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Biophysical characterization and molecular phylogeny of human KIN protein

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Abstract

The DNA/RNA-binding KIN protein was discovered in 1989, and since then, it has been found to participate in several processes, e.g., as a transcription factor in bacteria, yeasts, and plants, in immunoglobulin isotype switching, and in the repair and resolution of double-strand breaks caused by ionizing radiation. However, the complete three-dimensional structure and biophysical properties of KIN remain important information for clarifying its function and to help elucidate mechanisms associated with it not yet completely understood. The present study provides data on phylogenetic analyses of the different domains, as well as a biophysical characterization of the human KIN protein (HSAKIN) using bioinformatics techniques, circular dichroism spectroscopy, and differential scanning calorimetry to estimate the composition of secondary structure elements; further studies were performed to determine the biophysical parameters ΔHm and Tm. The phylogenetic analysis indicated that the zinc-finger and winged helix domains are highly conserved in KIN, with mean identity of 90.37% and 65.36%, respectively. The KOW motif was conserved only among the higher eukaryotes, indicating that this motif emerged later on the evolutionary timescale. HSAKIN has more than 50% of its secondary structure composed by random coil and β-turns. The highest values of ΔHm and Tm were found at pH 7.4 suggesting a stable structure at physiological conditions. The characteristics found for HSAKIN are primarily due to its relatively low composition of α-helices and β-strands, making up less than half of the protein structure.

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Acknowledgements

This work was supported by Fundação Araucária (Grant Numbers 147/14 and 40/16), Coordination for the Improvement of Higher Education Personnel—Brazil (CAPES, code 001), and the National Council for Scientific and Technological Development—Brazil (CNPq Grant Number 305960/2015-6). Dr. Fátima Pereira de Souza and Dr. Marcelo Andrés Fossey are gratefully acknowledged for the helpful discussion, and the authors thank IBILCE/UNESP and UFPR for the use of facilities.

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  1. Department of Technology, Universidade Estadual de Maringá-UEM, Av. Ângelo Moreira da Fonseca, 1800, Umuarama, PR, 87506-370, Brazil

    José Renato Pattaro Júnior & Flávio Augusto Vicente Seixas

  2. Department of Physics, Instituto de Biociências, Letras e Ciências Exatas-Universidade Estadual Paulista “Júlio de Mesquita Filho”, São José do Rio Preto, SP, Brazil

    Ícaro Putinhon Caruso

  3. Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Maringá, PR, Brazil

    Quirino Alves de Lima Neto, Francisco Ferreira Duarte Junior & Maria Aparecida Fernandez

  4. Center for Molecular, Structural and Functional Biology, CBM-Research Support Center Complex, Universidade Estadual de Maringá, Maringá, PR, Brazil

    Fabiana dos Santos Rando

  5. Department of Biochemistry, Universidade Federal do Paraná, Curitiba, PR, Brazil

    Edileusa Cristina Marques Gerhardt

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Pattaro Júnior, J.R., Caruso, Í.P., de Lima Neto, Q.A. et al. Biophysical characterization and molecular phylogeny of human KIN protein. Eur Biophys J 48, 645–657 (2019). https://doi.org/10.1007/s00249-019-01390-3

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