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Landolsi C, Salem-Berrabah OB, Feki M, Harrabi S, Hosseinian F. Unsaponifiable Compounds and Phenols Content, Antioxidant and Antitrypsin Activities of Prunus persica Kernel Oil. J Oleo Sci 2024; 73:865-874. [PMID: 38825540 DOI: 10.5650/jos.ess24027] [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] [Indexed: 06/04/2024] Open
Abstract
Although peach kernels are rich in oil, there is a lack of information about its chemical and biological properties. Therefore, the purpose of this study was to determine the lipid profile, antioxidant capacity, and trypsin inhibitory propriety of peach oil extracted from two varieties (sweet cap and O'Henry) cultivated in Tunisia. The investigated peach kernel oil contains significant amount of unsaponifiable (2.1±0.5-2.8±0.2% of oil) and phenolic compounds (45.8±0.92-74.6±1.3 mg GAE/g of oil). Its n-alkane profile was characterized by the predominance of tetracosane n-C24 (47.24%) followed by tricosane n-C23 (34.43%). An important total tocopherol content (1192.83±3.1 mg/kg oil) has been found in sweet cap cultivar. Although rich in polyphenols and tocopherols, the tested oil did not display an inhibitory effect on trypsin. However, all peach oil samples showed effective antioxidant capacity and the highest values (86.34±1.3% and 603.50±2.6 μmol TE/g oil for DPPH test and ORAC assay, respectively) were observed for sweet cap oil. Peach oil has an excellent potential for application in the food and pharmaceutical industries as source of naturally-occurring bioactive substances.
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Affiliation(s)
- Cyrine Landolsi
- Laboratory of Clinical Biochemistry, LR99ES11, Faculty of Medicine Tunis
| | - Olfa Ben Salem-Berrabah
- Laboratory of Environmental Science and Technologies, Higher Institute of Sciences and Technology of Environment, University of Carthage
| | - Moncef Feki
- Laboratory of Clinical Biochemistry, LR99ES11, Faculty of Medicine Tunis
| | - Saoussem Harrabi
- Laboratory of Clinical Biochemistry, LR99ES11, Faculty of Medicine Tunis
| | - Farah Hosseinian
- Food Science Program, Carleton University
- Institute of Biochemistry, Carleton University
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2
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Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT. Catalysts 2023. [DOI: 10.3390/catal13020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The enzyme OmpT of the outer membrane of Escherichia coli shows proteolytic activity and cleaves peptides and proteins. Using molecular dynamics simulations in a fully hydrated lipid bilayer on a time scale of hundreds of nanoseconds, we draw a detailed atomic picture of substrate recognition in the OmpT-holo enzyme complex. Hydrogen bonds and salt bridges are essential for maintaining the integrity of the active site and play a central role for OmpT in recognizing its substrate. Electrostatic interactions are critical at all stages from approaching the substrate to docking at the active site. Computational alanine scanning based on the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) approach confirms the importance of multiple residues in the active site that form salt bridges. The substrate fluctuates along the axis of the β-barrel, which is associated with oscillations of the binding cleft formed by the residue pairs D210-H212 and D83-D85. Principal component analysis suggests that substrate and protein movements are correlated. We observe the transient presence of putative catalytic water molecules near the active site, which may be involved in the nucleophilic attack on the cleavable peptide bond of the substrate.
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3
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Moi S, Shekh S, Dolle A, Vijayasarathy M, Gowd KH. Significance of D- tryptophan in Contryphan-Ar1131 Conus peptide: Oxidative folding, trypsin binding, and photostabilization activity. Peptides 2022; 156:170845. [PMID: 35902005 DOI: 10.1016/j.peptides.2022.170845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/06/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
Distinct differences have been observed between L-tryptophan and D-tryptophan containing contryphan-Ar1131 in oxidative folding, trypsin binding, and photostabilization activity on avobenzone. [W5] contryphan-Ar1131 and [w5] contryphan-Ar1131 were chemically synthesized and characterized using RP-HPLC and mass spectrometry. Structural differences due to the change of configuration of tryptophan were evident from the optimized structures of contryphan-Ar1131 using density functional theory (DFT). The comparison of early events of oxidative folding has revealed the role of D-tryptophan in accelerating the formation of a disulfide bond. The optimized structures of the reduced form of peptides revealed the occurrence of aromatic-aromatic and aromatic-proline interactions in [w5] contryphan-Ar1131 which may be critical in aiding the oxidative folding reaction. The presence of the Lys6-Pro7 peptide bond indicates that contryphan-Ar1131 is resistant but may bind to trypsin allowing to assign the binding affinity of peptides to the protein surface. Competitive binding studies and molecular docking along with molecular dynamic (MD) simulations have revealed that [w5] contryphan-Ar1131 has more affinity for the active site of trypsin. Given tryptophan is a photostabilizer of FDA-approved chemical UV-A filter avobenzone, the report has compared the photostabilization activity of [W5]/ [w5] contryphan-Ar1131 on avobenzone under natural sunlight. [w5] contryphan-Ar1131 has better photostabilization activity than that of [W5] contryphan-Ar1131 and also individual D-tryptophan and L-tryptophan amino acids. These biochemical studies have highlighted the significance of D-tryptophan in contryphan-Ar1131 and its photostabilization activity on avobenzone may find applications in cosmetics.
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Affiliation(s)
- Smriti Moi
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Shamasoddin Shekh
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Ashwini Dolle
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | | | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India.
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4
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Che K, Muttenthaler M, Kurzbach D. Conformational selection of vasopressin upon V 1a receptor binding. Comput Struct Biotechnol J 2021; 19:5826-5833. [PMID: 34765097 PMCID: PMC8567363 DOI: 10.1016/j.csbj.2021.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
The neuropeptide vasopressin (VP) and its three G protein-coupled receptors (V1aR, V1bR and V2R) are of high interest in a wide array of drug discovery programs. V1aR is of particular importance due to its cardiovascular functions and diverse roles in the central nervous system. The structure–activity relationships underpinning ligand-receptor interactions remain however largely unclear, hindering rational drug design. This is not least due to the high structural flexibility of VP in its free as well as receptor-bound states. In this work, we developed a novel approach to reveal features of conformational selectivity upon VP-V1aR complex formation. We employed virtual screening strategies to probe VP’s conformational space for transiently adopted structures that favor binding to V1aR. To this end, we dissected the VP conformational space into three sub-ensembles, each containing distinct structural sets for VP’s three-residue C-terminal tail. We validated the computational results with experimental nuclear magnetic resonance (NMR) data and docked each sub-ensemble to V1aR. We observed that the conformation of VP’s three-residue tail significantly modulated the complex dissociation constants. Solvent-exposed and proline trans-configured VP tail conformations bound to the receptor with three-fold enhanced affinities compared to compacted or cis-configured conformations. The solvent-exposed and more flexible structures facilitated unique interaction patterns between VP and V1aR transmembrane helices 3, 4, and 6 which led to high binding energies. The presented “virtual conformational space screening” approach, integrated with NMR spectroscopy, thus enabled identification and characterization of a conformational selection-type complex formation mechanism that confers novel perspectives on targeting the VP-V1aR interactions at the level of the encounter complex – an aspect that opens novel research avenues for understanding the functionality of the evolutionary selected conformational properties of VP, as well as guidance for ligand design strategies to provide more potent and selective VP analogues.
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Affiliation(s)
- Kateryna Che
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, A-1090 Vienna, Austria
| | - Markus Muttenthaler
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, A-1090 Vienna, Austria
- The University of Queensland, Institute for Molecular Bioscience, 306 Carmody Rd, 4072 St Lucia, Brisbane, Queensland, Australia
| | - Dennis Kurzbach
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, A-1090 Vienna, Austria
- Corresponding author.
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5
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Bous J, Orcel H, Floquet N, Leyrat C, Lai-Kee-Him J, Gaibelet G, Ancelin A, Saint-Paul J, Trapani S, Louet M, Sounier R, Déméné H, Granier S, Bron P, Mouillac B. Cryo-electron microscopy structure of the antidiuretic hormone arginine-vasopressin V2 receptor signaling complex. SCIENCE ADVANCES 2021; 7:7/21/eabg5628. [PMID: 34020960 PMCID: PMC8139594 DOI: 10.1126/sciadv.abg5628] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/01/2021] [Indexed: 05/08/2023]
Abstract
The antidiuretic hormone arginine-vasopressin (AVP) forms a signaling complex with the V2 receptor (V2R) and the Gs protein, promoting kidney water reabsorption. Molecular mechanisms underlying activation of this critical G protein-coupled receptor (GPCR) signaling system are still unknown. To fill this gap of knowledge, we report here the cryo-electron microscopy structure of the AVP-V2R-Gs complex. Single-particle analysis revealed the presence of three different states. The two best maps were combined with computational and nuclear magnetic resonance spectroscopy constraints to reconstruct two structures of the ternary complex. These structures differ in AVP and Gs binding modes. They reveal an original receptor-Gs interface in which the Gαs subunit penetrates deep into the active V2R. The structures help to explain how V2R R137H or R137L/C variants can lead to two severe genetic diseases. Our study provides important structural insights into the function of this clinically relevant GPCR signaling complex.
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Affiliation(s)
- Julien Bous
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Hélène Orcel
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Joséphine Lai-Kee-Him
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Gérald Gaibelet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Aurélie Ancelin
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Julie Saint-Paul
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Stefano Trapani
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Rémy Sounier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Hélène Déméné
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
| | - Patrick Bron
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France.
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
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6
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Wu M, Dorosh L, Schmitt-Ulms G, Wille H, Stepanova M. Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations. PLoS Comput Biol 2021; 17:e1008771. [PMID: 33711010 PMCID: PMC7990313 DOI: 10.1371/journal.pcbi.1008771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/24/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14’s presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42–SST14, Aβ42–AVP, and Aβ40–SST14. The Aβ42–SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42–SST14 system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ42–SST14 oligomerization. Improper folding of proteins causes disorders known as protein misfolding diseases. Under normal conditions most proteins adopt particular folds, which allow them functioning properly. However, for reasons that are not yet fully understood, proteins may misfold and aggregate, forming deposits known as amyloid fibrils, which accumulate in the brain or other tissues. This process affects functioning of the nervous system, gradually causing loss of cognitive abilities. Alzheimer’s disease is one of the most common diseases from this group. A better understanding of the aggregation of peptides implicated in Alzheimer’s disease, known as amyloid beta (Aβ) peptides, may facilitate the development of treatments that ameliorate or prevent the disease. We use detailed molecular dynamics simulations to investigate the influence of somatostatin-14 (SST14), a cyclic neuropeptide that might be involved in the amyloidogenic aggregation of Aβ, on molecular processes occurring at the onset of Aβ aggregation. Results of these simulations explain how the presence of SST14 might alter pathways of aggregation of Aβ, shedding light upon the possible role of extrinsic factors in the aggregation at a molecular level.
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Affiliation(s)
- Min Wu
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada
- Centre for Prions and Protein Folding Diseases, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
- * E-mail:
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7
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Damjanovic J, Miao J, Huang H, Lin YS. Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations. Chem Rev 2021; 121:2292-2324. [PMID: 33426882 DOI: 10.1021/acs.chemrev.0c01087] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.
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Affiliation(s)
- Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - He Huang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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8
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Kumar S, Venkatesha MA, Lall S, Prakash S, Balaram P. Mechanistic Insights into an Unusual Side-Chain-Mediated N-C α Bond Cleavage under Collision-Induced Dissociation Conditions in the Disulfide-Containing Peptide Conopressin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1083-1092. [PMID: 32175740 DOI: 10.1021/jasms.0c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Conopressin, a nonapeptide disulfide CFIRNCPKG amide present in cone snail venom, undergoes a facile cleavage at the Cys6-Pro7 peptide bond to yield a disulfide bridged b6 ion. Analysis of the mass spectral fragmentation pattern reveals the presence of a major fragment ion, which is unambiguously assigned as the tripeptide sequence IRN amide. The sequence dependence of this unusual fragmentation process has been investigated by comparing it with the fragmentation patterns of related peptides, oxytocin (CYIQNCPLG amide), Lys-vasopressin (CYFQNCPKG amide), and a series of synthetic analogues. The results establish the role of the Arg4 residue in facilitating the unusual N-Cα bond cleavage at Cys6. Structures are proposed for a modified disulfide bridged fragment containing the Cys1 and Cys6 residues. Gas-phase molecular dynamics simulations provide evidence for the occurrence of conformational states that permit close approach of the Arg4 side chain to the Cys6 Cβ methylene protons.
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Affiliation(s)
- Sanjeev Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - M Achanna Venkatesha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sahil Lall
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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9
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Yadav PK, Antonyraj CB, Basheer Ahamed SI, Srinivas S. Understanding Russell's viper venom factor V activator's substrate specificity by surface plasmon resonance and in-silico studies. PLoS One 2017; 12:e0181216. [PMID: 28732041 PMCID: PMC5521794 DOI: 10.1371/journal.pone.0181216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/28/2017] [Indexed: 11/18/2022] Open
Abstract
Blood coagulation factor V (FV) is activated either by Factor X or thrombin, cleaving at three different sites viz., Site I (Arg709-Ser710), site II (Arg1018-Thr1019), and site III (Arg1545-Ser1546). Russell's viper venom factor V activator (RVV-V) is a thrombin-like serine proteinase that activates FV with selective, single cleavage at site III. A long lasting effort is being pending in understanding the 'selective' binding specificity of the RVV-V towards site III. Here, we present the binding kinetic study of RVV-V with two designed peptides corresponding to the regions from site I (Gln699-Asn713) and site II (1008Lys-Pro1022), respectively, that include 15 amino acids. Our investigation for justifying the binding efficacy and kinetics of peptides includes SPR method, protein-peptide docking, molecular dynamics simulation, and principal component analysis (PCA). Surprisingly, the SPR experiment disclosed that the Peptide II showed a lower binding affinity with KD of 2.775 mM while the Peptide I showed none. Docking and simulation of both the peptides with RVV-V engaged either rooted or shallow binding for Peptide II and Peptide I respectively. The peptide binding resulted in global conformational changes in the native fold of RVV-V, whereas the similar studies for thrombin failed to make major changes in the native fold. In support, the PCA analysis for RVV-V showed the dislocation of catalytic triad upon binding both the peptides. Hence, RVV-V, a serine protease, is incompetent in cleaving these two sites. This study suggests a transition in RVV-V from the native rigid to the distorted flexible structure and paves a way to design a new peptide substrate/inhibitor.
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Affiliation(s)
- Pradeep K. Yadav
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
| | | | | | - Sistla Srinivas
- GE Healthcare Life Sciences, John F Welch Technology Centre, EPIP, Bengaluru, India
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10
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Haensele E, Saleh N, Read CM, Banting L, Whitley DC, Clark T. Can Simulations and Modeling Decipher NMR Data for Conformational Equilibria? Arginine–Vasopressin. J Chem Inf Model 2016; 56:1798-807. [PMID: 27585313 DOI: 10.1021/acs.jcim.6b00344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elke Haensele
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany
| | - Noureldin Saleh
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany
| | | | | | | | - Timothy Clark
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany
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11
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Semack A, Sandhu M, Malik RU, Vaidehi N, Sivaramakrishnan S. Structural Elements in the Gαs and Gαq C Termini That Mediate Selective G Protein-coupled Receptor (GPCR) Signaling. J Biol Chem 2016; 291:17929-40. [PMID: 27330078 DOI: 10.1074/jbc.m116.735720] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/06/2022] Open
Abstract
Although the importance of the C terminus of the α subunit of the heterotrimeric G protein in G protein-coupled receptor (GPCR)-G protein pairing is well established, the structural basis of selective interactions remains unknown. Here, we combine live cell FRET-based measurements and molecular dynamics simulations of the interaction between the GPCR and a peptide derived from the C terminus of the Gα subunit (Gα peptide) to dissect the molecular mechanisms of G protein selectivity. We observe a direct link between Gα peptide binding and stabilization of the GPCR conformational ensemble. We find that cognate and non-cognate Gα peptides show deep and shallow binding, respectively, and in distinct orientations within the GPCR. Binding of the cognate Gα peptide stabilizes the agonist-bound GPCR conformational ensemble resulting in favorable binding energy and lower flexibility of the agonist-GPCR pair. We identify three hot spot residues (Gαs/Gαq-Gln-384/Leu-349, Gln-390/Glu-355, and Glu-392/Asn-357) that contribute to selective interactions between the β2-adrenergic receptor (β2-AR)-Gαs and V1A receptor (V1AR)-Gαq The Gαs and Gαq peptides adopt different orientations in β2-AR and V1AR, respectively. The β2-AR/Gαs peptide interface is dominated by electrostatic interactions, whereas the V1AR/Gαq peptide interactions are predominantly hydrophobic. Interestingly, our study reveals a role for both favorable and unfavorable interactions in G protein selection. Residue Glu-355 in Gαq prevents this peptide from interacting strongly with β2-AR. Mutagenesis to the Gαs counterpart (E355Q) imparts a cognate-like interaction. Overall, our study highlights the synergy in molecular dynamics and FRET-based approaches to dissect the structural basis of selective G protein interactions.
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Affiliation(s)
- Ansley Semack
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Manbir Sandhu
- the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010, and
| | - Rabia U Malik
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, the Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Nagarajan Vaidehi
- the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010, and
| | - Sivaraj Sivaramakrishnan
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455,
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12
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Shao W, Zhu W, Wang Y, Lu J, Jin G, Wang Y, Su W. Rational design and molecular engineering of peptide aptamers to target human pancreatic trypsin in acute pancreatitis. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0638-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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13
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Mistarz UH, Brown JM, Haselmann KF, Rand KD. Probing the Binding Interfaces of Protein Complexes Using Gas-Phase H/D Exchange Mass Spectrometry. Structure 2015; 24:310-8. [PMID: 26749447 DOI: 10.1016/j.str.2015.11.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 12/20/2022]
Abstract
Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub-millisecond time span after electrospray ionization by ND3 gas can provide structural insights into protein conformers present in solution. Here, we have explored the use of gas-phase HDX-MS for probing the higher-order structure and binding interfaces of protein complexes originating from native solution conditions. Lysozyme ions bound by an oligosaccharide incorporated less deuterium than the unbound ion. Similarly, trypsin ions showed reduced deuterium uptake when bound by the peptide ligand vasopressin. Our results are in good agreement with crystal structures of the native protein complexes, and illustrate that gas-phase HDX-MS can provide a sensitive and simple approach to measure the number of heteroatom-bound non-amide side-chain hydrogens involved in the binding interface of biologically relevant protein complexes.
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Affiliation(s)
- Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Jeffery M Brown
- Waters MS Technologies Centre, Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Kim F Haselmann
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv 2670, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark.
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Conservation weighting functions enable covariance analyses to detect functionally important amino acids. PLoS One 2014; 9:e107723. [PMID: 25379728 PMCID: PMC4224327 DOI: 10.1371/journal.pone.0107723] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 07/31/2014] [Indexed: 01/22/2023] Open
Abstract
The explosive growth in the number of protein sequences gives rise to the possibility of using the natural variation in sequences of homologous proteins to find residues that control different protein phenotypes. Because in many cases different phenotypes are each controlled by a group of residues, the mutations that separate one version of a phenotype from another will be correlated. Here we incorporate biological knowledge about protein phenotypes and their variability in the sequence alignment of interest into algorithms that detect correlated mutations, improving their ability to detect the residues that control those phenotypes. We demonstrate the power of this approach using simulations and recent experimental data. Applying these principles to the protein families encoded by Dscam and Protocadherin allows us to make testable predictions about the residues that dictate the specificity of molecular interactions.
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15
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Haensele E, Banting L, Whitley DC, Clark T. Conformation and dynamics of 8-Arg-vasopressin in solution. J Mol Model 2014; 20:2485. [DOI: 10.1007/s00894-014-2485-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/06/2014] [Indexed: 01/12/2023]
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16
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Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants. J Phys Chem B 2014; 119:896-905. [PMID: 25231121 DOI: 10.1021/jp505902m] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Vasopressin and oxytocin are intrinsically disordered cyclic nonapeptides belonging to a family of neurohypophysial hormones. Although unique in their functions, these peptides differ only by two residues and both feature a tocin ring formed by the disulfide bridge between first and sixth cysteine residues. This sequence and structural similarity are experimentally linked to oxytocin agonism at vasopressin receptors and vasopressin antagonism at oxytocin receptors. Yet single- or double-residue mutations in both peptides have been shown to have drastic impacts on their activities at either receptor, and possibly the ability to bind to their neurophysin carrier protein. In this study we perform molecular dynamics simulations of the unbound native and mutant sequences of the oxytocin and vasopressin hormones to characterize their structural ensembles. We classify the subpopulations of these structural ensembles on the basis of the distributions of radius of gyration and secondary structure and hydrogen-bonding features of the canonical tocin ring and disordered tail region. We then relate the structural changes observed in the unbound form of the different hormone sequences to experimental information about peptide receptor binding, and more indirectly, carrier protein binding affinity, receptor activity, and protease degradation. This study supports the hypothesis that the structural characteristics of the unbound form of an IDP can be used to predict structural or functional preferences of its functional bound form.
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Affiliation(s)
- Eugene Yedvabny
- Department of Chemistry, ‡Department of Bioengineering, and §Department of Chemical and Biomolecular Engineering, University of California , Berkeley, California 94720-3220, United States
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17
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Sonti R, Rao KNS, Chidanand S, Gowd KH, Raghothama S, Balaram P. Conformational Analysis of a 20-Membered Cyclic Peptide Disulfide fromConus virgowith a WPW Segment: Evidence for an Aromatic-Proline Sandwich. Chemistry 2014; 20:5075-86. [DOI: 10.1002/chem.201303687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Indexed: 11/06/2022]
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18
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Pazderková M, Bednárová L, Dlouhá H, Flegel M, Lebl M, Hlaváček J, Setnička V, Urbanová M, Hynie S, Klenerová V, Baumruk V, Maloň P. Electronic and vibrational optical activity of several peptides related to neurohypophyseal hormones: Disulfide group conformation. Biopolymers 2012; 97:923-32. [DOI: 10.1002/bip.22105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Endele S, Nelkenbrecher C, Bördlein A, Schlickum S, Winterpacht A. C4ORF48, a gene from the Wolf-Hirschhorn syndrome critical region, encodes a putative neuropeptide and is expressed during neocortex and cerebellar development. Neurogenetics 2011; 12:155-63. [PMID: 21287218 DOI: 10.1007/s10048-011-0275-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/14/2011] [Indexed: 12/27/2022]
Abstract
In order to identify novel genes involved in mental retardation/intellectual disability, we focused on a microdeletion reported in a patient with a mild form of Wolf-Hirschhorn syndrome. This patient presented with attention-deficit hyperactivity disorder, some learning and fine motor deficits as well as facial abnormalities. The deleted region included three genes. Here, we report the first characterization of one of these genes, C4ORF48. C4ORF48 encodes a short (139 aa) evolutionarily conserved protein with a predicted signal peptide and two potential dibasic convertase cleavage sites. In mice, we demonstrated expression of the corresponding protein exclusively in brain tissue using an anti-mouse C4Orf48 polyclonal antibody. Detailed RNA in situ hybridization experiments revealed expression of C4Orf48 in different zones during cortical and cerebellar development, as well as in almost all cortical and subcortical regions of the adult mouse brain. Based on the present data, we propose that C4Orf48 probably encodes a novel neuropeptide, which, if hemizygously deleted, may be involved in the observed intellectual and fine motor disabilities and thus in the overall neurological aspects of Wolf-Hirschhorn syndrome.
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Affiliation(s)
- Sabine Endele
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
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20
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Zhao G, Yuan C, Wind T, Huang Z, Andreasen PA, Huang M. Structural basis of specificity of a peptidyl urokinase inhibitor, upain-1. J Struct Biol 2007; 160:1-10. [PMID: 17692534 DOI: 10.1016/j.jsb.2007.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/16/2007] [Accepted: 06/07/2007] [Indexed: 11/17/2022]
Abstract
Urokinase-type plasminogen activator (uPA) plays a crucial role in the regulation of plasminogen activation, tumor cell adhesion and migration. The inhibition of uPA activity is a promising mechanism for anti-cancer therapy. A cyclic peptidyl inhibitor, upain-1, CSWRGLENHRMC, was identified recently as a competitive and highly specific uPA inhibitor. We determined the crystal structure of uPA in complex with upain-1 at 2.15 A. The structure reveals that the cyclic peptide adopts a rigid conformation stabilized by a disulfide bond (residues 1-12) and three tight beta turns (residues 3-6, 6-9, 9-12). The Glu7 residue of upain-1 forms hydrogen bonds with the main chain nitrogen atoms of residues 4, 5, and 6 of upain-1, and is also critical for maintaining the active conformation of upain-1. The Arg4 of upain-1 is inserted into the uPA's specific S1 pocket. The Ser2 residue of upain-1 locates close to the S1beta pocket of uPA. The Gly5 and Glu7 residues of upain-1 occupy the S2 pocket and the oxyanion hole of uPA, respectively. Furthermore, the Asn8 residue of upain-1 binds to the 37- and 60-loops of uPA and renders the specificity of upain-1 for uPA. Based on this structure, a new pharmacophore for the design of highly specific uPA inhibitors was proposed.
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Affiliation(s)
- Gengxiang Zhao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002, China
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21
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Möller C, Marí F. A vasopressin/oxytocin-related conopeptide with gamma-carboxyglutamate at position 8. Biochem J 2007; 404:413-9. [PMID: 17331075 PMCID: PMC1896288 DOI: 10.1042/bj20061480] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Vasopressins and oxytocins are homologous, ubiquitous and multifunctional peptides present in animals. Conopressins are vasopressin/oxytocin-related peptides that have been found in the venom of cone snails, a genus of marine predatory molluscs that envenom their prey with a complex mixture of neuroactive peptides. In the present paper, we report the purification and characterization of a unique conopressin isolated from the venom of Conus villepinii, a vermivorous cone snail species from the western Atlantic Ocean. This novel peptide, designated gamma-conopressin-vil, has the sequence CLIQDCPgammaG* (gamma is gamma-carboxyglutamate and * is C-terminal amidation). The unique feature of this vasopressin/oxytocin-like peptide is that the eighth residue is gamma-carboxyglutamate instead of a neutral or basic residue; therefore it could not be directly classified into either the vasopressin or the oxytocin peptide families. Nano-NMR spectroscopy of the peptide isolated directly from the cone snails revealed that the native gamma-conopressin-vil undergoes structural changes in the presence of calcium. This suggests that the peptide binds calcium, and the calcium-binding process is mediated by the gamma-carboxyglutamate residue. However, the negatively charged residues in the sequence of gamma-conopressin-vil may mediate calcium binding by a novel mechanism not observed in other peptides of this family.
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Affiliation(s)
- Carolina Möller
- Department of Chemistry and Biochemistry, and Center of Excellence in Biomedical and Marine Biotechnology, Florida Atlantic University, Boca Raton, FL 33431, U.S.A
| | - Frank Marí
- Department of Chemistry and Biochemistry, and Center of Excellence in Biomedical and Marine Biotechnology, Florida Atlantic University, Boca Raton, FL 33431, U.S.A
- To whom correspondence should be addressed (email )
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22
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Sikorska E, Rodziewicz-MotowidŁo S. Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part I: studies in water. J Pept Sci 2007; 14:76-84. [DOI: 10.1002/psc.918] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Rodziewicz-MotowidŁo S, Sikorska E, Oleszczuk M, Czaplewski C. Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: studies in the SDS micelle. J Pept Sci 2007; 14:85-96. [DOI: 10.1002/psc.917] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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