Anharmonic onsets in polypeptides revealed by neutron scattering: Experimental evidences and quantitative description of energy resolution dependence

Biophysical Chemistry

Volumn 180-181, Issue , 2013, Pages 29-36

  Schiró, Giorgio ^a  

^a CNRS   (France)

Author keywords

Anharmonic dynamics; Elastic neutron scattering; Protein dynamical transition

Indexed keywords

POLYPEPTIDE;

ARTICLE; ENERGY; NEUTRON SCATTERING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN POLYMORPHISM; QUANTITATIVE ANALYSIS; TEMPERATURE DEPENDENCE;

ANHARMONIC DYNAMICS; ELASTIC NEUTRON SCATTERING; PROTEIN DYNAMICAL TRANSITION;

CONCANAVALIN A; MODELS, THEORETICAL; MURAMIDASE; NEUTRON DIFFRACTION; PEPTIDES; SCATTERING, SMALL ANGLE; TEMPERATURE; THERMODYNAMICS; WATER;

EID: 84879821801     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2013.05.006     Document Type: Article

References (32)

1. J.H. Roh, V.N. Novikov, R.B. Gregory, J.E. Curtis, Z. Chowdhuri, A.P. Sokolov, Onsets of anharmonicity in protein dynamics, Physical Review Letters 95 (2005) 038101.
2. W. Doster, S. Cusack, W. Petry, Dynamical transition of myoglobin revealed by inelastic neutron scattering, Nature 337 (1989) 754.
3. G. Schiró, C. Caronna, F. Natali, A. Cupane, Direct evidence of the amino acid side chain and backbone contributions to protein anharmonicity, Journal of the American Chemical Society 132 (2010) 1371.
4. K. Wood, D.J. Tobias, B. Kessler, F. Gabel, D. Oesterhelt, F.A.A. Mulder, G. Zaccai, M. Weik, The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: direct evidence using isotope labeling and molecular dynamics simulations, Journal of the American Chemical Society 132 (2010) 4990.
5. G. Schiró, C. Caronna, F. Natali, A. Cupane, Molecular origin and hydration dependence of protein anharmonicity: an elastic neutron scattering study, Physical Chemistry Chemical Physics 12 (2010) 10215.
6. M. Krishnan, V. Kurkal-Siebert, J. Smith, Methyl group dynamics and the onset of anharmonicity in myoglobin, The Journal of Physical Chemistry B 112 (2008) 5522.
7. R.M. Daniel, J.C. Smith, M. Ferrand, S. Hery, R. Dunn, J.L. Finney, Enzyme activity below the dynamical transition at 220 K, Biophysical Journal 75 (1998) 2504.
8. E. Mamontov, H. O'Neill, Q. Zhang, Mean-squared atomic displacements in hydrated lysozyme, native and denatured, Journal of Biological Physics 36 (2010) 291-297.
9. G. Zaccai, How soft is a protein? A protein dynamics force constant measured by neutron scattering, Science 288 (2000) 1604.
10. S.-H. Chen, L. Liu, E. Fratini, P. Baglioni, A. Faraone, E. Mamontov, Observation of fragile-to-strong dynamic crossover in protein hydration water, Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 9012.
11. W. Doster, The two-step scenario of the protein dynamical transition, Journal of Non-Crystalline Solids 357 (2011) 622.
12. S. Khodadadi, S. Pawlus, J.H. Roh, V. Garcia Sakai, E. Mamontov, A.P. Sokolov, The origin of the dynamic transition in proteins, The Journal of Chemical Physics 128 (2008) 195106.
13. G. Chen, P.W. Fenimore, H. Frauenfelder, F. Mezei, J. Swenson, R.D. Young, Protein fluctuations explored by inelastic neutron scattering and dielectric relaxation spectroscopy, Philosophical Magazine 88 (2008) 1478.
14. S. Magazú, F. Migliardo, A. Benedetto, Puzzle of protein dynamical transition, The Journal of Physical Chemistry B 115 (2011) 7736.
15. T. Becker, J.C. Smith, Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems, Physical Review E 67 (2003) 021904.
16. D. Vural, H. Glyde, Intrinsic mean-square displacements in proteins, Physical Review E 86 (2012) 011926.
17. R.M. Daniel, J.L. Finney, V. Réat, R. Dunn, M. Ferrand, J.C. Smith, Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution, Biophysical Journal 77 (1999) 2184.
18. S. Magazú, F. Migliardo, M.T. Caccamo, Innovativewavelet protocols in analyzing elastic incoherent neutron scattering, The Journal of Physical Chemistry B 116 (2012) 9417.
19. G. Schiró, F. Natali, A. Cupane, Physical origin of anharmonic dynamics in proteins: new insights from resolution-dependent neutron scattering on homomeric polypeptides, Physical Review Letters 109 (2012) 10215.
20. A.M. Gaspar, S. Busch, M.-S. Appavou, W. Haeussler, R. Georgii, Y. Su, W. Doster, Using polarization analysis to separate the coherent and incoherent scattering from protein samples, Biochimica et Biophysica Acta 1804 (2010) 76.
21. J.H. Roh, R.M. Briber, A. Damjanovic, D. Thirumalai, S.A. Woodson, A.P. Sokolov, Dynamics of tRNA at different levels of hydration, Biophysical Journal 96 (2009) 2755.
22. A. Stoeckli, A. Furrer, Ch. Schoenenberger, B.H. Meier, R.R. Ernst, I. Anderson, Dynamics of hydrogen bonds in carboxylic acids, Physica 136B (1986) 161.
23. P. Fenimore, H. Frauenfelder, B.H. McMahon, F.G. Parak, Slaving: solvent fluctuations dominate protein dynamics and functions, Proceedings of the National Academy of Sciences of the United States of America 99 (2003) 16047.
24. H.W. Weber, R. Kimmich, Anomalous segment diffusion in polymers and NMR relaxation spectroscopy, Macromolecules 26 (1993) 2597.
25. A. Arbe, J. Colmenero, Dynamics of glass-forming polymers: "homogeneous" versus "heterogeneous" scenario, Physical Review Letters 81 (1998) 590.
26. H. Frauenfelder, S.G. Sligar, P.G. Wolynes, The energy landscapes and motions of proteins, Science 254 (1991) 1598.
27. G. Schiró, V. Vetri, B. Frick, V. Militello, M. Leone, A. Cupane, Neutron scattering reveals enhanced protein dynamics in concanavalin A amyloid fibrils, Journal of Physical Chemistry Letters 3 (2012) 992-996.
28. G. Schiró, C. Caronna, F. Natali, M.M. Koza, A. Cupane, The "protein dynamical transition" does not require the protein polypeptide chain, Journal of Physical Chemistry Letters 2 (2011) 2275.
29. L. Liu, S.-H. Chen, A. Faraone, C.-W. Yen, C.-Y. Mou, Pressure dependence of fragile-to-strong transition and a possible second critical point in supercooled confined water, Physical Review Letters 95 (2005) 117802.
30. H. Stanley, P. Kumar, S. Han, M.G. Mazza, K. Stokely, S.V. Buldyrev, G. Franzese, F. Mallamace, L. Xu, Heterogeneities in confined water and protein hydration water, Journal of Physics: Condensed Matter 21 (2009) 504105.
31. M. Lagi, X. Chu, C. Kim, F. Mallamace, P. Baglioni, S.-H. Chen, The low-temperature dynamic crossover phenomenon in protein hydration water: simulations vs experiments, The Journal of Physical Chemistry B 112 (2008) 1571.
32. G. Schiró, A. Cupane, S. Pagnotta, F. Bruni, Dynamic properties of solvent confined in silica gels studied by broadband dielectric spectroscopy, Journal of Non-Crystalline Solids 353 (2007) 4546.