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Insight into Biophysicochemical Principles of Biopolymers through Simulation and Theory

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Abstract

The development of biopolymers for biomedical applications has traditionally been based on new chemistries. However, there is growing recognition that the biological responses can be regulated by the physical as well as the chemical properties of biomaterials. Understanding the biophysicochemical principles regarding biopolymers is thereby of great importance in the generation of advanced biomaterials. Herein, this review article seeks to provide a conceptual framework demonstrating how the approaches of tailored computer simulations and theoretical analysis are harnessed to explore the physicochemical principles of biopolymer cellular interactions. We briefly introduce the theoretical and simulation methods used in this field, summarize the typical findings based on these approaches, and describe the correlations between theoretical results and experiments. Finally, the future prospects for the theoretical aspect of biopolymers and their biophysicochemical interactions are discussed. The knowledge might be critical from the perspective of advantageous and safe use of designer biomaterials.

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References

  1. Yadav, P.; Yadav, H.; Shah, V. G.; Shah, G.; Dhaka, G. Biomedical biopolymers, their origin and evolution in biomedical sciences: a systematic review. J. Clin. Diagn. Res. 2015, 9, ZE21–ZE25.

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Jadoun, S.; Riaz, U.; Budhiraja, V. Biodegradable conducting polymeric materials for biomedical applications: a review. Med. Devices Sens. 2021, 4, e10141.

    CAS  Google Scholar 

  3. Torchilin, V. P. Multifunctional nanocarriers. Adv. Drug Del. Rev. 2006, 58, 1532–1555.

    CAS  Google Scholar 

  4. Gref, R.; Minamitake, Y.; Peracchia, M. T.; Trubetskoy, V.; Torchilin, V.; Langer, R. Biodegradable long-circulating polymeric nanospheres. Science 1994, 263, 1600–1603.

    CAS  PubMed  Google Scholar 

  5. Langer, R.; Tirrell, D. A. Designing materials for biology and medicine. Nature 2004, 428, 487–492.

    CAS  PubMed  Google Scholar 

  6. Mitragotri, S.; Lahann, J. Physical approaches to biomaterial design. Nat. Mater. 2009, 8, 15–23.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Rolland, J. P.; Maynor, B. W.; Euliss, L. E.; Exner, A. E.; Denison, G. M.; DeSimone, J. M. Direct fabrication and harvesting of monodisperse, shape-specific nanobiomaterials. J. Am. Chem. Soc. 2005, 127, 10096–10100.

    CAS  PubMed  Google Scholar 

  8. Champion, J. A.; Mitragotri, S. Role of target geometry in phagocytosis. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 4930–4934.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Champion, J. A.; Katare, Y. K.; Mitragotri, S. Making polymeric micro- and nanoparticles of complex shapes. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 11901–11904.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Geng, Y.; Dalhaimer, P.; Cai, S.; Tsai, R.; Tewari, M.; Minko, T.; Discher, D. E. Shape effects of filaments versus spherical particles in flow and drug delivery. Nat. Nanotechnol. 2007, 2, 249–255.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Dalhaimer, P.; Bates, F. S.; Discher, D. E. Single molecule visualization of stable, stiffness-tunable, flow-conforming worm micelles. Macromolecules 2003, 36, 6873–6877.

    CAS  Google Scholar 

  12. Ding, H. M.; Ma, Y. Q. Theoretical and computational investigations of nanoparticle-biomembrane interactions in cellular delivery. Small 2015, 11, 1055–71.

    CAS  PubMed  Google Scholar 

  13. Chithrani, B. D.; Chan, W. C. W. Elucidating the mechanism of cellular uptake and removal of protein-coated gold nanoparticles of different sizes and shapes. Nano Lett. 2007, 7, 1542–1550.

    CAS  PubMed  Google Scholar 

  14. Gratton, S. E.; Ropp, P. A.; Pohlhaus, P. D.; Luft, J. C.; Madden, V. J.; Napier, M. E.; DeSimone, J. M. The effect of particle design on cellular internalization pathways. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11613–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Qu, Z. G.; He, X. C.; Lin, M.; Sha, B. Y.; Shi, X. H.; Lu, T. J.; Xu, F. Advances in the understanding of nanomaterial-biomembrane interactions and their mathematical and numerical modeling. Nanomedicine 2013, 8, 995–1011.

    CAS  PubMed  Google Scholar 

  16. Tian, W. D.; Ma, Y. Q. Theoretical and computational studies of dendrimers as delivery vectors. Chem. Soc. Rev. 2013, 42, 705–727.

    CAS  PubMed  Google Scholar 

  17. Tachikawa, M.; Mochizuki, A. Golgi apparatus self-organizes into the characteristic shape via postmitotic reassembly dynamics. Proc. Natl. Acad. Sci. U.S.A. 2017, 114, 5177–5182.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Huang, C.; Zhang, Y.; Yuan, H.; Gao, H.; Zhang, S. Role of nanoparticle geometry in endocytosis: laying down to stand up. Nano Lett. 2013, 13, 4546–50.

    CAS  PubMed  Google Scholar 

  19. Chen, P.; Yue, H.; Zhai, X.; Huang, Z.; Ma, G. H.; Wei, W.; Yan, L. T. Transport of a graphene nanosheet sandwiched inside cell membranes. Sci. Adv. 2019, 5, eaaw3192.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Escriba, P. V.; Gonzalez-Ros, J. M.; Goni, F. M.; Kinnunen, P. K.; Vigh, L.; Sanchez-Magraner, L.; Fernandez, A. M.; Busquets, X.; Horvath, I.; Barcelo-Coblijn, G. Membranes: a meeting point for lipids, proteins and therapies. J. Cell. Mol. Med. 2008, 12, 829–75.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Ge, Z.; Li, Q.; Wang, Y. Free energy calculation of nanodiamond-membrane association—the effect of shape and surface functionalization. J. Chem. Theory Comput. 2014, 10, 2751–2758.

    CAS  PubMed  Google Scholar 

  22. Tu, Y.; Lv, M.; Xiu, P.; Huynh, T.; Zhang, M.; Castelli, M.; Liu, Z.; Huang, Q.; Fan, C.; Fang, H.; Zhou, R. Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets. Nat. Nanotechnol. 2013, 8, 594–601.

    CAS  PubMed  Google Scholar 

  23. Marrink, S. J.; de Vries, A. H.; Tieleman, D. P. Lipids on the move: Simulations of membrane pores, domains, stalks and curves. Biochim. Biophys. Acta 2009, 1788, 149–168.

    CAS  PubMed  Google Scholar 

  24. Marrink, S. J.; de Vries, A. H.; Mark, A. E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 2004, 108, 750–760.

    CAS  Google Scholar 

  25. Reynwar, B. J.; Illya, G.; Harmandaris, V. A.; Müller, M. M.; Kremer, K.; Deserno, M. Aggregation and vesiculation of membrane proteins by curvature-mediated interactions. Nature 2007, 447, 461–464.

    CAS  PubMed  Google Scholar 

  26. Pluhackova, K.; Böckmann, R. A. Biomembranes in atomistic and coarse-grained simulations. J. Phys.: Condens. Matter 2015, 27, 323103.

    PubMed  Google Scholar 

  27. Klauda, J. B.; Venable, R. M.; Freites, J. A.; O’Connor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D.,Jr.; Pastor, R. W. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 2010, 114, 7830–7843.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Provasi, D.; Bortolato, A.; Filizola, M. Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics. Biochemistry 2009, 48, 10020–10029.

    CAS  PubMed  Google Scholar 

  29. Berka, K.; Hendrychová, T.; Anzenbacher, P.; Otyepka, M. Membrane position of Ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 Active Site. J. Phys. Chem. A 2011, 115, 11248–11255.

    CAS  PubMed Central  Google Scholar 

  30. Schmid, N.; Eichenberger, A. P.; Choutko, A.; Riniker, S.; Winger, M.; Mark, A. E.; van Gunsteren, W. F. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur. Biophys. J. 2011, 40, 843–856.

    CAS  PubMed  Google Scholar 

  31. Venturoli, M.; Sperotto, M.; Kranenburg, M.; Smit, B. J. P. R. Mesoscopic models of biological membranes. Phys. Rep. 2006, 437, 1–54.

    CAS  Google Scholar 

  32. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 2007, 111, 7812–7824.

    CAS  PubMed  Google Scholar 

  33. Español, P.; Warren, P. Statistical mechanics of dissipative particle dynamics. Europhys. Lett. 1995, 30, 191.

    Google Scholar 

  34. Groot, R. D.; Warren, P. B. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys. 1997, 107, 4423–4435.

    CAS  Google Scholar 

  35. Hoogerbrugge, P. J.; Koelman, J. M. V. A. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys. Lett. 1992, 19, 155–160.

    Google Scholar 

  36. Cooke, I. R.; Deserno, M. Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials. J. Chem. Phys. 2005, 123, 224710.

    PubMed  Google Scholar 

  37. Cooke, I. R.; Kremer, K.; Deserno, M. Tunable generic model for fluid bilayer membranes. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2005, 72, 011506.

    PubMed  Google Scholar 

  38. Yuan, H.; Huang, C.; Li, J.; Lykotrafitis, G.; Zhang, S. One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2010, 82, 011905.

    PubMed  Google Scholar 

  39. Hollingsworth, S. A.; Dror, R. O. Molecular dynamics simulation for all. Neuron 2018, 99, 1129–1143.

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Plimpton, S. Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 1995, 117, 1–19.

    CAS  Google Scholar 

  41. Chávez Thielemann, H.; Cardellini, A.; Fasano, M.; Bergamasco, L.; Alberghini, M.; Ciorra, G.; Chiavazzo, E.; Asinari, P. From GROMACS to LAMMPS: GRO2LAM. J. Mol. Model. 2019, 25, 147.

    PubMed  Google Scholar 

  42. Lyubartsev, A. P. Multiscale modeling of lipids and lipid bilayers. Eur. Biophys. J. 2005, 35, 53–61.

    CAS  PubMed  Google Scholar 

  43. Chen, P.; Xu, Z.; Zhu, G.; Dai, X.; Yan, L. T. Cellular uptake of active particles. Phys. Rev. Lett. 2020, 124, 198102.

    CAS  PubMed  Google Scholar 

  44. Lelimousin, M.; Limongelli, V.; Sansom, M. S. P. Conformational changes in the epidermal growth factor receptor: role of the transmembrane domain investigated by coarse-grained metadynamics free energy calculations. J. Am. Chem. Soc. 2016, 138, 10611–10622.

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Deng, Z. X.; Li, J. L.; Yuan, B.; Yang, K. Residue-specialized membrane poration kinetics of melittin and its variants: insight from mechanistic landscapes. Commun. Theor. Phys. 2019, 71, 887–902.

    CAS  Google Scholar 

  46. Duncan, A. L.; Corey, R. A.; Sansom, M. S. P. Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels. Proc. Natl. Acad. Sci. U.S.A. 0200, 117, 7803–7813.

    Google Scholar 

  47. Ma, W.; Jiang, X.; Dou, Y.; Zhang, Z.; Li, J.; Yuan, B.; Yang, K. Biophysical impact of lipid a modification caused by mobile colistin resistance gene on bacterial outer membranes. J. Phys. Chem. Lett. 2021, 12, 11629–11635.

    CAS  PubMed  Google Scholar 

  48. Yuan, B.; Liu, J.; Deng, Z.; Wei, L.; Li, W.; Dou, Y.; Chen, Z.; Zhang, C.; Xia, Y.; Wang, J.; Zhang, M.; Yang, K.; Ma, Y.; Kang, Z. A molecular architectural design that promises potent antimicrobial activity against multidrug-resistant pathogens. NPG Asia Mater. 2021, 13, 18.

    CAS  Google Scholar 

  49. Deng, Z.; Yuan, B.; Yang, K. Cardiolipin selectively binds to the interface of VsSemiSWEET and regulates its dimerization. J Phys. Chem. Lett. 2021, 12, 1940–1946.

    CAS  PubMed  Google Scholar 

  50. Liu, G.; Xu, Z.; Dai, X.; Zeng, Y.; Wei, Y.; He, X.; Yan, L. T.; Tao, L. De Novo design of entropy-driven polymers resistant to bacterial attachment via multicomponent reactions. J. Am. Chem. Soc. 2021, 143, 17250–17260.

    CAS  PubMed  Google Scholar 

  51. Li, J.; Lu, X. M.; Ma, W. D.; Chen, Z. L.; Sun, S. Q.; Wang, Q. H.; Yuan, B.; Yang, K. Cholesterols work as a molecular regulator of the antimicrobial peptide-membrane interactions. Front. Mol. Biosci. 2021, 8, 638988.

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Zhang, S. L.; Li, J.; Lykotrafitis, G.; Bao, G.; Suresh, S. Size-dependent endocytosis of nanoparticles. Adv. Mater. 2009, 21, 419–424.

    PubMed  PubMed Central  Google Scholar 

  53. He, K.; Wei, Y.; Zhang, Z.; Chen, H.; Yuan, B.; Pang, H. B.; Yang, K. Membrane-curvature-mediated co-endocytosis of bystander and functional nanoparticles. Nanoscale 2021, 13, 9626–9633.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Wei, Y.; Chen, H.; Li, Y. X.; He, K.; Yang, K.; Pang, H. B. Synergistic entry of individual nanoparticles into mammalian cells driven by free energy decline and regulated by their sizes. ACS Nano 2022, 16, 5885–5897.

    CAS  PubMed  Google Scholar 

  55. Yang, K.; Ma, Y. Q. Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer. Nat. Nanotechnol. 2010, 5, 579–583.

    CAS  PubMed  Google Scholar 

  56. Ding, H. M.; Tian, W. D.; Ma, Y. Q. Designing nanoparticle translocation through membranes by computer simulations. ACS Nano 2012, 6, 1230–1238.

    CAS  PubMed  Google Scholar 

  57. Wang, Y.-F.; Zhang, Q.; Tian, F.; Wang, H.; Wang, Y.; Ma, X.; Huang, Q.; Cai, M.; Ji, Y.; Wu, X.; Gan, Y.; Yan, Y.; Dawson, K. A.; Guo, S.; Zhang, J.; Shi, X.; Shan, Y.; Liang, X. J. Spatiotemporal tracing of the cellular internalization process of rod-shaped nanostructures. ACS Nano 2022, 16, 4059–4071.

    CAS  PubMed  Google Scholar 

  58. Ding, H.; Li, J.; Chen, N.; Hu, X.; Yang, X.; Guo, L.; Li, Q.; Zuo, X.; Wang, L.; Ma, Y.; Fan, C. DNA nanostructure-programmed like-charge attraction at the cell-membrane interface. ACS Cent. Sci. 2018, 4, 1344–1351.

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Li, Y.; Yue, T.; Yang, K.; Zhang, X. Molecular modeling of the relationship between nanoparticle shape anisotropy and endocytosis kinetics. Biomaterials 2012, 33, 4965–4973.

    CAS  PubMed  Google Scholar 

  60. Shi, X.; von dem Bussche, A.; Hurt, R. H.; Kane, A. B.; Gao, H. Cell entry of one-dimensional nanomaterials occurs by tip recognition and rotation. Nat. Nanotechnol. 2011, 6, 714–719.

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Guo, R.; Mao, J.; Yan, L. T. Computer simulation of cell entry of graphene nanosheet. Biomaterials 2013, 34, 4296–4301.

    CAS  PubMed  Google Scholar 

  62. Mao, J.; Chen, P.; Liang, J.; Guo, R.; Yan, L. T. Receptor-mediated endocytosis of two-dimensional nanomaterials undergoes flat vesiculation and occurs by revolution and self-rotation. ACS Nano 2016, 10, 1493–1502.

    CAS  PubMed  Google Scholar 

  63. Lu, X. M.; Liu, J. J.; Gou, L.; Li, J. L.; Yuan, B.; Yang, K.; Ma, Y. Q. Designing melittin-graphene hybrid complexes for enhanced antibacterial activity. Adv. Healthc. Mater. 2019, 8, 1801521.

    Google Scholar 

  64. Qian, R.; Maiti, D.; Zhong, J.; Xiong, S. S.; Zhou, H. L.; Zhu, R.; Wan, J. M.; Yang, K. Multifunctional nano-graphene based nanocomposites for multimodal imaging guided combined radioisotope therapy and chemotherapy. Carbon 2019, 149, 55–62.

    CAS  Google Scholar 

  65. Li, Y.; Feng, D.; Zhang, X.; Cao, D. Design strategy of cell-penetrating copolymers for high efficient drug delivery. Biomaterials 2015, 52, 171–179.

    CAS  PubMed  Google Scholar 

  66. Ou, L.; Chen, H.; Yuan, B.; Yang, K. Membrane-specific binding of 4 nm lipid nanoparticles mediated by an entropy-driven interaction mechanism. ACS Nano 2022, 16, 18090–18100.

    CAS  PubMed  Google Scholar 

  67. Tang, Y.; Bera, S.; Yao, Y.; Zeng, J.; Lao, Z.; Dong, X.; Gazit, E.; Wei, G. Prediction and characterization of liquid-liquid phase separation of minimalistic peptides. Cell Rep. Phys. Sci. 2021, 2, 100579.

    CAS  Google Scholar 

  68. Dong, X.; Bera, S.; Qiao, Q.; Tang, Y.; Lao, Z.; Luo, Y.; Gazit, E.; Wei, G. Liquid-liquid phase separation of tau protein is encoded at the monomeric level. J. Phys. Chem. Lett. 2021, 12, 2576–2586.

    CAS  PubMed  Google Scholar 

  69. Ren, C.-L.; Shan, Y.; Zhang, P.; Ding, H. M.; Ma, Y. Q. Uncovering the molecular mechanism for dual effect of ATP on phase separation in FUS solution. Sci. Adv. 2022, 8, eabo7885.

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Sun, J. S.; Zhang, L.; Wang, J. L.; Feng, Q.; Liu, D. B.; Yin, Q. F.; Xu, D. Y.; Wei, Y. J.; Ding, B. Q.; Shi, X. H.; Jiang, X. Y. Tunable rigidity of (polymeric core)-(lipid shell) nanoparticles for regulated cellular uptake. Adv. Mater. 2015, 27, 1402–1407.

    CAS  PubMed  Google Scholar 

  71. Yi, X.; Shi, X.; Gao, H. Cellular uptake of elastic nanoparticles. Phys. Rev. Lett. 2011, 107, 098101.

    PubMed  Google Scholar 

  72. Hu, C.-M. J.; Fang, R. H.; Wang, K.-C.; Luk, B. T.; Thamphiwatana, S.; Dehaini, D.; Nguyen, P.; Angsantikul, P.; Wen, C. H.; Kroll, A. V.; Carpenter, C.; Ramesh, M.; Qu, V.; Patel, S. H.; Zhu, J.; Shi, W.; Hofman, F. M.; Chen, T. C.; Gao, W.; Zhang, K.; Chien, S.; Zhang, L. Nanoparticle biointerfacing by platelet membrane cloaking. Nature 2015, 526, 118–121.

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Xia, Q. S.; Zhu, T.; Jiang, Z. Y.; Ding, H. M.; Ma, Y. Q. Enhancing the targeting ability of nanoparticles via protected copolymers. Nanoscale 2020, 12, 7804–7813.

    CAS  PubMed  Google Scholar 

  74. Xu, C.; Ma, W.; Wang, K.; He, K.; Chen, Z.; Liu, J.; Yang, K.; Yuan, B. Correlation between single-molecule dynamics and biological functions of antimicrobial peptide melittin. J. Phys. Chem. Lett. 2020, 11, 4834–4841.

    CAS  PubMed  Google Scholar 

  75. Chen, P.; Huang, Z.; Liang, J.; Cui, T.; Zhang, X.; Miao, B.; Yan, L. T. Diffusion and directionality of charged nanoparticles on lipid bilayer membrane. ACS Nano 2016, 10, 11541–11547.

    CAS  PubMed  Google Scholar 

  76. Dai, X.; Zhu, Z.; Li, Y.; Yang, B.; Xu, J. F.; Dong, Y.; Zhou, X.; Yan, L. T.; Liu, D. “Shutter” effects enhance protein diffusion in dynamic and rigid molecular networks. J. Am. Chem. Soc. 2022, 144, 19017–19025.

    CAS  PubMed  Google Scholar 

  77. Cho, W. K.; Spille, J. H.; Hecht, M.; Lee, C.; Li, C.; Grube, V.; Cisse, I. I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 2018, 361, 412–415.

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Franzmann, T. M.; Jahnel, M.; Pozniakovsky, A.; Mahamid, J.; Holehouse, A. S.; Nuske, E.; Richter, D.; Baumeister, W.; Grill, S. W.; Pappu, R. V.; Hyman, A. A.; Alberti, S. Phase separation of a yeast prion protein promotes cellular fitness. Science 2018, 359, eaao5654.

    PubMed  Google Scholar 

  79. Zhang, H.; Ji, X.; Li, P.; Liu, C.; Lou, J.; Wang, Z.; Wen, W.; Xiao, Y.; Zhang, M.; Zhu, X. Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci. China: Life Sci. 2020, 63, 953–985.

    PubMed  Google Scholar 

  80. Li, P.; Banjade, S.; Cheng, H.-C.; Kim, S.; Chen, B.; Guo, L.; Llaguno, M.; Hollingsworth, J. V.; King, D. S.; Banani, S. F.; Russo, P. S.; Jiang, Q.-X.; Nixon, B. T.; Rosen, M. K. Phase transitions in the assembly of multivalent signalling proteins. Nature 2012, 483, 336–340.

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Patel, A.; Lee, Hyun O.; Jawerth, L.; Maharana, S.; Jahnel, M.; Hein, Marco Y.; Stoynov, S.; Mahamid, J.; Saha, S.; Franzmann, Titus M.; Pozniakovski, A.; Poser, I.; Maghelli, N.; Royer, Loic A.; Weigert, M.; Myers, Eugene W.; Grill, S.; Drechsel, D.; Hyman, Anthony A.; Alberti, S. A Liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell 2015, 162, 1066–1077.

    CAS  PubMed  Google Scholar 

  82. Murray, D. T.; Kato, M.; Lin, Y.; Thurber, K. R.; Hung, I.; McKnight, S. L.; Tycko, R. Structure of FUS protein fibrils and its relevance to self-assembly and phase separation of low-complexity domains. Cell 2017, 171, 615–627.

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Wei, X.; Zhou, J.; Wang, Y.; Meng, F. Modeling elastically mediated liquid-liquid phase separation. Phys. Rev. Lett. 2020, 125, 268001.

    CAS  PubMed  Google Scholar 

  84. Zhang, L.; Granick, S. Slaved diffusion in phospholipid bilayers. Proc. Natl. Acad. Sci. USA 2005, 102, 9118–9121.

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Wang, B.; Anthony, S. M.; Bae, S. C.; Granick, S. Anomalous yet Brownian. Proc. Natl. Acad. Sci. USA 2009, 106, 15160–15164.

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Barkai, E.; Garini, Y.; Metzler, R. Strange kinetics of single molecules in living cells. Phys. Today 2012, 65, 29–35.

    CAS  Google Scholar 

  87. Wang, B.; Kuo, J.; Bae, S. C.; Granick, S. When Brownian diffusion is not Gaussian. Nat. Mater. 2012, 11, 481–485.

    CAS  PubMed  Google Scholar 

  88. Saffman, P. G.; Delbruck, M. Brownian-motion in biological-membranes. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 3111–3113.

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Javanainen, M.; Martinez-Seara, H.; Metzler, R.; Vattulainen, I. Diffusion of integral membrane proteins in protein-rich membranes. J. Phys. Chem. Lett. 2017, 8, 4308–4313.

    CAS  PubMed  Google Scholar 

  90. Jeon, J. H.; Monne, H. M. S.; Javanainen, M.; Metzler, R. Anomalous diffusion of phospholipids and cholesterols in a lipid bilayer and its origins. Phys. Rev. Lett. 2012, 109, 188103.

    PubMed  Google Scholar 

  91. Jeon, J. H.; Javanainen, M.; Martinez-Seara, H.; Metzler, R.; Vattulainen, I. Protein crowding in lipid bilayers gives rise to non-Gaussian anomalous lateral diffusion of phospholipids and proteins. Phys. Rev. X 2016, 6, 021006.

    Google Scholar 

  92. Ji, Q. J.; Yuan, B.; Lu, X. M.; Yang, K.; Ma, Y. Q. Controlling the nanoscale rotational behaviors of nanoparticles on the cell membranes: a computational model. Small 2016, 12, 1140–1146.

    CAS  PubMed  Google Scholar 

  93. Osaki, F.; Kanamori, T.; Sando, S.; Sera, T.; Aoyama, Y. A Quantum dot conjugated sugar ball and its cellular uptake. on the size effects of endocytosis in the subviral region. J. Am. Chem. Soc. 2004, 126, 6520–6521.

    CAS  PubMed  Google Scholar 

  94. Chithrani, B. D.; Ghazani, A. A.; Chan, W. C. W. Determining the size and shape dependence of gold nanoparticle uptake into mammalian cells. Nano Lett. 2006, 6, 662–668.

    CAS  PubMed  Google Scholar 

  95. Gao, H. J.; Shi, W. D.; Freund, L. B. Mechanics of receptor-mediated endocytosis. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 9469–9474.

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Gu, Y.; Sun, W.; Wang, G. F.; Zimmermann, M. T.; Jernigan, R. L.; Fang, N. Revealing rotational modes of functionalized gold nanorods on live cell membranes. Small 2013, 9, 785–792.

    CAS  PubMed  Google Scholar 

  97. Chu, Z.; Zhang, S.; Zhang, B.; Zhang, C.; Fang, C. Y.; Rehor, I.; Cigler, P.; Chang, H.-C.; Lin, G.; Liu, R.; Li, Q. Unambiguous observation of shape effects on cellular fate of nanoparticles. Sci. Rep. 2014, 4, 4495.

    PubMed  PubMed Central  Google Scholar 

  98. Cho, E. C.; Xie, J.; Wurm, P. A.; Xia, Y. Understanding the role of surface charges in cellular adsorption versus internalization by selectively removing gold nanoparticles on the cell surface with a I-2/KI Etchant. Nano Lett. 2009, 9, 1080–1084.

    CAS  PubMed  Google Scholar 

  99. Ding, H. M.; Ma, Y. Q. Interactions between Janus particles and membranes. Nanoscale 2012, 4, 1116–1122.

    CAS  PubMed  Google Scholar 

  100. Gao, Y.; Yu, Y. How half-coated janus particles enter cells. J. Am. Chem. Soc. 2013, 135, 19091–19094.

    CAS  PubMed  Google Scholar 

  101. Ding, H. M.; Ma, Y. Q. Role of physicochemical properties of coating ligands in receptor-mediated endocytosis of nanoparticles. Biomaterials 2012, 33, 5798–5802.

    CAS  PubMed  Google Scholar 

  102. Chelladurai, R.; Debnath, K.; Jana, N. R.; Basu, J. K. Nanoscale heterogeneities drive enhanced binding and anomalous diffusion of nanoparticles in model biomembranes. Langmuir 2018, 34, 1691–1699.

    CAS  PubMed  Google Scholar 

  103. Salvati, A.; Pitek, A. S.; Monopoli, M. P.; Prapainop, K.; Bombelli, F. B.; Hristov, D. R.; Kelly, P. M.; Åberg, C.; Mahon, E.; Dawson, K. A. Transferrin-functionalized nanoparticles lose their targeting capabilities when a biomolecule corona adsorbs on the surface. Nat. Nanotechnol. 2013, 8, 137–143.

    CAS  PubMed  Google Scholar 

  104. Ding, H. M.; Ma, Y. Q. Computer simulation of the role of protein corona in cellular delivery of nanoparticles. Biomaterials 2014, 35, 8703–8710.

    CAS  PubMed  Google Scholar 

  105. Hartmann, R.; Weidenbach, M.; Neubauer, M.; Fery, A.; Parak, W. J. Stiffness-dependent in vitro uptake and lysosomal acidification of colloidal particles. Angew. Chem. Int. Ed. 2015, 54, 1365–1368.

    CAS  Google Scholar 

  106. Dai, X.; Zhang, X.; Gao, L.; Yan, L. T. Superentropy effect and macromolecular entropy control strategy. Acta Polymerica Sinica (in Chinese) 2021, 52, 1076–1099.

    CAS  Google Scholar 

  107. Beningo, K. A.; Wang, Y. L. Fc-receptor-mediated phagocytosis is regulated by mechanical properties of the target. J. Cell Sci. 2002, 115, 849–856.

    CAS  PubMed  Google Scholar 

  108. Banquy, X.; Suarez, F.; Argaw, A.; Rabanel, J. M.; Grutter, P.; Bouchard, J. F.; Hildgen, P.; Giasson, S. Effect of mechanical properties of hydrogel nanoparticles on macrophage cell uptake. Soft Matter 2009, 5, 3984–3991.

    CAS  Google Scholar 

  109. Dai, X.; Zhang, X.; Gao, L.; Xu, Z.; Yan, L. T. Topology mediates transport of nanoparticles in macromolecular networks. Nat. Commun. 2022, 13, 4094.

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Guo, R.; Mao, J.; Yan, L. T. Unique dynamical approach of fully wrapping dendrimer-like soft nanoparticles by lipid bilayer membrane. ACS Nano 2013, 7, 10646–10653.

    CAS  PubMed  Google Scholar 

  111. Teng, Z. G.; Wang, C. Y.; Tang, Y. X.; Li, W.; Bao, L.; Zhang, X. H.; Su, X. D.; Zhang, F.; Zhang, J. J.; Wang, S. J.; Zhao, D. Y.; Lu, G. M. Deformable hollow periodic mesoporous organosilica nanocapsules for significantly improved cellular uptake. J. Am. Chem. Soc. 2018, 140, 1385–1393.

    CAS  PubMed  Google Scholar 

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Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (Nos. 22025302, 21873053 and 32230063). K.Y. thanks the financial support from the open research fund of Songshan Lake Materials Laboratory (No. 2021SLABFK10).

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Correspondence to Kai Yang or Li-Tang Yan.

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Kai Yang received his Ph.D. degree in soft matter physics from Nanjing University in 2009. He was appointed as an Associate Professor at Soochow University in 2010 and was promoted as a full Professor in 2015. During 2014–2015, he was a visiting professor at the Cornell University with Prof. Gerald W. Feigenson. His research interests include biophysics, Nano-Bio interactions, and simulations and theory of soft matter systems.

Li-Tang Yan received his Ph.D. in polymer physics and chemistry at Tsinghua University in 2007. Then he went to Bayreuth University in Germany as a Humboldt Research Fellowship. In 2010, he joined Prof. Anna Balazs’ group at University of Pittsburgh in USA as a Postdoctoral Research Fellowship. He returned to Tsinghua University as a faculty from May 2011, and now is a full professor with tenure. He leads a polymer theory and physics group working on polymer theory and simulation, soft condense matter physics, biophysics and nonequilibrium physics.

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Wan, HX., Xu, D., Dong, XW. et al. Insight into Biophysicochemical Principles of Biopolymers through Simulation and Theory. Chin J Polym Sci 41, 1342–1354 (2023). https://doi.org/10.1007/s10118-023-2954-y

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  • DOI: https://doi.org/10.1007/s10118-023-2954-y

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