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Dr Fabio Parmeggiani
(e/fe)
- Ar gael fel goruchwyliwr ôl-raddedig
Timau a rolau for Fabio Parmeggiani
Darlithydd, Cymrawd gyrfa gynnar EPSRC
Trosolwyg
Mae fy ngrŵp yn gweithio ar y croestoriad rhwng bioleg arbrofol a chyfrifiadurol i ddatblygu proteinau diagnostig a therapiwtig newydd, a dulliau newydd ar gyfer peirianneg a dethol proteinau. Rydym yn cyfuno offer cyfrifiadurol o'r radd flaenaf ar gyfer dylunio proteinau, sy'n seiliedig ar ffiseg a dysgu peiriannau, gyda mynegiant a nodweddu protein.
Meysydd ymchwil
Dylunio protein modiwlaidd: gwneud proteinau trwy ychwanegu a chyfnewid blociau adeiladu dilysu
Rhwymo carbohydradau: dylunio proteinau newydd i adnabod siwgrau, oligosacaridau a glycanau
Strwythurau protein anhyblyg a deinamig: dyluniad ar gyfer symudiad rheoledig
Ymwrthedd gwrthficrobaidd: dylunio proteinau i oresgyn ymwrthedd bioffilm i driniaethau
Swyddi agored
Rydym bob amser yn chwilio am israddedigion, ôl-raddedigion ac ôl-ddoethurol sydd â diddordeb mewn dylunio protein, o gefndiroedd arbrofol a chyfrifiadurol/mathemategol.
Ar gael ar hyn o bryd:
1 swydd myfyriwr PhD. Rydym yn chwilio am fyfyriwr sydd â diddordeb mewn dylunio protein cyfrifiadurol ar gyfer adnabod carbohydradau a chymwysiadau gwrthficrobaidd, gan ddechrau ym mis Hydref 2026, mewn cydweithrediad â Dr Angela Nobbs (Prifysgol Bryste). Mae'r prosiect yn rhan o bartneriaeth hyfforddiant doethurol GW4 MRC. Gwnewch gais drwy'r ffurflen gais rhaglen . Y dyddiad cau ar gyfer ceisiadau yw Hydref 20fed 2025.
1 swydd ôl-ddoethurol. Rydym yn chwilio am gydymaith ymchwil gydag arbenigedd bioleg biocemegol, bioffisegol a strwythurol i'w gymhwyso i ddylunio a nodweddu strwythurau protein modiwlaidd. Mae'r swydd am 1 flwyddyn gydag estyniad posibl. Gwnewch gais drwy borth Prifysgol Caerdydd. Y dyddiad cau ar gyfer ceisiadau yw Medi 17eg 2025.
Cyhoeddiad
2026
- Luo, Y. and Parmeggiani, F. 2026. CLIMBS: Assessing carbohydrate–protein interactions through a graph neural network classifier using synthetic negative data. Journal of Chemical Information and Modeling 66 (11), pp.6271-6280. (10.1021/acs.jcim.6c00126)
2025
- Costa, F. et al., 2025. A global survey of intramolecular isopeptide bonds. Protein Science 34 (12) e70342. (10.1002/pro.70342)
2024
- Zelenka, N. R. et al., 2024. Data hazards in synthetic biology. Synthetic Biology 9 (1) ysae010. (10.1093/synbio/ysae010)
- Moreno-Tortolero, R. O. et al., 2024. Molecular organization of fibroin heavy chain and mechanism of fibre formation in Bombyx mori. Communications Biology 7 786. (10.1038/s42003-024-06474-1)
- Sarvaharman, S. et al., 2024. Scalable design of repeat protein structural dynamics via probabilistic coarse-grained models. [Online].medRxiv. (10.1101/2024.03.13.584748)Available at: https://doi.org/10.1101/2024.03.13.584748.
2023
- Bethel, N. et al., 2023. Precisely patterned nanofibres made from extendable protein multiplexes. Nature Chemistry 15 (Decemb), pp.1664-1671. (10.1038/s41557-023-01314-x)
- Moreno-Tortolero, R. et al., 2023. Silk road revealed: Mechanism of silk fibre formation inBombyx mori. [Online].bioRxiv: Cold Spring Harbor Laboratory. (10.1101/2023.06.02.543394)Available at: https://doi.org/10.1101/2023.06.02.543394.
2021
- Gidley, F. and Parmeggiani, F. 2021. Repeat proteins: designing new shapes and functions for solenoid folds. Current Opinion in Structural Biology 68 , pp.208-214. (10.1016/j.sbi.2021.02.002)
2020
- Yeh, C. , Obendorf, L. and Parmeggiani, F. 2020. Elfin UI. Frontiers in Bioengineering and Biotechnology 8 568318. (10.3389/fbioe.2020.568318)
2018
- Geiger-Schuller, K. et al., 2018. Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions. Proceedings of the National Academy of Sciences 115 (29), pp.7539-7544. (10.1073/pnas.1800283115)
- Yeh, C. et al., 2018. Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. Journal of Structural Biology X 201 (2), pp.100-107. (10.1016/j.jsb.2017.09.001)
2017
- Parmeggiani, F. and Huang, P. 2017. Designing repeat proteins. Current Opinion in Structural Biology 45 (8), pp.116-123. (10.1016/j.sbi.2017.02.001)
2016
- Mills, J. et al., 2016. Computational design of a homotrimeric metalloprotein with a trisbipyridyl core. Proceedings of the National Academy of Sciences 113 (52), pp.15012-15017. (10.1073/pnas.1600188113)
- Fallas, J. et al., 2016. Computational design of self-assembling cyclic protein homo-oligomers. Nature Chemistry 9 (4), pp.353-360. (10.1038/nchem.2673)
- Reichen, C. et al., 2016. Computationally designed armadillo repeat proteins for modular peptide recognition. Journal of Molecular Biology 428 (22), pp.4467-4489. (10.1016/j.jmb.2016.09.012)
2015
- Brunette, T. et al., 2015. Exploring the repeat protein universe through computational protein design. Nature 528 (7583), pp.580-584. (10.1038/nature16162)
- Doyle, L. et al., 2015. Rational design of alpha-helical tandem repeat proteins with closed architectures. Nature 528 (7583), pp.585-588. (10.1038/nature16191)
- Huang, P. et al., 2015. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chemical Biology 12 (1), pp.29-34. (10.1038/nchembio.1966)
- Park, K. et al., 2015. Control of repeat-protein curvature by computational protein design. Nature Structural and Molecular Biology 22 (2), pp.167-174. (10.1038/nsmb.2938)
2014
- Parmeggiani, F. et al. 2014. A general computational approach for repeat protein design. Journal of Molecular Biology 427 (2), pp.563-575. (10.1016/j.jmb.2014.11.005)
2013
- Prindle, M. et al., 2013. A substitution in the fingers domain of DNA polymerase delta reduces fidelity by altering nucleotide discrimination in the catalytic site. Journal of Biological Chemistry 288 (8), pp.5572-5580. (10.1074/jbc.M112.436410)
2012
- Alfarano, P. et al., 2012. Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science 21 (9), pp.1298-1314. (10.1002/pro.2117)
- Baxter, S. et al., 2012. Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Nucleic Acids Research 40 (16), pp.7985-8000. (10.1093/nar/gks502)
- Reichen, C. et al., 2012. Design and Selection of Armadillo Repeat Proteins: A novel technology for modular peptide recognition. Protein Science 21 (Supple), pp.82.
2008
- Parmeggiani, F. et al. 2008. Designed armadillo repeat proteins as general peptide-binding scaffolds: Consensus design and computational optimization of the hydrophobic core. Journal of Molecular Biology 376 (5), pp.1282-1304. (10.1016/j.jmb.2007.12.014)
2007
- Radeghieri, A. et al., 2007. Tyrosine83 is essential for the activity of E-coli galactoside transacetylase. Biochimica Et Biophysica Acta-Proteins and Proteomics 1774 (2), pp.243-248. (10.1016/j.bbapap.2006.11.013)
- Navratilova, I. et al., 2007. Thermodynamic benchmark study using Biacore technology. Analytical Biochemistry 364 (1), pp.67-77. (10.1016/j.ab.2007.01.031)
Erthyglau
- Luo, Y. and Parmeggiani, F. 2026. CLIMBS: Assessing carbohydrate–protein interactions through a graph neural network classifier using synthetic negative data. Journal of Chemical Information and Modeling 66 (11), pp.6271-6280. (10.1021/acs.jcim.6c00126)
- Costa, F. et al., 2025. A global survey of intramolecular isopeptide bonds. Protein Science 34 (12) e70342. (10.1002/pro.70342)
- Zelenka, N. R. et al., 2024. Data hazards in synthetic biology. Synthetic Biology 9 (1) ysae010. (10.1093/synbio/ysae010)
- Moreno-Tortolero, R. O. et al., 2024. Molecular organization of fibroin heavy chain and mechanism of fibre formation in Bombyx mori. Communications Biology 7 786. (10.1038/s42003-024-06474-1)
- Bethel, N. et al., 2023. Precisely patterned nanofibres made from extendable protein multiplexes. Nature Chemistry 15 (Decemb), pp.1664-1671. (10.1038/s41557-023-01314-x)
- Gidley, F. and Parmeggiani, F. 2021. Repeat proteins: designing new shapes and functions for solenoid folds. Current Opinion in Structural Biology 68 , pp.208-214. (10.1016/j.sbi.2021.02.002)
- Yeh, C. , Obendorf, L. and Parmeggiani, F. 2020. Elfin UI. Frontiers in Bioengineering and Biotechnology 8 568318. (10.3389/fbioe.2020.568318)
- Geiger-Schuller, K. et al., 2018. Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions. Proceedings of the National Academy of Sciences 115 (29), pp.7539-7544. (10.1073/pnas.1800283115)
- Yeh, C. et al., 2018. Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. Journal of Structural Biology X 201 (2), pp.100-107. (10.1016/j.jsb.2017.09.001)
- Parmeggiani, F. and Huang, P. 2017. Designing repeat proteins. Current Opinion in Structural Biology 45 (8), pp.116-123. (10.1016/j.sbi.2017.02.001)
- Mills, J. et al., 2016. Computational design of a homotrimeric metalloprotein with a trisbipyridyl core. Proceedings of the National Academy of Sciences 113 (52), pp.15012-15017. (10.1073/pnas.1600188113)
- Fallas, J. et al., 2016. Computational design of self-assembling cyclic protein homo-oligomers. Nature Chemistry 9 (4), pp.353-360. (10.1038/nchem.2673)
- Reichen, C. et al., 2016. Computationally designed armadillo repeat proteins for modular peptide recognition. Journal of Molecular Biology 428 (22), pp.4467-4489. (10.1016/j.jmb.2016.09.012)
- Brunette, T. et al., 2015. Exploring the repeat protein universe through computational protein design. Nature 528 (7583), pp.580-584. (10.1038/nature16162)
- Doyle, L. et al., 2015. Rational design of alpha-helical tandem repeat proteins with closed architectures. Nature 528 (7583), pp.585-588. (10.1038/nature16191)
- Huang, P. et al., 2015. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chemical Biology 12 (1), pp.29-34. (10.1038/nchembio.1966)
- Park, K. et al., 2015. Control of repeat-protein curvature by computational protein design. Nature Structural and Molecular Biology 22 (2), pp.167-174. (10.1038/nsmb.2938)
- Parmeggiani, F. et al. 2014. A general computational approach for repeat protein design. Journal of Molecular Biology 427 (2), pp.563-575. (10.1016/j.jmb.2014.11.005)
- Prindle, M. et al., 2013. A substitution in the fingers domain of DNA polymerase delta reduces fidelity by altering nucleotide discrimination in the catalytic site. Journal of Biological Chemistry 288 (8), pp.5572-5580. (10.1074/jbc.M112.436410)
- Alfarano, P. et al., 2012. Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science 21 (9), pp.1298-1314. (10.1002/pro.2117)
- Baxter, S. et al., 2012. Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Nucleic Acids Research 40 (16), pp.7985-8000. (10.1093/nar/gks502)
- Reichen, C. et al., 2012. Design and Selection of Armadillo Repeat Proteins: A novel technology for modular peptide recognition. Protein Science 21 (Supple), pp.82.
- Parmeggiani, F. et al. 2008. Designed armadillo repeat proteins as general peptide-binding scaffolds: Consensus design and computational optimization of the hydrophobic core. Journal of Molecular Biology 376 (5), pp.1282-1304. (10.1016/j.jmb.2007.12.014)
- Radeghieri, A. et al., 2007. Tyrosine83 is essential for the activity of E-coli galactoside transacetylase. Biochimica Et Biophysica Acta-Proteins and Proteomics 1774 (2), pp.243-248. (10.1016/j.bbapap.2006.11.013)
- Navratilova, I. et al., 2007. Thermodynamic benchmark study using Biacore technology. Analytical Biochemistry 364 (1), pp.67-77. (10.1016/j.ab.2007.01.031)
Gwefannau
- Sarvaharman, S. et al., 2024. Scalable design of repeat protein structural dynamics via probabilistic coarse-grained models. [Online].medRxiv. (10.1101/2024.03.13.584748)Available at: https://doi.org/10.1101/2024.03.13.584748.
- Moreno-Tortolero, R. et al., 2023. Silk road revealed: Mechanism of silk fibre formation inBombyx mori. [Online].bioRxiv: Cold Spring Harbor Laboratory. (10.1101/2023.06.02.543394)Available at: https://doi.org/10.1101/2023.06.02.543394.
Ymchwil
Rydym yn grŵp rhyngddisgyblaethol sy'n dod â dylunio cyfrifiadol a nodweddu arbrofol o broteinau ynghyd. Rydym yn defnyddio meddalwedd o'r radd flaenaf (e.e. AlphaFold, Rosetta, RFdiffusion) ac yn datblygu offer newydd (Elfin, CLIMBS) i ddatrys problemau heriol trwy ddylunio'r protein cywir ar gyfer y swydd.
Dyluniad protein modiwlaidd
Rydym yn gweithio ar ddylunio proteinau newydd gyda strwythurau arfer, gan ddefnyddio blociau adeiladu wedi'u nodweddu'n dda y gellir eu hasio trwy ryngwynebau hysbys ac Elfin, meddalwedd ar gyfer cynulliad modiwlaidd yr ydym wedi'i ddylunio. Mae'r broses yn caniatáu i gyflawni cyfradd llwyddiant uchel yn arbrofol. Gwnaethom ddefnyddio'r strwythurau modiwlaidd hyn, yn seiliedig ar broteinau ailadroddus naturiol ac wedi'u dylunio, i adeiladu nanoronynnau wedi'u teilwra â swyddogaethau wedi'u hymgorffori lluosog ar gyfer adnabod celloedd ac actifadu trwy glystyru a chyd-glystyru derbynyddion.
Rhwymo carbohydrad
Rydym wedi datblygu meddalwedd dysgu peiriannau, CLIMBS, ar gyfer cydnabod a graddio rhwymo carbohydrad, fel dewis amgen i swyddogaethau sgôr sy'n seiliedig ar ynni. Gall CLIMBS adnabod rhwymwyr tebyg i frodoriaeth yn effeithlon, ac rydym yn ei ddefnyddio i werthuso canlyniadau docio moleciwlaidd a dylunio canllaw proteinau rhwymo carbohydradau newydd fel diagnosteg a therapiwteg bosibl newydd.
Strwythurau protein anhyblyg a deinamig
Rydym wedi datblygu dulliau cyfrifiadurol i werthuso'n gyflym y ddeinameg a chydffurfiadau sydd ar gael o broteinau modiwlaidd. Rydym yn defnyddio'r offer hyn i ddylunio proteinau newydd gyda chynigion penodol, a newid rhwng cydffurfiadau caeedig ac agored o dan amodau penodol, megis newidiadau amgylcheddol a chydnabod targedau. Mae gan hyn geisiadau posibl wrth ddylunio nanoronyn ar gyfer cyflenwi cyffuriau a biosynwyryddion.
Aelodau presennol o'r grŵp
Fabio Parmeggiani (PI)
Yijie (Jacky) Luo (myfyriwr PhD, gyda grŵp Woolfson, Prifysgol Bryste)
Srikanth Lingappa (myfyriwr PhD, gyda grŵp Berger, Prifysgol Bryste)
Pierpaolo Foddai (myfyriwr MSC)
Cydweithredwyr
Ash Toye (Prifysgol Bryste): rhwymo derbynnydd wyneb celloedd
Louis Luk (Prifysgol Caerdydd): dylunio proteinau D
Angela Nobbs (Prifysgol Bryste): gwrthficrobau ar gyfer bioffilmiau
Imre Berger (Prifysgol Bryste): peirianneg proteinau gwenwyn neidr ar gyfer cynhyrchu brechlyn
Bywgraffiad
Rwy'n ddarlithydd yn Ysgol Fferylliaeth a Gwyddorau Fferyllol Caerdydd ers 2024. Cefais fy PhD mewn Biocemeg o Brifysgol Zurich gan weithio yng ngrŵp Andreas Pluckthun, yna ymunais â grŵp David Baker ym Mhrifysgol Washington i weithio ar ddylunio protein cyfrifiadurol a dod yn arweinydd grŵp a chymrawd ymchwil gyrfa gynnar EPSRC ym Mhrifysgol Bryste, cyn ymuno â Phrifysgol Caerdydd. Rwyf wedi gweithio ar flaen y gad o ran peirianneg a dylunio protein arbrofol a chyfrifiannol ac ar hyn o bryd rwy'n datblygu dulliau newydd o ddylunio proteinau gyda strwythurau modiwlaidd, gwerthuso dynameg protein wrth ddylunio, a dylunio proteinau newydd i adnabod carbohydradau, fel antigenau wyneb celloedd ac mewn bioffilmiau bacteriol. Y nod yw cymhwyso'r offer hyn ar gyfer datblygu diagnosteg a therapiwteg newydd.
Aelodaethau proffesiynol
Rosetta Commons https://rosettacommons.org/
Cymdeithas Biocemegol https://www.biochemistry.org/
Safleoedd academaidd blaenorol
Darlithydd, Ysgol y Gwyddorau Plwyfol a Phahrmaceutical, Prifysgol Caerdydd (2024-)
Cymrawd Ymchwil, Ysgol Cemeg ac Ysgol Biocemeg, Prifysgol Bryste (2016-2024)
Cymrawd Ymchwil Ôl-ddoethurol a Hyfforddwr Dros Dro, Adran Biocemeg a'r Sefydliad Dylunio Protein, Prifysgol Washington (2009-2016)
Contact Details
Themâu ymchwil
Arbenigeddau
- Biocemeg
- Dylunio a pheirianneg protein
- Nanobiotechnoleg
- Biowybodeg a bioleg gyfrifiadurol
- Nodweddu macromolecylau biolegol