Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA

被引：2
|
作者：
Rodriguez, Jessica [1 ,2 ,3 ]
Battistini, Federica [3 ,4 ]
Learte-Aymami, Soraya [1 ,2 ]
Orozco, Modesto [3 ,4 ]
Mascarenas, Jose L. [1 ,2 ]
机构：
[1] Univ Santiago De Compostela, Ctr Singular Invest Quim Biol & Mat Mol CIQUS, Rua Jenaro De La Fuente S-N, Santiago De Compostela 15782, Spain
[2] Univ Santiago De Compostela, Dept Quim Organ, Rua Jenaro De La Fuente S-N, Santiago De Compostela 15782, Spain
[3] Barcelona Inst Sci & Technol BIST, Inst Res Biomed IRB Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain
[4] Univ Barcelona, Dept Biochem & Mol Biol, Barcelona 08028, Spain
来源：
RSC CHEMICAL BIOLOGY | 2023年 / 4卷 / 07期
关键词：
BINDING PROTEINS; RECOGNITION; PEPTIDE; COMPLEX; DOMAIN; SIMULATION; SEQUENCES; SELECTION; VERSATILE; DESIGN;
D O I：
10.1039/d3cb00053b
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
引用
收藏
页码：486 / 493
页数：8
相关论文
共 50 条
  • [31] NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex
    Tsui, V
    Radhakrishnan, I
    Wright, PE
    Case, DA
    JOURNAL OF MOLECULAR BIOLOGY, 2000, 302 (05) : 1101 - 1117
  • [32] DNA RECOGNITION OF C2H2 ZINC-FINGER PROTEINS - EVIDENCE FOR A ZINC-FINGER-SPECIFIC DNA RECOGNITION CODE
    THIESEN, HJ
    BACH, C
    ANNALS OF THE NEW YORK ACADEMY OF SCIENCES-SERIES, 1993, 684 : 246 - 249
  • [33] Efficient double-stranded DNA cleavage by artificial zinc-finger nucleases composed of one zinc-finger protein and a single-chain FokI dimer
    Mino, Takashi
    Aoyama, Yasuhiro
    Sera, Takashi
    JOURNAL OF BIOTECHNOLOGY, 2009, 140 (3-4) : 156 - 161
  • [34] Novel role of zinc-finger protein 518 in heterochromatin formation on α-satellite DNA
    Ohta, Shinya
    Ohzeki, Jun-Ichirou
    Sato, Nobuko
    Tanizawa, Hideki
    Chung, Claire Yik-Lok
    Noma, Ken-Ichi
    Masumoto, Hiroshi
    NUCLEIC ACIDS RESEARCH, 2024, 53 (02)
  • [35] Speed-stability paradox in DNA-scanning by zinc-finger proteins
    Iwahara, Junji
    Levy, Yaakov
    TRANSCRIPTION-AUSTIN, 2013, 4 (02): : 58 - 61
  • [36] Sequence-specific recognition of methylated DNA by human zinc-finger proteins
    Sasai, Nobuhiro
    Nakao, Mitsuyoshi
    Defossez, Pierre-Antoine
    NUCLEIC ACIDS RESEARCH, 2010, 38 (15) : 5015 - 5022
  • [37] STRUCTURES OF DNA-BINDING MUTANT ZINC-FINGER DOMAINS - IMPLICATIONS FOR DNA-BINDING
    HOFFMAN, RC
    HORVATH, SJ
    KLEVIT, RE
    PROTEIN SCIENCE, 1993, 2 (06) : 951 - 965
  • [38] DNA-BINDING AND TRANSCRIPTION REGULATION BY THE PROMYELOCYTIC LEUKEMIA ZINC-FINGER PROTEIN
    LI, JY
    ENGLISH, MA
    BISHT, S
    WAXMAN, S
    LICHT, JD
    BLOOD, 1994, 84 (10) : A41 - A41
  • [39] MOLECULAR-BASIS FOR NUCLEIC-ACID RECOGNITION BY ZINC-FINGER PROTEINS
    WRIGHT, PE
    BRUSCHWEILER, R
    CLEMENS, K
    FOSTER, M
    GOTTESFELD, J
    JAHNKE, W
    LIAO, X
    MILLAR, D
    WUTTKE, D
    JOURNAL OF CELLULAR BIOCHEMISTRY, 1995, : 16 - 16
  • [40] Molecular cloning and characterization of FX3, a novel zinc-finger protein
    Xu, F
    Wang, Y
    Hall, FL
    ONCOLOGY REPORTS, 2000, 7 (05) : 995 - 1001
12345