Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8

Kaushal Parikh, Sander H. Diks, Jurriaan H B Tuynman, Auke Verhaar, Mark Löwenberg, Daan W. Hommes, Jos Joore, Akhilesh Pandey, Maikel P. Peppelenbosch

Research output: Contribution to journalArticle

Abstract

Kinases are pivotal regulators of cellular physiology. The human genome contains more than 500 putative kinases, which exert their action via the phosphorylation of specific substrates. The determinants of this specificity are still only partly understood and as a consequence it is difficult to predict kinase substrate preferences from the primary structure, hampering the understanding of kinase function in physiology and prompting the development of technologies that allow easy assessment of kinase substrate consensus sequences. Hence, we decided to explore the usefulness of phosphorylation of peptide arrays comprising of 1176 different peptide substrates with recombinant kinases for determining kinase substrate preferences, based on the contribution of individual amino acids to total array phosphorylation. Employing this technology, we were able to determine the consensus peptide sequences for substrates of both c-Raf and Mitogen Activated Protein Kinase Kinase Kinase 8, two highly homologous kinases with distinct signalling roles in cellular physiology. The results show that although consensus sequences for these two kinases identified through our analysis share important chemical similarities, there is still some sequence specificity that could explain the different biological action of the two enzymes. Thus peptide arrays are a useful instrument for deducing substrate consensus sequences and highly homologous kinases can differ in their requirement for phosphorylation events.

Original languageEnglish (US)
Article numbere6440
JournalPLoS One
Volume4
Issue number7
DOIs
StatePublished - Jun 30 2009

Fingerprint

mitogen-activated protein kinase kinase kinase
MAP Kinase Kinase Kinases
Phosphorylation
phosphorylation
phosphotransferases (kinases)
Phosphotransferases
peptides
Peptides
Substrates
Consensus Sequence
consensus sequence
Physiology
physiology
Technology
Human Genome
Genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Parikh, K., Diks, S. H., Tuynman, J. H. B., Verhaar, A., Löwenberg, M., Hommes, D. W., ... Peppelenbosch, M. P. (2009). Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PLoS One, 4(7), [e6440]. https://doi.org/10.1371/journal.pone.0006440

Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. / Parikh, Kaushal; Diks, Sander H.; Tuynman, Jurriaan H B; Verhaar, Auke; Löwenberg, Mark; Hommes, Daan W.; Joore, Jos; Pandey, Akhilesh; Peppelenbosch, Maikel P.

In: PLoS One, Vol. 4, No. 7, e6440, 30.06.2009.

Research output: Contribution to journalArticle

Parikh, K, Diks, SH, Tuynman, JHB, Verhaar, A, Löwenberg, M, Hommes, DW, Joore, J, Pandey, A & Peppelenbosch, MP 2009, 'Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8', PLoS One, vol. 4, no. 7, e6440. https://doi.org/10.1371/journal.pone.0006440
Parikh, Kaushal ; Diks, Sander H. ; Tuynman, Jurriaan H B ; Verhaar, Auke ; Löwenberg, Mark ; Hommes, Daan W. ; Joore, Jos ; Pandey, Akhilesh ; Peppelenbosch, Maikel P. / Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. In: PLoS One. 2009 ; Vol. 4, No. 7.
@article{7a50ae82ffda4ee2971add5cb8f93429,
title = "Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8",
abstract = "Kinases are pivotal regulators of cellular physiology. The human genome contains more than 500 putative kinases, which exert their action via the phosphorylation of specific substrates. The determinants of this specificity are still only partly understood and as a consequence it is difficult to predict kinase substrate preferences from the primary structure, hampering the understanding of kinase function in physiology and prompting the development of technologies that allow easy assessment of kinase substrate consensus sequences. Hence, we decided to explore the usefulness of phosphorylation of peptide arrays comprising of 1176 different peptide substrates with recombinant kinases for determining kinase substrate preferences, based on the contribution of individual amino acids to total array phosphorylation. Employing this technology, we were able to determine the consensus peptide sequences for substrates of both c-Raf and Mitogen Activated Protein Kinase Kinase Kinase 8, two highly homologous kinases with distinct signalling roles in cellular physiology. The results show that although consensus sequences for these two kinases identified through our analysis share important chemical similarities, there is still some sequence specificity that could explain the different biological action of the two enzymes. Thus peptide arrays are a useful instrument for deducing substrate consensus sequences and highly homologous kinases can differ in their requirement for phosphorylation events.",
author = "Kaushal Parikh and Diks, {Sander H.} and Tuynman, {Jurriaan H B} and Auke Verhaar and Mark L{\"o}wenberg and Hommes, {Daan W.} and Jos Joore and Akhilesh Pandey and Peppelenbosch, {Maikel P.}",
year = "2009",
month = "6",
day = "30",
doi = "10.1371/journal.pone.0006440",
language = "English (US)",
volume = "4",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",

}

TY - JOUR

T1 - Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8

AU - Parikh, Kaushal

AU - Diks, Sander H.

AU - Tuynman, Jurriaan H B

AU - Verhaar, Auke

AU - Löwenberg, Mark

AU - Hommes, Daan W.

AU - Joore, Jos

AU - Pandey, Akhilesh

AU - Peppelenbosch, Maikel P.

PY - 2009/6/30

Y1 - 2009/6/30

N2 - Kinases are pivotal regulators of cellular physiology. The human genome contains more than 500 putative kinases, which exert their action via the phosphorylation of specific substrates. The determinants of this specificity are still only partly understood and as a consequence it is difficult to predict kinase substrate preferences from the primary structure, hampering the understanding of kinase function in physiology and prompting the development of technologies that allow easy assessment of kinase substrate consensus sequences. Hence, we decided to explore the usefulness of phosphorylation of peptide arrays comprising of 1176 different peptide substrates with recombinant kinases for determining kinase substrate preferences, based on the contribution of individual amino acids to total array phosphorylation. Employing this technology, we were able to determine the consensus peptide sequences for substrates of both c-Raf and Mitogen Activated Protein Kinase Kinase Kinase 8, two highly homologous kinases with distinct signalling roles in cellular physiology. The results show that although consensus sequences for these two kinases identified through our analysis share important chemical similarities, there is still some sequence specificity that could explain the different biological action of the two enzymes. Thus peptide arrays are a useful instrument for deducing substrate consensus sequences and highly homologous kinases can differ in their requirement for phosphorylation events.

AB - Kinases are pivotal regulators of cellular physiology. The human genome contains more than 500 putative kinases, which exert their action via the phosphorylation of specific substrates. The determinants of this specificity are still only partly understood and as a consequence it is difficult to predict kinase substrate preferences from the primary structure, hampering the understanding of kinase function in physiology and prompting the development of technologies that allow easy assessment of kinase substrate consensus sequences. Hence, we decided to explore the usefulness of phosphorylation of peptide arrays comprising of 1176 different peptide substrates with recombinant kinases for determining kinase substrate preferences, based on the contribution of individual amino acids to total array phosphorylation. Employing this technology, we were able to determine the consensus peptide sequences for substrates of both c-Raf and Mitogen Activated Protein Kinase Kinase Kinase 8, two highly homologous kinases with distinct signalling roles in cellular physiology. The results show that although consensus sequences for these two kinases identified through our analysis share important chemical similarities, there is still some sequence specificity that could explain the different biological action of the two enzymes. Thus peptide arrays are a useful instrument for deducing substrate consensus sequences and highly homologous kinases can differ in their requirement for phosphorylation events.

UR - http://www.scopus.com/inward/record.url?scp=68149145821&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=68149145821&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0006440

DO - 10.1371/journal.pone.0006440

M3 - Article

VL - 4

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 7

M1 - e6440

ER -