Did “Nobelitis” over-inflate the capabilities of X-ray crystallography as Best Practice?

The reason I summarised Georgina Ferry's biography of Max Perutz in my post of 17 Nov 2021 is that Max Perutz was the main driver in the establishment of x-ray crystallography as Best Practice in all aspects of protein structure. I would say he went too far. Max became an effective promoter of his views about the capabilities of the method. He himself confessed, according to the biography, that winning a Nobel Prize changed his approach. It seems he developed a case of “Nobelitis” that also infected those around him and persists to this day. Because of it's long duration, it may be the most costly case of “Nobelitis” there has ever been. Max was never a scientist of the philosophical kind. He assiduously collected data and, especially after winning a Nobel, would form a view about what it meant and vigorously promote that view. His organisation, the Laboratory for Molecular Biology (LMB), never published any of their own work to validate the method. Under Max's leadership the priority was promotion, not scientific validation. Quite likely some of his more scientifically-minded staff did try experimental validation but, from what we now know, they would have failed. Whatever the case, nothing was ever published. In 1976 Max was under considerable pressure to justify his views, his laboratory having recently been subjected to a Government enquiry in 1974 (the Phillips report) because of the cost and lack of useful results of his work. In 1976 Max made a contribution to a paper by Asakura et al. about a hemoglobin mutant (JMB 104 185-195) in which he claimed that agreement between NMR signal assignments and the crystal structure was evidence that the crystal structure was the same as the solution structure of hemoglobin. This claim ignored the fact that the NMR assignments were derived from the crystal structure. At the same time Max's assistant, Alan Fersht, wrote a textbook entitled “Enzyme Structure and Mechanism” (1977) drawing on the resources of the LMB, in which he addressed the question “Are the crystal and solution structures of an enzyme identical?” on page 15. The discussion can be criticised for dealing with the question as a false dichotomy, for arguing from the particular to the general, and not least for the fact that none of the cited evidence concerning quaternary structure bears scrutiny. With current search engines it is easy to check the claims – perhaps it was not so easy then. Later editions of the book were published in 1985 and 1999 with little change in this section. Statistically, it would take hundreds of well documented examples to reach the sought-after general conclusion. Fersht rightly points out the difficulty of doing the experiments. Nowadays it is widely conceded that crystallised proteins lose most or all of their biological function. There are no known examples of quantitative retention of biological activity. The reason given is that proteins need to breathe. That is, it is claimed the crystal structure is correct but the protein needs some more freedom to move in a way that is beyond knowing. This is a social construct to reconcile current Best Practice with the absence of supporting evidence. Hopefully it is abandoned soon.

About Best Practice in Protein Science

X-ray crystallography has been the Best Practice method for determining all aspects of protein structure for nearly 60 years. This includes quaternary structure and binding to ligands. All the work described in this blog is therefore not Best Practice. We need to think about how Best Practice came about and whether Best Practice should change. Best Practice is socially constructed and enforced. As far as possible, the community of scientists defining Best Practice use scientific evidence. In a complex field, such as Medicine, where we teach and learn from Authority, it is common for Best Practice to lack scientific evidence. In Medicine, the Cochrane Collaboration has a mission to examine Best Practice and, where evidence is lacking, seek to have it changed to be more evidence-based. Protein Science has also been a seemingly complex field and has largely developed as a branch of Medical Research. There is no "Cochrane Collaboration" to review the evidence base. It is up to us individual scientists to do so. More posts on this theme to follow.

Revised Summary of Perutz Biography

I first posted the summary a year ago and then took it down a few months ago thinking it might alienate readers who had known and followed Max Perutz. This version is a little more sympathetic to Max, emphasizing the influence of the extraordinary circumstances in which he found himself. Nevertheless, in dispelling some of the mythology I am bound to cause offence, for which I apologise. Read the summary here.

Hemoglobin: NMR evidence for transition between T state and i conformation.

Fan et al (2013) measured changes in chemical shifts (if any) of most amino acids in carbonmonoxyhemoglobin with and without the polyanionic effector, inositol hexaphosphate. See their Figure 2. As expected, amino acids at or near the accepted polyanion binding site between beta chains experienced shift changes greater than average. However there were many amino acids elsewhere that also experienced above average changes of chemical shift. About 6 of these were internal and in contact with heme or proximal or distal histidines of alpha and beta chains. This indicates a change in the immediate electronic environment. Perhaps the effector caused CO to dissociate from Hb, or almost so. Of the other changes, most can be explained by a transition between the t and i conformations shown in the Nativeproteins Gallery . This transition involves change of neighbouring subunit from alpha chain to beta chain across the extensive Chain A - Chain B interface and the smaller Chain A - Chain C interface. There is no change across the Chain A - Chain D interface. The NMR reflects this. Alpha 38, 39, 41, 86, 93, 94, 95, 96, 97, and 137 experienced above average NMR changes and make up most of the A - B interface. Similarly, beta 41, 96, 98, 99, 101, 142, and 146 experienced above average changes and make up most of the A - B interface. Alpha 100 and beta 34 and 43 also experienced above average NMR changes and are at the A -C interface. There were no above average NMR changes at the A - D interface. As a consequence I have renamed the t2 conformation the i conformation, reflecting the fact that it is possibly an intermediate state between r conformation and t conformation and not just a hypothetical structure. Possibly the i conformation is the true R state, pending further investigation.

Summary of Perutz biography by Georgina Ferry

I have now finished tracing the origins of false beliefs about protein crystallization. It seems that J. D. Bernal and the young Max Perutz in 1946 decided to create the impression that proteins in crystals did not contact each other or exert forces on each other. They needed to do this in order to win support for Perutz and his project. At the time the prevailing expert opinion was that globular proteins were very soft, perhaps even partially liquid. Protein chemists were well aware that most globular proteins in solution were readily denatured by very minor changes in the chemical or physical environment and would have argued that crystallization was bound to affect structure. This decision to discount expert opinion created a silo in which protein x-ray crystallography could survive and eventually flourish but at the expense of consistency with the rest of physics. The biography of Max Perutz by Georgina Ferry (2007) contains enough detail about the personality, circumstances, talents and limitations of Perutz to enable understanding of subsequent events. Click here to view summary notes from the book.

Native Protein Data Bank and Gallery of Protein Structure Animations

The Gallery of 3D Native Protein Structures has been renamed "Native Protein Data Bank and Gallery of Protein Structure Animations" because it includes the facility to download full structural coordinates of native proteins and because it is expected the collection will grow. The reliability of most of these structures is now known to be very high. For barrel structures, the practice of pointing the barrels towards the origin and docking them symmetrically can be shown to produce structures with very high statistical correlation with other features and functions. For the viral neuraminadases, the appropriate locations of glycosylation sites, each with a probability of appropriate location by chance of about 2 in 3, taken together amount to a probability by chance of less than 1 in a thousand. For the hemoglobins of mammals, crocodiles, rays and sharks, the appropriate locations of allosteric binding sites and a variation in structure coordinated between alpha and beta chains, the combined probability of happening by chance is again about 1 in a thousand. Both these groups of protein structures were achieved by the same pointing and docking procedure and so we can say that the probability of this procedure producing meaningful structures by chance is about 1 in a million. As successful examples accumulate, while unsuccessful examples are rare, it seems that the statistical significance will continue to rise. Users of the Gallery part of the site will now find it easier to use as I have obtained a Symantec/Verisign Code Signing certificate. This allows Java to run the Jmol molecular viewer with only one request for permission from the user.

Gallery of 3D Native Protein Structures has been repaired

The Gallery of 3D Native Protein Structures has been repaired so that users can operate the script box, buttons and checkboxes. There are still security warnings generated by Java (the underlying system) but this is the best that can be done without a complete reconstruction.

Technical difficulty with the Gallery

The animations of protein structures in the Gallery may no longer work as they should. This is because the Jmol applet requires Java to run and the latest version of Java treats the Jmol applet as a security risk. I will update the Jmol software as soon as possible. In the meantime, Java will display security warnings to users and, even if you accept the nativeproteins site as a trusted site, many of the animation options will not function. The opening page of the Gallery provides links to the raw structure data in pdb format and it is suggested that readers download files of interest and use their own structure viewer. I apologise for this interruption. Fixing the problem is not straightforward. An update will fix the (false) security issue and will make the animations accessible on tablets and phones as well as computers, but might make them inaccessible to older computers and browsers.

Lack of Evidence to Support the Belief that Crystal Quaternary Structures are the same as Solution Quaternary Structures. Part 1: The Current State of Knowledge

In the introduction to this blog I said that "The fundamental starting point of this discussion is that the arrangements seen in protein crystals are not necessarily the native arrangements." Since then I have not found any examples where the crystal quaternary structure even resembles the native functional structure, although parts of the native protein-protein interfaces usually also participate in crystal contacts between proteins. Therefore I have tried to find the source of the belief that crystal quaternary structures reflect solution structures. This exploration brings with it mixed emotions. On the one hand comes the satisfaction of understanding the underlying truths. On the other hand there is some embarrassment at the human capacity to get it wrong. Over the coming weeks I will write further posts dealing with the historical roots of the belief, the use of NMR and SAXS to support crystal quaternary structures, the nature of forces within protein crystals and possibly other matters that emerge in the process. This is not a full review. In the future, scientific historians will no doubt provide a fuller picture of how a much-hoped-for result of 50 years ago was transformed into dogma. Click here to begin the exploration.

Bird Flu Neuraminidase type N9 native structure

Currently a new strain of avian influenza is causing concern for human health. This H7N9 strain has a coat containing N9 neuraminidase. It is timely to place the native structure of this enzyme in the Gallery (click here for link). While adding N9 neuraminidase to the Gallery, I noticed that the N2 neuraminidase listed there was not displaying. I have corrected that error and now all three neuraminidases on display can be compared. Note that the details of the native structures of these neuraminidases and 8 others were published on this blog in the post of April 14 2007. Careful inspection of the native structures of N9 and N2 neuraminidases shows that the differences are minute although the amino acid sequences differ significantly. This reflects the fact that both proteins perform the same tasks in almost identical environments. In contrast, the crystal structures clearly differ in subunit orientation. It is an emerging fact that crystal quaternary structures are much more diverse than native quaternary structures, presumably because crystal quaternary structures are artefacts of the interaction of surface charges with water in the crystal phase. The relationship between native structure and function, together with the phenomena determining crystal structures were discussed on this blog in the two posts of December 9 2011.

Immunoglobulin Structure and Function in a nutshell

The two principal structures of immunoglobulins are now available in the Gallery. The trans form is the stable form in the absence of antigen, while the cis form is stable in the presence of antigen and complement. The two forms are quaternary isomers, differing almost only in the arrangement of subunits. It is now possible to give names to the various domains that suggest their shapes and functions. The word "elbow" is already used to describe the short flexible linking sequences between domains and the word "bridge" is already used to describe the longer flexible sequence in the middle of the heavy chain. These names can be retained. The light chain has two domains separated by an elbow of residues 104-109. Residues 1-103, previously named N_L, can now be named "antigen jaw_L", while residues 110-214, previously named C_L can be named "left-hand_L". The heavy chain domains can be similarly renamed (old names in parentheses): 1-111 "antigen jaw_H" (N_H); 114-230 "left-hand_H" (C_H1); 232-243 "bridge" or now possibly "latch"; 244-357 "right-hand" (C_H2); and 365-478 "complement jaw" (C_H3). Elbows are 112-113 and 358-364. The orientational relationship between a jaw and a left-hand is similar to that seen in the L chain of IgG2 (1YEF.pdb). Left hands clasp each other to form the antigen-binding complex, with the Complementarity Determining Regions on the inner surfaces of the jaws. Right-hands clasp right-hands to form the complement-binding complex. The switch between isomers involves four disulfide bridges exchanging partners, first the disulfides linking “left-hands” and then the disulfides in the “bridge”. This last exchange of disulfide partners may serve to lock the complement-binding domains into their binding conformation – hence the “bridge” may be better described as a “latch”. More work required!

Conventions for naming files

The structure files of native proteins draw most of their information from Protein Data Bank files and are expressed in the same format. Therefore it is appropriate to name the native protein files by adding short prefixes or suffixes to the names of the original crystal structures supplied by the Protein Data Bank. I have chosen to use the prefix "n" to indicate a native structure, together with a numeral. "n1_" indicates a first approximation to the native structure using subunit rearrangement only. "n2_" indicates a second approximation achieved by restoring the conformation of a small number of residues, usually less than 10% of the total sequence. "n3_" would be used for a full relaxation of the crystal structure into a native structure using a force field. For α₂β₂ heterotetramers, e.g. hemoglobin, there are 3 possible quaternary isomers and I have chosen to use suffixes to indicate which isomer the file describes. Where there are existing abbreviations for the isomers it is best to retain them. For hemoglobin, I use the suffix "_r" for the R state, "_t" for the principal T state and "_t2" for the alternate T state that might be significant in the absence of polyanions. In the case of elongated proteins in α₂β₂ heterotetramers, such as the heavy chain of immunoglobulin, one isomer can be described as "cis" and the other two as "trans". A pair of immunogobulin structures will be placed in the Gallery shortly, the cis form with the suffix "_cis" and the principal trans form with the suffix "_tr".

Improved site for Structure Gallery

The Gallery of 3D Structures has now been made a free-standing site with all its software on the Nativeproteins server. This has fixed some failings in the control buttons and check-boxes of the Jmol interface. This new version of Jmol has been chosen so that it is prevented from writing to your computer - it will not be seen by your browser as a potential threat, but, on the other hand, it cannot write a jpg file to save an image. For those who prefer to use their own structure viewer, the files of atomic coordinates are also provided for download. I have established some conventions for constructing and naming the files of reassembled atomic coordinates. These will be detailed in a future post.

Gallery restored with updated Jmol

The Gallery of 3D Native Protein Structures has now been restored. The files use the updated version of Jmol supplied by the RCSB Protein Data Bank. Please advise me if any functionality is missing by email to dvanselow@hotmail.com

Gallery temporarily out-of-order

Apologies for the temporary loss of function in the Gallery of 3D Native Protein Structures linked to this blog. The Gallery depends on the software used by the RCSB Protein Data Bank. As they have updated their software, the html files in the Gallery now need to be updated.

A naturally occurring cross-linked TIM validates these Native Structures

Triose phosphate isomerase (TIM) from the hyperthermophilic bacterium Thermotoga maritima crystallizes as a tetramer that appears to be a pair of dimers similar to those observed in crystals of other TIMs (Maes et al. 1999). The two dimers are joined by disulphide bonds between pairs of Cys142. As noticed by Gayathri et al.(2007) this linkage is not consistent with the dimer seen in crystals being the same as the dimer in solution and Gayathri et al. conclude that the "tetramerization appears to be a crystallization artifact."
However, when the TIM monomers are docked by the methods described in this blog, the pairs of Cys142 are naturally in close proximity. The native structure of TIM from T. maritima is now included in the Gallery. It can be seen that the disulfide bond is indeed a natural part of the quaternary structure and the form of dimer seen in crystals is the actual artifact.

Mirror site for scientists in China

It has come to my notice that our colleagues in China cannot access this blog but can access the Structure Gallery. Therefore I will maintain a copy of this blog and the companion Enzyme Function blog on the server used by the Gallery. Please direct any colleagues who cannot access Blogspot to
www.nativeproteins.com/blog/

Symmetry, Pseudo-symmetry and Evolution in Protein Structures

This poster was displayed at BioPhysChem 2011 at the University of Wollongong 3-6 December 2011. Reasoning from the effect of Natural Selection on symmetry, it shows examples of the arrangement of subunits in a complex and the alignment of "barrel" structures pointing towards the centre of the complex. Click on the title of this post or here to view the poster.

Effect of Crystallization on Protein Quaternary Structure

This talk was given at BioPhysChem2011 (3-6 December at the University of Wollongong) on 6 December 2011. It deals quantitatively with the expected changes to protein structure when the protein-in-water phase is changed to a water-in-protein phase during crystallization. For the first time there is a chemical explanation of why crystal structures differ from native structures as detailed throughout this blog. Click on the title of this post or here to view the slides, including animation.

Galactose oxidase now in the Gallery

The reassembled structure of galactose oxidase has been placed in the Gallery. My earlier work on this enzyme was posted, below, on September 30, 2007. I remarked then that the docking could be improved and I have done so in preparing the structure for the Gallery. The improved structure brings the copper centres of adjacent subunits closer together and the surrounding aromatic groups into closer contact. To achieve this I have accepted that the amino-acid chain 148-153 has been displaced by crystallization. This chain links the N-terminal auxilliary domain to the catalytic domain. It is quite likely that the N-terminal domain is also slightly out of place but it does not clash significantly with other subunits. The clash of 148-153 with the symmetry-related subunit can be seen in the reassembled structure but it is an artefact of crystallization.
Galactose oxidase shares many features with other proteins in the Gallery. Like hemocyanin it has pairs of copper-histidine centres but unlike hemocyanin, the partners in each pair are in different subunits. Like hemoglobin, the metal centres are electronically linked by an extended π-electron network. Like neuraminidases, the structural motif that focusses compressive force is a "propeller" of β-sheets. Also like some neuraminidases, galactose oxidase has auxilliary domains. These may have a role in interactions with the oligo- or poly-saccharides that are the natural substrates for both enzymes.
In coming days I will modify the preprint, linked through the 30 September 2007 post, to reflect the improved structure.

Hemocyanin structure

I was curious to see whether there were any obvious similarities in the subunit interactions of hemocyanin and hemoglobin. I downloaded 1NOL.pdb of Hazes et al. (1993). They reported it as a homohexamer and so I tried to dock the structure as a compact hexamer. In the crystal the hexamer has a large central cavity, which is unsatisfactory on physical grounds (see the first post of this Blog). Docking of a hexamer was unsatisfactory but a tetramer docked very well.
I have added the tetramer to the Gallery. The implication is that the tetramer has a physiological role.
Like hemoglobin, hemocyanin has an extensive aromatic network linked to the oxygen binding sites. Unlike hemoglobin the network does not appear to link oxygen binding sites on adjacent subunits. It is also unclear how the reported reverse Bohr effect could work.

Hemoglobin of the goose.

I have placed the R state and T state of hemoglobin from the Bar-Headed Goose, Anser indicus, in the Gallery. Inositol hexaphosphate is the polyanionic effector of avian hemoglobins and I have included a molecule of inositol hexaphosphate in the polyanion binding site of the T state. The positive charges of the polyanion binding site can be visualised by following the instructions in the Gallery. It can be seen that there are more positive charges than in human hemoglobin. The number of positive charges able to interact with the inositol hexaphosphate is more than appears at first sight, because allowance must be made for the flexibility of lysine side-chains. The larger number of positive charges accords with the fact that the avian effector has more negative charges than does diphosphoglycerate, the effector in human hemoglobin.

The Gallery can be accessed by clicking on the Title of this Post.

Quaternary Isomers of Hemoglobin

Perhaps a suitable term for the T state and R state conformations of hemoglobin would be "Quaternary Isomers". I have previously described them as interchangeable by subunit exchange. Subunit exchange is geometrically equivalent to concerted rotation of each subunit about its radial axis by 120º and perhaps this would be the preferred pathway of isomerisation in nature. For an α₂β₂ tetrahedron there are 3 different quaternary isomers. For vertebrate hemoglobins, a clockwise rotation of each subunit of the R state by 120º produces the T state with a polyanion binding site. An anticlockwise rotation of each R state subunit by 120º produces an alternate T state without an intact polyanion binding site. The alternate T state probably has a minor role physiologically. In the presence of the appropriate polyanion effector the isomerisation equilibrium would shift towards the main T state.
I have placed all 3 isomers in the Gallery.

Hemoglobin poster added to F1000 poster collection

The 2008 "Haemoglobin Revisited" poster presented at WATOC 08 has been accepted into the Faculty of 1000 Poster Collection and can be accessed by clicking on the heading of this post. It is slightly modified from the original by inclusion of the instructions for generating the structures and by crossing out the claim that the crystal structure cannot account for the inability to form crosslinks between the N-terminals of the beta chains. The crystal structure can account for this phenomenon if it is also assumed that the N-terminals are not very mobile. On the other hand, the native structure of the T-state proposed in the poster (click on the Gallery link) can account for the crosslinking properties only if the lysine side chains are considered mobile.
In summary, the crosslinking study cannot distinguish between these opposing views of protein structure.

Dihydrodipicolinate Synthase (DHDPS)

The structure of this enzyme from Bacillus anthracis is now available in the Gallery. It is the first alpha/beta barrel native quaternary structure to be reassembled. Using this structure as a template should help in the reassembly of other alpha/beta barrel structures. There is a ragged edge on the z-axis of this structure that corresponds to an area of inter-subunit contact in the crystal. Probably this is an example of damage to the tertiary structure caused by crystallization.

Dihydrofolate reductase Type 1 tetramer

In the course of discussions about Enzyme Function arising from the companion blog, I became aware that DHFR Type 1 is described as a monomer. It is divided into two sub-domains. As this is inconsistent with the physics of catalysis (see the first post of this blog), I explored possible dimeric and tetrameric complexes of this enzyme. The tetramer docks very well. The tetrameric structure is now included in the gallery. Click on the title of this post to study the 3D structure.
I checked the sources of reports that DHFR Type 1 is a monomer and found that the direct evidence came from experiments in the absence of cofactor. I am now planning to repeat the MW determination in the presence of cofactor.

Gallery of 3D Protein Structures

I have begun a gallery of 3D structures of the proteins mentioned on this blog. The structures are rendered by the powerful Jmol applet using the same graphic interface used by the Protein Data Bank. Jmol can display spacefill, backbone or cartoon representations. Jmol can calculate and display surfaces and cavities. It can rotate the structure in any way requested by the user and responds to scripts similar to those of RASMOL and other protein display programs. Click here to enter the gallery.

Companion Blog on Enzyme Function

Today I created a companion blog to this one, dealing with the emerging non-structural evidence in support of the role of constraint in enzyme catalysis. The blog is called "Enzyme Function" and can be viewed by clicking here. The evidence is from measurements of the kinetic isotope effects in enzymic hydride transfer reactions and subsequent attempts to simulate those effects by quantum mechanics. It is found that the effects can be simulated if atoms are brought significantly closer together than their van der Waals radii would allow. In other words the observed kinetic isotope effects imply that the active site is compressed at the time of catalysis. It is the need for compression at the time of catalysis that created the need to look for rigid protein structures as described in the current blog.

Citations of the Biophysics paper that started this blog

So far there are three laboratories that cite this work. Most active is the group of Atsushi Imai in Tokyo. They cite this work as a reason for research into the mechanical properties of single protein molecules. Their citing papers have been published in 2009, 2008, 2007, 2005a, 2005b, 2004a, and 2004b.
Another group is the Yeates group at UCLA. Their 2006 paper on knots in protein folds cited my work as justifying interest in sites of protein rigidity.
A third group (Tsekova and Sakov in Sofia, Bulgaria) published work on protein adsorption in 2005 and cited my work as justifying the study of protein-protein interactions.

Immunoglobulin structure

Last year I said that a full paper detailing all the haemoglobin work would be the next project for this blog. As it happens I realised a few months ago that IgG (an immunoglobulin) is like haemoglobin in being an α₂β₂ tetramer and so I explored tetrahedral rearrangements of the published crystal structure. This project has been very successful. I will present the IgG results on this blog before I complete the larger haemoglobin document.

Rotation-translation operators.

I have changed the form of the rotation and translation operations used to present the results of my earlier studies on neuraminidases, galactose oxidase and haemoglobin. The Convention used by the International Union of Crystallographers is that the rotation should precede the translation. I have now amended the papers linked to this blog to conform with that Convention. Previously I specified the translation before the rotation. The one paper I have not yet amended is the older pdf version of the neuraminidase paper.

I just noticed tonight that some of the punctuation and special characters in my linked htm files were not shown by Internet Explorer. Sorry about that. I have fixed the problems and added a few links back to this page to aid navigation. I'm still thinking about a novel approach to writing up the haemoglobin work. I think I have a good idea. I've also noticed that the original Biophysical Journal paper (see the bottom of this blog) is getting more citations as the years pass.

The WATOC Poster released.

Click on the text to download the poster "Haemoglobin Revisited" and instructions for generating the 3-dimensional coordinates of the structures shown in the poster.
WATOC (World Association of Theoretical and Computational Chemists) was a meeting characterised by very diverse interests.
In relation to the contentious issue raised by this blog, namely, whether a molecular structure in a crystal accurately reflects the structure in solution, the speakers expressed opinions on both sides. Those presenting work with biomolecules implicity believed that the crystal structures reflected solution structures. Those working with organo-metallic complexes, for which contradictory evidence existed, were quick to state that crystal structures could differ from solution structures. Among other participants I found a reasonable willingness to accept that crystal structures could differ from solution structures.
In relation to the "Haemoglobin Revisited" poster, one scientist was concerned that the proposed R-state differed from the T-state by too great a translocation of subunits. A number encouraged me to develop my work further and I am very grateful for their support. Perhaps reflecting the interests of participants, there was a suggestion that the proposed structures be subjected to molecular dynamics simulation to improve the docking and demonstrate stability. I agree that the docking could be improved. I am not sure that the Force Fields for Molecular Dynamics are accurate enough to simulate the weak energy of association of the haemoglobin tetramer. However, if the simulation does suggest that the proposed structures are stable, that will certainly help in the presentation of the structures.

WATOC 2008 Poster

"HAEMOGLOBIN REVISITED", poster to be shown at WATOC2008, Sydney 14-19 August
A theoretical study of catalysis by soft materials, such as protein, has shown the relationship between the degree of catalysis and local transient rigidity [1]. Since the intrinsic rigidity of protein is quite low, a theoretical source of local rigidity has been found in the effects of surface tension on multi-subunit proteins [1]. This concept has already been used to generate new quaternary structures for the neuraminidases and galactose oxidase [2]. It was assumed that crystallisation of the proteins in preparation for x-ray crystallography had left their tertiary structures essentially the same as in solution, but their quaternary (multi-subunit) structures were possibly very different.
This poster will show a new model structure for haemoglobin based on the same concepts. The new structure is consistent with the complex chemical properties of haemoglobin and is supported by cross-linking studies.
Natural haemoglobin occurs as an α2β2 tetramer (α and β being different forms of haemoglobin) that shows cooperative binding of O2. There are also other interactions between the O2 binding, the pH and the concentrations of certain other chemicals. These interactions require that a binding site at one location in the tetramer does work on binding sites elsewhere in the tetramer. Some degree of rigidity would be required to allow specific transmission of this energy to the correct location.
The widely accepted structure of haemoglobin is based on x-ray crystallography, initially by Muirhead and Perutz in 1963. (Some recent NMR studies suggest that the solution structure is similar to the crystal, but they have problems with assumptions and verifiability.) In 1965 Monod, Wyman and Changeux proposed a new mechanism to explain cooperative O2 binding, as it was previously thought that the hemes interacted directly [3]. In Perutz’s structure the hemes could not directly interact and an intricate mechanical and chemical mechanism was proposed. As the complexity of haemoglobin chemistry has emerged since then, much ingenuity has been applied to modifying the models to fit the data. However, serious inconsistencies remain [4, 5]
The new quaternary structure to be shown in this poster differs markedly from Perutz’s structure. It provides an explanation for the apparent necessity that highly cooperative O2 binding involves α2β2 tetramers rather than homotetramers. The “switch” between high and low affinity forms involves isomeric quaternary structures only achievable with an α2β2 tetramer. The interactions between sites are mediated by delocalised π-electrons connected through the rigid central core of the tetramer. This mechanism is reminiscent of the mechanism proposed by Pauling before the x-ray crystal structure became known [3].
[1] Vanselow, D. G. Biophys. J. 2002, 82, 2293-2203.
[2] Vanselow, D. G. Native Proteins; http://nativeproteins.blogspot.com, 2008.
[3] Eaton, W.A.; Henry. E.R.; Hofrichter, J.; Mozzarelli, A. Nat. Struct. Biol. 1999, 6, 351-358.
[4] Yonetani, T.; Park, S.; Tsuneshige, A.; Imai, K.; Kanaori, K. J. Biol. Chem. 2002, 277, 34508-34520.
[5] Eaton, W. A..; Henry, E. R.; Hofrichter, J.; Bettati, S.; Viappiani, C.; Mozzarelli, A. IUBMB Life 2007, 59, 586-599.

A preprint of a full paper describing this work will be posted after the conference.

Proposed tetrahedral quaternary structure for Galactose Oxidase.

Galactose Oxidase has structural similarity to neuraminidase but its function and active site are very different. This preprint shows how a compact tetrahedral structure can be assembled from the X-ray crystal structure. This is the first protein reconstruction that confronts earlier physical measurements that suggest the native form is a monomer. The preprint therefore addresses the limitations of the earlier physical measurements.
Galactose oxidase is a copper enzyme with an aromatic electron-relay system connecting copper ions in adjacent subunits, thus allowing two-electron reduction of molecular oxygen. Apart from this novel feature the enzyme is similar to neuraminidases in having a channel from the active site to the enzyme exterior in order that substrate moieties can be oxidised while still part of a polysaccharide or glycoprotein.

Link here to the preprint.

Feedback most welcome.

Can you help to get this work published and more widely known?

I am interested to hear from anyone with a suggestion about a journal that might be receptive to the neuraminidase work. I would be especially delighted to hear from anyone who would be prepared to act as a referee.
Please bring this BLOG to the attention of any of your colleagues who might be interested.

Expert reviews of neuraminidase paper with author's comments

I have put together the reviews I received on the two occasions I tried to publish this work in high-profile journals. I have included my formal responses and later annotations. The reviews indicate a generally defensive position by X-ray crystallography experts. Have a look. I would appreciate your views.

Link

Please submit a Posting or email me direct at dvanselow@hotmail.com

Don Vanselow

New Native Structures in Neuraminidases

Following on from the theory, I have produced model quaternary structures for a number of neuraminidase enzymes, based on the x-ray crystal structures. Click on these links to view this paper. html linked here. An earlier pdf version is linked here. The paper is copyright 2007 to myself, Dr Don Vanselow, 54 Greenways Road, Glen Waverley, Victoria 3150. Australia. All rights reserved.

The Fundamental Biophysics of Protein Function

The theory of catalysis and other functions displayed by soft biomaterials such as proteins is described in the paper "The Role of Constraint in Catalysis and High-Affinity Binding by Proteins" published in the Biophysical Journal in May 2002. Use the link provided by clicking on the title of this Post.