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Khakimzhan A, Izri Z, Thompson S, Dmytrenko O, Fischer P, Beisel C, Noireaux V. Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Commun Biol 2024; 7:1005. [PMID: 39152195 PMCID: PMC11329788 DOI: 10.1038/s42003-024-06690-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report cell-free transcription-translation in a quartz crystal microbalance with dissipation (TXTL-QCMD) to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes, and the multiple-IIMP dynamical pattern-forming association of the E. coli division-coordinating proteins MinCDE. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system that is unamenable to labeling, we discovered that ZorA and ZorB integrate within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.
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Affiliation(s)
- Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ziane Izri
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Oleg Dmytrenko
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Patrick Fischer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Chase Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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2
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Griffo A, Sparn C, Lolicato F, Nolle F, Khangholi N, Seemann R, Fleury JB, Brinkmann M, Nickel W, Hähl H. Mechanics of biomimetic free-standing lipid membranes: insights into the elasticity of complex lipid compositions. RSC Adv 2024; 14:13044-13052. [PMID: 38655466 PMCID: PMC11034475 DOI: 10.1039/d4ra00738g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
The creation of free-standing lipid membranes has been so far of remarkable interest to investigate processes occurring in the cell membrane since its unsupported part enables studies in which it is important to maintain cell-like physicochemical properties of the lipid bilayer, that nonetheless depend on its molecular composition. In this study, we prepare pore-spanning membranes that mimic the composition of plasma membranes and perform force spectroscopy indentation measurements to unravel mechanistic insights depending on lipid composition. We show that this approach is highly effective for studying the mechanical properties of such membranes. Furthermore, we identify a direct influence of cholesterol and sphingomyelin on the elasticity of the bilayer and adhesion between the two leaflets. Eventually, we explore the possibilities of imaging in the unsupported membrane regions. For this purpose, we investigate the adsorption and movement of a peripheral protein, the fibroblast growth factor 2, on the complex membrane.
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Affiliation(s)
- Alessandra Griffo
- Center for Biophysics, Experimental Physics, Saarland University Saarbrücken Germany
- Department of Experimental Physics, Saarland University Saarbrücken Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg Germany
| | - Carola Sparn
- Heidelberg University Biochemistry Center Heidelberg Germany
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center Heidelberg Germany
| | - Friederike Nolle
- Center for Biophysics, Experimental Physics, Saarland University Saarbrücken Germany
- Department of Experimental Physics, Saarland University Saarbrücken Germany
| | - Navid Khangholi
- Center for Biophysics, Experimental Physics, Saarland University Saarbrücken Germany
- Department of Experimental Physics, Saarland University Saarbrücken Germany
| | - Ralf Seemann
- Center for Biophysics, Experimental Physics, Saarland University Saarbrücken Germany
| | - Jean-Baptiste Fleury
- Center for Biophysics, Experimental Physics, Saarland University Saarbrücken Germany
- Department of Experimental Physics, Saarland University Saarbrücken Germany
| | - Martin Brinkmann
- Department of Experimental Physics, Saarland University Saarbrücken Germany
| | - Walter Nickel
- Heidelberg University Biochemistry Center Heidelberg Germany
| | - Hendrik Hähl
- Center for Biophysics, Experimental Physics, Saarland University Saarbrücken Germany
- Department of Experimental Physics, Saarland University Saarbrücken Germany
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3
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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: 2] [Impact Index Per Article: 2.0] [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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4
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Regmi D, Shen F, Stanic A, Islam M, Du D. Effect of phospholipid liposomes on prion fragment (106-128) amyloid formation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184199. [PMID: 37454869 DOI: 10.1016/j.bbamem.2023.184199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/08/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Misfolding and aggregation of cellular prion protein (PrPc) is a major molecular process involved in the pathogenesis of prion diseases. Here, we studied the aggregation properties of a prion fragment peptide PrP(106-128). The results show that the peptide aggregates in a concentration-dependent manner in an aqueous solution and that the aggregation is sensitive to pH and the preformed amyloid seeds. Furthermore, we show that the zwitterionic POPC liposomes moderately inhibit the aggregation of PrP(106-128), whereas POPC/cholesterol (8:2) vesicles facilitate peptide aggregation likely due to the increase of the lipid packing order and membrane rigidity in the presence of cholesterol. In addition, anionic lipid vesicles of POPG and POPG/cholesterol above a certain concentration accelerate the aggregation of the peptide remarkably. The strong electrostatic interactions between the N-terminal region of the peptide and POPG may constrain the conformational plasticity of the peptide, preventing insertion of the peptide into the inner side of the membrane and thus promoting fibrillation on the membrane surface. The results suggest that the charge properties of the membrane, the composition of the liposomes, and the rigidity of lipid packing are critical in determining peptide adsorption on the membrane surface and the efficiency of the membrane in catalyzing peptide oligomeric nucleation and amyloid formation. The peptide could be used as an improved model molecule to investigate the mechanistic role of the crucial regions of PrP in aggregation in a membrane-rich environment and to screen effective inhibitors to block key interactions between these regions and membranes for preventing PrP aggregation.
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Affiliation(s)
- Deepika Regmi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Aleksander Stanic
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA.
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5
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El-Fakharany EM, El-Gendi H, Abdel-Wahhab K, Abu-Serie MM, El-Sahra DG, Ashry M. Therapeutic efficacy of α-lactalbumin coated oleic acid based liposomes against colorectal carcinoma in Caco-2 cells and DMH-treated albino rats. J Biomol Struct Dyn 2023:1-15. [PMID: 37624964 DOI: 10.1080/07391102.2023.2250452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
Colorectal cancer (CRC) is a malignant tumor recognized as a major cause of morbidity and mortality throughout the world. Therefore, novel liposomes of oleic acid coated with camel α-lactalbumin (α-LA coated liposomes) were developed for their potential antitumor activity against CRC, both in vitro and in DMH-induced CRC-modeled animal. In vitro results indicated the high safety of α-LA coated liposomes towards normal human cells with potent antitumor activity against Caco-2 cells at an IC50 value of 57.01 ± 3.55 µM with selectivity index of 6.92 ± 0.48. This antitumor activity has been attributed to induction of the apoptotic mechanism, as demonstrated by nuclear condensation and arrest of Caco-2 cells in sub-G1 populations. α-LA coated liposomes also revealed a significant up-regulation of the p53 gene combined with a down-regulation of the Bcl2 gene. Moreover, in vivo results revealed that treatment of induced-CRC modeled animals with α-LA coated liposomes for six weeks markedly improved the CRC-disorders; this was achieved from the significant reduction in the values of AFP, CEA, CA19.9, TNF-α, IL-1β, MDA, and NO coupled with remarkable rise in SOD, GPx, GSH, CAT, and CD4+ levels. The histopathological findings asserted the therapeutic potential of α-LA coated liposomes in the treatment of CRC. Therefore, the present results proved the antitumor activity of α-LA coated liposomes against CRC through the restoration of impaired oxidative stress, improved immune response, and reduced inflammation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Esmail M El-Fakharany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA- City), Alexandria, Egypt
| | - Hamada El-Gendi
- Bioprocess Development Department, GEBRI, SRTA-City, Alexandria, Egypt
| | | | - Marwa M Abu-Serie
- Medical Biotechnology Department, GEBRI, SRTA-City, Alexandria, Egypt
| | - Doaa Galal El-Sahra
- Medical Surgical Nursing Department, Faculty of Nursing, Modern University for Technology and Information, Cairo, Egypt
| | - Mahmoud Ashry
- Zoology Department, Faculty of Science, Al-Azhar University, Assuit, Egypt
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6
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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: 1] [Impact Index Per Article: 1.0] [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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7
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Pašalić L, Pem B, Bakarić D. Lamellarity-Driven Differences in Surface Structural Features of DPPS Lipids: Spectroscopic, Calorimetric and Computational Study. MEMBRANES 2023; 13:83. [PMID: 36676890 PMCID: PMC9865892 DOI: 10.3390/membranes13010083] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/27/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Although single-lipid bilayers are usually considered models of eukaryotic plasma membranes, their research drops drastically when it comes to exclusively anionic lipid membranes. Being a major anionic phospholipid in the inner leaflet of eukaryote membranes, phosphatidylserine-constituted lipid membranes were occasionally explored in the form of multilamellar liposomes (MLV), but their inherent instability caused a serious lack of efforts undertaken on large unilamellar liposomes (LUVs) as more realistic model membrane systems. In order to compensate the existing shortcomings, we performed a comprehensive calorimetric, spectroscopic and MD simulation study of time-varying structural features of LUV made from 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS), whereas the corresponding MLV were examined as a reference. A substantial uncertainty of UV/Vis data of LUV from which only Tm was unambiguously determined (53.9 ± 0.8 °C), along with rather high uncertainty on the high-temperature range of DPPS melting profile obtained from DSC (≈50-59 °C), presumably reflect distinguished surface structural features in LUV. The FTIR signatures of glycerol moiety and those originated from carboxyl group serve as a strong support that in LUV, unlike in MLV, highly curved surfaces occur continuously, whereas the details on the attenuation of surface features in MLV were unraveled by molecular dynamics.
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8
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Tikhonov AM, Asadchikov VE, Volkov YO, Roshchin BS, Nuzhdin AD, Makrinsky KI, Ermakov YA. X-ray Reflectivity Study of Polylysine Adsorption on the Surface of DMPS Monolayers. MEMBRANES 2022; 12:1223. [PMID: 36557131 PMCID: PMC9785213 DOI: 10.3390/membranes12121223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The results of a systematic study on the adsorption of polylysine molecules of different lengths on the surface of a 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) monolayer in the liquid (LE) and condensed (LC) states are presented. A compressibility diagram and the Volta potential were recorded with the Langmuir monolayer technique and further analyzed with the empirical approach. The structure of the monolayer films with adsorbed polypeptides was studied with synchrotron X-ray reflectometry. Two- and three-layer slab models describe the reflectivity data fairly well and reveal both the significant structural changes and the dehydration of the polar groups induced by all polylysines used at the maximal coverage of the monolayer interface in both the LE and LC states. On the one hand, in the LE phase of the monolayer (area per molecule A ≅ 70 Ǻ2), the integrated electron density of the lipid headgroup region is approximately half the density contained in the clean monolayer. This indicates both significant compaction and dehydration in the polar groups of the lipids, caused by the adsorption of polypeptides. On the other hand, in the LC state (A ≅ 40 Ǻ2), the degree of the hydration of the polar region is similar to that for the initial DMPS monolayer. However, both the electron density and the thickness of the head group region differ significantly from the values of these parameters for the clean monolayer in the LC state.
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Affiliation(s)
- Aleksey M. Tikhonov
- Kapitza Institute for Physical Problems, Russian Academy of Sciences, Moscow 119334, Russia
| | - Victor E. Asadchikov
- Shubnikov Institute of Crystallography, Federal Research Center Crystallography and Photonics, Russian Academy of Sciences, Moscow 119333, Russia
| | - Yury O. Volkov
- Shubnikov Institute of Crystallography, Federal Research Center Crystallography and Photonics, Russian Academy of Sciences, Moscow 119333, Russia
- Institute of Solid State Physics, Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Boris S. Roshchin
- Shubnikov Institute of Crystallography, Federal Research Center Crystallography and Photonics, Russian Academy of Sciences, Moscow 119333, Russia
| | - Alexander D. Nuzhdin
- Shubnikov Institute of Crystallography, Federal Research Center Crystallography and Photonics, Russian Academy of Sciences, Moscow 119333, Russia
| | - Kirill I. Makrinsky
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - Yury A. Ermakov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
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9
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Strazdaite S, Roeters SJ, Sakalauskas A, Sneideris T, Kirschner J, Pedersen KB, Schiøtt B, Jensen F, Weidner T, Smirnovas V, Niaura G. Interaction of Amyloid-β-(1-42) Peptide and Its Aggregates with Lipid/Water Interfaces Probed by Vibrational Sum-Frequency Generation Spectroscopy. J Phys Chem B 2021; 125:11208-11218. [PMID: 34597059 DOI: 10.1021/acs.jpcb.1c04882] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we use surface-sensitive vibrational sum-frequency generation (VSFG) spectroscopy to investigate the interaction between model lipid monolayers and Aβ(1-42) in its monomeric and aggregated states. Combining VSFG with atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence measurements, we found that only small aggregates with probably a β-hairpin-like structure adsorbed to the zwitterionic lipid monolayer (DOPC). In contrast, larger aggregates with an extended β-sheet structure adsorbed to a negatively charged lipid monolayer (DOPG). The adsorption of small, initially formed aggregates strongly destabilized both monolayers, but only the DOPC monolayer was completely disrupted. We showed that the intensity of the amide-II' band in achiral (SSP) and chiral (SPP) polarization combinations increased in time when Aβ(1-42) aggregates accumulated at the DOPG monolayer. Nevertheless, almost no adsorption of preformed mature fibrils to DOPG monolayers was detected. By performing spectral VSFG calculations, we revealed a clear correlation between the amide-II' signal and the degree of amyloid aggregates (e.g., oligomers or (proto)fibrils) of various Aβ(1-42) structures. The calculations showed that only structures with a significant amyloid β-sheet content have a strong amide-II' intensity, in line with previous Raman studies. The combination of the presented results substantiates the amide-II(') band as a legitimate amyloid marker.
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Affiliation(s)
- S Strazdaite
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
| | - S J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - A Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - T Sneideris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - J Kirschner
- Institute of Solid State Physics, TU Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - K B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - B Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - F Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - T Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - V Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - G Niaura
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
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10
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Amiss AS, Henriques ST, Lawrence N. Antimicrobial peptides provide wider coverage for targeting drug‐resistant bacterial pathogens. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anna S. Amiss
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland Australia
- School of Biomedical Sciences Queensland University of Technology, Translational Research Institute Brisbane Queensland Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland Australia
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11
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Jakubec M, Bariås E, Furse S, Govasli ML, George V, Turcu D, Iashchishyn IA, Morozova-Roche LA, Halskau Ø. Cholesterol-containing lipid nanodiscs promote an α-synuclein binding mode that accelerates oligomerization. FEBS J 2021; 288:1887-1905. [PMID: 32892498 DOI: 10.1111/febs.15551] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 07/28/2020] [Accepted: 09/01/2020] [Indexed: 01/09/2023]
Abstract
Dysregulation of the biosynthesis of cholesterol and other lipids has been implicated in many neurological diseases, including Parkinson's disease. Misfolding of α-synuclein (α-Syn), the main actor in Parkinson's disease, is associated with changes in a lipid environment. However, the exact molecular mechanisms underlying cholesterol effect on α-Syn binding to lipids as well as α-Syn oligomerization and fibrillation remain elusive, as does the relative importance of cholesterol compared to other factors. We probed the interactions and fibrillation behaviour of α-Syn using styrene-maleic acid nanodiscs, containing zwitterionic and anionic lipid model systems with and without cholesterol. Surface plasmon resonance and thioflavin T fluorescence assays were employed to monitor α-Syn binding, as well as fibrillation in the absence and presence of membrane models. 1 H-15 N-correlated NMR was used to monitor the fold of α-Syn in response to nanodisc binding, determining individual residue apparent affinities for the nanodisc-contained bilayers. The addition of cholesterol inhibited α-Syn interaction with lipid bilayers and, however, significantly promoted α-Syn fibrillation, with a more than a 20-fold reduction of lag times before fibrillation onset. When α-Syn bilayer interactions were analysed at an individual residue level by solution-state NMR, we observed two different effects of cholesterol. In nanodiscs made of DOPC, the addition of cholesterol modulated the NAC part of α-Syn, leading to stronger interaction of this region with the lipid bilayer. In contrast, in the nanodiscs comprising DOPC, DOPE and DOPG, the NAC part was mostly unaffected by the presence of cholesterol, while the binding of the N and the C termini was both inhibited.
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Affiliation(s)
- Martin Jakubec
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Espen Bariås
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Samuel Furse
- Department of Molecular Biology, University of Bergen, Norway
| | - Morten L Govasli
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
- Division of Infection and Immunity, University College London, London, UK
| | - Vinnit George
- Department of Chemistry, University of Bergen, Norway
| | - Diana Turcu
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Igor A Iashchishyn
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | | | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
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12
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Chen P, Vorobyov I, Roux B, Allen TW. Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness. J Phys Chem B 2021; 125:1020-1035. [PMID: 33493394 DOI: 10.1021/acs.jpcb.0c08613] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Different mechanisms have been proposed to explain the permeation of charged compounds through lipid membranes. Overall, it is expected that an ion-induced defect permeation mechanism, where substantial membrane deformations accompany ion movement, should be dominant in thin membranes but that a solubility-diffusion mechanism, where ions partition into the membrane core with large associated dehydration energy costs, becomes dominant in thicker membranes. However, while this physical picture is intuitively reasonable, capturing the interconversion between these two permeation mechanisms in molecular dynamics (MD) simulations based on atomic models is challenging. In particular, simulations relying on nonpolarizable force fields are artificially unfavorable to the solubility-diffusion mechanism, as induced polarization of the nonpolar hydrocarbon is ignored, causing overestimated free energy costs for charged molecules to enter into this region of the membrane. In this study, all-atom MD simulations based on nonpolarizable and polarizable force fields are used to quantitatively characterize the permeation process for the arginine side chain analog methyl-guanidinium through bilayer membranes of mono-unsaturated phosphatidylcholine lipids with and without cholesterol, resulting in thicknesses spanning from ∼24 to ∼42 Å. With simulations based on a nonpolarizable force field, ion translocation can take place solely through an ion-induced defect mechanism, with free energy barriers increasing linearly from 14 to 40 kcal/mol, depending on the thickness. However, with simulations based on a polarizable force field, ion translocation is predominantly dominated by an ion-induced defect mechanism in thin membranes, which progressively converts to a solubility-diffusion mechanism as the membranes get thicker. The transition between the two mechanisms occurs at a thickness of ∼29 Å, with lipid tails of 22 or more carbon atoms. This situation appears to represent the upper limit for ion-induced defect permeation within the current polarizable models. Beyond this thickness, it becomes energetically preferable for the ion to dehydrate and partition into the membrane core-a phenomenon that cannot be captured using the nonpolarizable models. Induced electronic polarizability therefore leads not just to a shift in permeation energetics but to an interconversion between two strikingly different physical mechanisms. The result highlights the importance of induced polarizability in modeling lipid membranes.
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Affiliation(s)
- Peiran Chen
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology, Department of Pharmacology, University of California, Davis, California 95616, United States
| | - Benoît Roux
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Toby W Allen
- School of Science, RMIT University, Melbourne 3001, Australia
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13
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Kopec W, Żak A, Jamróz D, Nakahata R, Yusa SI, Gapsys V, Kepczynski M. Polycation-Anionic Lipid Membrane Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12435-12450. [PMID: 33058724 PMCID: PMC7594277 DOI: 10.1021/acs.langmuir.0c01062] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Natural or synthetic polycations are used as biocides or as drug/gene carriers. Understanding the interactions between these macromolecules and cell membranes at the molecular level is therefore of great importance for the design of effective polymer biocides or biocompatible polycation-based delivery systems. Until now, details of the processes at the interface between polycations and biological systems have not been fully recognized. In this study, we consider the effect of strong polycations with quaternary ammonium groups on the properties of anionic lipid membranes that we use as a model system for protein-free cell membranes. For this purpose, we employed experimental measurements and atomic-scale molecular dynamics (MD) simulations. MD simulations reveal that the polycations are strongly hydrated in the aqueous phase and do not lose the water shell after adsorption at the bilayer surface. As a result of strong hydration, the polymer chains reside at the phospholipid headgroup and do not penetrate to the acyl chain region. The polycation adsorption involves the formation of anionic lipid-rich domains, and the density of anionic lipids in these domains depends on the length of the polycation chain. We observed the accumulation of anionic lipids only in the leaflet interacting with the polymer, which leads to the formation of compositionally asymmetric domains. Asymmetric adsorption of the polycation on only one leaflet of the anionic membrane strongly affects the membrane properties in the polycation-membrane contact areas: (i) anionic lipid accumulates in the region near the adsorbed polymer, (ii) acyl chain ordering and lipid packing are reduced, which results in a decrease in the thickness of the bilayer, and (iii) polycation-anionic membrane interactions are strongly influenced by the presence and concentration of salt. Our results provide an atomic-scale description of the interactions of polycations with anionic lipid bilayers and are fully supported by the experimental data. The outcomes are important for understanding the correlation of the structure of polycations with their activity on biomembranes.
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Affiliation(s)
- Wojciech Kopec
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
- Computational
Biomolecular Dynamics Group, Max Planck
Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Agata Żak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Dorota Jamróz
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Rina Nakahata
- Department
of Applied Chemistry, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Shin-ichi Yusa
- Department
of Applied Chemistry, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Vytautas Gapsys
- Computational
Biomolecular Dynamics Group, Max Planck
Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mariusz Kepczynski
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
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14
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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15
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Martínez-Navarro I, Díaz-Molina R, Pulido-Capiz A, Mas-Oliva J, Luna-Reyes I, Rodríguez-Velázquez E, Rivero IA, Ramos-Ibarra MA, Alatorre-Meda M, García-González V. Lipid Modulation in the Formation of β-Sheet Structures. Implications for De Novo Design of Human Islet Amyloid Polypeptide and the Impact on β-Cell Homeostasis. Biomolecules 2020; 10:biom10091201. [PMID: 32824918 PMCID: PMC7563882 DOI: 10.3390/biom10091201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/25/2022] Open
Abstract
Human islet amyloid polypeptide (hIAPP) corresponds to a 37-residue hormone present in insulin granules that maintains a high propensity to form β-sheet structures during co-secretion with insulin. Previously, employing a biomimetic approach, we proposed a panel of optimized IAPP sequences with only one residue substitution that shows the capability to reduce amyloidogenesis. Taking into account that specific membrane lipids have been considered as a key factor in the induction of cytotoxicity, in this study, following the same design strategy, we characterize the effect of a series of lipids upon several polypeptide domains that show the highest aggregation propensity. The characterization of the C-native segment of hIAPP (residues F23-Y37), together with novel variants F23R and I26A allowed us to demonstrate an effect upon the formation of β-sheet structures. Our results suggest that zwitterionic phospholipids promote adsorption of the C-native segments at the lipid-interface and β-sheet formation with the exception of the F23R variant. Moreover, the presence of cholesterol did not modify this behavior, and the β-sheet structural transitions were not registered when the N-terminal domain of hIAPP (K1-S20) was characterized. Considering that insulin granules are enriched in phosphatidylserine (PS), the property of lipid vesicles containing negatively charged lipids was also evaluated. We found that these types of lipids promote β-sheet conformational transitions in both the C-native segment and the new variants. Furthermore, these PS/peptides arrangements are internalized in Langerhans islet β-cells, localized in the endoplasmic reticulum, and trigger critical pathways such as unfolded protein response (UPR), affecting insulin secretion. Since this phenomenon was associated with the presence of cytotoxicity on Langerhans islet β-cells, it can be concluded that the anionic lipid environment and degree of solvation are critical conditions for the stability of segments with the propensity to form β-sheet structures, a situation that will eventually affect the structural characteristics and stability of IAPP within insulin granules, thus modifying the insulin secretion.
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Affiliation(s)
- Israel Martínez-Navarro
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali 21000, Baja California, Mexico; (I.M.-N.); (R.D.-M.); (A.P.-C.)
| | - Raúl Díaz-Molina
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali 21000, Baja California, Mexico; (I.M.-N.); (R.D.-M.); (A.P.-C.)
| | - Angel Pulido-Capiz
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali 21000, Baja California, Mexico; (I.M.-N.); (R.D.-M.); (A.P.-C.)
- Laboratorio de Biología Molecular, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali 21000, Baja California, Mexico
| | - Jaime Mas-Oliva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (J.M.-O.); (I.L.-R.)
| | - Ismael Luna-Reyes
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (J.M.-O.); (I.L.-R.)
| | - Eustolia Rodríguez-Velázquez
- Facultad de Odontología, Universidad Autónoma de Baja California, Tijuana 22390, Mexico;
- Tecnológico Nacional de México/I.T. Tijuana, Centro de Graduados e Investigación en Química-Grupo de Biomateriales y Nanomedicina, Tijuana 22510, Mexico
| | - Ignacio A. Rivero
- Tecnológico Nacional de México/Instituto Tecnológico de Tijuana, Centro de Graduados e Investigación en Química, Tijuana 22510, Baja California, Mexico;
| | - Marco A. Ramos-Ibarra
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Tijuana 22390, Baja California, Mexico;
| | - Manuel Alatorre-Meda
- Cátedras CONACyT- Tecnológico Nacional de México/I.T. Tijuana, Centro de Graduados e Investigación en Química-Grupo de Biomateriales y Nanomedicina, Tijuana 22510, Mexico;
| | - Victor García-González
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali 21000, Baja California, Mexico; (I.M.-N.); (R.D.-M.); (A.P.-C.)
- Correspondence: ; Tel.: +52-68-6557-1622
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16
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Trombik P, Cieślik-Boczula K. Influence of phenothiazine molecules on the interactions between positively charged poly-l-lysine and negatively charged DPPC/DPPG membranes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117563. [PMID: 31689607 DOI: 10.1016/j.saa.2019.117563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/20/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
Phenothiazines are very effective antipsychotic drugs, which also have anticancer and antimicrobial activities. Despite being used in human treatment, the molecular mechanism of the biological actions of these molecules is not yet understood in detail. The role of the interactions between phenothiazines and proteins or lipid membranes has been much discussed. Herein, fourier-transform infrared (FTIR) spectroscopic studies were used to investigate the effect of three phenothiazines: fluphenazine (FPh); chlorpromazine (ChP); and propionylpromazine (PP) on the structures of a positively charged poly-l-lysine (PLL) peptide, a negatively charged dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylglycerol (DPPC/DPPG) membrane, and on the mutual interactions between electrostatically associated PLL molecules and DPPC/DPPG membranes. Phenothiazine-induced alterations in the secondary structure of PLL, the conformational state (trans/gauche) of the hydrocarbon lipid chains, and the hydration of the DPPC/DPPG membrane interface were studied on the basis of amide I' vibrations, antisymmetric and symmetric stretching vibrations of the CH2 groups of the lipid hydrocarbon chains (νsCH2), and stretching vibrations of the lipid C=O groups (νC = O), respectively. It was shown that in the presence of negatively charged DPPC/DPPG membranes, the phenothiazines were able to modify the secondary structure of charged PLL molecules. Additionally, the effect of PLL on the structure of DPPC/DPPG membranes was also altered by the presence of the phenothiazine molecules.
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Affiliation(s)
- Paulina Trombik
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383, Wroclaw, Poland
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17
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Huff HC, Maroutsos D, Das A. Lipid composition and macromolecular crowding effects on CYP2J2-mediated drug metabolism in nanodiscs. Protein Sci 2019; 28:928-940. [PMID: 30861250 DOI: 10.1002/pro.3603] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023]
Abstract
Lipid composition and macromolecular crowding are key external effectors of protein activity and stability whose role varies between different proteins. Therefore, it is imperative to study their effects on individual protein function. CYP2J2 is a membrane-bound cytochrome P450 in the heart involved in the metabolism of fatty acids and xenobiotics. In order to facilitate this metabolism, cytochrome P450 reductase (CPR), transfers electrons to CYP2J2 from NADPH. Herein, we use nanodiscs to show that lipid composition of the membrane bilayer affects substrate metabolism of the CYP2J2-CPR nanodisc (ND) system. Differential effects on both NADPH oxidation and substrate metabolism by CYP2J2-CPR are dependent on the lipid composition. For instance, sphingomyelin containing nanodiscs produced more secondary substrate metabolites than discs of other lipid compositions, implying a possible conformational change leading to processive metabolism. Furthermore, we demonstrate that macromolecular crowding plays a role in the lipid-solubilized CYP2J2-CPR system by increasing the Km and decreasing the Vmax , and effect that is size-dependent. Crowding also affects the CYP2J2-CPR-ND system by decreasing both the Km and Vmax for Dextran-based macromolecular crowding agents, implying an increase in substrate affinity but a lack of metabolism. Finally, protein denaturation studies show that crowding agents destabilize CYP2J2, while the multidomain protein CPR is stabilized. Overall, these studies are the first report on the role of the surrounding lipid environment and macromolecular crowding in modulating enzymatic function of CYP2J2-CPR membrane protein system.
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Affiliation(s)
- Hannah C Huff
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Demetri Maroutsos
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Aditi Das
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Beckman Institute for Advanced Science and Technology, Division of Nutritional Science, Neuroscience Program, and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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18
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Gál M, Sokolová R, Naumowicz M, Híveš J, Krahulec J. Electrochemical and AFM study of the interaction of recombinant human cathelicidin LL-37 with various supported bilayer lipid membranes. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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19
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Abstract
Outer-membrane porins are often considered as passive conduits of small molecules across lipid bilayers. Using native mass spectrometry experiments we identify a pH-sensitive lipid-binding mechanism of outer membrane porin F, which enables increased threading of a colicin-derived peptide through open channels. Supported by molecular dynamics simulations and channel recording experiments, we posit that this mechanism attenuates channel opening in response to changes in environmental conditions, specifically pH. These findings have important consequences for mass spectrometry experiments, wherein the role of charge is often overlooked, and they also could help provide understanding of antibiotics that gain access to Gram-negative bacteria through porin-mediated pathways. Strong interactions between lipids and proteins occur primarily through association of charged headgroups and amino acid side chains, rendering the protonation status of both partners important. Here we use native mass spectrometry to explore lipid binding as a function of charge of the outer membrane porin F (OmpF). We find that binding of anionic phosphatidylglycerol (POPG) or zwitterionic phosphatidylcholine (POPC) to OmpF is sensitive to electrospray polarity while the effects of charge are less pronounced for other proteins in outer or mitochondrial membranes: the ferripyoverdine receptor (FpvA) or the voltage-dependent anion channel (VDAC). Only marginal charge-induced differences were observed for inner membrane proteins: the ammonia channel (AmtB) or the mechanosensitive channel. To understand these different sensitivities, we performed an extensive bioinformatics analysis of membrane protein structures and found that OmpF, and to a lesser extent FpvA and VDAC, have atypically high local densities of basic and acidic residues in their lipid headgroup-binding regions. Coarse-grained molecular dynamics simulations, in mixed lipid bilayers, further implicate changes in charge by demonstrating preferential binding of anionic POPG over zwitterionic POPC to protonated OmpF, an effect not observed to the same extent for AmtB. Moreover, electrophysiology and mass-spectrometry–based ligand-binding experiments, at low pH, show that POPG can maintain OmpF channels in open conformations for extended time periods. Since the outer membrane is composed almost entirely of anionic lipopolysaccharide, with similar headgroup properties to POPG, such anionic lipid binding could prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways.
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20
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DeMarco KR, Bekker S, Clancy CE, Noskov SY, Vorobyov I. Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations. Front Pharmacol 2018; 9:26. [PMID: 29449809 PMCID: PMC5799612 DOI: 10.3389/fphar.2018.00026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022] Open
Abstract
Interactions of drug molecules with lipid membranes play crucial role in their accessibility of cellular targets and can be an important predictor of their therapeutic and safety profiles. Very little is known about spatial localization of various drugs in the lipid bilayers, their active form (ionization state) or translocation rates and therefore potency to bind to different sites in membrane proteins. All-atom molecular simulations may help to map drug partitioning kinetics and thermodynamics, thus providing in-depth assessment of drug lipophilicity. As a proof of principle, we evaluated extensively lipid membrane partitioning of d-sotalol, well-known blocker of a cardiac potassium channel Kv11.1 encoded by the hERG gene, with reported substantial proclivity for arrhythmogenesis. We developed the positively charged (cationic) and neutral d-sotalol models, compatible with the biomolecular CHARMM force field, and subjected them to all-atom molecular dynamics (MD) simulations of drug partitioning through hydrated lipid membranes, aiming to elucidate thermodynamics and kinetics of their translocation and thus putative propensities for hydrophobic and aqueous hERG access. We found that only a neutral form of d-sotalol accumulates in the membrane interior and can move across the bilayer within millisecond time scale, and can be relevant to a lipophilic channel access. The computed water-membrane partitioning coefficient for this form is in good agreement with experiment. There is a large energetic barrier for a cationic form of the drug, dominant in water, to cross the membrane, resulting in slow membrane translocation kinetics. However, this form of the drug can be important for an aqueous access pathway through the intracellular gate of hERG. This route will likely occur after a neutral form of a drug crosses the membrane and subsequently re-protonates. Our study serves to demonstrate a first step toward a framework for multi-scale in silico safety pharmacology, and identifies some of the challenges that lie therein.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Department of Pharmacology, University of California, Davis, Davis, CA, United States.,Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Hartnell College, Salinas, CA, United States
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Sergei Y Noskov
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Department of Pharmacology, University of California, Davis, Davis, CA, United States
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21
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Exploration of the role of the virulence factor ElrA during Enterococcus faecalis cell infection. Sci Rep 2018; 8:1749. [PMID: 29379180 PMCID: PMC5788860 DOI: 10.1038/s41598-018-20206-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/15/2018] [Indexed: 12/15/2022] Open
Abstract
Enterococcus faecalis, an organism generally not pathogenic for healthy humans, has the potential to cause disease in susceptible hosts. While it seems to be equipped to interact with and circumvent host immune defense, most of the molecular and cellular mechanisms underlying the enterococcal infectious process remain elusive. Here, we investigated the role of the Enterococcal Leucine Rich protein A (ElrA), an internalin-like protein of E. faecalis also known as a virulence factor. ElrA was previously shown to prevent adhesion to macrophages. We show that ElrA does not inhibit the basic phagocytic process, but is able to prevent sensing and migration of macrophages toward E. faecalis. Presence or absence of FHL2, a eukaryotic partner of ElrA, does not affect the ElrA-dependent mechanism preventing macrophage migration. However, we highlight a partial contribution of FHL2 in ElrA-mediated virulence in vivo. Our results indicate that ElrA plays at least a dual role of which anti-phagocytic activity may contribute to dissemination of extracellular E. faecalis during infection.
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22
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Kuć M, Cieślik-Boczula K, Rospenk M. Anesthetic-dependent changes in the chain-melting phase transition of DPPG liposomes studied using near-infrared spectroscopy supported by PCA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 186:37-43. [PMID: 28605687 DOI: 10.1016/j.saa.2017.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/18/2017] [Accepted: 06/05/2017] [Indexed: 06/07/2023]
Abstract
The effect of inhalation anesthetics (enflurane, isoflurane, sevoflurane or halothane) on the lipid chain-melting phase transition of negatively charged phospholipid membranes was studied using near-infrared (NIR) spectroscopy supported by Principal Component Analysis (PCA). NIR spectra of anesthetics-mixed dipalmitoylphosphatidylglycerol (DPPG) membranes were recorded in a range of the first overtone of the symmetric and antisymmetric stretching vibrations of CH2 groups of lipid aliphatic chains as a function of increasing temperature. Anesthetic-dependent changes in the trans to gauche conformers ratio of CH2 groups in the hydrocarbon lipid chains were characterized in detail and compared with the zwitterionic lipid membranes, which were built of dipalmitoylphosphatidylcholine (DPPC) molecules.
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Affiliation(s)
- Marta Kuć
- Faculty of Chemistry, University of Wroclaw, Joliot- Curie 14, 50-383 Wroclaw, Poland
| | | | - Maria Rospenk
- Faculty of Chemistry, University of Wroclaw, Joliot- Curie 14, 50-383 Wroclaw, Poland
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23
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Takechi-Haraya Y, Aki K, Tohyama Y, Harano Y, Kawakami T, Saito H, Okamura E. Glycosaminoglycan Binding and Non-Endocytic Membrane Translocation of Cell-Permeable Octaarginine Monitored by Real-Time In-Cell NMR Spectroscopy. Pharmaceuticals (Basel) 2017; 10:ph10020042. [PMID: 28420127 PMCID: PMC5490399 DOI: 10.3390/ph10020042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/13/2022] Open
Abstract
Glycosaminoglycans (GAGs), which are covalently-linked membrane proteins at the cell surface have recently been suggested to involve in not only endocytic cellular uptake but also non-endocytic direct cell membrane translocation of arginine-rich cell-penetrating peptides (CPPs). However, in-situ comprehensive observation and the quantitative analysis of the direct membrane translocation processes are challenging, and the mechanism therefore remains still unresolved. In this work, real-time in-cell NMR spectroscopy was applied to investigate the direct membrane translocation of octaarginine (R8) into living cells. By introducing 4-trifluoromethyl-l-phenylalanine to the N terminus of R8, the non-endocytic membrane translocation of 19F-labeled R8 (19F-R8) into a human myeloid leukemia cell line was observed at 4 °C with a time resolution in the order of minutes. 19F NMR successfully detected real-time R8 translocation: the binding to anionic GAGs at the cell surface, followed by the penetration into the cell membrane, and the entry into cytosol across the membrane. The NMR concentration analysis enabled quantification of how much of R8 was staying in the respective translocation processes with time in situ. Taken together, our in-cell NMR results provide the physicochemical rationale for spontaneous penetration of CPPs in cell membranes.
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Affiliation(s)
- Yuki Takechi-Haraya
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Kenzo Aki
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Yumi Tohyama
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Yuichi Harano
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroyuki Saito
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto 607-8414, Japan.
| | - Emiko Okamura
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
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24
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Kadonosono T, Yimchuen W, Tsubaki T, Shiozawa T, Suzuki Y, Kuchimaru T, Sato Y, Kizaka-Kondoh S. Domain architecture of vasohibins required for their chaperone-dependent unconventional extracellular release. Protein Sci 2017; 26:452-463. [PMID: 27879017 DOI: 10.1002/pro.3089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023]
Abstract
Vasohibins (VASH1 and VASH2) are recently identified regulators of angiogenesis and cancer cell functions. They are secreted proteins without any classical secretion signal sequences, and are thought to be secreted instead via an unconventional protein secretion (UPS) pathway in a small vasohibin-binding protein (SVBP)-dependent manner. However, the precise mechanism of SVBP-dependent UPS is poorly understood. In this study, we identified a novel UPS regulatory system in which essential domain architecture (VASH-PS) of VASHs, comprising regions VASH191-180 and VASH280-169 , regulate the cytosolic punctate structure formation in the absence of SVBP. We also demonstrate that SVBP form a complex with VASH1 through the VASH1274-282 (SIa), VASH1139-144 (SIb), and VASH1133-137 (SIc), leading to the dispersion in the cytosol and extracellular release of VASH1. The amino acid sequences of VASH-SIa and VASH-PS, containing SIb and SIc, are highly conserved among VASH family members in vertebrates, suggesting that SVBP-dependent UPS may be common within the VASH family. This novel UPS regulatory system may open up new avenues for understanding fundamental protein secretion in vertebrates.
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Affiliation(s)
- Tetsuya Kadonosono
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Wanaporn Yimchuen
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Takuya Tsubaki
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Tadashi Shiozawa
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yasuhiro Suzuki
- Department of Vascular Biology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Takahiro Kuchimaru
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yasufumi Sato
- Department of Vascular Biology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Shinae Kizaka-Kondoh
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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25
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Bradbury R, Nagao M. Effect of charge on the mechanical properties of surfactant bilayers. SOFT MATTER 2016; 12:9383-9390. [PMID: 27830216 DOI: 10.1039/c6sm01686c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Charge effects on the mechanical properties of surfactant bilayers have been measured, for a system with a low ionic strength, using small-angle neutron scattering and neutron spin echo spectroscopy. We report that, not only does increasing the surface charge density lead to greater structural ordering and a stiffening of the membrane, which is consistent with classical theory of charge effects on membranes, but also that the relaxation rate of the membrane thickness fluctuations decreases without affecting the fluctuation amplitude. From the relaxation rate we demonstrate, using recent theory, that the viscosity of the surfactant membrane is increased with surface charge density, which suggests that the amount of charge controls the diffusion behavior of inclusions inside the membrane. The present results confirm that the thickness fluctuation relaxation rate and amplitude are tuned independently since the membrane viscosity is only influencing the relaxation rate. This work demonstrates that charge stabilization of lamellar bilayers is not merely affected by intermembrane interactions and structural ordering but that intramembrane dynamics also have a significant contribution.
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Affiliation(s)
- Robert Bradbury
- Center for Exploration of Energy and Matter, Department of Physics, Indiana University, Bloomington, Indiana, USA. and National Institute of Standards and Technology Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland, USA
| | - Michihiro Nagao
- Center for Exploration of Energy and Matter, Department of Physics, Indiana University, Bloomington, Indiana, USA. and National Institute of Standards and Technology Center for Neutron Research, 100 Bureau Drive, Gaithersburg, Maryland, USA
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26
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Xing B, Wang L, Li Q, Cao Y, Dong X, Liang J, Wu X. Hsp70 plays an important role in high-fat diet induced gestational hyperglycemia in mice. J Physiol Biochem 2015; 71:649-58. [PMID: 26318018 DOI: 10.1007/s13105-015-0430-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/14/2015] [Indexed: 02/07/2023]
Abstract
Gestational diabetes mellitus (GDM) has emerged as an epidemic disease during the last decade, affecting about 2 to 5% pregnant women. Even among women who have gestational hyperglycemia may also be positively related to adverse outcomes as GDM. Since heat shock protein (Hsp) 70 has been reported to be associated with diabetes and insulin resistance and its expression was reported to be negatively regulated by the membrane-permeable Hsp70 inhibitor MAL3-101 while positively regulated by the Hsp70 activator BGP-15, we investigated whether Hsp70 played a role in a gestational hyperglycemia mouse model. Mice were divided into non-pregnant and pregnant groups, and each comprised three subgroups: control, high-fat diet (HFD) + MAL3-101, and HFD + BGP-15. We examined the serum levels of triglycerides, total cholesterol, glucose, and insulin, as well as conducted thermal detection of brown adipose tissue (BAT). The role of Hsp70 in BAT apoptosis was also investigated by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay and caspase-3 staining. Higher serum level of Hsp70 was associated with increased bodyweight gain after pregnancy in mice fed HFD. Circulating Hsp70 was elevated in control pregnant mice compared to control non-pregnant mice. BGP-induced serum Hsp70 expression reduced triglycerides, total cholesterol, glucose, and insulin levels in the serum. Additionally, thermal detection of BAT, TUNEL, and caspase-3 staining revealed relationship correlation between Hsp70 and BAT functions. Hsp70 level is associated with hyperglycemia during pregnancy. Our results support the role of Hsp70 in facilitating BAT activities and protecting BAT cells from apoptosis via caspase-3 pathway.
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Affiliation(s)
- Baoheng Xing
- Department of Obstetrics, Cangzhou City Central Hospital, Cangzhou, 061001, China.
| | - Lili Wang
- Department of Neurology, Cangzhou City People's Hospital, Cangzhou, 061000, China
| | - Qin Li
- Department of Obstetrics, Cangzhou City Central Hospital, Cangzhou, 061001, China
| | - Yalei Cao
- Department of Obstetrics, Cangzhou City Central Hospital, Cangzhou, 061001, China
| | - Xiujuan Dong
- Department of Obstetrics, Cangzhou City Central Hospital, Cangzhou, 061001, China
| | - Jun Liang
- Department of Gynecology and Obstetrics, Bethune International Peace Hospital, Zhongshan West Road, Shijiazhuang, 050051, People's Republic of China
| | - Xiaohua Wu
- Department of Gynecology and Obstetrics, Bethune International Peace Hospital, Zhongshan West Road, Shijiazhuang, 050051, People's Republic of China.
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27
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De Marothy MT, Elofsson A. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding. Protein Sci 2015; 24:1057-74. [PMID: 25970811 DOI: 10.1002/pro.2698] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/24/2015] [Indexed: 01/12/2023]
Abstract
Cells have developed an incredible machinery to facilitate the insertion of membrane proteins into the membrane. While we have a fairly good understanding of the mechanism and determinants of membrane integration, more data is needed to understand the insertion of membrane proteins with more complex insertion and folding pathways. This review will focus on marginally hydrophobic transmembrane helices and their influence on membrane protein folding. These weakly hydrophobic transmembrane segments are by themselves not recognized by the translocon and therefore rely on local sequence context for membrane integration. How can such segments reside within the membrane? We will discuss this in the light of features found in the protein itself as well as the environment it resides in. Several characteristics in proteins have been described to influence the insertion of marginally hydrophobic helices. Additionally, the influence of biological membranes is significant. To begin with, the actual cost for having polar groups within the membrane may not be as high as expected; the presence of proteins in the membrane as well as characteristics of some amino acids may enable a transmembrane helix to harbor a charged residue. The lipid environment has also been shown to directly influence the topology as well as membrane boundaries of transmembrane helices-implying a dynamic relationship between membrane proteins and their environment.
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Affiliation(s)
- Minttu T De Marothy
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
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28
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Di Pisa M, Chassaing G, Swiecicki JM. Translocation Mechanism(s) of Cell-Penetrating Peptides: Biophysical Studies Using Artificial Membrane Bilayers. Biochemistry 2014; 54:194-207. [DOI: 10.1021/bi501392n] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Margherita Di Pisa
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- ENS, UMR 7203, Laboratoire des Biomolécules,
Département de Chimie, Ecole Normale Supérieure, 24 Rue Lhomond, F-75005 Paris, France
| | - Gérard Chassaing
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- ENS, UMR 7203, Laboratoire des Biomolécules,
Département de Chimie, Ecole Normale Supérieure, 24 Rue Lhomond, F-75005 Paris, France
| | - Jean-Marie Swiecicki
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- ENS, UMR 7203, Laboratoire des Biomolécules,
Département de Chimie, Ecole Normale Supérieure, 24 Rue Lhomond, F-75005 Paris, France
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29
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Srivastava A, Voth GA. Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems. J Chem Theory Comput 2014; 10:4730-4744. [PMID: 25328498 PMCID: PMC4196741 DOI: 10.1021/ct500474a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Indexed: 12/13/2022]
Abstract
![]()
We
present a methodology to develop coarse-grained lipid models
such that electrostatic interactions between the coarse-grained sites
can be derived accurately from an all-atom molecular dynamics trajectory
and expressed as an effective pairwise electrostatic potential with
appropriate screening functions. The reference nonbonded forces from
the all-atom trajectory are decomposed into separate electrostatic
and van der Waals (vdW) forces, based on the multiscale coarse-graining
method. The coarse-grained electrostatic potential is assumed to be
a general function of unknown variables and the final site–site
interactions are obtained variationally, where the residual of the
electrostatic forces from the assumed field is minimized. The resulting
electrostatic interactions are fitted to screened electrostatics functions,
with a special treatment for distance-dependent dielectrics and screened
dipole–dipole interactions. The vdW interactions are derived
separately. The resulting charged hybrid coarse-graining method is
applied to various solvent-free three-site models of anionic lipid
systems.
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Affiliation(s)
- Anand Srivastava
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
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30
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Chaudhuri A, Chattopadhyay A. Lipid binding specificity of bovine α-lactalbumin: A multidimensional approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2078-86. [DOI: 10.1016/j.bbamem.2014.04.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 10/25/2022]
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31
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Virkki MT, Agrawal N, Edsbäcker E, Cristobal S, Elofsson A, Kauko A. Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Sci 2014; 23:981-92. [PMID: 24777974 PMCID: PMC4088982 DOI: 10.1002/pro.2483] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 12/29/2022]
Abstract
The folding of most integral membrane proteins follows a two-step process: initially, individual transmembrane helices are inserted into the membrane by the Sec translocon. Thereafter, these helices fold to shape the final conformation of the protein. However, for some proteins, including Aquaporin 1 (AQP1), the folding appears to follow a more complicated path. AQP1 has been reported to first insert as a four-helical intermediate, where helix 2 and 4 are not inserted into the membrane. In a second step, this intermediate is folded into a six-helical topology. During this process, the orientation of the third helix is inverted. Here, we propose a mechanism for how this reorientation could be initiated: first, helix 3 slides out from the membrane core resulting in that the preceding loop enters the membrane. The final conformation could then be formed as helix 2, 3, and 4 are inserted into the membrane and the reentrant regions come together. We find support for the first step in this process by showing that the loop preceding helix 3 can insert into the membrane. Further, hydrophobicity curves, experimentally measured insertion efficiencies and MD-simulations suggest that the barrier between these two hydrophobic regions is relatively low, supporting the idea that helix 3 can slide out of the membrane core, initiating the rearrangement process.
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Affiliation(s)
- Minttu T Virkki
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Nitin Agrawal
- Department of Biosciences, Biochemistry, Åbo AkademiTurku, FI-20520, Finland
| | - Elin Edsbäcker
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Health Science, Linköping UniversityLinköping, Sweden
- Department of Physiology, IKERBASQUE, Basque Foundation for Science, Faculty of Medicine and Dentistry, University of the Basque CountryLeioa, Spain
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm UniversitySolna, SE-171 21, Sweden
| | - Anni Kauko
- Department of Biosciences, Biochemistry, Åbo AkademiTurku, FI-20520, Finland
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32
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Li L, Vorobyov I, Allen TW. The different interactions of lysine and arginine side chains with lipid membranes. J Phys Chem B 2013; 117:11906-20. [PMID: 24007457 DOI: 10.1021/jp405418y] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The basic amino acids lysine (Lys) and arginine (Arg) play important roles in membrane protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin, and cell-penetrating peptides. These roles are thought to stem from the strong interactions and disruptive influences of these amino acids on lipid membranes. In this study, we employ fully atomistic molecular dynamics simulations to observe, quantify, and compare the interactions of Lys and Arg with saturated phosphatidylcholine membranes of different thickness. We make use of both charged (methylammonium and methylguanidinium) and neutral (methylamine and methylguanidine) analogue molecules, as well as Lys and Arg side chains on transmembrane helix models. We find that the free energy barrier experienced by a charged Lys crossing the membrane is strikingly similar to that of a charged Arg (to within 2 kcal/mol), despite the two having different chemistries, H-bonding capability, and hydration free energies that differ by ∼10 kcal/mol. In comparison, the barrier for neutral Arg is higher than that for neutral Lys by around 5 kcal/mol, being more selective than that for the charged species. This can be explained by the different transport mechanisms for charged or neutral amino acid side chains in the membrane, involving membrane deformations or simple dehydration, respectively. As a consequence, we demonstrate that Lys would be deprotonated in the membrane, whereas Arg would maintain its charge. Our simulations also reveal that Arg attracts more phosphate and water in the membrane, and can form extensive H-bonding with its five H-bond donors to stabilize Arg-phosphate clusters. This leads to enhanced interfacial binding and membrane perturbations, including the appearance of a trans-membrane pore in a thinner membrane. These results highlight the special role played by Arg as an amino acid to bind to, disrupt, and permeabilize lipid membranes, as well as to sense voltages for a range of peptide and protein activities in nature and in engineered bionanodevices.
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Affiliation(s)
- Libo Li
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
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33
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Vazdar M, Wernersson E, Khabiri M, Cwiklik L, Jurkiewicz P, Hof M, Mann E, Kolusheva S, Jelinek R, Jungwirth P. Aggregation of Oligoarginines at Phospholipid Membranes: Molecular Dynamics Simulations, Time-Dependent Fluorescence Shift, and Biomimetic Colorimetric Assays. J Phys Chem B 2013; 117:11530-40. [DOI: 10.1021/jp405451e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mario Vazdar
- Division
of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, P.O.B.
180, HR-10002 Zagreb, Croatia
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Erik Wernersson
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Morteza Khabiri
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Lukasz Cwiklik
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Martin Hof
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Ella Mann
- Department
of Chemistry and the Ilse Katz Institute for Nanoscale Science and
Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sofiya Kolusheva
- Department
of Chemistry and the Ilse Katz Institute for Nanoscale Science and
Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Raz Jelinek
- Department
of Chemistry and the Ilse Katz Institute for Nanoscale Science and
Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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Crosstalk between DnaA protein, the initiator of Escherichia coli chromosomal replication, and acidic phospholipids present in bacterial membranes. Int J Mol Sci 2013; 14:8517-37. [PMID: 23595001 PMCID: PMC3645759 DOI: 10.3390/ijms14048517] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/03/2013] [Accepted: 04/06/2013] [Indexed: 11/16/2022] Open
Abstract
Anionic (i.e., acidic) phospholipids such as phosphotidylglycerol (PG) and cardiolipin (CL), participate in several cellular functions. Here we review intriguing in vitro and in vivo evidence that suggest emergent roles for acidic phospholipids in regulating DnaA protein-mediated initiation of Escherichia coli chromosomal replication. In vitro acidic phospholipids in a fluid bilayer promote the conversion of inactive ADP-DnaA to replicatively proficient ATP-DnaA, yet both PG and CL also can inhibit the DNA-binding activity of DnaA protein. We discuss how cellular acidic phospholipids may positively and negatively influence the initiation activity of DnaA protein to help assure chromosomal replication occurs once, but only once, per cell-cycle. Fluorescence microscopy has revealed that PG and CL exist in domains located at the cell poles and mid-cell, and several studies link membrane curvature with sub-cellular localization of various integral and peripheral membrane proteins. E. coli DnaA itself is found at the cell membrane and forms helical structures along the longitudinal axis of the cell. We propose that there is cross-talk between acidic phospholipids in the bacterial membrane and DnaA protein as a means to help control the spatial and temporal regulation of chromosomal replication in bacteria.
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35
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Structure and dynamics of the two amphipathic arginine-rich peptides RW9 and RL9 in a lipid environment investigated by solid-state NMR and MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:824-33. [DOI: 10.1016/j.bbamem.2012.11.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 11/09/2012] [Accepted: 11/12/2012] [Indexed: 02/06/2023]
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36
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Gombos I, Crul T, Piotto S, Güngör B, Török Z, Balogh G, Péter M, Slotte JP, Campana F, Pilbat AM, Hunya Á, Tóth N, Literati-Nagy Z, Vígh L, Glatz A, Brameshuber M, Schütz GJ, Hevener A, Febbraio MA, Horváth I, Vígh L. Membrane-lipid therapy in operation: the HSP co-inducer BGP-15 activates stress signal transduction pathways by remodeling plasma membrane rafts. PLoS One 2011; 6:e28818. [PMID: 22174906 PMCID: PMC3236211 DOI: 10.1371/journal.pone.0028818] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 11/15/2011] [Indexed: 01/22/2023] Open
Abstract
Aging and pathophysiological conditions are linked to membrane changes which modulate membrane-controlled molecular switches, causing dysregulated heat shock protein (HSP) expression. HSP co-inducer hydroxylamines such as BGP-15 provide advanced therapeutic candidates for many diseases since they preferentially affect stressed cells and are unlikely have major side effects. In the present study in vitro molecular dynamic simulation, experiments with lipid monolayers and in vivo ultrasensitive fluorescence microscopy showed that BGP-15 alters the organization of cholesterol-rich membrane domains. Imaging of nanoscopic long-lived platforms using the raft marker glycosylphosphatidylinositol-anchored monomeric green fluorescent protein diffusing in the live Chinese hamster ovary (CHO) cell plasma membrane demonstrated that BGP-15 prevents the transient structural disintegration of rafts induced by fever-type heat stress. Moreover, BGP-15 was able to remodel cholesterol-enriched lipid platforms reminiscent of those observed earlier following non-lethal heat priming or membrane stress, and were shown to be obligate for the generation and transmission of stress signals. BGP-15 activation of HSP expression in B16-F10 mouse melanoma cells involves the Rac1 signaling cascade in accordance with the previous observation that cholesterol affects the targeting of Rac1 to membranes. Finally, in a human embryonic kidney cell line we demonstrate that BGP-15 is able to inhibit the rapid heat shock factor 1 (HSF1) acetylation monitored during the early phase of heat stress, thereby promoting a prolonged duration of HSF1 binding to heat shock elements. Taken together, our results indicate that BGP-15 has the potential to become a new class of pharmaceuticals for use in ‘membrane-lipid therapy’ to combat many various protein-misfolding diseases associated with aging.
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Affiliation(s)
- Imre Gombos
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Tim Crul
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Stefano Piotto
- Department of Pharmaceutical and Biomedical Sciences, University of Salerno, Salerno, Italy
| | - Burcin Güngör
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsolt Török
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gábor Balogh
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Mária Péter
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - J. Peter Slotte
- Department of Biosciences, Abo Akademi University, Turku, Finland
| | - Federica Campana
- Department of Pharmaceutical and Biomedical Sciences, University of Salerno, Salerno, Italy
| | - Ana-Maria Pilbat
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | | | - Noémi Tóth
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsuzsanna Literati-Nagy
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - László Vígh
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
| | - Attila Glatz
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Mario Brameshuber
- Institute of Applied Physics, Vienna University of Technology, Vienna, Austria
| | - Gerhard J. Schütz
- Institute of Applied Physics, Vienna University of Technology, Vienna, Austria
| | - Andrea Hevener
- Department of Medicine, Division of Endocrinology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Mark A. Febbraio
- Cellular and Molecular Metabolism Laboratory, Baker Heart and Diabetes Institute, Prahran, Victoria, Australia
| | - Ibolya Horváth
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - László Vígh
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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Li LB, Vorobyov I, Allen TW. The role of membrane thickness in charged protein-lipid interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:135-45. [PMID: 22063722 DOI: 10.1016/j.bbamem.2011.10.026] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/23/2011] [Accepted: 10/24/2011] [Indexed: 02/01/2023]
Abstract
Charged amino acids are known to be important in controlling the actions of integral and peripheral membrane proteins and cell disrupting peptides. Atomistic molecular dynamics studies have shed much light on the mechanisms of membrane binding and translocation of charged protein groups, yet the impact of the full diversity of membrane physico-chemical properties and topologies has yet to be explored. Here we have performed a systematic study of an arginine (Arg) side chain analog moving across saturated phosphatidylcholine (PC) bilayers of variable hydrocarbon tail length from 10 to 18 carbons. For all bilayers we observe similar ion-induced defects, where Arg draws water molecules and lipid head groups into the bilayers to avoid large dehydration energy costs. The free energy profiles all exhibit sharp climbs with increasing penetration into the hydrocarbon core, with predictable shifts between bilayers of different thickness, leading to barrier reduction from 26 kcal/mol for 18 carbons to 6 kcal/mol for 10 carbons. For lipids of 10 and 12 carbons we observe narrow transmembrane pores and corresponding plateaus in the free energy profiles. Allowing for movements of the protein and side chain snorkeling, we argue that the energetic cost for burying Arg inside a thin bilayer will be small, consistent with recent experiments, also leading to a dramatic reduction in pK(a) shifts for Arg. We provide evidence that Arg translocation occurs via an ion-induced defect mechanism, except in thick bilayers (of at least 18 carbons) where solubility-diffusion becomes energetically favored. Our findings shed light on the mechanisms of ion movement through membranes of varying composition, with implications for a range of charged protein-lipid interactions and the actions of cell-perturbing peptides. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Libo B Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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MacCallum JL, Bennett WFD, Tieleman DP. Transfer of arginine into lipid bilayers is nonadditive. Biophys J 2011; 101:110-7. [PMID: 21723820 DOI: 10.1016/j.bpj.2011.05.038] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/29/2011] [Accepted: 05/17/2011] [Indexed: 01/21/2023] Open
Abstract
Computer simulations suggest that the translocation of arginine through the hydrocarbon core of a lipid membrane proceeds by the formation of a water-filled defect that keeps the arginine molecule hydrated even at the center of the bilayer. We show here that adding additional arginine molecules into one of these water defects causes only a small change in free energy. The barrier for transferring multiple arginines through the membrane is approximately the same as for a single arginine and may even be lower depending on the exact geometry of the system. We discuss these results in the context of arginine-rich peptides such as antimicrobial and cell-penetrating peptides.
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Affiliation(s)
- Justin L MacCallum
- Department of Biological Sciences, Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta, Canada
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