Thursday, April 9, 2009
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.
Monday, September 22, 2008
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 (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.
Wednesday, August 13, 2008
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.
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.
Sunday, September 30, 2007
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.
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.
Tuesday, July 10, 2007
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.
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
Link
Please submit a Posting or email me direct at dvanselow@hotmail.com
Don Vanselow
Saturday, April 14, 2007
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.
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