Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: A nitrogen-15 relaxation study

Junji Iwahara, Robert D. Peterson, Robert T. Clubb

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

AT-rich interaction domains (ARIDs) are found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation, and development. Previously we elucidated how ARIDs recognize DNA by determining the solution structure of the Drosophila melanogaster Dead ringer protein in both its DNA-free and -bound states. In order to quantitatively determine how ARIDs alter their mobility to recognize DNA, we have measured the relaxation parameters of the backbone nitrogen-15 nuclei of Dead ringer in its free and bound forms, and interpreted these data using the model-free approach. We show that Dead ringer undergoes significant changes in its mobility upon binding, with residues in the loop connecting helices H5 and H6 becoming immobilized in the major groove and contacts to the minor groove slowing down the motion of residues at the C terminus. A DNA-induced rotation and displacement of the N-terminal subdomain of the protein increases the mobility of helix H1 located distal to the DNA interface and may partially negate the entropic cost of immobilizing interfacial residues. Elevated motions on the micro- to millisecond timescale in the N-terminal domain prior to DNA binding appear to foreshadow the DNA-induced conformation change.

Original languageEnglish (US)
Pages (from-to)1140-1150
Number of pages11
JournalProtein Science
Volume14
Issue number5
DOIs
StatePublished - May 2005
Externally publishedYes

Fingerprint

Nitrogen
DNA
Proteins
Nucleic Acid Conformation
Drosophila melanogaster
Cell proliferation
Cell Differentiation
Transcription Factors
Conformations
Cell Proliferation
Costs and Cost Analysis
Costs

Keywords

  • N-relaxation
  • ARID
  • AT-rich interaction domain
  • Backbone dynamics
  • Dead ringer protein
  • NMR
  • Protein-DNA interaction

ASJC Scopus subject areas

  • Biochemistry

Cite this

Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA : A nitrogen-15 relaxation study. / Iwahara, Junji; Peterson, Robert D.; Clubb, Robert T.

In: Protein Science, Vol. 14, No. 5, 05.2005, p. 1140-1150.

Research output: Contribution to journalArticle

@article{084ee45000e8423fb285b6aa2faae1ec,
title = "Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: A nitrogen-15 relaxation study",
abstract = "AT-rich interaction domains (ARIDs) are found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation, and development. Previously we elucidated how ARIDs recognize DNA by determining the solution structure of the Drosophila melanogaster Dead ringer protein in both its DNA-free and -bound states. In order to quantitatively determine how ARIDs alter their mobility to recognize DNA, we have measured the relaxation parameters of the backbone nitrogen-15 nuclei of Dead ringer in its free and bound forms, and interpreted these data using the model-free approach. We show that Dead ringer undergoes significant changes in its mobility upon binding, with residues in the loop connecting helices H5 and H6 becoming immobilized in the major groove and contacts to the minor groove slowing down the motion of residues at the C terminus. A DNA-induced rotation and displacement of the N-terminal subdomain of the protein increases the mobility of helix H1 located distal to the DNA interface and may partially negate the entropic cost of immobilizing interfacial residues. Elevated motions on the micro- to millisecond timescale in the N-terminal domain prior to DNA binding appear to foreshadow the DNA-induced conformation change.",
keywords = "N-relaxation, ARID, AT-rich interaction domain, Backbone dynamics, Dead ringer protein, NMR, Protein-DNA interaction",
author = "Junji Iwahara and Peterson, {Robert D.} and Clubb, {Robert T.}",
year = "2005",
month = "5",
doi = "10.1110/ps.041154405",
language = "English (US)",
volume = "14",
pages = "1140--1150",
journal = "Protein Science",
issn = "0961-8368",
publisher = "Cold Spring Harbor Laboratory Press",
number = "5",

}

TY - JOUR

T1 - Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA

T2 - A nitrogen-15 relaxation study

AU - Iwahara, Junji

AU - Peterson, Robert D.

AU - Clubb, Robert T.

PY - 2005/5

Y1 - 2005/5

N2 - AT-rich interaction domains (ARIDs) are found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation, and development. Previously we elucidated how ARIDs recognize DNA by determining the solution structure of the Drosophila melanogaster Dead ringer protein in both its DNA-free and -bound states. In order to quantitatively determine how ARIDs alter their mobility to recognize DNA, we have measured the relaxation parameters of the backbone nitrogen-15 nuclei of Dead ringer in its free and bound forms, and interpreted these data using the model-free approach. We show that Dead ringer undergoes significant changes in its mobility upon binding, with residues in the loop connecting helices H5 and H6 becoming immobilized in the major groove and contacts to the minor groove slowing down the motion of residues at the C terminus. A DNA-induced rotation and displacement of the N-terminal subdomain of the protein increases the mobility of helix H1 located distal to the DNA interface and may partially negate the entropic cost of immobilizing interfacial residues. Elevated motions on the micro- to millisecond timescale in the N-terminal domain prior to DNA binding appear to foreshadow the DNA-induced conformation change.

AB - AT-rich interaction domains (ARIDs) are found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation, and development. Previously we elucidated how ARIDs recognize DNA by determining the solution structure of the Drosophila melanogaster Dead ringer protein in both its DNA-free and -bound states. In order to quantitatively determine how ARIDs alter their mobility to recognize DNA, we have measured the relaxation parameters of the backbone nitrogen-15 nuclei of Dead ringer in its free and bound forms, and interpreted these data using the model-free approach. We show that Dead ringer undergoes significant changes in its mobility upon binding, with residues in the loop connecting helices H5 and H6 becoming immobilized in the major groove and contacts to the minor groove slowing down the motion of residues at the C terminus. A DNA-induced rotation and displacement of the N-terminal subdomain of the protein increases the mobility of helix H1 located distal to the DNA interface and may partially negate the entropic cost of immobilizing interfacial residues. Elevated motions on the micro- to millisecond timescale in the N-terminal domain prior to DNA binding appear to foreshadow the DNA-induced conformation change.

KW - N-relaxation

KW - ARID

KW - AT-rich interaction domain

KW - Backbone dynamics

KW - Dead ringer protein

KW - NMR

KW - Protein-DNA interaction

UR - http://www.scopus.com/inward/record.url?scp=17744363273&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=17744363273&partnerID=8YFLogxK

U2 - 10.1110/ps.041154405

DO - 10.1110/ps.041154405

M3 - Article

C2 - 15802641

AN - SCOPUS:17744363273

VL - 14

SP - 1140

EP - 1150

JO - Protein Science

JF - Protein Science

SN - 0961-8368

IS - 5

ER -