Publications

Journal articles:

* Corresponding or co-corresponding author

# Equal first authorship.

51. Calcium-driven in silico inactivation of a human olfactory receptor.

L. Pirona, F. Ballabio, M. Alfonso-Prieto, R. Capelli, J. Chem. Info. Model.  64, 2971–2978 (2024). (Link)

50. Fluoride permeation mechanism of the Fluc channel in liposomes revealed by solid-state NMR.

J. Zhang, D. Song, F. K. Schackert, J. Li, S. Xiang, C. Tian, W. Gong, P. Carloni, M. Alfonso-Prieto, C. Shi, Sci. Adv. 9, eadg9709 (2023). (Link)

49. Low Molecular Weight Inhibitors Targeting the RNA-Binding Protein HuR.

B. P. Joseph, V. Weber, L. Knüpfer, A. Giorgetti, M. Alfonso-Prieto, S. Krauß, P. Carloni, G. Rossetti, Intl. J. Mol. Sci. 24, 13127 (2023). (Link)

48. Machine learning-based modeling of olfactory receptors: Human OR51E2 as a case study.

M. Alfonso-Prieto*, R. Capelli*, J. Chem. Info. Model. 63, 2911–2917 (2023). (Link)

47. Substrate-assisted mechanism for the degradation of N‐glycans by a gut bacterial mannoside phosphorylase.

M. Alfonso-Prieto#, I. Cuxart#, G. Potocki-Véronèse, I. André, C. Rovira, ACS Catal., 13, 4283–4289 (2023). (Link)

46. Molecular determinants of acrylamide neurotoxicity through covalent docking.

N.P. F. Mueller, P. Carloni, M. Alfonso-Prieto*, Front. Pharmacol., 14, 1125871 (2023). (Link)

45. Neprilysin-dependent neuropeptide Y cleavage in the liver promotes fibrosis by blocking NPY-receptor 1.

C. Ortiz, S. Klein, W. H. Reul, F. Magdaleno, S. Gröschl, P. Dietrich, R. Schierwagen, F. E. Uschner, S. Torres, C. Hieber, C. Meier, N. Kraus, O. Tyc, M. Brol, S. Zeuzem, C. Welsch, M. Poglitsch, C. Hellerbrand, M. Alfonso-Prieto, F. Mira, U. auf dem Keller, A. Tetzner, A. Moore, T. Walther, J. Trebicka, Cell Reports, 42, 112059 (2023). (Link)

44. Hydrogen-bond networks for proton couplings in G-Protein Coupled Receptors.

A.-N. Bondar, M. Alfonso-Prieto, Front. Phys., 10, 963716 (2022). (Link)

43. OLHA (Nα-oleoylhistamine) modulates activity of mouse brain histaminergic neurons.

O.A. Sergeeva, K. Mazur, D. Reiner-Link, K. Lutsenko, H.L. Haas, M. Alfonso-Prieto, H. Stark, Neuropharmacol., 215, 109167 (2022). (Link)

42. Structure-function relationships of the disease-linked A218T oxytocin receptor variant.

M. Meyer, B. Jurek, M. Alfonso-Prieto, R. Ribeiro, V. M. Milenkovic, J. Winter, P. Hoffmann, C. H. Wetzel, A. Giorgetti, P. Carloni, I. D. Neumann, Mol. Psych.,  27, 907–917 (2022). (Link)

• FZJ press release 

• UR press release

• HBP press release

41. Photopharmacology of ion channels through the light of the computational microscope.

A. Nin-Hill, N.P.F. Mueller, C. Molteni, C. Rovira, M. Alfonso-Prieto*, Int. J. Mol. Sci., 22, 12072 (2021). (Link)

40. Bitter taste and olfactory receptors: Beyond chemical sensing in the tongue and the nose.

M. Alfonso-Prieto*, J. Membr. Biol., 254, 343–352 (2021). (Link)

39. Mechanisms underlying proton release in CLC-type F–/H+ antiporters.

M. G. Chiariello,  M. Alfonso-Prieto, E. Ippoliti, Ch. Fahlke, P. Carloni, J. Phys. Chem. Lett., 12, 4415–4420 (2021). (Link)

38. Robust principal component analysis‐based prediction of protein‐protein interaction hot spots.

D. Sitani, A. Giorgetti,  M. Alfonso-Prieto, P. Carloni, Proteins, 89, 639-647 (2021). (Link)

37. Subunit-specific photocontrol of glycine receptors by azobenzene-nitrazepam photoswitcher.

G. Maleeva*, A. Nin-Hill,  K. Rustler, E. Petukhova, D. Ponomareva, E. Mukhametova, A. Gomila-Juaneda,  D. Wutz, M. Alfonso-Prieto*, B. König, P. Gorostiza, P. Bregestovski*, eNeuro, 8, ENEURO.0294-20.2020 (2021). (Link)

• IBEC press release

36. Photocontrol of endogenous glycine receptors in vivo.

A. Gomila-Juaneda, K. Rustler, G. Maleeva, A. Nin-Hill, D. Wutz, A. Bautista-Barrufet, X. Rovira, M. Bosch, E. Mukhametova, F. Mukhamedyarov, F. Peiretti, M. Alfonso-Prieto, C. Rovira, B. König, P. Bregestovski, P. Gorostiza, Cell Chem. Biol., 27, 1425-1433 (2020). (Link)

35. Hybrid MM/CG Webserver: Automatic set up of molecular mechanics/coarse-grained simulations for human G protein-coupled receptor/ligand complexes.

J. Schneider, R. Ribeiro,  M. Alfonso-Prieto, P. Carloni, Alejandro Giorgetti,  Front. Mol. Biosci., 7, 576689 (2020). (Link)

34. Ligand pose predictions for human G protein-coupled receptors: insights from the Amber-based hybrid Molecular Mechanics/Coarse-Grained approach.

J. Schneider, K. Korshunova, Z. Si Chaib, A. Giorgetti, M. Alfonso-Prieto, P. Carloni, J. Chem. Inf. Model., 60, 5103-5116 (2020). (Link)

33. Dual binding mode of “bitter sugars” to their human bitter taste receptor target.

F. Fierro, A. Giorgetti, P. Carloni, W. Meyerhof, M. Alfonso-Prieto*, Sci. Rep. 9, 8437 (2019). (Link)

32. A photoswitchable GABA receptor channel blocker.

G. Maleeva,  D. Wutz,  K. Rustler,  A. Nin‐Hill,  C. Rovira, E. Petukhova,  A. Bautista‐Barrufet,  A. Gomila‐Juaneda,  P.  Scholze,  F. Peiretti,  M. Alfonso-Prieto*,  B. König,  P. Gorostiza*,  P. Bregestovski*, Br. J. Pharmacol. 176, 2661-2677 (2019). (Link)

31. Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.

V. A. Streltsov, S. Luang, A. Peisley, J. N. Varghese, J. R. Ketudat Cairns, S. Fort, M. Hijnen, I. Tvaroška, A. Ardá, J. Jiménez-Barbero, M. Alfonso-Prieto, C. Rovira, F. Mendoza, L. Tiessler-Sala, J.-E. Sánchez-Aparicio, J. Rodríguez-Guerra, J. M. Lluch, J.-D. Maréchal, L. Masgrau, M. Hrmova, Nature Comm. 10, 2222 (2019). (Link)

30. Characterization of cancer-associated IDH2 mutations that differ in tumorigenicity, chemosensitivity and 2-hydroxyglutarate production.

K. P. Kotredes, R. Razmpour, E. Lutton, M. Alfonso-Prieto, S. H. Ramirez, A. M. Gamero, Oncotarget, 10, 2675-2692 (2019). (Link)

• Featured cover paper in the journal Oncotarget Volume 10, Issue 28.

29. Understanding ligand binding to G-protein coupled receptors using multiscale simulations.

M. Alfonso-Prieto, L. Navarini, P. Carloni, Front. Mol. Biosci. 6, 29 (2019). (Link)

28. Multiscale simulations on human Frizzled and Taste2 GPCRs.

M. Alfonso-Prieto#, A. Giorgetti#, P. Carloni, Curr. Opin. Struct. Biol. 55, 8-16 (2019). (Link)

27. Oxazoline or oxazolinium ion? The protonation state and conformation of the reaction intermediate of chitinase enzymes revisited.

J. Coines,  M. Alfonso-Prieto,  X. Biarnés,  A. Planas, C. Rovira, Chem. Eur. J. 24(72), 19258-19265 (2018). (Link)

26.  Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations.

J. Schneider, K. Korshunova, F. Musiani, M. Alfonso-Prieto*, A. Giorgetti, P. Carloni*, Biochem. Biophys. Res. Comm. 498(2), 366-374 (2018). (Link)

25. Agonist binding to chemosensory receptors: a systematic bioinformatics analysis.

F. Fierro, E. Suku, M. Alfonso-Prieto*, A. Giorgetti*, S. Cichon, P. Carloni, Front. Mol. Biosci. 4, 63 (2017). (Link)

24. Multi-scale simulations of membrane proteins: the case of bitter taste receptors.

E. Suku, F. Fierro, A. Giorgetti*, M. Alfonso-Prieto*, P. Carloni, J. Sci. Adv. Mat. Dev. 2, 15-21 (2017). (Link)

23. Mechanism of ribonuclease III regulation by site-specific serine phosphorylation. 

S. Gone#, M. Alfonso-Prieto#, S. Paudyal and A.W. Nicholson, Sci. Rep. 6, 25448 (2016). (Link)

22. High resolution structures of the M2 proton channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction. 

J. L. Thomaston, M. Alfonso-Prieto, R. A. Woldeyes, J. S. Fraser, M. L. Klein, G. Fiorin and W. F. DeGrado, Proc. Natl. Acad. Sci. USA. 112(46), 14260-14265 (2015). (Link)

21. The molecular mechanism of the catalase-like activity in horseradish peroxidase.

P. Campomanes, U. Roethlisberger, M. Alfonso-Prieto* and C. Rovira*, J. Am. Chem. Soc. 137(34), 11170-11178 (2015). (Link)

20. Catalytic metal ions and enzymatic processing of DNA and RNA. 

G. Palermo, A. Cavalli, M. L. Klein, M. Alfonso-Prieto, M. Dal Peraro and M. De Vivo, Acc. Chem. Res. 48(2), 220-228 (2015). (Link)

19. Combined computational and experimental analysis of a complex of  ribonuclease III and the regulatory macrodomain protein YmdB. 

S. Paudyal#, M. Alfonso-Prieto#,  V. Carnevale, S. K. Redhu, M. L. Klein and A. W. Nicholson, Proteins 83(3), 459-472 (2015). (Link)  

• Cover image in the journal Proteins Volume 83, Issue 3. 

18. An integrated biological approach to guide the development of metal-chelating inhibitors of influenza virus PA endonuclease. 

A. Stevaert, S. Nurra, N. Pala, M. Carcelli, D. Rogolino, C. Shepard, R. A. Domaoal, B. Kim, M. Alfonso-Prieto, S. A. E. Marras, M. Sechi and L. Naesens, Mol. Pharm. 87(2), 323-337  (2015). (Link) 

17. Magnesium-dependent RNA binding to the PA endonuclease domain of the avian influenza polymerase. 

S. Xiao, M. L. Klein, D. N. LeBard, B. G. Levine, H. Liang, C. M. MacDermaid and M. Alfonso-Prieto*, J. Phys. Chem. B 118, 873-889  (2014). (Link) 

16. The reaction mechanisms of heme catalases: an atomistic view by ab initio molecular dynamics. 

M. Alfonso-Prieto, P. Vidossich, C. Rovira, Arch. Biochem. Biophys. 525(2), 121-30 (2012).  (Link)

15. Catalases versus peroxidases: DFT investigation of H2O2 oxidation in models systems and implications for heme protein  engineering. 

P. Vidossich, M. Alfonso-Prieto and C. Rovira, J. Inorg. Biochem. 117, 292-297 (2012).  (Link)

14. Role of the axial base in the modulation of the  cob(I)alamin electronic properties: insight from QM/MM, DFT, and CASSCF  calculations. 

N. Kumar, M. Alfonso-Prieto, C. Rovira, P. Lodowski, M. Jaworska and P. M. Kozlowski, J. Chem. Theor. Comput. 7(5), 1541-1551 (2011). (Link)

13. Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase. 

M. Alfonso-Prieto, H. Oberhofer, M. L. Klein, C. Rovira and J. Blumberger, J. Am. Chem. Soc. 133(12), 4285-4298 (2011). (Link)

12. Re-engineering specificity in 1,3-1,4-β-glucanase to accept branched xyloglucan substrates. 

T. Addington, B. Calisto, M. Alfonso-Prieto, C. Rovira, I. Fita and A. Planas, Proteins 79(2), 365-375 (2011). (Link)

11. Reductive cleavage mechanism of Co-C bond in cobalamin-dependent methionine synthase. 

M. Alfonso-Prieto, X. Biarnés, M. Kumar, C. Rovira and P. M. Kozlowski, J. Phys. Chem. B 114(40), 12965-12971 (2010). (Link) 

10. Substrate recognition in the Escherichia coli ammonia channel AmtB: a QM/MM investigation. 

T. P. Nygaard, M. Alfonso-Prieto, G. H. Peters, M. Jensen and C. Rovira, J. Phys. Chem. B 114(36), 11859-11865 (2010). (Link)

09. Modulation of Aβ42 fibrillogenesis by glycosaminoglycan structure.

J. J. Valle-Delgado, M. Alfonso-Prieto, N. S. deGroot, S. Ventura, J. Samitier, C. Rovira and X. Fernández-Busquets, FASEB J. 24(11), 4250-4261 (2010). (Link)

08. The dynamic role of distal side residues in heme hydroperoxidase catalysis.  Interplay between X-ray crystallography and ab initio simulations.

P. Vidossich, M. Alfonso-Prieto, X. Carpena, I. Fita, P. C. Loewen and C. Rovira, Arch. Biochem. Biophys., 500(1), 37-44 (2010). (Link)

07. On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation.

P. Vidossich, G. Fiorin, M. Alfonso-Prieto, E. Derat, S. Shaik and C. Rovira, J. Phys. Chem. B 114(15), 5161-5169 (2010). (Link)

• Selected by Journal of Physical Chemistry senior editor Pavel Jungwirth as one  of the 8 published articles in 2010 that highlighted the field of  Biophysical Chemistry.

06. The molecular mechanism of the catalase reaction. 

M. Alfonso-Prieto, X. Biarnés, P. Vidossich and C. Rovira, J. Am. Chem. Soc., 131(33), 11751-11761 (2009). (Link)

• My most cited paper (360 citations as of March 2023)

05. Electronic state of the molecular oxygen released by catalase. 

M. Alfonso-Prieto, P. Vidossich, A. Rodríguez-Fortea, X. Carpena, I. Fita, P. C. Loewen and C. Rovira, J. Phys. Chem. A, 112(50), 12842-12848 (2008). (Link)

04. The effect of a water molecule on the mechanism of formation of compound 0 in horseradish peroxidase.

E. Derat, S. Shaik, C. Rovira, P. Vidossich and M. Alfonso-Prieto, J. Am. Chem. Soc. (Comm.), 129(20), 6346-6347 (2007). (Link)

03. Versatility of the electronic structure of compound I in catalases-peroxidases. 

P. Vidossich, M. Alfonso-Prieto, X. Carpena, P. C. Loewen, I. Fita and C. Rovira, J. Am. Chem. Soc., 129(44), 13436-13446 (2007). (Link) 

02. The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by  X-ray crystallography and QM/MM density functional theory calculations. 

M. Alfonso-Prieto, A. Borovik, X. Carpena, G. Murshudov, W. Melik-Adamyan, I. Fita, C. Rovira and P. C. Loewen, J. Am. Chem. Soc., 129(14), 4193-4205 (2007). (Link) 

01. A first principles study of the binding of formic acid in catalase  complementing high resolution X-ray structures. 

C. Rovira, M. Alfonso-Prieto, X. Biarnés, X. Carpena, I. Fita and P. C. Loewen, Chem. Phys., 323(1), 129-137 (2006).  (Link)