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Amelio I, Tsvetkov PO, Knight RA, Lisitsa A, Melino G, Antonov AV. SynTarget: an online tool to test the synergetic effect of genes on survival outcome in cancer. Cell Death Differ 2016; 23:912. [PMID: 26915292 PMCID: PMC4832110 DOI: 10.1038/cdd.2016.12] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- I Amelio
- Medical Research Council, Toxicology Unit, Leicester University, Lancaster Road, P.O. Box 138, Leicester, UK
| | - P O Tsvetkov
- Aix-Marseille Université, Inserm, CRO2 UMR S 911, Faculté de Pharmacie, Marseille, France.,Institute of General Pathology and Pathophysiology, RAMS, 125315 Moscow, Russia
| | - R A Knight
- Medical Research Council, Toxicology Unit, Leicester University, Lancaster Road, P.O. Box 138, Leicester, UK
| | - A Lisitsa
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Street, Moscow, Russia
| | - G Melino
- Medical Research Council, Toxicology Unit, Leicester University, Lancaster Road, P.O. Box 138, Leicester, UK.,Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy.,Institute of Cytology, Saint-Petersburg 194064, Russia
| | - A V Antonov
- Medical Research Council, Toxicology Unit, Leicester University, Lancaster Road, P.O. Box 138, Leicester, UK.,Institute of Cytology, Saint-Petersburg 194064, Russia
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Mitkevich VA, Petrushanko IY, Yegorov YE, Simonenko OV, Vishnyakova KS, Kulikova AA, Tsvetkov PO, Makarov AA, Kozin SA. Isomerization of Asp7 leads to increased toxic effect of amyloid-β42 on human neuronal cells. Cell Death Dis 2013; 4:e939. [PMID: 24287700 PMCID: PMC3847340 DOI: 10.1038/cddis.2013.492] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- V A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, Russia
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Indeykina MI, Popov IA, Kozin SA, Kononikhin AS, Kharybin ON, Tsvetkov PO, Makarov AA, Nikolaev EN. Capabilities of MS for Analytical Quantitative Determination of the Ratio of α- and βAsp7 Isoforms of the Amyloid-β Peptide in Binary Mixtures. Anal Chem 2011; 83:3205-10. [DOI: 10.1021/ac103213j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria I. Indeykina
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Igor A. Popov
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Alexey S. Kononikhin
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Oleg N. Kharybin
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Philippe O. Tsvetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Evgenij N. Nikolaev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
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Lafitte D, Tsvetkov PO, Devred F, Toci R, Barras F, Briand C, Makarov AA, Haiech J. Cation binding mode of fully oxidised calmodulin explained by the unfolding of the apostate. Biochim Biophys Acta 2002; 1600:105-10. [PMID: 12445465 DOI: 10.1016/s1570-9639(02)00450-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Calmodulin is the most ubiquitous calcium binding protein. The protein is very sensitive to oxidation and this modification has pronounced effects on calmodulin function. In this work, we decided to fully oxidise calmodulin in order to study the consequences on cation binding, domain stability, and alpha helicity. Oxidation of methionines unfolds completely the apostate of the protein, which upon calcium binding recovers the major part of its secondary and tertiary structure. However, the unstructuring of the apostate results in a protein that binds calcium to any site in an independent manner, does not bind magnesium and does not possess auxiliary sites anymore.
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Affiliation(s)
- Daniel Lafitte
- UMR CNRS 6032, UFR de Pharmacie, 27 Bd Jean Moulin 13385 Cedex 5, Marseilles, France.
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Lafitte D, Lamour V, Tsvetkov PO, Makarov AA, Klich M, Deprez P, Moras D, Briand C, Gilli R. DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose. Biochemistry 2002; 41:7217-23. [PMID: 12044152 DOI: 10.1021/bi0159837] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA gyrase is a major bacterial protein that is involved in replication and transcription and catalyzes the negative supercoiling of bacterial circular DNA. DNA gyrase is a known target for antibacterial agents since its blocking induces bacterial death. Quinolones, coumarins, and cyclothialidines have been designed to inhibit gyrase. Significant improvements can still be envisioned for a better coumarin-gyrase interaction. In this work, we obtained the crystal costructures of the natural coumarin clorobiocin and a synthetic analogue with the 24 kDa gyrase fragment. We used isothermal titration microcalorimetry and differential scanning calorimetry to obtain the thermodynamic parameters representative of the molecular interactions occurring during the binding process between coumarins and the 24 kDa gyrase fragment. We provide the first experimental evidence that clorobiocin binds gyrase with a stronger affinity than novobiocin. We also demonstrate the crucial role of both the hydroxybenzoate isopentenyl moiety and the 5'-alkyl group on the noviose of the coumarins in the binding affinity for gyrase.
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Affiliation(s)
- Daniel Lafitte
- UMR CNRS 6032, UFR de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France.
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Baladi S, Tsvetkov PO, Petrova TV, Takagi T, Sakamoto H, Lobachov VM, Makarov AA, Cox JA. Folding units in calcium vector protein of amphioxus: Structural and functional properties of its amino- and carboxy-terminal halves. Protein Sci 2001; 10:771-8. [PMID: 11274468 PMCID: PMC2373976 DOI: 10.1110/ps.40601] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Muscle of amphioxus contains large amounts of a four EF-hand Ca2+-binding protein, CaVP, and its target, CaVPT. To study the domain structure of CaVP and assess the structurally important determinants for its interaction with CaVPT, we expressed CaVP and its amino (N-CaVP) and carboxy-terminal halves (C-CaVP). The interactive properties of recombinant and wild-type CaVP are very similar, despite three post-translational modifications in the wild-type protein. N-CaVP does not bind Ca2+, shows a well-formed hydrophobic core, and melts at 44 degrees C. C-CaVP binds two Ca2+ with intrinsic dissociation constants of 0.22 and 140 microM (i.e., very similar to the entire CaVP). The metal-free domain in CaVP and C-CaVP shows no distinct melting transition, whereas its 1Ca2+ and 2Ca2+) forms melt in the 111 degrees -123 degrees C range, suggesting that C-CaVP and the carboxy- domain of CaVP are natively unfolded in the metal-free state and progressively gain structure upon binding of 1Ca2+ and 2Ca2+. Thermal denaturation studies provide evidence for interdomain interaction: the apo, 1Ca2+ and 2Ca2+ states of the carboxy-domain destabilize to different degrees the amino-domain. Only C-CaVP forms a Ca2+-dependent 1:1 complex with CaVPT. Our results suggest that the carboxy-terminal domain of CaVP interacts with CaVPT and that the amino-terminal lobe modulates this interaction.
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Affiliation(s)
- S Baladi
- Department of Biochemistry, University of Geneva, 1211 Geneva 4, Switzerland
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Hill TJ, Lafitte D, Wallace JI, Cooper HJ, Tsvetkov PO, Derrick PJ. Calmodulin-peptide interactions: apocalmodulin binding to the myosin light chain kinase target-site. Biochemistry 2000; 39:7284-90. [PMID: 10852728 DOI: 10.1021/bi000139m] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncovalent binding of the synthetic peptide RS20 to calmodulin in the presence of calcium was confirmed by electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry to form a complex with a 1:1:4 calmodulin/RS20/calcium stoichiometry. There was no evidence for formation of a calmodulin-RS20-Ca(2) species. The absence of calmodulin-RS20-Ca(2) would be consistent with models in which the two globular domains are coupled functionally. There was evidence that calmodulin, RS20-calmodulin without associated calcium, and calmodulin-RS20-Ca(4) existed together in solution, whereas calmodulin-calcium complexes were absent. It is proposed that calcium binding to form the calmodulin-RS20-Ca(4) complex occurs after an initial RS20-calmodulin binding event, and serves to secure the target within the calmodulin structure. The binding of more than one RS20 molecule to calmodulin was observed to induce unfolding of calmodulin.
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Affiliation(s)
- T J Hill
- Institute of Mass Spectrometry and Department of Chemistry, University of Warwick, Coventry, UK
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Tsvetkov PO, Protasevich II, Gilli R, Lafitte D, Lobachov VM, Haiech J, Briand C, Makarov AA. Apocalmodulin binds to the myosin light chain kinase calmodulin target site. J Biol Chem 1999; 274:18161-4. [PMID: 10373414 DOI: 10.1074/jbc.274.26.18161] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of a 20-residue-long peptide derived from the calmodulin-binding domain of the smooth muscle myosin light chain kinase with calcium-free calmodulin (apocalmodulin) was studied using a combination of isothermal titration calorimetry and differential scanning calorimetry. We showed that: (i) a significant binding between apocalmodulin and the target peptide (RS20) exists in the absence of salt (Ka = 10(6) M-1), (ii) the peptide interacts with the C-terminal lobe of calmodulin and adopts a partly helical conformation, and (iii) the presence of salt weakens the affinity of the peptide for apocalmodulin, emphasizing the importance of electrostatic interactions in the complex. Based on these results and taking into account the work of Bayley et al. (Bayley, P. M., Findlay, W.A., and Martin, S. R. (1996) Protein Sci. 5, 1215-1228), we suggest a physiological role for apocalmodulin.
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Affiliation(s)
- P O Tsvetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 117984 Moscow, Russia
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Starikov NS, Yaroslavtsev IV, Tsvetkov PO, Yudin AN, Denisov MV, Slavsky AA, Vedenov AA, Karamov EV. Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid hamming distances. J Biomol Struct Dyn 1998; 15:877-85. [PMID: 9619510 DOI: 10.1080/07391102.1998.10508209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures for HIV-1 V3 classification. Two-mode distribution for the subtype E could sertificate that this subtype includes two thinner taxons.
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