1
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Lal J, Prajapati G, Meena R, Kant R, Sankar Ampapathi R, Reddy DN. Influence of Proline Chirality on Neighbouring Azaproline Residue Stereodynamic Nitrogen Preorganization. Chem Asian J 2023; 18:e202201023. [PMID: 36349404 DOI: 10.1002/asia.202201023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/04/2022] [Indexed: 11/10/2022]
Abstract
We report herein the first systematic crystal structural investigation of azaproline incorporated in homo- and heterochiral diprolyl peptides. The X-ray crystallography data of peptides 1-5 illustrates that stereodynamic nitrogen in azaproline adopted the stereochemistry of neighbouring proline residue without depending on its position in the peptide sequence. Natural bond orbital analysis of crystal structures indicates OazPro -C'Pro of peptides 4 and 5 participating in n→π* interaction with stabilization energy about 1.21-1.33 kcal/mol. Density functional theory calculations suggested that the endo-proline ring puckering favoured over exo-conformation by 6.72-7.64 kcal/mol. NBO and DFT data reveals that the n→π* interactions and proline ring puckering stabilize azaproline chirality with the neighbouring proline stereochemistry. The CD, solvent titration, variable-temperature and 2D NMR experimental results further supported the crystal structures conformation.
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Affiliation(s)
- Jhajan Lal
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Gurudayal Prajapati
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-CDRI, Lucknow, 226031, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Rachana Meena
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Ruchir Kant
- Biochemistry and Structural Biology Division, CSIR-CDRI, Lucknow, 226031, India
| | - Ravi Sankar Ampapathi
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-CDRI, Lucknow, 226031, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Damodara N Reddy
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
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2
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Gupta SK, Banerjee S, Prabhakaran EN. Understanding the anomaly of cis-trans isomerism in Pro-His sequence. Bioorg Med Chem Lett 2022; 76:128985. [PMID: 36165914 DOI: 10.1016/j.bmcl.2022.128985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/05/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022]
Abstract
The anomalous absence of cisPro stabilizing CαHαXaa···πAro interactions at Xaa-Pro-Aro exclusively when Aro is His, is understood by NMR structural analyses of model peptides, as due to i → i backbone-side chain C6 H-bond that forms uniquely when Aro is His, which significantly decreases its χ1-g- population essential for CαHαXaa···πAro formation.
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Affiliation(s)
- Sunil K Gupta
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Erode N Prabhakaran
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.
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3
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Goyal B, Srivastava KR, Durani S. N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent. J Pept Sci 2017; 23:431-437. [PMID: 28425159 DOI: 10.1002/psc.3005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 12/25/2022]
Abstract
Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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4
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Milano T, Angelaccio S, Tramonti A, Di Salvo ML, Contestabile R, Pascarella S. Structural properties of the linkers connecting the N- and C- terminal domains in the MocR bacterial transcriptional regulators. BIOCHIMIE OPEN 2016; 3:8-18. [PMID: 29450126 PMCID: PMC5801912 DOI: 10.1016/j.biopen.2016.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/10/2016] [Indexed: 12/03/2022]
Abstract
Peptide inter-domain linkers are peptide segments covalently linking two adjacent domains within a protein. Linkers play a variety of structural and functional roles in naturally occurring proteins. In this work we analyze the sequence properties of the predicted linker regions of the bacterial transcriptional regulators belonging to the recently discovered MocR subfamily of the GntR regulators. Analyses were carried out on the MocR sequences taken from the phyla Actinobacteria, Firmicutes, Alpha-, Beta- and Gammaproteobacteria. The results suggest that MocR linkers display phylum-specific characteristics and unique features different from those already described for other classes of inter-domain linkers. They show an average length significantly higher: 31.8 ± 14.3 residues reaching a maximum of about 150 residues. Compositional propensities displayed general and phylum-specific trends. Pro is dominating in all linkers. Dyad propensity analysis indicate Pro–Pro as the most frequent amino acid pair in all linkers. Physicochemical properties of the linker regions were assessed using amino acid indices relative to different features: in general, MocR linkers are flexible, hydrophilic and display propensity for β-turn or coil conformations. Linker sequences are hypervariable: only similarities between MocR linkers from organisms related at the level of species or genus could be found with sequence searches. The results shed light on the properties of the linker regions of the new MocR subfamily of bacterial regulators and may provide knowledge-based rules for designing artificial linkers with desired properties. An overview of the structural properties of MocR inter-domain linkers is reported. Linker length distribution is heterogeneous in different phyla. Linkers are flexible, hydrophilic and have coil conformation propensity. Pro and Pro–Pro dyads are very frequent in all the linkers. MocR linkers display a few properties different from those reported for other linkers.
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Affiliation(s)
- Teresa Milano
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Sebastiana Angelaccio
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | - Martino Luigi Di Salvo
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
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5
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Wani NA, Gupta VK, Singh UP, Aravinda S, Rai R. Folded Structure Stabilized by C 7, C 10and C 12Hydrogen Bonds in αγ Hybrid Peptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Naiem Ahmad Wani
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
| | - Vivek Kumar Gupta
- X-ray Crystallography Laboratory; Post-Graduate Department of Physics and Electronics; University of Jammu; Jammu Tawi 180 006 India
| | - Umesh Prasad Singh
- CSIR-Indian Institute of Chemical Biology; 4, Raja, S.C. Mullick Road Kolkata- 700032 India
| | - Subrayashastry Aravinda
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
| | - Rajkishor Rai
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
- Academy of Scientific and Innovative Research; New Delhi India
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6
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Goyal B, Kumar A, Srivastava KR, Durani S. Computational scrutiny of the effect of N-terminal proline and residue stereochemistry in the nucleation of α-helix fold. RSC Adv 2016. [DOI: 10.1039/c6ra10934a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
N-Terminal l- to d-residue mutation nucleate helical fold in Ac–DAla–LAla3–NHMe (Ib, m2), Ac–DPro–LAla3–NHMe (IIb, m1), and Ac–DPro–LPro–LAla2–NHMe (IIIb, m2) peptides.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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7
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Goyal B, Srivastava KR, Kumar A, Patwari GN, Durani S. Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models. RSC Adv 2016. [DOI: 10.1039/c6ra22870d] [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] Open
Abstract
Energetics of folding (ΔHE→F, in kcal mol−1) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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8
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Kharrat M, Hsairi I, Fendri-Kriaa N, Kenoun H, Othmen HB, Ben Mahmoud A, Ghorbel R, Abid I, Triki C, Fakhfakh F. A Novel Mutation p.A59P in N-Terminal Domain of Methyl-CpG-Binding Protein 2 Confers Phenotypic Variability in 3 Cases of Tunisian Rett Patients: Clinical Evaluations and In Silico Investigations. J Child Neurol 2015; 30:1715-21. [PMID: 25862735 DOI: 10.1177/0883073815578529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/18/2015] [Indexed: 11/16/2022]
Abstract
Rett syndrome is a monogenic X-linked dominant neurodevelopmental disorder related to mutation in MECP2, which encodes the methyl-CpG-binding protein MeCP2. The aim of this study was to search for mutations of MECP2 gene in Tunisian Rett patients and to evaluate the impact of the found variants on structural and functional features of MeCP2. The result of mutation analysis revealed that 3 Rett patients shared the same novel heterozygous point mutation c.175G>C (p.A59P). The p.A59P mutation was located in a conserved amino acid in the N-terminal segment of MeCP2. This novel mutation confers a phenotypic variability with different clinical severity scores (3, 8, and 9) and predicted by Sift and PolyPhen to be damaging. Modeling results showed that p.A59P adds 2 hydrogen bonds and changes the structural conformation of MeCP2 with a significant root mean square deviation value (9.66 Å), suggesting that this mutation could probably affect the conformation, function and stability of MeCP2.
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Affiliation(s)
- Marwa Kharrat
- Laboratory of Human Molecular Genetics, The Sfax Faculty of Medicine, Sfax, Tunisia
| | - Ines Hsairi
- Service de Neurologie Infantile, C.H.U. Hédi Chaker de Sfax, Tunisia
| | | | - Houda Kenoun
- Laboratory of Human Molecular Genetics, The Sfax Faculty of Medicine, Sfax, Tunisia
| | - Houda Ben Othmen
- Laboratory of Human Molecular Genetics, The Sfax Faculty of Medicine, Sfax, Tunisia
| | - Afif Ben Mahmoud
- Laboratory of Human Molecular Genetics, The Sfax Faculty of Medicine, Sfax, Tunisia
| | - Rania Ghorbel
- Laboratory of Human Molecular Genetics, The Sfax Faculty of Medicine, Sfax, Tunisia
| | - Imen Abid
- Service de Neurologie Infantile, C.H.U. Hédi Chaker de Sfax, Tunisia
| | - Chahnez Triki
- Service de Neurologie Infantile, C.H.U. Hédi Chaker de Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Human Molecular Genetics, The Sfax Faculty of Medicine, Sfax, Tunisia
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9
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Guan X, Noble KA, Tao Y, Roux KH, Sathe SK, Young NL, Marshall AG. Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:812-819. [PMID: 26169135 DOI: 10.1002/jms.3589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution-phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX-MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope-contributing segments.
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Affiliation(s)
- Xiaoyan Guan
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Kyle A Noble
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Shridhar K Sathe
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
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10
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Abstract
In addition to the small and large ribosomal subunits, aminoacyl-tRNAs, and an mRNA, cellular protein synthesis is dependent on translation factors. The eukaryotic translation initiation factor 5A (eIF5A) and its bacterial ortholog elongation factor P (EF-P) were initially characterized based on their ability to stimulate methionyl-puromycin (Met-Pmn) synthesis, a model assay for protein synthesis; however, the function of these factors in cellular protein synthesis has been difficult to resolve. Interestingly, a conserved lysine residue in eIF5A is post-translationally modified to hypusine and the corresponding lysine residue in EF-P from at least some bacteria is modified by the addition of a β-lysine moiety. In this review, we provide a summary of recent data that have identified a novel role for the translation factor eIF5A and its hypusine modification in the elongation phase of protein synthesis and more specifically in stimulating the production of proteins containing runs of consecutive proline residues.
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Affiliation(s)
- Thomas E. Dever
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Erik Gutierrez
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Byung-Sik Shin
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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11
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Zotti MD, Formaggio F, Crisma M, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part I: Helices based on protein amino acids. J Pept Sci 2014; 20:307-22. [DOI: 10.1002/psc.2638] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Marta De Zotti
- Department of Chemistry; University of Padua; Padua Italy
| | | | | | | | | | - Claudio Toniolo
- Department of Chemistry; University of Padua; Padua Italy
- ICB, Padua Unit; CNR; Italy
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12
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McClure-Begley TD, Papke RL, Stone KL, Stokes C, Levy AD, Gelernter J, Xie P, Lindstrom J, Picciotto MR. Rare human nicotinic acetylcholine receptor α4 subunit (CHRNA4) variants affect expression and function of high-affinity nicotinic acetylcholine receptors. J Pharmacol Exp Ther 2014; 348:410-20. [PMID: 24385388 DOI: 10.1124/jpet.113.209767] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Nicotine, the primary psychoactive component in tobacco smoke, produces its behavioral effects through interactions with neuronal nicotinic acetylcholine receptors (nAChRs). α4β2 nAChRs are the most abundant in mammalian brain, and converging evidence shows that this subtype mediates the rewarding and reinforcing effects of nicotine. A number of rare variants in the CHRNA4 gene that encode the α4 nAChR subunit have been identified in human subjects and appear to be underrepresented in a cohort of smokers. We compared three of these variants (α4R336C, α4P451L, and α4R487Q) to the common variant to determine their effects on α4β2 nAChR pharmacology. We examined [(3)H]epibatidine binding, interacting proteins, and phosphorylation of the α4 nAChR subunit with liquid chromatography and tandem mass spectrometry (LC-MS/MS) in HEK 293 cells and voltage-clamp electrophysiology in Xenopus laevis oocytes. We observed significant effects of the α4 variants on nAChR expression, subcellular distribution, and sensitivity to nicotine-induced receptor upregulation. Proteomic analysis of immunopurified α4β2 nAChRs incorporating the rare variants identified considerable differences in the intracellular interactomes due to these single amino acid substitutions. Electrophysiological characterization in X. laevis oocytes revealed alterations in the functional parameters of activation by nAChR agonists conferred by these α4 rare variants, as well as shifts in receptor function after incubation with nicotine. Taken together, these experiments suggest that genetic variation at CHRNA4 alters the assembly and expression of human α4β2 nAChRs, resulting in receptors that are more sensitive to nicotine exposure than those assembled with the common α4 variant. The changes in nAChR pharmacology could contribute to differences in responses to smoked nicotine in individuals harboring these rare variants.
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Affiliation(s)
- T D McClure-Begley
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut (T.D.M.-B., A.D.L., J.G., M.R.P.); Institute for Behavioral Genetics, University of Colorado, Boulder, Boulder, Colorado (T.D.M.-B.); Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida (R.L.P., C.S.); W.M. Keck Biotechnology Research Laboratory (K.S.), Interdepartmental Neuroscience Program (A.D.L., M.R.P.), Department of Genetics (J.G., P.X.), and Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut (M.R.P.); Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, Connecticut (J.G.); Center for Human Genome Variation, Duke University, Durham, North Carolina (P.X.); and Department of Neuroscience, Medical School of the University of Pennsylvania, Philadelphia, Pennsylvania (J.L.)
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13
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Lombardi C, Ayach M, Beaurepaire L, Chenon M, Andreani J, Guerois R, Jupin I, Bressanelli S. A compact viral processing proteinase/ubiquitin hydrolase from the OTU family. PLoS Pathog 2013; 9:e1003560. [PMID: 23966860 PMCID: PMC3744425 DOI: 10.1371/journal.ppat.1003560] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 07/02/2013] [Indexed: 01/06/2023] Open
Abstract
Turnip yellow mosaic virus (TYMV) - a member of the alphavirus-like supergroup of viruses - serves as a model system for positive-stranded RNA virus membrane-bound replication. TYMV encodes a precursor replication polyprotein that is processed by the endoproteolytic activity of its internal cysteine proteinase domain (PRO). We recently reported that PRO is actually a multifunctional enzyme with a specific ubiquitin hydrolase (DUB) activity that contributes to viral infectivity. Here, we report the crystal structure of the 150-residue PRO. Strikingly, PRO displays no homology to other processing proteinases from positive-stranded RNA viruses, including that of alphaviruses. Instead, the closest structural homologs of PRO are DUBs from the Ovarian tumor (OTU) family. In the crystal, one molecule's C-terminus inserts into the catalytic cleft of the next, providing a view of the N-terminal product complex in replication polyprotein processing. This allows us to locate the specificity determinants of PRO for its proteinase substrates. In addition to the catalytic cleft, at the exit of which the active site is unusually pared down and solvent-exposed, a key element in molecular recognition by PRO is a lobe N-terminal to the catalytic domain. Docking models and the activities of PRO and PRO mutants in a deubiquitylating assay suggest that this N-terminal lobe is also likely involved in PRO's DUB function. Our data thus establish that DUBs can evolve to specifically hydrolyze both iso- and endopeptide bonds with different sequences. This is achieved by the use of multiple specificity determinants, as recognition of substrate patches distant from the cleavage sites allows a relaxed specificity of PRO at the sites themselves. Our results thus shed light on how such a compact protein achieves a diversity of key functions in viral genome replication and host-pathogen interaction. Positive-stranded RNA viruses are ultimate parasites. In order to replicate their genome, they first need to invade a host cell and, with usually very limited viral genetic material, subvert the host's molecular machinery. Turnip yellow mosaic virus (TYMV) is an excellent model system for studying positive-stranded RNA virus replication. As for many such viruses, TYMV genome replication is dependent on the activity of a viral proteinase (PRO) to properly process the virus' replication molecules. We have recently established that PRO is a multifunctional enzyme and is also used by TYMV to subvert a key host defense against pathogens. We report here the atomic structure of PRO as well as new functional data on PRO's interaction with the host. Our data shed light on how PRO can perform such multiple activities despite its small size, providing TYMV with a Swiss army knife in its ongoing fight with a vastly more complex host.
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Affiliation(s)
- Charlotte Lombardi
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Maya Ayach
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Lionel Beaurepaire
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Mélanie Chenon
- Laboratoire de Virologie Moléculaire, CNRS - Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, Paris, France
| | - Jessica Andreani
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
| | - Raphaël Guerois
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
| | - Isabelle Jupin
- Laboratoire de Virologie Moléculaire, CNRS - Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, Paris, France
- * E-mail: (IJ); (SB)
| | - Stéphane Bressanelli
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
- * E-mail: (IJ); (SB)
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Saha I, Shamala N. Investigating proline puckering states in diproline segments in proteins. Biopolymers 2013; 99:605-10. [DOI: 10.1002/bip.22224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Indranil Saha
- Department of Physics; Indian Institute of Science; Bangalore; 560012; Karnataka; India
| | - Narayanaswamy Shamala
- Department of Physics; Indian Institute of Science; Bangalore; 560012; Karnataka; India
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15
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Hagen CM, Aidt FH, Havndrup O, Hedley PL, Jespersgaard C, Jensen M, Kanters JK, Moolman-Smook JC, Møller DV, Bundgaard H, Christiansen M. MT-CYB mutations in hypertrophic cardiomyopathy. Mol Genet Genomic Med 2013; 1:54-65. [PMID: 24498601 PMCID: PMC3893158 DOI: 10.1002/mgg3.5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/18/2013] [Accepted: 02/21/2013] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial dysfunction is a characteristic of heart failure. Mutations in mitochondrial DNA, particularly in MT-CYB coding for cytochrome B in complex III (CIII), have been associated with isolated hypertrophic cardiomyopathy (HCM). We hypothesized that MT-CYB mutations might play an important causal or modifying role in HCM. The MT-CYB gene was sequenced from DNA isolated from blood from 91 Danish HCM probands. Nonsynonymous variants were analyzed by bioinformatics, molecular modeling and simulation. Two germline-inherited, putative disease-causing, nonsynonymous variants: m.15024G>A; p.C93Y and m.15482T>C; p.S246P were identified. Modeling showed that the p.C93Y mutation leads to disruption of the tertiary structure of Cytb by helix displacement, interfering with protein–heme interaction. The p.S246P mutation induces a diproline structure, which alters local secondary structure and induces a kink in the protein backbone, interfering with macromolecular interactions. These molecular effects are compatible with a leaky phenotype, that is, limited but progressive mitochondrial dysfunction. In conclusion, we find that rare, putative leaky mtDNA variants in MT-CYB can be identified in a cohort of HCM patients. We propose that further patients with HCM should be examined for mutations in MT-CYB in order to clarify the role of these variants.
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Affiliation(s)
- Christian M Hagen
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark ; Department of Biomedical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Frederik H Aidt
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark ; Institute of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Ole Havndrup
- Department of Cardiology, Roskilde Sygehus Roskilde, Denmark
| | - Paula L Hedley
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark ; Department of Biomedical Sciences, Stellenbosch University Cape Town, South Africa
| | - Cathrine Jespersgaard
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark
| | - Morten Jensen
- Department of Medicine B, The Heart Center, Rigshospitalet Copenhagen, Denmark
| | - Jørgen K Kanters
- Department of Biomedical Sciences, University of Copenhagen Copenhagen, Denmark
| | | | - Daniel V Møller
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Medicine B, The Heart Center, Rigshospitalet Copenhagen, Denmark
| | - Michael Christiansen
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark
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16
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Brown AM, Zondlo NJ. A propensity scale for type II polyproline helices (PPII): aromatic amino acids in proline-rich sequences strongly disfavor PPII due to proline-aromatic interactions. Biochemistry 2012; 51:5041-51. [PMID: 22667692 DOI: 10.1021/bi3002924] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type II polyproline helices (PPII) are a fundamental secondary structure of proteins, common in globular and nonglobular regions and important in cellular signaling. We developed a propensity scale for PPII using a host-guest system with sequence Ac-GPPXPPGY-NH(2), where X represents any amino acid. We found that proline has the highest PPII propensity, but most other amino acids display significant PPII propensities. The PPII propensity of leucine was the highest of all propensities of non-proline residues. Alanine and residues with linear side chains displayed the next highest PPII propensities. Three classes of residues displayed lower PPII propensities: β-branched amino acids (Thr, Val, and Ile), short amino acids with polar side chains (Asn, protonated Asp, Ser, Thr, and Cys), and aromatic amino acids (Phe, Tyr, and Trp). tert-Leucine particularly disfavored PPII. The basis of the low PPII propensities of aromatic amino acids in this context was significant cis-trans isomerism, with proline-rich peptides containing aromatic residues exhibiting 45-60% cis amide bonds, due to Pro-cis-Pro-aromatic and aromatic-cis-Pro amide bonds.
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Affiliation(s)
- Alaina M Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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