Computational approaches for understanding and predicting the self-assembled peptide hydrogels
Tài liệu tham khảo
Zhang, 2003, Fabrication of novel biomaterials through molecular self-assembly, Nat Biotechnol, 21, 1171, 10.1038/nbt874
Chakraborty, 2020, Unusual two-step assembly of a minimalistic dipeptide-based functional hypergelator, Adv Mater, 32, 10.1002/adma.201906043
Wang, 2016, Peptide self-assembly: thermodynamics and kinetics, Chem Soc Rev, 45, 5589, 10.1039/C6CS00176A
Yuan, 2019, Hierarchically oriented organization in supramolecular peptide crystals, Nat Rev Chem, 3, 567, 10.1038/s41570-019-0129-8
Xue, 2021, Gas-induced phase transition of dipeptide supramolecular assembly, CCS Chemistry, 3, 8, 10.31635/ccschem.021.202000601
Zhao, 2010, Molecular self-assembly and applications of designer peptide amphiphiles, Chem Soc Rev, 39, 3480, 10.1039/b915923c
Matson, 2011, Peptide self-assembly for crafting functional biological materials, Curr Opin Solid State Mater Sci, 15, 225, 10.1016/j.cossms.2011.08.001
Li, 2020, Surfactant-like peptides: from molecular design to controllable self-assembly with applications, Coord Chem Rev, 421, 10.1016/j.ccr.2020.213418
Aggeli, 2001, Hierarchical self-assembly of chiral rod-like molecules as a model for peptide β-sheet tapes, ribbons, fibrils, and fibers, Proc Natl Acad Sci USA, 98, 11857, 10.1073/pnas.191250198
Yuan, 2019, Nucleation and growth of amino acid and peptide supramolecular polymers through liquid–liquid phase separation, Angew Chem, 131, 18284, 10.1002/ange.201911782
Gelain, 2021, Self-assembling peptide EAK16 and RADA16 nanofiber scaffold hydrogel, Chem Rev, 121, 5093, 10.1021/acs.chemrev.1c00215
Van Lommel, 2021, Computational tools to rationalize and predict the self-assembly behavior of supramolecular gels, Gels, 7, 87, 10.3390/gels7030087
Li, 2019, Recent advances of self-assembling peptide-based hydrogels for biomedical applications, Soft Matter, 15, 1704, 10.1039/C8SM02573H
Wang, 2020, Role of thermolysin in catalytic-controlled self-assembly of fmoc-dipeptides, CCS Chemistry, 2, 317, 10.31635/ccschem.020.201900116
Prince, 2019, Design and applications of man-made biomimetic fibrillar hydrogels, Nat Rev Mater, 4, 99, 10.1038/s41578-018-0077-9
Zhang, 2018, An injectable dipeptide–fullerene supramolecular hydrogel for photodynamic antibacterial therapy, J Mater Chem B, 6, 7335, 10.1039/C8TB01487F
Mei, 2019, Self-assembling Collagen/Alginate hybrid hydrogels for combinatorial photothermal and immuno tumor therapy, Colloids Surf, A, 577, 570, 10.1016/j.colsurfa.2019.06.023
Xing, 2019, Self-assembled injectable biomolecular hydrogels towards phototherapy, Nanoscale, 11, 22182, 10.1039/C9NR06266A
Yang, 2019, A versatile cyclic dipeptide hydrogelator: self-assembly and rheology in various physiological conditions, Colloids Surf, A, 572, 259, 10.1016/j.colsurfa.2019.04.020
You, 2019, High-tolerance crystalline hydrogels formed from self-assembling cyclic dipeptide, Beilstein J Nanotechnol, 10, 1894, 10.3762/bjnano.10.184
Zou, 2020, Injectable self-assembled bola-dipeptide hydrogels for sustained photodynamic prodrug delivery and enhanced tumor therapy, J Contr Release, 319, 344, 10.1016/j.jconrel.2020.01.002
Frederix, 2018, Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments, Chem Soc Rev, 47, 3470, 10.1039/C8CS00040A
Manandhar, 2017, Molecular simulations of peptide amphiphiles, Org Biomol Chem, 15, 7993, 10.1039/C7OB01290J
Zhou, 2019, Amino acid conformations control the morphological and chiral features of the self-assembled peptide nanostructures: Young investigators perspective, J Colloid Interface Sci, 548, 244, 10.1016/j.jcis.2019.04.019
Li, 2020, Ordered nanofibers fabricated from hierarchical self-assembling processes of designed α-helical peptides, Small, 16
Brauner, 2004, A quantitative reconstruction of the amide I contour in the IR spectra of globular proteins: from structure to spectrum, J Am Chem Soc, 127, 100, 10.1021/ja0400685
Greenfield, 2007, Using circular dichroism spectra to estimate protein secondary structure, Nat Protoc, 1, 2876, 10.1038/nprot.2006.202
Luca, 2007, Peptide conformation and supramolecular organization in amylin fibrils: constraints from solid-state NMR, Biochemistry, 46, 13505, 10.1021/bi701427q
Wang, 2021, Unexpected role of achiral Glycine in determining the suprastructural handedness of peptide nanofibrils, ACS Nano, 15, 10328, 10.1021/acsnano.1c02547
Matthes, 2009, Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes, Biophys J, 97, 599, 10.1016/j.bpj.2009.04.061
Gopal, 2021, Conformational preferences of an intrinsically disordered protein domain: a case study for modern force fields, J Phys Chem B, 125, 24, 10.1021/acs.jpcb.0c08702
Jephthah, 2021, Force field effects in simulations of flexible peptides with varying polyproline II propensity, J Chem Theor Comput, 17, 6634, 10.1021/acs.jctc.1c00408
Siwy, 2017, Is the conformational ensemble of alzheimer's aβ10-40 peptide force field dependent?, PLoS Comput Biol, 13, 10.1371/journal.pcbi.1005314
Moore SJ, Deplazes E, Mancera RL. Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide. Proteins: Struct, Funct, Bioinf 2022, [n/a].
Tang, 2019, Stimuli-responsive, pentapeptide, nanofiber hydrogel for tissue engineering, J Am Chem Soc, 141, 4886, 10.1021/jacs.8b13363
Zhou, 2016, Interplay between intrinsic conformational propensities and intermolecular interactions in the self-assembly of short surfactant-like peptides composed of leucine/isoleucine, Langmuir, 32, 4662, 10.1021/acs.langmuir.6b00287
Noble Jesus, 2021, Amphiphilic histidine-based oligopeptides exhibit pH-reversible fibril formation, ACS Macro Lett, 10, 984, 10.1021/acsmacrolett.1c00142
Wang, 2018, Nanoribbons self-assembled from short peptides demonstrate the formation of polar zippers between β-sheets, Nat Commun, 9, 5118, 10.1038/s41467-018-07583-2
Zhou, 2016, Different nanostructures caused by competition of intra- and inter-β-sheet interactions in hierarchical self-assembly of short peptides, J Colloid Interface Sci, 464, 219, 10.1016/j.jcis.2015.11.030
Zanuy, 2016, Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly, Phys Chem Chem Phys, 18, 1265, 10.1039/C5CP04269K
Chakraborty, 2021, Nanoengineered peptide-based antimicrobial conductive supramolecular biomaterial for cardiac tissue engineering, Adv Mater, 33, 10.1002/adma.202008715
Shamovsky, 2000, Theoretical studies on the origin of β-sheet twisting, J Phys Chem B, 104, 11296, 10.1021/jp002590t
Wang, 2016, Tuning self-assembled morphology of the Aβ(16–22) peptide by substitution of phenylalanine residues, Colloids Surf B Biointerfaces, 147, 116, 10.1016/j.colsurfb.2016.07.052
Chen, 2019, Sequence isomerism-dependent self-assembly of glycopeptide mimetics with switchable antibiofilm properties, Chem Sci, 10, 8171, 10.1039/C9SC00193J
Casalini, 2019, From microscale to macroscale: nine orders of magnitude for a comprehensive modeling of hydrogels for controlled drug delivery, Gels, 5, 28, 10.3390/gels5020028
Sather, 2021, 3D printing of supramolecular polymer hydrogels with hierarchical structure, Small, 17, 10.1002/smll.202005743
Sasselli, 2022, Modeling interactions within and between peptide amphiphile supramolecular filaments, J Phys Chem B, 126, 650, 10.1021/acs.jpcb.1c09258
Abul-Haija, 2017, Cooperative, ion-sensitive co-assembly of tripeptide hydrogels, Chem Commun, 53, 9562, 10.1039/C7CC04796G
Garcia, 2021, Nanoscale Assembly of functional peptides with divergent programming elements, ACS Nano, 15, 3015, 10.1021/acsnano.0c09386
Lan, 2015, To gel or not to gel: correlating molecular gelation with solvent parameters, Chem Soc Rev, 44, 6035, 10.1039/C5CS00136F
Lin, 2017, To gel or not to gel: a prior prediction of gelation in solvent mixtures, Chin Chem Lett, 28, 771, 10.1016/j.cclet.2016.12.024
Delbecq, 2020, Gelation properties of various long chain amidoamines: prediction of solvent gelation via machine learning using Hansen solubility parameters, J Mol Liq, 303, 10.1016/j.molliq.2020.112587
Hashemnejad, 2017, Molecular insights into gelation of di-fmoc-l-lysine in organic solvent–water mixtures, ACS Omega, 2, 1864, 10.1021/acsomega.7b00108
van Teijlingen, 2021, Beyond tripeptides two-step active machine learning for very large data sets, J Chem Theor Comput, 17, 3221, 10.1021/acs.jctc.1c00159
Gupta, 2016, Will it gel? Successful computational prediction of peptide gelators using physicochemical properties and molecular fingerprints, Chem Sci, 7, 4713, 10.1039/C6SC00722H
Li, 2019, Design of self-assembly dipeptide hydrogels and machine learning via their chemical features, Proc Natl Acad Sci USA, 116, 11259, 10.1073/pnas.1903376116
Frederix, 2015, Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels, Nat Chem, 7, 30, 10.1038/nchem.2122
Frederix, 2011, Virtual screening for dipeptide aggregation: toward predictive tools for peptide self-assembly, J Phys Chem Lett, 2, 2380, 10.1021/jz2010573
Tang, 2021, Prediction and characterization of liquid-liquid phase separation of minimalistic peptides, Cell Reports Physical Science, 2, 10.1016/j.xcrp.2021.100579
Moreira, 2019, Computational prediction of tripeptide-dipeptide co-assembly, Mol Phys, 117, 1151, 10.1080/00268976.2018.1523482
Van Lommel, 2020, Molecular dynamics based descriptors for predicting supramolecular gelation, Chem Sci, 11, 4226, 10.1039/D0SC00129E
Wang, 2019, Thermodynamic phase diagram of amyloid-β (16–22) peptide, Proc Natl Acad Sci USA, 116, 2091, 10.1073/pnas.1819592116
Sun, 2020, Proteinaceous fibers with outstanding mechanical properties manipulated by supramolecular interactions, CCS Chemistry, 3, 1669, 10.31635/ccschem.020.202000231
Wang, 2021, Regulating mechanical properties of polymer-supramolecular double-network hydrogel by supramolecular self-assembling structures, Chin J Chem, 39, 2711, 10.1002/cjoc.202100370
