The extracellular matrix (ECM) is a complex, hierarchical material containing structural and bioactive components. This complexity makes decoupling the effects of biomechanical properties and cell-matrix interactions difficult, especially when studying cellular processes in a 3D environment. Matrix mechanics and cell adhesion are both known regulators of specific cellular processes such as stem cell proliferation and differentiation. However, more information is required about how such variables impact various neural lineages that could, upon transplantation, therapeutically improve neural function after a central nervous system injury or disease. Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are one biomaterial approach to meet these goals, consisting of a family of peptide sequences that assemble into physical hydrogels in physiological media. In this study, we studied our previously reported supramolecularly-assembling RAPID hydrogels functionalized with the ECM-derived cell-adhesive peptide ligands RGD, IKVAV, and YIGSR. Using molecular dynamics simulations and experimental rheology, we demonstrated that these integrin-binding ligands at physiological concentrations (3–12 m<sc>m</sc>) did not impact the assembly of the KYFIL peptide system. In simulations, molecular measures of assembly such as hydrogen bonding and pi-pi interactions appeared unaffected by cell-adhesion sequence or concentration. Visualizations of clustering and analysis of solvent-accessible surface area indicated that the integrin-binding domains remained exposed. KYFIL or AYFIL hydrogels containing 3 m<sc>m</sc> of integrin-binding domains resulted in mechanical properties consistent with their non-functionalized equivalents. This strategy of doping RAPID gels with cell-adhesion sequences allows for the precise tuning of peptide ligand concentration, independent of the rheological properties. The controllability of the RAPID hydrogel system provides an opportunity to investigate the effect of integrin-binding interactions on encapsulated neural cells to discern how hydrogel microenvironment impacts growth, maturation, or differentiation.

Small molecules can assemble together into larger structures to impact biological outcomes. One such type of assembly occurs between peptides, short chains of amino acids bonded together. When carefully designed, some peptides can assemble into fibers and hydrogels. However, adding additional amino acids to the peptide, in order to have a different biological effect, may interfere with the structural assembly. This paper examines how some peptide modifications may or may not interrupt assembly. We use both computational simulations and experimental methods to characterize material mechanical properties. Our results indicate that at concentrations appropriate for biological systems, the modifications do not dramatically impact peptide assembly.

1.
Alegre-Requena JV, Saldías C, Inostroza-Rivera R, Díaz Díaz D. Understanding hydrogelation processes through molecular dynamics. J Mater Chem B. 2019;7(10):1652–73.
2.
Álvarez Z, Ortega JA, Sato K, Sasselli IR, Kolberg-Edelbrock AN, Qiu R, et al. Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons. Cell Stem Cell. 2023;30(2):219–38.e14.
3.
Asmani MN, Ai J, Amoabediny G, Noroozi A, Azami M, Ebrahimi-Barough S, et al. Three-dimensional culture of differentiated endometrial stromal cells to oligodendrocyte progenitor cells (OPCs) in fibrin hydrogel. Cell Biol Int. 2013;37(12):1340–9.
4.
Banerjee A, Arha M, Choudhary S, Ashton RS, Bhatia SR, Schaffer DV, et al. The influence of hydrogel modulus on the proliferation and differentiation of encapsulated neural stem cells. Biomaterials. 2009;30(27):4695–9.
5.
Bordo D, Argos P. The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins. J Mol Biol. 1994;243(3):504–19.
6.
Brown TE, Anseth KS. Spatiotemporal hydrogel biomaterials for regenerative medicine. Chem Soc Rev. 2017;46(21):6532–52.
7.
Clarke DE, Pashuck ET, Bertazzo S, Weaver JVM, Stevens MM. Self-healing, self-assembled β-sheet peptide-poly(γ-glutamic acid) hybrid hydrogels. J Am Chem Soc. 2017;139(21):7250–5.
8.
Condon JE, Jayaraman A. Jayaraman A: development of a coarse-grained model of collagen-like peptide (CLP) for studies of CLP triple helix melting. J Phys Chem B. 2018;122(6):1929–39.
9.
Contreras-Riquelme S, Garate J-A, Perez-Acle T, Martin AJM. RIP-MD: a tool to study residue interaction networks in protein molecular dynamics. PeerJ. 2018;6:e5998.
10.
Cui GH, Shao SJ, Yang JJ, Liu JR, Guo HD. Designer self-assemble peptides maximize the therapeutic benefits of neural stem cell transplantation for alzheimer’s disease via enhancing neuron differentiation and paracrine action. Mol Neurobiol. 2016;53(2):1108–23.
11.
Dånmark S, Aronsson C, Aili D. Tailoring supramolecular peptide–poly(ethylene glycol) hydrogels by coiled coil self-assembly and self-sorting. Biomacromolecules. 2016;17(6):2260–7.
12.
Diao HJ, Low WC, Milbreta U, Lu QR, Chew SY. Nanofiber-mediated microRNA delivery to enhance differentiation and maturation of oligodendroglial precursor cells. J Control Release. 2015;208:85–92.
13.
Ding L, Jiang Y, Zhang J, Klok H-A, Zhong Z. pH-sensitive coiled-coil peptide-cross-linked hyaluronic acid nanogels: synthesis and targeted intracellular protein delivery to CD44 positive cancer cells. Biomacromolecules. 2018;19(2):555–62.
14.
Edwards-Gayle CJC, Hamley IW. Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials. Org Biomol Chem. 2017;15(28):5867–76.
15.
Farrukh A, Ortega F, Fan W, Marichal N, Paez JI, Berninger B, et al. Bifunctional hydrogels containing the laminin motif IKVAV promote neurogenesis. Stem Cell Rep. 2017;9(5):1432–40.
16.
Fischer SE, Liu X, Mao H-Q, Harden JL. Controlling cell adhesion to surfaces via associating bioactive triblock proteins. Biomaterials. 2007;28(22):3325–37.
17.
Frederix PWJM, Scott GG, Abul-Haija YM, Kalafatovic D, Pappas CG, Javid N, et al. Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels. Nat Chem. 2015;7(1):30–7.
18.
Gartner TEI, Jayaraman A. Modeling and simulations of polymers: a roadmap. Macromolecules. 2019;52(3):755–86.
19.
Gelain F, Lomander A, Vescovi AL, Zhang S. Systematic studies of a self-assembling peptide nanofiber scaffold with other scaffolds. J Nanosci Nanotechnol. 2007;7(2):424–34.
20.
Gray VP, Amelung CD, Duti IJ, Laudermilch EG, Letteri RA, Lampe KJ. Biomaterials via peptide assembly: design, characterization, and application in tissue engineering. Acta Biomater. 2022;140:43–75.
21.
Haines-Butterick L, Rajagopal K, Branco M, Salick D, Rughani R, Pilarz M, et al. Controlling hydrogelation kinetics by peptide design for three-dimensional encapsulation and injectable delivery of cells. Proc Natl Acad Sci U S A. 2007;104(19):7791–6.
22.
Hartgerink JD, Beniash E, Stupp SI. Self-assembly and mineralization of peptide-amphiphile nanofibers. Science. 2001;294(5547):1684–8.
23.
Hilderbrand AM, Taylor PA, Stanzione F, LaRue M, Guo C, Jayaraman A, et al. Combining simulations and experiments for the molecular engineering of multifunctional collagen mimetic peptide-based materials. Soft Matter. 2021;17(7):1985–98.
24.
Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph. 1996;14(1):33–8, 27-8.
25.
Jayawarna V, Ali M, Jowitt TA, Miller AF, Saiani A, Gough JE, et al. Nanostructured hydrogels for three-dimensional cell culture through self-assembly of fluorenylmethoxycarbonyl–dipeptides. Adv Mater. 2006;18(5):611–4.
26.
Jung JP, Moyano JV, Collier JH. Multifactorial optimization of endothelial cell growth using modular synthetic extracellular matrices. Integr Biol. 2011;3:185–96.
27.
Lampe KJ, Antaris AL, Heilshorn SC. Design of three-dimensional engineered protein hydrogels for tailored control of neurite growth. Acta Biomater. 2013;9(3):5590–9.
28.
Larsen PH, Yong VW. The expression of matrix metalloproteinase-12 by oligodendrocytes regulates their maturation and morphological differentiation. J Neurosci. 2004;24(35):7597–603.
29.
LeBaron RG, Athanasiou KA. Extracellular matrix cell adhesion peptides: functional applications in orthopedic materials. Tissue Eng. 2000;6(2):85–103.
30.
Lee S, Leach MK, Redmond SA, Chong SYC, Mellon SH, Tuck SJ, et al. A culture system to study oligodendrocyte myelination processes using engineered nanofibers. Nat Methods. 2012;9:917–22.
31.
Li NK, García Quiroz F, Hall CK, Chilkoti A, Yingling YG. Molecular description of the LCST behavior of an elastin-like polypeptide. Biomacromolecules. 2014;15(10):3522–30.
32.
Liedmann A, Rolfs A, Frech MJ. Cultivation of human neural progenitor cells in a 3-dimensional self-assembling peptide hydrogel. J Vis Exp. 2012(59):3830.
33.
Lourenço T, Grãos M. Modulation of oligodendrocyte differentiation by mechanotransduction. Front Cell Neurosci. 2016;10:277.
34.
Madl CM, Katz LM, Heilshorn SC. Bio-orthogonally crosslinked, engineered protein hydrogels with tunable mechanics and biochemistry for cell encapsulation. Adv Funct Mater. 2016;26(21):3612–20.
35.
Mann JL, Yu AC, Agmon G, Appel EA. Supramolecular polymeric biomaterials. Biomater Sci. 2017;6(1):10–37.
36.
Mansbach RA, Ferguson AL. Coarse-grained molecular simulation of the hierarchical self-assembly of π-conjugated optoelectronic peptides. J Phys Chem B. 2017;121(7):1684–706.
37.
Marquardt LM, Doulames VM, Wang AT, Dubbin K, Suhar RA, Kratochvil MJ, et al. Designer, injectable gels to prevent transplanted Schwann cell loss during spinal cord injury therapy. Sci Adv. 2020;6(14):eaaz1039.
38.
McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 1994;238(5):777–93.
39.
Meco E, Zheng WS, Sharma AH, Lampe KJ. Guiding oligodendrocyte precursor cell maturation with urokinase plasminogen activator-degradable elastin-like protein hydrogels. Biomacromolecules. 2020;21(12):4724–36.
40.
Miller JS, Shen CJ, Legant WR, Baranski JD, Blakely BL, Chen CS. Bioactive hydrogels made from step-growth derived PEG-peptide macromers. Biomaterials. 2010;31(13):3736–43.
41.
Murphy NP, Lampe KJ. Mimicking biological phenomena in hydrogel-based biomaterials to promote dynamic cellular responses. J Mater Chem B. 2015;3(40):7867–80.
42.
Patel R, Santhosh M, Dash JK, Karpoormath R, Jha A, Kwak J. A moldy application of MALDI: MALDI-ToF mass spectrometry for fungal identification. J Fungi. 2019;5(1):4–12.
43.
Payne SL, Tuladhar A, Obermeyer JM, Varga BV, Teal CJ, Morshead CM, et al. Initial cell maturity changes following transplantation in a hyaluronan-based hydrogel and impacts therapeutic success in the stroke-injured rodent brain. Biomaterials. 2019;192:309–22.
44.
Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys. 2020;153(4):044130.
45.
Prhashanna A, Taylor PA, Qin J, Kiick KL, Jayaraman A. Effect of peptide sequence on the LCST-like transition of elastin-like peptides and elastin-like peptide–collagen-like peptide conjugates: simulations and experiments. Biomacromolecules. 2019;20(3):1178–89.
46.
Rodell CB, Kaminski AL, Burdick JA. Rational design of network properties in guest-host assembled and shear-thinning hyaluronic acid hydrogels. Biomacromolecules. 2013;14(11):4125–34.
47.
Rodrigues GMC, Gaj T, Adil MM, Wahba J, Rao AT, Lorbeer FK, et al. Defined and scalable differentiation of human oligodendrocyte precursors from pluripotent stem cells in a 3D culture system. Stem Cell Rep. 2017;8(6):1770–83.
48.
Russell LN, Lampe KJ. Engineering biomaterials to influence oligodendroglial growth, maturation, and myelin production. Cells Tissues Organs. 2016;202(1-2):85–101.
49.
Russell LN, Lampe KJ. Oligodendrocyte precursor cell viability, proliferation, and morphology is dependent on mesh size and storage modulus in 3D poly(ethylene glycol)-based hydrogels. ACS Biomater Sci Eng. 2017;3(12):3459–68.
50.
Schneider JP, Pochan DJ, Ozbas B, Rajagopal K, Pakstis L, Kretsinger J. Responsive hydrogels from the intramolecular folding and self-assembly of a designed peptide. J Am Chem Soc. 2002;124(50):15030–7.
51.
Silva GA, Czeisler C, Niece KL, Beniash E, Harrington DA, Kessler JA, et al. Selective differentiation of neural progenitor cells by high-epitope density nanofibers. Science. 2004;303(5662):1352–5.
52.
Smith AV, Hall CK. Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model. J Mol Biol. 2001;312(1):187–202.
53.
Smith AM, Williams RJ, Tang C, Coppo P, Collins RF, Turner ML, et al. Fmoc-diphenylalanine self assembles to a hydrogel via a novel architecture based on π–π interlocked β-sheets. Adv Mater. 2008;20(1):37–41.
54.
Sumey JL, Johnston PC, Harrell AM, Caliari SR. Hydrogel mechanics regulate fibroblast DNA methylation and chromatin condensation. Biomater Sci. 2023;11(8):2886–97.
55.
Tang JD, Mura C, Lampe KJ. Stimuli-responsive, pentapeptide, nanofiber hydrogel for tissue engineering. J Am Chem Soc. 2019a;141(12):4886–99.
56.
Tang JD, Roloson EB, Amelung CD, Lampe KJ. Rapidly assembling pentapeptides for injectable delivery (RAPID) hydrogels as cytoprotective cell carriers. ACS Biomater Sci Eng. 2019b;5:2117–21.
57.
Taylor PA, Huang H, Kiick KL, Jayaraman A. Placement of tyrosine residues as a design element for tuning the phase transition of elastin-peptide-containing conjugates: experiments and simulations. Mol Syst Des Eng. 2020;5(7):1239–54.
58.
Taylor PA, Kloxin AM, Jayaraman A. Impact of collagen-like peptide (CLP) heterotrimeric triple helix design on helical thermal stability and hierarchical assembly: a coarse-grained molecular dynamics simulation study. Soft Matter. 2022;18(16):3177–92.
59.
Thompson HL, Burbelo PD, Yamada Y, Kleinman HK, Metcalfe DD. Identification of an amino acid sequence in the laminin A chain mediating mast cell attachment and spreading. Immunology. 1991;72(1):144–9.
60.
Tibbitt MW, Anseth KS. Hydrogels as extracellular matrix mimics for 3D cell culture. Biotechnol Bioeng. 2009;103(4):655–63.
61.
Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO. Maximum allowed solvent accessibilites of residues in proteins. PLoS One. 2013;8(11):e80635.
62.
Cheng TY, Chen MH, Chang WH, Huang MY, Wang TW. Neural stem cells encapsulated in a functionalized self-assembling peptide hydrogel for brain tissue engineering. Biomaterials. 2013;34(8):2005–16.
63.
Tysseling VM, Sahni V, Pashuck ET, Birch D, Hebert A, Czeisler C, et al. Self-assembling peptide amphiphile promotes plasticity of serotonergic fibers following spinal cord injury. J Neurosci Res. 2010;88(14):3161–70.
64.
Unal DB, Caliari SR, Lampe KJ. 3D hyaluronic acid hydrogels for modeling oligodendrocyte progenitor cell behavior as a function of matrix stiffness. Biomacromolecules. 2020;21(12):4962–71.
65.
Urbanski MM, Kingsbury L, Moussouros D, Kassim I, Mehjabeen S, Paknejad N, et al. Myelinating glia differentiation is regulated by extracellular matrix elasticity. Sci Rep. 2016;6:33751.
66.
Veiga S, Ly J, Chan PH, Bresnahan JC, Beattie MS. SOD1 overexpression improves features of the oligodendrocyte precursor response in vitro. Neurosci Lett. 2011;503(1):10–4.
67.
Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods. 2020;17(3):261–72.
68.
Wang J, Liu K, Xing R, Yan X. Peptide self-assembly: thermodynamics and kinetics. Chem Soc Rev. 2016;45(20):5589–604.
69.
Wang Y, An Y, Shmidov Y, Bitton R, Deshmukh SA, Matson JB. A combined experimental and computational approach reveals how aromatic peptide amphiphiles self-assemble to form ion-conducting nanohelices. Mater Chem Front. 2020;4(10):3022–31.
70.
Weber LM, Hayda KN, Haskins K, Anseth KS. The effects of cell-matrix interactions on encapsulated beta-cell function within hydrogels functionalized with matrix-derived adhesive peptides. Biomaterials. 2007;28(19):3004–11.
71.
Weinhold F, Klein RA. What is a hydrogen bond? Mutually consistent theoretical and experimental criteria for characterizing H-bonding interactions. Mol Phys. 2012;110(9-10):565–79.
72.
Wong Po Foo CTS, Lee JS, Mulyasasmita W, Parisi-Amon A, Heilshorn SC. Two-component protein-engineered physical hydrogels for cell encapsulation. Proc Natl Acad Sci U S A. 2009;106(52):22067–72.
73.
Ylä-Outinen L, Joki T, Varjola M, Skottman H, Narkilahti S. Three-dimensional growth matrix for human embryonic stem cell-derived neuronal cells. J Tissue Eng Regen Med. 2014;8(3):186–94.
74.
Yu X, Dillon GP, Bellamkonda RB. A laminin and nerve growth factor-laden three-dimensional scaffold for enhanced neurite extension. Tissue Eng. 1999;5(4):291–304.
75.
Zhong J, Chan A, Morad L, Kornblum HI, Fan G, Carmichael ST. Hydrogel matrix to support stem cell survival after brain transplantation in stroke. Neurorehabil Neural Repair. 2010;24(7):636–44.
You do not currently have access to this content.