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    • 𝛽- and 𝛾-turns in proteins revisited: A new set of amino acid turn-type de-pendent positional preferences and potentials

      Kunchur Guruprasad Sasidharan Rajkumar

      Articles Volume 25 Issue 2 June 2000 pp 143-156

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      Permanent link:
      https://www.ias.ac.in/article/fulltext/jbsc/025/02/0143-0156

    • Keywords

       

      Amino acid preferences; amino acid potentials; 𝛽- and 𝛾-turns in proteins

    • Abstract

       

      The number of 𝛽-turns in a representative set of 426 protein three-dimensional crystal structures selected from the recent Protein Data Bank has nearly doubled and the number of 𝛾-turns in a representative set of 320 proteins has increased over seven times since the previous analysis. 𝛽-turns (7153) and 𝛾-turns (911) extracted from these proteins were used to derive a revised set of type-dependent amino acid positional preferences and potentials. Compared with previous results, the preference for proline, methionine and tryptophan has increased and the preference for glutamine, valine, glutamic acid and alanine has decreased for 𝛽-turns. Certain new amino acid preferences were observed for both turn types and individual amino acids showed turn-type dependent positional preferences. The rationale for new amino acid preferences are discussed in the light of hydrogen bonds and other interactions involving the turns. Where main-chain hydrogen bonds of the type NH(𝑖 + 3)→CO(𝑖) were not observed for some 𝛽-turns, other main-chain hydrogen bonds or solvent interactions were observed that possibly stabilize such 𝛽-turns. A number of unexpected isolated 𝛽-turns with proline at 𝑖 + 2 position were also observed. The NH(𝑖 + 2)→CO(𝑖) hydrogen bond was observed for almost all 𝛾-turns. Nearly 20% classic 𝛾-turns and 43% inverse 𝛾-turns are isolated turns.

    • Author Affiliations

       

      Kunchur Guruprasad1 Sasidharan Rajkumar1

      1. Centre for DNA Fingerprinting and Diagnostics (CDFD), ECIL Road, Nacharam, Hyderabad 500 076, India

    • Dates

       
      Published
      June 2000
      Manuscript received
      15 November 1999
      Accepted
      8 February 2000

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