Abstract
Single-chain equilibrium conformation and dimerization of the three types of ionic EAK16 peptide are studied under three pH conditions using all-atom molecular dynamics simulations. It is found that both the single-chain conformation and the dimerization process of EAK16-IV are considerably different from those of the two other types, EAK16-I and EAK16-II. The value of pH is found to have a stronger effect on the single-chain conformation and dimerization of EAK16-IV. It is shown that in addition to the charge pattern on the peptide chains, the size of the side chains of the charged amino acids plays role in the conformation of the peptide chains and their dimerization. The results shed light on the pH-dependent self-assembly behavior of EAK16 peptide in the bulk solution, which has been reported in the literature.
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References
Baratlo M, Fazli H (2009) Molecular dynamics simulation of semiflexible polyampholyte brushes–the effect of charged monomers sequence. Eur Phys J E 29:131–138. doi:10.1140/epje/i2009-10458-x
Baratlo M, Fazli H (2010) Brushes of flexible, semiflexible, and rodlike diblock polyampholytes: molecular dynamics simulation and scaling analysis. Phys Rev E 81:011801. doi:10.1103/PhysRevE.81.011801
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. Intermol Forces 14:331–342. doi:10.1007/978-94-015-7658-1_21
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690. doi:10.1063/1.448118
Carrell RW, Gooptut B (1998) Conformational changes and disease—serpins, prions and Alzheimer’s. Curr Opin Struct Biol 8:799–809. doi:10.1016/S0959-440X(98)80101-2
Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092. doi:10.1063/1.464397
Dubrynin AV, Colby RH, Rubinstein M (2004) Polyampholytes. J Polym Sci Part B Polym Phys 42:3513–3538. doi:10.1002/polb.20207
Emamyari S, Fazli H (2014) pH-dependent self-assembly of EAK16 peptides in the presence of a hydrophobic surface: coarse-grained molecular dynamics simulation. Soft Matter (to be published)
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8592. doi:10.1063/1.470117
Fernández-Carneado J, Kogan MJ, Pujals S, Giralt E (2004) Amphipathic peptides and drug delivery. Pept Sci 76:196–203. doi:10.1002/bip.10585
Ferreira ST, De Felice FG (2001) Protein dynamics, folding and misfolding: from basic physical chemistry to human conformational diseases. FEBS Lett 498:129–134. doi:10.1016/S0014-5793(01)02491-7
Fung SY, Keyes C, Duhamel J, Chen P (2003) Concentration effect on the aggregation of a self-assembling oligopeptide. Biophys J 85:537–548. doi:10.1016/S0006-3495(03)74498-1
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comp Chem 18:1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447. doi:10.1021/ct700301q
Holmes TC, de Lacalle S, Su X, Liu G, Rich A, Zhang S (2000) Extensive neurite outgrowth and active synapse formation on self-assembling peptide scaffolds. Proc Natl Acad Sci USA 97:6728–6733. doi:10.1073/pnas.97.12.6728
Hong Y, Legge RL, Zhang S, Chen P (2003) Effect of amino acid sequence and pH on nanofiber formation of self-assembling peptides EAK16-II and EAK16-IV. Biomacromolecules 4:1433–1442. doi:10.1021/bm0341374
Hong Y, Lau LS, Legge RL, Chen P (2004) Critical self-assembly concentration of an ionic-complementary peptide EAK16-I. J Adhesion 80:913–931. doi:10.1080/00218460490508616
Hong Y, Pritzker MD, Legge RL, Chen P (2005) Effect of NaCl and peptide concentration on the self-assembly of an ionic-complementary peptide EAK16-II. Colloids Surf B 46:152–161. doi:10.1016/j.colsurfb.2005.11.004
Houseman BT, Mrksich M (2002) Towards quantitative assays with peptide chips: a surface engineering approach. Trends Biotechnol 20:279–281. doi:10.1016/S0167-7799(02)01984-4
Humphrey W, Dalkeand A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38. doi:10.1016/0263-7855(96)00018-5
HyperChem(TM), Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA
Jorgensen WL, Tirado-Rives J (1988) The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657–1666. doi:10.1021/ja00214a001
Jun S, Hong Y, Imamura H, Ha B-Y, Bechhoefer J, Chen P (2004) Self-assembly of the ionic peptide EAK16: the effect of charge distributions on self-assembly. Biophys J 87:1249–1259. doi:10.1529/biophysj.103.038166
Kisiday J, Jin M, Kurz B, Hung H, Semino C, Zhang S, Grodzinsky AJ (2002) Self-assembling peptide hydrogel fosters chondrocyte extracellular matrix production and cell division: implications for cartilage tissue repair. Proc Natl Acad Sci USA 99:9996–10001. doi:10.1073/pnas.142309999
Lim HS, Han JT, Kwak D, Jin M, Cho K (2006) Photoreversibly switchable superhydrophobic surface with erasable and rewritable pattern. J Am Chem Soc 128:14458–14459. doi:10.1021/ja0655901
Luo Z, Zhao X, Zhang S (2008) Structural dynamic of a self-assembling peptide d-EAK16 made of only d-amino acids. PLoS ONE 3(5):e2364. doi:10.1371/journal.pone.0002364
Miyamoto S, Kollman PA (1992) Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comp Chem 13:952–962. doi:10.1002/jcc.540130805
Sheng Y, Wang Y, Chen P (2010) Interaction of an ionic complementary peptide with a hydrophobic graphite surface. Protein Sci 19:1639–1648. doi:10.1002/pro.444
Soto C, Saborio GP (2001) Prions: disease propagation and disease therapy by conformational transmission. TRENDS Mol Med 7:109–114. doi:10.1016/S1471-4914(01)01931-1
van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005a) GROMACS: fast, flexible, and free. J Comp Chem 26:1701–1718. doi:10.1002/jcc.20291
van der Spoel D, Lindahl E, Hess B, Kutzner C, van Buuren AR, Apol E, Meulenhoff PJ, Tieleman DP, Sijbers ALTM, Feenstra KA, van Drunen R, Berendsen HJC (2005b). Gromacs user manual version 4.0. www.gromacs.org
van Gunsteren WF, Berendsen HJC (1988) A Leap-frog algorithm for stochastic dynamics. Mol Sim 1:173–185. doi:10.1080/08927028808080941
Wang J, Tang F, Li F, Lin J, Zhang Y, Du L, Zhao X (2008a) The amphiphilic self-assembling peptide EAK16-I as a potential hydrophobic drug carrier. J Nanomater 2008:516286–516294. doi:10.1155/2008/516286
Wang X, Horii A, Zhang S (2008b) Designer functionalized self-assembling peptide nanofiber scaffolds for growth, migration, and tubulogenesis of human umbilical vein endothelial cells. Soft Matter 4:2388–2395. doi:10.1039/B807155A
Wei Y, Tong W, Wise C, Wei X, Armbrust K, Zimmt M (2006) Dipolar control of monolayer morphology: spontaneous SAM patterning. J Am Chem Soc 128:13362–13363. doi:10.1021/ja065338t
Whitesides GM, Boncheva M (2002) Beyond molecules: self-assembly of mesoscopic and macroscopic components. Proc Natl Acad Sci USA 99:4769–4774. doi:10.1073/pnas.082065899
Whitesides GM, Grzybowski B (2002) Self-assembly at all scales. Science 295:2418–2421. doi:10.1126/science.1070821
Whitesides GM, Mathias JP, Seto C (1991) Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures. Science 254:1312–1319. doi:10.1126/science.1962191
Wouters D, Schubert US (2004) Nanolithography and nanochemistry: probe-related patterning techniques and chemical modification for nanometer-sized devices. Angew Chem Int Ed 43:2480–2495. doi:10.1002/anie.200300609
Yan Z, Wang J, Wang W (2008) Folding and dimerization of the ionic peptide EAK16-IV. Proteins 72:150–162. doi:10.1002/prot.21903
Yang H, Fung S-Yu, Pritzker M, Chen P (2007a) Surface-assisted assembly of an ionic-complementary peptide: controllable growth of nanofibers. J Am Chem Soc 129(12200):12210. doi:10.1021/ja073168u
Yang H, Fung S-Yu, Pritzker M, Chen P (2007b) Modification of hydrophilic and hydrophobic surfaces using an ionic-complementary peptide. PLoS ONE 2:e1325. doi:10.1371/journal.pone.0001325
Zerovnik E (2002) Amyloid-fibril formation: proposed mechanisms and relevance to conformational disease. Eur J Biochem 269:3362–3371. doi:10.1046/j.1432-1033.2002.03024.x
Zhang S (2003) Fabrication of novel biomaterials through molecular self-assembly. Nat Biotechnol 21:1171–1178. doi:10.1038/nbt874
Zhang S, Lockshin C, Herbert A, Winter E, Rich A (1992) Zuotin, a putative Z-DNA binding protein in Saccharomyces cerevisiae. EMBO J 11:3787–3796
Zhang S, Holmes T, Lockshin C, Rich A (1993) Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane. Proc Natl Acad Sci USA 90:3334–3338. doi:10.1073/pnas.90.8.3334
Zhang S, Holmes TC, Michael DiPersio C, Hynes RO, Su X, Rich A (1995) Self-complementary oligopeptide matrices support mammalian cell attachment. Biomaterials 16:1385–1393. doi:10.1016/0142-9612(95)96874-Y
Zhang S, Yan L, Altman M, Lässle M, Nugent H, Frankel F, Lauffenburger DA, Whitesides GM, Rich A (1999) Biological surface engineering: a simple system for cell pattern formation. Biomaterials 20:1213–1220. doi:10.1016/S0142-9612(99)00014-9
Zhang S, Marini DM, Hwang W, Santoso S (2002) Design of nanostructured biological materials through self-assembly of peptides and proteins. Curr Opin Chem Biol 6:865–871. doi:10.1016/s1367-5931(02)00391-5
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Emamyari, S., Fazli, H. All-atom molecular dynamics study of EAK16 peptide: the effect of pH on single-chain conformation, dimerization and self-assembly behavior. Eur Biophys J 43, 143–155 (2014). https://doi.org/10.1007/s00249-014-0949-x
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DOI: https://doi.org/10.1007/s00249-014-0949-x