Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome

Charles A. Galea, Anthony A. High, John C. Obenauer, Ashutosh Mlshra, Cheon Gil Park, Marco Punta, Avner Schlesslnger, Ma Jing, Burkhard Rost, Clive A. Slaughter, Richard W. Kriwacki

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

Intrinsically disordered proteins are predicted to be highly abundant and play broad biological roles in eukaryotic cells. In particular, by virtue of their structural malleability and propensity to interact with multiple binding partners, disordered proteins are thought to be specialized for roles in signaling and regulation. However, these concepts are based on in silico analyses of translated whole genome sequences, not on large-scale analyses of proteins expressed in living cells. Therefore, whether these concepts broadly apply to expressed proteins is currently unknown. Previous studies have shown that heat-treatment of cell extracts lead to partial enrichment of soluble, disordered proteins. On the basis of this observation, we sought to address the current dearth of knowledge about expressed, disordered proteins by performing a large-scale proteomics study of thermostable proteins isolated from mouse fibroblast cells. With the use of novel multidimensional chromatography methods and mass spectrometry, we identified a total of 1320 thermostable proteins from these cells. Further, we used a variety of bioinformatics methods to analyze the structural and biological properties of these proteins. Interestingly, more than 900 of these expressed proteins were predicted to be substantially disordered. These were divided into two categories, with 514 predicted to be predominantly disordered and 395 predicted to exhibit both disordered and ordered/folded features. In addition, 411 of the thermostable proteins were predicted to be folded. Despite the use of heat treatment (60 min at 98 °C) to partially enrich for disordered proteins, which might have been expected to select for small proteins, the sequences of these proteins exhibited a wide range of lengths (622 ± 555 residues (average length ± standard deviation) for disordered proteins and 569 ± 598 residues for folded proteins). Computational structural analyses revealed several unexpected features of the thermostable proteins: (1) disordered domains and coiled-coil domains occurred together in a large number of disordered proteins, suggesting functional interplay between these domains; and (2) more than 170 proteins contained lengthy domains (>300 residues) known to be folded. Reference to Gene Ontology Consortium functional annotations revealed that, while disordered proteins play diverse biological roles in mouse fibroblasts, they do exhibit heightened involvement in several functional categories, including, cytoskeletal structure and cell movement, metabolic and biosynthetic processes, organelle structure, cell division, gene transcription, and ribonucleoprotein complexes. We believe that these results reflect the general properties of the mouse intrinsically disordered proteome (IDP-ome) although they also reflect the specialized physiology of fibroblast cells. Large-scale identification of expressed, thermostable proteins from other cell types in the future, grown under varied physiological conditions, will dramatically expand our understanding of the structural and biological properties of disordered eukaryotic proteins.

Original languageEnglish (US)
Pages (from-to)211-226
Number of pages16
JournalJournal of Proteome Research
Volume8
Issue number1
DOIs
StatePublished - Jan 1 2009
Externally publishedYes

Fingerprint

Proteome
Proteins
Cells
Fibroblasts
Genes
Hot Temperature
Heat treatment
Intrinsically Disordered Proteins
Cell Physiological Phenomena
Gene Ontology
Ribonucleoproteins
Sexual Partners

Keywords

  • Intrinsically disordered proteins
  • Intrinsically unstructured proteins
  • Mammalian proteome
  • Proteomics
  • Thermostable proteins

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Galea, C. A., High, A. A., Obenauer, J. C., Mlshra, A., Park, C. G., Punta, M., ... Kriwacki, R. W. (2009). Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. Journal of Proteome Research, 8(1), 211-226. https://doi.org/10.1021/pr800308v

Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. / Galea, Charles A.; High, Anthony A.; Obenauer, John C.; Mlshra, Ashutosh; Park, Cheon Gil; Punta, Marco; Schlesslnger, Avner; Jing, Ma; Rost, Burkhard; Slaughter, Clive A.; Kriwacki, Richard W.

In: Journal of Proteome Research, Vol. 8, No. 1, 01.01.2009, p. 211-226.

Research output: Contribution to journalArticle

Galea, CA, High, AA, Obenauer, JC, Mlshra, A, Park, CG, Punta, M, Schlesslnger, A, Jing, M, Rost, B, Slaughter, CA & Kriwacki, RW 2009, 'Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome', Journal of Proteome Research, vol. 8, no. 1, pp. 211-226. https://doi.org/10.1021/pr800308v
Galea, Charles A. ; High, Anthony A. ; Obenauer, John C. ; Mlshra, Ashutosh ; Park, Cheon Gil ; Punta, Marco ; Schlesslnger, Avner ; Jing, Ma ; Rost, Burkhard ; Slaughter, Clive A. ; Kriwacki, Richard W. / Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. In: Journal of Proteome Research. 2009 ; Vol. 8, No. 1. pp. 211-226.
@article{bd7230e190d64308bf842187686d3b01,
title = "Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome",
abstract = "Intrinsically disordered proteins are predicted to be highly abundant and play broad biological roles in eukaryotic cells. In particular, by virtue of their structural malleability and propensity to interact with multiple binding partners, disordered proteins are thought to be specialized for roles in signaling and regulation. However, these concepts are based on in silico analyses of translated whole genome sequences, not on large-scale analyses of proteins expressed in living cells. Therefore, whether these concepts broadly apply to expressed proteins is currently unknown. Previous studies have shown that heat-treatment of cell extracts lead to partial enrichment of soluble, disordered proteins. On the basis of this observation, we sought to address the current dearth of knowledge about expressed, disordered proteins by performing a large-scale proteomics study of thermostable proteins isolated from mouse fibroblast cells. With the use of novel multidimensional chromatography methods and mass spectrometry, we identified a total of 1320 thermostable proteins from these cells. Further, we used a variety of bioinformatics methods to analyze the structural and biological properties of these proteins. Interestingly, more than 900 of these expressed proteins were predicted to be substantially disordered. These were divided into two categories, with 514 predicted to be predominantly disordered and 395 predicted to exhibit both disordered and ordered/folded features. In addition, 411 of the thermostable proteins were predicted to be folded. Despite the use of heat treatment (60 min at 98 °C) to partially enrich for disordered proteins, which might have been expected to select for small proteins, the sequences of these proteins exhibited a wide range of lengths (622 ± 555 residues (average length ± standard deviation) for disordered proteins and 569 ± 598 residues for folded proteins). Computational structural analyses revealed several unexpected features of the thermostable proteins: (1) disordered domains and coiled-coil domains occurred together in a large number of disordered proteins, suggesting functional interplay between these domains; and (2) more than 170 proteins contained lengthy domains (>300 residues) known to be folded. Reference to Gene Ontology Consortium functional annotations revealed that, while disordered proteins play diverse biological roles in mouse fibroblasts, they do exhibit heightened involvement in several functional categories, including, cytoskeletal structure and cell movement, metabolic and biosynthetic processes, organelle structure, cell division, gene transcription, and ribonucleoprotein complexes. We believe that these results reflect the general properties of the mouse intrinsically disordered proteome (IDP-ome) although they also reflect the specialized physiology of fibroblast cells. Large-scale identification of expressed, thermostable proteins from other cell types in the future, grown under varied physiological conditions, will dramatically expand our understanding of the structural and biological properties of disordered eukaryotic proteins.",
keywords = "Intrinsically disordered proteins, Intrinsically unstructured proteins, Mammalian proteome, Proteomics, Thermostable proteins",
author = "Galea, {Charles A.} and High, {Anthony A.} and Obenauer, {John C.} and Ashutosh Mlshra and Park, {Cheon Gil} and Marco Punta and Avner Schlesslnger and Ma Jing and Burkhard Rost and Slaughter, {Clive A.} and Kriwacki, {Richard W.}",
year = "2009",
month = "1",
day = "1",
doi = "10.1021/pr800308v",
language = "English (US)",
volume = "8",
pages = "211--226",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "1",

}

TY - JOUR

T1 - Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome

AU - Galea, Charles A.

AU - High, Anthony A.

AU - Obenauer, John C.

AU - Mlshra, Ashutosh

AU - Park, Cheon Gil

AU - Punta, Marco

AU - Schlesslnger, Avner

AU - Jing, Ma

AU - Rost, Burkhard

AU - Slaughter, Clive A.

AU - Kriwacki, Richard W.

PY - 2009/1/1

Y1 - 2009/1/1

N2 - Intrinsically disordered proteins are predicted to be highly abundant and play broad biological roles in eukaryotic cells. In particular, by virtue of their structural malleability and propensity to interact with multiple binding partners, disordered proteins are thought to be specialized for roles in signaling and regulation. However, these concepts are based on in silico analyses of translated whole genome sequences, not on large-scale analyses of proteins expressed in living cells. Therefore, whether these concepts broadly apply to expressed proteins is currently unknown. Previous studies have shown that heat-treatment of cell extracts lead to partial enrichment of soluble, disordered proteins. On the basis of this observation, we sought to address the current dearth of knowledge about expressed, disordered proteins by performing a large-scale proteomics study of thermostable proteins isolated from mouse fibroblast cells. With the use of novel multidimensional chromatography methods and mass spectrometry, we identified a total of 1320 thermostable proteins from these cells. Further, we used a variety of bioinformatics methods to analyze the structural and biological properties of these proteins. Interestingly, more than 900 of these expressed proteins were predicted to be substantially disordered. These were divided into two categories, with 514 predicted to be predominantly disordered and 395 predicted to exhibit both disordered and ordered/folded features. In addition, 411 of the thermostable proteins were predicted to be folded. Despite the use of heat treatment (60 min at 98 °C) to partially enrich for disordered proteins, which might have been expected to select for small proteins, the sequences of these proteins exhibited a wide range of lengths (622 ± 555 residues (average length ± standard deviation) for disordered proteins and 569 ± 598 residues for folded proteins). Computational structural analyses revealed several unexpected features of the thermostable proteins: (1) disordered domains and coiled-coil domains occurred together in a large number of disordered proteins, suggesting functional interplay between these domains; and (2) more than 170 proteins contained lengthy domains (>300 residues) known to be folded. Reference to Gene Ontology Consortium functional annotations revealed that, while disordered proteins play diverse biological roles in mouse fibroblasts, they do exhibit heightened involvement in several functional categories, including, cytoskeletal structure and cell movement, metabolic and biosynthetic processes, organelle structure, cell division, gene transcription, and ribonucleoprotein complexes. We believe that these results reflect the general properties of the mouse intrinsically disordered proteome (IDP-ome) although they also reflect the specialized physiology of fibroblast cells. Large-scale identification of expressed, thermostable proteins from other cell types in the future, grown under varied physiological conditions, will dramatically expand our understanding of the structural and biological properties of disordered eukaryotic proteins.

AB - Intrinsically disordered proteins are predicted to be highly abundant and play broad biological roles in eukaryotic cells. In particular, by virtue of their structural malleability and propensity to interact with multiple binding partners, disordered proteins are thought to be specialized for roles in signaling and regulation. However, these concepts are based on in silico analyses of translated whole genome sequences, not on large-scale analyses of proteins expressed in living cells. Therefore, whether these concepts broadly apply to expressed proteins is currently unknown. Previous studies have shown that heat-treatment of cell extracts lead to partial enrichment of soluble, disordered proteins. On the basis of this observation, we sought to address the current dearth of knowledge about expressed, disordered proteins by performing a large-scale proteomics study of thermostable proteins isolated from mouse fibroblast cells. With the use of novel multidimensional chromatography methods and mass spectrometry, we identified a total of 1320 thermostable proteins from these cells. Further, we used a variety of bioinformatics methods to analyze the structural and biological properties of these proteins. Interestingly, more than 900 of these expressed proteins were predicted to be substantially disordered. These were divided into two categories, with 514 predicted to be predominantly disordered and 395 predicted to exhibit both disordered and ordered/folded features. In addition, 411 of the thermostable proteins were predicted to be folded. Despite the use of heat treatment (60 min at 98 °C) to partially enrich for disordered proteins, which might have been expected to select for small proteins, the sequences of these proteins exhibited a wide range of lengths (622 ± 555 residues (average length ± standard deviation) for disordered proteins and 569 ± 598 residues for folded proteins). Computational structural analyses revealed several unexpected features of the thermostable proteins: (1) disordered domains and coiled-coil domains occurred together in a large number of disordered proteins, suggesting functional interplay between these domains; and (2) more than 170 proteins contained lengthy domains (>300 residues) known to be folded. Reference to Gene Ontology Consortium functional annotations revealed that, while disordered proteins play diverse biological roles in mouse fibroblasts, they do exhibit heightened involvement in several functional categories, including, cytoskeletal structure and cell movement, metabolic and biosynthetic processes, organelle structure, cell division, gene transcription, and ribonucleoprotein complexes. We believe that these results reflect the general properties of the mouse intrinsically disordered proteome (IDP-ome) although they also reflect the specialized physiology of fibroblast cells. Large-scale identification of expressed, thermostable proteins from other cell types in the future, grown under varied physiological conditions, will dramatically expand our understanding of the structural and biological properties of disordered eukaryotic proteins.

KW - Intrinsically disordered proteins

KW - Intrinsically unstructured proteins

KW - Mammalian proteome

KW - Proteomics

KW - Thermostable proteins

UR - http://www.scopus.com/inward/record.url?scp=60849128834&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=60849128834&partnerID=8YFLogxK

U2 - 10.1021/pr800308v

DO - 10.1021/pr800308v

M3 - Article

VL - 8

SP - 211

EP - 226

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 1

ER -