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Liekkinen J, Olżyńska A, Cwiklik L, Bernardino de la Serna J, Vattulainen I, Javanainen M. Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein-Lipid Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4338-4350. [PMID: 36917773 PMCID: PMC10061932 DOI: 10.1021/acs.langmuir.2c03349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The lining of the alveoli is covered by pulmonary surfactant, a complex mixture of surface-active lipids and proteins that enables efficient gas exchange between inhaled air and the circulation. Despite decades of advancements in the study of the pulmonary surfactant, the molecular scale behavior of the surfactant and the inherent role of the number of different lipids and proteins in surfactant behavior are not fully understood. The most important proteins in this complex system are the surfactant proteins SP-B and SP-C. Given this, in this work we performed nonequilibrium all-atom molecular dynamics simulations to study the interplay of SP-B and SP-C with multicomponent lipid monolayers mimicking the pulmonary surfactant in composition. The simulations were complemented by z-scan fluorescence correlation spectroscopy and atomic force microscopy measurements. Our state-of-the-art simulation model reproduces experimental pressure-area isotherms and lateral diffusion coefficients. In agreement with previous research, the inclusion of either SP-B and SP-C increases surface pressure, and our simulations provide a molecular scale explanation for this effect: The proteins display preferential lipid interactions with phosphatidylglycerol, they reside predominantly in the lipid acyl chain region, and they partition into the liquid expanded phase or even induce it in an otherwise packed monolayer. The latter effect is also visible in our atomic force microscopy images. The research done contributes to a better understanding of the roles of specific lipids and proteins in surfactant function, thus helping to develop better synthetic products for surfactant replacement therapy used in the treatment of many fatal lung-related injuries and diseases.
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Affiliation(s)
- Juho Liekkinen
- Department
of Physics, University of Helsinki, FI-00560 Helsinki, Finland
| | - Agnieszka Olżyńska
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, CZ-18223 Prague, Czech Republic
| | - Lukasz Cwiklik
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, CZ-18223 Prague, Czech Republic
| | - Jorge Bernardino de la Serna
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
- NIHR
Imperial Biomedical Research Centre, London SW7 2AZ, U.K.
| | - Ilpo Vattulainen
- Department
of Physics, University of Helsinki, FI-00560 Helsinki, Finland
| | - Matti Javanainen
- Institute
of Biotechnology, University of Helsinki, FI-00790 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, CZ-16100 Prague 6, Czech Republic
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2
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The lung surfactant activity probed with molecular dynamics simulations. Adv Colloid Interface Sci 2022; 304:102659. [PMID: 35421637 DOI: 10.1016/j.cis.2022.102659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 01/17/2023]
Abstract
The surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins. This lung surfactant plays a crucial role in lung functioning. It shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants. For studying multicomponent biological systems, it is of interest to couple experimental approach with computational modelling yielding atomic-scale information. Simple two, three, or four-component model systems showed to be useful for getting more insight in the interaction between lipids, lipids and proteins or lipids and proteins with drugs and impurities. These systems were studied theoretically using molecular dynamic simulations and experimentally by means of the Langmuir technique. A better understanding of the structure and behavior of lung surfactants obtained from this research is relevant for developing new synthetic surfactants for efficient therapies, and may contribute to public health protection.
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3
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Nele V, Holme MN, Rashid MH, Barriga HMG, Le TC, Thomas MR, Doutch JJ, Yarovsky I, Stevens MM. Design of Lipid-Based Nanocarriers via Cation Modulation of Ethanol-Interdigitated Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11909-11921. [PMID: 34581180 DOI: 10.1021/acs.langmuir.1c02076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Short-chain alcohols (i.e., ethanol) can induce membrane interdigitation in saturated-chain phosphatidylcholines (PCs). In this process, alcohol molecules intercalate between phosphate heads, increasing lateral separation and favoring hydrophobic interactions between opposing acyl chains, which interpenetrate forming an interdigitated phase. Unraveling mechanisms underlying the interactions between ethanol and model lipid membranes has implications for cell biology, biochemistry, and for the formulation of lipid-based nanocarriers. However, investigations of ethanol-lipid membrane systems have been carried out in deionized water, which limits their applicability. Here, using a combination of small- and wide-angle X-ray scattering, small-angle neutron scattering, and all-atom molecular dynamics simulations, we analyzed the effect of varying CaCl2 and NaCl concentrations on ethanol-induced interdigitation. We observed that while ethanol addition leads to the interdigitation of bulk phase 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers in the presence of CaCl2 and NaCl regardless of the salt concentration, the ethanol-induced interdigitation of vesicular DPPC depends on the choice of cation and its concentration. These findings unravel a key role for cations in the ethanol-induced interdigitation of lipid membranes in either bulk phase or vesicular form.
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Affiliation(s)
- Valeria Nele
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Margaret N Holme
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - M Harunur Rashid
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- Department of Mathematics and Physics, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Hanna M G Barriga
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Michael R Thomas
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
- London Centre for Nanotechnology and Department of Biochemical Engineering, University College London, 17-19 Gordon Street, London WC1H 0AH, U.K
| | - James J Doutch
- ISIS Neutron and Muon Source, STFC, Rutherford Appleton Laboratory, Didcot OX11 ODE, U.K
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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4
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Dupuis JH, Wang S, Song C, Yada RY. The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics. PLoS One 2020; 15:e0237884. [PMID: 32841243 PMCID: PMC7447066 DOI: 10.1371/journal.pone.0237884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/04/2020] [Indexed: 01/31/2023] Open
Abstract
The Solanum tuberosum plant specific insert (StPSI) has a defensive role in potato plants, with the requirements of acidic pH and anionic lipids. The StPSI contains a set of three highly conserved disulfide bonds that bridge the protein’s helical domains. Removal of these bonds leads to enhanced membrane interactions. This work examined the effects of their sequential removal, both individually and in combination, using all-atom molecular dynamics to elucidate the role of disulfide linkages in maintaining overall protein tertiary structure. The tertiary structure was found to remain stable at both acidic (active) and neutral (inactive) pH despite the removal of disulfide linkages. The findings include how the dimer structure is stabilized and the impact on secondary structure on a residue-basis as a function of disulfide bond removal. The StPSI possesses an extensive network of inter-monomer hydrophobic interactions and intra-monomer hydrogen bonds, which is likely the key to the stability of the StPSI by stabilizing local secondary structure and the tertiary saposin-fold, leading to a robust association between monomers, regardless of the disulfide bond state. Removal of disulfide bonds did not significantly impact secondary structure, nor lead to quaternary structural changes. Instead, disulfide bond removal induces regions of amino acids with relatively higher or lower variation in secondary structure, relative to when all the disulfide bonds are intact. Although disulfide bonds are not required to preserve overall secondary structure, they may have an important role in maintaining a less plastic structure within plant cells in order to regulate membrane affinity or targeting.
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Affiliation(s)
- John H. Dupuis
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, Beijing, People's Republic of China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People’s Republic of China
| | - Rickey Y. Yada
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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5
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Kumar V, Hoag H, Sader S, Scorese N, Liu H, Wu C. GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β 2 Adrenergic Receptor. J Chem Inf Model 2020; 60:4064-4075. [PMID: 32786510 DOI: 10.1021/acs.jcim.0c00432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
G-protein-coupled receptors (GPCRs) transmit signals into the cell in response to ligand binding at its extracellular domain, which is characterized by the coupling of agonist-induced receptor conformational change to guanine nucleotide (GDP) exchange with guanosine triphosphate on a heterotrimeric (αβγ) guanine nucleotide-binding protein (G-protein), leading to the activation of the G-protein. The signal transduction mechanisms have been widely researched in vivo and in silico. However, coordinated communication from stimulating ligands to the bound GDP still remains elusive. In the present study, we used microsecond (μS) molecular dynamic (MD) simulations to directly probe the communication from the β2 adrenergic receptor (β2AR) with an agonist or an antagonist or no ligand to GDP bound to the open conformation of the Gα protein. Molecular mechanism-general Born surface area calculation results indicated either the agonist or the antagonist destabilized the binding between the receptor and the G-protein but the agonist caused a higher level of destabilization than the antagonist. This is consistent with the role of agonist in the activation of the G-protein. Interestingly, while GDP remained bound with the Gα-protein for the two inactive systems (antagonist-bound and apo form), GDP dissociated from the open conformation of the Gα protein for the agonist activated system. Data obtained from MD simulations indicated that the receptor and the Gα subunit play a big role in coordinated communication and nucleotide exchange. Based on residue interaction network analysis, we observed that engagement of agonist-bound β2AR with an α5 helix of Gα is essential for the GDP release and the residues in the phosphate-binding loop, α1 helix, and α5 helix play very important roles in the GDP release. The insights on GPCR-G-protein communication will facilitate the rational design of agonists and antagonists that target both active and inactive GPCR binding pockets, leading to more precise drugs.
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Affiliation(s)
- Vikash Kumar
- Complex Systems Division, Beijing Computational Science Research Center, Haidian district, Beijing 100193, China
| | - Hannah Hoag
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Safaa Sader
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Nicolas Scorese
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, Haidian district, Beijing 100193, China
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
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6
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Liekkinen J, Enkavi G, Javanainen M, Olmeda B, Pérez-Gil J, Vattulainen I. Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex. J Mol Biol 2020; 432:3251-3268. [DOI: 10.1016/j.jmb.2020.02.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 12/11/2022]
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7
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Analysis of vismodegib resistance in D473G and W535L mutants of SMO receptor and design of novel drug derivatives using molecular dynamics simulations. Life Sci 2020; 244:117302. [DOI: 10.1016/j.lfs.2020.117302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/02/2020] [Accepted: 01/11/2020] [Indexed: 01/30/2023]
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8
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Robichaud NAS, Khatami MH, Saika-Voivod I, Booth V. All-Atom Molecular Dynamics Simulations of Dimeric Lung Surfactant Protein B in Lipid Multilayers. Int J Mol Sci 2019; 20:ijms20163863. [PMID: 31398818 PMCID: PMC6719169 DOI: 10.3390/ijms20163863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Although lung surfactant protein B (SP-B) is an essential protein that plays a crucial role in breathing, the details of its structure and mechanism are not well understood. SP-B forms covalent homodimers, and in this work we use all-atom molecular dynamics simulations to study dimeric SP-B’s structure and its behavior in promoting lipid structural transitions. Four initial system configurations were constructed based on current knowledge of SP-B’s structure and mechanism, and the protein maintained a helicity consistent with experiment in all systems. Several SP-B-induced lipid reorganization behaviors were observed, and regions of the protein particularly important for these activities included SP-B’s “central loop” and “hinge” regions. SP-B dimers with one subunit initially positioned in each of two adjacent bilayers appeared to promote close contact between two bilayers. When both subunits were initially positioned in the same bilayer, SP-B induced the formation of a defect in the bilayer, with water penetrating into the centre of the bilayer. Similarly, dimeric SP-B showed a propensity to interact with preformed interpores in the bilayer. SP-B dimers also promoted bilayer thinning and creasing. This work fleshes out the atomistic details of the dimeric SP-B structures and SP-B/lipid interactions that underlie SP-B’s essential functions.
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Affiliation(s)
- Nicholas A S Robichaud
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
| | - Mohammad Hassan Khatami
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
| | - Ivan Saika-Voivod
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada.
| | - Valerie Booth
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada.
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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9
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Zhao X, Zhai L, Dang L, Wei H. Impact of Additives on the Microstructural Properties of DIDMAMS Bilayers: Studied by Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:6112-6119. [PMID: 30938534 DOI: 10.1021/acs.langmuir.9b00605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To further understand the mechanism of the impact of perfume raw materials (PRMs) such as allyl heptoate (AHT) and cashmeran (CMR) on distearoyl isopropyl dimethylammonium methyl sulfate (DIDMAMS) bilayers, 90 ns molecular dynamics simulations were conducted to investigate the structure of bilayers consisting of DIDMAMS and PRMs at 350 K on the molecular scale. Structural properties such as density profiles, order parameters, radial distribution functions (RDFs), and bilayer thickness were analyzed. The bilayers appear to be the structure of the ripple phase whether PRMs are added or not. The RDF and density profiles show that CMR molecules tend to locate in the region close to head groups and AHT molecules prefer to uniformly distribute among hydrocarbon chains. The special distribution of CMR molecules results in hydrocarbon chains twining around CMR molecules. The existence of CMR molecules between bilayers and the consequent highest bilayer thickness may be the main cause of higher viscosity. We expect that this work can help to screen stable vesicular formula and understand the relationship between microstructures of the vesicles and macroscopic fluidic properties.
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Affiliation(s)
- Xueying Zhao
- School of Chemical Engineering and Technology , Tianjin University , No.135 Yaguan Road , Jinnan District, Tianjin 300072 , P.R. China
| | - Lina Zhai
- Tianjin TJU-XEDA Synergetic Innovation Institute Co., Ltd , No.5 Xinghua 8th Branch Rd , Xiqing Economic-Technological Development Area, Tianjin 300385 , China
| | - Leping Dang
- School of Chemical Engineering and Technology , Tianjin University , No.135 Yaguan Road , Jinnan District, Tianjin 300072 , P.R. China
| | - Hongyuan Wei
- School of Chemical Engineering and Technology , Tianjin University , No.135 Yaguan Road , Jinnan District, Tianjin 300072 , P.R. China
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10
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Walther FJ, Gupta M, Gordon LM, Waring AJ. A sulfur-free peptide mimic of surfactant protein B (B-YL) exhibits high in vitro and in vivo surface activities. Gates Open Res 2018; 2:13. [PMID: 30234192 PMCID: PMC6139377 DOI: 10.12688/gatesopenres.12799.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2018] [Indexed: 11/23/2022] Open
Abstract
Background: Animal-derived surfactants containing surfactant proteins B (SP-B) and C (SP-C) are used to treat respiratory distress syndrome (RDS) in preterm infants. SP-B (79 residues) plays a pivotal role in lung function and the design of synthetic lung surfactant. Super Mini-B (SMB), a 41-residue peptide based on the N- and C-domains of SP-B covalently joined with a turn and two disulfides, folds as an α-helix hairpin mimicking the properties of these domains in SP-B. Here, we studied ‘B-YL’, a 41-residue SMB variant that has its four cysteine and two methionine residues replaced by tyrosine and leucine, respectively, to test whether these hydrophobic substitutions produce a surface-active, α-helix hairpin. Methods: Structure and function of B-YL and SMB in surfactant lipids were compared with CD and FTIR spectroscopy, and surface activity with captive bubble surfactometry and in lavaged, surfactant-deficient adult rabbits. Results: CD and FTIR spectroscopy of B-YL in surfactant lipids showed secondary structures compatible with peptide folding as an α-helix hairpin, similar to SMB in lipids. B-YL in surfactant lipids demonstrated excellent
in vitro surface activity and good oxygenation and dynamic compliance in lavaged, surfactant-deficient adult rabbits, suggesting that the four tyrosine substitutions are an effective replacement for the disulfide-reinforced helix-turn of SMB. Here, the B-YL fold may be stabilized by a core of clustered tyrosines linking the N- and C-helices through non-covalent interactions involving aromatic rings. Conclusions: ‘Sulfur-free’ B-YL forms an amphipathic helix-hairpin in surfactant liposomes with high surface activity and is functionally similar to SMB and native SP-B. The removal of the cysteines makes B-YL more feasible to scale up production for clinical application. B-YL’s possible resistance against free oxygen radical damage to methionines by substitutions with leucine provides an extra edge over SMB in the treatment of respiratory failure in preterm infants with RDS.
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Affiliation(s)
- Frans J Walther
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Monik Gupta
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Larry M Gordon
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Alan J Waring
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
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