Skip to main content
SpringerLink
Log in

Multi-Scale Approach for Self-Assembly and Protein Folding

  • Chapter
  • First Online:
Book cover Design of Self-Assembling Materials

Abstract

We develop a multi-scale approach to simulate hydrated nanobio systems under realistic conditions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of water at bio-interfaces (e.g., proteins or membranes) and nano-interfaces (e.g., nanoparticles or graphene sheets) and coarse-grain models of hydration water for protein folding and protein design. We study protein self-assembly and crystallization, in bulk or under confinement, and the kinetics of protein adsorption onto nanoparticles, verifying our predictions in collaboration with several experimental groups. We try to find answers for fundamental questions (Why water is so important for life? Which properties make water unique for biological processes?) and applications (Can we design better drugs? Can we limit protein-aggregations causing Alzheimer? How to implement nanotheranostic?). Here we focus only on the two larger scales of our approach: (1) The coarse-grain description of hydrated proteins and protein folding at sub-nanometric length-scale and milliseconds-to-seconds time-scales, and (2) the coarse-grain modeling of protein self-assembly on nanoparticles at 10-to-100 nm length-scale and seconds-to-hours time-scales.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 54.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Levy Y, Onuchic JN. Water and proteins: a love-hate relationship. Proc Natl Acad Sci USA. 2004;101(10):3325–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Levy Y, Onuchic JN. Mechanisms of protein assembly: lessons from minimalist models. Acc Chem Res. 2006;39(2):135–42.

    Article  CAS  PubMed  Google Scholar 

  3. Raschke TM. Water structure and interactions with protein surfaces. Curr Opin Struct Biol. 2006;16(2):152–9.

    Article  CAS  PubMed  Google Scholar 

  4. Zipp A, Kauzmann W. Pressure denaturation of metmyoglobin. Biochemistry 1973;12(21):4217–28.

    Article  CAS  PubMed  Google Scholar 

  5. Privalov PL. Cold denaturation of proteins. Crit Rev Biochem Mol Biol. 1990;25(4):281–305.

    Article  CAS  PubMed  Google Scholar 

  6. Hummer G, Garde S, García AE, Paulaitis ME, Pratt LR. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proc Natl Acad Sci. 1998;95(4):1552–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Meersman F, Smeller L, Heremans K. Pressure-assisted cold unfolding of proteins and its effects on the conformational stability compared to pressure and heat unfolding. High Pressure Res. 2000;19(1–6):263–8.

    Article  Google Scholar 

  8. Lassalle MW, Yamada H, Akasaka K. The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR. J Mol Biol. 2000;298(2):293–302.

    Article  CAS  PubMed  Google Scholar 

  9. Smeller L. Pressure-temperature phase diagrams of biomolecules. Biochim Biophys Acta Protein Struct Mol Enzymol. 2002;1595(1–2):11–29.

    Article  CAS  Google Scholar 

  10. Herberhold H, Winter R. Temperature- and pressure-induced unfolding and refolding of ubiquitin: a static and kinetic Fourier transform infrared spectroscopy study. Biochemistry 2002;41(7):2396–401.

    Article  CAS  PubMed  Google Scholar 

  11. Lesch H, Stadlbauer H, Friedrich J, Vanderkooi JM. Stability diagram and unfolding of a modified cytochrome c: what happens in the transformation regime? Biophys J. 2002;82(3):1644–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ravindra R, Winter R. On the temperature–pressure free-energy landscape of proteins. Chem Phys Chem. 2003;4(4):359–65.

    Article  CAS  PubMed  Google Scholar 

  13. Meersman F, Dobson CM, Heremans K. Protein unfolding, amyloid fibril formation and configurational energy landscapes under high pressure conditions. Chem Soc Rev. 2006;35(10):908–17.

    Article  CAS  PubMed  Google Scholar 

  14. Pastore A, Martin SR, Politou A, Kondapalli KC, Stemmler T, Temussi PA. Unbiased cold denaturation: low- and high-temperature unfolding of yeast Frataxin under physiological conditions. J Am Chem Soc. 2007;129(17):5374–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wiedersich J, Köhler S, Skerra A, Friedrich J. Temperature and pressure dependence of protein stability: the engineered fluorescein-binding lipocalin FluA shows an elliptic phase diagram. Proc Natl Acad Sci USA. 2008;105(15):5756–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Maeno A, Matsuo H, Akasaka K. The pressure–temperature phase diagram of hen lysozyme at low pH. Biophysics 2009;5:1–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Somkuti J, Mártonfalvi Z, Kellermayer MSZ, Smeller L. Different pressure–temperature behavior of the structured and unstructured regions of titin. Biochim. Biophys. Acta 2013;1834(1):112–8.

    Article  CAS  PubMed  Google Scholar 

  18. Somkuti J, Jain S, Ramachandran S, Smeller L. Folding-unfolding transitions of Rv3221c on the pressure-temperature plane. High Pressure Res. 2013;33(2):250–7.

    Article  CAS  Google Scholar 

  19. Nucci NV, Fuglestad B, Athanasoula EA, Wand AJ. Role of cavities and hydration in the pressure unfolding of T4 lysozyme. Proc Natl Acad Sci USA. 2014;111(38):13846–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Griko YV, Privalov PL, Sturtevant JM, Venyaminov SY. Cold denaturation of staphylococcal nuclease. Proc Natl Acad Sci. 1988;85(10):3343–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Goossens K, Smeller L, Frank J, Heremans K. Pressure-tuning the conformation of bovine pancreatic trypsin inhibitor studied by fourier-transform infrared spectroscopy. Eur J Biochem. 1996;236(1):254–62.

    Article  CAS  PubMed  Google Scholar 

  22. Nash DP, Jonas J. Structure of the pressure-assisted cold denatured state of ubiquitin. Biochem Biophys Res Commun. 1997;238(2):289–91.

    Article  CAS  PubMed  Google Scholar 

  23. Nash DP, Jonas J . Structure of pressure-assisted cold denatured lysozyme and comparison with lysozyme folding intermediates. Biochemistry 1997;36(47):14375–83.

    Article  CAS  PubMed  Google Scholar 

  24. De Los Rios P, Caldarelli G. Putting proteins back into water. Phys Rev E. 2000;62(6):8449–52.

    Article  Google Scholar 

  25. Marqués MI, Borreguero JM, Stanley HE, Dokholyan NV. Possible mechanism for cold denaturation of proteins at high pressure. Phys Rev Lett. 2003;91(13):138103.

    Article  PubMed  CAS  Google Scholar 

  26. Patel BA, Debenedetti PG, Stillinger FH, Rossky PJ. A water-explicit lattice model of heat-, cold-, and pressure-induced protein unfolding. Biophys J. 2007;93(12):4116–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Athawale MV, Goel G, Ghosh T, Truskett TM, Garde S. Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water. Proc Natl Acad Sci USA. 2007;104(3):733–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Nettels D, Müller-Späth S, Küster F, Hofmann H, Haenni D, Rüegger S, Reymond L, Hoffmann A, Kubelka J, Heinz B, Gast K, Best RB, Schuler B. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci. 2009;106(49):20740–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Best RB, Mittal J. Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse. J Phys Chem B. 2010;114(46):14916–23.

    Article  CAS  PubMed  Google Scholar 

  30. Jamadagni SN, Bosoy C, Garde S. Designing heteropolymers to fold into unique structures via water-mediated interactions. J Phys Chem B. 2010;114(42):13282–8.

    Article  CAS  PubMed  Google Scholar 

  31. Badasyan AV, Tonoyan SA, Mamasakhlisov YS, Giacometti A, Benight AS, Morozov VF. Competition for hydrogen-bond formation in the helix-coil transition and protein folding. Phys Rev E Stat Nonlin Soft Matter Phys. 2011;83(5 Pt 1):051903.

    Article  CAS  PubMed  Google Scholar 

  32. Matysiak S, Debenedetti PG, Rossky PJ. Role of hydrophobic hydration in protein stability: a 3D water-explicit protein model exhibiting cold and heat denaturation. J Phys Chem B. 2012;116(28):8095–104.

    Article  CAS  PubMed  Google Scholar 

  33. Bianco V, Iskrov S, Franzese G. Understanding the role of hydrogen bonds in water dynamics and protein stability. J Biol Phys. 2012;38(1):27–48.

    Article  CAS  PubMed  Google Scholar 

  34. Bianco V, Franzese G. Contribution of water to pressure and cold denaturation of proteins. Phys Rev Lett. 2015;115(10):108101.

    Article  PubMed  CAS  Google Scholar 

  35. Paschek D, García AE. Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study. Phys Rev Lett. 2004;93(23):238105.

    Article  PubMed  CAS  Google Scholar 

  36. Paschek D, Gnanakaran S, Garcia AE. Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proc Natl Acad Sci USA. 2005;102(19):6765–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Sumi T, Sekino H. Possible mechanism underlying high-pressure unfolding of proteins: formation of a short-period high-density hydration shell. Phys Chem Chem Phys. 2011;13(35):15829–32.

    Article  CAS  PubMed  Google Scholar 

  38. Coluzza I. A coarse-grained approach to protein design: learning from design to understand folding. PloS One 2011;6(7):e20853.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Dias CL. Unifying microscopic mechanism for pressure and cold denaturations of proteins. Phys Rev Lett. 2012;109(4):048104.

    Article  PubMed  CAS  Google Scholar 

  40. Das P, Matysiak S. Direct characterization of hydrophobic hydration during cold and pressure denaturation. J Phys Chem B. 2012;116(18):5342–8.

    Article  CAS  PubMed  Google Scholar 

  41. Sarma R, Paul S. Effect of pressure on the solution structure and hydrogen bond properties of aqueous N-methylacetamide. Chem Phys. 2012;407:115–23.

    Article  CAS  Google Scholar 

  42. Franzese G, Bianco V. Water at biological and inorganic interfaces. Food Biophys. 2013;8(3):153–69.

    Article  Google Scholar 

  43. Abeln S, Vendruscolo M, Dobson CM, Frenkel D. A simple lattice model that captures protein folding, aggregation and amyloid formation. PloS One 2014;9(1):e85185.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Yang C, Jang S, Pak Y. A fully atomistic computer simulation study of cold denaturation of a β-hairpin. Nat Commun. 2014;5:5773.

    Article  CAS  PubMed  Google Scholar 

  45. Roche J, Caro JA, Norberto DR, Barthe P, Roumestand C, Schlessman JL, Garcia AE, García-Moreno BE, Royer CA, Garc∖’ia AE, Garcia-Moreno BE, Royer CA. Cavities determine the pressure unfolding of proteins. Proc Natl Acad Sci USA. 2012;109(18):6945–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Nisius L, Grzesiek S. Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network. Nat Chem. 2012;4(9):711–7.

    Article  CAS  PubMed  Google Scholar 

  47. van Dijk E, Varilly P, Knowles TP, Frenkel D, Abeln S. Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation. arXiv e-prints 2015;116(7):078101.

    Google Scholar 

  48. Larios E. Gruebele M. Protein stability at negative pressure. Methods (San Diego, Calif.) 2010;52(1):51–6.

    Google Scholar 

  49. Hatch HW, Stillinger FH, Debenedetti PG. Computational study of the stability of the miniprotein Trp-cage, the GB1 β-hairpin, and the AK16 peptide, under negative pressure. J Phys Chem B. 2014;118(28):7761–9.

    Article  CAS  PubMed  Google Scholar 

  50. Hawley SA. Reversible pressure–temperature denaturation of chymotrypsinogen. Biochemistry 1971;10(13):2436–42.

    Article  CAS  PubMed  Google Scholar 

  51. Meersman F, Smeller L, Heremans K. Protein stability and dynamics in the pressure-temperature plane. Biochim Biophys Acta. 2006;1764(3):346–54.

    Article  CAS  PubMed  Google Scholar 

  52. Stokely K, Mazza MG, Stanley HE, Franzese G. Effect of hydrogen bond cooperativity on the behavior of water. Proc Natl Acad Sci USA. 2010;107:1301–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Strekalova EG, Mazza MG, Stanley HE, Franzese G. Large decrease of fluctuations for supercooled water in hydrophobic nanoconfinement. Phys Rev Lett. 2011;106:145701.

    Article  PubMed  CAS  Google Scholar 

  54. Franzese G, Bianco V, Iskrov S. Water at interface with proteins. Food Biophys. 2011;6:186–98. https://doi.org/10.1007/s11483-010-9198-4.

    Article  Google Scholar 

  55. Mazza MG, Stokely K, Pagnotta SE, Bruni F, Stanley HE, Franzese G. More than one dynamic crossover in protein hydration water. Proc Natl Acad Sci. 2011;108(50):19873–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Bianco V, Vilanova O, Franzese G. Polyamorphism and polymorphism of a confined water monolayer: liquid–liquid critical point, liquid–crystal and crystal–crystal phase transitions. In: Proceedings of perspectives and challenges in statistical physics and complex systems for the next decade: a conference in honor of Eugene Stanley and Liacir Lucen; 2013. p. 126–49.

    Google Scholar 

  57. de los Santos F, Franzese G. Understanding diffusion and density anomaly in a coarse-grained model for water confined between hydrophobic walls. J Phys Chem B. 2011;115:14311–20.

    Google Scholar 

  58. Bianco V, Franzese G. Critical behavior of a water monolayer under hydrophobic confinement. Sci Rep. 2014;4:4440.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  59. Coronas LE, Bianco V, Zantop A, Franzese G. Liquid–liquid critical point in 3D many-body water model. arXiv e-prints, October 2016.

    Google Scholar 

  60. Corradini D, Gallo P. Liquid–liquid coexistence in NaCl aqueous solutions: a simulation study of concentration effects. J Phys Chem B. 2011;115(48):14161–6.

    Article  CAS  PubMed  Google Scholar 

  61. Hernández de la Peña L, Kusalik PG. Temperature dependence of quantum effects in liquid water. J Am Chem Soc. 2005;127(14):5246–51.

    Article  PubMed  CAS  Google Scholar 

  62. Soper AK, Antonietta Ricci M. Structures of high-density and low-density water. Phys Rev Lett. 2000;84(13):2881–4.

    Article  CAS  PubMed  Google Scholar 

  63. Lau FK, Dill KA. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules 1989;22(10):3986–97.

    Article  CAS  Google Scholar 

  64. Caldarelli G, De Los Rios P. Cold and warm denaturation of proteins. J Biol Phys. 2001;27(2–3):229–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Dias CL, Ala-Nissila T, Karttunen M, Vattulainen I, Grant M. Microscopic mechanism for cold denaturation. Phys Rev Lett. 2008;100(11):118101–4.

    Article  PubMed  CAS  Google Scholar 

  66. Petersen CL, Tielrooij K-J, Bakker HJ. Strong temperature dependence of water reorientation in hydrophobic hydration shells. J Chem Phys. 2009;130(21):214511.

    Article  CAS  PubMed  Google Scholar 

  67. Sarupria S. Garde S. Quantifying water density fluctuations and compressibility of hydration shells of hydrophobic solutes and proteins. Phys Rev Lett. 2009;103(3):37803.

    Article  CAS  Google Scholar 

  68. Tarasevich YI. State and structure of water in vicinity of hydrophobic surfaces. Colloid J. 2011;73(2):257–66.

    Article  CAS  Google Scholar 

  69. Davis JG, Gierszal KP, Wang P, Ben-Amotz D. Water structural transformation at molecular hydrophobic interfaces. Nature 2012;491(7425):582–5.

    Article  CAS  PubMed  Google Scholar 

  70. Muller N. Search for a realistic view of hydrophobic effects. Acc Chem Res. 1990;23(1):23–8.

    Article  CAS  Google Scholar 

  71. Lum K, Chandler D, Weeks JD. Hydrophobicity at small and large length scales. J Phys Chem B. 1999;103(22):4570–7.

    Article  CAS  Google Scholar 

  72. Schwendel D, Hayashi T, Dahint R, Pertsin A, Grunze M, Steitz R, Schreiber F . Interaction of water with self-assembled monolayers: neutron reflectivity measurements of the water density in the interface region. Langmuir 2003;19(6):2284–93.

    Article  CAS  Google Scholar 

  73. Jensen TR, Østergaard Jensen M, Reitzel N, Balashev K, Peters GH, Kjaer K, Bjørnholm T. Water in contact with extended hydrophobic surfaces: direct evidence of weak dewetting. Phys Rev Lett. 2003;90(8):86101.

    Article  CAS  Google Scholar 

  74. Doshi DA, Watkins EB, Israelachvili JN, Majewski J. Reduced water density at hydrophobic surfaces: effect of dissolved gases. Proc Natl Acad Sci USA. 2005;102(27):9458–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Godawat R, Jamadagni SN, Garde S. Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations. Proc Natl Acad Sci USA. 2009;106(36):15119–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Ghosh T, García AE, Garde S. Molecular dynamics simulations of pressure effects on hydrophobic interactions. J Am Chem Soc. 2001;123(44):10997–1003.

    Article  CAS  PubMed  Google Scholar 

  77. Dias CL, Chan HS. Pressure-dependent properties of elementary hydrophobic interactions: ramifications for activation properties of protein folding. J Phys Chem B. 2014;118(27):7488–509.

    Article  CAS  PubMed  Google Scholar 

  78. Bianco V, Pagès Gelabert N, Coluzza I, Franzese G. How the stability of a folded protein depends on interfacial water properties and residue–residue interactions. arXiv e-prints, April 2017.

    Google Scholar 

  79. Frenkel D, Smit B. Understand molecular simulations. San Diego/London: Academic; 2002.

    Google Scholar 

  80. Habash M, Reid G. Microbial biofilms: their development and significance for medical device-related infections. J Clin Pharmacol. 1999;39(9):887–98.

    Article  CAS  PubMed  Google Scholar 

  81. Salvati A, Pitek AS, Monopoli MP, Prapainop K, Bombelli FB, Hristov DR, Kelly PM, Åberg C, Mahon E, Dawson KA. Transferrin-functionalized nanoparticles lose their targeting capabilities when a biomolecule corona adsorbs on the surface. Nat Nanotechnol. 2013;8(2):137–43.

    Article  CAS  PubMed  Google Scholar 

  82. Ding H-M, Ma YQ. Design strategy of surface decoration for efficient delivery of nanoparticles by computer simulation. Sci Rep. 2016;6:26783.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. De Simone A, Spadaccini R, Temussi PA, Fraternali F. Toward the understanding of MNEI sweetness from hydration map surfaces. Biophys J. 2006;90(9):3052–61.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  84. Puntes VF. Design and pharmacokinetical aspects for the use of inorganic nanoparticles in radiomedicine. Br J Radiol. 2016;89(1057):20150210.

    Article  PubMed  Google Scholar 

  85. Lindman S, Lynch I, Thulin E, Nilsson H, Dawson KA, Linse S. Systematic investigation of the thermodynamics of HSA adsorption to N-iso-propylacrylamide/N-tert-butylacrylamide copolymer nanoparticles. Effects of particle size and hydrophobicity. Nano Lett. 2007;7(4):914–20.

    Article  CAS  PubMed  Google Scholar 

  86. Dawson KA, Salvati A, Lynch I. Nanotoxicology: nanoparticles reconstruct lipids. Nat Nano. 2009;4(2):84–5.

    Article  CAS  Google Scholar 

  87. Lundqvist M, Stigler J, Elia G, Lynch I, Cedervall T, Dawson KA. Nanoparticle size and surface properties determine the protein corona with possible implications for biological impacts. Proc Natl Acad Sci. 2008;105(38):14265–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Pratap N, Casey A, Lynch I. Tenuta T, Dawson KA. Preparation, characterization and ecotoxicological evaluation of four environmentally relevant species of n- isopropylacrylamide and n-isopropylacrylamide-co-n-tert-butylacrylamide copolymer nanoparticles. Aquat Toxicol. 2009;92:146–54.

    Google Scholar 

  89. Rivera Gil P, Oberdörster G, Elder A, Puntes VF, Parak WJ. Correlating physico-chemical with toxicological properties of nanoparticles: the present and the future. ACS Nano. 2010;4(10):5227–31.

    Article  CAS  Google Scholar 

  90. Corbo C, Molinaro R, Parodi A, Furman NET, Salvatore F, Tasciotti E. The impact of nanoparticle protein corona on cytotoxicity, immunotoxicity and target drug delivery. Nanomedicine. 2016;11(1):81–100.

    Article  CAS  PubMed  Google Scholar 

  91. Lynch I, Cedervall T, Lundqvist M, Cabaleiro-Lago C, Linse S, Dawson KA. The nanoparticle-protein complex as a biological entity; a complex fluids and surface science challenge for the 21st century. Adv Colloid Interface Sci. 2007;134–135:167–74.

    Article  PubMed  CAS  Google Scholar 

  92. Cedervall T, Lynch I, Lindman S, Berggård T, Thulin E, Nilsson H, Dawson KA, Linse S. Understanding the nanoparticle-protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles. Proc Natl Acad Sci USA. 2007;104(7):2050–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Lynch I, Salvati A, Dawson KA. Protein-nanoparticle interactions: what does the cell see? Nat Nanotechnol. 2009;4(9):546–7.

    Article  CAS  PubMed  Google Scholar 

  94. Walczyk D, Bombelli FB, Monopoli MP, Lynch I, Dawson KA. What the cell “sees” in bionanoscience. J Am Chem Soc. 2010;132(16):5761–8.

    Article  CAS  PubMed  Google Scholar 

  95. Casals E, Pfaller T, Duschl A, Oostingh GJ, Puntes VF. Time evolution of the nanoparticle protein corona. ACS Nano. 2010;4(7):3623–32.

    Article  CAS  PubMed  Google Scholar 

  96. Dell’Orco D, Lundqvist M, Oslakovic C, Cedervall T, Linse S. Modeling the time evolution of the nanoparticle-protein corona in a body fluid. PLoS One 2010;5(6):e10949.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Milani S, Bombelli FB, Pitek AS, Dawson KA, Rädler J, Baldelli Bombelli F. Reversible versus irreversible binding of transferrin to polystyrene nanoparticles: soft and hard corona. ACS Nano. 2012;6(3):2532–41.

    Article  CAS  PubMed  Google Scholar 

  98. Pitek AS, O’Connell D, Mahon E, Monopoli MP, Bombelli FB, Dawson KA. Transferrin coated nanoparticles: study of the bionano interface in human plasma. PLoS One. 2012;7(7):e40685.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Monopoli MP, Åberg C, Salvati A, Dawson KA. Biomolecular coronas provide the biological identity of nanosized materials. Nat Nanotechnol. 2012;7(12):779–86.

    Article  CAS  PubMed  Google Scholar 

  100. Lundqvist M, Stigler J, Cedervall T, Berggård T, Flanagan MB, Lynch I, Elia G, Dawson K. The evolution of the protein corona around nanoparticles: a test study. ACS Nano. 2011;5(9):7503–9.

    Article  CAS  PubMed  Google Scholar 

  101. Shapero K, Fenaroli F, Lynch I, Cottell DC, Salvati A, Dawson KA. Time and space resolved uptake study of silica nanoparticles by human cells. Mol BioSyst. 2011;7:371–8.

    Article  CAS  PubMed  Google Scholar 

  102. Salvati A, Åberg C, dos Santos T, Varela J, Pinto P, Lynch I, Dawson KA. Experimental and theoretical comparison of intracellular import of polymeric nanoparticles and small molecules: toward models of uptake kinetics. Nanomed Nanotechnol Biol Med. 2011;7(6):818–26.

    Article  CAS  Google Scholar 

  103. Monopoli MP, Walczyk D, Campbell A, Elia G, Lynch I, Bombelli FB, Dawson KA. Physical-chemical aspects of protein corona: relevance to in vitro and in vivo biological impacts of nanoparticles. J Am Chem Soc. 2011;133(8):2525–34.

    Article  CAS  PubMed  Google Scholar 

  104. Monopoli MP, Bombelli FB, Dawson KA. Nanobiotechnology: nanoparticle coronas take shape. Nat Nano. 2011;6(1):11–2

    Article  CAS  Google Scholar 

  105. Vilaseca P, Dawson KA, Franzese G. Understanding and modulating the competitive surface-adsorption of proteins through coarse-grained molecular dynamics simulations. Soft Matter. 2013;9(29):6978–85.

    Article  CAS  Google Scholar 

  106. Vilanova O. Bionanointeractions: interactions between nanoscopic systems and biological macromolecules in solution. PhD thesis, Universitat de Barcelona. 2018.

    Google Scholar 

  107. Vilanova O, Mittag JJ, Kelly PM, Milani S, Dawson KA, Rädler JO, Franzese G. Understanding the kinetics of protein–nanoparticle corona formation. ACS Nano. 2016;10(12):10842–50

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Kumar P, Franzese G, Stanley HE. Dynamics and thermodynamics of water. J Phys Condens Matter. 2008;20(24):244114.

    Article  CAS  Google Scholar 

  109. Mazza MG , Stokely K, Strekalova EG, Stanley HE, Franzese G. Cluster Monte Carlo and numerical mean field analysis for the water liquid–liquid phase transition. Comput Phys Commun. 2009;180(4):497–502.

    Article  CAS  Google Scholar 

  110. Franzese G, Malescio G, Skibinsky A, Buldyrev SV, Stanley HE. Metastable liquid-liquid phase transition in a single-component system with only one crystal phase and no density anomaly. Phys Rev E. 2002;66(5):51206.

    Article  CAS  Google Scholar 

  111. Franzese G, Stanley HE. A theory for discriminating the mechanism responsible for the water density anomaly. Physica A. 2002;314(1–4):508–13.

    Article  CAS  Google Scholar 

  112. Franzese G, Stanley HE. Liquid–liquid critical point in a Hamiltonian model for water: analytic solution. J Phys Condens Matter. 2002;14(9):2201–9.

    Article  CAS  Google Scholar 

  113. https://github.com/bubbles-suite/BUBBLES (2015).

  114. Franzese G. Differences between discontinuous and continuous soft-core attractive potentials: the appearance of density anomaly. J Mol Liq. 2007;136(3):267–73.

    Article  CAS  Google Scholar 

  115. Vilaseca P, Franzese G. Isotropic soft-core potentials with two characteristic length scales and anomalous behaviour. J Non-Cryst Solids. 2011;357(2):419–26.

    Article  CAS  Google Scholar 

  116. Vilanova O, Franzese G. Structural and dynamical properties of nanoconfined supercooled water. arXiv.org, arXiv:1102.2864. 2011.

    Google Scholar 

  117. Bianco V, Franzese G, Dellago C, Coluzza I. Role of water in the selection of stable proteins at ambient and extreme thermodynamic conditions. Phys Rev X. 2017;7:021047.

    Google Scholar 

Download references

Acknowledgements

We are thankful to M. Bernabei, C. Calero, L. E. Coronas, F. Leoni, N. Pagès, and A. Zantop for helpful discussions. O.V. and G.F. acknowledge the support of Spanish MINECO grant FIS2012-31025 and FIS2015-66879-C2-2-P. I. C. acknowledges the support from the Austrian Science Fund (FWF) Grant No. 26253-N27. V.B. acknowledges the support of the FWF Grant No. 2150-N36 and P 26253-N27.

Author information

Authors and Affiliations

  1. Secció de Física Estadística i Interdisciplinària, Departament de Física de la Matèria Condensada, Facultat de Física & Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain

    Oriol Vilanova & Giancarlo Franzese

  2. Computational Physics Group, Faculty of Physics, Universität Wien, Sensengasse 8/10, 1090, Vienna, Austria

    Valentino Bianco

Authors
  1. Oriol Vilanova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Valentino Bianco
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Giancarlo Franzese
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Giancarlo Franzese .

Editor information

Editors and Affiliations

  1. Computational Biophysics, CIC biomaGUNE, Parque Científico y Tecnológico de Gipuzkoa, Donostia/San Sebastián, Gipuzkoa, Spain

    Ivan Coluzza

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Vilanova, O., Bianco, V., Franzese, G. (2017). Multi-Scale Approach for Self-Assembly and Protein Folding. In: Coluzza, I. (eds) Design of Self-Assembling Materials. Springer, Cham. https://doi.org/10.1007/978-3-319-71578-0_5

Download citation

Publish with us

Policies and ethics

Search

Navigation