Publications

Scientific Publications

  1. I. Maffucci, D. Laage, G. Stirnemann, F. Sterpone, "Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes", PCCP (2020) in press.
  2. I. Maffucci, D. Laage, F. Sterpone, G. Stirnemann, "Thermal Adaptation of Enzymes: Impacts of Conformational Shifts on Catalytic Activation Energy and Optimum Temperature", Chemistry (2020), 26,  10045-10056.
  3. Stepan Timr, David Gnutt, Simon Ebbinghaus, and Fabio Sterpone “The Unfolding Journey of Superoxide Dismutase 1 Barrels under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions with Crowders”, (2020) J. Phys. Chem. Lett. 11, 4206-421.
  4. S. Timr, D. Madern, F. Sterpone, “Protein thermal stability”, Academic Press (2020)
  5. P. Nguyen, F. Sterpone, P. Derreumaux, “Aggregation of disease-related peptides”, Academic Press (2020)
  6. M. Katava, M. Marchi, D. Madern, M. Sztucki, M. Maccarini, F. Sterpone, “Temperature Unmasks Allosteric Propensity in a Thermophilic Malate Dehydrogenase via Dewetting and Collapse”, J. Phys. Chem. B (2020) in press
  7. A. Brander, S. Timr, S. Melchionna, P. Derreumaux, M. Baaden, F. Sterpone, "Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics", Sci. Rep. (2019), 9, 16450
  8. F. Barroso da Silva, F. Sterpone, P. Derreumaux,"OPEP6: A new constant-pH Molecular Dynamics simulation scheme with OPEP coarse-grained force field", J. Chem. Theory Comput. (2019), 15, 3875-3888
  9. M. Chiricotto, S. Melchionna, P. Derreumaux, F. Sterpone, «Multiscale Aggregation of the Amyloid Aβ16–22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils», J. Phys. CHem. Lett.  (2019), 10, 1594–1599.
  10. D. Gnutt, S. Timr∥, J. Ahlers, B. König, E. Manderfeld, M. Heyden, F. Sterpone, and S Ebbinghaus "Stability Effect of Quinary Interactions Reversed by Single Point Mutations", (2019), J. Am. Chem. Soc., 141,  4660–4669.
  11. Y. Lu, X. Shi, P. Nguyen, F. Sterpone, F. R. Salsbury Jr., and P. Derreumaux, "Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids", (2019), J. Phys. Chem. B 123 , 2687–2696.
  12. P. Maiocchi, P. Derreumaux, F. Sterpone, S. Melchionna, "Mesoscale biosimulations within a unified framework: from proteins to plasmids", Molecular Simulation, DOI 10.1080/08927022.2018.1560439
  13. O. Languin-Cattoën, S. Melchionna, P. Derreumaux, G. Stirnemann, and F. Sterpone, "Three Weaknesses for Three Perturbations: Comparing Protein Unfolding Under Shear, Force, and Thermal Stresses", (2018), J. Phys. Chem. B in press.
  14. M. Bernaschi, S. Melchionna,P. Derreumaux, F. Sterpone, S. Succi, "Multilevel Lattice Boltzmann-Particle Dynamics simulations at the Physics-Biology interface", J. Phys. (2018), 1136 [Free here]
  15. M. Kinoshita, Y. Lin, I. Dai, M. Okumura, N. Markova, J. E. Ladbury, F Sterpone  and  Y-Ho Lee, “Energy landscape of polymorphic amyloid generation of β2-microglobulin revealed by calorimetry”, (2018) Chem. Commun., 2018,54, 7995-7998
    1. G. Sutherland et al,  «Probing the quality control mechanism of the Escherichia coli twin-arginine translocase using folding variants of a de novo-designed heme protein», (2018) J. Biol. Chem. in press. 
    2. S. Murail, T. Vasiliu, A. Neamtu, M. Barboiu, F. Sterpone, M. Baaden, « Modeling artificial water channels embedded in a membrane environment: dynamic properties of confined water in I-quartet channels.», (2018) in press Faraday Discussion.
    3. Fabio Sterpone, Philippe Derreumaux, and Simone Melchionna, "Molecular Mechanism of Protein Unfolding under Shear: A Lattice Boltzmann Molecular Dynamics Study", J. Phys. Chem. (2018), 122, 1573–1579.
    4. G. Stirnemann, F. Sterpone, "Mechanics of Protein Adaptation to High Temperatures", J. Phys. Chem. Lett.,(2017), 8, 5884–5890. 
    5. F. Sterpone, S. Melchionna, S. Doutreligne, T. Tran, P. Nguyen, M. Baaden, P. Derreumaux, PhD«Multi-scale and Multi-physics Simulations of Biological Systems using the OPEP Coarse-grained Model»,(2017) BBRC, 498, 296-30
    6. M. Katava, G. Stirnemann, M. Zanatta, S. Capaccioli, M. Pacchetti, K. Ngai, F. Sterpone, A. Paciaroni, «Critical structural fluctuations of proteins at the thermal unfolding: challenging the Lindemann criterion», (2017), PNAS, 114,  9361–9366.
    7. O.  Rahaman, M. Kalimeri, M. Katava, A. Paciaroni, and F. Sterpone «Configurational Disorder of Water Hydrogen Bond Network at the Protein Dynamical Transition» J. Phys. Chem. B (2017) 121, 6792−6798.
    8. A. J. Doig,  M. Castillo-Frias, O. Berthoumieu, B. Tarus, J. Nasica-Labouze, F. Sterpone, P. H. Nguyen, N. M. Hooper, P. Faller, and Philippe Derreumaux «Why Is Research on Amyloid-β Failing to Give New Drugs for Alzheimer’s Disease?», ACS Chem. Neurosci, (2017) 8, 1435–1437.
    9. M. Katava, M. Maccarini, G. Villain, A. Paciaroni, M. Sztucki, O. Ivanova, D. Madern, and F. Sterpone, «Thermal activation of ‘allosteric-like’ large-scale motions in a eukaryotic Lactate Dehydrogenase.», Sci. Reports. (2016) 7, 41092. [Free at Scientific Reports]
    10. P. H. Nguyen, F. Sterpone, R. Pouplana, P. Derreumaux, and J. M. Campanera, «Dimerization Mechanism of Alzheimer Aβ40 Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation», J. Phys. Chem. B (2016), 120 (47), pp 12111–12126.
    11. M. Chiricotto, P. Derreumaux, F. Sterpone, S. Melchionna, «Multiscale simulation of molecular processes in cellular environments», Phil. Trans. A (2016), 374 20160225.
    12. M. Chiricotto, T. T. Tran, P. H. Nguyen, S. Melchionna, F. Sterpone and P. Derreumaux, «Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation», Isr. J. Chem. (2016), DOI: 10.1002/ijch.201600048.
    13. M. Chiricotto, S. Melchionna, P. Derreumaux, F. Sterpone, «Hydrodynamic effects on β-amyloid (16-22) peptide aggregation», J. Chem. Phys. (2016), 145, 035102. 
    14. M-C. Bellissent-Funel, A. Hassanali, M. Havenith, R. Henchman∥, P. Pohl, F. Sterpone, D. van der Spoel, Y. Xu, and Angel E Garcia,  «Water Determines the Structure and Dynamics of Proteins», Chem.Rev. (2016) 116, 7673–7697
    15. P. H. Nguyen, F. Sterpone, J. M. Campanera, J. Nasica-Labouze , and Philippe Derreumaux, «Impact of the A2V mutation on the Heterozygous and Homozygous Aβ1-40 Dimer Structures from Atomistic Simulations», ACS Chem. Neurosci. (2016) 7, 823–832
    16. M. Katava, M. Kalimeri, G. Stirnemann, and F. Sterpone, «Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from its Mesophilic Homologue», J. Phys. Chem. B (2016), 120, 2721–2730
    17. G. Stirnemann, F. Sterpone, «Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent», J. Chem. Theory Comput. (2015), 11, 5573–5577 
    18. D.Chakraborty, A. Taly, F. Sterpone, «Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins», J. Phys. Chem. B (2015) 119 (40), 12760–12770. [Free at Europe PMC]
    19. B. Tarus , T. T. Tran , J. Nasica-Labouze , F. Sterpone , P. H. Nguyen , and P. Derreumaux, «Structures of the Alzheimer’s Wild-Type Aβ1-40 Dimer from Atomistic Simulations», J. Phys.Chem. B (2015) 119, 10478–1048.
    20. F. Sterpone, P. Derreumaux, S. Melchionna «Protein simulations in fluids: coupling the OPEP coarse-grained force field with hydrodynamics», J. Chem. Theory Comput. (2015) 11, 1843-1853. [Free at Europe PMC]
    21. J. Nasica-Labouze et al., « Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies», Chem. Rev. (2015), 115, 3518–3563.
    22. M. Kalimeri, P. Derreumaux, F. Sterpone «Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field », J. Non-Cryst. Solids (2015), 407, 494-501. [Free at Europe PMC]
    23. O. Rahaman, M. Kalimeri, S. Melchionna, J. Henin, F. Sterpone  «Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains», J. Phys. Chem. B (2015),119, 8939-49. [Free at Europe PMC]
    24. M. Kalimeri, E.Girard, D. Madern, F. Sterpone «Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase», Plos ONE (2014), 9, e113895. [Free at PlosONE] 
    25. F. Sterpone et al. « The OPEP coarse-grained protein model: from single molecules, amyloid formation, role of macromolecular crowding and hydrodynamics to RNA/DNA complexes», Chem.Soc.Rev. (2014), 43, 4871-4893. [Free at Europe PMC]
    26. M. Kalimeri, S. Melchionna, F. Sterpone, « Inquiring Protein Thermostability: Is Resistance to Temperature Stress a Rigidity/Flexibility Trade-off? », Proceedings of the European Conference on Complex Systems 2012, Springer Proceedings in Complexity 2013, pp 535-541.
    27. M. Kalimeri, O. Rahaman, S. Melchionna, F. Sterpone, « How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain », J. Phys. Chem . B (2013), 117, 13775-13785. [Free at Europe PMC]
    28. F. Sterpone, P. Nguyen, M. Kalimeri, P. Derreumaux, « Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation », J. Chem. Theory Comput. (2013), 9, 4574-4584. [Free at Europe PMC]
    29. A. Fogarty, E. Duboue-Dijon, F.Sterpone, J.T. Hynes, D. Laage, « Biomolecular hydration dynamics: a jump model perspective », Chem. Soc. Rev.(2013), 42, 5672-5683
    30. O. Rahamn, S. Melchionna, D. Laage, F. Sterpone « Effect of protein composition on hydration dynamics », PCCP (2013), 15, 3570-3576. [Free at Europe PMC]
    31. M. Montagna, F. Sterpone, L. Guidoni, « Structural and Spectroscopic Properties of Water around Small Hydrophobic Solutes », J. Phys. Chem. B (2012), 116, 11695-11700. [Free at Europe PMC] 
    32. F. Sterpone, S. Bonella, S. Meloni, « Exploring dehydrogenation process in Alanates via Temperature Accelerated ab initio Molecular dynamics », J. Phys. Chem. C (2012), 116, 19636-19643
    33. F. Sterpone,  G. Stirnemann, D. Laage, « Magnitude and molecular origin of water slowdown next to protein », J. Am. Chem. Soc. (2012), 134, 4116-4119.
    34. F. Sterpone and S. Melchionna, «Thermophilic proteins : insight and perspective from in silico experiments », Chem.Soc.Rev. (2012), 41, 1665-1676. [Free at Europe PMC]
    35. D. Laage, G. Stirnemann, F. Sterpone, J.T. Hynes, « Water Jump Reorientation : From Theoretical Prediction to Experimental Observation », Acc. Chem. Res. (2012), 45, 53-62. 
    36. F. Sterpone, R. Martinazzo, A.N. Panda, I. Burghardt, « Coherent Excitation Transfer Driven by Torsional Dynamics: a Model Hamiltonian for PPV Type Systems », Zeitschrift für Physikalische Chemie (2011), 255, 541-551.
    37. F.Sterpone, S.Melchionna, « Role of packing, hydration and fluctuation on Thermostability”, Chapter for “Thermostable proteins: Structural stability and design ». CRC Press- Taylor and Francis. L. Nilsson and S.Sen Eds.
    38. G. Stirnemann, F. Sterpone,  D. Laage, « Dynamics of water in concentrated solutions of amphiphiles: key roles of local structure and aggregation » J. Phys. Chem . B (2011), 115, 3254-3262. 
    39. D. Laage , G.Stirnemann, F.Sterpone, R. Rey, J.T. Hynes, «Reorientation and allied dynamics in water and aqueous solution », Ann. Rev. Phys. Chem.( 2011), 62, 395-416.
    40. M. Bedard-Hearn, F. Sterpone, P.J. Rossky, « Non adiabatic simulations of exciton dissociation in poly-p-phenylenevinylene oligomers ». J.Phys.Chem. A (2010), 114, 7661–7670.
    41. F. Sterpone, C. Bertonati, G. Briganti, S. Melchionna, “Water around thermophilic proteins: the role of charged and polar atoms », J. of Physics: Condensed Matter (2010), 22, 28413.
    42. F.Sterpone, G.Stirnemann, J.T. Hynes, D. Laage, “Water Hydrogen bond dynamics around amino acids: The key role of hydrophilic hydrogen-bond acceptor groups », J. Phys. Chem. B (2010), 114, 2083-2089.
    43. F. Sterpone, G. Briganti and C. Pierleoni, « Sphere vs Cylinder: The effect of packing on the structure on non ionic C12E6 micelles ». Langmuir (2009), 25, 8960-8967.
    44. F. Sterpone, M. Bedard-Hearn, P.J. Rossky, « Non adiabatic mixed quantum-classical simulation of p-stacked PPV oligomers in the groud state and excited states ». J.Phys.Chem. A (2009), 113, 3427–3430. 
    45. F. Sterpone, C. Bertonati, G. Briganti, S. Melchionna « Key role of proximal water on protein thermostability ». J.Phys.Chem.B. (2009), 113, 131-137.
    46. F. Sterpone, L. Spanu, L. Ferraro, S. Sorella, L. Guidoni « Water-water hydrogen bond studied by QMC ». J. Chem.Theory and Comput. (2008), 4, 1428-1432.
    47. F. Sterpone, G. Briganti, S. Melchionna, C. Pierleoni « Pressure induced core packing and interfacial dehydration in nonionic C12E6 micelle in acqueous solution ». Langmuir (2008), 24, 6067-6071. 
    48. F. Sterpone, P.J. Rossky, « Molecular modeling and simulation of conjugated polymer oligomers: Ground and excited state chain dynamics of PPV in the gas phase ». J. Phys. Chem. B (2008), 112, 4983-4993.
    49. F. Pizzitutti, M. Marchi, F. Sterpone, P.J. Rossky, « How Protein Surfaces Induce Anomalous Dynamics of Hydration Water ».  J. Phys. Chem. B. (2007), 111, 7584-7590.
    50. F. Sterpone, C. Pierleoni, G. Briganti, M. Marchi, « Structure and dynamics of hydrogen bonds in the interface of a C12E6 spherical micelle in water solution: A MD study at various temperatures ».  J. Phys. Chem. B. (2006), 110, 18254-18261.
    51. F. Sterpone, G. Marchetti, C. Pierleoni, M. Marchi, « Molecular modeling and simulation of water near model micelles : Diffusion, rotational relaxation and structure at the hydration interface ». J. Phys. Chem. B. (2006), 110, 11504-11510. 
    52. G.Briganti, G.D’Arrigo, M.Maccarini, C.Pierleoni, F. Sterpone, « Hydration and thermodynamic equilibrium of nonionic surfactant solution », Colloids and Surfaces (2005), 261, 93-99.
    53. S.Abel, F.Sterpone, S. Bandyopadhyay, M.Marchi, « Molecular modeling and simulation of AOT-water reverse Micelles in iso-octane: structural and dynamic properties », J. Phys. Chem. B. (2005), 108, 19458-19466. 
    54. F.Sterpone, C.Pierleoni, G.Briganti, M.Marchi, « Temperature dehydration of C12E6 micelle », Langmuir (2004), 20, 4311-4314. 
    55. F.Sterpone, M.Ceccarelli, M.Marchi, « Linear response and electron transfer in complex biomolecules systems and Reaction Center Protein », J. Phys. Chem. B (2003), 107, 11208-11215.
    56. M.Marchi, F.Sterpone, M.Ceccarelli, « Water rotational relaxation and diffusion in hydrated Lysozyme », J. Am. Chem. Soc. (2002), 124, 23, 6787-6791.
    57. F.Sterpone, M.Ceccarelli, M.Marchi, « Dynamics of hydration in Hen Egg White Lysozyme », J.Mol.Biol. (2001), 311, 429-439.
    58. F.Sterpone, G.Briganti, C.Pierleoni, « Molecular Dynamics study of spherical aggregates of chain molecules at different degree of hydrophilicity in water solution », Langmuir (2001), 17, 5103-5110.

    PhD Thesis

    Maria KALIMERI :: "Are thermophilic proteins rigid or flexible?" [here]
    Mara CHIRICOTTO :: "Hydrodynamic effect on b-amyloid peptide aggregation" [here]
    Marina KATAVA :: "Thermophilic proteins: stability and function" [here]. Award:: Best PHD Thesis GGMM Prize (2017)
    Astrid Brandner ::  "Multi-scale methods for membrane systems applied to confined systems and membrane fusion"

     

     

    Science & Society

     

    TOWARD NEW THERMOSTABLE PROTEINS

    The RESEARCH MEDIA crew publishes an highlight of the project THERMOS on the magazine International Innovation, N. 136

    The contribution is available below (Courtesy of International Innovation) and is published under the Creative Common License.

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    With the crew LASER ( think thank for discussing the horizons in Science, Epistemology and Research), I am coauthor of

     

    FREE KNOWLEDGE (Il sapere liberato)

    Feltrinelli (2005).

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    The free-software movement and its philosophy could inspire practices in the broad arena of the scientific research?   

     

     

     

     

    SCIENCE SPA

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    LASER. (publisher's catalog) 

    A quest for an appropriate description of the scientific workers in the "post-FORD" new-economy era. When science is more and more at the crossroad of business and technology, how science and society talk each others?

     

     

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