Trosolwyg
My main research interest is to understand the molecular organisation of $acirc; fibrous proteins$acirc; , in particular that of collagens forming networks and that of the proteins in the muscle sarcomere.
Network forming collagens do not form fibrils, but their general role appears to be to provide both mechanical strength and filtering properties. In some cases the open networks that they form are ordered enough that their structure can be analysed both by X-ray diffraction and by electron microscopy to reveal the basic molecular packing arrangements. I have taken advantage of the remarkably good order in the network-like structure of the egg case walls of the dogfish to reveal an open, body-centred, collagen molecular assembly. Intriguingly, something similar to this has been found in the human eye associated with a condition known as full thickness macular holes. In this case it appears to be collagen Type VI that is forming the aggregates. I am continuing to explore the nature of such collagen aggregates in the eye, especially in relation to Sorsby$acirc; s Fundus Dystrophy and Age-Related Macular Degeneration. I also carry out theoretical analyses of collagen amino acid sequences to try to understand the general principles that link collagen structures and functions.
The cornea is another system where collagen is organised as a network that possesses incredible optical properties. My aim is to understand which physical mechanisms are responsible for this organisation and how corneal optical properties arise. At present we are pursuing this by means of three-dimensional electron microscopy.
In collaboration with the Cell Signalling and Cell Biology Section at the University of Bristol, I am studying the ultrastructure of the myosin and actin filaments using X-ray fibre diffraction. In particular, we are following dynamic molecular changes in active muscle by means of fast (millisecond) time-resolved X-ray diffraction using very powerful X-ray beams from synchrotron X-ray sources, particularly the Advance Photon Source, at Argonne National Laboratory, in the US.
Cyhoeddiad
2024
- Regini, J. W. et al. 2024. Membrane structures and functional correlates in the bi-segmented eye lens of the cephalopod. Biology Open 13(9), article number: bio060445. (10.1242/bio.060445)
- Meek, K. M., Knupp, C., Lewis, P. N., Morgan, S. R. and Hayes, S. 2024. Structural control of corneal transparency, refractive power and dynamics. Eye (10.1038/s41433-024-02969-7)
2020
- Young, R. D. et al. 2020. Observations on nascent matrix structures in embryonic cornea: Important in cell interactions, or merely vestiges of the lens surface?. Archives of Clinical and Experimental Ophthalmology 2(2), pp. 67-72. (10.46439/ophthalmology.2.014)
2019
- Knupp, C. and Squire, J. M. 2019. Myosin cross-bridge behaviour in contracting muscle- The T1 Curve of Huxley and Simmons (1971) revisited. International Journal of Molecular Sciences 20(19), article number: 4892. (10.3390/ijms20194892)
- Young, R. D. et al. 2019. Cell-independent matrix configuration in early corneal development. Experimental Eye Research 187, article number: 107772. (10.1016/j.exer.2019.107772)
- Wild, J., Smith, P. E. M. and Knupp, C. 2019. Objective derivation of the morphology and staging of visual field loss associated with long-term vigabatrin therapy. CNS Drugs 33(8), pp. 817-829. (10.1007/s40263-019-00634-2)
- Burgoyne, T. et al. 2019. Three-dimensional structure of the basketweave Z-band in midshipman fish sonic muscle. Proceedings of the National Academy of Sciences 116(31), pp. 15534-15539. (10.1073/pnas.1902235116)
- Eakins, F., Knupp, C. and Squire, J. M. 2019. Monitoring the myosin crossbridge cycle in contracting muscle: steps towards 'Muscle-the Movie'. Journal of Muscle Research and Cell Motility 40(2), pp. 77-91. (10.1007/s10974-019-09543-9)
2016
- Eakins, F., Pinali, C., Gleeson, A., Knupp, C. and Squire, J. M. 2016. X-ray diffraction evidence for low force actin-attached and rigor-like cross-bridges in the contractile cycle. Biology 5(4), article number: 41. (10.3390/biology5040041)
- Kamma-Lorger, C. S. et al. 2016. Role of Decorin core protein in collagen organisation in Congenital Stromal Corneal Dystrophy (CSCD). PLoS ONE 11(2), article number: e0147948. (10.1371/journal.pone.0147948)
2015
- Meek, K. M. A. and Knupp, C. 2015. Corneal structure and transparency. Progress in Retinal and Eye Research 49, pp. 1-16. (10.1016/j.preteyeres.2015.07.001)
- Gardner, S. J., White, N., Albon, J., Knupp, C., Kamma-Lorger, C. S. and Meek, K. M. 2015. Measuring the refractive index of bovine corneal stromal cells using quantitative phase imaging. Biophysical Journal 109(8), pp. 1592-1599. (10.1016/j.bpj.2015.08.046)
2014
- Arkill, K. P. et al. 2014. Resolution of the three dimensional structure of components of the glomerular filtration barrier. BMC Nephrology 15, article number: 24. (10.1186/1471-2369-15-24)
- Young, R. D. et al. 2014. Three-dimensional aspects of matrix assembly by cells in the developing cornea. Proceedings of the National Academy of Sciences 111(2), pp. 687-692. (10.1073/pnas.1313561110)
2011
- Koudouna, E. et al. 2011. Preliminary electron microscopical studies of connective tissue in the human lamina cribrosa [Abstract]. International Journal of Experimental Pathology 92(6), pp. A26. (10.1111/j.1365-2613.2011.00780.x)
- Parfitt, G., Pinali, C., Akama, T. O., Young, R. D., Nishida, K., Quantock, A. J. and Knupp, C. 2011. Electron tomography reveals multiple self-association of chondroitin sulphate/dermatan sulphate proteoglycans in Chst5-null mouse corneas. Journal of Structural Biology 174(3), pp. 536-541. (10.1016/j.jsb.2011.03.015)
- Bushby, A. J., P'ng, K. M. Y., Young, R. D., Pinali, C., Knupp, C. and Quantock, A. J. 2011. Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy. Nature Protocols 6(6), pp. 845-858. (10.1038/nprot.2011.332)
- Young, R. D. et al. 2011. Large Proteoglycan Complexes and Disturbed Collagen Architecture in the Corneal Extracellular Matrix of Mucopolysaccharidosis Type VII (Sly Syndrome). Investigative Ophthalmology & Visual Science 52(9), pp. 6720-6728. (10.1167/iovs.11-7377)
2010
- Parfitt, G. J., Pinali, C., Young, R. D., Quantock, A. J. and Knupp, C. 2010. Three-dimensional reconstruction of collagen-proteoglycan interactions in the mouse corneal stroma by electron tomography. Journal of Structural Biology 170(2), pp. 392-397. (10.1016/j.jsb.2010.01.019)
- Lewis, P., Pinali, C., Young, R. D., Meek, K. M. A., Quantock, A. J. and Knupp, C. 2010. Structural interactions between collagen and proteoglycans are elucidated by three-dimensional electron tomography of bovine cornea. Structure 18(2), pp. 239-245. (10.1016/j.str.2009.11.013)
- Kamma-Lorger, C. S. et al. 2010. Collagen and mature elastic fibre organisation as a function of depth in the human cornea and limbus. Journal of Structural Biology 169(3), pp. 424-430. (10.1016/j.jsb.2009.11.004)
2009
- Knupp, C., Offer, G., Ranatunga, K. W. and Squire, J. M. 2009. Probing muscle myosin motor action: X-Ray (M3 and M6) interference measurements report motor domain not lever arm movement. Journal of Molecular Biology 390(2), pp. 168-181. (10.1016/j.jmb.2009.04.047)
- Knupp, C., Pinali, C., Lewis, P., Parfitt, G. J., Young, R. D., Meek, K. M. A. and Quantock, A. J. 2009. The architecture of the cornea and structural basis of its transparency. In: McPherson, A. ed. Advances in Protein Chemistry and Structural Biology., Vol. 78. London: Academic Press, pp. 25-49., (10.1016/S1876-1623(08)78002-7)
2008
- Luther, P. K. et al. 2008. Understanding the organisation and role of Myosin binding protein C in normal striated muscle by comparison with MyBP-C knockout cardiac muscle. Journal of Molecular Biology 384(1), pp. 60-72. (10.1016/j.jmb.2008.09.013)
2006
- Knupp, C., Pinali, C., Munro, P. M., Gruber, H. E., Sherratt, M. J., Baldock, C. and Squire, J. M. 2006. Structural correlation between collagen VI microfibrils and collagen VI banded aggregates. Journal of Structural Biology 154(3), pp. 312-326. (10.1016/j.jsb.2006.03.023)
2003
- Squire, J. M., AL-Khayat, H. A., Harford, J. J., Hudson, L., Irving, T. C., Knupp, C. and Reedy, M. K. 2003. Modelling muscle motor conformations using low-angle X-ray diffraction. IEE Proceedings -Nanobiotechnology 150(3), pp. 103-110. (10.1049/ip-nbt:20031094)
- Squire, J. M., Knupp, C., AL-Khayat, H. A. and Harford, J. J. 2003. Millisecond time-resolved low-angle x-ray fibre diffraction: a powerful, high-sensitivity technique for modelling real-time movements in biological macromolecular assemblies. Fibre diffraction review 11, pp. 28-35.
- Squire, J. M. et al. 2003. New CCP13 software and the strategy behind further developments: stripping and modelling of fibre diffraction data. Fibre Diffraction Review 11, pp. 7-19.
2002
- Knupp, C., Amin, S. Z., Munro, P. M. G., Luthert, P. J. and Squire, J. M. 2002. Collagen VI assemblies in age-related macular degeneration. Journal of Structural Biology 139(3), pp. 181-189. (10.1016/S1047-8477(02)00534-8)
- Knupp, C., Chong, N. H. V., Munro, P. M. G., Luthert, P. J. and Squire, J. M. 2002. Analysis of the collagen VI assemblies associated with Sorsby's fundus dystrophy. Journal of Structural Biology 137(1-2), pp. 31-40. (10.1006/jsbi.2002.4449)
2001
- Knupp, C. and Squire, J. M. 2001. A new twist in the collagen story - the type VI segmented supercoil. Embo Journal 20(3), pp. 372-376. (10.1093/emboj/20.3.372)
Adrannau llyfrau
- Knupp, C., Pinali, C., Lewis, P., Parfitt, G. J., Young, R. D., Meek, K. M. A. and Quantock, A. J. 2009. The architecture of the cornea and structural basis of its transparency. In: McPherson, A. ed. Advances in Protein Chemistry and Structural Biology., Vol. 78. London: Academic Press, pp. 25-49., (10.1016/S1876-1623(08)78002-7)
Erthyglau
- Regini, J. W. et al. 2024. Membrane structures and functional correlates in the bi-segmented eye lens of the cephalopod. Biology Open 13(9), article number: bio060445. (10.1242/bio.060445)
- Meek, K. M., Knupp, C., Lewis, P. N., Morgan, S. R. and Hayes, S. 2024. Structural control of corneal transparency, refractive power and dynamics. Eye (10.1038/s41433-024-02969-7)
- Young, R. D. et al. 2020. Observations on nascent matrix structures in embryonic cornea: Important in cell interactions, or merely vestiges of the lens surface?. Archives of Clinical and Experimental Ophthalmology 2(2), pp. 67-72. (10.46439/ophthalmology.2.014)
- Knupp, C. and Squire, J. M. 2019. Myosin cross-bridge behaviour in contracting muscle- The T1 Curve of Huxley and Simmons (1971) revisited. International Journal of Molecular Sciences 20(19), article number: 4892. (10.3390/ijms20194892)
- Young, R. D. et al. 2019. Cell-independent matrix configuration in early corneal development. Experimental Eye Research 187, article number: 107772. (10.1016/j.exer.2019.107772)
- Wild, J., Smith, P. E. M. and Knupp, C. 2019. Objective derivation of the morphology and staging of visual field loss associated with long-term vigabatrin therapy. CNS Drugs 33(8), pp. 817-829. (10.1007/s40263-019-00634-2)
- Burgoyne, T. et al. 2019. Three-dimensional structure of the basketweave Z-band in midshipman fish sonic muscle. Proceedings of the National Academy of Sciences 116(31), pp. 15534-15539. (10.1073/pnas.1902235116)
- Eakins, F., Knupp, C. and Squire, J. M. 2019. Monitoring the myosin crossbridge cycle in contracting muscle: steps towards 'Muscle-the Movie'. Journal of Muscle Research and Cell Motility 40(2), pp. 77-91. (10.1007/s10974-019-09543-9)
- Eakins, F., Pinali, C., Gleeson, A., Knupp, C. and Squire, J. M. 2016. X-ray diffraction evidence for low force actin-attached and rigor-like cross-bridges in the contractile cycle. Biology 5(4), article number: 41. (10.3390/biology5040041)
- Kamma-Lorger, C. S. et al. 2016. Role of Decorin core protein in collagen organisation in Congenital Stromal Corneal Dystrophy (CSCD). PLoS ONE 11(2), article number: e0147948. (10.1371/journal.pone.0147948)
- Meek, K. M. A. and Knupp, C. 2015. Corneal structure and transparency. Progress in Retinal and Eye Research 49, pp. 1-16. (10.1016/j.preteyeres.2015.07.001)
- Gardner, S. J., White, N., Albon, J., Knupp, C., Kamma-Lorger, C. S. and Meek, K. M. 2015. Measuring the refractive index of bovine corneal stromal cells using quantitative phase imaging. Biophysical Journal 109(8), pp. 1592-1599. (10.1016/j.bpj.2015.08.046)
- Arkill, K. P. et al. 2014. Resolution of the three dimensional structure of components of the glomerular filtration barrier. BMC Nephrology 15, article number: 24. (10.1186/1471-2369-15-24)
- Young, R. D. et al. 2014. Three-dimensional aspects of matrix assembly by cells in the developing cornea. Proceedings of the National Academy of Sciences 111(2), pp. 687-692. (10.1073/pnas.1313561110)
- Koudouna, E. et al. 2011. Preliminary electron microscopical studies of connective tissue in the human lamina cribrosa [Abstract]. International Journal of Experimental Pathology 92(6), pp. A26. (10.1111/j.1365-2613.2011.00780.x)
- Parfitt, G., Pinali, C., Akama, T. O., Young, R. D., Nishida, K., Quantock, A. J. and Knupp, C. 2011. Electron tomography reveals multiple self-association of chondroitin sulphate/dermatan sulphate proteoglycans in Chst5-null mouse corneas. Journal of Structural Biology 174(3), pp. 536-541. (10.1016/j.jsb.2011.03.015)
- Bushby, A. J., P'ng, K. M. Y., Young, R. D., Pinali, C., Knupp, C. and Quantock, A. J. 2011. Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy. Nature Protocols 6(6), pp. 845-858. (10.1038/nprot.2011.332)
- Young, R. D. et al. 2011. Large Proteoglycan Complexes and Disturbed Collagen Architecture in the Corneal Extracellular Matrix of Mucopolysaccharidosis Type VII (Sly Syndrome). Investigative Ophthalmology & Visual Science 52(9), pp. 6720-6728. (10.1167/iovs.11-7377)
- Parfitt, G. J., Pinali, C., Young, R. D., Quantock, A. J. and Knupp, C. 2010. Three-dimensional reconstruction of collagen-proteoglycan interactions in the mouse corneal stroma by electron tomography. Journal of Structural Biology 170(2), pp. 392-397. (10.1016/j.jsb.2010.01.019)
- Lewis, P., Pinali, C., Young, R. D., Meek, K. M. A., Quantock, A. J. and Knupp, C. 2010. Structural interactions between collagen and proteoglycans are elucidated by three-dimensional electron tomography of bovine cornea. Structure 18(2), pp. 239-245. (10.1016/j.str.2009.11.013)
- Kamma-Lorger, C. S. et al. 2010. Collagen and mature elastic fibre organisation as a function of depth in the human cornea and limbus. Journal of Structural Biology 169(3), pp. 424-430. (10.1016/j.jsb.2009.11.004)
- Knupp, C., Offer, G., Ranatunga, K. W. and Squire, J. M. 2009. Probing muscle myosin motor action: X-Ray (M3 and M6) interference measurements report motor domain not lever arm movement. Journal of Molecular Biology 390(2), pp. 168-181. (10.1016/j.jmb.2009.04.047)
- Luther, P. K. et al. 2008. Understanding the organisation and role of Myosin binding protein C in normal striated muscle by comparison with MyBP-C knockout cardiac muscle. Journal of Molecular Biology 384(1), pp. 60-72. (10.1016/j.jmb.2008.09.013)
- Knupp, C., Pinali, C., Munro, P. M., Gruber, H. E., Sherratt, M. J., Baldock, C. and Squire, J. M. 2006. Structural correlation between collagen VI microfibrils and collagen VI banded aggregates. Journal of Structural Biology 154(3), pp. 312-326. (10.1016/j.jsb.2006.03.023)
- Squire, J. M., AL-Khayat, H. A., Harford, J. J., Hudson, L., Irving, T. C., Knupp, C. and Reedy, M. K. 2003. Modelling muscle motor conformations using low-angle X-ray diffraction. IEE Proceedings -Nanobiotechnology 150(3), pp. 103-110. (10.1049/ip-nbt:20031094)
- Squire, J. M., Knupp, C., AL-Khayat, H. A. and Harford, J. J. 2003. Millisecond time-resolved low-angle x-ray fibre diffraction: a powerful, high-sensitivity technique for modelling real-time movements in biological macromolecular assemblies. Fibre diffraction review 11, pp. 28-35.
- Squire, J. M. et al. 2003. New CCP13 software and the strategy behind further developments: stripping and modelling of fibre diffraction data. Fibre Diffraction Review 11, pp. 7-19.
- Knupp, C., Amin, S. Z., Munro, P. M. G., Luthert, P. J. and Squire, J. M. 2002. Collagen VI assemblies in age-related macular degeneration. Journal of Structural Biology 139(3), pp. 181-189. (10.1016/S1047-8477(02)00534-8)
- Knupp, C., Chong, N. H. V., Munro, P. M. G., Luthert, P. J. and Squire, J. M. 2002. Analysis of the collagen VI assemblies associated with Sorsby's fundus dystrophy. Journal of Structural Biology 137(1-2), pp. 31-40. (10.1006/jsbi.2002.4449)
- Knupp, C. and Squire, J. M. 2001. A new twist in the collagen story - the type VI segmented supercoil. Embo Journal 20(3), pp. 372-376. (10.1093/emboj/20.3.372)
Ymchwil
Research Interests
Corneal Transparency
Why are corneas transparent?
Mammalian corneas, like much of the extracellular matrix, are made essentially of collagen and proteoglycans. However, unlike the rest of the extracellular matrix, they are exquisitely transparent. To understand why we need first to understand how light interacts with each collagen fibril in the cornea.
The top-left corner of the image above contains the representation of a single collagen fibril seen in cross section.
In the bottom-left corner, light is coming from the left and is represented as straight lines. You can think of this incoming light as ripples on the surface of a pond. The darker lines represent a wave-crest while the lighter lines a trough. When light interacts with the collagen fibrils, it forces the electrons of the atoms in the fibril to oscillate. Because accelerating charges produce electromagnetic waves, a secondary wave is produced. This wave has the same wavelength of the incoming wave, but it radiates in all directions in the plane. The crest of the secondary wave is represented in red, the trough in grey.
In the top-right corner the secondary wave is drawn on top of a greyscale representation of the wave itself. Since we are actually interested in the energy associated with the wave, we draw here the square of the wave amplitudes, so that crests and troughs look identical.
In the bottom-right corner we only draw the greyscale (intensity) representation of the secondary wave.
When two fibrils are present, the secondary waves produced by each fibril interfere. This means that the two sets of secondary waves simply add together, so that where two crests or two troughs meet we will have a wave twice as deep, but where a crest meets a trough the waves cancel out. Correspondingly, the greyscale representation of the intensity of the resulting wave in the top and the bottom right panels of the figure above is not two even sets of concentric rings radiating from the fibrils: the wave intensity is distributed unevenly in the plane. But what happens when more than two fibrils are present?
The figure above represents a situation in which many fibrils are randomly placed. Wave interference will take place also in this case, and the secondary waves from all fibrils will add together. As you might expect, the intensity of the resulting wave is not uniformly distributed in space. Most of the intensity from the secondary waves is travelling in the forward direction, but a considerable portion is travelling in other directions. This means that if the fibrils in the cornea were randomly distributed, not all the light would be transmitted through the cornea, but a considerable portion would be reflected back. What would happen if the fibrils were not randomly distributed?
In the figure above, the collagen fibrils are regularly placed on an hexagonal lattice. Secondary waves from these fibrils cancel out in all directions except the forward direction: light is travelling undisturbed through the cornea. A cornea with an ordered collagen fibril distribution of this type is therefore transparent.
It turns out that strict positional order for the collagen fibrils is not an absolute requirement for cornea transparency. It is in fact sufficient that the distance between adjacent collagen fibrils is approximately the same, as long as this distance is markedly less than the wavelength of the incoming wave. In addition, a final requirement is that the diameter of the fibrils must be the same for all fibrils.
To understand how the arrangement of the collagen fibrils in the cornea is maintained, we can look at it directly using a transmission electron microscope and reconstruct what we see in three dimensions.
ElectronTomography of the Cornea
By tilting a corneal specimen in the electron microscope, collecting a series of images at different tilt angles, and recombining these images using suitable computational algorithms, we can reconstruct the structure of the corneal stroma and observe the way proteoglycans and collagen fibrils interact with each other. These interactions are fundamental in maintaining the arrangement of the collagen fibrils, so important for transparency.
seen in cross-section, are painted in blue. Proteoglycans in yellow. We can see here that the
proteoglycans link two or more adjacent fibrils. The way proteoglycans extend from a collagen
fibril to a neighbouring one is not ordered and crystal-like, but it is sufficient to keep
neighbouring fibrils at defined distances (Reconstruction by Dr C. Pinali).
From reconstructions of bovine and mouse corneas, we proposed a model of how the distance between adjacent collagen fibrils is maintained thanks to the action of the proteoglycans. The model is based on the idea that proteoglycans are able to give rise to two opposite forces acting on the fibrils: an attractive force trying to pull fibrils close to each other and a repulsive one trying to push fibrils apart. The distance between fibrils in the cornea is the distance where the two opposing forces cancel out.
The repulsive force arise because of the Donnan effect. Since the proteoglycans are negatively charged they attract positive ions present in the corneal stroma. In turn, these ions attract water molecules by a process analogous to osmosis. Water accumulates between the fibrils and exert pressure that make the fibrils move apart.
The Attractive forces are due to thermal motion of the proteoglycans. Proteoglycans are continuously bombarded by molecules present in the stroma. The overall effect of the collisions is that the proteoglycans change their shape. They are no longer fully extended and their terminal ends are forced to move close to each other. Since these ends are linked to the collagen fibrils, also the fibrils move closer to each other.
The combination of these repulsive and attractive forces keep the fibrils at regular distances from each other. Note that the fibrils are not fixed in space in a crystalline way. They are able to vibrate and move around, making the cornea a fluid and resilient system.
References:
Lewis PN, Pinali C, Young RD, Meek KM, Quantock AJ, Knupp C. (2010) $acirc; Structural interactions between collagen and proteoglycans are elucidated by three-dimensional electron tomography of bovine cornea$acirc; . Structure. 18(2), 239-245.
Knupp C, Pinali C, Lewis PN, Parfitt GJ, Young RD, Meek KM, Quantock AJ (2010) $acirc; The architecture of the cornea and structural basis of its transparency$acirc; Advances in protein chemistry and structural biology,78, 25-49.