1
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Samanta R, Gray JJ. Implicit model to capture electrostatic features of membrane environment. PLoS Comput Biol 2024; 20:e1011296. [PMID: 38252688 PMCID: PMC10833867 DOI: 10.1371/journal.pcbi.1011296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 02/01/2024] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Membrane protein structure prediction and design are challenging due to the complexity of capturing the interactions in the lipid layer, such as those arising from electrostatics. Accurately capturing electrostatic energies in the low-dielectric membrane often requires expensive Poisson-Boltzmann calculations that are not scalable for membrane protein structure prediction and design. In this work, we have developed a fast-to-compute implicit energy function that considers the realistic characteristics of different lipid bilayers, making design calculations tractable. This method captures the impact of the lipid head group using a mean-field-based approach and uses a depth-dependent dielectric constant to characterize the membrane environment. This energy function Franklin2023 (F23) is built upon Franklin2019 (F19), which is based on experimentally derived hydrophobicity scales in the membrane bilayer. We evaluated the performance of F23 on five different tests probing (1) protein orientation in the bilayer, (2) stability, and (3) sequence recovery. Relative to F19, F23 has improved the calculation of the tilt angle of membrane proteins for 90% of WALP peptides, 15% of TM-peptides, and 25% of the adsorbed peptides. The performances for stability and design tests were equivalent for F19 and F23. The speed and calibration of the implicit model will help F23 access biophysical phenomena at long time and length scales and accelerate the membrane protein design pipeline.
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Affiliation(s)
- Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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2
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Samanta R, Gray JJ. Implicit model to capture electrostatic features of membrane environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546486. [PMID: 37425950 PMCID: PMC10327106 DOI: 10.1101/2023.06.26.546486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Membrane protein structure prediction and design are challenging due to the complexity of capturing the interactions in the lipid layer, such as those arising from electrostatics. Accurately capturing electrostatic energies in the low-dielectric membrane often requires expensive Poisson-Boltzmann calculations that are not scalable for membrane protein structure prediction and design. In this work, we have developed a fast-to-compute implicit energy function that considers the realistic characteristics of different lipid bilayers, making design calculations tractable. This method captures the impact of the lipid head group using a mean-field-based approach and uses a depth-dependent dielectric constant to characterize the membrane environment. This energy function Franklin2023 (F23) is built upon Franklin2019 (F19), which is based on experimentally derived hydrophobicity scales in the membrane bilayer. We evaluated the performance of F23 on five different tests probing (1) protein orientation in the bilayer, (2) stability, and (3) sequence recovery. Relative to F19, F23 has improved the calculation of the tilt angle of membrane proteins for 90% of WALP peptides, 15% of TM-peptides, and 25% of the adsorbed peptides. The performances for stability and design tests were equivalent for F19 and F23. The speed and calibration of the implicit model will help F23 access biophysical phenomena at long time and length scales and accelerate the membrane protein design pipeline.
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Affiliation(s)
- Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, United States
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3
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Price JR, Afrose F, Greathouse DV, Koeppe RE. Illuminating Disorder Induced by Glu in a Stable Arg-Anchored Transmembrane Helix. ACS OMEGA 2021; 6:20611-20618. [PMID: 34396006 PMCID: PMC8359125 DOI: 10.1021/acsomega.1c02800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Membrane proteins are vital for biological function and are complex to study. Even in model peptide-lipid systems, the combined influence or interaction of pairs of chemical groups still is not well understood. Disordered proteins, whether in solution or near lipid membranes, are an emerging paradigm for the initiation and control of biological function. The disorder can involve molecular orientation as well as molecular folding. This paper reports an astonishing induction of disorder when one Glu residue is introduced into a highly stable 23-residue transmembrane helix. The parent helix is anchored by a single Arg residue, tilted at a well-defined angle with respect to the DOPC bilayer normal and undergoes rapid cone precession. When Glu is introduced two residues away from Arg, with 200° (or 160°) radial separation, the helix properties change radically to exhibit a multiplicity of three or more disordered states. The helix characteristics have been monitored by deuterium (2H) NMR spectroscopy as functions of the pH and lipid bilayer composition. The disordered multistate behavior of the (Glu, Arg)-containing helix varies with the lipid bilayer thickness and pH. The results highlight a fundamental induction of protein multistate properties by a single Glu residue in a lipid membrane environment.
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4
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McKay M, Marr KA, Price JR, Greathouse DV, Koeppe RE. Lipid-Dependent Titration of Glutamic Acid at a Bilayer Membrane Interface. ACS OMEGA 2021; 6:8488-8494. [PMID: 33817510 PMCID: PMC8015139 DOI: 10.1021/acsomega.1c00276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The ionization properties of protein side chains in lipid-bilayer membranes will differ from the canonical values of side chains exposed to an aqueous solution. While the propensities of positively charged side chains of His, Lys, and Arg to release a proton in lipid membranes have been rather well characterized, the propensity for a negatively charged Glu side chain to receive a proton and achieve the neutral state in a bilayer membrane has been less well characterized. Indeed, the ionization of the glutamic acid side chain has been predicted to depend on its depth of burial in a lipid membrane but has been difficult to verify experimentally. To address the issue, we incorporated an interfacial Glu residue at position 4 of a distinct 23-residue transmembrane helix and used 2H NMR to examine the helix properties as a function of pH. We observe that the helix tilt and azimuthal rotation vary little with pH, but the extent of helix unraveling near residues 3 and 4 changes as the Glu residue E4 titrates. Remarkably, the 2H quadrupolar splitting for the side chain of alanine A3 responds to pH with an apparent pK a of 4.8 in 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 6.3 in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC), but is unchanged up to pH 8.0 in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) in the presence of residue E4. With bilayers composed of alkali-stable ether-linked lipids, the side chain of A3 responds to pH with an apparent pK a of 11.0 in the ether analogue of DOPC. These results suggest that the depth dependence of Glu ionization in lipid-bilayer membranes may be steeper than previously predicted or envisioned.
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5
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Afrose F, Martfeld AN, Greathouse DV, Koeppe RE. Examination of pH dependency and orientation differences of membrane spanning alpha helices carrying a single or pair of buried histidine residues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183501. [PMID: 33130099 DOI: 10.1016/j.bbamem.2020.183501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/08/2023]
Abstract
We have employed the peptide framework of GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide) to examine the orientation, dynamics and pH dependence of peptides having buried single or pairs of histidine residues. When residue L8 is substituted to yield GWALP23-H8, acetyl-GGALWLAH8ALALALALALWLAGA-amide, the deuterium NMR spectra of 2H-labeled core alanine residues reveal a helix that occupies a single transmembrane orientation in DLPC, or in DMPC at low pH, yet shows multiple states at higher pH or in bilayers of DOPC. Moreover, a single histidine at position 8 or 16 in the GWALP23 framework is sensitive to pH. Titration points are observed near pH 3.5 for the deprotonation of H8 in lipid bilayers of DLPC or DMPC, and for H16 in DOPC. When residues L8 and L16 both are substituted to yield GWALP23-H8,16, the 2H NMR spectra show, interestingly, no titration dependence from pH 2-8, yet bilayer thickness-dependent orientation differences. The helix with H8 and H16 is found to adopt a transmembrane orientation in thin bilayers of DLPC, a combination of transmembrane and surface orientations in DMPC, and then a complete transition to a surface bound orientation in the thicker DPoPC and DOPC lipid bilayers. In the surface orientations, alanine A7 no longer fits within the core helix. These results along with previous studies with different locations of histidine residues suggest that lipid hydrophobic thickness is a first determinant and pH a second determinant for the helical orientation, along with possible side-chain snorkeling, when the His residues are incorporated into the hydrophobic region of a lipid membrane-associated helix.
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Affiliation(s)
- Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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6
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McKay MJ, Greathouse DV, Koeppe RE. Flanking aromatic residue competition influences transmembrane peptide helix dynamics. FEBS Lett 2020; 594:4280-4291. [DOI: 10.1002/1873-3468.13926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Matthew J. McKay
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
| | - Denise V. Greathouse
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
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Syga Ł, de Vries RH, van Oosterhout H, Bartelds R, Boersma AJ, Roelfes G, Poolman B. A Trifunctional Linker for Palmitoylation and Peptide and Protein Localization in Biological Membranes. Chembiochem 2020; 21:1320-1328. [PMID: 31814256 PMCID: PMC7317724 DOI: 10.1002/cbic.201900655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 01/09/2023]
Abstract
Attachment of lipophilic groups is an important post-translational modification of proteins, which involves the coupling of one or more anchors such as fatty acids, isoprenoids, phospholipids, or glycosylphosphatidyl inositols. To study its impact on the membrane partitioning of hydrophobic peptides or proteins, we designed a tyrosine-based trifunctional linker. The linker allows the facile incorporation of two different functionalities at a cysteine residue in a single step. We determined the effect of the lipid modification on the membrane partitioning of the synthetic α-helical model peptide WALP with or without here and in all cases below; palmitoyl groups in giant unilamellar vesicles that contain a liquid-ordered (Lo ) and liquid-disordered (Ld ) phase. Introduction of two palmitoyl groups did not alter the localization of the membrane peptides, nor did the membrane thickness or lipid composition. In all cases, the peptide was retained in the Ld phase. These data demonstrate that the Lo domain in model membranes is highly unfavorable for a single membrane-spanning peptide.
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Affiliation(s)
- Łukasz Syga
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Reinder H. de Vries
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Hugo van Oosterhout
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Rianne Bartelds
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Arnold J. Boersma
- DWI Leibniz Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
| | - Gerard Roelfes
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Bert Poolman
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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8
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Strandberg E, Bentz D, Wadhwani P, Ulrich AS. Chiral supramolecular architecture of stable transmembrane pores formed by an α-helical antibiotic peptide in the presence of lyso-lipids. Sci Rep 2020; 10:4710. [PMID: 32170095 PMCID: PMC7070102 DOI: 10.1038/s41598-020-61526-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/20/2020] [Indexed: 01/10/2023] Open
Abstract
The amphipathic α-helical antimicrobial peptide MSI-103 (aka KIA21) can form stable transmembrane pores when the bilayer takes on a positive spontaneous curvature, e.g. by the addition of lyso-lipids. Solid-state 31P- and 15N-NMR demonstrated an enrichment of lyso-lipids in these toroidal wormholes. Anionic lyso-lipids provided additional stabilization by electrostatic interactions with the cationic peptides. The remaining lipid matrix did not affect the nature of the pore, as peptides maintained the same orientation independent of lipid charge, and a change in membrane thickness did not considerably affect their tilt angle. Under optimized conditions (i.e. in the presence of lyso-lipids and appropriate bilayer thickness), stable and well-aligned pores could be obtained for solid-state 2H-NMR analysis. These data revealed for the first time the complete 3D alignment of this representative amphiphilic peptide in fluid membranes, which is compatible with either monomeric helices as constituents, or left-handed supercoiled dimers as building blocks from which the overall toroidal wormhole is assembled.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - David Bentz
- KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany. .,KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.
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9
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Comparing Interfacial Trp, Interfacial His and pH Dependence for the Anchoring of Tilted Transmembrane Helical Peptides. Biomolecules 2020; 10:biom10020273. [PMID: 32053887 PMCID: PMC7072424 DOI: 10.3390/biom10020273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 11/27/2022] Open
Abstract
Charged and aromatic amino acid residues, being enriched toward the terminals of membrane-spanning helices in membrane proteins, help to stabilize particular transmembrane orientations. Among them, histidine is aromatic and can be positively charge at low pH. To enable investigations of the underlying protein-lipid interactions, we have examined the effects of single or pairs of interfacial histidine residues using the constructive low-dynamic GWALP23 (acetyl-GG2ALW5LALALALALALALW19LAG22A-amide) peptide framework by incorporating individual or paired histidines at locations 2, 5, 19 or 22. Analysis of helix orientation by means of solid-state 2H NMR spectra of labeled alanine residues reveals marked differences with H2,22 compared to W2,22. Nevertheless, the properties of membrane-spanning H2,22WALP23 helices show little pH dependence and are similar to those having Gly, Arg or Lys at positions 2 and 22. The presence of H5 or H19 influences the helix rotational preference but not the tilt magnitude. H5 affects the helical integrity, as residue 7 unwinds from the core helix; yet once again the helix orientation and dynamic properties show little sensitivity to pH. The overall results reveal that the detailed properties of transmembrane helices depend upon the precise locations of interfacial histidine residues.
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10
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Influence of interfacial tryptophan residues on an arginine-flanked transmembrane helix. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183134. [PMID: 31738898 DOI: 10.1016/j.bbamem.2019.183134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 10/25/2022]
Abstract
The transmembrane helices of membrane proteins often are flanked by interfacial charged or aromatic residues that potentially help to anchor the membrane-spanning protein. For isolated single-span helices, the interfacial residues may be especially important for stabilizing particular tilted transmembrane orientations. The peptide RWALP23 (acetyl-GR2ALW(LA)6LWLAR22A-amide) has been employed to investigate the interplay between interfacial arginines and tryptophans. Here we replace the tryptophans of RWALP23 with A5 and A19, to investigate arginines alone with respect to helix fraying and orientation in varying lipid bilayers. Deuterated alanines incorporated into the central sequence allow the orientation and stability of the core helix to be assessed by means of solid -state 2H NMR in bilayers of DOPC, DMPC and DLPC. The helix tilt from the bilayer normal is found to increase slightly when R2 and R22 are present, and increases still further when the tryptophans W5 and W19 are replaced by alanines. The extent of helix dynamic averaging remains low in all cases. The preferred helix azimuthal rotation is essentially constant for all of the helices in each of the lipid membranes considered here. The alanines located outside of the core region of the peptide are sensitive to helical integrity. The new alanines, A5 and A19, therefore, provide new information about the length of the core helix and the onset of unraveling of the terminals. Residue A19 remains essentially on the central helix in each lipid membrane, while residues A3, A5 and A21 deviate from the core helix to an extent that depends on the membrane thickness. Differential unraveling of the two ends to expose peptide backbone groups for hydrogen bonding therefore acts together with specific interfacial side chains to stabilize a transmembrane helix.
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Lipinski K, McKay MJ, Afrose F, Martfeld AN, Koeppe RE, Greathouse DV. Influence of Lipid Saturation, Hydrophobic Length and Cholesterol on Double-Arginine-Containing Helical Peptides in Bilayer Membranes. Chembiochem 2019; 20:2784-2792. [PMID: 31150136 DOI: 10.1002/cbic.201900282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Indexed: 12/12/2022]
Abstract
Membrane proteins are essential for many cell processes yet are more difficult to investigate than soluble proteins. Charged residues often contribute significantly to membrane protein function. Model peptides such as GWALP23 (acetyl-GGALW5 LAL8 LALALAL16 ALW19 LAGA-amide) can be used to characterize the influence of specific residues on transmembrane protein domains. We have substituted R8 and R16 in GWALP23 in place of L8 and L16, equidistant from the peptide center, and incorporated specific 2 H-labeled alanine residues within the central sequence for detection by solid-state 2 H NMR spectroscopy. The resulting pattern of [2 H]Ala quadrupolar splitting (Δνq ) magnitudes indicates the core helix for R8,16 GWALP23 is significantly tilted to give a similar transmembrane orientation in thinner bilayers with either saturated C12:0 or C14:0 acyl chains (1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)) or unsaturated C16:1 Δ9 cis acyl chains. In bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC; C18:1 Δ9 cis) multiple orientations are indicated, whereas in longer, unsaturated 1,2-dieicosenoyl-sn-glycero-3-phosphocholine (DEiPC; C20:1 Δ11 cis) bilayers, the R8,16 GWALP23 helix adopts primarily a surface orientation. The inclusion of 10-20 mol % cholesterol in DOPC bilayers drives more of the R8,16 GWALP23 helix population to the membrane surface, thereby allowing both charged arginines access to the interfacial lipid head groups. The results suggest that hydrophobic thickness and cholesterol content are more important than lipid saturation for the arginine peptide dynamics and helix orientation in lipid membranes.
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Affiliation(s)
- Karli Lipinski
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Matthew J McKay
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA.,Present address: Department Department of Neurobiology, Duke University Medical Center, 311 Research Drive, Durham, NC, 27710, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
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12
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McKay MJ, Fu R, Greathouse DV, Koeppe RE. Breaking the Backbone: Central Arginine Residues Induce Membrane Exit and Helix Distortions within a Dynamic Membrane Peptide. J Phys Chem B 2019; 123:8034-8047. [PMID: 31483653 DOI: 10.1021/acs.jpcb.9b06034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane domains of membrane proteins sometimes contain conserved charged or ionizable residues which may be essential for protein function and regulation. This work examines the molecular interactions of single Arg residues within a highly dynamic transmembrane peptide helix. To this end, we have modified the GW4,20ALP23 (acetyl-GGAW4(AL)7AW20AGA-amide) model peptide framework to incorporate Arg residues near the center of the peptide. Peptide helix formation, orientation and dynamics were analyzed by means of solid-state NMR spectroscopy to monitor specific 2H- or 15N-labeled residues. GW4,20ALP23 itself adopts a tilted orientation within lipid bilayer membranes. Nevertheless, the GW4,20ALP23 helix exhibits moderate to high dynamic averaging of NMR observables, such as 2H quadrupolar splittings or 15N-1H dipolar couplings, due to competition between the interfacial Trp residues on opposing helix faces. Here we examine how the helix dynamics are impacted by the introduction of a single Arg residue at position 12 or 14. Residue R14 restricts the helix to low dynamic averaging and a well-defined tilt that varies inversely with the lipid bilayer thickness. To compensate for the dominance of R14, the competing Trp residues cause partial unwinding of the helix at the C-terminal. By contrast, R12GW4,20ALP23 exits the DOPC bilayer to an interfacial surface-bound location. Interestingly, multiple orientations are exhibited by a single residue, Ala-9. Quadrupolar splittings generated by 2H-labeled residues A3, A5, A7, and A9 do not fit to the α-helical quadrupolar wave plot defined by residues A11, A13, A15, A17, A19, and A21. The discontinuity at residue A9 implicates a helical swivel distortion and an apparent 310-helix involving the N-terminal residues preceding A11. These molecular features suggest that, while arginine residues are prominent factors controlling transmembrane helix dynamics, the influence of interfacial tryptophan residues cannot be ignored.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University , Tallahassee , Florida 32310 , United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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13
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Götz A, Mylonas N, Högel P, Silber M, Heinel H, Menig S, Vogel A, Feyrer H, Huster D, Luy B, Langosch D, Scharnagl C, Muhle-Goll C, Kamp F, Steiner H. Modulating Hinge Flexibility in the APP Transmembrane Domain Alters γ-Secretase Cleavage. Biophys J 2019; 116:2103-2120. [PMID: 31130234 PMCID: PMC6554489 DOI: 10.1016/j.bpj.2019.04.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 04/15/2019] [Indexed: 01/27/2023] Open
Abstract
Intramembrane cleavage of the β-amyloid precursor protein C99 substrate by γ-secretase is implicated in Alzheimer's disease pathogenesis. Biophysical data have suggested that the N-terminal part of the C99 transmembrane domain (TMD) is separated from the C-terminal cleavage domain by a di-glycine hinge. Because the flexibility of this hinge might be critical for γ-secretase cleavage, we mutated one of the glycine residues, G38, to a helix-stabilizing leucine and to a helix-distorting proline. Both mutants impaired γ-secretase cleavage and also altered its cleavage specificity. Circular dichroism, NMR, and backbone amide hydrogen/deuterium exchange measurements as well as molecular dynamics simulations showed that the mutations distinctly altered the intrinsic structural and dynamical properties of the substrate TMD. Although helix destabilization and/or unfolding was not observed at the initial ε-cleavage sites of C99, subtle changes in hinge flexibility were identified that substantially affected helix bending and twisting motions in the entire TMD. These resulted in altered orientation of the distal cleavage domain relative to the N-terminal TMD part. Our data suggest that both enhancing and reducing local helix flexibility of the di-glycine hinge may decrease the occurrence of enzyme-substrate complex conformations required for normal catalysis and that hinge mobility can thus be conducive for productive substrate-enzyme interactions.
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Affiliation(s)
- Alexander Götz
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany
| | - Nadine Mylonas
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Philipp Högel
- Center for Integrated Protein Science Munich at the Lehrstuhl Chemie der Biopolymere, Technical University Munich, Freising, Germany
| | - Mara Silber
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Hannes Heinel
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Simon Menig
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany
| | - Alexander Vogel
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Hannes Feyrer
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dieter Langosch
- Center for Integrated Protein Science Munich at the Lehrstuhl Chemie der Biopolymere, Technical University Munich, Freising, Germany
| | - Christina Scharnagl
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany.
| | - Claudia Muhle-Goll
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany.
| | - Frits Kamp
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany
| | - Harald Steiner
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
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14
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Aisenbrey C, Kemayo-Koumkoua P, Salnikov ES, Glattard E, Bechinger B. Investigations of the Structure, Topology, and Interactions of the Transmembrane Domain of the Lipid-Sorting Protein p24 Being Highly Selective for Sphingomyelin-C18. Biochemistry 2019; 58:2782-2795. [PMID: 31120242 DOI: 10.1021/acs.biochem.9b00375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The p24 proteins play an important role in the secretory pathway where they selectively connect various cargo to other proteins, thereby being involved in the controlled assembly and disassembly of the coat protein complexes and lipid sorting. Recently, a highly selective lipid interaction motif has been identified within the p24 transmembrane domain (TMD) that recognizes the combination of the sphingomyelin headgroup and the exact length of the C18 fatty acyl chain (SM-C18). Here, we present investigations of the structure, dynamics, and sphingomyelin interactions of the p24 transmembrane region using circular dichroism, tryptophan fluorescence, and solid-state nuclear magnetic resonance (NMR) spectroscopies of the polypeptides and the surrounding lipids. Membrane insertion and/or conformation of the TMD is strongly dependent on the membrane lipid composition where the transmembrane helical insertion is strongest in the presence of 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) and SM-C18. By analyzing solid-state NMR angular restraints from a large number of labeled sites, we have found a tilt angle of 19° for the transmembrane helical domain at a peptide-to-lipid ratio of 1 mol %. Only minor changes in the solid-state NMR spectra are observed due to the presence of SM-C18; the only visible alterations are associated with the SM-C18 recognition motif close to the carboxy-terminal part of the hydrophobic transmembrane region in the proximity of the SM headgroup. Finally, the deuterium order parameters of POPC- d31 were nearly unaffected by the presence of SM-C18 or the polypeptide alone but decreased noticeably when the sphingomyelin and the polypeptide were added in combination.
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Affiliation(s)
- Christopher Aisenbrey
- Université de Strasbourg/CNRS, UMR7177 , Institut de Chimie , 4, rue Blaise Pascal , 67070 Strasbourg , France
| | - Patricia Kemayo-Koumkoua
- Université de Strasbourg/CNRS, UMR7177 , Institut de Chimie , 4, rue Blaise Pascal , 67070 Strasbourg , France
| | - Evgeniy S Salnikov
- Université de Strasbourg/CNRS, UMR7177 , Institut de Chimie , 4, rue Blaise Pascal , 67070 Strasbourg , France
| | - Elise Glattard
- Université de Strasbourg/CNRS, UMR7177 , Institut de Chimie , 4, rue Blaise Pascal , 67070 Strasbourg , France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177 , Institut de Chimie , 4, rue Blaise Pascal , 67070 Strasbourg , France
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15
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Affiliation(s)
- Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, Biophysics Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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16
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Afrose F, McKay MJ, Mortazavi A, Suresh Kumar V, Greathouse DV, Koeppe RE. Transmembrane Helix Integrity versus Fraying To Expose Hydrogen Bonds at a Membrane-Water Interface. Biochemistry 2019; 58:633-645. [PMID: 30565458 DOI: 10.1021/acs.biochem.8b01119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Transmembrane helices dominate the landscape for many membrane proteins. Often flanked by interfacial aromatic residues, these transmembrane helices also contain loops and interhelix segments, which could help in stabilizing a transmembrane orientation. Using 2H nuclear magnetic resonance spectroscopy to monitor bilayer-incorporated model GWALP23 family peptides, we address systematically the issue of helix fraying in relation to the dynamics and orientation of highly similar individual transmembrane helices. We inserted aromatic (Phe, Trp, Tyr, and His) or non-aromatic residues (Ala and Gly) into positions 4 and 5 adjacent to a core transmembrane helix to examine the side-chain dependency of the transmembrane orientation, dynamics, and helix integrity (extent and location of unraveling). Incorporation of [2H]alanine labels enables one to assess the helicity of the core sequence and the peptide termini. For most of the helices, we observed substantial unwinding involving at least three residues at both ends. For the unique case of histidine at positions 4 and 5, an extended N-terminal unwinding was observed up to residue 7. For further investigation of the onset of fraying, we employed A4,5GWALP23 with 2H labels at residues 4 and 5 and found that the number of terminal residues involved in the unwinding depends on bilayer thicknesses and helps to govern the helix dynamics. The combined results enable us to compare and contrast the extent of fraying for each related helix, as reflected by the deviation of experimental 2H quadrupolar splitting magnitudes of juxta-terminal alanines A3 and A21 from those represented by an ideal helix geometry.
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Affiliation(s)
- Fahmida Afrose
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Armin Mortazavi
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Vasupradha Suresh Kumar
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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17
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Reißer S, Strandberg E, Steinbrecher T, Elstner M, Ulrich AS. Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR. J Chem Theory Comput 2018; 14:6002-6014. [PMID: 30289704 DOI: 10.1021/acs.jctc.8b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane alignment of helical amphiphilic peptides in oriented phospholipid bilayers can be obtained as ensemble and time averages from solid state 2H NMR by fitting the quadrupolar splittings to ideal α-helices. At the same time, molecular dynamics (MD) simulations can provide atomistic insight into peptide-membrane systems. Here, we evaluate the potential of MD simulations to complement the experimental NMR data that is available on three exemplary systems: the natural antimicrobial peptide PGLa and the two designer-made peptides MSI-103 and KIA14, whose sequences were derived from PGLa. Each peptide was simulated for 1 μs in a DMPC lipid bilayer. We calculated from the MD simulations the local angles which define the side chain geometry with respect to the peptide helix. The peptide orientation was then calculated (i) directly from the simulation, (ii) from back-calculated MD-derived NMR splittings, and (iii) from experimental 2H NMR splittings. Our findings are that (1) the membrane orientation and secondary structure of the peptides found in the NMR analysis are generally well reproduced by the simulations; (2) the geometry of the side chains with respect to the helix backbone can deviate significantly from the ideal structure depending on the specific residue, but on average all side chains have the same orientation; and (3) for all of our peptides, the azimuthal rotation angle found from the MD-derived splittings is about 15° smaller than the experimental value.
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Affiliation(s)
- Sabine Reißer
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
| | - Thomas Steinbrecher
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Anne S Ulrich
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany.,Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
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18
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Pal S, Koeppe RE, Chattopadhyay A. Wavelength-Selective Fluorescence of a Model Transmembrane Peptide: Constrained Dynamics of Interfacial Tryptophan Anchors. J Fluoresc 2018; 28:1317-1323. [PMID: 30225736 DOI: 10.1007/s10895-018-2293-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/03/2018] [Indexed: 11/27/2022]
Abstract
WALPs are prototypical, α-helical transmembrane peptides that represent a consensus sequence for transmembrane segments of integral membrane proteins and serve as excellent models for exploring peptide-lipid interactions and hydrophobic mismatch in membranes. Importantly, the WALP peptides are in direct contact with the lipids. They consist of a central stretch of alternating hydrophobic alanine and leucine residues capped at both ends by tryptophans. In this work, we employ wavelength-selective fluorescence approaches to explore the intrinsic fluorescence of tryptophan residues in WALP23 in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes. Our results show that the four tryptophan residues in WALP23 exhibit an average red edge excitation shift (REES) of 6 nm, implying their localization at the membrane interface, characterized by a restricted microenvironment. This result is supported by fluorescence anisotropy and lifetime measurements as a function of wavelength displayed by WALP23 tryptophans in POPC membranes. These results provide a new approach based on intrinsic fluorescence of interfacial tryptophans to address protein-lipid interaction and hydrophobic mismatch.
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Affiliation(s)
- Sreetama Pal
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Amitabha Chattopadhyay
- Academy of Scientific and Innovative Research, Ghaziabad, India.
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
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19
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McKay MJ, Martfeld AN, De Angelis AA, Opella SJ, Greathouse DV, Koeppe RE. Control of Transmembrane Helix Dynamics by Interfacial Tryptophan Residues. Biophys J 2018; 114:2617-2629. [PMID: 29874612 PMCID: PMC6129553 DOI: 10.1016/j.bpj.2018.04.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 01/12/2023] Open
Abstract
Transmembrane protein domains often contain interfacial aromatic residues, which may play a role in the insertion and stability of membrane helices. Residues such as Trp or Tyr, therefore, are often found situated at the lipid-water interface. We have examined the extent to which the precise radial locations of interfacial Trp residues may influence peptide helix orientation and dynamics. To address these questions, we have modified the GW5,19ALP23 (acetyl-GGALW5(LA)6LW19LAGA-[ethanol]amide) model peptide framework to relocate the Trp residues. Peptide orientation and dynamics were analyzed by means of solid-state nuclear magnetic resonance (NMR) spectroscopy to monitor specific 2H- and 15N-labeled residues. GW5,19ALP23 adopts a defined, tilted orientation within lipid bilayer membranes with minimal evidence of motional averaging of NMR observables, such as 2H quadrupolar or 15N-1H dipolar splittings. Here, we examine how peptide dynamics are impacted by relocating the interfacial Trp (W) residues on both ends and opposing faces of the helix, for example by a 100° rotation on the helical wheel for positions 4 and 20. In contrast to GW5,19ALP23, the modified GW4,20ALP23 helix experiences more extensive motional averaging of the NMR observables in several lipid bilayers of different thickness. Individual and combined Gaussian analyses of the 2H and 15N NMR signals confirm that the extent of dynamic averaging, particularly rotational "slippage" about the helix axis, is strongly coupled to the radial distribution of the interfacial Trp residues as well as the bilayer thickness. Additional 2H labels on alanines A3 and A21 reveal partial fraying of the helix ends. Even within the context of partial unwinding, the locations of particular Trp residues around the helix axis are prominent factors for determining transmembrane helix orientation and dynamics within the lipid membrane environment.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Anna A De Angelis
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas.
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20
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Strandberg E, Grau-Campistany A, Wadhwani P, Bürck J, Rabanal F, Ulrich AS. Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. J Phys Chem B 2018; 122:6236-6250. [DOI: 10.1021/acs.jpcb.8b02661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Ariadna Grau-Campistany
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
- KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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21
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Abstract
Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.
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22
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Molugu TR, Lee S, Brown MF. Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes. Chem Rev 2017; 117:12087-12132. [PMID: 28906107 DOI: 10.1021/acs.chemrev.6b00619] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Concepts of solid-state NMR spectroscopy and applications to fluid membranes are reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups are studied using 2H NMR to yield knowledge of their atomistic structures in relation to equilibrium properties. This review demonstrates the principles and applications of solid-state NMR by unifying dipolar and quadrupolar interactions and highlights the unique features offered by solid-state 2H NMR with experimental illustrations. For randomly oriented multilamellar lipids or aligned membranes, solid-state 2H NMR enables direct measurement of residual quadrupolar couplings (RQCs) due to individual C-2H-labeled segments. The distribution of RQC values gives nearly complete profiles of the segmental order parameters SCD(i) as a function of acyl segment position (i). Alternatively, one can measure residual dipolar couplings (RDCs) for natural abundance lipid samples to obtain segmental SCH order parameters. A theoretical mean-torque model provides acyl-packing profiles representing the cumulative chain extension along the normal to the aqueous interface. Equilibrium structural properties of fluid bilayers and various thermodynamic quantities can then be calculated, which describe the interactions with cholesterol, detergents, peptides, and integral membrane proteins and formation of lipid rafts. One can also obtain direct information for membrane-bound peptides or proteins by measuring RDCs using magic-angle spinning (MAS) in combination with dipolar recoupling methods. Solid-state NMR methods have been extensively applied to characterize model membranes and membrane-bound peptides and proteins, giving unique information on their conformations, orientations, and interactions in the natural liquid-crystalline state.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Soohyun Lee
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Michael F Brown
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
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23
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Affiliation(s)
- Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
- Department of Physics, University of Arizona, Tucson, Arizona 85721
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24
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Rajagopalan V, Greathouse DV, Koeppe RE. Influence of glutamic acid residues and pH on the properties of transmembrane helices. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:484-492. [PMID: 28069412 DOI: 10.1016/j.bbamem.2017.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/13/2016] [Accepted: 01/04/2017] [Indexed: 11/13/2022]
Abstract
Negatively charged side chains are important for the function of particular ion channels and certain other membrane proteins. To investigate the influence of single glutamic acid side chains on helices that span lipid-bilayer membranes, we have employed GWALP23 (acetyl-GGALW5LALALALALALALW19LAGA-amide) as a favorable host peptide framework. We substituted individual Leu residues with Glu residues (L12E or L14E or L16E) and incorporated specific 2H-labeled alanine residues within the core helical region or near the ends of the sequence. Solid-state 2H NMR spectra reveal little change for the core labels in GWALP23-E12, -E14 and -E16 over a pH range of 4 to 12.5, with the spectra being broader for samples in DOPC compared to DLPC bilayers. The spectra for samples with deuterium labels near the helix ends on alanines 3 and 21 show modest pH-dependent changes in the extent of unwinding of the helix terminals in DLPC and DOPC bilayers. The combined results indicate minor overall responses of these transmembrane helices to changes in pH, with the most buried residue E12 showing no pH dependence. While the Glu residues E14 and E16 may have high pKa values in the lipid bilayer environment, it is also possible that a paucity of helix response is masking the pKa values. Interestingly, when E16 is present, spectral changes at high pH report significant local unwinding of the core helix. Our results are consistent with the expectation that buried carboxyl groups aggressively hold their protons and/or waters of hydration.
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Affiliation(s)
- Venkatesan Rajagopalan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States.
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25
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Marquardt D, Heberle FA, Greathouse DV, Koeppe RE, Standaert RF, Van Oosten BJ, Harroun TA, Kinnun JJ, Williams JA, Wassall SR, Katsaras J. Lipid bilayer thickness determines cholesterol's location in model membranes. SOFT MATTER 2016; 12:9417-9428. [PMID: 27801465 DOI: 10.1039/c6sm01777k] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cholesterol is an essential biomolecule of animal cell membranes, and an important precursor for the biosynthesis of certain hormones and vitamins. It is also thought to play a key role in cell signaling processes associated with functional plasma membrane microdomains (domains enriched in cholesterol), commonly referred to as rafts. In all of these diverse biological phenomena, the transverse location of cholesterol in the membrane is almost certainly an important structural feature. Using a combination of neutron scattering and solid-state 2H NMR, we have determined the location and orientation of cholesterol in phosphatidylcholine (PC) model membranes having fatty acids of different lengths and degrees of unsaturation. The data establish that cholesterol reorients rapidly about the bilayer normal in all the membranes studied, but is tilted and forced to span the bilayer midplane in the very thin bilayers. The possibility that cholesterol lies flat in the middle of bilayers, including those made from PC lipids containing polyunsaturated fatty acids (PUFAs), is ruled out. These results support the notion that hydrophobic thickness is the primary determinant of cholesterol's location in membranes.
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Affiliation(s)
- Drew Marquardt
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada and Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA and Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Robert F Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Brad J Van Oosten
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Jacob J Kinnun
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Justin A Williams
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Stephen R Wassall
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - John Katsaras
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada and The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Shull Wollan Center-a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
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26
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Thibado JK, Martfeld AN, Greathouse DV, Koeppe RE. Influence of High pH and Cholesterol on Single Arginine-Containing Transmembrane Peptide Helices. Biochemistry 2016; 55:6337-6343. [PMID: 27782382 PMCID: PMC5266483 DOI: 10.1021/acs.biochem.6b00896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
An essential component
of mammalian cells, cholesterol exerts significant
influence on the physical properties of the cell membrane and in turn
its constituents, including membrane proteins. Although sparse, polar
amino acid residues are highly conserved in membrane proteins and
play pivotal roles in determining specific structural and functional
properties. To improve our understanding of particular polar residues
in the membrane environment, we have examined two specific “guest”
Arg residues within a well-defined and deuterium-labeled “host”
framework provided by the transmembrane helical peptide GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide).
Solid-state 2H nuclear magnetic resonance (NMR) spectra
from aligned bilayer membrane samples effectively report changes in
the host helix properties because of the incorporation of the guest
residues. The focus of this work is two-pronged. First, GWALP23-R14
was examined over a pH range of 2–13 in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) ester- or ether-linked
bilayer membranes. Our findings indicate that the Arg guanidinium
side chain remains charged over this entire range, in agreement with
numerous molecular dynamics simulations. Second, GWALP23-R12 and GWALP23-R14
peptides were characterized in DOPC bilayers with varying cholesterol
content. Our findings suggest that 10 or 20% cholesterol content has
minimal impact on the orientation of the R14 peptide. Although the
NMR signals are broader and weaker in the presence of 20% cholesterol,
the deuterium quadrupolar splittings for [2H]Ala residues
in GWALP23-R14 change very little. Conversely, cholesterol appears
to modulate the multistate behavior of GWALP23-R12 and to favor a
major interfacial state for the helix, bound at the bilayer surface.
These results indicate a conditional sensitivity of a complex multistate
transmembrane Arg-containing peptide helix to the presence of cholesterol.
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Affiliation(s)
- Jordana K Thibado
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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27
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Pyne A, Pfeil MP, Bennett I, Ravi J, Iavicoli P, Lamarre B, Roethke A, Ray S, Jiang H, Bella A, Reisinger B, Yin D, Little B, Muñoz-García JC, Cerasoli E, Judge PJ, Faruqui N, Calzolai L, Henrion A, Martyna GJ, Grovenor CRM, Crain J, Hoogenboom BW, Watts A, Ryadnov MG. Engineering monolayer poration for rapid exfoliation of microbial membranes. Chem Sci 2016; 8:1105-1115. [PMID: 28451250 PMCID: PMC5369539 DOI: 10.1039/c6sc02925f] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/25/2016] [Indexed: 12/04/2022] Open
Abstract
A novel mechanism of monolayer poration leading to the rapid exfoliation and lysis of microbial membranes is reported.
The spread of bacterial resistance to traditional antibiotics continues to stimulate the search for alternative antimicrobial strategies. All forms of life, from bacteria to humans, are postulated to rely on a fundamental host defense mechanism, which exploits the formation of open pores in microbial phospholipid bilayers. Here we predict that transmembrane poration is not necessary for antimicrobial activity and reveal a distinct poration mechanism that targets the outer leaflet of phospholipid bilayers. Using a combination of molecular-scale and real-time imaging, spectroscopy and spectrometry approaches, we introduce a structural motif with a universal insertion mode in reconstituted membranes and live bacteria. We demonstrate that this motif rapidly assembles into monolayer pits that coalesce during progressive membrane exfoliation, leading to bacterial cell death within minutes. The findings offer a new physical basis for designing effective antibiotics.
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Affiliation(s)
- Alice Pyne
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK . .,London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , London WC1E 6BT , UK
| | - Marc-Philipp Pfeil
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK . .,Department of Biochemistry , University of Oxford , Oxford OX1 3QU , UK
| | - Isabel Bennett
- London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , London WC1E 6BT , UK
| | - Jascindra Ravi
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK .
| | - Patrizia Iavicoli
- European Commission , Joint Research Centre , Institute for Health and Consumer Protection , Ispra (VA) , Italy
| | - Baptiste Lamarre
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK .
| | - Anita Roethke
- Physikalisch-Technische Bundesanstalt , 38116 Braunschweig , Germany
| | - Santanu Ray
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK .
| | - Haibo Jiang
- Centre for Microscopy , Characterisation and Analysis , The University of Western Australia , Crawley , Western Australia 6009 , Australia
| | - Angelo Bella
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK .
| | - Bernd Reisinger
- Physikalisch-Technische Bundesanstalt , 38116 Braunschweig , Germany
| | - Daniel Yin
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK . .,Department of Biochemistry , University of Oxford , Oxford OX1 3QU , UK
| | - Benjamin Little
- School of Physics and Astronomy , University of Edinburgh , Edinburgh EH9 3JZ , UK
| | | | - Eleonora Cerasoli
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK .
| | - Peter J Judge
- Department of Biochemistry , University of Oxford , Oxford OX1 3QU , UK
| | - Nilofar Faruqui
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK .
| | - Luigi Calzolai
- European Commission , Joint Research Centre , Institute for Health and Consumer Protection , Ispra (VA) , Italy
| | - Andre Henrion
- Physikalisch-Technische Bundesanstalt , 38116 Braunschweig , Germany
| | - Glenn J Martyna
- IBM T. J. Watson Research Center , Yorktown Heights , NY 10598 , USA
| | | | - Jason Crain
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK . .,School of Physics and Astronomy , University of Edinburgh , Edinburgh EH9 3JZ , UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , London WC1E 6BT , UK
| | - Anthony Watts
- Department of Biochemistry , University of Oxford , Oxford OX1 3QU , UK
| | - Maxim G Ryadnov
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , UK .
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28
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Martfeld AN, Greathouse DV, Koeppe RE. Ionization Properties of Histidine Residues in the Lipid Bilayer Membrane Environment. J Biol Chem 2016; 291:19146-56. [PMID: 27440045 PMCID: PMC5009283 DOI: 10.1074/jbc.m116.738583] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/12/2016] [Indexed: 01/22/2023] Open
Abstract
We address the critically important ionization properties of histidine side chains of membrane proteins, when exposed directly to lipid acyl chains within lipid bilayer membranes. The problem is important for addressing general principles that may underlie membrane protein function. To this end, we have employed a favorable host peptide framework provided by GWALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide). We inserted His residues into position 12 or 14 of GWALP23 (replacing either Leu(12) or Leu(14)) and incorporated specific [(2)H]Ala labels within the helical core sequence. Solid-state (2)H NMR spectra report the folding and orientation of the core sequence, revealing marked differences in the histidine-containing transmembrane helix behavior between acidic and neutral pH conditions. At neutral pH, the GWALP23-H12 and GWALP23-H14 helices exhibit well defined tilted transmembrane orientations in dioleoylphosphatidylcholine (DOPC)and dilauroylphosphatidylcholine (DLPC) bilayer membranes. Under acidic conditions, when His(12) is protonated and charged, the GWALP23-H12 helix exhibits a major population that moves to the DOPC bilayer surface and a minor population that occupies multiple transmembrane states. The response to protonation of His(14) is an increase in helix tilt, but GWALP23-H14 remains in a transmembrane orientation. The results suggest pKa values of less than 3 for His(12) and about 3-5 for His(14) in DOPC membranes. In the thinner DLPC bilayers, with increased water access, the helices are less responsive to changes in pH. The combined results enable us to compare the ionization properties of lipid-exposed His, Lys, and Arg side chains in lipid bilayer membranes.
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Affiliation(s)
- Ashley N Martfeld
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Denise V Greathouse
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Roger E Koeppe
- From the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
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29
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Grau-Campistany A, Strandberg E, Wadhwani P, Rabanal F, Ulrich AS. Extending the Hydrophobic Mismatch Concept to Amphiphilic Membranolytic Peptides. J Phys Chem Lett 2016; 7:1116-1120. [PMID: 26963560 DOI: 10.1021/acs.jpclett.6b00136] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A series of nine amphiphilic, pore-forming α-helical KIA peptides (KIAGKIA repeats) with lengths between 14 and 28 residues were studied by solid-state (15)N NMR to determine their alignment in oriented lipid bilayers. In a 2:1 mixture of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) with its corresponding 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (lyso-MPC), which has a highly positive spontaneous curvature, the helix tilt angle was found to vary steadily with peptide length. The shortest peptide was aligned transmembrane and upright, while the longer ones successively became tilted away from the membrane normal. This behavior is in agreement with the hydrophobic matching concept, conceived so far only for hydrophobic helices. In 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine, with a negative spontaneous curvature, all KIA peptides remained flat on the bilayer surface, while the cylindrical DMPC lipids permitted a slight tilt. Peptide insertion thus depends critically on the intrinsic lipid curvature, and helix orientation is then fine-tuned by membrane thickness. A refined toroidal pore model is proposed.
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Affiliation(s)
- Ariadna Grau-Campistany
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry , KIT , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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30
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Mortazavi A, Rajagopalan V, Sparks KA, Greathouse DV, Koeppe RE. Juxta-terminal Helix Unwinding as a Stabilizing Factor to Modulate the Dynamics of Transmembrane Helices. Chembiochem 2016; 17:462-5. [PMID: 26749271 PMCID: PMC4820057 DOI: 10.1002/cbic.201500656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 12/24/2022]
Abstract
Transmembrane helices of integral membrane proteins often are flanked by interfacial aromatic residues that can serve as anchors to aid the stabilization of a tilted transmembrane orientation. Yet, physical factors that govern the orientation or dynamic averaging of individual transmembrane helices are not well understood and have not been adequately explained. Using solid-state (2) H NMR spectroscopy to examine lipid bilayer-incorporated model peptides of the GWALP23 (acetyl-GGALW(LA)6 LWLAGA-amide) family, we observed substantial unwinding at the terminals of several tilted helices spanning the membranes of DLPC, DMPC, or DOPC lipid bilayers. The fraying of helix ends might be vital for defining the dynamics and orientations of transmembrane helices in lipid bilayer membranes.
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Affiliation(s)
- Armin Mortazavi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Venkatesan Rajagopalan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kelsey A Sparks
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, 72701, USA.
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31
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Zamora-Carreras H, Strandberg E, Mühlhäuser P, Bürck J, Wadhwani P, Jiménez MÁ, Bruix M, Ulrich AS. Alanine scan and (2)H NMR analysis of the membrane-active peptide BP100 point to a distinct carpet mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1328-38. [PMID: 26975251 DOI: 10.1016/j.bbamem.2016.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/23/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
The short membrane-active peptide BP100 [KKLFKKILKYL-NH2] is known as an effective antimicrobial and cell penetrating agent. For a functional alanine scan each of the 11 amino acids was replaced with deuterated Ala-d3, one at a time. MIC assays showed that a substitution of Lys did not affect the antimicrobial activity, but it decreased when a hydrophobic residue was replaced. In most cases, a reduction in hydrophobicity led to a decrease in hemolysis, and some peptide analogues had an improved therapeutic index. Circular dichroism showed that BP100 folds as an amphiphilic α-helix in a bilayer. Its alignment was determined from (2)H NMR in oriented membranes of different composition. The azimuthal rotation angle was the same under all conditions, but the average helix tilt angle and the dynamical behavior of the peptide varied in a systematic manner. In POPC/POPG bilayers, with a negative spontaneous curvature, the peptide was found to lie flat on the bilayer surface, and with little wobble. In DMPC/DMPG, with a positive spontaneous curvature, BP100 at higher concentrations became tilted obliquely into the membrane, with the uncharged C-terminus inserted more deeply into the lipid bilayer, experiencing significant fluctuations in tilt angle. In DMPC/DMPG/lyso-MPC, with a pronounced positive spontaneous curvature, the helix tilted even further and became even more mobile. The 11-mer BP100 is obviously too short to form transmembrane pores. We conclude that BP100 operates via a carpet mechanism, whereby the C-terminus gets inserted into the hydrophobic core of the bilayer, which leads to membrane perturbation and induces transient permeability.
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Affiliation(s)
| | - Erik Strandberg
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Philipp Mühlhäuser
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - M Ángeles Jiménez
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Marta Bruix
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Anne S Ulrich
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany; KIT, Institute of Organic Chemistry and CFN, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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32
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Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol 2015; 11:e1004368. [PMID: 26505197 PMCID: PMC4624691 DOI: 10.1371/journal.pcbi.1004368] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/01/2015] [Indexed: 11/25/2022] Open
Abstract
The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced. Knowledge of multiple conformational states of membrane transport proteins is a prerequisite to understand their function. However, the determination of atomic structures for all these states with conventional high-resolution approaches can be very challenging due to inherent difficulties in high yield purification of functional membrane transport proteins. Various complementary structural information of proteins in their native states can be obtained by a variety of biophysical and biochemical methods with site-directed mutations. Here, a novel restrained molecular dynamics structural refinement method is developed to help derive a structural model that is consistent with experimental data by incorporating all the experimental constraints simultaneously through the use of non-interacting all-atom molecular fragments. The method can be easily and effectively extended to incorporate many kinds of structural constraints from a variety of biophysical and biochemical experiments, and should be very useful in generating and refining models of proteins in specific functional states.
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33
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Membrane interactions of phylloseptin-1, -2, and -3 peptides by oriented solid-state NMR spectroscopy. Biophys J 2015; 107:901-11. [PMID: 25140425 DOI: 10.1016/j.bpj.2014.07.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/30/2014] [Accepted: 07/07/2014] [Indexed: 01/10/2023] Open
Abstract
Phylloseptin-1, -2, and -3 are three members of the family of linear cationic antimicrobial peptides found in tree frogs. The highly homologous peptides encompass 19 amino acids, and only differ in the amino acid composition and charge at the six most carboxy-terminal residues. Here, we investigated how such subtle changes are reflected in their membrane interactions and how these can be correlated to their biological activities. To this end, the three peptides were labeled with stable isotopes, reconstituted into oriented phospholipid bilayers, and their detailed topology determined by a combined approach using (2)H and (15)N solid-state NMR spectroscopy. Although phylloseptin-2 and -3 adopt perfect in-plane alignments, the tilt angle of phylloseptin-1 deviates by 8° probably to assure a more water exposed localization of the lysine-17 side chain. Furthermore, different azimuthal angles are observed, positioning the amphipathic helices of all three peptides with the charged residues well exposed to the water phase. Interestingly, our studies also reveal that two orientation-dependent (2)H quadrupolar splittings from methyl-deuterated alanines and one (15)N amide chemical shift are sufficient to unambiguously determine the topology of phylloseptin-1, where quadrupolar splittings close to the maximum impose the most stringent angular restraints. As a result of these studies, a strategy is proposed where the topology of a peptide structure can be determined accurately from the labeling with (15)N and (2)H isotopes of only a few amino acid residues.
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Strandberg E, Ulrich AS. AMPs and OMPs: Is the folding and bilayer insertion of β-stranded outer membrane proteins governed by the same biophysical principles as for α-helical antimicrobial peptides? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1944-54. [PMID: 25726906 DOI: 10.1016/j.bbamem.2015.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 11/24/2022]
Abstract
The folding and function of membrane proteins is controlled not only by specific but also by unspecific interactions with the constituent lipids. In this review, we focus on the influence of the spontaneous lipid curvature on the folding and insertion of peptides and proteins in membranes. Amphiphilic α-helical peptides, as represented by various antimicrobial sequences, are compared with β-barrel proteins, which are found in the outer membrane of Gram-negative bacteria. It has been shown that cationic amphiphilic peptides are always surface-bound in lipids with a negative spontaneous curvature like POPC, i.e. they are oriented parallel to the membrane plane. On the other hand, in lipids like DMPC with a positive curvature, these peptides can get tilted or completely inserted in a transmembrane state. Remarkably, the folding and spontaneous membrane insertion of β-barrel outer membrane proteins also proceeds more easily in lipids with a positive intrinsic curvature, while it is hampered by negative curvature. We therefore propose that a positive spontaneous curvature of the lipids promotes the ability of a surface-bound molecule to insert more deeply into the bilayer core, irrespective of the conformation, size, or shape of the peptide, protein, or folding intermediate. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B. 3640, 76021 Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B. 3640, 76021 Karlsruhe, Germany; KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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35
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3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides. Biophys J 2015; 106:2385-94. [PMID: 24896117 DOI: 10.1016/j.bpj.2014.04.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 11/22/2022] Open
Abstract
The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/.
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36
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Sparks KA, Gleason NJ, Gist R, Langston R, Greathouse DV, Koeppe RE. Comparisons of interfacial Phe, Tyr, and Trp residues as determinants of orientation and dynamics for GWALP transmembrane peptides. Biochemistry 2014; 53:3637-45. [PMID: 24829070 PMCID: PMC4053069 DOI: 10.1021/bi500439x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Aromatic
amino acids often flank the transmembrane alpha helices
of integral membrane proteins. By favoring locations within the membrane–water
interface of the lipid bilayer, aromatic residues Trp, Tyr, and sometimes
Phe may serve as anchors to help stabilize a transmembrane orientation.
In this work, we compare the influence of interfacial Trp, Tyr, or
Phe residues upon the properties of tilted helical transmembrane peptides.
For such comparisons, it has been critical to start with no more than
one interfacial aromatic residue near each end of a transmembrane
helix, for example, that of GWALP23 (acetyl-GGALW5(LA)6LW19LAGA-[ethanol]amide). To this end, we have
employed 2H-labeled alanines and solid-state NMR spectroscopy
to investigate the consequences of moving or replacing W5 or W19 in
GWALP23 with selected Tyr, Phe, or Trp residues at the same or proximate
locations. We find that GWALP23 peptides having F5, Y5, or W5 exhibit
essentially the same average tilt and similar dynamics in bilayer
membranes of 1,2-dilauroylphosphatidylcholine (DLPC) or 1,2-dioleoylphosphatidylcholine
(DOPC). When double Tyr anchors are present, in Y4,5GWALP23
the NMR observables are markedly more subject to dynamic averaging
and at the same time are less responsive to the bilayer thickness.
Decreased dynamics are nevertheless observed when ring hydrogen bonding
is removed, such that F4,5GWALP23 exhibits a similar extent
of low dynamic averaging as GWALP23 itself. When F5 is the sole aromatic
group in the N-interfacial region, the dynamic averaging is (only)
slightly more extensive than with W5, Y5, or Y4 alone or with F4,5,
yet it is much less than that observed for Y4,5GWALP23.
Interestingly, moving Y5 to Y4 or W19 to W18, while retaining only
one hydrogen-bond-capable aromatic ring at each interface, maintains
the low level of dynamic averaging but alters the helix azimuthal
rotation. The rotation change is about 40° for Y4 regardless
of whether the host lipid bilayer is DLPC or DOPC. The rotational
change (Δρ) is more dramatic and more complex when W19
is moved to W18, as Δρ is about +90° in DLPC but
about −60° in DOPC. Possible reasons for this curious
lipid-dependent helix rotation could include not only the separation
distances between flanking aromatic or hydrophobic residues but also
the absolute location of the W19 indole ring. For the more usual cases,
when the helix azimuthal rotation shows little dependence on the host
bilayer identity, excepting W18GWALP23, the transmembrane
helices adapt to different lipids primarily by changing the magnitude
of their tilt. We conclude that, in the absence of other functional
groups, interfacial aromatic residues determine the preferred orientations
and dynamics of membrane-spanning peptides. The results furthermore
suggest possibilities for rotational and dynamic control of membrane
protein function.
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Affiliation(s)
- Kelsey A Sparks
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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37
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Wadhwani P, Strandberg E, van den Berg J, Mink C, Bürck J, Ciriello RA, Ulrich AS. Dynamical structure of the short multifunctional peptide BP100 in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:940-9. [DOI: 10.1016/j.bbamem.2013.11.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/25/2013] [Accepted: 11/01/2013] [Indexed: 11/26/2022]
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38
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Gleason NJ, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Single tryptophan and tyrosine comparisons in the N-terminal and C-terminal interface regions of transmembrane GWALP peptides. J Phys Chem B 2013; 117:13786-94. [PMID: 24111589 DOI: 10.1021/jp407542e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrophobic membrane-spanning helices often are flanked by interfacial aromatic or charged residues. In this paper, we compare the consequences of single Trp → Tyr substitutions at each interface for the properties of a defined transmembrane helix in the absence of charged residues. The choice of molecular framework is critical for these single-residue experiments because the presence of "too many" aromatic residues (more than one at either membrane-water interface) introduces excess dynamic averaging of solid state NMR observables. To this end, we compare the outcomes when changing W(5) or W(19), or both of them, to tyrosine in the well-characterized transmembrane peptide acetyl-GGALW(5)(LA)6LW(19)LAGA-amide ("GWALP23"). By means of solid-state (2)H and (15)N NMR experiments, we find that Y(19)GW(5)ALP23 displays similar magnitudes of peptide helix tilt as Y(5)GW(19)ALP23 and responds similarly to changes in bilayer thickness, from DLPC to DMPC to DOPC. The presence of Y(19) changes the azimuthal rotation angle ρ (about the helix axis) to a similar extent as Y(5), but in the opposite direction. When tyrosines are substituted for both tryptophans to yield GY(5,19)ALP23, the helix tilt angle is again of comparable magnitude, and furthermore, the preferred azimuthal rotation angle ρ is relatively unchanged from that of GW(5,19)ALP23. The extent of dynamic averaging increases marginally when Tyr replaces Trp. Yet, importantly, all members of the peptide family having single Tyr or Trp residues near each interface exhibit only moderate and not highly extensive dynamic averaging. The results provide important benchmarks for evaluating conformational and dynamic control of membrane protein function.
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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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39
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Vostrikov VV, Mote KR, Verardi R, Veglia G. Structural dynamics and topology of phosphorylated phospholamban homopentamer reveal its role in the regulation of calcium transport. Structure 2013; 21:2119-30. [PMID: 24207128 DOI: 10.1016/j.str.2013.09.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 01/25/2023]
Abstract
Phospholamban (PLN) inhibits the sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA), thereby regulating cardiac diastole. In membranes, PLN assembles into homopentamers that in both the phosphorylated and nonphosphorylated states have been proposed to form ion-selective channels. Here, we determined the structure of the phosphorylated pentamer using a combination of solution and solid-state nuclear magnetic resonance methods. We found that the pinwheel architecture of the homopentamer is preserved upon phosphorylation, with each monomer having an L-shaped conformation. The TM domains form a hydrophobic pore approximately 24 Å long and 2 Å in diameter, which is inconsistent with canonical Ca²⁺-selective channels. Phosphorylation, however, enhances the conformational dynamics of the cytoplasmic region of PLN, causing partial unwinding of the amphipathic helix. We propose that PLN oligomers act as storage for active monomers, keeping SERCA function within a physiological window.
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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40
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Sánchez-Muñoz OL, Strandberg E, Esteban-Martín E, Grage SL, Ulrich AS, Salgado J. Canonical azimuthal rotations and flanking residues constrain the orientation of transmembrane helices. Biophys J 2013; 104:1508-16. [PMID: 23561527 DOI: 10.1016/j.bpj.2013.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/31/2013] [Accepted: 02/20/2013] [Indexed: 12/22/2022] Open
Abstract
In biological membranes the alignment of embedded proteins provides crucial structural information. The transmembrane (TM) parts have well-defined secondary structures, in most cases α-helices and their orientation is given by a tilt angle and an azimuthal rotation angle around the main axis. The tilt angle is readily visualized and has been found to be functionally relevant. However, there exist no general concepts on the corresponding azimuthal rotation. Here, we show that TM helices prefer discrete rotation angles. They arise from a combination of intrinsic properties of the helix geometry plus the influence of the position and type of flanking residues at both ends of the hydrophobic core. The helical geometry gives rise to canonical azimuthal angles for which the side chains of residues from the two ends of the TM helix tend to have maximum or minimum immersion within the membrane. This affects the preferential position of residues that fall near hydrophobic/polar interfaces of the membrane, depending on their hydrophobicity and capacity to form specific anchoring interactions. On this basis, we can explain the orientation and dynamics of TM helices and make accurate predictions, which correspond well to the experimental values of several model peptides (including dimers), and TM segments of polytopic membrane proteins.
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41
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Strandberg E, Zerweck J, Wadhwani P, Ulrich AS. Synergistic insertion of antimicrobial magainin-family peptides in membranes depends on the lipid spontaneous curvature. Biophys J 2013; 104:L9-11. [PMID: 23528099 DOI: 10.1016/j.bpj.2013.01.047] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 01/09/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022] Open
Abstract
PGLa and magainin 2 (MAG2) are amphiphilic antimicrobial peptides from frog skin with known synergistic activity. The orientation of the two helices in membranes was studied using solid-state (15)N-NMR, for each peptide alone and for a 1:1 mixture of the peptides, in a range of different lipid systems. Two types of orientational behavior emerged. 1), In lipids with negative spontaneous curvature, both peptides remain flat on the membrane surface, when assessed both alone and in a 1:1 mixture. 2), In lipids with positive spontaneous curvature, PGLa alone assumes a tilted orientation but inserts into the bilayer in a transmembrane alignment in the presence of MAG2, whereas MAG2 stays on the surface or gets only slightly tilted, when observed both alone and in the presence of PGLa. The behavior of PGLa alone is identical to that of another antimicrobial peptide, MSI-103, in the same lipid systems, indicating that the curvature-dependent helix orientation is a general feature of membrane-bound peptides and also influences their synergistic intermolecular interactions.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
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42
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Buried lysine, but not arginine, titrates and alters transmembrane helix tilt. Proc Natl Acad Sci U S A 2013; 110:1692-5. [PMID: 23319623 DOI: 10.1073/pnas.1215400110] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ionization states of individual amino acid residues of membrane proteins are difficult to decipher or assign directly in the lipid-bilayer membrane environment. We address this issue for lysines and arginines in designed transmembrane helices. For lysines (but not arginines) at two locations within dioleoyl-phosphatidylcholine bilayer membranes, we measure pK(a) values below 7.0. We find that buried charged lysine, in fashion similar to arginine, will modulate helix orientation to maximize its own access to the aqueous interface or, if occluded by aromatic rings, may cause a transmembrane helix to exit the lipid bilayer. Interestingly, the influence of neutral lysine (vis-à-vis leucine) upon helix orientation also depends upon its aqueous access. Our results suggest that changes in the ionization states of particular residues will regulate membrane protein function and furthermore illustrate the subtle complexity of ionization behavior with respect to the detailed lipid and protein environment.
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Caputo GA. Analyzing the effects of hydrophobic mismatch on transmembrane α-helices using tryptophan fluorescence spectroscopy. Methods Mol Biol 2013; 1063:95-116. [PMID: 23975773 DOI: 10.1007/978-1-62703-583-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydrophobic matching between transmembrane protein segments and the lipid bilayer in which they are embedded is a significant factor in the behavior and orientation of such transmembrane segments. The condition of hydrophobic mismatch occurs when the hydrophobic thickness of a lipid bilayer is significantly different than the length of the membrane spanning segment of a protein, resulting in a mismatch. This mismatch can result in altered function of proteins as well as nonnative structural arrangements including effects on transmembrane α-helix tilt angles, oligomerization state, and/or the formation of non-transmembrane topographies. Here, a fluorescence-based protocol is described for testing model transmembrane α-helices and their sensitivity to hydrophobic mismatch by measuring the propensity of these helices to form non-transmembrane structures. Overall, good hydrophobic matching between the bilayer and transmembrane segments is an important factor that must be considered when designing membrane proteins or peptides.
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Affiliation(s)
- Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, USA
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Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations. Biophys J 2012; 103:29-37. [PMID: 22828329 DOI: 10.1016/j.bpj.2012.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/30/2012] [Accepted: 05/07/2012] [Indexed: 02/02/2023] Open
Abstract
Elemental biological functions such as molecular signal transduction are determined by the dynamic interplay between polypeptides and the membrane environment. Determining such supramolecular arrangements poses a significant challenge for classical structural biology methods. We introduce an iterative approach that combines magic-angle spinning solid-state NMR spectroscopy and atomistic molecular dynamics simulations for the determination of the structure and topology of membrane-bound systems with a resolution and level of accuracy difficult to obtain by either method alone. Our study focuses on the Shaker B ball peptide that is representative for rapid N-type inactivating domains of voltage-gated K(+) channels, associated with negatively charged lipid bilayers.
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Rankenberg JM, Vostrikov VV, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Properties of membrane-incorporated WALP peptides that are anchored on only one end. Biochemistry 2012; 51:10066-74. [PMID: 23171005 DOI: 10.1021/bi301394z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides of the "WALP" family, acetyl-GWW(LA)(n)LWWA-[ethanol]amide, have proven to be opportune models for investigating lipid-peptide interactions. Because the average orientations and motional behavior of the N- and C-terminal Trp (W) residues differ, it is of interest to investigate how the positions of the tryptophans influence the properties of the membrane-incorporated peptides. To address this question, we synthesized acetyl-GGWW(LA)(n)-ethanolamide and acetyl-(AL)(n)WWG-ethanolamide, in which n = 4 or 8, which we designate as "N-anchored" and "C-anchored" peptides, respectively. Selected (2)H or (15)N labels were incorporated for solid-state nuclear magnetic resonance (NMR) spectroscopy. These peptides can be considered "half"-anchored WALP peptides, having only one pair of interfacial Trp residues near either the amino or the carboxyl terminus. The hydrophobic lengths of the (n = 8) peptides are similar to that of WALP23. These longer half-anchored WALP peptides incorporate into lipid bilayers as α-helices, as reflected in their circular dichroism spectra. Solid-state NMR experiments indicate that the longer peptide helices assume defined transmembrane orientations with small non-zero average tilt angles and moderate to high dynamic averaging in bilayer membranes of 1,2-dioleoylphosphatidylcholine, 1,2-dimyristoylphosphatidylcholine, and 1,2-dilauroylphosphatidylcholine. The intrinsically small apparent tilt angles suggest that interactions of aromatic residues with lipid headgroups may play an important role in determining the magnitude of the peptide tilt in the bilayer membrane. The shorter (n = 4) peptides, in stark contrast to the longer peptides, display NMR spectra that are characteristic of greatly reduced motional averaging, probably because of peptide aggregation in the bilayer environment, and CD spectra that are characteristic of β-structure.
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Affiliation(s)
- Johanna M Rankenberg
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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Vostrikov VV, Hall BA, Sansom MSP, Koeppe RE. Accommodation of a central arginine in a transmembrane peptide by changing the placement of anchor residues. J Phys Chem B 2012; 116:12980-90. [PMID: 23030363 DOI: 10.1021/jp308182b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Both Trp and Arg in transmembrane protein domains make important interactions with lipids at the membrane/water interface, but at different depths. Derivatives of the designed peptide GWALP23, acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide, with single Trp anchors, have proven useful for characterizing such interactions. Indeed, previous work revealed quite different effects emanating from Arg substitutions at positions 12 and 14 within GWALP23, with the R12 peptide exhibiting multiple positions and orientations with respect to DOPC bilayer membranes (Vostrikov et al. J. Am. Chem. Soc. 2010, 132, 5803-5811). To gain further understanding of the multistate behavior, we moved the Trp "anchor" residues to more outer positions 3 and 21 in GWALP23 itself, and in the R12 and R14 derivatives. The locations and orientations of the peptides with respect to lipid bilayer membranes of differing thickness were investigated by means of solid-state (2)H NMR spectroscopy, using labeled alanines, and coarse-grained molecular dynamics simulations. Interestingly, relatively intense and narrow (2)H resonances from selected backbone C(α) deuterons were observed over quite narrow ranges of frequency and sample orientation. The backbone resonances reflect dynamic complexities and at the same time provide important contributions for the analysis of peptide transmembrane orientation. With the Trp(3,21) anchors relatively far from the peptide and bilayer center, the results indicate significantly large apparent tilt angles, for example, close to 30° for the new R12 and R14 peptides with respect to the bilayer normal of DLPC membranes. The R12 side chain indeed is "rescued" to a stable position, where it is accommodated within the transmembrane helix, when the Trp anchors are moved outward and to another face of the helix. At the same time, the R14 side chain of transmembrane GW(3,21)ALP23 also retains a stable favored position.
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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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Callenberg KM, Latorraca NR, Grabe M. Membrane bending is critical for the stability of voltage sensor segments in the membrane. ACTA ACUST UNITED AC 2012; 140:55-68. [PMID: 22732310 PMCID: PMC3382720 DOI: 10.1085/jgp.201110766] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The interaction between membrane proteins and the surrounding membrane is becoming increasingly appreciated for its role in regulating protein function, protein localization, and membrane morphology. In particular, recent studies have suggested that membrane deformation is needed to stably accommodate proteins harboring charged amino acids in their transmembrane (TM) region, as it is energetically prohibitive to bury charge in the hydrophobic core of the bilayer. Unfortunately, current computational methods are poorly equipped for describing such deformations, as atomistic simulations are often too short to observe large-scale membrane reorganization and most continuum approaches assume a flat membrane. Previously, we developed a method that overcomes these shortcomings by using elasticity theory to characterize equilibrium membrane distortions in the presence of a TM protein, while using traditional continuum electrostatic and nonpolar energy models to determine the energy of the protein in the membrane. Here, we linked the elastostatics, electrostatics, and nonpolar numeric solvers to permit the calculation of energies for nontrivial membrane deformations. We then coupled this procedure to a robust search algorithm that identifies optimal membrane shapes for a TM protein of arbitrary chemical composition. This advance now permits us to explore a host of biological phenomena that were beyond the scope of our original method. We show that the energy required to embed charged residues in the membrane can be highly nonadditive, and our model provides a simple mechanical explanation for this nonadditivity. Our results also predict that isolated voltage sensor segments do not insert into rigid membranes, but membrane bending dramatically stabilizes these proteins in the bilayer despite their high charge content. Additionally, we use the model to explore hydrophobic mismatch with regard to nonpolar peptides and mechanosensitive channels. Our method is in quantitative agreement with molecular dynamics simulations at a tiny fraction of the computational cost.
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Affiliation(s)
- Keith M Callenberg
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA 15213, USA
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de Jesus AJ, Allen TW. The determinants of hydrophobic mismatch response for transmembrane helices. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:851-63. [PMID: 22995244 DOI: 10.1016/j.bbamem.2012.09.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 10/27/2022]
Abstract
Hydrophobic mismatch arises from a difference in the hydrophobic thickness of a lipid membrane and a transmembrane protein segment, and is thought to play an important role in the folding, stability and function of membrane proteins. We have investigated the possible adaptations that lipid bilayers and transmembrane α-helices undergo in response to mismatch, using fully-atomistic molecular dynamics simulations totaling 1.4 μs. We have created 25 different tryptophan-alanine-leucine transmembrane α-helical peptide systems, each composed of a hydrophobic alanine-leucine stretch, flanked by 1-4 tryptophan side chains, as well as the β-helical peptide dimer, gramicidin A. Membrane responses to mismatch include changes in local bilayer thickness and lipid order, varying systematically with peptide length. Adding more flanking tryptophan side chains led to an increase in bilayer thinning for negatively mismatched peptides, though it was also associated with a spreading of the bilayer interface. Peptide tilting, bending and stretching were systematic, with tilting dominating the responses, with values of up to ~45° for the most positively mismatched peptides. Peptide responses were modulated by the number of tryptophan side chains due to their anchoring roles and distributions around the helices. Potential of mean force calculations for local membrane thickness changes, helix tilting, bending and stretching revealed that membrane deformation is the least energetically costly of all mismatch responses, except for positively mismatched peptides where helix tilting also contributes substantially. This comparison of energetic driving forces of mismatch responses allows for deeper insight into protein stability and conformational changes in lipid membranes.
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Strandberg E, Tiltak D, Ehni S, Wadhwani P, Ulrich AS. Lipid shape is a key factor for membrane interactions of amphipathic helical peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1764-76. [DOI: 10.1016/j.bbamem.2012.02.027] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/22/2012] [Accepted: 02/27/2012] [Indexed: 02/07/2023]
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50
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Gofman Y, Haliloglu T, Ben-Tal N. The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation. J Chem Theory Comput 2012; 8:2896-2904. [PMID: 24932138 PMCID: PMC4053537 DOI: 10.1021/ct300128x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Indexed: 11/29/2022]
Abstract
Hydrophobic helical peptides interact with lipid bilayers
in various
modes, determined by the match between the length of the helix’s
hydrophobic core and the thickness of the hydrocarbon region of the
bilayer. For example, long helices may tilt with respect to the membrane
normal to bury their hydrophobic cores in the membrane, and the lipid
bilayer may stretch to match the helix length. Recent molecular dynamics
simulations and potential of mean force calculations have shown that
some TM helices whose lengths are equal to, or even shorter than,
the bilayer thickness may also tilt. The tilt is driven by a gain
in the helix precession entropy, which compensates for the free energy
penalty resulting from membrane deformation. Using this free energy
balance, we derived theoretically an equation of state, describing
the dependence of the tilt on the helix length and membrane thickness.
To this end, we conducted coarse-grained Monte Carlo simulations of
the interaction of helices of various lengths with lipid bilayers
of various thicknesses, reproducing and expanding the previous molecular
dynamics simulations. Insight from the simulations facilitated the
derivation of the theoretical model. The tilt angles calculated using
the theoretical model agree well with our simulations and with previous
calculations and measurements.
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Affiliation(s)
- Yana Gofman
- Helmholtz-Zentrum, 21502 Geesthacht, Germany ; The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Turkan Haliloglu
- Chemical Engineering Department, Polymer Research Center, Life Sciences and Technologies Research Center, Bogazici University, 34342 Bebek-Istanbul, Turkey
| | - Nir Ben-Tal
- The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
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