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Protein & Peptide Letters

Editor-in-Chief

ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Letter Article

Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

Author(s): Gaurav Pandey, Prem Prakash Das and Vibin Ramakrishnan*

Volume 27 , Issue 9 , 2020

Page: [923 - 929] Pages: 7

DOI: 10.2174/0929866527666200224114627

Price: $65

Abstract

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications.

Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly.

Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide.

Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies.

Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

Keywords: Functional peptides, microenvironments, biophysical techniques, nanofibers, peptide self-assembly, RADA peptide.

Graphical Abstract
[1]
Yokoi, H.; Kinoshita, T.; Zhang, S. Dynamic reassembly of peptide RADA16 nanofiber scaffold. Proc. Natl. Acad. Sci. USA, 2005, 102(24), 8414-8419.
[http://dx.doi.org/10.1073/pnas.0407843102 ] [PMID: 15939888]
[2]
Zhang, S.; Holmes, T.; Lockshin, C.; Rich, A. Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane. Proc. Natl. Acad. Sci. USA, 1993, 90(8), 3334-3338.
[http://dx.doi.org/10.1073/pnas.90.8.3334 ] [PMID: 7682699]
[3]
Chen, P. Self-assembly of ionic-complementary peptides: A physicochemical viewpoint. Colloids Surf. A Physicochem. Eng. Asp., 2005, 261, 3-24.
[http://dx.doi.org/10.1016/j.colsurfa.2004.12.048]
[4]
Zhang, S.; Greenfield, M.A.; Mata, A.; Palmer, L.C.; Bitton, R.; Mantei, J.R.; Aparicio, C.; de la Cruz, M.O.; Stupp, S.I. A self-assembly pathway to aligned monodomain gels. Nat. Mater., 2010, 9(7), 594-601.
[http://dx.doi.org/10.1038/nmat2778 ] [PMID: 20543836]
[5]
Cavalli, S.; Albericio, F.; Kros, A. Amphiphilic peptides and their cross-disciplinary role as building blocks for nanoscience. Chem. Soc. Rev., 2010, 39(1), 241-263.
[http://dx.doi.org/10.1039/B906701A ] [PMID: 20023851]
[6]
Zhao, X.; Pan, F.; Xu, H.; Yaseen, M.; Shan, H.; Hauser, C.A.; Zhang, S.; Lu, J.R. Molecular self-assembly and applications of designer peptide amphiphiles. Chem. Soc. Rev., 2010, 39(9), 3480-3498.
[http://dx.doi.org/10.1039/b915923c ] [PMID: 20498896]
[7]
Schnur, J.M. Lipid tubules: A paradigm for molecularly engineered structures. Science, 1993, 262(5140), 1669-1676.
[http://dx.doi.org/10.1126/science.262.5140.1669 ] [PMID: 17781785]
[8]
Zhang, S. Emerging biological materials through molecular self-assembly. Biotechnol. Adv., 2002, 20(5-6), 321-339.
[http://dx.doi.org/10.1016/S0734-9750(02)00026-5 ] [PMID: 14550019]
[9]
Mirkin, C.A.; Letsinger, R.L.; Mucic, R.C.; Storhoff, J.J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature, 1996, 382(6592), 607-609.
[http://dx.doi.org/10.1038/382607a0 ] [PMID: 8757129]
[10]
Lvov, Y.M.; Price, R.R.; Selinger, J.V.; Singh, A.; Spector, M.S.; Schnur, J.M. Imaging nanoscale patterns on biologically derived microstructures. Langmuir, 2000, 16, 5932-5935.
[http://dx.doi.org/10.1021/la000069k]
[11]
Ravichandran, R.; Griffith, M.; Phopase, J. Applications of self-assembling peptide scaffolds in regenerative medicine: The way to the clinic. J. Mater. Chem. B Mater. Biol. Med., 2014, 2, 8466-8478.
[http://dx.doi.org/10.1039/C4TB01095G]
[12]
Tsuda, Y.; Morimoto, Y.; Takeuchi, S. Monodisperse cell-encapsulating peptide microgel beads for 3D cell culture. Langmuir, 2010, 26(4), 2645-2649.
[http://dx.doi.org/10.1021/la902827y ] [PMID: 19845343]
[13]
Maude, S.; Ingham, E.; Aggeli, A. Biomimetic self-assembling peptides as scaffolds for soft tissue engineering. Nanomedicine (Lond.), 2013, 8(5), 823-847.
[http://dx.doi.org/10.2217/nnm.13.65 ] [PMID: 23656267]
[14]
Kisiday, J.; Jin, M.; Kurz, B.; Hung, H.; Semino, C.; Zhang, S.; Grodzinsky, A.J. Self-assembling peptide hydrogel fosters chondrocyte extracellular matrix production and cell division: Implications for cartilage tissue repair. Proc. Natl. Acad. Sci. USA, 2002, 99(15), 9996-10001.
[http://dx.doi.org/10.1073/pnas.142309999 ] [PMID: 12119393]
[15]
Narmoneva, D.A.; Oni, O.; Sieminski, A.L.; Zhang, S.; Gertler, J.P.; Kamm, R.D.; Lee, R.T. Self-assembling short oligopeptides and the promotion of angiogenesis. Biomaterials, 2005, 26(23), 4837-4846.
[http://dx.doi.org/10.1016/j.biomaterials.2005.01.005 ] [PMID: 15763263]
[16]
Davis, M.E.; Motion, J.P.; Narmoneva, D.A.; Takahashi, T.; Hakuno, D.; Kamm, R.D.; Zhang, S.; Lee, R.T. Injectable self-assembling peptide nanofibers create intramyocardial microenvironments for endothelial cells. Circulation, 2005, 111(4), 442-450.
[http://dx.doi.org/10.1161/01.CIR.0000153847.47301.80 ] [PMID: 15687132]
[17]
Wang, X.; Horii, A.; Zhang, S. Designer functionalized self-assembling peptide nanofiber scaffolds for growth, migration, and tubulogenesis of human umbilical vein endothelial cells. Soft Matter, 2008, 4, 2388-2395.
[http://dx.doi.org/10.1039/b807155a]
[18]
Koutsopoulos, S.; Unsworth, L.D.; Nagai, Y.; Zhang, S. Controlled release of functional proteins through designer self-assembling peptide nanofiber hydrogel scaffold. Proc. Natl. Acad. Sci. USA, 2009, 106(12), 4623-4628.
[http://dx.doi.org/10.1073/pnas.0807506106 ] [PMID: 19273853]
[19]
Nagai, Y.; Unsworth, L.D.; Koutsopoulos, S.; Zhang, S. Slow release of molecules in self-assembling peptide nanofiber scaffold. J. Control. Release, 2006, 115(1), 18-25.
[http://dx.doi.org/10.1016/j.jconrel.2006.06.031 ] [PMID: 16962196]
[20]
Davis, M.E.; Hsieh, P.C.; Takahashi, T.; Song, Q.; Zhang, S.; Kamm, R.D.; Grodzinsky, A.J.; Anversa, P.; Lee, R.T. Local myocardial insulin-like growth factor 1 (IGF-1) delivery with biotinylated peptide nanofibers improves cell therapy for myocardial infarction. Proc. Natl. Acad. Sci. USA, 2006, 103(21), 8155-8160.
[http://dx.doi.org/10.1073/pnas.0602877103 ] [PMID: 16698918]
[21]
Gelain, F.; Unsworth, L.D.; Zhang, S. Slow and sustained release of active cytokines from self-assembling peptide scaffolds. J. Control. Release, 2010, 145(3), 231-239.
[http://dx.doi.org/10.1016/j.jconrel.2010.04.026 ] [PMID: 20447427]
[22]
Ye, Z.; Zhang, H.; Luo, H.; Wang, S.; Zhou, Q.; Du, X.; Tang, C.; Chen, L.; Liu, J.; Shi, Y.K. Temperature and pH effects on biophysical and morphological properties of self‐assembling peptide RADA16‐I. J. Pept. Sci., 2008, 14, 152-162.
[http://dx.doi.org/10.1002/psc.988] [PMID: 18196533]
[23]
Arosio, P.; Owczarz, M.; Wu, H.; Butté, A.; Morbidelli, M. End-to-end self-assembly of RADA 16-I nanofibrils in aqueous solutions. Biophys. J., 2012, 102(7), 1617-1626.
[http://dx.doi.org/10.1016/j.bpj.2012.03.012 ] [PMID: 22500762]
[24]
Ramakrishnan, V.; Ranbhor, R.; Durani, S. Existence of specific “folds” in polyproline II ensembles of an “unfolded” alanine peptide detected by molecular dynamics. J. Am. Chem. Soc., 2004, 126(50), 16332-16333.
[http://dx.doi.org/10.1021/ja045787y ] [PMID: 15600329]
[25]
Ramakrishnan, V.; Ranbhor, R.; Kumar, A.; Durani, S. The link between sequence and conformation in protein structures appears to be stereochemically established. J. Phys. Chem. B, 2006, 110(18), 9314-9323.
[http://dx.doi.org/10.1021/jp056417e ] [PMID: 16671750]
[26]
Marqusee, S.; Robbins, V.H.; Baldwin, R.L. Unusually stable helix formation in short alanine-based peptides. Proc. Natl. Acad. Sci. USA, 1989, 86(14), 5286-5290.
[http://dx.doi.org/10.1073/pnas.86.14.5286 ] [PMID: 2748584]
[27]
Stanger, H.E.; Syud, F.A.; Espinosa, J.F.; Giriat, I.; Muir, T.; Gellman, S.H. Length-dependent stability and strand length limits in antiparallel β -sheet secondary structure. Proc. Natl. Acad. Sci. USA, 2001, 98(21), 12015-12020.
[http://dx.doi.org/10.1073/pnas.211536998 ] [PMID: 11593011]
[28]
Escobedo, A.; Topal, B.; Kunze, M.B.A.; Aranda, J.; Chiesa, G.; Mungianu, D.; Bernardo-Seisdedos, G.; Eftekharzadeh, B.; Gairí, M.; Pierattelli, R.; Felli, I.C.; Diercks, T.; Millet, O.; García, J.; Orozco, M.; Crehuet, R.; Lindorff-Larsen, K.; Salvatella, X. Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor. Nat. Commun., 2019, 10(1), 2034.
[http://dx.doi.org/10.1038/s41467-019-09923-2 ] [PMID: 31048691]
[29]
Adler, J.; Scheidt, H.A.; Lemmnitzer, K.; Krueger, M.; Huster, D. N-terminal lipid conjugation of amyloid β(1-40) leads to the formation of highly ordered N-terminally extended fibrils. Phys. Chem. Chem. Phys., 2017, 19(3), 1839-1846.
[http://dx.doi.org/10.1039/C6CP05982A ] [PMID: 28000812]
[30]
Srinivasan, R. Ribosome - program to build coordinates for peptides from sequence, Jenkins Department of Biophysics, Johns Hopkins University. Available from: https://biophysics.jhu.edu/graduate/jenkins-biophysics-program/
[31]
Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M.R.; Smith, J.C.; Kasson, P.M.; van der Spoel, D.; Hess, B.; Lindahl, E. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 2013, 29(7), 845-854.
[http://dx.doi.org/10.1093/bioinformatics/btt055 ] [PMID: 23407358]
[32]
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(7), 843-856.
[http://dx.doi.org/10.1007/s00249-011-0700-9 ] [PMID: 21533652]
[33]
Sasidharan, S.; Hazam, P.K.; Ramakrishnan, V. Symmetry-directed self-organization in peptide nanoassemblies through aromatic π-π interactions. J. Phys. Chem. B, 2017, 121(2), 404-411.
[http://dx.doi.org/10.1021/acs.jpcb.6b09474 ] [PMID: 27935713]

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