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Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions

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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Year of Publication: 2016
Authors:
Avneet Saini
10.5120/ijca2016910265

Avneet Saini. Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions. International Journal of Computer Applications 143(7):46-56, June 2016. BibTeX

@article{10.5120/ijca2016910265,
	author = {Avneet Saini},
	title = {Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions},
	journal = {International Journal of Computer Applications},
	issue_date = {June 2016},
	volume = {143},
	number = {7},
	month = {Jun},
	year = {2016},
	issn = {0975-8887},
	pages = {46-56},
	numpages = {11},
	url = {http://www.ijcaonline.org/archives/volume143/number7/25093-2016910265},
	doi = {10.5120/ijca2016910265},
	publisher = {Foundation of Computer Science (FCS), NY, USA},
	address = {New York, USA}
}

Abstract

Conformations of achiral and chiral aromatic homo-polypeptoids of Nphe, Nspe and Nrpe were studied by quantum mechanics and molecular dynamics approaches. The amide bond geometry in model peptoids Ac-X-NMe2 could be both cis and trans and the Nphe peptoids adopted degenerate conformations of opposite handedness with Φ, Ψ values of ~ ± 120º, ± 150º with trans amide bond geometry. This degeneracy was lifted with increase in chain length; in favor of the structure with Φ = -120º, Ψ = -150º. Polypeptoids of Nspe and Nrpe with and without protecting groups populated states with Φ, Ψ values of ~ 110º, 155º & -110º, -165º respectively with trans amide bond geometry.

Simulation studies in water revealed that with protecting groups peptoid Ac-(Nspe/Nrpe)5-NMe2 populated with cis amide bond geometry in PP type I and inverse PP type I helices respectively due to interactions between the solvent molecules and carbonyl oxygens of the backbone. Without protecting groups these polypeptoids populated poly-L-proline type II conformations. In DMSO these peptoids were shown to populate in PP type-I and inverse PP type-I helices and without protecting groups they could be realized in PP type-I as well as inverse PP type-I conformation whereas the peptoid -Nrpe6-NH2 could be realized in inverse PP type-I conformation. Analysis of simulation results as a function of time ruled out amide bond inter-conversions between cis and trans geometry. Hence, like polyproline peptoids can also be exploited as molecular spacers.

References

  1. Miller S M, Simon R J, Ng S, Zuckermann R N, Kerr J M & Moos W H (1995) Drug. Dev. Res. 35, 20-32
  2. Kwon Y & Kodadek T (2007) J. Am. Chem. Soc. 129, 1508-1509
  3. Miller S M, Simon R J, Ng S, Zuckermann R N, Kerr J M & Moos W H (1994) Bioorg. Med. Chem. Lett. 4, 2657–2662
  4. Proulx C, Yoo S, Connolly M D & Zuckermann R N (2015) J. Org. Chem., Article ASAP
  5. Huang M L, Benson M A, Shin S B Y, Torres V J & Kirshenbaum K (2013) Eur. J. Org. Chem. 2013, 3560–3566
  6. Huang W, Seo J, Willingham S B, Czyzewski, A M, Gonzalgo M L, Weissman I L & Barron A E (2014) PLOSOne 9, e90397
  7. Mojsoska B, Zuckermann R N & Jenssena H (2015) Antimicrob. Agents Chemother. 59, 4112-20
  8. Patch J A & Barron A E (2003) J. Am. Chem. Soc. 123, 12092-12093
  9. Seurynck S L, Patch J A & Barron A E (2005) Chem. Biol. 12, 77-88
  10. Rossa T M, Zuckermann R N, William C R & Frey H (2008) Neuroscience Letters 439, 30–33
  11. Statz A R, Meagher R J, Barron A E & Messersmith P B (2005) J. Am. Chem. Soc.127, 7972-7973
  12. Statz A R, Meagher R J, Barron A E & Messersmith P B (2008) Soft Matter 4, 131–139
  13. Lau K H A, Ren C, Sileika T S, Park S H, Szleifer I & Messersmith P B (2012) Langmuir 28, 16099−16107
  14. Ham H O, Park S H, Kurutz J W, Szleifer I G & Messersmith P B (2013) J. Am. Chem. Soc. 135, 13015–13022
  15. Wender P A, Mitchell D J, Pattabiraman K, Pelkey E T, Steinman L & Rothbard J B (2000) Proc. Natl. Acad. Sci. USA. 97, 13003–13008
  16. Schröder T, Schmitz K, Niemeier N, Balaban T S, Krug H F, Schepers U & Bräse S (2007) Bioconjugate Chem. 18, 342–354
  17. Nnanabu E & Burgess K (2006) Org. Lett. 8,1259-1262
  18. Shin S B Y, Yoo B, Todaro L J & Kirshenbaum K (2007) J. Am. Chem. Soc.129, 3218-3225
  19. Pokorski J K, Jenkins L M M, Feng H, Durell S R, Bai Y & Appella D H (2007) Org. Lett. 9, 2381-2383
  20. Nandel F S & Jaswal R R (2013) Ind J. Biochem. Biophys. 51, 7-18
  21. Maigret B, Perahia D & Pullman B (1970) J. Theor. Biol. 29, 275-291
  22. Subramanian E & Parthasarathy R (1989) Int. J. Pept. Prot. Res. 33, 345-347
  23. Armand P, Kirshenbaum K, Falicov A, Dunbarck Jr R L, Dill K A, Zuckermann R N & Cohen F E (1997) Folding and Design 2, 369-375
  24. Baldauf C, Günther R & Hofmann H J (2006) Phys. Biol. 3, S1–S9
  25. Zuckermann R N, Kerr J M, Kent S B H & Moost W H (1992) J. Am. Chem. Soc. 114, 10646-10647
  26. Sui Q, Borchardt D & Rabenstein D L (2007) J. Am. Chem. Soc. 129, 12042-12048
  27. Wu C W, Kirshenbaum K, Sanborn T J, Huang K, Zuckermann R N, Barron A E, Patch J A, Dill K A (2003) J. Am. Chem. Soc. 125, 13525-13530
  28. Wu C W, Sanborn T J, Huang K, Zuckermann R N & Barron A E (2001) J. Am. Chem. Soc. 123, 6778-6784
  29. Wu C W, Sanborn T J, Zuckermann R N & Barron A E (2001) J. Am. Chem. Soc. 123, 2958-2963
  30. Kirshenbaum K, Zuckermann R N, Dill K A, Barron A E, Armand P, Goldsmith R & Cohen E (1998). Proc. Natl. Acad. Sci. 95, 4303-4308
  31. Jordan P A, Paul B, Butterfoss G L, Renfrew P D, Bonneau R & Kirshenbaum K (2011) Biopoymers (Peptide Science) 96, 617-625
  32. Shah N H, Butterfoss G L, Nguyen K, Yoo B, Bonneau R, Rabenstein D L & Kirshenbaum K (2008) J. Am. Chem. Soc. 130, 16622-16632
  33. Zhang S, Prabpai S, Kongsaeree P & Arvidsson P I (2006) Chem. Commun 497-499
  34. Fowler S A, Luechapanichkul R & Blackwell H E (2009) J. Org. Chem. 74, 1440–1449
  35. Stringer J R, Crapster J A, Guzei I A & Blackwell H E (2011) Biopolymer peptide Science 96, 604-616
  36. Stringer J R, Crapster J A, Guzei I A & Blackwell H E (2010) J. Org. Chem. 75, 6068-6078
  37. Stringer J R, Crapster J A, Guzei I A & Blackwell H E (2011) J. Am. Chem. Soc. 133, 15559-15567
  38. Qiu Y, Chen P, Guo P, Li Y & Liu M (2008) Advanced Materials 20, 2908-2913
  39. Moretto A, Peggion C, Formaggio F, Crisma M, Kaptein B, Boxteman Q B & Toniolo C (2005) Chirality 17, 481-487
  40. Pullman B & Pullman A (1974) Adv. Protein Chem. 28, 347-526
  41. Lawrence R P & Thompson C(1982) J. Mol. Str: Theochem. 88, 37-43
  42. Aleman C & Casanovas J (1994) Chem Soc Perkins Trans 2, 563-568
  43. Aleman C & Casanovas J (1995) Biopolymers 36, 71-82
  44. Nandel F S & Khare B (2005) Biopolymers 77, 63-73
  45. Nandel F S, Malik N, Singh B & Jain D V S (1999) Int. J. Quant. Chem. 72, 15-23
  46. Nandel F S, Malik N, Singh B & Virdi M (1999) Indian J. Biochem. Biophys. 36, 195-203
  47. Weiner S J, Singh U C, Donell T J O & Kollman P A (1984) J. Am. Chem. Soc. 106, 6243-6245
  48. Mohle K & Hoffman H J (1998) J. Pept. Res. 51, 19-28
  49. Aduzbei A A & Sternberg J E (1993) J. Mol. Biol. 229, 472-493
  50. Adzubei A A, Eisenmenger F, Tumanyan V G, Zinke M & Esipova NG (1987) Biophys Biochem Res Commun 146, 934-938
  51. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark A E & Berendsen H J C (2005) J. Comp. Chem. 26, 1701–1718
  52. Butterfoss G L, Renfren P D, Kuhlman B & Kirshenbaum K A (2009) J. Am. Chem. Soc. 131, 16798-16807
  53. Schuettelkopf A W & Van Aalten D M F (2004) Acta Crystallogr. D60, 1355-1363
  54. Berendsen H J C, Postma, J P M, Van Gunsteren W F & Hermans J (1981) In B. Pullman, editor, Intermolecular Forces, Dordrecht: D. Reidel Publishing Company,331–342
  55. Liu H, Muller-Plathe F & Van Gunsteren W F (1995) J. Am. Chem. Soc. 117, 4363-4366
  56. Van Gunsteren W F, Billeter S R, Eising A A, Hünenberger P H, Krüger P, Mark A E, Scott W R P & Tironi I G (1996) Biomolecular Simulation: The GROMOS96 manual and user guide, Zürich, Switzerland: Hochschulverlag AG an der ETH Zürich
  57. TingGuang S, Ming L, WeiZu C & CunXin W (2010) Sci China Life Sci 53, 620-630
  58. Hockney R W & Eastwood J W (1981) Computer simulation using particles, New York, McGraw-Hill
  59. Berendsen HJC, Postma JPM, DiNola A, Haak JR (1984) J. Chem. Phys. 81: 3684–3690
  60. Hess B, Bekker H, Berendsen H J C & Fraaije J G E M (1997) J. Comp. Chem. 18, 1463–1472
  61. Essmann U, Perera L, Berkowitz M L, Darden T, Lee H & Pedersen L G (1995) J. Chem. Phys.103, 8577–8592
  62. Voelz V A, Dill K A & Chorny I (2011) Peptide Science 96, 639-650
  63. Zi H F & Zang H X (2005) J. Mol. Structure (Theochem) 756, 109-112
  64. Jain A, Purohit C K, Verma S & Shankararamankrishnan R (2007) The J. of Physical Chemistry B Letters 111, 8680-8683
  65. Egli M & Sarkhel S (2007) Acc. Chem. Res. 40, 197-205
  66. Gautrot J E, Hodge P, Cupertino D & Helliwell M (2006) New J. of Chemistry 30, 1801-1807
  67. Maccallum P H, Poet R & Milner-White E J (1995) J. Mol. Biol. 48, 374-384
  68. Maccallum P H, Poet R & Milner-White E J (1995) J. Mol. Biol. 248, 361-373
  69. Allen F H, Baalham C A, Lommerse J P M & Raithby P R(1998) Acta Crystallogr B54, 320-329
  70. Allen F H, Dacies J E, Galloy J J, Johnson O, Kennard O, Macrae C F, Mitchell E M, Mitchell G F, Smith J M & Watson D G (1991) J Chem Inf Comput Sci 31, 187-204
  71. Deane C M, Allen F H, Taylor R & Blundell T L (1999) Protein Engineering 12, 1025-1028
  72. Nandel F S, Kaur H, Malik N, Shankar N & Jain D V S (2001) Indian J. Biochem. Biophys. 38, 417-425
  73. Nandel F S & Kaur H (2003) Indian J. Biochem. Biophys. 40, 265-273
  74. Nandel F S & Saini A (2011) J. of Biophysical Chemistry 2, 37-48
  75. Nandel F S, Jaswal R R, Saini A, Nandel V & Shafique M (2014) Journal of Molecular Modeling 20, 24-29
  76. Desiraju G R & Steiner T(1999) The Weak Hydrogen Bond: In Structural Chemistry and Biology, Oxford Science Publications
  77. Peggion E, Cosani A, Verdini A S, Del Pra A & Mammi M (1968) Biopolymers 6, 1477-1486
  78. Urry D W, Glicksan J D, Mayery D F & Haider J (1972) Biochemistry 11, 487-493
  79. Schuler B, Lipman E A, Steinbach P J, Kumke M & Eaton W A (2005) Proc Natl Acad Sci USA 102, 2754–2759
  80. Ungar-waron H, Gurari D, Hurwitz E & Sela M (1973) Eur J Immunol 3, 201–205
  81. Miranda L P & Alewood P (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 1181-1186
  82. Sato S, Kwon Y, Kamisuki S, Srivastava N, Mao Q A, Kawazoe Y & Uesugi M (2007) J Am Chem Soc 129, 873–880
  83. Jitariu L C, Wilson C & Hirst D M (1997) Journal of Molecular Structure (Theochem) 391, 111-116.
  84. Schmid E D & Brodbek E (1985) Can. J. Biophys. 63, 1365-1371.

Keywords

biomimetic, Nphe/Nrpe/Nspe peptoids, simulations, conformational analysis, PP and inverse PP structures.