Mutagenesis study on the zebra fish SOX9 high-mobility group

Comparison of sequence and non-sequence specific HMG domains

Nai-Wan Hsiao, Dharmaraj Samuel, Yu Nan Liu, Li Chuan Chen, Tzu Ying Yang, Gurunathan Jayaraman, Ping Chiang Lyu

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

A unique class of proteins, containing high-mobility group (HMG) domain(s), recognizes unusual DNA structures and/or bends specific to AT-rich linear double-stranded DNA. The DNA binding feature of these proteins is exhibited in the HMG domain(s). Although the sequence specific and non-sequence specific HMG domains exhibit very high degrees of sequence similarity, the reasons for the difference between their DNA recognition mechanisms are unclear. A series of zebra fish SOX9 HMG domain mutants was prepared in an effort to elucidate the importance of various residues on protein stability and DNA binding. This study is the first of a comprehensive mutagenesis study on a sequence specific HMG domain. Comparing how various residues influence sequence specific and non-sequence specific HMG domains helps us to rationalize their mode of action. Positively charged amino acids concentrated at the surface of sequence specific HMG domains recognize specific, linear AT-rich DNA segments. After the negative charges at the surface of the DNA are neutralized, the hydrophobic residues of the protein may intercalate DNA. Phenylalanine at position 12 plays a crucial role in the sequence specific HMG domain. The differences in pI values, the instability index, and DNA contact regions between sequence and non-sequence specific HMG domains are associated with their functional modes.

Original languageEnglish
Pages (from-to)11183-11193
Number of pages11
JournalBiochemistry
Volume42
Issue number38
DOIs
Publication statusPublished - 2003 Sep 30

Fingerprint

Mutagenesis
Zebrafish
Fish
DNA
High Mobility Group Proteins
Proteins
Protein Stability
DNA-Binding Proteins
Phenylalanine
Amino Acids

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

Hsiao, Nai-Wan ; Samuel, Dharmaraj ; Liu, Yu Nan ; Chen, Li Chuan ; Yang, Tzu Ying ; Jayaraman, Gurunathan ; Lyu, Ping Chiang. / Mutagenesis study on the zebra fish SOX9 high-mobility group : Comparison of sequence and non-sequence specific HMG domains. In: Biochemistry. 2003 ; Vol. 42, No. 38. pp. 11183-11193.
@article{1985c1801e9f4734a94cf635d40acbe9,
title = "Mutagenesis study on the zebra fish SOX9 high-mobility group: Comparison of sequence and non-sequence specific HMG domains",
abstract = "A unique class of proteins, containing high-mobility group (HMG) domain(s), recognizes unusual DNA structures and/or bends specific to AT-rich linear double-stranded DNA. The DNA binding feature of these proteins is exhibited in the HMG domain(s). Although the sequence specific and non-sequence specific HMG domains exhibit very high degrees of sequence similarity, the reasons for the difference between their DNA recognition mechanisms are unclear. A series of zebra fish SOX9 HMG domain mutants was prepared in an effort to elucidate the importance of various residues on protein stability and DNA binding. This study is the first of a comprehensive mutagenesis study on a sequence specific HMG domain. Comparing how various residues influence sequence specific and non-sequence specific HMG domains helps us to rationalize their mode of action. Positively charged amino acids concentrated at the surface of sequence specific HMG domains recognize specific, linear AT-rich DNA segments. After the negative charges at the surface of the DNA are neutralized, the hydrophobic residues of the protein may intercalate DNA. Phenylalanine at position 12 plays a crucial role in the sequence specific HMG domain. The differences in pI values, the instability index, and DNA contact regions between sequence and non-sequence specific HMG domains are associated with their functional modes.",
author = "Nai-Wan Hsiao and Dharmaraj Samuel and Liu, {Yu Nan} and Chen, {Li Chuan} and Yang, {Tzu Ying} and Gurunathan Jayaraman and Lyu, {Ping Chiang}",
year = "2003",
month = "9",
day = "30",
doi = "10.1021/bi034678d",
language = "English",
volume = "42",
pages = "11183--11193",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "38",

}

Mutagenesis study on the zebra fish SOX9 high-mobility group : Comparison of sequence and non-sequence specific HMG domains. / Hsiao, Nai-Wan; Samuel, Dharmaraj; Liu, Yu Nan; Chen, Li Chuan; Yang, Tzu Ying; Jayaraman, Gurunathan; Lyu, Ping Chiang.

In: Biochemistry, Vol. 42, No. 38, 30.09.2003, p. 11183-11193.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Mutagenesis study on the zebra fish SOX9 high-mobility group

T2 - Comparison of sequence and non-sequence specific HMG domains

AU - Hsiao, Nai-Wan

AU - Samuel, Dharmaraj

AU - Liu, Yu Nan

AU - Chen, Li Chuan

AU - Yang, Tzu Ying

AU - Jayaraman, Gurunathan

AU - Lyu, Ping Chiang

PY - 2003/9/30

Y1 - 2003/9/30

N2 - A unique class of proteins, containing high-mobility group (HMG) domain(s), recognizes unusual DNA structures and/or bends specific to AT-rich linear double-stranded DNA. The DNA binding feature of these proteins is exhibited in the HMG domain(s). Although the sequence specific and non-sequence specific HMG domains exhibit very high degrees of sequence similarity, the reasons for the difference between their DNA recognition mechanisms are unclear. A series of zebra fish SOX9 HMG domain mutants was prepared in an effort to elucidate the importance of various residues on protein stability and DNA binding. This study is the first of a comprehensive mutagenesis study on a sequence specific HMG domain. Comparing how various residues influence sequence specific and non-sequence specific HMG domains helps us to rationalize their mode of action. Positively charged amino acids concentrated at the surface of sequence specific HMG domains recognize specific, linear AT-rich DNA segments. After the negative charges at the surface of the DNA are neutralized, the hydrophobic residues of the protein may intercalate DNA. Phenylalanine at position 12 plays a crucial role in the sequence specific HMG domain. The differences in pI values, the instability index, and DNA contact regions between sequence and non-sequence specific HMG domains are associated with their functional modes.

AB - A unique class of proteins, containing high-mobility group (HMG) domain(s), recognizes unusual DNA structures and/or bends specific to AT-rich linear double-stranded DNA. The DNA binding feature of these proteins is exhibited in the HMG domain(s). Although the sequence specific and non-sequence specific HMG domains exhibit very high degrees of sequence similarity, the reasons for the difference between their DNA recognition mechanisms are unclear. A series of zebra fish SOX9 HMG domain mutants was prepared in an effort to elucidate the importance of various residues on protein stability and DNA binding. This study is the first of a comprehensive mutagenesis study on a sequence specific HMG domain. Comparing how various residues influence sequence specific and non-sequence specific HMG domains helps us to rationalize their mode of action. Positively charged amino acids concentrated at the surface of sequence specific HMG domains recognize specific, linear AT-rich DNA segments. After the negative charges at the surface of the DNA are neutralized, the hydrophobic residues of the protein may intercalate DNA. Phenylalanine at position 12 plays a crucial role in the sequence specific HMG domain. The differences in pI values, the instability index, and DNA contact regions between sequence and non-sequence specific HMG domains are associated with their functional modes.

UR - http://www.scopus.com/inward/record.url?scp=0141456382&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0141456382&partnerID=8YFLogxK

U2 - 10.1021/bi034678d

DO - 10.1021/bi034678d

M3 - Article

VL - 42

SP - 11183

EP - 11193

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 38

ER -