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Genomics Inform > Volume 9(2); 2011 > Article
Analysis of the Globular Nature of Proteins.
Sunghoon Jung, Hyeon Seok Son
1Laboratory of Computational Biology & Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul 151-742, Korea.
2Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, Seoul 151-742, Korea.
3SNU Bioinformatics Institute, Seoul 151-742, Korea.
Numerous restraints and simplifications have been developed for methods that anticipate protein structure to reduce the colossal magnitude of possible conformational states. In this study, we investigated if globularity is a general characteristic of proteins and whether they can be applied as a valid constraint in protein structure simulations with approximated measurements (Gb-index). Unexpectedly, most of the proteins showed strong structural globularity (i.e., mode of approximately 76% similarity to the perfect globe) with only a few percent of proteins being outliers. Small proteins tended to be significantly non-globular (R2=0.79) and the minimum Gb-index showed a logarithmic increase with the increase in protein size (R2=0.62), strongly implying that the non-globular characteristics might be more acceptable for smaller proteins than larger ones. The strong perfect globe-like character and the relationship between small size and the loss of globular structure of a protein may imply that living organisms have mechanisms to aid folding into the globular structure to reduce irreversible aggregation. This also implies the possible mechanisms of diseases caused by protein aggregation, including some forms of trinucleotide repeat expansion-mediated diseases.
Keywords: protein aggregation disease; protein globularity; protein structure analysis
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