Skip to main content
SpringerLink
Log in

Screens Displaying Structural Properties of Aminoacids in Polypeptide Chains: Alanine as a Case Study

  • Conference paper
  • First Online:
Computational Science and Its Applications – ICCSA 2019 (ICCSA 2019)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11624))

Included in the following conference series:

Abstract

Large sets of data need to be compacted for classification and extraction of information regarding structural changes of aminoacid units in specific sequences of proteins. The screen is constructed by opposite sides of the virtual tetrahedron built by the six distances between four centers and provides coordinates for a two-dimensional square plot. As alternative e.g. to Ramachandran diagrams based on angles, it may offer greater accuracy and sensitivity. The screen was initially employed to peroxides and persulfides, to monitor the distances relevant to chirality changing processes and successively to show some electric and kinetic properties. The smallest chiral aminoacid, alanine, was therefore chosen for the basic illustration presented here. A virtual tetrahedron is built by the six distances between four centers of the aminoacid skeleton: they do not necessarily coincide with bonds, so a computer program permits their calculation from tabulations of experimental and theoretical data. Here, the screen is applied to treat significant geometrical features of alanine as affected by adjacent aminoacids in peptide chains, as available on protein databases. In this exemplary presentation applications of screen plots are limited to biochemistry: elsewhere have been shown useful in other areas, such as spin networks and the kinematics of a four-bar mechanism.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Bibliography

  1. Palazzetti, F., Maciel, G.S., Lombardi, A., Grossi, G., Aquilanti, V.: The astrochemical observatory: molecules in the laboratory and in the cosmos. J. Chin. Chem. Soc. 59 (2012). https://doi.org/10.1002/jccs.201200242

  2. Gianturco, F.A., et al.: Exploring a chemical route for the formation of stable anions of polyynes [Cn H−(n = 2, 4)] in molecular clouds. Astrophys. J. 830, 2 (2016). https://doi.org/10.3847/0004-637X/830/1/2

    Article  Google Scholar 

  3. Wang, X., Li, Y., Yang, Z., Lu, C., Zhu, T.: A quantum mechanical computational method for modeling electrostatic and solvation effects of protein. Sci. Rep. 8, 5475 (2018)

    Article  Google Scholar 

  4. Lombardi, A., Palazzetti, F., Aquilanti, V., Pirani, F., Casavecchia, P.: The astrochemical observatory: experimental and computational focus on the chiral molecule propylene oxide as a case study. In: Gervasi, O., et al. (eds.) ICCSA 2017. LNCS, vol. 10408, pp. 267–280. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-62404-4_20

    Chapter  Google Scholar 

  5. Palazzetti, F., et al.: Stereodirectional photodynamics: experimental and theoretical perspectives. In: AIP Conference Proceedings, vol. 1790, p. 020020 (2016). https://doi.org/10.1063/1.4968646

  6. Kasai, T., et al.: Directions of chemical change: experimental characterization of the stereodynamics of photodissociation and reactive processes. Phys. Chem. Chem. Phys. 16, 9776–9790 (2014). https://doi.org/10.1039/c4cp00464g

    Article  Google Scholar 

  7. Barreto, P.R.P., et al.: Potential energy surface for the interaction of helium with the chiral molecule propylene oxide. In: Gervasi, O., et al. (eds.) ICCSA 2018. LNCS, vol. 10964, pp. 593–604. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-95174-4_46

    Chapter  Google Scholar 

  8. Su, T.-M., Palazzetti, F., Lombardi, A., Grossi, G., Aquilanti, V.: Molecular alignment and chirality in gaseous streams and vortices. Rend. Lincei 24, 291–297 (2013). https://doi.org/10.1007/s12210-013-0249-x

    Article  Google Scholar 

  9. Che, D.-C., Kanda, K., Palazzetti, F., Aquilanti, V., Kasai, T.: Electrostatic hexapole state-selection of the asymmetric-top molecule propylene oxide: rotational and orientational distributions. Chem. Phys. 399, 180–192 (2012). https://doi.org/10.1016/j.chemphys.2011.11.020

    Article  Google Scholar 

  10. Lombardi, A., Maciel, G.S., Palazzetti, F., Grossi, G., Aquilanti, V.: Alignment and chirality in gaseous flows. J. Vac. Soc. Jpn. 53, 645–653 (2010). https://doi.org/10.3131/jvsj2.53.645

    Article  Google Scholar 

  11. Albernaz, A.F., Barreto, P.R.P., Aquilanti, V., Lombardi, A., Palazzetti, F., Pirani, F.: The astrochemical observatory: the interaction between helium and the chiral molecule propylene oxide. In: AIP Conference Proceedings, vol. 2040, p. 020018 (2018). https://doi.org/10.1063/1.5079060

  12. Lin, K.-C., et al.: Angular distribution of bromine atomic photofragment in oriented 2-bromobutane via hexapole state selector. In: AIP Conference Proceedings, p. 020001 (2017). https://doi.org/10.1063/1.5012287

  13. Nakamura, M., et al.: Stereodirectional images of molecules oriented by a variable-voltage hexapolar field: fragmentation channels of 2-bromobutane electronically excited at two photolysis wavelengths. J. Chem. Phys. 147 (2017). https://doi.org/10.1063/1.4981025

  14. Falcinelli, S., et al.: Double photoionization of propylene oxide: a coincidence study of the ejection of a pair of valence-shell electrons. J. Chem. Phys. 148, 114302 (2018). https://doi.org/10.1063/1.5024408

    Article  Google Scholar 

  15. Lombardi, A., Palazzetti, F., Aquilanti, V., Grossi, G.: Chirality in molecular collisions. In: AIP Conference Proceedings, vol. 1906, p. 030012 (2017). https://doi.org/10.1063/1.5012291

  16. Aquilanti, V., et al.: The astrochemical observatory: computational and theoretical focus on molecular chirality changing torsions around O–O and S–S bonds. In: AIP Conference Proceedings, vol. 1906, p. 030010 (2017). https://doi.org/10.1063/1.5012289

  17. Che, D.-C., Palazzetti, F., Okuno, Y., Aquilanti, V., Kasai, T.: Electrostatic hexapole state-selection of the asymmetric-top molecule propylene oxide. J. Phys. Chem. A 114, 3280–3286 (2010). https://doi.org/10.1021/jp909553t

    Article  Google Scholar 

  18. Carrascoza, F., Zaric, S., Silaghi-Dumitrescu, R.: Computational study of protein secondary structure elements: Ramachandran plots revisited. J. Mol. Graph. Model. 50, 125–133 (2014)

    Article  Google Scholar 

  19. Lombardi, A., Palazzetti, F., Maciel, G.S., Aquilanti, V., Sevryuk, M.B.: Simulation of oriented collision dynamics of simple chiral molecules. Int. J. Quantum Chem. 111, 1651–1658 (2011). https://doi.org/10.1002/qua.22816

    Article  Google Scholar 

  20. Barreto, P.R.P., Palazzetti, F., Grossi, G., Lombardi, A., Maciel, G.S., Vilela, A.F.A.: Range and strength of intermolecular forces for van der Waals complexes of the type H2Xn-Rg, with X = O, S and n = 1, 2. Int. J. Quantum Chem. 110, 777–786 (2010). https://doi.org/10.1002/qua.22127

    Article  Google Scholar 

  21. Barreto, P.R.P., Vilela, A.F.A., Lombardi, A., Maciel, G.S., Palazzetti, F., Aquilanti, V.: The hydrogen peroxide-rare gas systems: quantum chemical calculations and hyperspherical harmonic representation of the potential energy surface for atom-floppy molecule interactions. J. Phys. Chem. A 111, 12754–12762 (2007). https://doi.org/10.1021/jp076268v

    Article  Google Scholar 

  22. Maciel, G.S., Barreto, P.R.P., Palazzetti, F., Lombardi, A., Aquilanti, V.: A quantum chemical study of H2S2: intramolecular torsional mode and intermolecular interactions with rare gases. J. Chem. Phys. 129, 164302 (2008). https://doi.org/10.1063/1.2994732

    Article  Google Scholar 

  23. Aquilanti, V., Caglioti, C., Lombardi, A., Maciel, G.S., Palazzetti, F.: Screens for displaying chirality changing mechanisms of a series of peroxides and persulfides from conformational structures computed by quantum chemistry. In: Gervasi, O., et al. (eds.) ICCSA 2017. LNCS, vol. 10408, pp. 354–368. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-62404-4_26

    Chapter  Google Scholar 

  24. Caglioti, C., Santos, R.F.D., Aquilanti, V., Lombardi, A., Palazzetti, F.: Screen mapping of structural and electric properties, chirality changing rates and racemization times of chiral peroxides and persulfides. In: AIP Conference Proceedings, vol. 2040, p. 020021 (2018). https://doi.org/10.1063/1.5079063

  25. Protein Data Bank, PDB. https://www.rcsb.org/

  26. Bitencourt, A.C.P., Ragni, M., Littlejohn, R.G., Anderson, R., Aquilanti, V.: The screen representation of vector coupling coefficients or Wigner 3j symbols: exact computation and illustration of the asymptotic behavior. In: Murgante, B., et al. (eds.) ICCSA 2014. LNCS, vol. 8579, pp. 468–481. Springer, Cham (2014). https://doi.org/10.1007/978-3-319-09144-0_32

    Chapter  Google Scholar 

  27. Aquilanti, V., et al.: Quadrilaterals on the square screen of their diagonals: Regge symmetries of quantum mechanical spin networks and Grashof classical mechanisms of four-bar linkages. Rend. Lincei 30, 67–81 (2019). https://doi.org/10.1007/s12210-019-00776-x

    Article  Google Scholar 

  28. Littlejohn, R.G., Yu, L.: Uniform semiclassical approximation for the Wigner 6j-symbol in terms of rotation matrices. J. Phys. Chem. A 113, 14904–14922 (2009)

    Article  Google Scholar 

  29. Aquilanti, V., Haggard, H.M., Hedeman, A., Jeevangee, N., Littlejohn, R., Yu, L.: Semiclassical mechanics of the Wigner 6j-symbol. J. Phys. A. 45, 065209 (2012)

    Article  MathSciNet  Google Scholar 

  30. Aquilanti, V., Capecchi, G.: Harmonic analysis and discrete polynomials from semiclassical angular momentum theory to the hyperquantization algorithm. Theoret. Chem. Acc. 104, 183–188 (2000)

    Article  Google Scholar 

  31. De Fazio, D., Cavalli, S., Aquilanti, V.: Orthogonal polynomials of a discrete variable as expansion basis sets in quantum mechanics the hyperquantization algorithm. Int. J. Quantum Chem. 93, 91–111 (2003)

    Article  Google Scholar 

  32. Aquilanti, V., Cavalli, S., De Fazio, D.: Angular and hyperangular momentum coupling coefficients as hahn polynomials. J. Phys. Chem. 99, 15694–15698 (1995)

    Article  Google Scholar 

  33. Bitencourt, A.C.P., Marzuoli, A., Ragni, M., Anderson, R.W., Aquilanti, V.: Exact and asymptotic computations of elementary spin networks: classification of the quantum–classical boundaries. In: Murgante, B., et al. (eds.) ICCSA 2012. LNCS, vol. 7333, pp. 723–737. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-31125-3_54

    Chapter  Google Scholar 

  34. Aquilanti, V., Bitencourt, A.C.P., da S. Ferreira, C., Marzuoli, A., Ragni, M.: Combinatorics of angular momentum recoupling theory: spin networks, their asymptotics and applications. Theoret. Chem. Acc. 123, 237 (2009)

    Google Scholar 

  35. Ponzano, G., Regge, T.: Semiclassical limit of Racah coefficients. In: Spectroscopic and Group Theoretical Methods in Physics. North-Holland, Amsterdam (1968)

    Google Scholar 

  36. Neville, D.: A technique for solving recurrence relations approximately and its application to the 3j and 6j symbols. J. Math. Phys. 12, 2438 (1971)

    Article  MathSciNet  Google Scholar 

  37. Schulten, K., Gordon, R.: Semiclassical approximations to 3j- and 6j-coefficients for quantum-mechanical coupling of angular momenta. J. Math. Phys. 16, 1971–1988 (1975)

    Article  MathSciNet  Google Scholar 

  38. Schulten, K., Gordon, R.: Exact recursive evaluation of 3j- and 6j-coefficients for quantum mechanical coupling of angular momenta. J. Math. Phys. 16, 1961–1970 (1975)

    Article  MathSciNet  Google Scholar 

  39. Ragni, M., Bitencourt, A.C.P., Aquilanti, V., Anderson, R.W., Littlejohn, R.G.: Exact computation and asymptotic approximations of 6j symbols: illustration of their semiclassical limits. Int. J. Quantum Chem. 110, 731–742 (2010)

    Article  Google Scholar 

  40. Aquilanti, V., Cavalli, S., Coletti, C.: Angular and hyperangular momentum recoupling, harmonic superposition and Racah polynomials: a recursive algorithm. Chem. Phys. Lett. 344, 587–600 (2001)

    Article  Google Scholar 

  41. Berlin ab-initio amino acid DB. http://aminoaciddb.rz-berlin.mpg.de/

Download references

Acknowledgements

The authors acknowledge the Italian Ministry for Education, University and Research, MIUR, for financial supporting through SIR 2014 Scientific Independence for young Researchers (RBSI14U3VF).

Author information

Authors and Affiliations

  1. Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto 8, 06123, Perugia, Italy

    Concetta Caglioti, Andrea Lombardi, Federico Palazzetti & Vincenzo Aquilanti

  2. Instituto de Fìsica, Universidade Federal da Bahia, Campus Universitario de Ondina, Salvador, BA, 40210-340, Brazil

    Robenilson Ferreira Dos Santos

  3. Instituto Federal de Alagoas-Campus Piranhas, Piranhas, AL, 57460-000, Brazil

    Robenilson Ferreira Dos Santos

  4. Istituto di Struttura della Materia-Consiglio Nazionale delle Ricerche, 00016, Rome, Italy

    Vincenzo Aquilanti

Authors
  1. Concetta Caglioti
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robenilson Ferreira Dos Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Andrea Lombardi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Federico Palazzetti
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Vincenzo Aquilanti
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Federico Palazzetti .

Editor information

Editors and Affiliations

  1. Covenant University, Ota, Nigeria

    Sanjay Misra

  2. University of Perugia, Perugia, Italy

    Osvaldo Gervasi

  3. University of Basilicata, Potenza, Italy

    Beniamino Murgante

  4. Saint Petersburg State University, Saint Petersburg, Russia

    Elena Stankova

  5. Saint Petersburg State University, Saint Petersburg, Russia

    Vladimir Korkhov

  6. Polytechnic University of Bari, Bari, Italy

    Carmelo Torre

  7. University of Minho, Braga, Portugal

    Ana Maria A.C. Rocha

  8. Monash University, Clayton, VIC, Australia

    David Taniar

  9. Kyushu Sangyo University, Fukuoka, Japan

    Bernady O. Apduhan

  10. Polytechnic University of Bari, Bari, Italy

    Eufemia Tarantino

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Caglioti, C., Dos Santos, R.F., Lombardi, A., Palazzetti, F., Aquilanti, V. (2019). Screens Displaying Structural Properties of Aminoacids in Polypeptide Chains: Alanine as a Case Study. In: Misra, S., et al. Computational Science and Its Applications – ICCSA 2019. ICCSA 2019. Lecture Notes in Computer Science(), vol 11624. Springer, Cham. https://doi.org/10.1007/978-3-030-24311-1_32

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-24311-1_32

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-24310-4

  • Online ISBN: 978-3-030-24311-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation