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Andrew's publications

Andrew's Publications

Publications002

 

 

(63) Martínez-Lumbreras, S., Alfano, C., Evans, N.J., Collins, K.M., Flanagan, K.A., Atkinson, R.A., Krysztofinska, E.M., Vydyanath, A., Jackter, J., Fixon-Owoo, S., Camp, A.H. and Isaacson, R.L. (2018) Structure, doi: 10.1016/j.str.2018.02.007.

Structural and functional insights into Bacillus subtilis sigma factor inhibitor, CsfB.


(62) O’Brien, K.A., Pollock, R.D., Stroud, M., Lambert, R.J., Kumar, A., Atkinson, R.A., Green, D.A., Anton-Solanas, A., Edwards, L.M. and Harridge, S.D.R. (2018) Physiol. Rep., doi: 10.14814/phy2.13613.

Human physiological and metabolic responses to an attempted winter crossing of Antarctica: the effects of prolonged hypobaric hypoxia.


(61) Zervou, S., Yin, X., Nabeebaccus, A.A., O’Brien, B.A., Cross, R.L., McAndrew, D.J., Atkinson, R.A., Eykyn, T.R., Mayr, M., Neubauer, S. and Legate, C.A. (2016) Amino Acids, 48, 11969-1981.

Proteomic and metabolomic changes driven by elevating myocardial creatine suggest novel metabolic feedback mechanisms.


(60) Martino, L., Pennell, S., Kelly, G., Busi, B., Brown, P.., Atkinson, R.A., Salisbury, N.J., Ooi, Z.H., See, K.W., Smerdon, S.J., Alfano, C., Bui, T.T., Conte, M.R. (2015) Nucleic Acids Res., 43, 645-660.

Synergic interplay of the La motif, RRM1 and the inter domain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module.


(59) Martino, L., Salisbury, N.J., Brown, P., Kelly, G., Atkinson, R.A., Conte, M.R. (2015) Biomol. NMR Assign., 9, 337-340.

1H, 15N and 13C chemical shift assignments of the La motif and RRM1 from human LARP6.


(58) Ramírez, J., Recht, R., Charbonnier, S., Ennifar, E., Atkinson, R.A., Travé, G., Nominé, Y. and Kieffer, B. (2015) Biochemistry, 54, 1327-1337.

Disorder-to-order transition of MAGI-1 PDZ1 C-terminal extension upon peptide binding: thermodynamic and dynamic insights.

 

(57) Lu, Z., Bergeron, J.R., Atkinson, R.A., Schaller, T., Veselkov, D.A., Oregioni, A., Yang, Y., Matthews, S.J., Malim, M.H. and Sanderson, M.R. (2013) Open Biol., 3(11):130100.

Insight into the HIV-1 Vif SOCS-box-ElonginBC interaction.

 

(56) De Nicola, G.F., Martin E.D., Chaikuad, A., Bassi, R., Clark, J., Martino, L., Verma, S., Sicard, P., Tata, R., Atkinson, R.A., Knapp, S., Conte, M.R. and Marber, M.S. (2013) Nat. Struct. Mol. Biol., 20, 1182-1190.

Mechanism and consequence of the autoactivation of p38α mitogen-activated protein kinase promoted by TAB1.

 

(55) Takacs, M., Petoukhov, M.V., Atkinson, R.A., Roblin, P., Ogi, F.-X., Demeler, B., Potier, N., Chebaro, Y., Dejaegere, A., Svergun, D.I., Moras, D. and Billas, I.M.L. (2013) PLoS One, 8:e67810.

The asymmetric binding of PGC-1α to the ERRα and ERRg nuclear receptor homodimers involves a similar recognition mechanism.

 

(54) Vermeer, L.S., Lan, Y., Abbate, V., Ruh, E., Bui, T.T., Wilkinson, L.J., Kanno, T., Jumagulova, E., Kozlowska, J., Patel, J., McIntyre, C.A., Yam, W.C., Siu, G., Atkinson, R.A., Lam, L.K., Bansal, S.S., Drake, A.F., Mitchell, G.H. and Mason, A.J. (2012) J. Biol. Chem., 287, 34120-34133.

Conformational flexibility determines selectivity and antibacterial, antiplasmodial, and anticancer potency of cationic α-helical peptides.

 

(53) Zanier, K., Ould M'hamed Ould Sidi, A., Boulade-Ladame, C., Rybin, V., Chappelle, A., Atkinson, A., Kieffer, B. and Travé, G. (2012) Structure, 20, 604-617.

Solution structure analysis of the HPV16 E6 oncoprotein reveals a self-association mechanism required for E6-mediated degradation of p53.

 

(52) Kappo, M.A., AB, E., Hassem, F., Atkinson, R.A., Faro, A., Muleya, V., Mulaudzi, T., Poole, J.O., McKenzie, J.M., Chibi, M., Moolman-Smook, J.C., Rees, D.J.G. and Pugh, D.J.R. (2012) J. Biol. Chem., 287, 7146-7158.

Solution structure of the RING finger domain of retinoblastoma binding protein-6 (RBBP6) suggests it functions as a U-box.

(51) Charbonnier, S., Nominé, Y., Ramirez, J., Luck, K., Chapelle, A., Stote, R.H., Travé, G., Kieffer, B. and Atkinson, R.A. (2011) J. Mol. Biol., 406, 745-763.
The structural and dynamic response of MAGI-1 PDZ1 with non-canonical domain boundaries to the binding of human papillomavirus E6.

(50) Bonnet, J., Wang, Y.-H., Spedale, G., Atkinson, R.A., Romier, C., Hamiche, A., Pijnappel, W.W., Timmers, H.T., Tora, L., Devys, D. and Kieffer, B. (2010) EMBO Rep., 11, 612-618.
The structural plasticity of SCA7 domains defines their differential nucleosome-binding properties.

(49) Susini, L., Besse, S., Duflaut, D., Lespagnol, A., Beekman, C., Fiucci, G., Atkinson, R.A., Busso, D., Poussin, P., Marine, J.-C., Martinou, J.-C., Cavarelli, J., Moras, D., Amson, R. and Telerman, A. (2008) Cell Death Differ., 15, 1211-1220.
TCTP protects from apoptotic cell death by antagonizing bax function.

(48) Desplancq, D., Rinaldi, A.-S., Hörzer, H., Ho, Y., Nierengarten, H., Atkinson, R.A., Kieffer, B. and Weiss, E. (2008) Biotechnol. Appl. Biochem., 51, 53-61.
Automated overexpression and isotopic labeling of biologically active oncoproteins in the cyanobacterium Anabaena sp. PCC 7120.

(47) Charbonnier, S., Stier, G., Orfanoudakis, G., Kieffer, B., Atkinson, R.A. and Travé, G. (2008) Protein Expr. Purif., 60, 64-73.
Defining the minimal interacting regions of the tight junction protein MAGI-1 and HPV16 E6 oncoprotein for solution structure studies.

(46) Wasielewski, E., Tzou, D.L., Dillmann, B., Czaplicki, J., Abdallah, M.A., Atkinson, R.A. and Kieffer, B. (2008) Biochemistry, 47, 3397-3406.
Multiple conformations of the metal-bound pyoverdine PvdI, a siderophore of Pseudomonas aeruginosa: a nuclear magnetic resonance study.

(45) Vitorino, M., Coin, F., Zlobinskaya, O., Atkinson, R.A., Moras, D., Egly, J.-M., Poterszman, A. and Kieffer, B. (2007) J. Mol. Biol., 368, 473-480.
Solution structure and self-association properties of the p8 TFIIH subunit responsible for trichothiodystrophy.

(44) AB, E., Atkinson, R.A., Banci, L., Bertini, I., Ciofi-Baffoni, S., Brunner, K., Diercks, T., Dötsch, V., Engelke, F., Folkers, G.E., Griesinger, C., Gronwald, W., Günther, U., Habeck, M., de Jong, R.N., Kalbitzer, H.R., Kieffer, B., Leeflang, B.R., Loss, S., Luchinat, C., Marquardsen, T., Moskau, D., Neidig, K.-P., Nilges, M., Piccioli, M., Pierattelli, R., Rieping, W., Schippmann, T., Schwalbe, H., Travé, G., Trenner, J., Wöhnert, J., Zweckstetter, M. and Kaptein, R. (2006) Acta Cryst., D62, 1150-1161.
NMR in the SPINE structural proteomics project.

(43) Oblak, M., Grdadolnik, S.G., Kotnik, M., Poterszman, A., Atkinson, R.A., Nierengarten, H., Desplancq, D., Moras, D. and Solmajer, T. (2006) Biochem. Biophys. Res. Commun., 349, 1206-1213.
Biophysical characterization of an indolinone inhibitor in the ATP-binding site of DNA gyrase.

(42) Aukrust, I., Evensen, L., Hollås, H., Berven, F., Atkinson, R.A., Travé, G., Flatmark, T. and Vedeler, A. (2006) J. Mol. Biol., 363, 469-481.
Engineering, biophysical characterisation and binding properties of a soluble mutant form of annexin A2 domain IV that adopts a partially folded conformation.

(41) Charbonnier, S., Coutouly, M.-A., Kieffer, B., Travé, G. and Atkinson, R.A. (2006) J. Biomol. NMR, online April 26 2006.
13C, 15N and 1H resonance assignment of the PDZ1 domain of MAGI-1 using QUASI.

(40) Nominé, Y., Masson, M., Charbonnier, S., Zanier, K., Ristriani, T., Deryckère, F., Sibler, A.-P., Desplancq, D., Atkinson, R.A., Weiss, E., Orfanoudakis, G., Kieffer, B. and Travé, G. (2006) Mol. Cell, 21, 665-678.
Structural and functional analysis of E6 oncoprotein: insights in the molecular pathways of human papillomavirus-mediated pathogenesis.

(39) Schons, V., Atkinson, R.A., Dugave, C., Graff, R., Mislin, G.L.A., Rochet, L., Hennard, C., Kieffer, B., Abdallah, B. and Schalk, I.J. (2005) Biochemistry,  44, 14069-14079.
The structure-activity relationship of ferric-pyoverdine bound to its outer membrane transporter: implications for the mechanism of iron uptake.

(38) Tzou, D.L., Wasielewski, E., Abdallah, M.A., Kieffer, B. and Atkinson, R.A. (2005) Biopolymers, 79, 139-149.
A low temperature heteronuclear NMR study of two exchanging conformations of metal-bound pyoverdin PaA from Pseudomonas aeruginosa.

(37) Houben, K., Wasielewski, E., Dominguez, C., Kellenberger, E., Atkinson, R.A., Timmers, H.T.M., Kieffer, B. and Boelens, R. (2005) J. Mol. Biol., 349, 621-637.
Dynamics and metal exchange properties of C4C4 RING domains from CNOT4 and the p44 subunit of TFIIH.

(36) Nominé, Y., Charbonnier, S., Miguet, L., Potier, N., van Dorsselaer, A., Atkinson, R.A., Travé, G. and Kieffer, B. (2005) J. Biomol. NMR, 31, 129-141.
1H and 15N resonance assignments, secondary structure and dynamic behaviour of the C-terminal domain of human papillomavirus oncoprotein E6.

(35) Klein, F.A.C, Atkinson, R.A., Potier, N., Moras, D. and Cavarelli, J. (2005) J. Biol. Chem, 280, 5682-5692.
Biochemical and NMR mapping of the interface between CBP and ligand binding domains of nuclear receptors: beyond the LXXLL motif.

(34) Jawhari, A., Boussert, S., Lamour, V., Atkinson, R.A., Kieffer, B., Poch, O., Potier, N., van Dorsselaer, A, Moras, D. and Poterszman, A. (2004) Biochemistry 43, 14420-14430.
Domain architecture of the p62 subunit from the human transcription/repair factor TFIIH deduced by limited proteolysis and mass spectrometry analysis.

(33) Au, Y., Atkinson, R.A., Guerrini, R., Kelly, G., Joseph, C., Martin, S.R., Muskett, F.W., Pallavicini, A., Faulkner, G. and Pastore, A. (2004) Structure, 12, 611-622.
Solution structure of ZASP PDZ domain: Implications for sarcomere ultrastructure and enigma family redundancy.

(32) Atkinson, R.A. and Kieffer, B. (2004) Progress in NMR Spectroscopy, 44, 141-187.
The role of protein motions in molecular recognition: insights from heteronuclear NMR relaxation measurements.

(31) Coutouly, M.-A., Kieffer, B. and Atkinson, R.A. (2004) Comptes Rendus Chimie, 7, 335-341.
QUASI: Quick Access to Spectral Interpretation.

(30) Wasielewski, E., Atkinson, R.A., Abdallah, M.A. and Kieffer, B. (2002) Biochemistry, 41, 12488-12497.
The three-dimensional structure of the gallium complex of azoverdin, a siderophore of Azomonas macrocytogenes ATCC 12334, determined by NMR using residual dipolar coupling constants.

(29) Ramboarina, S., Srividya, N., Atkinson, R.A., Morellet, N., Roques, B.P., Lefèvre, J.-F., Mély, Y. and Kieffer, B. (2002) J. Mol. Biol., 316, 611-627.
Effects of temperature on the dynamic behaviour of the HIV-1 nucleocapsid NCp7 and its DNA complex.

(28) Atkinson R.A. and Saudek, V. (2002) FEBS Lett., 510, 1-4.
Hypothesis : The direct determination of protein structure by NMR without assignment.

(27) Atkinson R.A., Joseph, C., Kelly, G., Muskett, F.W., Frenkiel, T.A., Nietlispach, D. and Pastore, A. (2001) Nature Struct. Biol., 8, 853-857.
Ca2+-independent binding of an EF-hand domain to a novel motif in the α-actinin-titin complex.

(26) Joseph, C., Stier, G., O’Brien, R., Politou, A.S., Atkinson, R.A., Bianco, A., Ladbury, J.E., Martin, S.R. and Pastore, A. (2001) Biochemistry, 40, 4957-4965.
A structural characterization of the interactions between titin Z-repeats and the α-actinin C-terminal domain.

(25) Atkinson, R.A., Kieffer, B., Dejaegere, A., Sirockin, F. and Lefèvre, J.-F. (2000) Biochemistry, 39, 3908-3919.
Structural and dynamic characterisation of ω-conotoxin MVIIA: the binding loop exhibits slow conformational exchange.

(24) Atkinson, R.A., Joseph, C., Kelly, G., Muskett, F.W., Frenkiel, T.A. and Pastore, A. (2000) J. Biomol. NMR, 16, 277-278.
Assignment of the 1H, 13C and 15N resonances of the C-terminal EF-hands of α-actinin in a 14 kDa complex with Z-repeat 7 of titin.

(23) Atkinson, R.A., Joseph, C., Dal Piaz, F., Birolo, L., Stier, G., Pucci, P. and Pastore, A. (2000) Biochemistry, 39, 5255-5264.
The binding of α-actinin to titin: implications for Z-disk assembly.

(22) Atkinson, R.A. and Lefèvre, J.-F. (1999) J. Biomol. NMR, 13, 83-88.
Reduced spectral density mapping for proteins: validity for studies of 13C relaxation.

(21) Improta, S., Krueger, J.K., Gautel, M., Atkinson, R.A., Lefèvre, J.-F., Moulton, S., Trewhella, J. and Pastore, A. (1998) J. Mol. Biol., 284, 761-777.
The assembly of immunoglobulin-like modules in titin: implications for muscle elasticity.

(20) Fraternali, F., Do, Q.-T., Doan, B.-T., Atkinson, R.A., Palmas, P., Sklenár, V., Safar, P., Wildgoose, P., Strop, P. and Saudek, V. (1998) Proteins, 30, 264-274.
Mapping the active site of Factor Xa by selective inhibitors: an NMR and MD study.

(19) Doan, B.T., Fraternali, F., Do, Q.-T., Atkinson, R.A., Palmas, P., Sklenár, V., Wildgoose, P., Strop, P. and Saudek, V. (1998) J. Chim. Phys., 95, 443-446.
A NMR and MD study of the active site of Factor Xa by selective inhibitors.

(18) Atkinson, R.A. and Lefèvre, J.-F. (1998) in Protein Dynamics, Function and Design, pp. 129-145. ed. O. Jardetzky and J.-F. Lefèvre, Plenum Press, New York.
The investigation of protein dynamics via the spectral density function.

(17) Atkinson, R.A., Salah El Din, A.L., Kieffer, B., Lefèvre, J.-F. and Abdallah, M. (1998) Biochemistry, 37, 15965-15973.
Bacterial iron transport: 1H NMR determination of the three-dimensional structure of the gallium complex of pyoverdin G4R, the peptidic siderophore of Pseudomonas putida G4R.

(16) Atkinson, R.A. and Saudek, V. (1997) J. Chem. Soc., Faraday Trans., 93, 3319-3323.
Direct fitting of structure and chemical shift to NMR spectra.

(15) Saudek, V., Vincendon, P., Do, Q.-T., Atkinson, R.A., Sklenàr, V., Pelton, P.D., Piriou, F. and Ganzhorn, A.J. (1996) Eur. J. Biochem., 240, 288-291.
7Li nuclear magnetic resonance study of lithium binding to myo-inositol monophosphatase.

(14) Atkinson, R.A. and Saudek, V. (1996) in Dynamics and the Problem of Recognition in Biological Macromolecules, ed. O. Jardetzky and J.-F. Lefèvre, Plenum Press, New York. pp. 49-55.
The direct determination of protein structure from multidimensional NMR spectra without assignment. An evaluation of the concept.

(13) Atkinson, R.A., Evans, J.S., Hauschka, P.V., Levine, B.A., Meats, R., Triffitt, J.T., Virdi, A.S. and Williams, R.J.P. (1995) Eur. J. Biochem., 232, 515-521.
Conformational studies of osteocalcin in solution.

(12) Huggins, J.P., Ganzhorn, A.J., Saudek, V., Pelton, J.T. and Atkinson, R.A. (1994) Eur. J. Biochem., 221, 581-593.
Stimulation of cyclic GMP-dependent protein kinase 1α by a peptide from its own sequence. An investigation by enzymology, circular dichroism and 1H NMR of the activity and structure of cyclic GMP-dependent protein kinase 1α-(546-576)-amide.

(11) Atkinson, R.A., Saudek, V. and Pelton, J.T. (1994) Int. J. Peptide Protein Res., 43, 563-572.
Echistatin: the refined structure of a disintegrin in solution by 1H NMR and restrained molecular dynamics.

(10) Atkinson, R.A. and Pelton, J.T. (1992) FEBS Lett., 296, 1-6.
Conformational study of cyclo(D-Trp-D-Asp-Pro-D-Val-Leu), an endothelin-A receptor selective antagonist.

(9) Saudek, V., Atkinson, R.A. and Pelton, J.T. (1991) Biochemistry, 30, 7369-7372.
Three-dimensional structure of echistatin, the smallest active RGD protein.

(8) Saudek, V., Atkinson, R.A., Lepage, P. and Pelton, J.T. (1991) Eur. J. Biochem., 202, 329-338.
The secondary structure of echistatin from proton NMR, circular dichroism and Raman spectroscopy.

(7) Pastore, A., Atkinson, R.A., Saudek, V. and Williams, R.J.P. (1991) Proteins: Struct. Funct. Genet., 10, 22-32.
Topological mirror images in protein structure computation: an underestimated problem.

(6) Atkinson, R.A., Saudek, V., Huggins, J.P. and Pelton, J.T. (1991) Biochemistry, 30, 9387-9395.
Proton NMR and circular dichroism studies of the N-terminal domain of cyclic GMP-dependent protein kinase: a leucine/isoleucine zipper.

(5) Atkinson, R.A. and Williams, R.J.P. (1990) J. Mol. Biol., 212, 541-552.
Solution structure of the kringle 4 domain from human plasminogen by proton nuclear magnetic resonance spectroscopy and distance geometry.

(4) Atkinson, R.A., Fairbrother, W.J., Kaiser, D.A., Machesky, L., Pollard, T.D. and Levine, B.A. (1990) Biophys. J., 57, A334.
NMR studies of the solution structure of Acanthamoeba profilin-1 (meeting abstract).

(3) Saudek, V., Atkinson, R.A., Williams, R.J.P. and Ramponi, G. (1989) J. Mol. Biol., 205, 229-239.
Identification and description of α-helical regions in horse muscle acylphosphatase by proton nuclear magnetic resonance spectroscopy.

(2) Atkinson, R.A., Fairbrother, W.J., Levine, B.A., Tavare, J., Clark, B. and Ellis, L. (1989) Biochem. Soc. Trans., 17, 899.
NMR structural studies on the tyrosine kinase domain of the human insulin receptor (meeting abstract).

(1) Pielak, G.J., Atkinson, R.A., Boyd, J. and Williams, R.J.P. (1988) Eur. J. Biochem., 177, 179-185.
Two-dimensional NMR as a probe of structural similarity applied to mutants of cytochrome c.
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