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Avcibas R, Vermul A, Gluhovic V, Boback N, Arroyo R, Kingma P, Isasi-Campillo M, Garcia-Ortega L, Griese M, Kuebler WM, Ochs M, Lauster D, Lopez-Rodriguez E. Multivalent, calcium-independent binding of surfactant protein A and D to sulfated glycosaminoglycans of the alveolar epithelial glycocalyx. Am J Physiol Lung Cell Mol Physiol 2024; 326:L524-L538. [PMID: 38375572 DOI: 10.1152/ajplung.00283.2023] [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: 09/05/2023] [Revised: 01/22/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
Lung surfactant collectins, surfactant protein A (SP-A) and D (SP-D), are oligomeric C-type lectins involved in lung immunity. Through their carbohydrate recognition domain, they recognize carbohydrates at pathogen surfaces and initiate lung innate immune response. Here, we propose that they may also be able to bind to other carbohydrates present in typical cell surfaces, such as the alveolar epithelial glycocalyx. To test this hypothesis, we analyzed and quantified the binding affinity of SP-A and SP-D to different sugars and glycosaminoglycans (GAGs) by microscale thermophoresis (MST). In addition, by changing the calcium concentration, we aimed to characterize any consequences on the binding behavior. Our results show that both oligomeric proteins bind with high affinity (in nanomolar range) to GAGs, such as hyaluronan (HA), heparan sulfate (HS) and chondroitin sulfate (CS). Binding to HS and CS was calcium-independent, as it was not affected by changing calcium concentration in the buffer. Quantification of GAGs in bronchoalveolar lavage (BAL) fluid from animals deficient in either SP-A or SP-D showed changes in GAG composition, and electron micrographs showed differences in alveolar glycocalyx ultrastructure in vivo. Taken together, SP-A and SP-D bind to model sulfated glycosaminoglycans of the alveolar epithelial glycocalyx in a multivalent and calcium-independent way. These findings provide a potential mechanism for SP-A and SP-D as an integral part of the alveolar epithelial glycocalyx binding and interconnecting free GAGs, proteoglycans, and other glycans in glycoproteins, which may influence glycocalyx composition and structure.NEW & NOTEWORTHY SP-A and SP-D function has been related to innate immunity of the lung based on their binding to sugar residues at pathogen surfaces. However, their function in the healthy alveolus was considered as limited to interaction with surfactant lipids. Here, we demonstrated that these proteins bind to glycosaminoglycans present at typical cell surfaces like the alveolar epithelial glycocalyx. We propose a model where these proteins play an important role in interconnecting alveolar epithelial glycocalyx components.
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Affiliation(s)
- Rabia Avcibas
- Institute of Functional Anatomy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Vermul
- Institute of Functional Anatomy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Vladimir Gluhovic
- Institute of Functional Anatomy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nico Boback
- Core Facility Electron Microscopy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Raquel Arroyo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Paul Kingma
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Miriam Isasi-Campillo
- Department of Biochemistry and Molecular Biology, Complutense University Madrid, Madrid, Spain
| | - Lucia Garcia-Ortega
- Department of Biochemistry and Molecular Biology, Complutense University Madrid, Madrid, Spain
| | - Matthias Griese
- Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German Center for Lung Research, Munich, Germany
| | - Wolfgang M Kuebler
- Institute of Physiology, Charité - Universitätsmedizin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Keenan Research Centre, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- German Center for Lung Research (DZL), Berlin, Germany
| | - Matthias Ochs
- Institute of Functional Anatomy, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- German Center for Lung Research (DZL), Berlin, Germany
- Core Facility Electron Microscopy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel Lauster
- Institute of Pharmacy, Biopharmaceuticals, Freie Universität Berlin, Berlin, Germany
| | - Elena Lopez-Rodriguez
- Institute of Functional Anatomy, Charité - Universitätsmedizin Berlin, Berlin, Germany
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Geng Y, Cao Y, Li Y, Zhao Q, Liu D, Fan G, Tian S. A Deeper Insight into the Interfacial Behavior and Structural Properties of Mixed DPPC/POPC Monolayers: Implications for Respiratory Health. MEMBRANES 2022; 13:33. [PMID: 36676840 PMCID: PMC9864691 DOI: 10.3390/membranes13010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1-palmitoyl-2-oleyl-sn-glycerol-3-phosphorcholine (POPC) are important components in pulmonary surfactants (PSs), of which the relative content is related to lung compliance. Herein, the phase behavior and thermodynamic structure of mixed DPPC/POPC monolayers were studied to elucidate the intermolecular interaction between DPPC and POPC molecules. Surface pressure-molecular area isotherms demonstrated that POPC significantly affected the phase behavior of the lipid domain structure as a function of its concentration. The compression modulus of the mixed monolayers reduced with the increase in POPC proportion, which can be attributed to the intermolecular repulsion between DPPC and POPC. Brewster angle microscopy analysis showed that the ordered structure of the monolayers trended toward fluidization in the presence of POPC. Raman spectroscopy results revealed that the change in C-C skeleton stretching vibration was the main cause of the decrease in the monolayer packing density. These findings provide new insights into the role of different phospholipid components in the function of PS film at a molecular level, which can help us to understand the synergy effects of the proportional relationship between DPPC and POPC on the formation and progression of lung disease and provide some references for the synthesis of lung surfactants.
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Affiliation(s)
- Yingxue Geng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
- Faculty of Civil and Hydraulic Engineering, Xichang University, Xichang 615013, China
| | - Yan Cao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Yingjie Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Qun Zhao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Dan Liu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Ge Fan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Senlin Tian
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
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Roberts MF, Gershenson A, Reuter N. Phosphatidylcholine Cation—Tyrosine π Complexes: Motifs for Membrane Binding by a Bacterial Phospholipase C. Molecules 2022; 27:molecules27196184. [PMID: 36234717 PMCID: PMC9572076 DOI: 10.3390/molecules27196184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 10/27/2022] Open
Abstract
Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes are a virulence factor in many Gram-positive organisms. The specific activity of the Bacillus thuringiensis PI-PLC is significantly increased by adding phosphatidylcholine (PC) to vesicles composed of the substrate phosphatidylinositol, in part because the inclusion of PC reduces the apparent Kd for the vesicle binding by as much as 1000-fold when comparing PC-rich vesicles to PI vesicles. This review summarizes (i) the experimental work that localized a site on BtPI-PLC where PC is bound as a PC choline cation—Tyr-π complex and (ii) the computational work (including all-atom molecular dynamics simulations) that refined the original complex and found a second persistent PC cation—Tyr-π complex. Both complexes are critical for vesicle binding. These results have led to a model for PC functioning as an allosteric effector of the enzyme by altering the protein dynamics and stabilizing an ‘open’ active site conformation.
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Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
- Correspondence: ; Tel.: +1-617-460-5194
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics and Chemistry, University of Bergen, 5020 Bergen, Norway
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4
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Elucidating the enhanced binding affinity of a double mutant SP-D with trimannose on the influenza A virus using molecular dynamics. Comput Struct Biotechnol J 2022; 20:4984-5000. [PMID: 36097510 PMCID: PMC9452405 DOI: 10.1016/j.csbj.2022.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 12/02/2022] Open
Abstract
The Asp325Ala mutation in SP-D promotes a trimannose conformational change to a more stable state. The Arg343Val mutation in SP-D reduces its interaction with Glu333 to increase the binding affinity with trimannose. The Arg343Val mutation contributes more to the increase of SP-D’s binding affinity with trimannose than Asp325Ala.
Surfactant protein D (SP-D) is an essential component of the human pulmonary surfactant system, which is crucial in the innate immune response against glycan-containing pathogens, including Influenza A viruses (IAV) and SARS-CoV-2. Previous studies have shown that wild-type (WT) SP-D can bind IAV but exhibits poor antiviral activities. However, a double mutant (DM) SP-D consisting of two point mutations (Asp325Ala and Arg343Val) inhibits IAV more potently. Presently, the structural mechanisms behind the point mutations’ effects on SP-D’s binding affinity with viral surface glycans are not fully understood. Here we use microsecond-scale, full-atomistic molecular dynamics (MD) simulations to understand the molecular mechanism of mutation-induced SP-D’s higher antiviral activity. We find that the Asp325Ala mutation promotes a trimannose conformational change to a more stable state. Arg343Val increases the binding with trimannose by increasing the hydrogen bonding interaction with Glu333. Free energy perturbation (FEP) binding free energy calculations indicate that the Arg343Val mutation contributes more to the increase of SP-D’s binding affinity with trimannose than Asp325Ala. This study provides a molecular-level exploration of how the two mutations increase SP-D binding affinity with trimannose, which is vital for further developing preventative strategies for related diseases.
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Key Words
- CRD, Carbohydrate Recognition Domain
- DM, Double mutant
- FEP, Free Energy Perturbation
- Free Energy Perturbation
- HA, Hemagglutinin
- IAV, Influenza A Viruses
- MD, Molecular Dynamics
- Molecular Dynamics Simulation
- PAP, Pulmonary Alveolar Proteinosis
- PME, Particle Mesh Ewald
- PS, Pulmonary Surfactant
- Protein-Glycan Complexes
- RMSD, Root Mean Square Deviation
- RMSF, Root Mean Square Fluctuation
- SP-A, Surfactant Protein A
- SP-B, Surfactant Protein B
- SP-C, Surfactant Protein C
- SP-D, Surfactant Protein D
- Surfactant Protein D
- WT, Wild-type
- λ-REMD, λ-Replica-Exchange Molecular Dynamics
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5
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Aramyan S, McGregor K, Sandeep S, Haczku A. SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK. Front Immunol 2022; 13:945317. [PMID: 36189278 PMCID: PMC9519185 DOI: 10.3389/fimmu.2022.945317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022] Open
Abstract
The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.
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Affiliation(s)
- Sona Aramyan
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
| | - Kirk McGregor
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
| | - Samarth Sandeep
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
- *Correspondence: Samarth Sandeep, ; Angela Haczku,
| | - Angela Haczku
- University of California (UC) Davis Lung Center Pulmonary, Critical Care and Sleep Division, Department of Medicine, School of Medicine, University of California, Davis, CA, United States
- *Correspondence: Samarth Sandeep, ; Angela Haczku,
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6
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Coya JM, Fraile-Ágreda V, de Tapia L, García-Fojeda B, Sáenz A, Bengoechea JA, Kronqvist N, Johansson J, Casals C. Cooperative action of SP-A and its trimeric recombinant fragment with polymyxins against Gram-negative respiratory bacteria. Front Immunol 2022; 13:927017. [PMID: 36159837 PMCID: PMC9493720 DOI: 10.3389/fimmu.2022.927017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 08/10/2022] [Indexed: 11/19/2022] Open
Abstract
The exploration of therapies combining antimicrobial lung proteins and conventional antibiotics is important due to the growing problem of multidrug-resistant bacteria. The aim of this study was to investigate whether human SP-A and a recombinant trimeric fragment (rfhSP-A) have cooperative antimicrobial activity with antibiotics against pathogenic Gram-negative bacteria. We found that SP-A bound the cationic peptide polymyxin B (PMB) with an apparent dissociation constant (K D) of 0.32 ± 0.04 µM. SP-A showed synergistic microbicidal activity with polymyxin B and E, but not with other antibiotics, against three SP-A-resistant pathogenic bacteria: Klebsiella pneumoniae, non-typable Haemophilus influenzae (NTHi), and Pseudomonas aeruginosa. SP-A was not able to bind to K. pneumoniae, NTHi, or to mutant strains thereof expressing long-chain lipopolysaccharides (or lipooligosaccharides) and/or polysaccharide capsules. In the presence of PMB, SP-A induced the formation of SP-A/PMB aggregates that enhance PMB-induced bacterial membrane permeabilization. Furthermore, SP-A bound to a molecular derivative of PMB lacking the acyl chain (PMBN) with a K D of 0.26 ± 0.02 μM, forming SP-A/PMBN aggregates. PMBN has no bactericidal activity but can bind to the outer membrane of Gram-negative bacteria. Surprisingly, SP-A and PMBN showed synergistic bactericidal activity against Gram-negative bacteria. Unlike native supratrimeric SP-A, the trimeric rfhSP-A fragment had small but significant direct bactericidal activity against K. pneumoniae, NTHi, and P. aeruginosa. rfhSP-A did not bind to PMB under physiological conditions but acted additively with PMB and other antibiotics against these pathogenic bacteria. In summary, our results significantly improve our understanding of the antimicrobial actions of SP-A and its synergistic action with PMB. A peptide based on SP-A may aid the therapeutic use of PMB, a relatively cytotoxic antibiotic that is currently being reintroduced into clinics due to the global problem of antibiotic resistance.
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Affiliation(s)
- Juan Manuel Coya
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain
| | - Víctor Fraile-Ágreda
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain
| | - Lidia de Tapia
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain
| | - Belén García-Fojeda
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain
| | - Alejandra Sáenz
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain
| | - José A. Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Nina Kronqvist
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, Huddinge, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, Huddinge, Sweden
| | - Cristina Casals
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain
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7
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Depicolzuane LC, Roberts CM, Thomas NJ, Anderson-Fears K, Liu D, Barbosa JPP, Souza FR, Pimentel AS, Floros J, Gandhi CK. Hydrophilic But Not Hydrophobic Surfactant Protein Genetic Variants Are Associated With Severe Acute Respiratory Syncytial Virus Infection in Children. Front Immunol 2022; 13:922956. [PMID: 35903101 PMCID: PMC9317530 DOI: 10.3389/fimmu.2022.922956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection-related hospitalization in the first year of life. Surfactant dysfunction is central to pathophysiologic mechanisms of various pulmonary diseases including RSV. We hypothesized that RSV severity is associated with single nucleotide polymorphisms (SNPs) of surfactant proteins (SPs). We prospectively enrolled 405 RSV-positive children and divided them into moderate and severe RSV disease. DNA was extracted and genotyped for sixteen specific SP gene SNPs. SP-A1 and A2 haplotypes were assigned. The association of RSV severity with SP gene SNPs was investigated by multivariate logistic regression. A likelihood ratio test was used to test the goodness of fit between two models (one with clinical and demographic data alone and another that included genetic variants). p ≤ 0.05 denotes statistical significance. A molecular dynamics simulation was done to determine the impact of the SFTPA2 rs1965708 on the SP-A behavior under various conditions. Infants with severe disease were more likely to be younger, of lower weight, and exposed to household pets and smoking, as well as having co-infection on admission. A decreased risk of severe RSV was associated with the rs17886395_C of the SFTPA2 and rs2243639_A of the SFTPD, whereas an increased risk was associated with the rs1059047_C of the SFTPA1. RSV severity was not associated with SNPs of SFTPB and SFTPC. An increased risk of severe RSV was associated with the 1A0 genotype of SFTPA2 in its homozygous or heterozygous form with 1A3. A molecular dynamic simulation study of SP-A variants that differ in amino acid 223, an important amino acid change (Q223K) between 1A0 and 1A3, showed no major impact on the behavior of these two variants except for higher thermodynamic stability of the K223 variant. The likelihood ratio test showed that the model with multi-allelic variants along with clinical and demographic data was a better fit to predict RSV severity. In summary, RSV severity was associated with hydrophilic (but not with hydrophobic) SPs gene variants. Collectively, our findings show that SP gene variants may play a key role in RSV infection and have a potential role in prognostication.
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Affiliation(s)
- Lynnlee C. Depicolzuane
- Center for Host defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State College of Medicine, Hershey, PA, United States
| | - Catherine M. Roberts
- Center for Host defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State College of Medicine, Hershey, PA, United States
| | - Neal J. Thomas
- Center for Host defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State College of Medicine, Hershey, PA, United States
| | - Keenan Anderson-Fears
- Department of Public Health Science, The Pennsylvania State College of Medicine, Hershey, PA, United States
| | - Dajiang Liu
- Department of Public Health Science, The Pennsylvania State College of Medicine, Hershey, PA, United States
| | | | - Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joanna Floros
- Center for Host defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State College of Medicine, Hershey, PA, United States
- Department of Obstetrics & Gynecology, The Pennsylvania State College of Medicine, Hershey, PA, United States
- *Correspondence: Joanna Floros, ; Chintan K. Gandhi,
| | - Chintan K. Gandhi
- Center for Host defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State College of Medicine, Hershey, PA, United States
- *Correspondence: Joanna Floros, ; Chintan K. Gandhi,
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8
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Moutoussamy EE, Waheed Q, Binford GJ, Khan HM, Moran SM, Eitel AR, Cordes MHJ, Reuter N. Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage. PLoS Comput Biol 2022; 18:e1009871. [PMID: 35180220 PMCID: PMC8893692 DOI: 10.1371/journal.pcbi.1009871] [Citation(s) in RCA: 2] [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: 08/17/2021] [Revised: 03/03/2022] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (Sicarius terrosus, St_βIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_βIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and β clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments. Envenomation following bites from recluse spiders (Loxosceles) causes loxoscelism, a necrotic tissue breakdown in mammals, and leads to skin degeneration and systemic reactions in the worst case. Recluse spiders belong to the Sicariidae family which also includes six-eyed sand spiders in the genera Sicarius and Hexopthalma. While sicariid spiders are found natively on all continents except Australia, treatments of loxoscelism are typically antibody based and available in some regions of the Americas. Sphingomyelinase D/phospholipase D enzymes are one of the major toxins in venom of sicariid spiders, and have been divided in two clades called α and β. The activity of α and β clades toxins differs; most α clade toxins present high activity against lipids with choline headgroups (-N (CH3)3+) such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (-NH3+). When comparing the structures of two α clade toxins and one β clade toxin, we noticed the presence in the α clade toxins only of a cage consisting of three aromatic amino acids. In this work we used numerical molecular simulations to probe the role of this cage in the preference of α clade toxins for choline head groups over ethanolamine head groups.
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Affiliation(s)
- Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Qaiser Waheed
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Greta J. Binford
- Department of Biology, Lewis and Clark College, Portland, Oregon, United States
| | - Hanif M. Khan
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Shane M. Moran
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Anna R. Eitel
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Matthew H. J. Cordes
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
- * E-mail:
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9
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Ugarte La Torre D, Takada S. Modeling lipid-protein interactions for coarse-grained lipid and Cα protein models. J Chem Phys 2021; 155:155101. [PMID: 34686048 DOI: 10.1063/5.0057278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Biological membranes that play major roles in diverse functions are composed of numerous lipids and proteins, making them an important target for coarse-grained (CG) molecular dynamics (MD) simulations. Recently, we have developed the CG implicit solvent lipid force field (iSoLF) that has a resolution compatible with the widely used Cα protein representation [D. Ugarte La Torre and S. Takada, J. Chem. Phys. 153, 205101 (2020)]. In this study, we extended it and developed a lipid-protein interaction model that allows the combination of the iSoLF and the Cα protein force field, AICG2+. The hydrophobic-hydrophilic interaction is modeled as a modified Lennard-Jones potential in which parameters were tuned partly to reproduce the experimental transfer free energy and partly based on the free energy profile normal to the membrane surface from previous all-atom MD simulations. Then, the obtained lipid-protein interaction is tested for the configuration and placement of transmembrane proteins, water-soluble proteins, and peripheral proteins, showing good agreement with prior knowledge. The interaction is generally applicable and is implemented in the publicly available software, CafeMol.
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Affiliation(s)
- Diego Ugarte La Torre
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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10
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Awasthi S, Kumar G, Ramani V, Awasthi V, Rodgers KK, Xie J, Beierle J, Kyere-Davies G, Singh B, Rahman N, Chowdhury AA, Chataut N. Mechanism of Anti-Inflammatory Activity of TLR4-Interacting SPA4 Peptide. Immunohorizons 2021; 5:659-674. [PMID: 34429343 PMCID: PMC8673433 DOI: 10.4049/immunohorizons.2100067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 12/05/2022] Open
Abstract
The TLR4-interacting SPA4 peptide suppresses inflammation. We assessed the structural and physicochemical properties and binding of SPA4 peptide to TLR4-MD2. We also studied the changes at the whole transcriptome level, cell morphology, viability, secreted cytokines and chemokines, and cell influx in cell systems and mouse models challenged with LPS and treated with SPA4 peptide. Our results demonstrated that the SPA4 peptide did not alter the cell viability and size and only moderately affected the transcriptome of the cells. Computational docking and rendering suggested that the SPA4 peptide intercalates with LPS-induced TLR4-MD2 complex. Results with alanine mutations of D-2 amino acid and NYTXXXRG-12-19 motif of SPA4 peptide suggested their role in binding to TLR4 and in reducing the cytokine response against LPS stimulus. Furthermore, therapeutically administered SPA4 peptide significantly suppressed the secreted levels of cytokines and chemokines in cells and bronchoalveolar lavage fluids of LPS-challenged mice. The results suggest that the SPA4 peptide intercalates with LPS-induced TLR4 complex and signaling for the suppression of inflammation.
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Affiliation(s)
- Shanjana Awasthi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK;
| | - Gaurav Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Vijay Ramani
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Vibhudutta Awasthi
- Research Imaging Facility, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK; and
| | - Karla K Rodgers
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jun Xie
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jacob Beierle
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Gertrude Kyere-Davies
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Bhupinder Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Negar Rahman
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Asif Alam Chowdhury
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Neha Chataut
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK
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11
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Moqadam M, Tubiana T, Moutoussamy EE, Reuter N. Membrane models for molecular simulations of peripheral membrane proteins. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1932589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Thibault Tubiana
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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12
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Lipid-Protein and Protein-Protein Interactions in the Pulmonary Surfactant System and Their Role in Lung Homeostasis. Int J Mol Sci 2020; 21:ijms21103708. [PMID: 32466119 PMCID: PMC7279303 DOI: 10.3390/ijms21103708] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Pulmonary surfactant is a lipid/protein complex synthesized by the alveolar epithelium and secreted into the airspaces, where it coats and protects the large respiratory air–liquid interface. Surfactant, assembled as a complex network of membranous structures, integrates elements in charge of reducing surface tension to a minimum along the breathing cycle, thus maintaining a large surface open to gas exchange and also protecting the lung and the body from the entrance of a myriad of potentially pathogenic entities. Different molecules in the surfactant establish a multivalent crosstalk with the epithelium, the immune system and the lung microbiota, constituting a crucial platform to sustain homeostasis, under health and disease. This review summarizes some of the most important molecules and interactions within lung surfactant and how multiple lipid–protein and protein–protein interactions contribute to the proper maintenance of an operative respiratory surface.
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13
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Khan HM, Souza PCT, Thallmair S, Barnoud J, de Vries AH, Marrink SJ, Reuter N. Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field. J Chem Theory Comput 2020; 16:2550-2560. [PMID: 32096995 PMCID: PMC7175457 DOI: 10.1021/acs.jctc.9b01194] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Cation−π
interactions play an important
role in biomolecular recognition, including interactions between membrane
phosphatidylcholine lipids and aromatic amino acids of peripheral
proteins. While molecular mechanics coarse grain (CG) force fields
are particularly well suited to simulate membrane proteins in general,
they are not parameterized to explicitly reproduce cation−π
interactions. We here propose a modification of the polarizable MARTINI
coarse grain (CG) model enabling it to model membrane binding events
of peripheral proteins whose aromatic amino acid interactions with
choline headgroups are crucial for their membrane binding. For this
purpose, we first collected and curated a dataset of eight peripheral
proteins from different families. We find that the MARTINI CG model
expectedly underestimates aromatics–choline interactions and
is unable to reproduce membrane binding of the peripheral proteins
in our dataset. Adjustments of the relevant interactions in the polarizable
MARTINI force field yield significant improvements in the observed
binding events. The orientation of each membrane-bound protein is
comparable to reference data from all-atom simulations and experimental
binding data. We also use negative controls to ensure that choline–aromatics
interactions are not overestimated. We finally check that membrane
properties, transmembrane proteins, and membrane translocation potential
of mean force (PMF) of aromatic amino acid side-chain analogues are
not affected by the new parameter set. This new version “MARTINI
2.3P” is a significant improvement over its predecessors and
is suitable for modeling membrane proteins including peripheral membrane
binding of peptides and proteins.
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Affiliation(s)
- Hanif M Khan
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway.,Department of Chemistry, University of Bergen, N-5020 Bergen, Norway
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14
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Nalian A, Umstead TM, Yang CH, Silveyra P, Thomas NJ, Floros J, McCormack FX, Chroneos ZC. Structural and Functional Determinants of Rodent and Human Surfactant Protein A: A Synthesis of Binding and Computational Data. Front Immunol 2019; 10:2613. [PMID: 31781112 PMCID: PMC6856657 DOI: 10.3389/fimmu.2019.02613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/21/2019] [Indexed: 11/23/2022] Open
Abstract
Surfactant protein A (SP-A) provides surfactant stability, first line host defense, and lung homeostasis by binding surfactant phospholipids, pathogens, alveolar macrophages (AMs), and epithelial cells. Non-primates express one SP-A protein whereas humans express two: SP-A1 and SP-A2 with core intra- and inter-species differences in the collagen-like domain. Here, we used macrophages and solid phase binding assays to discern structural correlates of rat (r) and human (h) SP-A function. Binding assays using recombinant rSP-A expressed in insect cells showed that lack of proline hydroxylation, truncations of amino-terminal oligomerization domains, and site-directed serine (S) or alanine (A) mutagenesis of cysteine 6 (C6S), glutamate 195 (E195A), and glutamate 171 (E171A) in the carbohydrate recognition domain (CRD) all impaired SP-A binding. Replacement of arginine 197 with alanine found in hSP-A (R197A), however, restored the binding of hydroxyproline-deficient rSP-A to the SP-A receptor SP-R210 similar to native rat and human SP-A. In silico calculation of Ca++ coordination bond length and solvent accessibility surface area revealed that the “humanized” R197A substitution alters topology and solvent accessibility of the Ca++ coordination residues of the CRD domain. Binding assays in mouse AMs that were exposed to either endogenous SP-A or hSP-A1 (6A2) and hSP-A2 (1A0) isoforms in vivo revealed that mouse SP-A is a functional hybrid of hSP-A1 and hSP-A2 in regulating SP-A receptor occupancy and binding affinity. Binding assays using neonatal and adult human AMs indicates that the interaction of SP-A1 and SP-A2 with AMs is developmentally regulated. Furthermore, our data indicate that the auxiliary ion coordination loop encompassing the conserved E171 residue may comprise a conserved site of interaction with macrophages, and SP-R210 specifically, that merits further investigation to discern conserved and divergent SP-A functions between species. In summary, our findings support the notion that complex structural adaptation of SP-A regulate conserved and species specific AM functions in vertebrates.
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Affiliation(s)
- Armen Nalian
- Department of Biology, Stephen F. Austin State University, Nacogdoches, TX, United States.,The Center of Biomedical Research, University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Todd M Umstead
- Department of Pediatrics, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States.,Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States
| | - Ching-Hui Yang
- The Center of Biomedical Research, University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Patricia Silveyra
- Department of Pediatrics, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States.,Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States
| | - Neal J Thomas
- Department of Pediatrics, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States.,Department of Public Health Sciences, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States
| | - Joanna Floros
- Department of Pediatrics, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States.,Center of Host Defense and Inflammatory Disease Research, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States.,Department of Obstetrics and Gynecology, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States
| | - Francis X McCormack
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Zissis C Chroneos
- The Center of Biomedical Research, University of Texas Health Science Center at Tyler, Tyler, TX, United States.,Department of Pediatrics, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States.,Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States.,Department of Microbiology and Immunology, Pennsylvania State University College of Medicine and PennState Health Children's Hospital, Hershey, PA, United States
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15
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Waheed Q, Khan HM, He T, Roberts M, Gershenson A, Reuter N. Interfacial Aromatics Mediating Cation-π Interactions with Choline-Containing Lipids Can Contribute as Much to Peripheral Protein Affinity for Membranes as Aromatics Inserted below the Phosphates. J Phys Chem Lett 2019; 10:3972-3977. [PMID: 31246477 DOI: 10.1021/acs.jpclett.9b01639] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Membrane-binding interfaces of peripheral proteins are restricted to a small part of their exposed surface, so the ability to engage in strong selective interactions with membrane lipids at various depths in the interface, both below and above the phosphates, is an advantage. Driven by their hydrophobicity, aromatic amino acids preferentially partition into membrane interfaces, often below the phosphates, yet enthalpically favorable interactions with the lipid headgroups, above the phosphate plane, are likely to further stabilize high interfacial positions. Using free-energy perturbation, we calculate the energetic cost of alanine substitution for 11 interfacial aromatic amino acids from 3 peripheral proteins. We show that the involvement in cation-π interactions with the headgroups (i) increases the ΔΔGtransfer as compared with insertion at the same depth without cation-π stabilization and (ii) can contribute at least as much as deeper insertion below the phosphates, highlighting the multiple roles of aromatics in peripheral membrane protein affinity.
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Affiliation(s)
- Qaiser Waheed
- Department of Biological Sciences , University of Bergen , N-5020 Bergen , Norway
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
| | - Hanif M Khan
- Department of Biological Sciences , University of Bergen , N-5020 Bergen , Norway
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
| | - Tao He
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Mary Roberts
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
- Molecular and Cellular Biology Graduate Program , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
- Department of Chemistry , University of Bergen , N-5020 Bergen , Norway
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16
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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17
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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18
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A model for hydrophobic protrusions on peripheral membrane proteins. PLoS Comput Biol 2018; 14:e1006325. [PMID: 30048443 PMCID: PMC6080788 DOI: 10.1371/journal.pcbi.1006325] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 08/07/2018] [Accepted: 06/24/2018] [Indexed: 11/19/2022] Open
Abstract
With remarkable spatial and temporal specificities, peripheral membrane proteins bind to biological membranes. They do this without compromising solubility of the protein, and their binding sites are not easily distinguished. Prototypical peripheral membrane binding sites display a combination of patches of basic and hydrophobic amino acids that are also frequently present on other protein surfaces. The purpose of this contribution is to identify simple but essential components for membrane binding, through structural criteria that distinguish exposed hydrophobes at membrane binding sites from those that are frequently found on any protein surface. We formulate the concepts of protruding hydrophobes and co-insertability and have analysed more than 300 families of proteins that are classified as peripheral membrane binders. We find that this structural motif strongly discriminates the surfaces of membrane-binding and non-binding proteins. Our model constitutes a novel formulation of a structural pattern for membrane recognition and emphasizes the importance of subtle structural properties of hydrophobic membrane binding sites. Peripheral membrane proteins bind cellular membranes transiently, and are otherwise soluble proteins. As the interaction between proteins and membranes happens at cellular interfaces they are naturally involved in important interfacial processes such as recognition, signaling and trafficking. Commonly their binding sites are also soluble, and their binding mechanisms poorly understood. This complicates the elaboration of conceptual and quantitative models for peripheral membrane binding and makes binding site prediction difficult. It is therefore of great interest to discover traits that are common between these binding sites and that distinguishes them from other protein surfaces. In this work we identify simple and general structural features that facilitate membrane recognition by soluble proteins. We show that these motifs are highly over-represented on peripheral membrane proteins.
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19
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Visualization of lipid directed dynamics of perilipin 1 in human primary adipocytes. Sci Rep 2017; 7:15011. [PMID: 29118433 PMCID: PMC5678101 DOI: 10.1038/s41598-017-15059-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/19/2017] [Indexed: 12/20/2022] Open
Abstract
Perilipin 1 is a lipid droplet coating protein known to regulate lipid metabolism in adipocytes by serving as a physical barrier as well as a recruitment site for lipases to the lipid droplet. Phosphorylation of perilipin 1 by protein kinase A rapidly initiates lipolysis, but the detailed mechanism on how perilipin 1 controls lipolysis is unknown. Here, we identify specific lipid binding properties of perilipin 1 that regulate the dynamics of lipolysis in human primary adipocytes. Cellular imaging combined with biochemical and biophysical analyses demonstrate that perilipin 1 specifically binds to cholesteryl esters, and that their dynamic properties direct segregation of perilipin 1 into topologically distinct micro domains on the lipid droplet. Together, our data points to a simple unifying mechanism that lipid assembly and segregation control lipolysis in human primary adipocytes.
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20
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Pohjolainen E, Malola S, Groenhof G, Häkkinen H. Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. Bioconjug Chem 2017; 28:2327-2339. [DOI: 10.1021/acs.bioconjchem.7b00367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmi Pohjolainen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Sami Malola
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Gerrit Groenhof
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Hannu Häkkinen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
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21
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Takamiya R, Uchida K, Shibata T, Maeno T, Kato M, Yamaguchi Y, Ariki S, Hasegawa Y, Saito A, Miwa S, Takahashi H, Akaike T, Kuroki Y, Takahashi M. Disruption of the structural and functional features of surfactant protein A by acrolein in cigarette smoke. Sci Rep 2017; 7:8304. [PMID: 28814727 PMCID: PMC5559459 DOI: 10.1038/s41598-017-08588-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/11/2017] [Indexed: 02/06/2023] Open
Abstract
The extent to which defective innate immune responses contribute to chronic obstructive pulmonary disease (COPD) is not fully understood. Pulmonary surfactant protein A (SP-A) plays an important role in regulating innate immunity in the lungs. In this study, we hypothesised that cigarette smoke (CS) and its component acrolein might influence pulmonary innate immunity by affecting the function of SP-A. Indeed, acrolein-modified SP-A was detected in the lungs of mice exposed to CS for 1 week. To further confirm this finding, recombinant human SP-A (hSP-A) was incubated with CS extract (CSE) or acrolein and then analysed by western blotting and nanoscale liquid chromatography-matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry. These analyses revealed that CSE and acrolein induced hSP-A oligomerisation and that acrolein induced the modification of six residues in hSP-A: His39, His116, Cys155, Lys180, Lys221, and Cys224. These modifications had significant effects on the innate immune functions of hSP-A. CSE- or acrolein-induced modification of hSP-A significantly decreased hSP-A's ability to inhibit bacterial growth and to enhance macrophage phagocytosis. These findings suggest that CS-induced structural and functional defects in SP-A contribute to the dysfunctional innate immune responses observed in the lung during cigarette smoking.
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Affiliation(s)
- Rina Takamiya
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Hokkaido, 060-8556, Japan.
| | - Koji Uchida
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takahiro Shibata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Toshitaka Maeno
- Department of Medicine and Biological Science, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Masaki Kato
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Shigeru Ariki
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Hokkaido, 060-8556, Japan
| | - Yoshihiro Hasegawa
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Hokkaido, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Atsushi Saito
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Hokkaido, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Soichi Miwa
- Department of Cellular Pharmacology, Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroki Takahashi
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshio Kuroki
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Hokkaido, 060-8556, Japan
| | - Motoko Takahashi
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Hokkaido, 060-8556, Japan
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