Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acid, and Valine

Oda, Akifumi; Fukuyoshi, Shuichi

doi:10.1007/s11084-015-9418-5

ORIGINS 2014
Published: 21 March 2015

Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acid, and Valine

Akifumi Oda^1,2 &
Shuichi Fukuyoshi¹

Origins of Life and Evolution of Biospheres volume 45, pages 183–193 (2015)Cite this article

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Abstract

The GADV hypothesis is a form of the protein world hypothesis, which suggests that life originated from proteins (Lacey et al. 1999; Ikehara 2002; Andras 2006). In the GADV hypothesis, life is thought to have originated from primitive proteins constructed of only glycine, alanine, aspartic acid, and valine ([GADV]-proteins). In this study, the three-dimensional (3D) conformations of randomly generated short [GADV]-peptides were computationally investigated using replica-exchange molecular dynamics (REMD) simulations (Sugita and Okamoto 1999). Because the peptides used in this study consisted of only 20 residues each, they could not form certain 3D structures. However, the conformational tendencies of the peptides were elucidated by analyzing the conformational ensembles generated by REMD simulations. The results indicate that secondary structures can be formed in several randomly generated [GADV]-peptides. A long helical structure was found in one of the hydrophobic peptides, supporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup. In addition, these results indicate that REMD simulations can be used for the structural investigation of short peptides.

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References

Ajay, Murcko MA (1995) Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem 38:4953–4967. doi:10.1021/jm00026a001
CAS PubMed Article Google Scholar
Andras P (2006) The protein interaction world hypothesis of the origins of life. Viva Origino 34:40–50
CAS Google Scholar
Case DA (2005) Re: AMBER: value of SALTCON. Amber mailing list archive. http://archive.ambermd.org/200504/0085.html. Accessed 7 Jan 2015
Case DA, Darden TA, Cheatham TA III et al (2012) AMBER 12. University of California, San Francisco
Google Scholar
Crick FHC, Griffith JS, Orgel LE (1957) Codes without commas. Proc Natl Acad Sci U S A 43:416–421
CAS PubMed Central PubMed Article Google Scholar
Dyson F (1985) Origin of life. Cambridge University Press, Cambridge
Google Scholar
Ferris JP, Hill AR Jr, Liu R, Orgel LE (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381:59–61. doi:10.1038/381059a0
CAS PubMed Article Google Scholar
Futamura Y, Yamamoto K (2005) Hydrothermal synthesis of oligoglycines with adiabatic expansion cooling. Viva Origino 33:269–274
CAS Google Scholar
Huang C (2002) DMS. University of California, San Francisco
Google Scholar
Ikebe J, Kamiya N, Ito J, Shindo H, Higo J (2007) Simulation study on the disordered state of an Alzheimer’s β amyloid peptide Aβ(12–36) in water consisting of random-structural, β-structural, and helical clusters. Protein Sci 16:1596–1608. doi:10.1110/ps.062721907
CAS PubMed Central PubMed Article Google Scholar
Ikehara K (2002) Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis. J Biosci 27:165–186. doi:10.1007/BF02703773
CAS PubMed Article Google Scholar
Ikehara K (2005) Possible steps to the emergence of life: the [GADV]-protein world hypothesis. Chem Rec 5:107–118. doi:10.1002/tcr.20037
CAS PubMed Article Google Scholar
Ikehara K (2009) Pseudo-replication of [GADV]-proteins and origin of life. Int J Mol Sci 10:1525–1537. doi:10.3390/ijms10041525
CAS PubMed Central PubMed Article Google Scholar
Ikehara K, Omori Y, Arai R, Hirose A (2002) A novel theory on the origin of the genetic code: a GNC-SNS hypothesis. J Mol Evol 54:530–538. doi:10.1007/s00239-001-0053-6
CAS PubMed Article Google Scholar
Imai E, Honda H, Hatori K, Brack A, Matsuno K (1999) Elongation of oligopeptides in a simulated submarine hydrothermal system. Science 283:831–833. doi:10.1126/science.283.5403.831
CAS PubMed Article Google Scholar
Jin L, Briggs SL, Chandrasekhar S, Chirgadze NY, Clawson DK, Schevitz RW, Smiley DL, Tashjian AH, Zhang F (2000) Crystal structure of human parathyroid hormone 1–34 at 0.9 Å resolution. J Biol Chem 275:27238–27244. doi:10.1074/jbc.M001134200
CAS PubMed Google Scholar
Jordan IK, Kondrashov FA, Adzhubel IA, Wolf YI, Koonin EV, Kondrashov AS, Sunyaev S (2005) A universal trend of amino acid gain and loss in protein evolution. Nature 433:633–638. doi:10.1038/nature03306
CAS PubMed Article Google Scholar
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637. doi:10.1002/bip.360221211
CAS PubMed Article Google Scholar
Kobayashi K, Kaneko T, Saito T, Oshima T (1998) Amino acid formation in gas mixtures by high energy particle irradiation. Orig Life Evol Biosph 28:155–165. doi:10.1023/A:1006561217063
CAS PubMed Article Google Scholar
Kobayashi K, Kaneko T, Saito T (1999) Characterization of complex organic compounds formed in simulated planetary atmospheres by the action of high energy particles. Adv Space Res 24:461–464. doi:10.1016/S0273-1177(99)00088-5
CAS PubMed Article Google Scholar
Kobayashi K, Kaneko T, Takahashi J, Takano Y, Yoshida S (2010) High molecular weight complex organics in interstellar space and their relevance to origins of life. In: Basiuk V (ed) Astrobiology: from simple molecules to primitive life. American Scientific Publishers, Valencia, pp 175–186
Google Scholar
Lacey JC, Cook GW, Mullins DW (1999) Concepts related to the origin of coded protein synthesis. Chemtracts 12:398–418
CAS Google Scholar
Lönnberg H (2011) Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight. Org Biomol Chem 9:1687–1703. doi:10.1039/C0OB00486C
PubMed Article Google Scholar
Miller SL (1953) A production of amino acids under possible primitive earth conditions. Science 117:528–529. doi:10.1126/science.117.3046.528
CAS PubMed Article Google Scholar
Mongan J, Simmerling C, McCammon JA, Case DA, Onufriev A (2006) Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput 3:156–169. doi:10.1021/ct600085e
Article Google Scholar
Nguyen H, Roe DR, Simmerling C (2013) Improved generalized Born solvent model parameters for protein simulations. J Chem Theory Comput 9:2020–2034. doi:10.1021/ct3010485
CAS PubMed Central PubMed Article Google Scholar
Oba T, Fukushima J, Maruyama M, Iwamoto R, Ikehara K (2005) Catalytic activities of [GADV]-peptides. Formation and establishment of [GADV]-protein world for the emergence of life. Orig Life Evol Biosph 35:447–460. doi:10.1007/s11084-005-3519-5
CAS PubMed Article Google Scholar
Oda A, Yamaotsu N, Hirono S (2009) Evaluation of the searching abilities of HBOP and HBSITE for binding pocket detection. J Comput Chem 30:2728–2737. doi:10.1002/jcc.21299
CAS PubMed Article Google Scholar
Oda A, Kobayashi K, Takahashi O (2011) Comparison of molecular dynamics simulation methods for amyloid β_1–42 monomers containing d-aspartic acid residues for predicting retention times in chromatography. J Chromatogr B 873:3337–3343. doi:10.1016/j.jchromb.2011.08.011
Article Google Scholar
Oda A, Fukuyoshi S, Nakagaki R (2013) Structural prediction of [GADV]-proteins using threading and ab initio modeling for investigations of the origin of life. J Comput Aided Chem 14:23–35. doi:10.2751/jcac.14.23
Article Google Scholar
Oshima T (2011) Magic 20 and the origins of life. Viva Origino 39:45–47
CAS Google Scholar
Palm K, Stenberg P, Luthman K, Artursson P (1997) Polar molecular surface properties predict the intestinal absorption of drugs in humans. Pharm Res 14:568–571. doi:10.1023/A:1012188625088
CAS PubMed Article Google Scholar
Richards FM (1977) Areas, volumes, packing, and protein structure. Ann Rev Biophys Bioeng 6:151–176. doi:10.1146/annurev.bb.06.060177.001055
CAS Article Google Scholar
Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–341. doi:10.1016/0021-9991(77)90098-5
CAS Article Google Scholar
Schlesinger G, Miller SL (1983) Prebiotic synthesis in atmospheres containing CH₄, CO, and CO₂. I. Amino acids. J Mol Evol 19:376–382. doi:10.1007/BF02101642
CAS PubMed Article Google Scholar
Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314:141–151. doi:10.1016/S0009-2614(99)01123-9
CAS Article Google Scholar
Takahashi J, Hosokawa T, Masuda H, Kaneko T, Kobayashi K, Saito T, Utsumi Y (1999) Abiotic synthesis of amino acids by x-ray irradiation of simple inorganic gases. Appl Phys Lett 74:877–879. doi:10.1063/1.123396
CAS Article Google Scholar
van der Gulik P, Massar S, Gilis D, Buhrman H, Rooman M (2009) The first peptides: the evolutionary transition between prebiotic amino acids and early proteins. J Theor Biol 261:531–539. doi:10.1016/j.jtbi.2009.09.004
PubMed Article Google Scholar
Vékey K, Somogyi Á, Wysocki VH (1996) Average activation energies of low-energy fragmentation processes of protonated peptides determined by a new approach. Rapid Commun Mass Spectrom 10:911–918. doi:10.1002/(SICI)1097-0231(19960610)10:8<911::AID-RCM593>3.0.CO;2-7
PubMed Article Google Scholar
Xu D, Zhang Y (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80:1715–1735. doi:10.1002/prot.24065
CAS PubMed Central PubMed Article Google Scholar
Yamaotsu N, Oda A, Hirono S (2008) Determination of ligand-binding sites on proteins using long-range hydrophobic potential. Biol Pharm Bull 31:1552–1558. doi:10.1248/bpb.31.1552
CAS PubMed Article Google Scholar
Zuckerkandl E, Derancourt J, Vogel H (1971) Mutational trends and random processes in the evolution of informational macromolecules. J Mol Biol 59:473–490. doi:10.1016/0022-2836(71)90311-1
CAS PubMed Article Google Scholar

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Acknowledgments

Parts of the computations were performed by the Research Center for Computational Science, Okazaki. This work was supported by a grant-in-aid for scientific research [26460034] from the Japan Society for the Promotion of Science.

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Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
Akifumi Oda & Shuichi Fukuyoshi
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
Akifumi Oda

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Akifumi Oda
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Shuichi Fukuyoshi
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Correspondence to Akifumi Oda.

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Oda, A., Fukuyoshi, S. Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acid, and Valine. Orig Life Evol Biosph 45, 183–193 (2015). https://doi.org/10.1007/s11084-015-9418-5

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Received: 29 October 2014
Accepted: 09 January 2015
Published: 21 March 2015
Issue Date: June 2015
DOI: https://doi.org/10.1007/s11084-015-9418-5

Keywords

GADV hypothesis
Protein structure prediction
Secondary structure formation
Replica-exchange molecular dynamics simulation