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Publication . Preprint . 2019

Variants of intrinsic disorder: structural characterization

Sergio Forcelloni; Antonio Deiana; Andrea Giansanti;
Open Access
Published: 01 Aug 2019
Publisher: Cold Spring Harbor Laboratory

AbstractIn a recent study, we have introduced an operational classification of the human proteome in three variants of disorder: ordered proteins (ORDPs), structured proteins with intrinsically disordered protein regions (IDPRs), intrinsically disordered proteins (IDPs). That classification was useful in functionally separating IDPRs from IDPs, which up until now have been generally considered as a whole. In this study, we corroborate this distinction by considering different physical-chemical and structural properties. Both ORDPs and IDPRs are enriched in order-promoting amino acids, whereas only IDPs show an enrichment in disordered-promoting amino acids. Consistently, ORDPs and IDPRs are preferentially located in the ordered phase of the charge-hydropathy plot, whereas IDPs are widespread over the disordered phase. We introduce the mean packing - mean pairwise energy (MP-MPE) plane to structurally characterize these variants even in the absence of a structural model. As expected for well-packed proteins, a negative linear correlation is observed between MP and MPE for ORDPs and IDPRs, whereas IDPs break this linear dependence. Finally, we find that IDPs have a more extended conformation as measured by the scaling law between the radius of gyration and the length of these proteins, and accordingly they have higher solubility and accessible surface area than ORDPs and IDPRs. Overall, our results confirm the relevance of our operational separation of IDPRs from IDPs and provide further validation of our criteria to separate IDPs from the rest of human proteome.

Subjects by Vocabulary

Microsoft Academic Graph classification: Amino acid chemistry.chemical_classification chemistry Characterization (materials science) Accessible surface area Radius of gyration Linear correlation Computational biology Scaling law Human proteome project Intrinsically disordered proteins

46 references, page 1 of 5

1. Wright, P.E., Dyson, H.J. Intrinsically unstructured proteins: re-assessing the protein structurefunction paradigm. J Mol Biol. 31 (1999) 293-321.

2. Uversky, VN, Gillespie, JR, Fink, AL. Why Are “Natively Unfolded” Proteins Unstructured Under Physiologic Conditions?. PROTEINS: Structure, Function, and Genetics 41 (2000) 415- 427.

3. Dunker, A.K., Lawson, J.D., Brown, C.J., Williams, R.M., Romero, P., Oh, J.S., et al. Intrinsically disordered protein. J Mol Graph Model. 19 (2001) 26-59.

4. Tompa, P. Intrinsically unstructured proteins. Trends Biochem Sci. 27 (2002) 527-33.

5. Fink, A.L. Natively unfolded proteins. Curr Opin Struct Biol. 15 (2005) 35-41.

6. Daughdrill, G.W., Pielak, G.J., Uversky, V.N., Cortese, M.S., Dunker, K.A. Natively Disordered Proteins. In: Protein Folding Handbook. Wiley-Blackwell; 2008.

7. Tompa, P., Fersht, A. Structure and function of intrinsically disordered proteins. New York: Chapman and Hall/CRC; 2009. [OpenAIRE]

8. Schlessinger, A., Schaefer, C., Vicedo, E., Schmidberger, M., Punta, M., Rost, B. Protein disorder - a breakthrough invention of evolution?. Curr Opin Struct Biol. 21 (2011) 412-418.

9. Uversky, V.N. Under-Folded Proteins: conformational Ensembles and Their Roles in Protein Folding, Function, and Pathogenesis. Biopolymers 99 (2013) 870-887.

10. Xie, H., Vucetic, S., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Uversky, V.N., et al. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res. 6 (2007) 1882-98.