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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
Trosolwg
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 2027, 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 gwneud cais yw Hydref 21ain 2026.
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)
Articles
- 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)
Websites
- 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 dwyn ynghyd ddylunio cyfrifiadurol a nodweddu arbrofol o broteinau. 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 arferol, gan ddefnyddio blociau adeiladu wedi'u nodweddu'n dda y gellir eu cyfuno trwy ryngwynebau hysbys ac Elfin, meddalwedd ar gyfer cynulliad modiwlaidd yr ydym wedi'i ddylunio. Mae'r broses yn caniatáu cyflawni cyfradd llwyddiant uchel yn arbrofol. Defnyddiwyd y strwythurau modiwlaidd hyn, yn seiliedig ar broteinau ailadroddus naturiol a dylunio, i adeiladu nanoronynnau arferol gyda swyddogaethau lluosog wedi'u hymgorffori ar gyfer adnabod ac actifadu celloedd trwy glystyru a chyd-glystyru derbynyddion.
Rhwymo carbohydradau
Rydym wedi datblygu meddalwedd dysgu peiriant, CLIMBS, ar gyfer adnabod a graddio rhwymo carbohydradau, fel dewis arall i swyddogaethau sgôr sy'n seiliedig ar ynni. Gall CLIMBS adnabod rhwymwyr tebyg i frodorol yn effeithlon, ac rydym yn ei ddefnyddio i werthuso canlyniadau docio moleciwlaidd a dylunio proteinau rhwymo carbohydradau newydd fel diagnosteg a therapiwteg posibl newydd.
Strwythurau protein anhyblyg a deinamig
Rydym wedi datblygu dulliau cyfrifiadurol i werthuso deinameg a chydymffurfiadau sydd ar gael o broteinau modiwlaidd yn gyflym. Rydym yn defnyddio'r offer hyn i ddylunio proteinau newydd gyda symudiadau penodol, a newid rhwng cydymffurfiadau caeedig ac agored o dan amodau penodol, megis newidiadau amgylcheddol a chydnabod targedau. Mae gan hyn gymwysiadau posibl wrth ddylunio nanoronynnau ar gyfer cyflenwi cyffuriau a biosynwyryddion.
Aelodau presennol y grŵp
Fabio Parmeggiani (PI)
Olivia Little (myfyrwraig PhD)
Otsile Mojanaga (Ôl-ddoethurol)
Roberta Verde (myfyriwr MSc)
Cydweithwyr
Louis Luk (Prifysgol Caerdydd): dylunio proteinau synthetig
Angela Nobbs (Prifysgol Bryste): gwrthficrobyddion ar gyfer bioffilmiau
Addysgu
Meistr mewn Bioleg Canser: Biowybodeg protein PHT806
Cwrs MPharm: cydrannau cellog PH1123
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