FRM2-Munich CriticalReview DosterHome Personal


Physical background of protein dynamics and neutron scattering



by Wolfgang Doster
a unique Website devoted to graduate students, postdocs and all enthusiasts of Neutron Spectroscopy.
The post-Sankt Petersburg ECNS 2019 edition

Scope:
The peer-review of a scientific manuscript is not open. It occurs behind closed doors. The referees and Editors of scientific journals thus decide in a highly intransparent procedure, whether a manuscript is interesting enough and suitable for publication or not. The arguments remain secret. Their judgement is often biased by special interests, in particular off-main stream papers tend to be suppressed. The referee system is easily corrupted to reduce critical discussions and to exclude competitors. A recent submission to JCP was rejected, because we did not remove a critical discussion of related literature as requested. Once a paper has been published, even if it is obviously wrong, it is considered as established truth, writing critical comments is tedious and time consuming. One of my comments, concerning a basic mathematical error, was processed three times against the vote of the authors by JCP, before it was published. JCP does not publish letters anymore. The alternative would be a system of open reviews, practiced partially by PNAS, making it easier to get published, but at the same time, Comments would be facilitated to initiate a scientific discussion.

Motivation
The motivation of this Website is to document the unusually large number of scientifically questionable papers in bio-neutron scattering, published in high ranking journals like PNAS, PRL, BJ. Here I illustrate the idea of open critical reviews with published papers, where the referee system has obviouly failed. As the victim of a citation blockade, I found it increasingly difficult, to publish alternative and critical views in main stream journals.
Neutron scattering is an open access technique, which is provided by large scale facilities such as the FRM 2 in Garching FRM2. Biological inelastic neutron scattering can yield information on hydrogen based protein structural fluctuations and hydration water on a pico to nano-second time scale, comparable to the range covered by MD simulations.
Open access means that people with interesting ideas can get beam time, without demonstrating, that their knowledge of the technique is sufficient to perform such experiments. This aspect may account in part for the above mentioned deficiencies.

Background:

The field was initiated in 1989 by the "Nature Milestone" paper of Doster et al., "Dynamical transition of myoglobin revealed by inelastic neutron scattering". It was my second NS paper out of 100, the first one was with Martin Karplus. It showed for the first time wide temperature and frequency range spectra of a hydrated protein, combining data derived with two spectrometers IN6 and IN13 at the ILL in Grenoble. A small fraction of this paper was devoted to the Q and temperature dependence of elastic scattering, displaying two "dynamical transitions" near 160 and 240 K. At the transition temperature the relaxation times of protein motions overlap with the respective instrumental observation time.
During the next 30 years only the elastic section was picked up in 90 % of the citations, the equally important inelastic component was largely ignored.
G. Zaccai had the "ingenious" idea to reduce biodynamic neutron scattering to elastic scans. This approach can be justified for particular applications, specially if the biological material is available only in minor quantities ERS2003. From elastic scans a very useful molecular quantity, the "mean square displacement" can be deduced by fitting the data at low Q to straight lines.
This simple method convinced many biologists, experienced in static low angle scattering, to consider dynamic aspects. The possibility to deduce "biological dynamics" from elastic scattering experiments, boosted the field with a flood of publications. Not all of them were of high quality.
To cite a paper without reading it completely can be dangerous. For the "dynamical transition" the spectral analysis demonstrated that the nonlinear onset in the displacements at 240 K was resolution controlled. Thus with their "elastic only analysis", a wide range of questionable interpretations was possible..

Ignored problems:

(1) Most important, the elastic scans had to cover a wide temperature range, far below room temperature to spot the "dynamical transitions". To avoid ice formation, this required "hydrated" instead of solvated samples. The properties of solvents at low temperatures can lead to strange effects of demixing, ice formation and glass transitions, explaining some questionable interpretations. It was shown, that the "dynamical transition" can be recorded at room temperature by the new technique of "elastic resolution spectroscopy" with IN5 data, Doster et al. 2001. Thus also the low temperature transition at 160 K is resolution controlled and was assigned for the first time to methyl rotation.
(2) The restriction to the tiny elastic part of the spectrum near zero frequency, ignoring the rest of the energy window, reflects essentially the immobile, structurally static property of the biomolecule. Dynamics enters only via a diminishing elastic intensity with increasing temperature.

(3) Another problematic restriction is the focus on the narrow Q-range near zero momentum exchange, to derive mean square displacements, assuming the "Gaussian approximation".
Several workers did not fully understand the limitations of their method, its dependence on instrumental resolution and multiple scattering: The zero Q-extrapolated intensity decreases with increasing temperature. The "factor of two problem" with the Gaussian Lamb-Mössbauer factor lead to a confusion about the correct magnitude of mean square displacements Doster, EBJ 2008.

The "elastic intensity" approach recieved its final approvement, when the prestigious "Walter Hälg" prize was devoted to G. Zaccai in 2013. His publications provide very instructive examples of long lasting errors and sensational results. In his Science 2000 paper he interpreted the protein dynamical transition as resilence softening of the protein force constants. 13 years later at the "Les Houches School" , he presented the identical concept, although is was disproven by us in 1989 and many times later. G. Zaccai, Les Houches 2013 . It was the main topic of the laudatio for the prize given by J. Smith. The latter has published since 1990 a huge number of MD-papers, advertising "dynamic heterogeneity", including the "dynamical transition in a dry protein" Liu et al., PRL 2017 .

Biomolecular neutron scattering recieved a serious blow, when the nuclear physicist Hans Frauenfelder took control of the field beyond 2008, resulting in a dramatic decline of scientific quality. Now, energy landscapes and motional heterogeneity became main stream to explain bioneutron scattering. The complexity of dynamics, controlled by energy landscapes, naturally required the assistance of computer simulation. Elastic neutron scattering experiments are only needed to confirm the time resolved MD simulations. In his most recent papers (PNAS 2015/ 2017, discussed below) Frauenfelder suggests a complete re-interpretation of quasi-elastic neutron scattering theory in terms of inhomogeneous spectral broadening. Elastic scattering is dismissed. The hopping across an energy landscape is defined as the basic physical process in proteins. Spatial displacements, defining the Van Hove space-time correlation function, are replaced by diffusion in energy space. Frauenfelder, PNAS 2014.


The molecular view:

Our approach of discussing protein motions in terms of few well defined molecular components, standard in other fields (NMR), was misquoted by the heterogeneity group as a two-state model. Already in 1989 we started with two dynamic components, rotational transitions and water-coupled translational motions. Our new RT model describes wide range data successfully in the time domain without the need of low temperatures. The "protein dynamical transition" is no longer present in this model, since the data were corrected for the instrumental resolution.
It is revealing, that the respective manuscript, submitted to J. Chem. Phys. in 2018, with the provocative title, "Protein dynamics without energy landscape" was rejected, although the referees could not justify their verdict with decent scientific arguments. One referee, who sounded a lot like Hans Frauenfelder, was completely opposed to the landscape-free model: "not new", "self-citations". The second referee with MD background supported the publication, but requested to remove all critical comments to related work. This was rejected by us, since the purpose of this manuscript was to present an alternative view to dynamic heterogeneity. The Editors refused to involve a third referee, familiar with experimental neutron scattering. At the ECNS 2019 in St. Petersburg, our submitted oral contribution, a compact version of the JCP manuscript, was downgraded to the level of a Poster. By contrast, the "elastic only scattering group" recieved several invited talks from the organizers. One negative highlight was the dubious "water-protein decoupling" hypothesis of A. Benedetto, based on Q-averaged elastic scattering data (Phys. Chem. Lett. 2017). But the most scandalous talk was presented by Kearley and Benedetto on "Elastic Scattering Spectroscopy", which is a downgraded copy of what we had initially published in 2001 under the close, more appropriate name "Elastic Resolution Spectroscopy" (Doster et al. Physica B, 2001). According to their paper, elastic scattering experiments at different resolution are sufficient, after some numerical treatment, to determine the exact intermediate scattering function. This was shown to be incorrect (Doster et al. JCP, 2013). The citation blockade thus still exists, illustrating, why this Web Site is necessary.
Our new pedagogical version of how elastic and inelastic scattering with proteins can be combined, including a discussion of protein function, was published in Doster, 2018. "Are proteins dynamically heterogeneous?".


The role of errors and critical Comments to selected literature:

Said a big shot in this field to a young professor, the names are known,"in your last paper you said, I was wrong", "weren't you wrong?" "Yes, but you don't say it." This Web site is going to "say it". Hans Frauenfelder said to his postdoc: "Possibly I am wrong, but it will take them a long time to find out". Errors, according to Enrico Fermi, are quite common in Science. What matters is, how fast you find out. The philosoper Karl Popper proved, that Science proceeds essentially via disprove of errors and less by confirming results.
It is not the errors that strike me, it is their persistence and the political forces to prevent their correction.
To illustrate my point, I present below critical comments to selected publications, which contain "common" scientific errors or suggest conclusions, which are not properly justified. I emphasize, that this Web site reflects my personal view, which could be wrong, unjust or incomplete.
Of course, a lot of high quality work has been published in this field: The Berlin group around Jörg Fitter and the late Rueb Lechner combined successfully elastic and inelastic experiments to study bacteriorhodopsin, still valid today.
Another landmark paper, covering the transition from powder to solution was published by J Pérez, JM Zanotti, D Durand, Biophysical journal 77 (1), 454-469. Longeville and Stingaciu (2017) determine the role of hemoglobin diffusion inside blood cells to facilitate oxygen exchange in the lung with NSE (Sci. Rep. 7: 10448). The Munich-Jülich NSE group studies the polymer properties of partially folded proteins in the time domain, which has yielded interesting results.
Some rarely cited Doster papers: Lit.
Comments to: wdoster@bioneutron.de



by Wolfgang Doster, last changes: Nov. 10th, 2020