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Ma T, Li W, Tang Z, Sun X, Li L, Liu Z, Zhang G. ARIP: A Tool for Precise Interatomic Contact Area and Volume Calculation in Proteins. Int J Mol Sci 2024; 25:5176. [PMID: 38791216 PMCID: PMC11120937 DOI: 10.3390/ijms25105176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The interplay patterns of amino acid residues are pivotal in determining the tertiary structure and flexibility of proteins, which in turn are intricately linked to their functionality and interactions with other molecules. Here, we introduce ARIP, a novel tool designed to identify contact residues within proteins. ARIP employs a modified version of the dr_sasa algorithm and an atomic overlap weighted algorithm to directly calculate the contact area and volume between atoms based on their van der Waals radius. It also allows for the selection of solvent radii, recognizing that not every atom in proteins can interact with water molecules. The solvent parameters were derived from the analysis of approximately 5000 protein and nucleic acid structures with water molecules determined using X-ray crystallography. One advantage of the modified algorithm is its capability to analyze multiple models within a single PDB file, making it suitable for molecular dynamic capture. The contact volume is symmetrically distributed between the interacting atoms, providing more informative results than contact area for the analysis of intra- and intermolecular interactions and the development of scoring functions. Furthermore, ARIP has been applied to four distinct cases: capturing key residue-residue contacts in NMR structures of P4HB, protein-drug binding of CYP17A1, protein-DNA binding of SPI1, and molecular dynamic simulations of BRD4.
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Affiliation(s)
- Tao Ma
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (T.M.); (W.L.); (Z.T.); (X.S.); (L.L.)
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Wenhui Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (T.M.); (W.L.); (Z.T.); (X.S.); (L.L.)
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Zhiping Tang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (T.M.); (W.L.); (Z.T.); (X.S.); (L.L.)
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Xiangwei Sun
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (T.M.); (W.L.); (Z.T.); (X.S.); (L.L.)
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Lijuan Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (T.M.); (W.L.); (Z.T.); (X.S.); (L.L.)
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (T.M.); (W.L.); (Z.T.); (X.S.); (L.L.)
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
| | - Gaihua Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (T.M.); (W.L.); (Z.T.); (X.S.); (L.L.)
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China
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Characterization and Differential Cytotoxicity of Gramicidin Nanoparticles Combined with Cationic Polymer or Lipid Bilayer. Pharmaceutics 2022; 14:pharmaceutics14102053. [PMID: 36297488 PMCID: PMC9610547 DOI: 10.3390/pharmaceutics14102053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
Gramicidin (Gr) nanoparticles (NPs) and poly (diallyl dimethyl ammonium) chloride (PDDA) water dispersions were characterized and evaluated against Gram-positive and Gram-negative bacteria and fungus. Dynamic light scattering for sizing, zeta potential analysis, polydispersity, and colloidal stability over time characterized Gr NPs/PDDA dispersions, and plating and colony-forming units counting determined their microbicidal activity. Cell viabilities of Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans in the presence of the combinations were reduced by 6, 7, and 7 logs, respectively, at 10 μM Gr/10 μg·mL−1 PDDA, 0.5 μM Gr/0. 5μg·mL−1 PDDA, and 0.5 μM Gr/0.5 μg·mL−1 PDDA, respectively. In comparison to individual Gr doses, the combinations reduced doses by half (S. aureus) and a quarter (C. albicans); in comparison to individual PDDA doses, the combinations reduced doses by 6 times (P. aeruginosa) and 10 times (C. albicans). Gr in supported or free cationic lipid bilayers reduced Gr activity against S. aureus due to reduced Gr access to the pathogen. Facile Gr NPs/PDDA disassembly favored access of each agent to the pathogen: PDDA suctioned the pathogen cell wall facilitating Gr insertion in the pathogen cell membrane. Gr NPs/PDDA differential cytotoxicity suggested the possibility of novel systemic uses for the combination.
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Garnett JA, Atherton J. Structure Determination of Microtubules and Pili: Past, Present, and Future Directions. Front Mol Biosci 2022; 8:830304. [PMID: 35096976 PMCID: PMC8795688 DOI: 10.3389/fmolb.2021.830304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 11/30/2022] Open
Abstract
Historically proteins that form highly polymeric and filamentous assemblies have been notoriously difficult to study using high resolution structural techniques. This has been due to several factors that include structural heterogeneity, their large molecular mass, and available yields. However, over the past decade we are now seeing a major shift towards atomic resolution insight and the study of more complex heterogenous samples and in situ/ex vivo examination of multi-subunit complexes. Although supported by developments in solid state nuclear magnetic resonance spectroscopy (ssNMR) and computational approaches, this has primarily been due to advances in cryogenic electron microscopy (cryo-EM). The study of eukaryotic microtubules and bacterial pili are good examples, and in this review, we will give an overview of the technical innovations that have enabled this transition and highlight the advancements that have been made for these two systems. Looking to the future we will also describe systems that remain difficult to study and where further technical breakthroughs are required.
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Affiliation(s)
- James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Joseph Atherton
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
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Jäger M, Koslowski T, Wolf S. Predicting Ion Channel Conductance via Dissipation-Corrected Targeted Molecular Dynamics and Langevin Equation Simulations. J Chem Theory Comput 2021; 18:494-502. [PMID: 34928150 DOI: 10.1021/acs.jctc.1c00426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, here we applied dissipation-corrected targeted molecular dynamics in combination with Langevin equation simulations to potassium diffusion through the gramicidin A channel as a test system. Performing a nonequilibrium principal component analysis on backbone dihedral angles, we find coupled protein-ion dynamics to occur during ion transfer. The dissipation-corrected free energy profiles correspond well to predictions from other biased simulation methods. The incorporation of an external electric field in Langevin simulations enables the prediction of macroscopic observables in the form of I-V characteristics.
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Affiliation(s)
- Miriam Jäger
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - Thorsten Koslowski
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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Ngo V, Li H, MacKerell AD, Allen TW, Roux B, Noskov S. Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel. J Chem Theory Comput 2021; 17:1726-1741. [PMID: 33539082 DOI: 10.1021/acs.jctc.0c00968] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the progress in modeling complex molecular systems of ever-increasing complexity, a quantitatively accurate computational treatment of ion permeation through narrow membrane channels remains challenging. An important factor to reach this goal is induced electronic polarization, which is likely to impact the permeation rate of small ions through narrow molecular pores. In this work, we extended the recently developed polarizable force field based on the classical Drude oscillators to assess the role of induced polarization effects on the energetics of sodium and potassium ion transport across the gramicidin A (gA) ion channel. The inclusion of induced polarization lowers barriers present in 1D potential of mean force (PMF) for cation permeation by ∼50% compared to those obtained with the additive force field. Conductance properties calculated with 1D PMFs from Drude simulations are in better agreement with experimental results. Polarization of single-file water molecules and protein atoms forming the narrow pore has a direct impact on the free-energy barriers and cation-specific solid-state NMR chemical shifts. Sensitivity analysis indicates that small changes to water-channel interactions can alter the free energy barrier for ion permeation. These results, illustrating polarization effects present in the complex electrostatic environment of the gA channel, have broad implications for revising proposed mechanisms of ion permeation and selectivity in a variety of ion channels.
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Affiliation(s)
- Van Ngo
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N1N4, Canada.,Center for Nonlinear Studies, Los Alamos National Lab, Los Alamos, New Mexico 87544, United States
| | - Hui Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander D MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N1N4, Canada
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Sun D, He S, Bennett WFD, Bilodeau CL, Andersen OS, Lightstone FC, Ingólfsson HI. Atomistic Characterization of Gramicidin Channel Formation. J Chem Theory Comput 2021; 17:7-12. [PMID: 33378617 PMCID: PMC7808174 DOI: 10.1021/acs.jctc.0c00989] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 01/09/2023]
Abstract
We investigated gramicidin A (gA) subunit dimerization in lipid bilayers using microsecond-long replica-exchange umbrella sampling simulations, millisecond-long unbiased molecular dynamics simulations, and machine learning. Our simulations led to a dimer structure that is indistinguishable from the experimentally determined gA channel structures, with the two gA subunits joined by six hydrogen bonds (6HB). The simulations also uncovered two additional dimer structures, with different gA-gA stacking orientations that were stabilized by four or two hydrogen bonds (4HB or 2HB). When examining the temporal evolution of the dimerization, we found that two bilayer-inserted gA subunits can form the 6HB dimer directly, with no discernible intermediate states, as well as through paths that involve the 2HB and 4HB dimers.
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Affiliation(s)
- Delin Sun
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Stewart He
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - W. F. Drew Bennett
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Camille L. Bilodeau
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
- Howard
P. Isermann Department of Chemical and Biological Engineering and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Olaf S. Andersen
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10065, United States
| | - Felice C. Lightstone
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
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Abstract
Despite the well-characterized structural symmetry of the dimeric transmembrane antibiotic gramicidin A, we show that the symmetry is broken by selective hydrogen bonding between eight waters comprising a transmembrane water wire and a specific subset of the 26 pore-lining carbonyl oxygens of the gramicidin A channel. The 17O NMR spectroscopic resolution of the carbonyl resonances from the two subunits required the use of a world record high field magnet (35.2 T; 1,500 MHz for 1H). Uniquely, this result documented the millisecond timescale stability of the water wire orientation within the gramicidin A pore that had been reported to have only subnanosecond stability. These 17O spectroscopic results portend wide applications in molecular biophysics and beyond. Water wires are critical for the functioning of many membrane proteins, as in channels that conduct water, protons, and other ions. Here, in liquid crystalline lipid bilayers under symmetric environmental conditions, the selective hydrogen bonding interactions between eight waters comprising a water wire and a subset of 26 carbonyl oxygens lining the antiparallel dimeric gramicidin A channel are characterized by 17O NMR spectroscopy at 35.2 T (or 1,500 MHz for 1H) and computational studies. While backbone 15N spectra clearly indicate structural symmetry between the two subunits, single site 17O labels of the pore-lining carbonyls report two resonances, implying a break in dimer symmetry caused by the selective interactions with the water wire. The 17O shifts document selective water hydrogen bonding with carbonyl oxygens that are stable on the millisecond timescale. Such interactions are supported by density functional theory calculations on snapshots taken from molecular dynamics simulations. Water hydrogen bonding in the pore is restricted to just three simultaneous interactions, unlike bulk water environs. The stability of the water wire orientation and its electric dipole leads to opposite charge-dipole interactions for K+ ions bound at the two ends of the pore, thereby providing a simple explanation for an ∼20-fold difference in K+ affinity between two binding sites that are ∼24 Å apart. The 17O NMR spectroscopy reported here represents a breakthrough in high field NMR technology that will have applications throughout molecular biophysics, because of the acute sensitivity of the 17O nucleus to its chemical environment.
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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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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Na S, Steinbrecher T, Koslowski T. Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits. J Comput Chem 2018; 39:2539-2550. [DOI: 10.1002/jcc.25615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/27/2018] [Accepted: 09/03/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Sehee Na
- Fakultät für Chemie und Pharmazie, Institut für Physikalische ChemieUniversität Freiburg Albertstraße 23a, 79104, Freiburg im Breisgau Germany
| | | | - Thorsten Koslowski
- Fakultät für Chemie und Pharmazie, Institut für Physikalische ChemieUniversität Freiburg Albertstraße 23a, 79104, Freiburg im Breisgau Germany
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Identification of Effective Dimeric Gramicidin-D Peptide as Antimicrobial Therapeutics over Drug Resistance: In-Silico Approach. Interdiscip Sci 2018; 11:575-583. [PMID: 30182355 DOI: 10.1007/s12539-018-0304-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/25/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Discovering and developing the antimicrobial peptides are recently focused on pharmaceutical firm, since they serve as complementary to antibiotics in prevailing over drug resistance by eliciting the disruption of microbial membrane. Still, there are lots of challenges to bring up the structurally stable and functionally efficient antimicrobial peptides. It is well known that gramicidin D is the prominent antimicrobial peptide that exists as g-AB, g-BC, and g-AC. This study analyzes the structural stability and the functional activity of hetero-dimeric double-stranded gramicidin-D peptides, thereby demonstrating its potent antimicrobial activity against antibiotic-resistant micro-organisms. To investigate the structural stability and functionality of gramicidin D, we performed static and dynamic analysis. Initially, we observed a maximum number of intermolecular interactions and membrane penetration in g-AB as compared to g-BC and g-AC. To substantiate further, the geometrical and thermodynamic parameters revealed the retention of maximum stability in g-AB than g-AC and g-BC. Thus, the conformational free energy and the binding free energy showed the variation among gramicidin-D peptides for the prediction of increased stability and functionality. In conclusion, g-AB peptide has definitely demonstrated adequate structural stability and functionality and this work will need to be considered in peptide-based drug discovery.
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Azar E, Constantin D, Warschawski DE. The effect of gramicidin inclusions on the local order of membrane components. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:44. [PMID: 29582214 PMCID: PMC7088371 DOI: 10.1140/epje/i2018-11644-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
We study the local effect of the antimicrobial peptide Gramicidin A on bilayers composed of lipids or surfactants using nuclear magnetic resonance spectroscopy and wide-angle X-ray scattering, techniques that probe the orientational and positional order of the alkyl chains, respectively. The two types of order vary with temperature and peptide concentration in complex ways which depend on the membrane composition, highlighting the subtlety of the interaction between inclusions and the host bilayer. The amplitude of the variation is relatively low, indicating that the macroscopic constants used to describe the elasticity of the bilayer are unlikely to change with the addition of peptide.
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Affiliation(s)
- Elise Azar
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Doru Constantin
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France.
| | - Dror E Warschawski
- UMR 7099, CNRS-Université Paris Diderot, Institut de Biologie Physico-Chimique, Paris, France
- Département de Chimie, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, H3C 3P8, Montreal, Canada
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Reddy DN, Singh S, Ho CMW, Patel J, Schlesinger P, Rodgers S, Doctor A, Marshall GR. Design, synthesis, and biological evaluation of stable β 6.3-Helices: Discovery of non-hemolytic antibacterial peptides. Eur J Med Chem 2018; 149:193-210. [PMID: 29501941 DOI: 10.1016/j.ejmech.2018.02.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 01/26/2018] [Accepted: 02/16/2018] [Indexed: 11/25/2022]
Abstract
Gramicidin A, a topical antibiotic made from alternating L and D amino acids, is characterized by its wide central pore; upon insertion into membranes, it forms channels that disrupts ion gradients. We present helical peptidomimetics with this characteristic wide central pore that have been designed to mimic gramicidin A channels. Mimetics were designed using molecular modeling focused on oligomers of heterochiral dipeptides of proline analogs, in particular azaproline (AzPro). Molecular Dynamics simulations in water confirmed the stability of the designed helices. A sixteen-residue Formyl-(AzPro-Pro)8-NHCH2CH2OH helix was synthesized as well as a full thirty-two residue Cbz-(AzPro-Pro)16-OtBu channels. No liposomal lysis activity was observed suggesting lack of channel formation, possibly due to inappropriate hydrogen-bonding interactions in the membrane. These peptidomimetics also did not hemolyze red blood cells, unlike gramicidin A.
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Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Sukrit Singh
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chris M W Ho
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janki Patel
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paul Schlesinger
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephen Rodgers
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allan Doctor
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Garland R Marshall
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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15
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Li J, Richards MR, Kitova EN, Klassen JS. Delivering Transmembrane Peptide Complexes to the Gas Phase Using Nanodiscs and Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2054-2065. [PMID: 28681358 DOI: 10.1007/s13361-017-1735-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/25/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)2+ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å2 (conformation 1, C1), 708 Å2 (C2), and 737 Å2 (C3). The addition of NH4CH3CO2 produced (2GA + 2Na)2+ and (2GA + H + Na)2+ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)2+, (2GA + 2NH4)2+, and (2GA + H + NH4)2+ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH4)2+ dimer ions; the DMPC NDs produced both (2GA + 2H)2+ and (2GA + 2NH4)2+ dimer ions. While the Ω of (2GA + 2H)2+ is similar to that of C2, the (2GA + 2NH4)2+ ions from NDs adopt a more compact structure, with a Ω of 656 Å2. It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase. Graphical Abstract ᅟ.
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Affiliation(s)
- Jun Li
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada
| | - Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada.
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16
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Niroomand H, Mukherjee D, Khomami B. Tuning the photoexcitation response of cyanobacterial Photosystem I via reconstitution into Proteoliposomes. Sci Rep 2017; 7:2492. [PMID: 28559589 PMCID: PMC5449388 DOI: 10.1038/s41598-017-02746-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/19/2017] [Indexed: 12/25/2022] Open
Abstract
The role of natural thylakoid membrane housing of Photosystem I (PSI), the transmembrane photosynthetic protein, in its robust photoactivated charge separation with near unity quantum efficiency is not fundamentally understood. To this end, incorporation of suitable protein scaffolds for PSI incorporation is of great scientific and device manufacturing interest. Areas of interest include solid state bioelectronics, and photoelectrochemical devices that require bio-abio interfaces that do not compromise the photoactivity and photostability of PSI. Therefore, the surfactant-induced membrane solubilization of a negatively charged phospholipid (DPhPG) with the motivation of creating biomimetic reconstructs of PSI reconstitution in DPhPG liposomes is studied. Specifically, a simple yet elegant method for incorporation of PSI trimeric complexes into DPhPG bilayer membranes that mimic the natural thylakoid membrane housing of PSI is introduced. The efficacy of this method is demonstrated via absorption and fluorescence spectroscopy measurements as well as direct visualization using atomic force microscopy. This study provides direct evidence that PSI confinements in synthetic lipid scaffolds can be used for tuning the photoexcitation characteristics of PSI. Hence, it paves the way for development of fundamental understanding of microenvironment alterations on photochemical response of light activated membrane proteins.
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Affiliation(s)
- Hanieh Niroomand
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA.,Department of Chemical and Biomolecular Engineering, Knoxville, USA
| | - Dibyendu Mukherjee
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
| | - Bamin Khomami
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
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17
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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18
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Benigni P, Marin R, Molano-Arevalo JC, Garabedian A, Wolff JJ, Ridgeway ME, Park MA, Fernandez-Lima F. Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2016; 19:95-104. [PMID: 27818614 PMCID: PMC5091298 DOI: 10.1007/s12127-016-0201-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 01/02/2023]
Abstract
In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible and in good agreement with previously reported CCS values using other IMS analyzers (<5% difference). The main challenges for the analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~ 150 kDa) using TIMS-MS.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Rebecca Marin
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Alyssa Garabedian
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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19
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Setiadi J, Kuyucak S. Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A. MEMBRANES 2016; 6:membranes6010020. [PMID: 26999229 PMCID: PMC4812426 DOI: 10.3390/membranes6010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
Membrane proteins are embedded in a lipid bilayer and interact with the lipid molecules in subtle ways. This can be studied experimentally by examining the effect of different lipid bilayers on the function of membrane proteins. Understanding the causes of the functional effects of lipids is difficult to dissect experimentally but more amenable to a computational approach. Here we perform molecular dynamics simulations and free energy calculations to study the effect of two lipid types (POPC and NODS) on the conductance of the gramicidin A (gA) channel. A larger energy barrier is found for the K⁺ potential of mean force in gA embedded in POPC compared to that in NODS, which is consistent with the enhanced experimental conductance of cations in gA embedded in NODS. Further analysis of the contributions to the potential energy of K⁺ reveals that gA and water molecules in gA make similar contributions in both bilayers but there are significant differences between the two bilayers when the lipid molecules and interfacial waters are considered. It is shown that the stronger dipole moments of the POPC head groups create a thicker layer of interfacial waters with better orientation, which ultimately is responsible for the larger energy barrier in the K⁺ PMF in POPC.
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Affiliation(s)
- Jeffry Setiadi
- School of Physics, University of Sydney, Sydney NSW 2006, Australia.
| | - Serdar Kuyucak
- School of Physics, University of Sydney, Sydney NSW 2006, Australia.
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20
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Tanphaichitr N, Srakaew N, Alonzi R, Kiattiburut W, Kongmanas K, Zhi R, Li W, Baker M, Wang G, Hickling D. Potential Use of Antimicrobial Peptides as Vaginal Spermicides/Microbicides. Pharmaceuticals (Basel) 2016; 9:E13. [PMID: 26978373 PMCID: PMC4812377 DOI: 10.3390/ph9010013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/11/2022] Open
Abstract
The concurrent increases in global population and sexually transmitted infection (STI) demand a search for agents with dual spermicidal and microbicidal properties for topical vaginal application. Previous attempts to develop the surfactant spermicide, nonoxynol-9 (N-9), into a vaginal microbicide were unsuccessful largely due to its inefficiency to kill microbes. Furthermore, N-9 causes damage to the vaginal epithelium, thus accelerating microbes to enter the women's body. For this reason, antimicrobial peptides (AMPs), naturally secreted by all forms of life as part of innate immunity, deserve evaluation for their potential spermicidal effects. To date, twelve spermicidal AMPs have been described including LL-37, magainin 2 and nisin A. Human cathelicidin LL-37 is the most promising spermicidal AMP to be further developed for vaginal use for the following reasons. First, it is a human AMP naturally produced in the vagina after intercourse. Second, LL-37 exerts microbicidal effects to numerous microbes including those that cause STI. Third, its cytotoxicity is selective to sperm and not to the female reproductive tract. Furthermore, the spermicidal effects of LL-37 have been demonstrated in vivo in mice. Therefore, the availability of LL-37 as a vaginal spermicide/microbicide will empower women for self-protection against unwanted pregnancies and STI.
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Affiliation(s)
- Nongnuj Tanphaichitr
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Biochemistry, Microbiology, Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, ON, Canada.
| | - Nopparat Srakaew
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Rhea Alonzi
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Biochemistry, Microbiology, Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, ON, Canada.
| | - Wongsakorn Kiattiburut
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
| | - Kessiri Kongmanas
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Division of Dengue Hemorrhagic Fever Research Unit, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | - Ruina Zhi
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Key Laboratory of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, and School of Public Health, Fudan University, Shanghai 200032, China.
| | - Weihua Li
- Key Laboratory of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, and School of Public Health, Fudan University, Shanghai 200032, China.
| | - Mark Baker
- Reproductive Proteomics, Department of Science and Information technology, University of Newcastle, Callaghan Drive, Newcastle, NSW 2308 Australia.
| | - Guanshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA.
| | - Duane Hickling
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Division of Urology, Department of Surgery, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1Y 4E9, ON, Canada.
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21
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Zerfas BL, Joo Y, Gao J. Gramicidin A Mutants with Antibiotic Activity against Both Gram-Positive and Gram-Negative Bacteria. ChemMedChem 2016; 11:629-36. [PMID: 26918268 DOI: 10.1002/cmdc.201500602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 01/01/2023]
Abstract
Antimicrobial peptides (AMPs) have shown potential as alternatives to traditional antibiotics for fighting infections caused by antibiotic-resistant bacteria. One promising example of this is gramicidin A (gA). In its wild-type sequence, gA is active by permeating the plasma membrane of Gram-positive bacteria. However, gA is toxic to human red blood cells at similar concentrations to those required for it to exert its antimicrobial effects. Installing cationic side chains into gA has been shown to lower its hemolytic activity while maintaining the antimicrobial potency. In this study, we present the synthesis and the antibiotic activity of a new series of gA mutants that display cationic side chains. Specifically, by synthesizing alkylated lysine derivatives through reductive amination, we were able to create a broad selection of structures with varied activities towards Staphylococcus aureus and methicillin-resistant S. aureus (MRSA). Importantly, some of the new mutants were observed to have an unprecedented activity towards important Gram-negative pathogens, including Escherichia coli, Klebsiella pneumoniae and Psuedomonas aeruginosa.
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Affiliation(s)
- Breanna L Zerfas
- Department of Chemistry, Merkert Chemisty Center, Boston College, 2609 Beacon St., Chestnut Hill, MA, 02461, USA
| | - Yechaan Joo
- Department of Chemistry, Merkert Chemisty Center, Boston College, 2609 Beacon St., Chestnut Hill, MA, 02461, USA
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemisty Center, Boston College, 2609 Beacon St., Chestnut Hill, MA, 02461, USA.
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22
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23
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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24
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Wylie BJ, Dzikovski BG, Pawsey S, Caporini M, Rosay M, Freed JH, McDermott AE. Dynamic nuclear polarization of membrane proteins: covalently bound spin-labels at protein-protein interfaces. JOURNAL OF BIOMOLECULAR NMR 2015; 61:361-7. [PMID: 25828256 PMCID: PMC4819240 DOI: 10.1007/s10858-015-9919-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 03/05/2015] [Indexed: 05/07/2023]
Abstract
We demonstrate that dynamic nuclear polarization of membrane proteins in lipid bilayers may be achieved using a novel polarizing agent: pairs of spin labels covalently bound to a protein of interest interacting at an intermolecular interaction surface. For gramicidin A, nitroxide tags attached to the N-terminal intermolecular interface region become proximal only when bimolecular channels forms in the membrane. We obtained signal enhancements of sixfold for the dimeric protein. The enhancement effect was comparable to that of a doubly tagged sample of gramicidin C, with intramolecular spin pairs. This approach could be a powerful and selective means for signal enhancement in membrane proteins, and for recognizing intermolecular interfaces.
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Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
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25
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Patrick JW, Gamez RC, Russell DH. Elucidation of Conformer Preferences for a Hydrophobic Antimicrobial Peptide by Vesicle Capture-Freeze-Drying: A Preparatory Method Coupled to Ion Mobility-Mass Spectrometry. Anal Chem 2014; 87:578-83. [DOI: 10.1021/ac503163g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- John W. Patrick
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Roberto C. Gamez
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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26
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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27
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Cross TA, Ekanayake V, Paulino J, Wright A. Solid state NMR: The essential technology for helical membrane protein structural characterization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 239:100-9. [PMID: 24412099 PMCID: PMC3957465 DOI: 10.1016/j.jmr.2013.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.
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Affiliation(s)
- Timothy A Cross
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
| | - Vindana Ekanayake
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Joana Paulino
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Anna Wright
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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28
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Ion channel stability of Gramicidin A in lipid bilayers: Effect of hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:328-38. [DOI: 10.1016/j.bbamem.2013.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/20/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022]
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Wang F, Qin L, Wong P, Gao J. Effects of lysine methylation on gramicidin A channel folding in lipid membranes. Biopolymers 2013; 100:656-61. [DOI: 10.1002/bip.22268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/08/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Fang Wang
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
| | - Luoheng Qin
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
| | - Patrick Wong
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
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30
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Dreyer J, Zhang C, Ippoliti E, Carloni P. Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer. J Chem Theory Comput 2013; 9:3826-31. [PMID: 26584128 DOI: 10.1021/ct400374n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The membrane potential at the water/phospholipid interfaces may play a key role for proton conduction of gramicidin A (gA). Here we address this issue by Density Functional Theory-based molecular dynamics and metadynamics simulations. The calculations, performed on gA embedded in a solvated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model membrane environment (about 2,000 atoms), indicate that (i) the membrane dipole potential rises at the channel mouth by ∼0.4 V. A similar value has been measured for gA embedded in a DMPC monolayer; (ii) the calculated free energy barrier is located at the channel entrance, consistent with experiments comparing gA proton conduction in different bilayers. The electronic structures of the proton ligands (water molecules and peptide units) are similar to those in the bulk solvent. Based on these results, we suggest an important role of the membrane dipole potential for the free energy barrier of proton permeation of gA. This may provide a rationale for the large increase in the rate of proton conduction under application of a transmembrane voltage, as observed experimentally. Our calculations might suggest also a role for proton desolvation for the permeation process. This role has already emerged from EVB calculations on gA embedded in a model membrane.
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Affiliation(s)
- Jens Dreyer
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Chao Zhang
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emiliano Ippoliti
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
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31
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Szymański W, Beierle JM, Kistemaker HAV, Velema WA, Feringa BL. Reversible Photocontrol of Biological Systems by the Incorporation of Molecular Photoswitches. Chem Rev 2013; 113:6114-78. [DOI: 10.1021/cr300179f] [Citation(s) in RCA: 847] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wiktor Szymański
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - John M. Beierle
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Hans A. V. Kistemaker
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Willem A. Velema
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Ben L. Feringa
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
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32
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Jensen MØ, Jogini V, Eastwood MP, Shaw DE. Atomic-level simulation of current-voltage relationships in single-file ion channels. ACTA ACUST UNITED AC 2013; 141:619-32. [PMID: 23589581 PMCID: PMC3639580 DOI: 10.1085/jgp.201210820] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The difficulty in characterizing ion conduction through membrane channels at the level of individual permeation events has made it challenging to elucidate the mechanistic principles underpinning this fundamental physiological process. Using long, all-atom simulations enabled by special-purpose hardware, we studied K+ permeation across the KV1.2/2.1 voltage-gated potassium channel. At experimentally accessible voltages, which include the physiological range, the simulated permeation rate was substantially lower than the experimentally observed rate. The current–voltage relationship was also nonlinear but became linear at much higher voltages. We observed permeation consistent with a “knock-on” mechanism at all voltages. At high voltages, the permeation rate was in accordance with our previously reported KV1.2 pore-only simulations, after the simulated voltages from the previous study were recalculated using the correct method, new insight into which is provided here. Including the voltage-sensing domains in the simulated channel brought the linear current–voltage regime closer to the experimentally accessible voltages. The simulated permeation rate, however, still underestimated the experimental rate, because formation of the knock-on intermediate occurred too infrequently. Reducing the interaction strength between the ion and the selectivity filter did not increase conductance. In complementary simulations of gramicidin A, similar changes in interaction strength did increase the observed permeation rate. Permeation nevertheless remained substantially below the experimental value, largely because of infrequent ion recruitment into the pore lumen. Despite the need to apply large voltages to simulate the permeation process, the apparent voltage insensitivity of the permeation mechanism suggests that the direct simulation of permeation at the single-ion level can provide fundamental physiological insight into ion channel function. Notably, our simulations suggest that the knock-on permeation mechanisms in KV1.2 and KcsA may be different.
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33
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Abstract
The number of membrane protein structures in the Protein Data Bank is becoming significant and growing. Here, the transmembrane domain structures of the helical membrane proteins are evaluated to assess the influences of the membrane mimetic environments. Toward this goal, many of the biophysical properties of membranes are discussed and contrasted with those of the membrane mimetics commonly used for structure determination. Although the mimetic environments can perturb the protein structures to an extent that potentially gives rise to misinterpretation of functional mechanisms, there are also many structures that have a native-like appearance. From this assessment, an initial set of guidelines is proposed for distinguishing native-like from nonnative-like membrane protein structures. With experimental techniques for validation and computational methods for refinement and quality assessment and enhancement, there are good prospects for achieving native-like structures for these very important proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Institute of Molecular Biophysic, Florida State University, Tallahassee, USA
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34
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Rankenberg JM, Vostrikov VV, DuVall CD, Greathouse DV, Koeppe RE, Grant CV, Opella SJ. Proline kink angle distributions for GWALP23 in lipid bilayers of different thicknesses. Biochemistry 2012; 51:3554-64. [PMID: 22489564 DOI: 10.1021/bi300281k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By using selected (2)H and (15)N labels, we have examined the influence of a central proline residue on the properties of a defined peptide that spans lipid bilayer membranes by solid-state nuclear magnetic resonance (NMR) spectroscopy. For this purpose, GWALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-ethanolamide) is a suitable model peptide that employs, for the purpose of interfacial anchoring, only one tryptophan residue on either end of a central α-helical core sequence. Because of its systematic behavior in lipid bilayer membranes of differing thicknesses [Vostrikov, V. V., et al. (2010) J. Biol. Chem. 285, 31723-31730], we utilize GWALP23 as a well-characterized framework for introducing guest residues within a transmembrane sequence; for example, a central proline yields acetyl-GGALW(5)LALALAP(12)ALALALW(19)LAGA-ethanolamide. We synthesized GWALP23-P12 with specifically placed (2)H and (15)N labels for solid-state NMR spectroscopy and examined the peptide orientation and segmental tilt in oriented DMPC lipid bilayer membranes using combined (2)H GALA and (15)N-(1)H high-resolution separated local field methods. In DMPC bilayer membranes, the peptide segments N-terminal and C-terminal to the proline are both tilted substantially with respect to the bilayer normal, by ~34 ± 5° and 29 ± 5°, respectively. While the tilt increases for both segments when proline is present, the range and extent of the individual segment motions are comparable to or smaller than those of the entire GWALP23 peptide in bilayer membranes. In DMPC, the proline induces a kink of ~30 ± 5°, with an apparent helix unwinding or "swivel" angle of ~70°. In DLPC and DOPC, on the basis of (2)H NMR data only, the kink angle and swivel angle probability distributions overlap those of DMPC, yet the most probable kink angle appears to be somewhat smaller than in DMPC. As has been described for GWALP23 itself, the C-terminal helix ends before Ala(21) in the phospholipids DMPC and DLPC yet remains intact through Ala(21) in DOPC. The dynamics of bilayer-incorporated, membrane-spanning GWALP23 and GWALP23-P12 are less extensive than those observed for WALP family peptides that have more than two interfacial Trp residues.
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Affiliation(s)
- Johanna M Rankenberg
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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35
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Gleason NJ, Vostrikov VV, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Tyrosine replacing tryptophan as an anchor in GWALP peptides. Biochemistry 2012; 51:2044-53. [PMID: 22364236 DOI: 10.1021/bi201732e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic model peptides have proven useful for examining fundamental peptide-lipid interactions. A frequently employed peptide design consists of a hydrophobic core of Leu-Ala residues with polar or aromatic amino acids flanking each side at the interfacial positions, which serve to "anchor" a specific transmembrane orientation. For example, WALP family peptides (acetyl-GWW(LA)(n)LWWA-[ethanol]amide), anchored by four Trp residues, have received particular attention in both experimental and theoretical studies. A recent modification proved successful in reducing the number of Trp anchors to only one near each end of the peptide. The resulting GWALP23 (acetyl-GGALW(5)(LA)(6)LW(19)LAGA-[ethanol]amide) displays reduced dynamics and greater sensitivity to lipid-peptide hydrophobic mismatch than traditional WALP peptides. We have further modified GWALP23 to incorporate a single tyrosine, replacing W(5) with Y(5). The resulting peptide, Y(5)GWALP23 (acetyl-GGALY(5)(LA)(6)LW(19)LAGA-amide), has a single Trp residue that is sensitive to fluorescence experiments. By incorporating specific (2)H and (15)N labels in the core sequence of Y(5)GWALP23, we were able to use solid-state NMR spectroscopy to examine the peptide orientation in hydrated lipid bilayer membranes. The peptide orients well in membranes and gives well-defined (2)H quadrupolar splittings and (15)N/(1)H dipolar couplings throughout the core helical sequence between the aromatic residues. The substitution of Y(5) for W(5) has remarkably little influence on the tilt or dynamics of GWALP23 in bilayer membranes of the phospholipids DOPC, DMPC, or DLPC. A second analogue of the peptide with one Trp and two Tyr anchors, Y(4,5)GWALP23, is generally less responsive to the bilayer thickness and exhibits lower apparent tilt angles with evidence of more extensive dynamics. In general, the peptide behavior with multiple Tyr anchors appears to be quite similar to the situation when multiple Trp anchors are present, as in the original WALP series of model peptides.
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Affiliation(s)
- Nicholas J Gleason
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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36
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Chen L, Gao YQ, Russell DH. How Alkali Metal Ion Binding Alters the Conformation Preferences of Gramicidin A: A Molecular Dynamics and Ion Mobility Study. J Phys Chem A 2011; 116:689-96. [DOI: 10.1021/jp209430q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liuxi Chen
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yi Qin Gao
- Beijing National Lab for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China 100871
| | - David H. Russell
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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37
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Gopinath T, Mote KR, Veglia G. Proton evolved local field solid-state nuclear magnetic resonance using Hadamard encoding: theory and application to membrane proteins. J Chem Phys 2011; 135:074503. [PMID: 21861572 DOI: 10.1063/1.3622604] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
NMR anisotropic parameters such as dipolar couplings and chemical shifts are central to structure and orientation determination of aligned membrane proteins and liquid crystals. Among the separated local field experiments, the proton evolved local field (PELF) scheme is particularly suitable to measure dynamically averaged dipolar couplings and give information on local molecular motions. However, the PELF experiment requires the acquisition of several 2D datasets at different mixing times to optimize the sensitivity for the complete range of dipolar couplings of the resonances in the spectrum. Here, we propose a new PELF experiment that takes the advantage of the Hadamard encoding (HE) to obtain higher sensitivity for a broad range of dipolar couplings using a single 2D experiment. The HE scheme is obtained by selecting the spin operators with phase switching of hard pulses. This approach enables one to detect four spin operators, simultaneously, which can be processed into two 2D spectra covering a broader range of dipolar couplings. The advantages of the new approach are illustrated for a U-(15)N NAL single crystal and the U-(15)N labeled single-pass membrane protein sarcolipin reconstituted in oriented lipid bicelles. The HE-PELF scheme can be implemented in other multidimensional experiments to speed up the characterization of the structure and dynamics of oriented membrane proteins and liquid crystalline samples.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota 55455, USA
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38
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Winder PL, Pomponi SA, Wright AE. Natural products from the Lithistida: a review of the literature since 2000. Mar Drugs 2011; 9:2643-2682. [PMID: 22363244 PMCID: PMC3280575 DOI: 10.3390/md9122643] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/09/2011] [Accepted: 12/06/2011] [Indexed: 12/20/2022] Open
Abstract
Lithistid sponges are known to produce a diverse array of compounds ranging from polyketides, cyclic and linear peptides, alkaloids, pigments, lipids, and sterols. A majority of these structurally complex compounds have very potent and interesting biological activities. It has been a decade since a thorough review has been published that summarizes the literature on the natural products reported from this amazing sponge order. This review provides an update on the current taxonomic classification of the Lithistida, describes structures and biological activities of 131 new natural products, and discusses highlights from the total syntheses of 16 compounds from marine sponges of the Order Lithistida providing a compilation of the literature since the last review published in 2002.
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Affiliation(s)
- Priscilla L Winder
- Harbor Branch Oceanographic Institution at Florida Atlantic University, Center for Marine Biomedical and Biotechnology Research, 5600 US 1 North, Fort Pierce, FL 34946, USA
| | - Shirley A Pomponi
- Harbor Branch Oceanographic Institution at Florida Atlantic University, Center for Marine Biomedical and Biotechnology Research, 5600 US 1 North, Fort Pierce, FL 34946, USA
| | - Amy E Wright
- Harbor Branch Oceanographic Institution at Florida Atlantic University, Center for Marine Biomedical and Biotechnology Research, 5600 US 1 North, Fort Pierce, FL 34946, USA
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39
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Wang F, Qin L, Pace CJ, Wong P, Malonis R, Gao J. Solubilized Gramicidin A as Potential Systemic Antibiotics. Chembiochem 2011; 13:51-5. [DOI: 10.1002/cbic.201100671] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Indexed: 11/07/2022]
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40
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Wanasundara SN, Krishnamurthy V, Chung SH. Free energy calculations of gramicidin dimer dissociation. J Phys Chem B 2011; 115:13765-70. [PMID: 21988458 DOI: 10.1021/jp2084583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations, combined with umbrella sampling, is used to study how gramicidin A (gA) dimers dissociate in the lipid bilayer. The potential of mean force and intermolecular potential energy are computed as functions of the distance between center of masses of the two gA monomers in two directions of separation: parallel to the bilayer surface and parallel to the membrane normal. Results from this study show that the dissociation of gA dimers occurs via lateral displacement of gA monomers followed by tilting of dimers with respect to the lipid bilayer normal. It is found that the dissociation energy of gA dimers in the dimyristoylphosphatidylcholine bilayer is 14 kcal mol(-1) (~22 kT), which is approximately equal to the energy of breaking six intermolecular hydrogen bonds that stabilize the gA channel dimer.
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Affiliation(s)
- Surajith N Wanasundara
- Department of Electrical and Computer Engineering, University of British Columbia, 5500 - 2332 Main Mall, Vancouver, BC, V6T 1Z4 Canada
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41
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Vostrikov VV, Gu H, Ingólfsson HI, Hinton JF, Andersen OS, Roux B, Koeppe RE. Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments. J Phys Chem B 2011; 115:7427-32. [PMID: 21574558 PMCID: PMC3114435 DOI: 10.1021/jp200906y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motional properties are important for understanding protein function and are accessible to NMR relaxation measurements. The goal of this study is to investigate the internal dynamics occurring in gramicidin A (gA) channels in order to provide benchmark experimental data for comparison with the results of molecular dynamics simulations. We therefore synthesized several (15)N isotope-enriched gA samples, covering all backbone residues as well as the Trp indole side chains for NMR relaxation experiments. On the basis of the (15)N NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we determined T(1), T(2), and heteronuclear NOE values for backbone and indole (15)NH groups. The results indicate that the SDS-incorporated gA channel is a constrained structure without an especially "floppy" region. The NMR observables, particularly those for backbone groups, are predicted well by the molecular dynamics simulations in the accompanying article (DOI 10.1021/jp200904d ).
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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42
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Höfer N, Aragão D, Lyons JA, Caffrey M. Membrane Protein Crystallization in Lipidic Mesophases. Hosting lipid affects on the crystallization and structure of a transmembrane peptide. CRYSTAL GROWTH & DESIGN 2011; 11:1182-1192. [PMID: 22933857 PMCID: PMC3427940 DOI: 10.1021/cg101384p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Gramicidin is an apolar pentadecapeptide antibiotic consisting of alternating D-and L-amino acids. It functions, in part, by creating pores in membranes of susceptible cells rendering them leaky to monovalent cations. The peptide should be able to traverse the host membrane either as a double stranded, intertwined double helix (DSDH) or as a head-to-head single stranded helix (HHSH). Current structure models are based on macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR). However, the HHSH form has only been observed by NMR. The shape and size of the different gramicidin conformations differ. We speculated therefore that reconstituting it into a lipidic mesophase with bilayers of different microstructures would preferentially stabilize one form over the other. By using such mesophases for in meso crystallogenesis the expectation was that at least one would generate crystals of gramicidin in the HHSH form for structure determination by MX. This was tested using commercial and in-house synthesised lipids that support in meso crystallogenesis. Lipid acyl chain lengths were varied from 14 to 18 carbons to provide mesophases with a range of bilayer thicknesses. Unexpectedly, all lipids produced high quality, structure-grade crystals with gramicidin only in the DSDH conformation.
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Affiliation(s)
- Nicole Höfer
- Membrane Structural and Functional Biology Group, School of Biochemistry and Immunology, and School of Medicine, Trinity College, Dublin
- Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland
| | - David Aragão
- Membrane Structural and Functional Biology Group, School of Biochemistry and Immunology, and School of Medicine, Trinity College, Dublin
| | - Joseph A. Lyons
- Membrane Structural and Functional Biology Group, School of Biochemistry and Immunology, and School of Medicine, Trinity College, Dublin
- Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Biochemistry and Immunology, and School of Medicine, Trinity College, Dublin
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43
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The gramicidin channel ion permeation free-energy profile: direct and indirect effects of CHARMM force field improvements. Interdiscip Sci 2010; 1:113-27. [PMID: 20084184 DOI: 10.1007/s12539-009-0025-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A revised CHARMM force field for tryptophan residues is studied as well as a new grid-based correction algorithm, called CMAP, using molecular dynamics simulations of gramicidin A (1JNO) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl or KCl saline solution. The conformational stability of the interfacial side chains is studied, which shows good stability on the 10 ns time scale. The revised force field for the tryptophan side chain produces, in the decomposition, a Na(+) PMF(Trp) profile that is consonant with the prediction from the experimental results, analyzed with rate theory by Durrant et al. (2006), but in stark contrast to the prediction of the original CHARMM force field, version 22. However, the effect is diluted in the PMF profile due to indirect effects mediated by other components of the system (polypeptide, lipid molecules, ions, and water molecules). CMAP corrections to the L-amino acids help reduce the excessive translocation barrier. Decomposition demonstrates that this effect is due to effects on the K(+) PMF(H(2)O) profile rather than on the K(+) PMF(gA) profile. The results have been confirmed to be robust using an alternative umbrella-potential method. Further force field balancing efforts (direct and indirect) are required for future studies to evaluate whether these effects give rise to predictions that are consistent with those observables extracted from real experiments.
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44
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Verardi R, Traaseth NJ, Shi L, Porcelli F, Monfregola L, De Luca S, Amodeo P, Veglia G, Scaloni A. Probing membrane topology of the antimicrobial peptide distinctin by solid-state NMR spectroscopy in zwitterionic and charged lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:34-40. [PMID: 20719234 DOI: 10.1016/j.bbamem.2010.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 07/26/2010] [Accepted: 08/09/2010] [Indexed: 11/26/2022]
Abstract
Distinctin is a 47-residue antimicrobial peptide, which interacts with negatively charged membranes and is active against Gram-positive and Gram-negative bacteria. Its primary sequence comprises two linear chains of 22 (chain 1) and 25 (chain 2) residues, linked by a disulfide bridge between Cys19 of chain 1 and Cys23 of chain 2. Unlike other antimicrobial peptides, distinctin in the absence of the lipid membrane has a well-defined three-dimensional structure, which protects it from protease degradation. Here, we used static solid-state NMR spectroscopy in mechanically aligned lipid bilayers (charged or zwitterionic) to study the topology of distinctin in lipid bilayers. We found that this heterodimeric peptide adopts an ordered conformation absorbed on the surface of the membrane, with the long helix (chain 2), approximately parallel to the lipid bilayer (~5° from the membrane plane) and the short helix (chain 1) forming a ~24° angle with respect to the bilayer plane. Since the peptide does not disrupt the macroscopic alignment of charged or zwitterionic lipid bilayers at lipid-to-protein molar ratio of 50:1, it is possible that higher peptide concentrations might be needed for pore formation, or alternatively, distinctin elicits its cell disruption action by another mechanism.
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Affiliation(s)
- Raffaello Verardi
- Departments of Chemistry and Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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45
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Yin F, Kindt JT. Atomistic Simulation of Hydrophobic Matching Effects on Lipid Composition near a Helical Peptide Embedded in Mixed-Lipid Bilayers. J Phys Chem B 2010; 114:8076-80. [DOI: 10.1021/jp100931h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fuchang Yin
- Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - James T. Kindt
- Department of Chemistry, Emory University, Atlanta, Georgia 30322
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46
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Miloshevsky GV, Hassanein A, Jordan PC. Shape-Dependent Global Deformation Modes of Large Protein Structures. J Mol Struct 2010; 972:41-50. [PMID: 20526444 PMCID: PMC2878971 DOI: 10.1016/j.molstruc.2010.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT(Aa) proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT(Aa) biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod. The ClC-ec1 protein executes a splaying motion in the plane perpendicular to the lipid bilayer. These global collective deformations are determined by protein shape. New methods, all-atom Monte Carlo Normal Mode Following and its simplification using a rotation-translation of protein blocks (RTB), are described and applied to gain insight into the nature of gating transitions in gA and KcsA. These studies demonstrate the severe limitations of standard NMA in characterizing the structural rearrangements associated with gating transitions. Comparison of all-atom and RTB transition pathways in gA clearly illustrates the impact of the rigid protein block approximation and the need to include all degrees of freedom and their relaxation in computational studies of protein gating. The effects of atomic level structure, pH, hydrogen bonding and charged residues on the large scale conformational changes associated with gating transitions are discussed.
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Affiliation(s)
| | - Ahmed Hassanein
- School of Nuclear Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Peter C. Jordan
- Department of Chemistry, MS-015 Brandeis University, P.O. Box 549110, Waltham, MA 02454-9110, USA
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Shi L, Traaseth NJ, Verardi R, Cembran A, Gao J, Veglia G. A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints. JOURNAL OF BIOMOLECULAR NMR 2009; 44:195-205. [PMID: 19597943 PMCID: PMC2824793 DOI: 10.1007/s10858-009-9328-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 05/15/2009] [Indexed: 05/11/2023]
Abstract
To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, E (z) (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.
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Affiliation(s)
- Lei Shi
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nathaniel J. Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
| | - Alessandro Cembran
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA
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Sek S, Laredo T, Dutcher JR, Lipkowski J. Molecular resolution imaging of an antibiotic peptide in a lipid matrix. J Am Chem Soc 2009; 131:6439-44. [PMID: 19368392 DOI: 10.1021/ja808180m] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we show molecular resolution scanning tunneling microscopy (STM) images of gramicidin, a model antibacterial peptide, inserted into a phospholipid matrix. The resolution of the images is superior to that obtained in previous attempts to image gramicidin in a lipid environment using atomic force microscopy (AFM). This breakthrough has allowed visualization of individual peptide molecules surrounded by lipid molecules. We have observed several important features: the peptide molecules do not aggregate, the peptide molecules adopt a single conformation corresponding to a specific ion channel form, and the lipid molecules adjacent to the peptide molecules are systematically longer than those in the lipid matrix. These results constitute a new approach to obtain structural characteristics of antibiotic peptides in lipid assemblies that is necessary for the understanding of their biological activity.
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Affiliation(s)
- Slawomir Sek
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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49
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Gnandt D, Utz N, Blumen A, Koslowski T. Protein displacements under external forces: An atomistic Langevin dynamics approach. J Chem Phys 2009; 130:085104. [DOI: 10.1063/1.3077005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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50
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Siu SWI, Böckmann RA. Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin. J Phys Chem B 2009; 113:3195-202. [DOI: 10.1021/jp810302k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shirley W. I. Siu
- Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, 66041 Saarbrücken, Germany
| | - Rainer A Böckmann
- Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, 66041 Saarbrücken, Germany
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