List of Publications from the Leverhulme Centre

 

From April 2003 to April 2005 we have published 66 papers in international journals, including seven in Nature, one in Science, eight in PNAS and five in JACS. The complete list is:

 

 

1.         Azuaga, A. I., Canet, D., Smeenk, G., Berends, R., Titgemeijer, F., Duurkens, R., Mateo, P. L., Scheek, R. M., Robillard, G. T., Dobson, C. M. & van Nuland, N. A. J. (2003). Characterization of single-tryptophan mutants of histidine- containing phosphocarrier protein: Evidence for local rearrangements during folding from high concentrations of denaturan. Biochemistry 42, 4883-4895.

2.         Bastolla, U., Porto, M., Roman, H. E. & Vendruscolo, M. (2003). Statistical properties of neutral evolution. J. Mol. Evol. 57, S103-S119.

3.         Bastolla, U., Porto, M., Roman, H. E. & Vendruscolo, M. (2005). Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58, 22-30.

4.         Best, R. B. & Vendruscolo, M. (2004). Determination of protein structures consistent with NMR order parameters. J. Am. Chem. Soc. 126, 8090-8091.

5.         Bucciantini, M., Calloni, G., Chiti, F., Formigli, L., Nosi, D., Dobson, C. M. & Stefani, M. (2004). Prefibrillar amyloid protein aggregates share common features of cytotoxicity. J. Biol. Chem. 279, 31374-31382.

6.         Calamai, M., Canale, C., Relini, A., Stefani, M., Chiti, F. & Dobson, C. M. (2005). Reversal of protein aggregation provides evidence for multiple aggregated states. J. Mol. Biol. 346, 603-616.

7.         Canet, D., Lyon, C. E., Scheek, R. M., Robillard, G. T., Dobson, C. M., Hore, P. J. & van Nuland, N. A. J. (2003). Rapid formation of non-native contacts during the folding of HPr revealed by real-time photo-CIDNP NMR and stopped-flow fluorescence experiments. J. Mol. Biol. 330, 397-407.

8.         Chiti, F., Stefani, M., Taddei, N., Ramponi, G. & Dobson, C. M. (2003). Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424, 805-808.

9.         Christodoulou, J., Larsson, G., Fucini, P., Connell, S. R., Pertinhez, T. A., Hanson, C. L., Redfield, C., Nierhaus, K. H., Robinson, C. V., Schleucher, J. & Dobson, C. M. (2004). Heteronuclear NMR investigations of dynamic regions of intact Escherichia coli ribosomes. Proc. Natl. Acad. Sci. U. S. A. 101, 10949-10954.

10.       De Felice, F. G., Vieira, M. N. N., Meirelles, M. N. L., Morozova-Roche, L. A., Dobson, C. M. & Ferreira, S. T. (2004). Formation of amyloid aggregates from human lysozyme and its disease-associated variants using hydrostatic pressure. Faseb J. 18, U591-U605.

11.       de Laureto, P. P., Taddei, N., Frare, E., Capanni, C., Costantini, S., Zurdo, J., Chiti, F., Dobson, C. M. & Fontana, A. (2003). Protein aggregation and amyloid fibril formation by an SH3 domain probed by limited proteolysis. J. Mol. Biol. 334, 129-141.

12.       Dedmon, M. M., Lindorff-Larsen, K., Christodoulou, J., Vendruscolo, M. & Dobson, C. M. (2005). Mapping long-range interactions in alpha-synuclein using spin- label NMR and ensemble molecular dynamics simulations. J. Am. Chem. Soc. 127, 476-477.

13.       Dirix, C., Meersman, F., MacPhee, C. E., Dobson, C. M. & Heremans, K. (2005). High hydrostatic pressure dissociates early aggregates of TTR105-115, but not the mature amyloid fibrils. J. Mol. Biol. 347, 903-909.

14.       Dobson, C. M. (2004). Experimental investigation of protein folding and misfolding. Methods 34, 4-14.

15.       Dobson, C. M. (2003). Protein folding and misfolding. Nature 426, 884-890.

16.       Dobson, C. M. (2004). Chemical space and biology. Nature 432, 824-828.

17.       Dobson, C. M. (2004). Biological physics: Energy, information, life. Nature 432, 444-445.

18.       Dobson, C. M. (2004). In the footsteps of alchemists. Science 304, 1259-+.

19.       Dobson, C. M. (2005). Amyloidosis and protein folding - Response. Science 307, 43-44.

20.       Dobson, C. M. (2004). Principles of protein folding, misfolding and aggregation. Semin. Cell Dev. Biol. 15, 3-16.

21.       Dubay, K. F., Pawar, A. P., Chiti, F., Zurdo, J., Dobson, C. M. & Vendruscolo, M. (2004). Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. J. Mol. Biol. 341, 1317-1326.

22.       Dumoulin, M., Canet, D., Last, A. M., Pardon, E., Archer, D. B., Muyldermans, S., Wyns, L., Matagne, A., Robinson, C. V., Redfield, C. & Dobson, C. M. (2005). Reduced global copperativity is a common feature underlying the amyloidogenicity of pathogenic lysozyme mutations. J. Mol. Biol. 346, 773-788.

23.       Dumoulin, M. & Dobson, C. M. (2004). Probing the origins, diagnosis and treatment of amyloid diseases using antibodies. Biochimie 86, 589-600.

24.       Dumoulin, M., Last, A. M., Desmyter, A., Decanniere, K., Canet, D., Larsson, G. R., Spencer, A., Archer, D. B., Sasse, J., Muyldermans, S., Wyns, L., Redfield, C., Matagne, A., Robinson, C. V. & Dobson, C. M. (2003). A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme. Nature 424, 783-788.

25.       Fandrich, M., Forge, V., Buder, K., Kittler, M., Dobson, C. M. & Diekmann, S. (2003). Myoglobin forms amyloid fibrils by association of unfolded polypeptide segments. Proc. Natl. Acad. Sci. U. S. A. 100, 15463-15468.

26.       Frare, E., de Laureto, P. P., Zurdo, J., Dobson, C. M. & Fontana, A. (2004). A highly amyloidogenic region of hen lysozyme. J. Mol. Biol. 340, 1153-1165.

27.       Geierhaas, C. D., Paci, E., Vendruscolo, M. & Clarke, J. (2004). Comparison of the transition states for folding of two Ig-like proteins from different superfamilies. J. Mol. Biol. 343, 1111-1123.

28.       Gilbert, R. J. C., Fucini, P., Connell, S., Fuller, S. D., Nierhaus, K. H., Robinson, C. V., Dobson, C. M. & Stuart, D. I. (2004). Three-dimensional structures of translating ribosomes by cryo- EM. Mol. Cell 14, 57-66.

29.       Goyal, K., Tisi, L., Basran, A., Browne, J., Burnell, A., Zurdo, J. & Tunnacliffe, A. (2003). Transition from natively unfolded to folded state induced by desiccation in an anhydrobiotic nematode protein. J. Biol. Chem. 278, 12977-12984.

30.       Hatters, D. M., MacRaild, C. A., Daniels, R., Gosal, W. S., Thomson, N. H., Jones, J. A., Davis, J. J., MacPhee, C. E., Dobson, C. M. & Howlett, G. J. (2003). The circularization of amyloid fibrils formed by apolipoprotein C-II. Biophys. J. 85, 3979-3990.

31.       Jaroniec, C. P., MacPhee, C. E., Bajaj, V. S., McMahon, M. T., Dobson, C. M. & Griffin, R. G. (2004). High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 101, 711-716.

32.       Kamatari, Y. O., Dobson, C. M. & Konno, T. (2003). Structural dissection of alkaline-denatured pepsin. Protein Sci. 12, 717-724.

33.       Kamatari, Y. O., Dobson, C. M. & Konno, T. (2004). Structural dissection of alkaline-denatured pepsin. Spectr.-Int. J. 18, 227-236.

34.       Kammerer, R. A., Kostrewa, D., Zurdo, J., Detken, A., Garcia-Echeverria, C., Green, J. D., Muller, S. A., Meier, B. H., Winkler, F. K., Dobson, C. M. & Steinmetz, M. O. (2004). Exploring amyloid formation by a de novo design. Proc. Natl. Acad. Sci. U. S. A. 101, 4435-4440.

35.       Karplus, M., Dobson, C. M., Scoles, G., Zewail, A. H., McMillan, P. F. & Finney, J. L. (2005). Discussion. Philos. Trans. R. Soc. Lond. Ser. A-Math. Phys. Eng. Sci. 363, 389-391.

36.       Karplus, M., Wolynes, P. G., Dobson, C. M., Zewail, A. H., Clarke, J. & Schon, J. C. (2005). Energy landscapes and solved protein-folding problems - Discussion. Philos. Trans. R. Soc. Lond. Ser. A-Math. Phys. Eng. Sci. 363, 464-467.

37.       Korzhnev, D. M., Salvatella, X., Vendruscolo, M., Di Nardo, A. A., Davidson, A. R., Dobson, C. M. & Kay, L. E. (2004). Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature 430, 586-590.

38.       Krebs, M. R. H., MacPhee, C. E., Miller, A. F., Dunlop, L. E., Dobson, C. M. & Donald, A. M. (2004). The formation of spherulites by amyloid fibrils of bovine insulin. Proc. Natl. Acad. Sci. U. S. A. 101, 14420-14424.

39.       Krebs, M. R. H., Morozova-Roche, L. A., Daniel, K., Robinson, C. V. & Dobson, C. M. (2004). Observation of sequence specificity in the seeding of protein amyloid fibrils. Protein Sci. 13, 1933-1938.

40.       Kristjansdottir, S., Lindorff-Larsen, K., Fieber, W., Dobson, C. M., Vendruscolo, M. & Poulsen, F. M. (2005). Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies. J. Mol. Biol. 347, 1053-1062.

41.       Laurine, E., Gregoire, C., Fandrich, M., Engemann, S., Marchal, S., Thion, L., Mohr, M., Monsarrat, B., Michel, B., Dobson, C. M., Wanker, E., Erard, M. & Verdier, J. M. (2003). Lithostathine quadruple-helical filaments form proteinase K- resistant deposits in Creutzfeldt-Jakob disease. J. Biol. Chem. 278, 51770-51778.

42.       Lindorff-Larsen, K., Best, R. B., DePristo, M. A., Dobson, C. M. & Vendruscolo, M. (2005). Simultaneous determination of protein structure and dynamics. Nature 433, 128-132.

43.       Lindorff-Larsen, K., Kristjansdottir, S., Teilum, K., Fieber, W., Dobson, C. M., Poulsen, F. M. & Vendruscolo, M. (2004). Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein. J. Am. Chem. Soc. 126, 3291-3299.

44.       Lindorff-Larsen, K., Paci, E., Serrano, L., Dobson, C. M. & Vendruscolo, M. (2003). Calculation of mutational free energy changes in transition states for protein folding. Biophys. J. 85, 1207-1214.

45.       Lindorff-Larsen, K., Rogen, P., Paci, E., Vendruscolo, M. & Dobson, C. M. (2005). Protein folding and the organization of the protein topology universe. Trends Biochem.Sci. 30, 13-19.

46.       Lindorff-Larsen, K., Vendruscolo, M., Paci, E. & Dobson, C. M. (2004). Transition states for protein folding have native topologies despite high structural variability. Nat. Struct. Mol. Biol. 11, 443-449.

47.       MacPhee, C. E. & Woolfson, D. N. (2004). Engineered and designed peptide-based fibrous biomaterials. Curr. Opin. Solid State Mat. Sci. 8, 141-149.

48.       Malisauskas, M., Zamotin, V., Jass, J., Noppe, W., Dobson, C. M. & Morozova-Roche, L. A. (2003). Amyloid protofilaments from the calcium-binding protein equine lysozyme: Formation of ring and linear structures depends on pH and metal ion concentration. J. Mol. Biol. 330, 879-890.

49.       Marcon, G., Plakoutsi, G., Canale, C., Relini, A., Taddei, N., Dobson, C. M., Ramponi, G. & Chiti, F. (2005). Amyloid formation from HypF-N under conditions in which the protein is initially in its native state. J. Mol. Biol. 347, 323-335.

50.       Meehan, S., Berry, Y., Luisi, B., Dobson, C. M., Carver, J. A. & MacPhee, C. E. (2004). Amyloid fibril formation by lens crystallin proteins and its implications for cataract formation. J. Biol. Chem. 279, 3413-3419.

51.       Mok, K. H., Nagashima, T., Day, I. J., Jones, J. A., Jones, C. J. V., Dobson, C. M. & Hore, P. J. (2003). Rapid sample-mixing technique for transient NMR and photo-CIDNP spectroscopy: Applications to real-time protein folding. J. Am. Chem. Soc. 125, 12484-12492.

52.       Nilsson, M. R. & Dobson, C. M. (2003). Chemical modification of insulin in amyloid fibrils. Protein Sci. 12, 2637-2641.

53.       Paci, E., Cavalli, A., Vendruscolo, M. & Caflisch, A. (2003). Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc. Natl. Acad. Sci. U. S. A. 100, 8217-8222.

54.       Paci, E., Friel, C. T., Lindorff-Larsen, K., Radford, S. E., Karplus, M. & Vendruscolo, M. (2004). Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints. Proteins-Structure Function And Genetics 54, 513-525.

55.       Paci, E., Gsponer, J., Salvatella, X. & Vendruscolo, M. (2004). Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin. J. Mol. Biol. 340, 555-569.

56.       Porto, M., Bastolla, U., Roman, H. E. & Vendruscolo, M. (2004). Reconstruction of protein structures from a vectorial representation. Phys. Rev. Lett. 92, art. no.-218101.

57.       Porto, M., Roman, H. E., Vendruscolo, M. & Bastolla, U. (2005). Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences. Mol. Biol. Evol. 22, 630-638.

58.       Quezada, C. M., Schulman, B. A., Froggatt, J. J., Dobson, C. M. & Redfield, C. (2004). Local and global cooperativity in the human alpha-lactalbumin molten globule. J. Mol. Biol. 338, 149-158.

59.       Stefani, M. & Dobson, C. M. (2003). Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J. Mol. Med. 81, 678-699.

60.       Vendruscolo, M. & Dobson, C. M. (2005). Towards complete descriptions of the free-energy landscapes of proteins. Philos. Trans. R. Soc. Lond. Ser. A-Math. Phys. Eng. Sci. 363, 433-450.

61.       Vendruscolo, M., Paci, E., Dobson, C. M. & Karplus, M. (2003). Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. J. Am. Chem. Soc. 125, 15686-15687.

62.       Vendruscolo, M., Paci, E., Karplus, M. & Dobson, C. M. (2003). Structures and relative free energies of partially folded states of proteins. Proc. Natl. Acad. Sci. U. S. A. 100, 14817-14821.

63.       Vendruscolo, M., Zurdo, J., MacPhee, C. E. & Dobson, C. M. (2003). Protein folding and misfolding: a paradigm of self-assembly and regulation in complex biological systems. Philos. Trans. R. Soc. Lond. Ser. A-Math. Phys. Eng. Sci. 361, 1205-1222.

64.       Ventura, S., Zurdo, J., Narayanan, S., Parreno, M., Mangues, R., Reif, B., Chiti, F., Giannoni, E., Dobson, C. M., Aviles, F. X. & Serrano, L. (2004). Short amino acid stretches can mediate amyloid formation in globular proteins: The Src homology 3 (SH3) case. Proc. Natl. Acad. Sci. U. S. A. 101, 7258-7263.

65.       Wright, C. F., Christodoulou, J., Dobson, C. M. & Clarke, J. (2004). The importance of loop length in the folding of an immunoglobulin domain. Protein Eng. Des. Sel. 17, 443-453.

66.       Zurdo, J. (2005). Polypeptide models to understand misfolding and amyloidogenesis and their relevance in protein design and therapeutics. Protein Pept. Lett. 12, 171-187.