Bio-Neutron Scattering |
|
Neutron scattering is an open access technique, which is provided by large scale facilities such as the FRM 2 in Garching. Inelastic neutron scattering yields information on protein structural fluctuations and hydration water on a pico to nano-second time scale comparable to MD simulations. Most applications derive the properties of molecular motions from the narrow elastic scattering window. The figure shows the example of the protein elastic mean square displacements versus temperature of hydrated lysozyme (Doster, 1999 and Magazu et al. 2011) and xylanase in methanol/water (Daniel et al. 2002) observed at two instrumental resolutions. The "anharmonic enhancement" above 200 K is sometimes interpreted as the "protein dynamical transition" implying a softening of the elastic structural properties, or a water induced "visco-elastic cross-over" of protein flexibility. Magazu reports with the same instrument for the same sample deviating displacements, why? The xylanase peak is striking, and could be an artefact of the frozen solvent (below). To perform meaningful experiments requires, besides understanding the technique, a sound knowledge of condensed matter physics and biology, which is rare in this combination. Fragile interpretations, based on insufficient data are thus not uncommon. Since a scientific discussion hardly exists, errors tend to propagate. Critical comments are sometimes misinterpreted as personal attack: "Even if the opinions of the authors are correct regarding various neutron scattering studies and how data is treated, it is not necessary to attack persons (authors). For instance, such like Magazu´s and Chen´s such should be removed or rewritten.."(Comment of an unknown referee to Doster et al. JCP (2013)). Here I critically review selected publications with obvious (in my view) errors in historical order to trace the evolution of the field. The selection is made according to my expertise, that's why I often cite my own publications. Criticism should be taken literally but not personally. Errors are instructive, since science proceeds by disproving, not by proving (Karl Popper). |
|
Comments to: wdoster@bioneutron.de
posted Dec. 8 2017
2017: the Frauenfelder zero Q elastic scattering effect is due to multiple scattering
The role of momentum transfer during incoherent neutron scattering is explained by the energy landscape model
by H. Frauenfelder, R.D. Young, P.W. Fenimore PNAS vol 114, 5130(2017).
ref
Doster Comment
posted Dec. 2 2017
2014:The Protein Energy Landscape, a Case against Scattering Theory
Wave mechanical model of incoherent quasielastic in complex systems by Hans Frauenfelder, Paul Fenimore and Robert Young, PNAS , 111, 12764 (2014).
ref
Wuttke: No case against scattering theory, PNAS Letter
Doster Comment
posted Nov. 30 2017
2013: The Mössbauer Model of Quasi-elastic Neutron Scattering
Dynamics and Free Energy Landscape of Proteins, explored with the Mössbauer effect and quasi-elastic neutron scattering by Frauenfelder, Young and Fenimore, J.Phys.Chem.117 13301-
ref
Comment
posted Dec. 8 2017
2015: Dynamical Heterogeneity Models
Motional Displacement in Proteins, origin of wavevector-dependent values
by D. Vural, L. Hong, J. Smith, H. R. Glyde, Phys.Rev. E. 91 052705(2015). ref
Comment
2015: Spurious Pressure Effects on Protein Dynamics
Influence of Pressure and Crowding on the Subnanosecond Dynamics of Globular Proteins, by M. Erlkamp, J. Marion, N. Martinez, C. Czeslik, J. Peters and R. Winter J.Phys.Chem B 119 4842(2015). Comment
2014: The Freeze Drying Glass Transition in Dry Proteins
Does a dry protein undergo a glass transition by A. Frontzek, S. Strokov, ,J. Embs and S. Lushnikov J.Phys.Chem B 118(11) 2791-2802(2014). Comment
2012/3: Two step scenario of the protein dynamical transition
Change of caged dynamics of hydrated proteins by Capaccioli, Ngai, Ancherbak, Paciaroni, J. Chem.Phys. 138 (2013) 235102. Comment
Evidence of coexistence of change of caged dynamics.. by Capaccioli, Ngai, Paciaroni, J.Phys. Chem. B 116 (2012) 1745. Comment rejected by Editor of JPCB
2011: The RENS puzzle
Elastic incoherent neutron scattering operating by varying instrumental energy resolution: Principle, simulations, and experiments of the resolution elastic neutron scattering (RENS) S. Magazu, F. Migliardo, A. Benedetto Review of Scientific Instruments 82 (10), 105115 (2011)
nearly identical: Magazu, Migliardo, Benedetto, Vertessy in Chemical Physics 424(2013)26: Protein dynamics and neutron scattering.. Comment
Protein dynamical transition at 110 K, by C. Kim, M. Tate and S. Gruner PNAS 108, 20897 (2011) Comment
2011: The Frauenfelder Mössbauer effect and the PDT
Mössbauer effect in proteins, Young, Frauenfelder, Fenimore, PRL(2011)107, 158102 Comment
2008: Elliptical protein phase diagrams
Pressure and temperature dependent protein stability by Widersich, Skerra, Köhler, Friedrich, PNAS 105, 575 (2008) Comment
2006: Instrumental resolution effects interpreted as a fragile-strong crossover
Observation of fragile to strong dynamic cross-over of protein hydration water by S.H. Chen, L.Liu, E. Fratini, P. Bagliaoni, A. Faraone and E. Mamontov, PNAS USA 103, 9012 (2006) Comment
2004: Frauenfelders alpha/beta relaxation
Bulk solvent and hydration shell fluctuations by Fenimore, Frauenfelder, Mc Mahon, Young PNAS USA (2004)101,14408 Comment
2003: Neutron Hydrogen Displacement Distribution in Myoglobin
Hydrogen atoms in proteins, Engler, Ostermann, Nijmura, Parak, PNAS USA (2003)100,10243 Comment
2002: Slaving II
Solvent fluctuations dominate protein dynamics and function by Fenimore, Frauenfelder, Mc Mahon, Parak, PNAS USA (2002)99,16047 Comment
2002: Confined water and the two simple explanation
A model for water motion in crystals of lysozyme based on an incoherent quasi-elastic neutron scattering study by C.Bon, A.J. Dianoux, M. Ferrand and M.S. Lehmann, Biophys. J. 83( 2002) 1578 Comment
The protein dynamical transition may have a simple explanantion
by M. R. Daniel, J. Finney and J. Smith, Faraday Discussion (2002) 122,163 Comment
2000: Protein force constants from elastic displacements?
How soft is a protein? A protein dynamics force constant measured by neutron scattering by J. Zaccai, Science 288,1604( 2000) Comment
1998: Dynamic labelling of different functional parts of BR
by V. Reat, H. Patzelt, M. Ferrand, C. Pfister, D. Oesterhelt, G. Zaccai PNAS 95(1998)4970 Comment
1998: Activity below the transition?
Enzyme Activity below the Protein Dynamical Transition at 220K by R. Daniel, J.Smith, M. Ferrand, S. Hery, R. Dunn, J. Finney, Biophys. J. 75 (1998) 2504 Comment
1993: Melting of a frozen protein solution
Thermal motion and function of bacteriorhodopsin in purple membrane, effect of temperature and hydration observed by neutron scattering by M. Ferrand, A. Dianoux, W. Petry an G. Zaccai, PNAS 90, 9668 (1993)communicated by Hans Frauenfelder. Comment
1992: Confined water (I):
Single particle dynamics of hydration water in protein, M.C. Bellissent-Funel, J. Teixera, J.F. Bradley, S.H. Chen and L. Crespi, Physica B 181 &181, 740 (1992). Comment
1991: Review Article on MD Simulation and Experiments
Protein Dynamics: comparison of simulations with inelastic neutron scattering experiments, by J. Smith, Quat. Rev. Biophys.24 (1991), 227 Comment
1991: Frauenfelders Energy Landscape
The energy landscapes and motions in proteins, H. Frauenfelder, S. Sligar and P. Wolynes, Science 254 (1991) 1598 Comment
1990: Vacuum simulation of a hydrated protein
Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra, by J. Smith, K. Kuczera and M. Karplus, PNAS USA (1990)87, 1601. Comment
The temperature dependence of dynamics of hydrated myoglobin, comparison of force field calculations with neutron scattering data by R. Loncharich and B. Brooks, J. Mol. Biol. (1990)215, 439,
1989: first spectral analysis of protein dynamics:
Dynamical transition of myoglobin revealed by inelastic neutron scattering, W. Doster, W. Petry and S. Cusack, Nature 337,754(1989) Comment
Internal dynamics of globular proteins, comparison of neutron scattering measurements and theoretical models by J. Smith, K. Kuczera, B. Tidor, W. Doster, S.Cusack and M. Karplus, Physica B(1989) 156, 437. Comment
1982: Ligand Binding to Hexokinase
Inelastic neutron scattering analysis of hexokinase dynamics and its modification on binding of glucose by B. Jacrot, S. Cusack, A. Dianoux and D. Engelman, Nature 300 (1982)84
Comment
1980/1996: spurious oscillations of hydration water jump rate
Molecular dynamics of hydrated proteins, H. Middendorf, J. Randall and A. J. Leadbetter, Phil. Trans. R. Soc. Lond.B. (1980) 290, 639. and Middendorf, Phys. B. 226, 113 (1996) Comment