sensing affinity interactions by triggering disruption of self-assembly of ion channel-forming peptides in planar lipid bilayers. It shows that the binding of a derivative of alamethicin carrying a covalently attached sulfonamide ligand to carbonic anhydrase II (CA II) resulted in the inhibition of ion channel conductance through the bilayer. We propose that the binding of the bulky CA II protein (MW approximately 30 kD) to the ion channel-forming peptides (MW approximately 2.5 kD) either reduced the tendency of these peptides to self-assemble into a pore or extracted them from the bilayer altogether. In both outcomes, the interactions between the protein and the ligand lead to a disruption of self-assembled pores. Addition of a competitive inhibitor, 4-carboxybenzenesulfonamide, to the solution released CA II from the alamethicin-sulfonamide conjugate and restored the current flow across the bilayer by allowing reassembly of the ion channels in the bilayer. Time-averaged recordings of the current over discrete time intervals made it possible to quantify this monovalent ligand binding interaction. This method gave a dissociation constant of approximately 2 microM for the binding of CA II to alamethicin-sulfonamide in the bilayer recording chamber: this value is consistent with a value obtained independently with CA II and a related sulfonamide derivative by isothermal titration calorimetry.
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Affiliation(s)
- Michael Mayer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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Boucher J, Trudel E, Méthot M, Desmeules P, Salesse C. Organization, structure and activity of proteins in monolayers. Colloids Surf B Biointerfaces 2007; 58:73-90. [PMID: 17509839 DOI: 10.1016/j.colsurfb.2007.03.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 03/24/2007] [Accepted: 03/26/2007] [Indexed: 12/17/2022]
Abstract
Many different processes take place at the cell membrane interface. Indeed, for instance, ligands bind membrane proteins which in turn activate peripheral membrane proteins, some of which are enzymes whose action is also located at the membrane interface. Native cell membranes are difficult to use to gain information on the activity of individual proteins at the membrane interface because of the large number of different proteins involved in membranous processes. Model membrane systems, such as monolayers at the air-water interface, have thus been extensively used during the last 50 years to reconstitute proteins and to gain information on their organization, structure and activity in membranes. In the present paper, we review the recent work we have performed with membrane and peripheral proteins as well as enzymes in monolayers at the air-water interface. We show that the structure and orientation of gramicidin has been determined by combining different methods. Furthermore, we demonstrate that the secondary structure of rhodopsin and bacteriorhodopsin is indistinguishable from that in native membranes when appropriate conditions are used. We also show that the kinetics and extent of monolayer binding of myristoylated recoverin is much faster than that of the nonmyristoylated form and that this binding is highly favored by the presence polyunsaturated phospholipids. Moreover, we show that the use of fragments of RPE65 allow determine which region of this protein is most likely involved in membrane binding. Monomolecular films were also used to further understand the hydrolysis of organized phospholipids by phospholipases A2 and C.
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Affiliation(s)
- Julie Boucher
- Unité de recherche en ophtalmologie, Centre de Recherche du Centre Hospitalier Universitaire de Québec and Département d'Ophtalmologie, Faculté de médecine, Université Laval, Québec, Que. G1V 4G2, Canada
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Percec V, Smidrkal J, Peterca M, Mitchell CM, Nummelin S, Dulcey AE, Sienkowska MJ, Heiney PA. Self-assembly of hybrid dendrons with complex primary structure into functional helical pores. Chemistry 2007; 13:3989-4007. [PMID: 17304597 DOI: 10.1002/chem.200601582] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The synthesis of three libraries of self-assembling hybrid dendrons containing a primary structure based on the sequence (4-3,4-3,5)12G2-CO(2)CH(3) generated from benzyl ether, biphenyl-4-methyl ether, and AB(2) repeat units constructed from (AB)(y)--AB(2) combinations of benzyl ethers, is reported. The structural and retrostructural analysis of their supramolecular dendrimers facilitated the discovery of new architectural principles that lead to the assembly of functional helical pores. The self-assembly of an example of hybrid dendron containing -H, -CO(2)CH(3), -CH(2)OH, -COOH, -COOK, -CONH(2), -CONHCH(3), -CO(2)(CH(2))(2)OCH(3), -(R) and -(S)-CONHCH(CH(3))C(2)H(5) as X-groups at the apex demonstrated that these self-assembling dendrons provide the simplest strategy for the design and synthesis of porous columns containing a diversity of hydrophilic and hydrophobic functional groups in the inner part of the pore. The results reported here expand the scope and limitations of dendrons available for the self-assembly of functional pores that previously were generated mostly from dendritic dipeptides, to simpler architectures based on hybrid dendrons.
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Affiliation(s)
- Virgil Percec
- Roy and Diana Vagelos Laboratories, Department of Chemistry, Laboratory for Research on the Structure of Matter, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
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Percec V, Dulcey AE, Peterca M, Adelman P, Samant R, Balagurusamy VSK, Heiney PA. Helical Pores Self-Assembled from Homochiral Dendritic Dipeptides Based on l-Tyr and Nonpolar α-Amino Acids. J Am Chem Soc 2007; 129:5992-6002. [PMID: 17429976 DOI: 10.1021/ja071088k] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of dendritic dipeptides (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe where X = Gly, L-Val, L-Leu, L-Ile, L-Phe, and L-Pro is reported. Their self-assembly in bulk and in solution and the structural and retrostructural analysis of their periodic assemblies were compared to those of the previously reported and currently reinvestigated dendritic dipeptides with X = L-Ala. All dendritic dipeptides containing as X nonpolar alpha-amino acids self-assemble into helical porous columns. The substituent of X programs the structure of the helical pore and the resulting periodic array, in spite of the fact that its molar mass represents only between 0.05 and 4.77% from the molar mass of the dendritic dipeptide. In addition to the various 2-D columnar lattices, the dendritic dipeptides based on L-Ala, L-Leu, and L-Phe self-organize into 3-D hexagonal columnar crystals while those based on L-Val and L-Ile into an unknown columnar crystal. The principles via which the aliphatic and aromatic substituents of X program the structure of the helical pores indicate synthetic pathways to helical pores with bioinspired functions based on artificial nonpolar alpha-amino acids.
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Affiliation(s)
- Virgil Percec
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.
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Krummel AT, Zanni MT. Interpreting DNA Vibrational Circular Dichroism Spectra Using a Coupling Model from Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2006; 110:24720-7. [PMID: 17134235 DOI: 10.1021/jp063227a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.
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Affiliation(s)
- Amber T Krummel
- Department of Chemistry, University of Wisconsin at Madison, Madison, Wisconsin 53706-1396, USA
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Percec V. Bioinspired supramolecular liquid crystals. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2006; 364:2709-19. [PMID: 16973484 DOI: 10.1098/rsta.2006.1848] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A brief account on the historical events leading to the discovery of self-assembling dendrons that generate self-organizable supramolecular dendrimers, or supramolecular polymers, and self-organizable dendronized polymers is provided. These building blocks were accessed by an accelerated design strategy that involves structural and retrostructural analysis of periodic and quasi-periodic assemblies. This design strategy mediated the discovery of porous helical supramolecular structures that self-assembled from dendritic dipeptides. Helical porous columns are the closest mimics of biologically related structures, such as tobacco mosaic virus coat, porous transmembrane proteins, porous pathogens and antibiotics. It is expected that this concept will allow one to investigate the structural origin of functions in synthetic supramolecular materials.
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Affiliation(s)
- Virgil Percec
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
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Peterca M, Percec V, Dulcey AE, Nummelin S, Korey S, Ilies M, Heiney PA. Self-Assembly, Structural, and Retrostructural Analysis of Dendritic Dipeptide Pores Undergoing Reversible Circular to Elliptical Shape Change. J Am Chem Soc 2006; 128:6713-20. [PMID: 16704274 DOI: 10.1021/ja0611902] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of dendritic dipeptides (4-3,4-3,5-4)12G2-CH(2)-Boc-L-Tyr-L-Ala-OMe and (4-3, 4-3,5-4)12G2-CH(2)-Boc-D-Tyr-D-Ala-OMe is described. These dendritic dipeptides self-assemble into porous elliptical and circular columns that in turn self-organize into centered rectangular columnar and hexagonal columnar periodic arrays. The transition from porous elliptical to porous circular columns is mediated in a reversible or irreversible way by the thermal history of the sample. A method to determine the dimensions of hollow elliptical and circular columns by the reconstruction of the small-angle powder X-ray diffractograms of the centered rectangular or hexagonal columnar lattices was elaborated. This technique together with wide-angle X-ray experiments performed on aligned fibers provided access to the structural and retrostructural analysis of elliptical supramolecular pores. This procedure is general and can be adapted for the determination of the dimensions of pores of any columnar shape.
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Affiliation(s)
- Mihai Peterca
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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41
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Percec V, Dulcey AE, Peterca M, Ilies M, Nummelin S, Sienkowska MJ, Heiney PA. Principles of self-assembly of helical pores from dendritic dipeptides. Proc Natl Acad Sci U S A 2006; 103:2518-23. [PMID: 16469843 PMCID: PMC1413792 DOI: 10.1073/pnas.0509676103] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Indexed: 11/18/2022] Open
Abstract
The self-assembly of the dendritic dipeptides (4-3,4-3,5)nG2-CH2-Boc-L-Tyr-L-Ala-OMe and their achiral dendritic alcohol (4-3,4-3,5)nG2-CH2OH precursors, both with n = 1-16, where n represents the number of methylenic units in the alkyl groups of the dendron, are reported. All chiral dendritic dipeptides and achiral dendritic alcohols self-assemble into helical porous columns that are stable in both solution and solid state. The pore diameter (D(pore)) of the columns self-assembled from dendritic dipeptides is approximately 10 A larger than that of structures assembled from dendritic alcohols. The increase of the D(pore) at the transition from dendritic alcohol to dendritic dipeptide is accompanied by a decreased solid angle of the building block. This trend is in agreement with previous pore size-solid angle dependences observed with different protective groups of the dipeptide and primary structures of the dendron. However, within the series of dendritic alcohols and dendritic dipeptides with various n, the D(pore) increases when the solid angle increases. The results of these investigations together with those of previous studies on the role of dipeptide stereochemistry and protective groups on this self-assembly process provide the molecular principles required to program the construction of supramolecular helical pores with diameter controlled at the A level from a single dendritic dipeptide architecture. These principles are expected to be valid for libraries of dendritic dipeptides based on dendrons and dipeptides with various primary structures.
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Affiliation(s)
- Virgil Percec
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
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Percec V, Dulcey AE, Peterca M, Ilies M, Sienkowska MJ, Heiney PA. Programming the Internal Structure and Stability of Helical Pores Self-Assembled from Dendritic Dipeptides via the Protective Groups of the Peptide. J Am Chem Soc 2005; 127:17902-9. [PMID: 16351122 DOI: 10.1021/ja056313h] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of dendritic dipeptides (4-3,4-3,5)12G2-CH2-X-L-Tyr-L-Ala-OMe with X = Boc, Moc, and Ac; their self-assembly in bulk and in solution; and the structural and retrostructural analysis of their supramolecular helical porous assemblies are reported. The dimensions, structure, internal order, thermal stability of the supramolecular helical pores, and conformations of the dendron and supramolecular dendrimer are programmed by the nature of the protective groups of the dipeptide. The ability of the protective groups to program the structure of the helical pore reveals the simplest design strategy that complements the more complex strategies based on the architecture of the dendron, the stereochemistry, and the structure of the dipeptide.
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Affiliation(s)
- Virgil Percec
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.
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Gallagher GJ, Hong M, Thompson LK. Solid-State NMR Spin Diffusion for Measurement of Membrane-Bound Peptide Structure: Gramicidin A. Biochemistry 2004; 43:7899-906. [PMID: 15196034 DOI: 10.1021/bi0356101] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently developed solid-state NMR method for measurement of depths in membrane systems is applied to gramicidin A, a membrane-bound peptide of known structure, to investigate the potential of this method. (15)N-detected, (1)H spin diffusion experiments demonstrate the resolution of the technique by measuring the 4-5 A depth differences between three (15)N-labeled backbone sites (Trp13, Val7, Gly2) in gramicidin A. We also show that (13)C-detected, (1)H spin diffusion experiments on unlabeled gramicidin A are sufficient to discriminate between the end-to-end dimer and double-helix structures of gramicidin A. Thus, spin diffusion solid-state NMR experiments can provide a simple approach, which does not require labeled samples, for testing structural models of membrane-bound peptides.
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Affiliation(s)
- Greg J Gallagher
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003-9336, USA
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Kim JM, Patwardhan A, Bott A, Thompson DH. Preparation and electrochemical behavior of gramicidin-bipolar lipid monolayer membranes supported on gold electrodes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2003; 1617:10-21. [PMID: 14637015 DOI: 10.1016/j.bbamem.2003.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gramicidin-containing synthetic bolalipid membranes comprised of 2,2'-di-O-decyl-3,3'-O-1,20-eicosanyl-bis-rac-glycero-1,1'-diphosphocholine (C20BAS) have been synthesized and supported on gold electrodes. Supported membranes were prepared by first depositing a partial bolalipid layer on the electrode using a thioctic acid-modified bolalipid (1'-O-omega-thioctamidetetraethylene glycol-2,2'-di-O-decyl-3,3'-di-O-1,20-eicosanyl-bis-rac-glycero-1-phosphate, SSC20BAS) as an anchoring group, followed by a vesicle fusion step using either pure C20BAS or gramicidin-containing C20BAS (C20BAS-GA) vesicles. The latter configuration was designed to immobilize single, continuously-on channels of gramicidin in the C20BAS membrane. Vesicle deposition to form supported bolalipid monolayer membranes was monitored by impedance spectroscopy and cyclic voltammetry. Impedances were observed to increase with vesicle deposition time. Pretreatment of the impedance electrode with SSC20BAS accelerated the supported monolayer membrane deposition rate. Impedances decreased in a gramicidin concentration-dependent manner when gramicidin was incorporated into the C20BAS membrane. These supported bolalipid membranes are also surprisingly inert to organic solvent exposure (CH(3)CH(2)OH;CH(2)Cl(2)), suggesting that they may serve as robust host matrices for integral membrane protein-based sensors.
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Affiliation(s)
- J-M Kim
- Janus Biosystems, 3000 Kent Avenue, West Lafayette, IN 47906, USA
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45
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Abstract
Gramicidin is an antibiotic peptide that can be incorporated into the monolayers of cell membranes. Dimerization through hydrogen bonding between gramicidin monomers in opposing leaflets of the membrane results in the formation of an iontophoretic channel. Surrounding phospholipids influence the gating properties of this channel. Conversely, gramicidin incorporation has been shown to affect the structure of spontaneously formed lipid assemblies. Using small-angle x-ray diffraction and model systems composed of phospholipids and gramicidin, the effects produced by gramicidin on lipid layers were measured. These measurements explore how peptides are able to modulate the spontaneous curvature properties of phospholipid assemblies. The reverse hexagonal, H(II), phase formed by dioleoylphosphatidylethanolamine (DOPE) monolayers decreased in lattice dimension with increasing incorporation of gramicidin. This indicated that gramicidin itself was adding negative curvature to the lipid layers. In this system, gramicidin was measured to have an apparent intrinsic radius of curvature, R0pgram, of -7.1 A. The addition of up to 4 mol% gramicidin in DOPE did not result in the monolayers becoming stiffer, as measured by the monolayer bending moduli. Dioleoylphosphatidylcholine (DOPC) alone forms the lamellar (L(alpha)) phase when hydrated, but undergoes a transition into the reverse hexagonal (H(II)) phase when mixed with gramicidin. The lattice dimension decreases systematically with increased gramicidin content. Again, this indicated that gramicidin was adding negative curvature to the lipid monolayers but the mixture behaved structurally much less consistently than DOPE/gramicidin. Only at 12 mol% gramicidin in dioleoylphosphatidylcholine could an apparent radius of intrinsic curvature of gramicidin (R0pgram) be estimated as -7.4 A. This mixture formed monolayers that were very resistant to bending, with a measured bending modulus of 115 kT.
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Affiliation(s)
- J A Szule
- Biological Sciences, Brock University, St. Catharines, Ontario, Canada, L2S 3A1
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Lavoie H, Blaudez D, Vaknin D, Desbat B, Ocko BM, Salesse C. Spectroscopic [correction of eSpectroscopic] and structural properties of valine gramicidin A in monolayers at the air-water interface. Biophys J 2002; 83:3558-69. [PMID: 12496123 PMCID: PMC1302431 DOI: 10.1016/s0006-3495(02)75356-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Monomolecular films of valine gramicidin A (VGA) were investigated in situ at the air-water interface by x-ray reflectivity and x-ray grazing incidence diffraction as well as polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). These techniques were combined to obtain information on the secondary structure and the orientation of VGA and to characterize the shoulder observed in its pi-A isotherm. The thickness of the film was obtained by x-ray reflectivity, and the secondary structure of VGA was monitored using the frequency position of the amide I band. The PM-IRRAS spectra were compared with the simulated ones to identify the conformation adopted by VGA in monolayer. At large molecular area, VGA shows a disordered secondary structure, whereas at smaller molecular areas, VGA adopts an anti-parallel double-strand intertwined beta(5.6) helical conformation with 30 degrees orientation with respect to the normal with a thickness of 25 A. The interface between bulk water and the VGA monolayer was investigated by x-ray reflectivity as well as by comparing the experimental and the simulated PM-IRRAS spectra on D(2)O and H(2)O, which suggested the presence of oriented water molecules between the bulk and the monolayer.
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Affiliation(s)
- Hugo Lavoie
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec G9A 5H7, Canada
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Abstract
Volatile anesthetic agent, 1-chloro-1,2,2-trifluorocyclobutane (F3), was found to alter gramicidin A channel function by enhancing Na(+) transport (. Biophys. J. 77:739-746). Whether this functional change is associated with structural alternation is evaluated by circular dichroism and nuclear magnetic resonance spectroscopy. The circular dichroism and nuclear magnetic resonance results indicate that at low millimolar concentrations, 1-chloro-1,2,2-trifluorocyclobutane causes minimal changes in gramicidin A channel structure in sodium dodecyl sulfate micelles. All hydrogen bonds between channel backbones are well maintained in the presence of 1-chloro-1,2,2-trifluorocyclobutane, and the channel structure is stable. The finding supports the notion that low affinity drugs such as volatile anesthetics and alcohols can cause significant changes in protein function without necessarily producing associated changes in protein structure. To understand the molecular mechanism of general anesthesia, it is important to recognize that in addition to structural changes, other protein properties, including dynamic characteristics of channel motions, may also be of functional significance.
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Affiliation(s)
- Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261 USA.
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Fahsel S, Pospiech EM, Zein M, Hazlet TL, Gratton E, Winter R. Modulation of concentration fluctuations in phase-separated lipid membranes by polypeptide insertion. Biophys J 2002; 83:334-44. [PMID: 12080124 PMCID: PMC1302151 DOI: 10.1016/s0006-3495(02)75173-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The lateral membrane organization and phase behavior of the binary lipid mixture DMPC (1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine) - DSPC (1,2-distearoyl-sn-glycero-3-phosphatidylcholine) without and with incorporated gramicidin D (GD) as a model biomembrane polypeptide was studied by small-angle neutron scattering, Fourier-transform infrared spectroscopy, and by two-photon excitation fluorescence microscopy on giant unilamellar vesicles. The small-angle neutron scattering method allows the detection of concentration fluctuations in the range from 1 to 200 nm. Fluorescence microscopy was used for direct visualization of the lateral lipid organization and domain shapes on a micrometer length scale including information of the lipid phase state. In the fluid-gel coexistence region of the pure binary lipid system, large-scale concentration fluctuations appear. Infrared spectral parameters were used to determine the peptide conformation adopted in the different lipid phases. The data show that the structure of the temperature-dependent lipid phases is significantly altered by the insertion of 2 to 5 mol% GD. At temperatures corresponding to the gel-fluid phase coexistence region the concentration fluctuations drastically decrease, and we observe domains in the giant unilamellar vesicles, which mainly disappear by the incorporation of 2 to 5 mol% GD. Further, the lipid matrix has the ability to modulate the conformation of the inserted polypeptide. The balance between double-helical and helical dimer structures of GD depends on the phospholipid chain length and phase state. A large hydrophobic mismatch, such as in gel phase one-component DSPC bilayers, leads to an increase in population of double-helical structures. Using an effective molecular sorting mechanism, a large hydrophobic mismatch can be avoided in the DMPC-DSPC lipid mixture, which leads to significant changes in the heterogeneous lipid structure and in polypeptide conformation.
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Affiliation(s)
- S Fahsel
- University of Dortmund, Department of Chemistry, Physical Chemistry I, D-44221 Dortmund, Germany
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Mondal S, Ghosh S. Gramicidin A and its complexes with Cs+ and Tl+ ions in organic solvents. A study by steady state and time resolved emission spectroscopy. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2001; 60:12-24. [PMID: 11386676 DOI: 10.1016/s1011-1344(00)00138-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Gramicidin A (gr A), a linear pentadecapeptide containing four trp residues has been studied using steady state and time resolved fluorescence (at 298 K) and phosphorescence (at 77 K) in methanol (CH3OH), ethanol (C2H5OH), dimethyl sulfoxide (DMSO), 1,4-dioxane, 2-methyl tetrahydrofuran (2-MeTHF), ethanol/benzene (C2H5OH/C6H6) mixed solvent. Similar studies have also been carried out in CH3OH containing monovalent cations K+, Cs+, Tl+ and divalent cation Ca2+. Lambda(max) of fluorescence is found to be a good signature of the different forms having double helical structure [dh (1) to dh (4)] (J. Struct. Biol. 121 (1998) 123-141). Steady state and time resolved quenching studies of gr A by KI in CH3OH and DMSO and life time of the emitting singlet states of gr A support that gr A exists as a mixture of different forms of double helical (dh) structure [dh (1) to dh (4)] in CH3OH and as a random coil structure in DMSO. This study further indicates that emitting trp residue in DMSO is better shielded than that in CH3OH. Phosphorescence spectra of gr A at 77 K in CH3OH glass suggests that gr A retains a particular conformation dh (3) in this matrix. The phosphorescence spectra of gr A [conformation dh (4)] in 2-MeTHF at 77 K is further red shifted indicating that among all the dh forms, dh (4) has the emitting trp residue in most hydrophobic environment. The hydrophobicity of the emitting tryptophan environment is thus found to be in the order: dh (1)<dh (3)<dh (4). Since 2-MeTHF forms a clear glass at low temperature, it is thus possible to study the side chain arrangement of gr A dh (4) as a function of temperature. The phosphorescence spectra in different alcohol glassy matrix are in conformity with the observation of different side chain arrangement of gr A as one changes the polarity of alcohol. Steady state and time resolved quenching studies of gr A using Cs+ ion in CH3OH at 298 K clearly demonstrate the two binding sites for the metal ions and provide the value of equilibrium constant of the 'non-emitting' complex of gr A with Cs+ ion in the ground state. The observation of distinct red shift of the (0,0) band of the phosphorescence spectra of the complexes of gr A with K+, Cs+ and Tl+ ions at 77 K compared to that in CH3OH glass confirms the metal ion induced change of conformation in dh (3). The result also suggests that the emitting trp residues in the complexes are in somewhat more hydrophobic environment compared with that in the free gr A in CH3OH glass. The triplet state life time of these complexes indicate that the heavy metal ions Cs+ and Tl+ are within a Van der Waal's distance of emitting trp residue in gr A in CH3OH glass at 77 K so that they are capable of inducing increased spin-orbit coupling due to a heavy atom effect.
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Affiliation(s)
- S Mondal
- Department of Chemistry, Presidency College, Calcutta, India
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50
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Hao YH, Zhang GJ, Chen JW. The structure and function of gramicidin A embedded in interdigitated bilayer. Chem Phys Lipids 2000; 104:207-15. [PMID: 10669312 DOI: 10.1016/s0009-3084(99)00126-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The effects of phase transition from normal to interdigitated lipid bilayer on the function and structure of membrane proteins were studied using linear gramicidin (gramicidin A) as a model. Interdigitated bilayer structure of dipalmitoylphosphatidylglycerol (DPPG) liposomes that was induced by atropine could not be changed notably by intercalating of gramicidin. The K+ transportation of gramicidin in both normal and interdigitated bilayer was assayed by measuring the membrane potential. Results showed that gramicidin in interdigitated bilayer exhibited lower transport capability. Intrinsic fluorescence spectrum of gramicidin in interdigitated bilayer blue-shifted 2.8 nm from the spectrum in normal bilayer, which means that interdigitation provides a more hydrophobic environment for gramicidin. Circular dichroism measurement results indicated that the conformation of gramicidin in interdigitated bilayer is not the typical beta6.3 helix as in the normal bilayer. The results suggested that the interdigitated lipid bilayer might largely affect the structure and function of membrane proteins.
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Affiliation(s)
- Y H Hao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, People's Republic of China
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