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The importance of hydrophobic interactions in the structure of transcription systems

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Abstract

Hydrophobic forces play a crucial role in both the stability of B DNA and its interactions with proteins. In the present study, we postulate that the hydrophobic effect is an essential component in establishing specificity in the interaction transcription factor proteins with their consensus DNA sequence partners. The PDB coordinates of more than 50 transcription systems have been used to analyze the hydrophobic attraction of proteins towards their DNA consensus. This analysis includes computing the hydrophobic energy of the interacting molecules by means of their hydrophobic moments. Hydrophobic moments have successfully been used in previous studies involving self-assembly protein systems. In the present case, in spite of some variability, we found specificity in transcription factors when interacting with their respective consensus DNA sequences. By applying our model of biological membrane pattern for hydrophobic interactions, we postulate that hydrophobic forces constitute the necessary intermediate interaction between the unspecific electrostatic attraction for DNA phosphate groups and the very short-range interaction promoting hydrogen bonds. We conclude that hydrophobic interactions serve as the intermediate force guiding transcriptions factors towards the proper hydrogen bonds to their DNAs.

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Abbreviations

H :

Hydrophobic moment vector

enH :

Hydrophobic energy

h+ :

Total hydrophobicity

h– :

Total hydrophilicity

r i :

Position vector of element i (amino acid or nucleotide)

c +, c – :

Hydrophobic, hydrophilic centroids

prot.:

Protein

cons.:

Consensus motif DNA

nucl.acid:

Nucleic acid

PDB:

Protein data base

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Acknowledgements

This research was supported by Ministerio de Economía y Competitividad of Spain [BIO2017-84166R, BFU2013-50176-EXP and PID2020-116874R-100] and by the Centre de Referència de R+D de Biotecnologia de la Generalitat de Catalunya. We thank Mrs. Lynn Strother for revising the English text

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  1. Departament de Bioquímica i Biologia Molecular, Campus de Bellaterra, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain

    Angel Mozo-Villarías, Juan Cedano & Enrique Querol

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  1. Angel Mozo-Villarías
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  2. Juan Cedano
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  3. Enrique Querol
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Correspondence to Angel Mozo-Villarías.

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Mozo-Villarías, A., Cedano, J. & Querol, E. The importance of hydrophobic interactions in the structure of transcription systems. Eur Biophys J 50, 951–961 (2021). https://doi.org/10.1007/s00249-021-01557-x

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  • DOI: https://doi.org/10.1007/s00249-021-01557-x

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