Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Apr 18;12(4):592.
doi: 10.3390/biom12040592.

Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.)

Miloš Avramov  1 , Éva Schád  2 , Ágnes Révész  3 , Lilla Turiák  3 , Iva Uzelac  1 , Ágnes Tantos  2 , László Drahos  3 , Željko D Popović  1
Affiliations

Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.)

Miloš Avramov et al. Biomolecules. .

Abstract

Research in previous decades has shown that intrinsically disordered proteins (IDPs) and regions in proteins (IDRs) are as ubiquitous as highly ordered proteins. Despite this, research on IDPs and IDRs still has many gaps left to fill. Here, we present an approach that combines wet lab methods with bioinformatics tools to identify and analyze intrinsically disordered proteins in a non-model insect species that is cold-hardy. Due to their known resilience to the effects of extreme temperatures, these proteins likely play important roles in this insect's adaptive mechanisms to sub-zero temperatures. The approach involves IDP enrichment by sample heating and double-digestion of proteins, followed by peptide and protein identification. Next, proteins are bioinformatically analyzed for disorder content, presence of long disordered regions, amino acid composition, and processes they are involved in. Finally, IDP detection is validated with an in-house 2D PAGE. In total, 608 unique proteins were identified, with 39 being mostly disordered, 100 partially disordered, 95 nearly ordered, and 374 ordered. One-third contain at least one long disordered segment. Functional information was available for only 90 proteins with intrinsic disorders out of 312 characterized proteins. Around half of the 90 proteins are cytoskeletal elements or involved in translational processes.

Keywords: IUPred analysis; LC–MS/MS; Ostrinia nubilalis; cold hardiness; intrinsically disordered protein regions (IDRs); intrinsically disordered proteins (IDPs).

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Generalized workflow of the experiment. Detailed explanations are given in the relevant subsections. Aliquots from samples with the same symbol in the superscript (* or †) were pooled before being run on 2D PAGE. NCA—non-cold-acclimated diapausing group; CA—cold-acclimated diapausing group.
Figure 2
Figure 2
(A) Total unique and common proteins isolated from different experimental groups. (B) Effect of sample heating on the number of identified proteins. Unique Non-heated—proteins found only in the non-heated samples; Unique Heated—proteins found only in heated samples; Common—proteins that were found in both heated and non-heated samples; NCA—non-cold-acclimated diapausing group; CA—cold-acclimated diapausing group.
Figure 3
Figure 3
(A) Total number of proteins with varying degrees of intrinsic disorder—ordered (OPs, 10% at most), nearly ordered (NOPs, 10–30%), partially disordered (PDPs, 30–70%), mostly disordered (MDPs, at least 70%). (B) Effect of heat treatment on the percental distribution of proteins with varying degrees of intrinsic disorder in the two sample types of both experimental groups. NCA—non-cold-acclimated diapausing group; CA—cold-acclimated diapausing group.
Figure 4
Figure 4
Distribution of long intrinsically disordered regions in proteins with various degrees of intrinsic disorder in the (A) NCA (non-cold-acclimated diapausing) and (B) CA (cold-acclimated diapausing) experimental groups. The different numbers of long IDRs in proteins are color-coded.
Figure 5
Figure 5
Ratios of disorder-promoting (P, E, S, K, Q, H, D, R, G, A) and order-promoting amino acids (T, C, N, V, L, M, I, Y, F, W) in mostly disordered (MDPs), partially disordered (PDPs), nearly ordered (NOPs), and ordered proteins (OPs).
Figure 6
Figure 6
Ratios of individual disorder (A) and order-promoting amino acids (B) in mostly disordered (MDPs), partially disordered (PDPs), nearly ordered (NOPs), and ordered proteins (OPs), ordered by abundance in MDPs.
Figure 7
Figure 7
Results of in-house 2D PAGE for detecting intrinsically disordered proteins. (A) Proteins from heat-treated samples have successfully entered the second dimension. The black line represents the diagonal along which IDPs are located. Arrows denote ordered proteins that stay above the diagonal. (B) Proteins from non-heated samples are mostly locked in the gel from the first dimension (strip overlaying the larger gel).
Figure 8
Figure 8
Biological processes and molecular functions of intrinsically disordered proteins and proteins containing long IDRs. The category Other encompasses processes and functions that make up less than 4% of total hits each. Total unique—all uniquely identified proteins; Non-heated—all proteins identified in the non-heated sample types; Heated—all proteins identified in the heated sample types.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Chen J. Towards the physical basis of how intrinsic disorder mediates protein function. Arch. Biochem. Biophys. 2012;524:123–131. doi: 10.1016/j.abb.2012.04.024. - DOI - PubMed
    1. Tompa P. Intrinsically unstructured proteins. Trends Biochem. Sci. 2002;27:527–533. doi: 10.1016/S0968-0004(02)02169-2. - DOI - PubMed
    1. Uversky V.N., Gillespie J.R., Fink A.L. Why Are “Natively Unfolded” Proteins Unstructured Under Physiologic Conditions? Proteins. 2000;41:415–427. doi: 10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7. - DOI - PubMed
    1. Uversky V.N., Dunker A.K. Understanding Protein Non-Folding. Biochim. Biophys. Acta. 2010;1804:1231–1264. doi: 10.1016/j.bbapap.2010.01.017. - DOI - PMC - PubMed
    1. Dyson H.J., Wright P.E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell. Biol. 2005;6:197–208. doi: 10.1038/nrm1589. - DOI - PubMed

Publication types

Substances

LinkOut - more resources