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Vibrational spectrum and randomness of water at the interface of a protein–DNA complex

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Abstract

Molecular dynamics simulations have been carried out to explore the effect of complex formation between the N-terminal domain of the \(\lambda \)-repressor protein (in dimeric form) and the corresponding DNA operator on low-frequency intermolecular vibrational modes of water confined at the interface. The calculations demonstrated enhanced back-scattering of interfacial water due to increased caging effects, the effect being greater for water molecules that are associated with direct binding process. Highest degree of caging effect has been identified with the water molecules that are engaged in forming hydrogen-bonded bridges either near directly bound residues or in establishing contacts between the unbound DNA and protein residues. This leads to blue shifts of the O\(\cdots \)O\(\cdots \)O bending mode of water and the effect is maximum for the bridged water. The analyses further demonstrated that the local randomness of the interfacial water molecules strongly depends on the conformational rigidity of the DNA and the protein components.

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Data Availability

All data used in this study are openly available with contacting Sandip Mondal

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Acknowledgements

This study was supported by grant received from the Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Government of India (Ref. No. CRG/2020/000044) as well as grant received under DST-FIST programme. Sandip Mondal thanks University Grants Commission (UGC), Government of India (23/12/2012(ii)EU-V), while Krishna P. Ghanta and Souvik Mondal thank Council of Scientific and Industrial Research (CSIR), Government of India (09/081(1312)/2017-EMR-I, dated 18.10.2017 and 09/081(1272)/2015-EMR-I, dated 29.12.2015) for scholarships This work used the resources of the supercomputing facility of the Indian Institute of Technology Kharagpur established under National Supercomputing Mission (NSM), Government of India.

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  1. Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India

    Sandip Mondal, Krishna Prasad Ghanta, Souvik Mondal & Sanjoy Bandyopadhyay

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  1. Sandip Mondal
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  2. Krishna Prasad Ghanta
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SM performed the simulations and carried out partial analysis, KPG and SM carried out analysis and prepared the figures, SB conceptualized the idea of the manuscript. All the authors were involved in preparing the manuscript.

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Correspondence to Sanjoy Bandyopadhyay.

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Mondal, S., Ghanta, K.P., Mondal, S. et al. Vibrational spectrum and randomness of water at the interface of a protein–DNA complex. Theor Chem Acc 142, 75 (2023). https://doi.org/10.1007/s00214-023-03017-5

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