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Measuring Membrane Penetration Depths and Conformational Changes in Membrane Peptides and Proteins

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Abstract

The structural organization and dynamic nature of the biomembrane components are important determinants for numerous cellular functions. Particularly, membrane proteins are critically important for various physiological functions and are important drug targets. The mechanistic insights on the complex functionality of membrane lipids and proteins can be elucidated by understanding the interplay between structure and dynamics. In this regard, membrane penetration depth represents an important parameter to obtain the precise depth of membrane-embedded molecules that often define the conformation and topology of membrane probes and proteins. In this review, we discuss about the widely used fluorescence quenching-based methods (parallax method, distribution analysis, and dual-quencher analysis) to accurately determine the membrane penetration depths of fluorescent probes that are either membrane-embedded or attached to lipids and proteins. Further, we also discuss a relatively novel fluorescence quenching method that utilizes tryptophan residue as the quencher, namely the tryptophan-induced quenching, which is sensitive to monitor small-scale conformational changes (short distances of < 15 Å) and useful in mapping distances in proteins. We have provided numerous examples for the benefit of readers to appreciate the importance and applicability of these simple yet powerful methods to study membrane proteins.

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Fig. 1
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adapted from Caputo and London 2003a. See text for details

Fig. 6

Adapted from Mansoor et al. 2010. See text for more information

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Acknowledgements

R.B. thanks the Department of Atomic Energy, Government of India for the award of a Senior Research Fellowship. H.R. is a recipient of India Alliance DBT-Wellcome Trust Intermediate Fellowship (IA/I/17/2/503321). R.B. and H.R. thank the Department of Atomic Energy, Govt. of India for supporting this work. We thank members of our laboratory for critically reading the manuscript.

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  1. Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF, Bidhannagar, Kolkata, 700 064, India

    Rupasree Brahma & H. Raghuraman

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  1. Rupasree Brahma
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  2. H. Raghuraman
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RB and HR contributed to preparing figures and wrote the manuscript.

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Brahma, R., Raghuraman, H. Measuring Membrane Penetration Depths and Conformational Changes in Membrane Peptides and Proteins. J Membrane Biol 255, 469–483 (2022). https://doi.org/10.1007/s00232-022-00224-2

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