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Neutron scattering is an open access technique, which is provided by large scale
facilities such as the FRM 2 in Garching. FRM2 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 1998 and xylanase in methanol/water (Daniel et al. BJ 77,2184, 1999) 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, Zaccai or a water induced "visco-elastic cross-over" of protein flexibility Review JCP 2013. The xylanase peak is striking, likely an artefact of the frozen solvent, since incoherent displacements never decrease with increasing temperature. The open dots (IN13,lysozyme) illustrate unexplained discrepancies with Magazu et al. 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. I know few PNAS papers in this field, which are not seriously flawed. Recently Frauenfelder even questioned the validiy of basic scattering theory applied to proteins to save his energy landscape model. People, daring to correct their collegues, are turned down by embedded reviewers as being polemic. This attitude supresses any open scientific discussion with errors tending to propagate. I review selected publications with obvious (in my view) errors in historical order to trace the evolution of the field. My criticism should be taken literally, but not personally. Errors are instructive, since Science proceeds substantially by disproving and less by confirming. It is not the errors that strike me, it is their persistence. |
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2018: Are proteins dynamically heterogeneous? Neutron scattering analysis of hydrogen displacement distributions
peer reviewed research article by Wolfgang Doster, Int. Journ. Mol. and Math. Physics, Vol. 2 (1) 1-14 (2018).
review
Poster ECNS 2019
2018: Analysis of elastic incoherent neutron scattering data beyond the Gaussian approximation
by Zeller et al., J. Chem. Phys. 149, 234908 (2018)
referee comment, revised version by W. Doster
2018: Franck-Condon picture of incoherent neutron scattering
by G. Kneller, PNAS 115, 94509455 (2018), attempt to justify energy landscape models of proteins with quantum theoretical arguments.
Doster, PNAS Letter Apr. 2019,
G. Keller, Response to PNAS Letter Apr. 2019,
2017: 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).
Doster Comment: the Frauenfelder zero Q elastic scattering effect reflects multiple scattering
and not the energy landscape
2015: 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).
A more recent version was published by the same authors in Biophys. J. 114, 2397, 2018,
Determination of dynamical heterogeneity of proteins from dynamic neutron scattering
Comment Doster
2015: 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 Doster
2014: Wave mechanical model of incoherent quasielastic neutron scattering in complex systems
by Hans Frauenfelder, Paul Fenimore and Robert Young, PNAS , 111, 12764 (2014).
Wuttke: No case against scattering theory, PNAS Letter
Doster Comment
2014: 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
(The Freeze Drying Glass Transition in Dry Proteins)
2013: 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 (2013)
(The Mössbauer Model of Quasi-elastic Neutron Scattering) Comment Doster
2012/2013: Change of caged dynamics of hydrated proteins by Capaccioli, Ngai, Ancherbak, Paciaroni, J. Chem.Phys. 138 (2013) 235102. Comment Two step scenario of the protein dynamical transition
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
2013: 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, Comment
Evidence of coexistence of change of caged dynamics.. by Capaccioli, Ngai, Paciaroni, J.Phys. Chem. B 116 (2012) 1745. Comment
2011: The PDT puzzle and the Magazu copy and paste system
The puzzle of the protein dynamical transition by Magazu, Migliardo, Benedetti, J.Phys. Chem. B. 115, 7736(2011) Comment, 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
2008: 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 (2008) Comment, hydration water relaxation time
2004: Frauenfelders alpha/beta relaxation
Bulk solvent and hydration shell fluctuations by Fenimore, Frauenfelder, Mc Mahon, Young PNAS USA (2004)101,14408 Comment
2003: Hydrogen Distributions
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) PDF 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: spurious oscillations of hydration water
Molecular dynamics of hydrated proteins, H. Middendorf, J. Randall and A. J. Leadbetter, Phil. Trans. R. Soc. Lond.B. (1980) 290, 639. Comment