1
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Zea DJ, Teppa E, Marino-Buslje C. Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates. Methods Mol Biol 2023; 2627:83-100. [PMID: 36959443 DOI: 10.1007/978-1-0716-2974-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Homology modeling is the most common technique to build structural models of a target protein based on the structure of proteins with high-sequence identity and available high-resolution structures. This technique is based on the idea that protein structure shows fewer changes than sequence through evolution. While in this scenario single mutations would minimally perturb the structure, experimental evidence shows otherwise: proteins with high conformational diversity impose a limit of the paradigm of comparative modeling as the same protein sequence can adopt dissimilar three-dimensional structures. These cases present challenges for modeling; at first glance, they may seem to be easy cases, but they have a complexity that is not evident at the sequence level. In this chapter, we address the following questions: Why should we care about conformational diversity? How to consider conformational diversity when doing template-based modeling in a practical way?
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Affiliation(s)
- Diego Javier Zea
- Laboratory of Computational and Quantitative Biology, LCQB, UMR 7238 CNRS, IBPS, Sorbonne Université, Paris, France
| | - Elin Teppa
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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2
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Luchini A, Tidemand FG, Johansen NT, Sebastiani F, Corucci G, Fragneto G, Cárdenas M, Arleth L. Dark peptide discs for the investigation of membrane proteins in supported lipid bilayers: the case of synaptobrevin 2 (VAMP2). NANOSCALE ADVANCES 2022; 4:4526-4534. [PMID: 36341300 PMCID: PMC9595196 DOI: 10.1039/d2na00384h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Supported lipid bilayers (SLBs) are commonly used as model systems mimicking biological membranes. Recently, we reported a new method to produce SLBs with incorporated membrane proteins, which is based on the application of peptide discs [Luchini et al., Analytical Chemistry, 2020, 92, 1081-1088]. Peptide discs are small discoidal particles composed of a lipid core and an outer belt of self-assembled 18A peptides. SLBs including membrane proteins can be formed by depositing the peptide discs on a solid support and subsequently removing the peptide by buffer rinsing. Here, we introduce a new variant of the 18A peptide, named dark peptide (d18A). d18A exhibits UV absorption at 214 nm, whereas the absorption at 280 nm is negligible. This improves sample preparation as it enables a direct quantification of the membrane protein concentration in the peptide discs by measuring UV absorption at 280 nm. We describe the application of the peptide discs prepared with d18A (dark peptide discs) to produce SLBs with a membrane protein, synaptobrevin 2 (VAMP2). The collected data showed the successful formation of SLBs with high surface coverage and incorporation of VAMP2 in a single orientation with the extramembrane domain exposed towards the bulk solvent. Compared to 18A, we found that d18A was more efficiently removed from the SLB. Our data confirmed the structural organisation of VAMP2 as including both α-helical and β-sheet secondary structure. We further verified the orientation of VAMP2 in the SLBs by characterising the binding of VAMP2 with α-synuclein. These results point at the produced SLBs as relevant membrane models for biophysical studies as well as nanostructured biomaterials.
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Affiliation(s)
| | - Frederik Grønbæk Tidemand
- Department of Plant and Environmental Sciences, University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Nicolai Tidemand Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Federica Sebastiani
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University Per Albin Hanssons Väg 35 21432 Malmö Sweden
| | - Giacomo Corucci
- Institut Laue-Langevin 71 Avenue des Martyrs, BP 156 38042 Grenoble France
- Université Grenoble Alpes, Ecole Doctorale de Physique 110 Rue de la Chimie 38400 Saint-Martin-d'Hères France
| | - Giovanna Fragneto
- Institut Laue-Langevin 71 Avenue des Martyrs, BP 156 38042 Grenoble France
- Université Grenoble Alpes, Ecole Doctorale de Physique 110 Rue de la Chimie 38400 Saint-Martin-d'Hères France
| | - Marité Cárdenas
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University Per Albin Hanssons Väg 35 21432 Malmö Sweden
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5 2100 Copenhagen Denmark
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3
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Ghosh G, Barman R, Mukherjee A, Ghosh U, Ghosh S, Fernández G. Control over Multiple Nano‐ and Secondary Structures in Peptide Self‐Assembly. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Goutam Ghosh
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Correnstrasse 36 48149 Münster Germany
| | - Ranajit Barman
- School of Applied and Interdisciplinary Sciences Indian Association for the Cultivation Science 2A and 2B Raja S. C. Mullick Road Kolkata India
| | - Anurag Mukherjee
- School of Applied and Interdisciplinary Sciences Indian Association for the Cultivation Science 2A and 2B Raja S. C. Mullick Road Kolkata India
| | - Uttam Ghosh
- Department of Organic Chemistry Indian Institute of Science Bengaluru 560012 Karnataka India
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary Sciences Indian Association for the Cultivation Science 2A and 2B Raja S. C. Mullick Road Kolkata India
| | - Gustavo Fernández
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Correnstrasse 36 48149 Münster Germany
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4
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Ghosh G, Barman R, Mukherjee A, Ghosh U, Ghosh S, Fernández G. Control over Multiple Nano- and Secondary Structures in Peptide Self-Assembly. Angew Chem Int Ed Engl 2022; 61:e202113403. [PMID: 34758508 PMCID: PMC9300061 DOI: 10.1002/anie.202113403] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Indexed: 12/15/2022]
Abstract
Herein, we report the rich morphological and conformational versatility of a biologically active peptide (PEP-1), which follows diverse self-assembly pathways to form up to six distinct nanostructures and up to four different secondary structures through subtle modulation in pH, concentration and temperature. PEP-1 forms twisted β-sheet secondary structures and nanofibers at pH 7.4, which transform into fractal-like structures with strong β-sheet conformations at pH 13.0 or short disorganized elliptical aggregates at pH 5.5. Upon dilution at pH 7.4, the nanofibers with twisted β-sheet secondary structural elements convert into nanoparticles with random coil conformations. Interestingly, these two self-assembled states at pH 7.4 and room temperature are kinetically controlled and undergo a further transformation into thermodynamically stable states upon thermal annealing: whereas the twisted β-sheet structures and corresponding nanofibers transform into 2D sheets with well-defined β-sheet domains, the nanoparticles with random coil structures convert into short nanorods with α-helix conformations. Notably, PEP-1 also showed high biocompatibility, low hemolytic activity and marked antibacterial activity, rendering our system a promising candidate for multiple bio-applications.
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Affiliation(s)
- Goutam Ghosh
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrenstrasse 3648149MünsterGermany
| | - Ranajit Barman
- School of Applied and Interdisciplinary SciencesIndian Association for the Cultivation Science2A and 2B Raja S. C. Mullick RoadKolkataIndia
| | - Anurag Mukherjee
- School of Applied and Interdisciplinary SciencesIndian Association for the Cultivation Science2A and 2B Raja S. C. Mullick RoadKolkataIndia
| | - Uttam Ghosh
- Department of Organic ChemistryIndian Institute of ScienceBengaluru560012KarnatakaIndia
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary SciencesIndian Association for the Cultivation Science2A and 2B Raja S. C. Mullick RoadKolkataIndia
| | - Gustavo Fernández
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrenstrasse 3648149MünsterGermany
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5
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Das M, Chen N, LiWang A, Wang LP. Identification and characterization of metamorphic proteins: Current and future perspectives. Biopolymers 2021; 112:e23473. [PMID: 34528703 DOI: 10.1002/bip.23473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/06/2022]
Abstract
Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but it remains unknown the extent to which the proteome is populated by this class of proteins. We propose that uncovering the metamorphome will require a synergy of computational screening of protein sequences to identify potential metamorphic behavior and validation through experimental techniques. This perspective discusses computational and experimental approaches that are currently used to predict and characterize metamorphic proteins as well as the need for developing improved methodologies. Since metamorphic proteins act as molecular switches, understanding their properties and behavior could lead to novel applications of these proteins as sensors in biological or environmental contexts.
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Affiliation(s)
- Madhurima Das
- School of Natural Sciences, University of California, Merced, California, USA
| | - Nanhao Chen
- Department of Chemistry, University of California, Davis, California, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, California, USA.,Department of Chemistry and Biochemistry, University of California, Merced, California, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, California, USA.,Health Sciences Research Institute, University of California, Merced, California, USA.,Center for Circadian Biology, University of California, San Diego, California, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California, USA
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6
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He L, Ying L, Jingting X, Chen C, Shuntang G. Changes in the secondary structures and zeta potential of soybean peptide and its calcium complexes in different solution environments. Food Funct 2021; 12:5967-5974. [PMID: 34032239 DOI: 10.1039/d0fo03478a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To illustrate the relationship between environment hydrophobicity and soybean peptide and its calcium complexes when they are absorbed transmembrane, different solution environments (HBS buffer, TFE hydrophobic solution and cell suspension) were used to simulate hydrophilic and hydrophobic environments. In this study, soybean peptides (10-30 kDa) with a high calcium binding capacity were prepared by enzymatic hydrolysis and ultrafiltration. The results of cell experiments showed that the peptide could transport calcium into cells for absorption. Secondary structure changes of the peptide and its calcium complexes in different solution environments showed that the secondary structure of the peptide changed during the transmembrane absorption, and the contents of α-helix and β-sheet structures increased. Besides, the β-sheet structures in the peptide-calcium complexes were further converted to an α-helix structure. This conversion may be induced by the hydrophobicity of peptide solutions. In addition, when the conformation changes, the positively charged peptides in the sample will be exposed and then interact with cells, which is beneficial for the transmembrane of peptide-calcium complexes.
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Affiliation(s)
- Liu He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. and Yunnan Urban Agricultural Engineering and Technological Research Center, College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, China
| | - Lv Ying
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. and Department of Food Science, Beijing University of Agriculture, Beijing, 102206, China
| | - Xu Jingting
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Chen Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Guo Shuntang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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7
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Bozorgmehr JH. The origin of chromosomal histones in a 30S ribosomal protein. Gene 2020; 726:144155. [PMID: 31629821 DOI: 10.1016/j.gene.2019.144155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 11/18/2022]
Abstract
Histones are genes that regulate chromatin structure. They are present in both eukaryotes and archaea, and form nucleosomes with DNA, but their exact evolutionary origins have hitherto remained a mystery. A longstanding hypothesis is that they have precursors in ribosomal proteins with whom they share much in common in terms of size and chemistry. By examining the proteome of the Asgard archaeon, Lokiarchaeum, the most conserved of all the histones, H4, is found to plausibly be homologous with one of its 30S ribosomal proteins, RPS6. This is based on both sequence identity and statistical analysis. The N-terminal tail, containing key sites involved in post-translational modifications, is notably present in the precursor gene. Although other archaeal groups possess similar homologs, these are not as close to H4 as the one found in Lokiarchaeum. The other core histones, H2A, H2B and H3, appear to have also evolved from the same ribosomal protein. Parts of H4 are also similar to another ribosomal protein, namely RPS15, suggesting that the ancestral precursor could have resembled both. Eukaryotic histones, in addition, appear to have an independent origin to that of their archaeal counterparts that evolved from similar, but still different, 30S subunit proteins, some of which are much more like histones in terms of their physical structure. The nucleosome may, therefore, be not only of archaeal but also of ribosomal origin.
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8
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Chakraborty D, Chebaro Y, Wales DJ. A multifunnel energy landscape encodes the competing α-helix and β-hairpin conformations for a designed peptide. Phys Chem Chem Phys 2020; 22:1359-1370. [PMID: 31854397 DOI: 10.1039/c9cp04778f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Depending on the amino acid sequence, as well as the local environment, some peptides have the capability to fold into multiple secondary structures. Conformational switching between such structures is a key element of protein folding and aggregation. Specifically, understanding the molecular mechanism underlying the transition from an α-helix to a β-hairpin is critical because it is thought to be a harbinger of amyloid assembly. In this study, we explore the energy landscape for an 18-residue peptide (DP5), designed by Araki and Tamura to exhibit equal propensities for the α-helical and β-hairpin forms. We find that the degeneracy is encoded in the multifunnel nature of the underlying free energy landscape. In agreement with experiment, we also observe that mutation of tyrosine at position 12 to serine shifts the equilibrium in favor of the α-helix conformation, by altering the landscape topography. The transition from the α-helix to the β-hairpin is a complex stepwise process, and occurs via collapsed coil-like intermediates. Our findings suggest that even a single mutation can tune the emergent features of the landscape, providing an efficient route to protein design. Interestingly, the transition pathways for the conformational switch seem to be minimally perturbed upon mutation, suggesting that there could be universal microscopic features that are conserved among different switch-competent protein sequences.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
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9
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Aragón-Muriel A, Ausili A, Sánchez K, Rojas A OE, Londoño Mosquera J, Polo-Cerón D, Oñate-Garzón J. Studies on the Interaction of Alyteserin 1c Peptide and Its Cationic Analogue with Model Membranes Imitating Mammalian and Bacterial Membranes. Biomolecules 2019; 9:biom9100527. [PMID: 31557903 PMCID: PMC6843542 DOI: 10.3390/biom9100527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 01/17/2023] Open
Abstract
Antimicrobial peptides (AMPs) are effector molecules of the innate immune system and have been isolated from multiple organisms. Their antimicrobial properties are due to the fact that they interact mainly with the anionic membrane of the microorganisms, permeabilizing it and releasing the cytoplasmic content. Alyteserin 1c (+2), an AMP isolated from Alytes obstetricans and its more cationic and hydrophilic analogue (+5) were synthesized using the solid phase method, in order to study the interaction with model membranes by calorimetric and spectroscopic assays. Differential scanning calorimetry (DSC) showed that both peptides had a strong effect when the membrane contained phosphatidylcholine (PC) alone or was mixed with phosphatidylglycerol (PG), increasing membrane fluidization. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to study the secondary structure of the peptide. Peptide +2 exhibited a transition from β-sheet/turns to β-sheet/α-helix structures after binding with model membranes, whereas peptide +5 had a transition from aggregation/unordered to β-sheet/α-helix structures after binding with membrane-contained PC. Interestingly, the latter showed a β-sheet structure predominantly in the presence of PG lipids. Additionally, molecular dynamics (MD) results showed that the carboxy-terminal of the peptide +5 has the ability to insert into the surface of the PC/PG membranes, resulting in the increase of the membrane fluidity.
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Affiliation(s)
- Alberto Aragón-Muriel
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Alessio Ausili
- Departmento de Bioquímica y Biología Molecular-A, Facultad de Medicina Veterinaria, Campus of International Excellence Mare, Universidad de Murcia, E-30100 Murcia, Spain.
| | - Kevin Sánchez
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
| | - Oscar E Rojas A
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
| | - Juan Londoño Mosquera
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Dorian Polo-Cerón
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Jose Oñate-Garzón
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
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10
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Expression, purification and stabilization of human serotonin transporter from E. coli. Protein Expr Purif 2019; 164:105479. [PMID: 31442583 DOI: 10.1016/j.pep.2019.105479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/31/2019] [Accepted: 08/15/2019] [Indexed: 11/21/2022]
Abstract
The serotonin transporter belongs to the family of sodium-chloride coupled neurotransmitter transporter and is related to depression in humans. It is therefore an important drug target to support treatment of depression. Recently, structures of human serotonin transporter in complex with inhibitor molecules have been published. However, the production of large protein amounts for crystallization experiments remains a bottleneck. Here we present the possibility to obtain purified serotonin transporter from E. coli. Fos-choline 12 solubilized target protein was obtained with a purity of >95% and a yield of 1.2 mg L-1 culture in autoinduction medium. CD spectroscopic analysis of protein stability allowed identifying CHS and POPX as stabilizing components, which increased hSERT thermostability by 7 °C. The kinetic dissociation constant KD of 2.8 μM (±0.05) for of the inhibitor Desipramine was determined with a ka of 10,848 M - 1 s-1 (±220) and a kd of 0.03 s-1 (±4.7 × 10-5).
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11
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Fezoua-Boubegtiten Z, Hastoy B, Scotti P, Milochau A, Bathany K, Desbat B, Castano S, Oda R, Lang J. The transmembrane domain of the SNARE protein VAMP2 is highly sensitive to its lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:670-676. [DOI: 10.1016/j.bbamem.2018.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/15/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
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12
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Smirnova YG, Risselada HJ, Müller M. Thermodynamically reversible paths of the first fusion intermediate reveal an important role for membrane anchors of fusion proteins. Proc Natl Acad Sci U S A 2019; 116:2571-2576. [PMID: 30700547 PMCID: PMC6377489 DOI: 10.1073/pnas.1818200116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Biological membrane fusion proceeds via an essential topological transition of the two membranes involved. Known players such as certain lipid species and fusion proteins are generally believed to alter the free energy and thus the rate of the fusion reaction. Quantifying these effects by theory poses a major challenge since the essential reaction intermediates are collective, diffusive and of a molecular length scale. We conducted molecular dynamics simulations in conjunction with a state-of-the-art string method to resolve the minimum free-energy path of the first fusion intermediate state, the so-called stalk. We demonstrate that the isolated transmembrane domains (TMDs) of fusion proteins such as SNARE molecules drastically lower the free energy of both the stalk barrier and metastable stalk, which is not trivially explained by molecular shape arguments. We relate this effect to the local thinning of the membrane (negative hydrophobic mismatch) imposed by the TMDs which favors the nearby presence of the highly bent stalk structure or prestalk dimple. The distance between the membranes is the most crucial determinant of the free energy of the stalk, whereas the free-energy barrier changes only slightly. Surprisingly, fusion enhancing lipids, i.e., lipids with a negative spontaneous curvature, such as PE lipids have little effect on the free energy of the stalk barrier, likely because of its single molecular nature. In contrast, the lipid shape plays a crucial role in overcoming the hydration repulsion between two membranes and thus rather lowers the total work required to form a stalk.
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Affiliation(s)
- Yuliya G Smirnova
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany;
| | - Herre Jelger Risselada
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany
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13
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Yang Z, Jiang B, McNamara ME, Kearns SL, Pittman M, Kaye TG, Orr PJ, Xu X, Benton MJ. Pterosaur integumentary structures with complex feather-like branching. Nat Ecol Evol 2018; 3:24-30. [DOI: 10.1038/s41559-018-0728-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/23/2018] [Indexed: 01/24/2023]
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14
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Hastoy B, Clark A, Rorsman P, Lang J. Fusion pore in exocytosis: More than an exit gate? A β-cell perspective. Cell Calcium 2017; 68:45-61. [PMID: 29129207 DOI: 10.1016/j.ceca.2017.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/17/2017] [Accepted: 10/24/2017] [Indexed: 12/14/2022]
Abstract
Secretory vesicle exocytosis is a fundamental biological event and the process by which hormones (like insulin) are released into the blood. Considerable progress has been made in understanding this precisely orchestrated sequence of events from secretory vesicle docked at the cell membrane, hemifusion, to the opening of a membrane fusion pore. The exact biophysical and physiological regulation of these events implies a close interaction between membrane proteins and lipids in a confined space and constrained geometry to ensure appropriate delivery of cargo. We consider some of the still open questions such as the nature of the initiation of the fusion pore, the structure and the role of the Soluble N-ethylmaleimide-sensitive-factor Attachment protein REceptor (SNARE) transmembrane domains and their influence on the dynamics and regulation of exocytosis. We discuss how the membrane composition and protein-lipid interactions influence the likelihood of the nascent fusion pore forming. We relate these factors to the hypothesis that fusion pore expansion could be affected in type-2 diabetes via changes in disease-related gene transcription and alterations in the circulating lipid profile. Detailed characterisation of the dynamics of the fusion pore in vitro will contribute to understanding the larger issue of insulin secretory defects in diabetes.
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Affiliation(s)
- Benoit Hastoy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK.
| | - Anne Clark
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK; Metabolic Research, Institute of Neuroscience and Physiology, University of Goteborg, Medicinaregatan 11, S-41309 Göteborg, Sweden
| | - Jochen Lang
- Laboratoire de Chimie et Biologie des Membranes et Nano-objets (CBMN), CNRS UMR 5248, Université de Bordeaux, Allée de Geoffrey St Hilaire, 33600 Pessac, France.
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15
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Lella M, Mahalakshmi R. Metamorphic Proteins: Emergence of Dual Protein Folds from One Primary Sequence. Biochemistry 2017; 56:2971-2984. [DOI: 10.1021/acs.biochem.7b00375] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory,
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory,
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
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16
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Hastoy B, Scotti PA, Milochau A, Fezoua-Boubegtiten Z, Rodas J, Megret R, Desbat B, Laguerre M, Castano S, Perrais D, Rorsman P, Oda R, Lang J. A Central Small Amino Acid in the VAMP2 Transmembrane Domain Regulates the Fusion Pore in Exocytosis. Sci Rep 2017; 7:2835. [PMID: 28588281 PMCID: PMC5460238 DOI: 10.1038/s41598-017-03013-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 04/27/2017] [Indexed: 11/30/2022] Open
Abstract
Exocytosis depends on cytosolic domains of SNARE proteins but the function of the transmembrane domains (TMDs) in membrane fusion remains controversial. The TMD of the SNARE protein synaptobrevin2/VAMP2 contains two highly conserved small amino acids, G100 and C103, in its central portion. Substituting G100 and/or C103 with the β-branched amino acid valine impairs the structural flexibility of the TMD in terms of α-helix/β-sheet transitions in model membranes (measured by infrared reflection-absorption or evanescent wave spectroscopy) during increase in protein/lipid ratios, a parameter expected to be altered by recruitment of SNAREs at fusion sites. This structural change is accompanied by reduced membrane fluidity (measured by infrared ellipsometry). The G100V/C103V mutation nearly abolishes depolarization-evoked exocytosis (measured by membrane capacitance) and hormone secretion (measured biochemically). Single-vesicle optical (by TIRF microscopy) and biophysical measurements of ATP release indicate that G100V/C103V retards initial fusion-pore opening, hinders its expansion and leads to premature closure in most instances. We conclude that the TMD of VAMP2 plays a critical role in membrane fusion and that the structural mobility provided by the central small amino acids is crucial for exocytosis by influencing the molecular re-arrangements of the lipid membrane that are necessary for fusion pore opening and expansion.
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Affiliation(s)
- Benoît Hastoy
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Pier A Scotti
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France
| | - Alexandra Milochau
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France
| | - Zahia Fezoua-Boubegtiten
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France
| | - Jorge Rodas
- Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France.,Laboratoire de l'Intégration du Matériau au Système, UMR CNRS 5218, 351 Cours de la Libération, 33400 Talence, France.,Institut Polytechnique de Bordeaux, Avernue des Facultés, 33405, Talence, France
| | - Rémi Megret
- Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France.,Laboratoire de l'Intégration du Matériau au Système, UMR CNRS 5218, 351 Cours de la Libération, 33400 Talence, France.,Institut Polytechnique de Bordeaux, Avernue des Facultés, 33405, Talence, France
| | - Bernard Desbat
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France
| | - Michel Laguerre
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France
| | - Sabine Castano
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France
| | - David Perrais
- Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France.,Interdisciplinary Institute for Neuroscience, UMR CNRS 5287, 146, rue Léo-Saignat, 33077, Bordeaux, France
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Reiko Oda
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France.,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France
| | - Jochen Lang
- Laboratory of Membrane Chemistry and Biology (CBMN), UMR CNRS 5248, Université de Bordeaux, Allée de Geoffroy St Hilaire, 33600, Pessac, France. .,Université de Bordeaux, 351 Cours de la Libération, 33400, Talence, France.
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17
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Dagbay KB, Bolik-Coulon N, Savinov SN, Hardy JA. Caspase-6 Undergoes a Distinct Helix-Strand Interconversion upon Substrate Binding. J Biol Chem 2017; 292:4885-4897. [PMID: 28154009 DOI: 10.1074/jbc.m116.773499] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Caspases are cysteine aspartate proteases that are major players in key cellular processes, including apoptosis and inflammation. Specifically, caspase-6 has also been implicated in playing a unique and critical role in neurodegeneration; however, structural similarities between caspase-6 and other caspase active sites have hampered precise targeting of caspase-6. All caspases can exist in a canonical conformation, in which the substrate binds atop a β-strand platform in the 130's region. This caspase-6 region can also adopt a helical conformation that has not been seen in any other caspases. Understanding the dynamics and interconversion between the helical and strand conformations in caspase-6 is critical to fully assess its unique function and regulation. Here, hydrogen/deuterium exchange mass spectrometry indicated that caspase-6 is inherently and dramatically more conformationally dynamic than closely related caspase-7. In contrast to caspase-7, which rests constitutively in the strand conformation before and after substrate binding, the hydrogen/deuterium exchange data in the L2' and 130's regions suggested that before substrate binding, caspase-6 exists in a dynamic equilibrium between the helix and strand conformations. Caspase-6 transitions exclusively to the canonical strand conformation only upon substrate binding. Glu-135, which showed noticeably different calculated pK a values in the helix and strand conformations, appears to play a key role in the interconversion between the helix and strand conformations. Because caspase-6 has roles in several neurodegenerative diseases, exploiting the unique structural features and conformational changes identified here may provide new avenues for regulating specific caspase-6 functions for therapeutic purposes.
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Affiliation(s)
| | | | - Sergey N Savinov
- Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
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18
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Structure and interaction with lipid membrane models of Semliki Forest virus fusion peptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2671-2680. [PMID: 27425030 PMCID: PMC7172313 DOI: 10.1016/j.bbamem.2016.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/21/2016] [Accepted: 07/12/2016] [Indexed: 11/24/2022]
Abstract
Semliki Forest virus (SFV) is a well-characterized alphavirus that infects cells via endocytosis and an acid-triggered fusion step using class II fusion proteins. Membrane fusion is mediated by the viral spike protein, a heterotrimer of two transmembrane subunits, E1 and E2, and a peripheral protein, E3. Sequence analysis of the E1 ectodomain of a number of alphaviruses demonstrated the presence of a highly conserved hydrophobic domain on the E1 ectodomain. This sequence was proposed to be the fusion peptide of SFV and is believed to be the domain of E1 that interacts with the target membrane and triggers fusion. Here, we investigate the structure and the interaction with lipid membrane models of 76YQCKVYTGVYPFMWGGAYCFC96 sequence from SFV, named SFV21, using optical method (ellipsometry) and vibrational spectroscopiy approaches (Polarization Modulation infra-Red Reflection Absorption Spectroscopy, PMIRRAS, and polarized ATR-FTIR). We demonstrate a structural flexibility of SFV21 sequence whether the lateral pressure and the lipid environment. In a lipid environment that mimics eukaryotic cell membranes, a conformational transition from an α-helix to a β-sheet is induced in the presence of lipid by increasing the peptide to lipid ratio, which leads to important perturbations in the membrane organisation. SFV21 fusion peptide displays structural flexibility between α-helix and β-sheets. A conformational transition from an α-helix to a β-sheet is induced by the increase of the peptide to lipid ratio. SFV21 fusion peptide leads to important perturbations in the membrane organisation.
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19
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Khalil M, Boubegtiten-Fezoua Z, Hellmann N, Hellwig P. Extraordinary stability of hemocyanins from L. polyphemus and E. californicum studied using infrared spectroscopy from 294 to 20 K. Phys Chem Chem Phys 2016; 18:28732-28739. [DOI: 10.1039/c6cp03510h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infrared spectroscopic evidence of a high stability towards exposure to sub-zero temperatures for hemocyanins from the arthropods Limulus polyphemus and Eurypelma californicum.
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Affiliation(s)
- Mireille Khalil
- Laboratoire de Bioélectrochimie et Spectroscopie
- UMR 7140 Université de Strasbourg CNRS
- 1 Rue Blaise Pascal 67070
- France
| | - Zahia Boubegtiten-Fezoua
- Laboratoire de Bioélectrochimie et Spectroscopie
- UMR 7140 Université de Strasbourg CNRS
- 1 Rue Blaise Pascal 67070
- France
| | - Nadja Hellmann
- Institute for Molecular Biophysics
- University of Mainz
- 55128 Mainz
- Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie
- UMR 7140 Université de Strasbourg CNRS
- 1 Rue Blaise Pascal 67070
- France
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20
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Appadu A, Jelokhani-Niaraki M, DeBruin L. Conformational Changes and Association of Membrane-Interacting Peptides in Myelin Membrane Models: A Case of the C-Terminal Peptide of Proteolipid Protein and the Antimicrobial Peptide Melittin. J Phys Chem B 2015; 119:14821-30. [DOI: 10.1021/acs.jpcb.5b07375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashtina Appadu
- Department
of Chemistry and
Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario, Canada N2L 3C5
| | - Masoud Jelokhani-Niaraki
- Department
of Chemistry and
Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario, Canada N2L 3C5
| | - Lillian DeBruin
- Department
of Chemistry and
Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario, Canada N2L 3C5
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21
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Pieren M, Desfougères Y, Michaillat L, Schmidt A, Mayer A. Vacuolar SNARE protein transmembrane domains serve as nonspecific membrane anchors with unequal roles in lipid mixing. J Biol Chem 2015; 290:12821-32. [PMID: 25817997 DOI: 10.1074/jbc.m115.647776] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 12/23/2022] Open
Abstract
Membrane fusion is induced by SNARE complexes that are anchored in both fusion partners. SNAREs zipper up from the N to C terminus bringing the two membranes into close apposition. Their transmembrane domains (TMDs) might be mere anchoring devices, deforming bilayers by mechanical force. Structural studies suggested that TMDs might also perturb lipid structure by undergoing conformational transitions or by zipping up into the bilayer. Here, we tested this latter hypothesis, which predicts that the activity of SNAREs should depend on the primary sequence of their TMDs. We replaced the TMDs of all vacuolar SNAREs (Nyv1, Vam3, and Vti1) by a lipid anchor, by a TMD from a protein unrelated to the membrane fusion machinery, or by artificial leucine-valine sequences. Individual exchange of the native SNARE TMDs against an unrelated transmembrane anchor or an artificial leucine-valine sequence yielded normal fusion activities. Fusion activity was also preserved upon pairwise exchange of the TMDs against unrelated peptides, which eliminates the possibility for specific TMD-TMD interactions. Thus, a specific primary sequence or zippering beyond the SNARE domains is not a prerequisite for fusion. Lipid-anchored Vti1 was fully active, and lipid-anchored Nyv1 permitted the reaction to proceed up to hemifusion, and lipid-anchored Vam3 interfered already before hemifusion. The unequal contribution of proteinaceous TMDs on Vam3 and Nyv1 suggests that Q- and R-SNAREs might make different contributions to the hemifusion intermediate and the opening of the fusion pore. Furthermore, our data support the view that SNARE TMDs serve as nonspecific membrane anchors in vacuole fusion.
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Affiliation(s)
- Michel Pieren
- From the Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
| | - Yann Desfougères
- From the Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
| | - Lydie Michaillat
- From the Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
| | - Andrea Schmidt
- From the Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
| | - Andreas Mayer
- From the Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
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22
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Lhor M, Bernier SC, Horchani H, Bussières S, Cantin L, Desbat B, Salesse C. Comparison between the behavior of different hydrophobic peptides allowing membrane anchoring of proteins. Adv Colloid Interface Sci 2014; 207:223-39. [PMID: 24560216 PMCID: PMC4028306 DOI: 10.1016/j.cis.2014.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/11/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Membrane binding of proteins such as short chain dehydrogenase reductases or tail-anchored proteins relies on their N- and/or C-terminal hydrophobic transmembrane segment. In this review, we propose guidelines to characterize such hydrophobic peptide segments using spectroscopic and biophysical measurements. The secondary structure content of the C-terminal peptides of retinol dehydrogenase 8, RGS9-1 anchor protein, lecithin retinol acyl transferase, and of the N-terminal peptide of retinol dehydrogenase 11 has been deduced by prediction tools from their primary sequence as well as by using infrared or circular dichroism analyses. Depending on the solvent and the solubilization method, significant structural differences were observed, often involving α-helices. The helical structure of these peptides was found to be consistent with their presumed membrane binding. Langmuir monolayers have been used as membrane models to study lipid-peptide interactions. The values of maximum insertion pressure obtained for all peptides using a monolayer of 1,2-dioleoyl-sn-glycero-3-phospho-ethanolamine (DOPE) are larger than the estimated lateral pressure of membranes, thus suggesting that they bind membranes. Polarization modulation infrared reflection absorption spectroscopy has been used to determine the structure and orientation of these peptides in the absence and in the presence of a DOPE monolayer. This lipid induced an increase or a decrease in the organization of the peptide secondary structure. Further measurements are necessary using other lipids to better understand the membrane interactions of these peptides.
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Affiliation(s)
- Mustapha Lhor
- CUO-Recherche, Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement, Département d'ophtalmologie, Faculté de médecine, Université Laval, Québec, Québec G1V 0A6, Canada; Regroupement stratégique PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Sarah C Bernier
- CUO-Recherche, Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement, Département d'ophtalmologie, Faculté de médecine, Université Laval, Québec, Québec G1V 0A6, Canada; Regroupement stratégique PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Habib Horchani
- CUO-Recherche, Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement, Département d'ophtalmologie, Faculté de médecine, Université Laval, Québec, Québec G1V 0A6, Canada; Regroupement stratégique PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Sylvain Bussières
- CUO-Recherche, Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement, Département d'ophtalmologie, Faculté de médecine, Université Laval, Québec, Québec G1V 0A6, Canada; Regroupement stratégique PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Line Cantin
- CUO-Recherche, Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement, Département d'ophtalmologie, Faculté de médecine, Université Laval, Québec, Québec G1V 0A6, Canada; Regroupement stratégique PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Bernard Desbat
- CBMN-UMR 5248 CNRS, Université de Bordeaux, IPB, Allée Geoffroy Saint Hilaire, 33600 Pessac, France
| | - Christian Salesse
- CUO-Recherche, Centre de recherche du CHU de Québec, Hôpital du Saint-Sacrement, Département d'ophtalmologie, Faculté de médecine, Université Laval, Québec, Québec G1V 0A6, Canada; Regroupement stratégique PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada.
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23
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Oswal DP, Alter GM, Rider SD, Hostetler HA. A single amino acid change humanizes long-chain fatty acid binding and activation of mouse peroxisome proliferator-activated receptor α. J Mol Graph Model 2014; 51:27-36. [PMID: 24858253 DOI: 10.1016/j.jmgm.2014.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 04/09/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
Abstract
Peroxisome proliferator-activated receptor α (PPARα) is an important regulator of hepatic lipid metabolism which functions through ligand binding. Despite high amino acid sequence identity (>90%), marked differences in PPARα ligand binding, activation and gene regulation have been noted across species. Similar to previous observations with synthetic agonists, we have recently reported differences in ligand affinities and extent of activation between human PPARα (hPPARα) and mouse PPARα (mPPARα) in response to long chain fatty acids (LCFA). The present study was aimed to determine if structural alterations could account for these differences. The binding of PPARα to LCFA was examined through in silico molecular modeling and docking simulations. Modeling suggested that variances at amino acid position 272 are likely to be responsible for differences in saturated LCFA binding to hPPARα and mPPARα. To confirm these results experimentally, LCFA binding, circular dichroism, and transactivation studies were performed using a F272I mutant form of mPPARα. Experimental data correlated with in silico docking simulations, further confirming the importance of amino acid 272 in LCFA binding. Although the driving force for evolution of species differences at this position are yet unidentified, this study enhances our understanding of ligand-induced regulation by PPARα and demonstrates the efficacy of molecular modeling and docking simulations.
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Affiliation(s)
- Dhawal P Oswal
- Department of Biochemistry & Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, United States
| | - Gerald M Alter
- Department of Biochemistry & Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, United States
| | - S Dean Rider
- Department of Biochemistry & Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, United States
| | - Heather A Hostetler
- Department of Biochemistry & Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, United States.
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24
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Lella M, Mahalakshmi R. Pro-Gly mediated conformational switch of mycobacteriophage D29 holin transmembrane domain I is lipid concentration driven. Chem Commun (Camb) 2014; 49:9594-6. [PMID: 24018990 DOI: 10.1039/c3cc45058a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biophysical and spectroscopic analysis of synthetic transmembrane domain I (1) of mycobacteriophage D29 holin shows a lipid concentration dependent conformational switch from an α-helix to a β-sheet structure. The reversibility of this switch, upon change in the lipid-to-peptide ratio, requires a central Pro-Gly segment, and is abolished upon mutation to Ala-Ala or (D)Pro-Gly.
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Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.
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25
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Agopian A, Castano S. Structure and orientation study of Ebola fusion peptide inserted in lipid membrane models. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:117-26. [DOI: 10.1016/j.bbamem.2013.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 09/04/2013] [Accepted: 09/09/2013] [Indexed: 11/16/2022]
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26
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Bussières S, Cantin L, Desbat B, Salesse C. Binding of a truncated form of lecithin:retinol acyltransferase and its N- and C-terminal peptides to lipid monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:3516-3523. [PMID: 22260449 DOI: 10.1021/la203896n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Lecithin:retinol acyltransferase (LRAT) is a 230 amino acid membrane-associated protein which catalyzes the esterification of all-trans-retinol into all-trans-retinyl ester. A truncated form of LRAT (tLRAT), which contains the residues required for catalysis but which is lacking the N- and C-terminal hydrophobic segments, was produced to study its membrane binding properties. Measurements of the maximum insertion pressure of tLRAT, which is higher than the estimated lateral pressure of membranes, and the positive synergy factor a argue in favor of a strong binding of tLRAT to phospholipid monolayers. Moreover, the binding, secondary structure and orientation of the peptides corresponding to its N- and C-terminal hydrophobic segments of LRAT have been studied by circular dichroism and polarization-modulation infrared reflection absorption spectroscopy in monolayers. The results show that these peptides spontaneously bind to lipid monolayers and adopt an α-helical secondary structure. On the basis of these data, a new membrane topology model of LRAT is proposed where its N- and C-terminal segments allow to anchor this protein to the lipid bilayer.
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Affiliation(s)
- Sylvain Bussières
- LOEX/CUO-recherche, Centre hospitalier affilié universitaire de Québec, Hôpital du Saint-Sacrement, 1050 Chemin Ste-Foy, Québec (Québec), Canada
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27
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Schultz ZD, Levin IW. Vibrational spectroscopy of biomembranes. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:343-66. [PMID: 21456972 DOI: 10.1146/annurev-anchem-061010-114048] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Vibrational spectroscopy, commonly associated with IR absorption and Raman scattering, has provided a powerful approach for investigating interactions between biomolecules that make up cellular membranes. Because the IR and Raman signals arise from the intrinsic properties of these molecules, vibrational spectroscopy probes the delicate interactions that regulate biomembranes with minimal perturbation. Numerous innovative measurements, including nonlinear optical processes and confined bilayer assemblies, have provided new insights into membrane behavior. In this review, we highlight the use of vibrational spectroscopy to study lipid-lipid interactions. We also examine recent work in which vibrational measurements have been used to investigate the incorporation of peptides and proteins into lipid bilayers, and we discuss the interactions of small molecules and drugs with membrane structures. Emerging techniques and measurements on intact cellular membranes provide a prospective on the future of vibrational spectroscopic studies of biomembranes.
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Affiliation(s)
- Zachary D Schultz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.
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28
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Yassine W, Milochau A, Buchoux S, Lang J, Desbat B, Oda R. Effect of monolayer lipid charges on the structure and orientation of protein VAMP1 at the air–water interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:928-37. [DOI: 10.1016/j.bbamem.2010.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 12/02/2009] [Accepted: 01/13/2010] [Indexed: 12/20/2022]
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