Anne Kenworthy
Last active: 2/12/2016

On the use of Ripley's K-function and its derivatives to analyze domain size.

Kiskowski MA, Hancock JF, Kenworthy AK
Biophys J. 2009 97 (4): 1095-103

PMID: 19686657 · PMCID: PMC2726315 · DOI:10.1016/j.bpj.2009.05.039

Ripley's K-, H-, and L-functions are used increasingly to identify clustering of proteins in membrane microdomains. In this approach, aggregation (or clustering) is identified if the average number of proteins within a distance r of another protein is statistically greater than that expected for a random distribution. However, it is not entirely clear how the function may be used to quantitatively determine the size of domains in which clustering occurs. Here, we evaluate the extent to which the domain radius can be determined by different interpretations of Ripley's K-statistic in a theoretical, idealized context. We also evaluate the measures for noisy experimental data and use Monte Carlo simulations to separate the effects of different types of experimental noise. We find that the radius of maximal aggregation approximates the domain radius, while identifying the domain boundary with the minimum of the derivative of H(r) is highly accurate in idealized conditions. The accuracy of both measures is impacted by the noise present in experimental data; for example, here, the presence of a large fraction of particles distributed as monomers and interdomain interactions. These findings help to delineate the limitations and potential of Ripley's K in real-life scenarios.

MeSH Terms (8)

Algorithms Computer Simulation Models, Chemical Models, Molecular Molecular Weight Protein Conformation Proteins Protein Structure, Tertiary

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