Interfacial Structure Determination



The understanding of biomolecule structure at the nanoparticle interface is critical for the design of sensors containing nanoparticles and biological recognition elements. While many inorganic binding peptides have been identified from phage display and other experiments, the relationship between the peptide sequence, structure, and functional properties at the interface have not been identified. The structure of biomolecules at the interface can be determined with the tools (Circular Dichroism (CD), Fourier transform infra-red (FTIR), and nuclear magnetic resonance (NMR)) traditionally used for protein structure determination.


Nuclear Magnetic Resonance Nuclear Magnetic Resonance Spectrum Circular Dichroism Spectrum Cross Peak Dipolar Coupling 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Adey NB, Mataragnon AH, Rider JE, Carter JM, Kay BK (1995) Characterization of phage that bind plastic from phage-displayed random peptide libraries. Gene 156(1):27-31. doi: Google Scholar
  2. Andronesi OC, Heise H, Baldus M (2006) Determining protein 3D structure by magic angle spinning NMR. Mod Magn Reson 1:523–526Google Scholar
  3. Badia A, Cuccia L, Demers L, Morin F, Lennox RB (1997) Structure and dynamics in Alkanethiolate monolayers self-assembled on gold nanoparticles: a DSC, FT-IR, and deuterium NMR study. J Am Chem Soc 119(11):2682–2692CrossRefGoogle Scholar
  4. Bak M, Rasmussen JT, Nielsen NC (2000) SIMPSIN: a general simulation program for solid-state NMR spectroscopy. J Mag Reson 147:296–330CrossRefGoogle Scholar
  5. Baldus M (2006) Solid-state NMR spectroscopy: molecular structure and organization at the atomic level. Angew Chem Int Ed 45(8):1186–1188CrossRefGoogle Scholar
  6. Bartik K, Dobson CM, Redfield C (1993) H-1-NMR analysis of turkey egg-white lysozyme and comparison with hen egg-white lysozyme. Eur J Biochem 215(2):255–266. doi: 10.1111/j.1432-1033.1993.tb18030.x CrossRefGoogle Scholar
  7. Brown S (1997) Metal-recognition by repeating polypeptides. Nat Biotechnol 15(3):269–272CrossRefGoogle Scholar
  8. Calzolai L, Franchini F, Gilliland D, Rossi F (2010) Protein-nanoparticle interaction: identification of the ubiquitin-gold nanoparticle interaction site. Nano Lett 10(8):3101–3105. doi: 10.1021/nl101746v CrossRefGoogle Scholar
  9. Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci 104:9615–9620CrossRefGoogle Scholar
  10. Cavanagh J, Fairbrother WJ, Parlmer AG III, Rance M, Skelton NJ (2007) Protein NMR spectroscopy: principles and practice. Elsevier Academic Press, BurlingtonGoogle Scholar
  11. Coppage R, Slocik JM, Sethi M, Pacardo DB, Naik RR, Knecht MR (2010) Elucidation of peptide effects that control the activity of nanoparticles. Angew Chem Int Ed 122(22):3855–3858. doi: 10.1002/ange.200906949 CrossRefGoogle Scholar
  12. Coppage R, Slocik JM, Briggs BD, Frenkel AI, Heinz H, Naik RR, Knecht MR (2011) Crystallographic recognition controls peptide binding for bio-based nanomaterials. J Am Chem Soc 133(32):12346–12349. doi: 10.1021/ja203726n CrossRefGoogle Scholar
  13. Coppage R, Slocik JM, Briggs BD, Frenkel AI, Naik RR, Knecht MR (2012) Determining peptide sequence effects that control the size, structure, and function of nanoparticles. ACS Nano 6(2):1625–1636. doi: 10.1021/nn204600d CrossRefGoogle Scholar
  14. Croasmun WR, Carlson MK (eds) (1994) Two-Dimensional NMR. Applications for Chemists and Biochemists. Methods in Stereochemical Analysis. VCH Publishers, Inc., New YorkGoogle Scholar
  15. Dickerson MB, Sandhage KH, Naik RR (2008) Protein- and Peptide-directed syntheses of inorganic materials. Chem Rev 108(11):4935–4978CrossRefGoogle Scholar
  16. Drobny GP, Long JR, Karlsson T, Shaw W, Popham J, Oyler N, Bower P, Stringer J, Gregory D, Mehta M, Stayton PS (2003) Structural studies of biomaterials using double-quantum solid-state NMR spectroscopy. Ann Rev Phys Chem 54:531–571CrossRefGoogle Scholar
  17. Elgavish GA, Hay DI, Schlesinger DH (1984) 1H and 31P nuclear magnetic resonance studies of human salivary statherin. Int J Pept Protein Res 23(3):230–234. doi: 10.1111/j.1399-3011.1984.tb02714.x CrossRefGoogle Scholar
  18. Fernandez VL, Reimer JA, Denn MM (1992) Magnetic Resonance Studies of Polypeptides Adsorbed on Silica and Hydroxyapatite Surfaces. J Am Chem Soc 114:9634-9642Google Scholar
  19. Gibson JM, Raghunathan V, Popham JM, Stayton PS, Drobny GP (2005) A REDOR NMR study of a phosphorylated statherin fragment bound to hydroxyapatite crystals. J Am Chem Soc 127(26):9350–9351CrossRefGoogle Scholar
  20. Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP (2006) Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proc Natl Acad Sci USA 103(44):16083–16088CrossRefGoogle Scholar
  21. Greenfield NJ (2006) Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc 1(6):2876–2890CrossRefGoogle Scholar
  22. Greenfield NJ, Fasman GD (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8(10):4108–4116CrossRefGoogle Scholar
  23. Gullion T, Schaefer J (1989) Rotational-echo double resonance NMR. J Magn Reson 81:196–200Google Scholar
  24. Heinz H, Vaia RA, Farmer BL, Naik RR (2008) Accurate simulation of surfaces and interfaces of face-centered cubic metals using 12−6 and 9−6 Lennard-Jones Potentials. J Phys Chem C 112(44):17281–17290. doi: 10.1021/jp801931d CrossRefGoogle Scholar
  25. Heinz H, Farmer BL, Pandey RB, Slocik JM, Patnaik SS, Pachter R, Naik RR (2009) Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution. J Am Chem Soc 131(28):9704–9714. doi: 10.1021/ja900531f CrossRefGoogle Scholar
  26. Hnilova M, Oren EE, Seker UOS, Wilson BR, Collino S, Evans JS, Tamerler C, Sarikaya M (2008) Effect of molecular conformations on the adsorption behavior of gold-binding peptides. Langmuir 24(21):12440–12445. doi: 10.1021/la801468c CrossRefGoogle Scholar
  27. Jackson M, Mantsch HH (1995) The use and misuse of FTIR spectroscopy in the determination of protein-structure. Crit Rev Biochem Mol Biol 30(2):95–120. doi: 10.3109/10409239509085140 CrossRefGoogle Scholar
  28. Katoch J, Kim SN, Kuang Z, Farmer BL, Naik RR, Tatulian SA, Ishigami M (2012) Structure of a peptide adsorbed on graphene and graphite. Nano Lett 12(5):2342–2346. doi: 10.1021/nl300286k CrossRefGoogle Scholar
  29. Kogot JM, Parker AM, Lee J, Blaber M, Strouse GF, Logan TM (2009) Analysis of the Dynamics of assembly and structural impact for a histidine tagged FGF1–1.5 nm Au Nanoparticle Bioconjugate. Bioconjug Chem 20(11):2106–2113. doi: 10.1021/bc900224d CrossRefGoogle Scholar
  30. Kroger N, Deutzmann R, Sumper M (1999) Polycationic peptides from diatom biosilica that direct silica nanosphere formation. Science 286:1129–1132CrossRefGoogle Scholar
  31. Kuang ZF, Kim SN, Crookes-Goodson WJ, Farmer BL, Naik RR (2010) Biomimetic chemosensor: designing peptide recognition elements for surface functionalization of carbon nanotube field effect transistors. ACS Nano 4(1):452–458. doi: 10.1021/nn901365g CrossRefGoogle Scholar
  32. Long JR, Shaw WJ, Stayton PS, Drobny GP (2001) Structure and dynamics of hydrated statherin on hydroxyapatite as determined by solid-state NMR. Biochemistry 40(51):15451–15455CrossRefGoogle Scholar
  33. Luckarift HR, Spain JC, Naik RR, Stone MO (2004) Enzyme immobilization in a biomimetic silica support. Nat Biotech 22:211CrossRefGoogle Scholar
  34. Mafra L, Siegel R, Fernandez C, Schneider D, Aussenac F, Rocha J (2009) High-resolution 1H homonuclear dipolar recoupling NMR spectra of biological solids at MAS rates of to 67 kHz. J Magn Reson 199:111–114CrossRefGoogle Scholar
  35. Mandal HS, Kraatz H-B (2007) Effect of the surface curvature on the secondary structure of peptides adsorbed on nanoparticles. J Am Chem Soc 129(20):6356–6357. doi: 10.1021/ja0703372 CrossRefGoogle Scholar
  36. Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ (2010) Toward a structure determination method for biomineral-associated protein using combined solid-state NMR and computational structure prediction. Structure 18(12):1678–1687. doi: 10.1016/j.str.2010.09.013 CrossRefGoogle Scholar
  37. Mayer M, Mayer B (2001) Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc 123:6108–6117Google Scholar
  38. Mirau PA, Serres JL, Lyons M (2008) The structure and dynamics of Poly(l-lysine) in templated silica nanocomposites. Chem Mater 20(6):2218–2223. doi: 10.1021/cm702283u CrossRefGoogle Scholar
  39. Mirau PA, Naik RR, Gehring P (2011) Structure of peptides on metal oxide surfaces probed by NMR. J Am Chem Soc 133(45):18243–18248. doi: 10.1021/ja205454t CrossRefGoogle Scholar
  40. Miura Y, Kimura S, Imanishi Y, Umemura J (1999) Oriented helical peptide layer on the carboxylate-terminated alkanethiol immobilized on a gold surface. Langmuir 15(4):1155–1160. doi: 10.1021/la9803878 CrossRefGoogle Scholar
  41. Mirau PA, Naik RR, Coppage R, Knecht MR, Ramezani-DakHel H, Heinz H, Vaia RA, Kotlarchyk M (2014) The Structure of peptides at the palladium nanoparticle interface (submitted)Google Scholar
  42. Naganagowda GA, Gururaja TL, Levine MJ (1998) Delineation of conformational preferences in human salivary statherin by 1H, 31P NMR and CD studies: sequential assignments and structure-function correlations. J Biomol Struct Dyn 16:91–107CrossRefGoogle Scholar
  43. Naik RR, Brott LL, Clarson SJ, Stone MO (2002a) Silica-precipitating peptides isolated from a combinatorial phage display peptide library. J Nanosci Nanotechnol 2(1):95–100CrossRefGoogle Scholar
  44. Naik RR, Stringer SJ, Agarwal G, Jones SE, Stone MO (2002b) Biomimetic synthesis and patterning of silver nanoparticles. Nat Mater 1(3):169–172CrossRefGoogle Scholar
  45. Ndao M, Ash JT, Breen NF, Goobes G, Stayton PS, Drobny GP (2009) A 13C{31P} REDOR NMR investigation of the role of glutamic acid residues in statherin-hydroxyapatite recognition. Langmuir 25(20):12136–12143CrossRefGoogle Scholar
  46. Ndao M, Ash JT, Stayton PS, Drobny GP (2010) The role of basic amino acids in the molecular recognition of hydroxyapatite by statherin using solid state NMR. Surf Sci 604(15–16):L39–L42. doi: 10.1016/j.susc.2010.02.026 CrossRefGoogle Scholar
  47. Oren EE, Notman R, Kim IW, Evans JS, Walsh TR, Samudrala R, Tamerler C, Sarikaya M (2010) Probing the molecular mechanisms of quartz-binding peptides. Langmuir 26(13):11003–11009CrossRefGoogle Scholar
  48. Pacardo DB, Sethi M, Jones SE, Naik RR, Knecht MR (2009) Biomimetic synthesis of Pd nanocatalysts for the stille coupling reaction. ACS Nano 3(5):1288–1296CrossRefGoogle Scholar
  49. Parmar AS, Muschol M (2009) Hydration and hydrodynamic interactions of lysozyme: effects of chotropic versus kosmotropic ions. Biophys J 97(2):590–598CrossRefGoogle Scholar
  50. Renault M, Cukkemane A, Baldus M (2010) Solid-state NMR spectroscopy on complex biomolecules. Angewandte Chemie Int Ed 49(45):8346–8357. doi: 10.1002/anie.201002823 CrossRefGoogle Scholar
  51. Sano KI, Shiba K (2003) A hexapeptide mofif that electrostatically binds to the surface of titanium. J Am Chem Soc 125:14234–14235CrossRefGoogle Scholar
  52. Sano KI, Sasaki H, Shiba K (2005) Specificity and biomineralization activities of Ti-binding peptide-1 (TBP-1). Langmuir 21:3090–3095CrossRefGoogle Scholar
  53. Schmidt-Rohr K, Speiss HW (1994) Multidimensional solid-state NMR and polymers. Academic Press, New YorkGoogle Scholar
  54. Schwietters CD, Kuszewski JJ, Clore G (2006) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Mag Res Spectrosc 48:47–62CrossRefGoogle Scholar
  55. Shaw CP, Middleton DA, Volk M, Levy R (2012) Amyloid-derived peptide forms self-assembled mono layers on gold nanoparticle with a curvature-dependent beta-sheet structure. ACS Nano 6(2):1416–1426. doi: 10.1021/nn204214x CrossRefGoogle Scholar
  56. Slocik JM, Stone MO, Naik RR (2005) Synthesis of gold nanoparticles using multifunctional peptides. Small 1(11):1048–1052CrossRefGoogle Scholar
  57. Slocik JM, Zabinski JS Jr, Phillips DM, Naik Rajesh R (2008) Colorimentric response of peptide-functionalized gold nanoparticles to metal ions. Small 4:548–551Google Scholar
  58. Slocik JM, Govorov AO, Naik RR (2011) Plasmonic circular dichroism of peptide-functionalized gold nanoparticles. Nano Lett 11:701–705. doi: 10.1021/nl1038242 CrossRefGoogle Scholar
  59. Surewicz WK, Mantsch HH, Chapman D (1993) Determination of protein secondary structure by fourier transform infrared spectroscopy: a critical assessment. Biochemistry 32(2):389–394. doi: 10.1021/bi00053a001 CrossRefGoogle Scholar
  60. Swanson SC, Bryand RG (1991) The hydration response of Poly(L-Lysine) dynamics measured by 13C NMR spectroscopy. Biopolymers 31:967–973CrossRefGoogle Scholar
  61. Tjandra N, Tate S-i, Ono A, Kainosho M, Bax A (2000) The NMR structure of a DNA dodecamer in an aqueous dilute liquid crystalline phase. J Am Chem Soc 122(26):6190–6200Google Scholar
  62. Tycko R (2001) Biomolecular solid state NMR: advances in structural methodology and applications to peptide and protein fibrils. Ann Rev Phys Chem 52:575–606CrossRefGoogle Scholar
  63. Wang SS, Hemphreys ES, Chung SY, Delduco DF, Lustig SR, Wang H, Parker KN, Rizzo NW, Subramoney S, Chiang YM, Jagota A (2003) Peptides with selective affinity for carbon nanotubes. Nat Mater 2:196CrossRefGoogle Scholar
  64. Whaley SR, English DS, Hu EL, Barbara PF, Belcher AM (2000) Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature 405:665–668CrossRefGoogle Scholar
  65. Wishart DS, Sykes BD (1994) The 13C chemical -shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4(2):171–180CrossRefGoogle Scholar
  66. Wishart DS, Bigam CG, Holm A, Hodges RS, Sykes BD (1995) 1H, 13C and 15 N random coil NMR chemical shifts of the common amino acid. I. investigation of nearest neighbor effects. J Biomol NMR 5:67–81CrossRefGoogle Scholar
  67. Wuthrich K (1986) NMR of proteins and nucleic acids. Wiley, New YorkGoogle Scholar
  68. Zelakiewicz BS, de Dios AC, Tong YY (2003) 13C NMR spectroscopy of 13C1-labeled octanethiol-protected Au nanoparticles: shifts, relaxations, and particle-size effect. J Am Chem Soc 125(1):18–19CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Soft Matter Materials Branch (AFRL/RXAS), Air Force Research LaboratoriesWright-Patterson AFBDaytonUSA

Personalised recommendations