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A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure

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Abstract

The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: α-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their Cβ and Cγ atoms that predicts their preference for a particular secondary structure. All α-helix preferrers have neither polar heteroatoms on Cβ and Cγ atoms, nor branching or aromatic group on the Cβ atom. All strand preferrers have aromatic groups or branching groups on the Cβ atom. All turn and bend preferrers have a polar heteroatom on the Cβ or Cγ atoms or do not have a Cβ atom at all. These new rules could be helpful in making predictions about non-natural amino acids.

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Notes

  1. The correlations were calculated for some other thresholds with no significant differences. While specific correlation values differ, the trends and general conclusions are the same. The threshold of 25% is subjectively estimated as a good measure because smaller thresholds raise redundancy and larger thresholds reduce the sample size.

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Acknowledgements

This work was supported under projects, No 142037 and No 144030 by the Ministry of Science of the Republic of Serbia. M.B.H. acknowledges the support of the National Science Foundation, USA (CHE-0518074).

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Authors and Affiliations

  1. Department of Mathematics, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia

    Saša N. Malkov & Miodrag V. Živković

  2. Institute of General and Physical Chemistry, Studentski trg 16, 11000, Belgrade, Serbia

    Miloš V. Beljanski

  3. Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA

    Michael B. Hall

  4. Department of Chemistry, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia

    Snežana D. Zarić

Authors
  1. Saša N. Malkov
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  2. Miodrag V. Živković
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  3. Miloš V. Beljanski
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  4. Michael B. Hall
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  5. Snežana D. Zarić
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Correspondence to Snežana D. Zarić.

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Malkov, S.N., Živković, M.V., Beljanski, M.V. et al. A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. J Mol Model 14, 769–775 (2008). https://doi.org/10.1007/s00894-008-0313-0

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  • DOI: https://doi.org/10.1007/s00894-008-0313-0

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