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Biophysical and Computational Approaches to Unravel pH-Dependent Conformational Change of PspA Assist PspA-PspF Complex Formation in Yersinia enterocolitica

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Abstract

In enteropathogen, Yersinia enterocolitica, the genes encoding phage shock proteins are organized in an operon (pspA-E), which is activated at the various types of cellular stress (i.e., extracytoplasmic or envelop stress) whereas, PspA negatively regulates PspF, a transcriptional activator of pspA-E and pspG, and is also involved in other cellular machinery maintenance processes. The exact mechanism of association and dissociation of PspA and PspF during the stress response is not entirely clear. In this concern, we address conformational change of PspA in different pH conditions using various in-silico and biophysical methods. At the near-neutral pH, CD and FTIR measurements reveal a ß-like conformational change of PspA; however, AFM measurement indicates the lower oligomeric form at the above-mentioned pH. Additionally, the results of the MD simulation also support the conformational changes which indicate salt-bridge strength takes an intermediate position compared to other pHs. Furthermore, the bio-layer interferometry study confirms the stable complex formation that takes place between PspA and PspF at the near-neutral pH. It, thus, appears that PspA conformational change in adverse pH conditions abandons PspF from having a stable complex with it, and thus, the latter can act as a trans-activator. Taken together, it seems that PspA alone can transduce adverse signals by changing its conformation.

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Abbreviations

PspA:

Phage shock protein A

PspF:

Phage shock protein F

CD:

Circular dichrorism

FTIR:

Fourier transform infrared spectroscopy

BLI:

Bio-layer interferometry

SB:

Salt-bridge

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Author notes

  1. Chittran Roy and Rajeev Kumar have contributed equally to this work.

Authors and Affiliations

  1. Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research – Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India

    Chittran Roy, Rajeev Kumar, Md Maruf Hossain, Arkaprava Das & Saumen Datta

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Correspondence to Saumen Datta.

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Supplementary Information

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Supplementary materials

The supplementary material contains 11 Tables and 7 Figures. Table S1 contains the scores for models of PspF and PspA obtained using various online tools. Table S2 contain the percentile of alpha, beta, and other conformer of PspA at various pH. Table S3 has deconvoluted Amide I band frequencies and assignments of the secondary structure of PspA at different pH solution and Table S4 contain the binding kinetics of PspA and PspF. Table S5-10 contain component and net SB energy terms along with accessible surface area and a list of weak interactions has been shown in table S11. In figure, S1 shows near UV CD spectra of PspA, PspF, and PspA-PspF complex. Figure S2 shows the deconvolution of FTIR spectra of PspA at different pH. S3 shows CD spectra of PspF. Fig. S4 has Kye-Dollite hydrophobicity analysis of PspA and PspF, Fig. S5 shows the interaction between PspF-His with Ni-NTA at different pH. In Fig. S6 and S7, plot RMSD and H-bond interaction respectively. (DOC 3252 kb)

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Roy, C., Kumar, R., Hossain, M.M. et al. Biophysical and Computational Approaches to Unravel pH-Dependent Conformational Change of PspA Assist PspA-PspF Complex Formation in Yersinia enterocolitica. Protein J 41, 403–413 (2022). https://doi.org/10.1007/s10930-022-10061-w

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