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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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2
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Lum K, Ingólfsson HI, Koeppe RE, Andersen OS. Exchange of Gramicidin between Lipid Bilayers: Implications for the Mechanism of Channel Formation. Biophys J 2017; 113:1757-1767. [PMID: 29045870 DOI: 10.1016/j.bpj.2017.08.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 11/30/2022] Open
Abstract
The canonical mechanism of gramicidin (gA) channel formation is transmembrane dimerization of nonconducting subunits that reside in opposite bilayer leaflets. The channels do not open and close; they appear and disappear due to subunit association and dissociation. Many different types of experiments support this monomer ↔ dimer mechanism. Recently, however, this mechanism was challenged, based on experiments with lipid vesicle-incorporated gA under conditions where vesicle fusion could be controlled. In these experiments, sustained channel activity was observed long after fusion had been terminated, which led to the proposal that gA single-channel current transitions result from closed-open transitions in long-lived bilayer-spanning dimers. This proposal is at odds with 40 years of experiments, but involves the key assumption that gA monomers do not exchange between bilayers. We tested the possibility of peptide exchange between bilayers using three different types of experiments. First, we demonstrated the exchange of gA between 1,2-dierucoyl-sn-glycero-3-phosphocholine (DC22:1PC) or 1,2-dioleoyl-sn-glycero-3-phosphocholine (DC18:1PC) lipid vesicles using a fluorescence assay for gA channel activity. Second, we added gA-free DC22:1PC vesicles to both sides of planar DC18:1PC bilayers preincubated with gA, which reduced channel activity up to 10-fold. Third, we added gA-containing DC22:1PC vesicles to one or both sides of DC18:1PC planar bilayers, which produced much higher channel activity when the gA-containing vesicles were added to both sides of the bilayer, as compared to one side only. All three types of experiments show that gA subunits can exchange between lipid bilayers. The exchange of subunits between bilayers thus is firmly established, which becomes a crucial consideration with respect to the mechanism of channel formation.
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Affiliation(s)
- Kevin Lum
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Helgi I Ingólfsson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
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3
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Nerdal W, Nilsen TRS, Steinkopf S. CoenzymeQ10 localizations in model membranes. A Langmuir monolayer study. Biophys Chem 2015; 207:74-81. [PMID: 26408828 DOI: 10.1016/j.bpc.2015.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Willy Nerdal
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | | | - Signe Steinkopf
- Department of Biomedical Laboratory Science, Bergen University College, Inndalsveien 28, N-5020 Bergen, Norway.
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Sychev SV, Ivanov VT. Large scale conformational transitions in β
-structural motif of gramicidin A: kinetic analysis based on CD and FT-IR data. J Pept Sci 2014; 20:657-67. [DOI: 10.1002/psc.2643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/21/2014] [Accepted: 03/28/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Sergei V. Sychev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; 16/10 Miklukho-Maklaya Str. Moscow 117997 Russia
| | - Vadim T. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; 16/10 Miklukho-Maklaya Str. Moscow 117997 Russia
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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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6
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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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7
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Gopinath T, Veglia G. Improved Resolution in Dipolar NMR Spectra Using Constant Time Evolution PISEMA Experiment. Chem Phys Lett 2010; 494:104-110. [PMID: 20814452 PMCID: PMC2929988 DOI: 10.1016/j.cplett.2010.05.078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The atomic structure of small molecules and polypeptides can be attained from anisotropic NMR parameters such as dipolar couplings (DC) and chemical shifts (CS). Separated local field experiments resolve DC and CS correlations into two dimensions. However, crowded NMR spectra represent a significant obstacle for the complete resolution of these anisotropic parameters. Using the PISEMA (Polarization Inversion Spin Exchange at the Magic Angle) experiment as a foundation, we designed new pulse schemes that use a constant time evolution in the dipolar (indirect) dimension to measure DC and CS correlations at high resolution. We demonstrated this approach on a 4-pentyl-4'-cyanobiphenyl (5CB) liquid crystal sample, achieving a resolution enhancement ranging from 30 to 60 % for the resonances in the dipolar dimension. These new experiments open the possibility of obtaining significant resolution enhancement for multidimensional NMR experiments carried out on oriented liquid crystalline samples as well as oriented membrane proteins.
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Affiliation(s)
- T. Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
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Jones TL, Fu R, Nielson F, Cross TA, Busath DD. Gramicidin channels are internally gated. Biophys J 2010; 98:1486-93. [PMID: 20409467 DOI: 10.1016/j.bpj.2009.11.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/20/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022] Open
Abstract
Gramicidin channels are archetypal molecular subjects for solid-state NMR studies and investigations of single-channel or cation conductance. Until now, the transitions between on and off conductance states have been thought, based on multichannel studies, to represent monomer <--> dimer reactions. Here we use a single-molecule deposition method (vesicle fusion to a planar bilayer) to show that gramicidin dimer channels do not normally dissociate when conductance terminates. Furthermore, the observation of two 13C peaks in solid-state NMR indicates very stable dichotomous conformations for both the first and second peptide bonds in the monomers, and a two-dimensional chemical exchange spectrum with a 12-s mixing time demonstrates that the Val1 carbonyl conformations exchange slowly, with lifetimes of several seconds. It is proposed that gramicidin channels are gated by small conformational changes in the channel near the permeation pathway. These studies demonstrate how regulation of conformations governing closed <--> open transitions may be achieved and studied at the molecular level.
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Affiliation(s)
- Tyson L Jones
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah, USA
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Ravault S, Soubias O, Saurel O, Thomas A, Brasseur R, Milon A. Fusogenic Alzheimer's peptide fragment Abeta (29-42) in interaction with lipid bilayers: secondary structure, dynamics, and specific interaction with phosphatidyl ethanolamine polar heads as revealed by solid-state NMR. Protein Sci 2005; 14:1181-9. [PMID: 15840826 PMCID: PMC2253267 DOI: 10.1110/ps.041291405] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The interaction of the native Alzheimer's peptide C-terminal fragment Abeta (29-42), and two mutants (G33A and G37A) with neutral lipid bilayers made of POPC and POPE in a 9:1 molar ratio was investigated by solid-state NMR. This fragment and the lipid composition were selected because they represent the minimum requirement for the fusogenic activity of the Alzheimer's peptide. The chemical shifts of alanine methyl isotropic carbon were determined by MAS NMR, and they clearly demonstrated that the major form of the peptide equilibrated in membrane is not in a helical conformation. (2)H NMR, performed with acyl chain deuterated POPC, demonstrated that there is no perturbation of the acyl chain's dynamics and of the lipid phase transition temperature. (2)H NMR, performed with alanine methyl-deuterated peptide demonstrated that the peptide itself has a limited mobility below and above the lipid phase transition temperature (molecular order parameter equal to 0.94). MAS (31)P NMR revealed a specific interaction with POPE polar head as seen by the enhancement of POPE phosphorus nuclei T(2) relaxation. All these results are in favor of a beta-sheet oligomeric association of the peptide at the bilayer interface, preferentially recruiting phosphatidyl ethanolamine polar heads.
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Miloshevsky GV, Jordan PC. Gating gramicidin channels in lipid bilayers: reaction coordinates and the mechanism of dissociation. Biophys J 2004; 86:92-104. [PMID: 14695253 PMCID: PMC1303840 DOI: 10.1016/s0006-3495(04)74087-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Accepted: 09/17/2003] [Indexed: 11/26/2022] Open
Abstract
The dissociation of gramicidin A (gA) channels into monomers is the simplest example of a channel gating process. The initial steps in this process are studied via a computational model that simulates the reaction coordinate for dimer-monomer dissociation. The nonbonded interaction energy between the monomers is determined, allowing for their free relative translational and rotational motion. Lowest energy pathways and reaction coordinates of the gating process are determined. Partial rupture of the six hydrogen bonds (6HB) at the dimer junction takes place by coupling monomer rotation and lateral displacement. Coupling rotation with axial separation is far more expensive energetically. The transition state for channel dissociation occurs when monomers are displaced laterally by approximately 4-6 A, separated by approximately 1.6-2 A, and rotated by approximately 120 degrees, breaking two hydrogen bonds. In membranes with significant hydrophobic mismatch there is a much greater likelihood of forming 4HB and possibly even 2HB states. In the 4HB state the pore remains fully open and conductive. However, transitions from the 6HB to 4HB and 4HB to 2HB states take place via intermediates in which the gA pore is closed and nonconductive. These lateral monomer displacements give rise to transitory pore occlusion at the dimer junction, which provides a rationale for fast closure events (flickers). Local dynamics of gA monomers also leads to lateral and rotational diffusion of the whole gA dimer, giving rise to diffusional rotation of the dimer about the channel axis.
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Affiliation(s)
- Gennady V Miloshevsky
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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