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
  • [21] Overcharging of the Zinc Ion in the Structure of the Zinc-Finger Protein Is Needed for DNA Binding Stability
    Nguyen, Ly H.
    Tran, Tuyen T.
    Lien Thi Ngoc Truong
    Hanh Hong Mai
    Nguyen, Toan T.
    BIOCHEMISTRY, 2020, 59 (13) : 1378 - 1390
  • [22] SPECIFIC DNA-RNA HYBRID BINDING BY ZINC-FINGER PROTEINS
    SHI, YG
    BERG, JM
    SCIENCE, 1995, 268 (5208) : 282 - 284
  • [23] Donor DNA Utilization During Gene Targeting with Zinc-Finger Nucleases
    Beumer, Kelly J.
    Trautman, Jonathan K.
    Mukherjee, Kusumika
    Carroll, Dana
    G3-GENES GENOMES GENETICS, 2013, 3 (04): : 657 - 664
  • [24] Disease Related Mutation Effects on Conformations and Dynamics of the Zinc-Finger NEMO
    Godwin, Ryan
    Gmeiner, William
    Salsbury, Freddie
    PROTEIN SCIENCE, 2015, 24 : 164 - 165
  • [25] Towards understanding the molecular recognition process in prokaryotic zinc-finger domain
    Russo, Luigi
    Palmieri, Maddalena
    Caso, Jolanda Valentina
    D' Abrosca, Gianluca
    Diana, Donatella
    Malgieri, Gaetano
    Baglivo, Ilaria
    Isernia, Carla
    Pedone, Paolo V.
    Fattorusso, Roberto
    EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 2015, 91 : 100 - 108
  • [26] Solution structure and DNA binding of the zinc-finger domain from DNA ligase IIIα
    Kulczyk, AW
    Yang, JC
    Neuhaus, D
    JOURNAL OF MOLECULAR BIOLOGY, 2004, 341 (03) : 723 - 738
  • [27] Advances in the molecular mechanisms of zinc-finger transcription factors in neurodevelopmental disorders
    Wang, Hailin
    Yang, Ying
    Ni, Ziwei
    Qiao, Xiaoting
    Guo, Yaqian
    Wang, Xiaomin
    Cao, Duo
    Wang, Yayun
    Ruan, Cailian
    IBRO NEUROSCIENCE REPORTS, 2025, 18 : 409 - 413
  • [28] An orphan nuclear receptor lacking a zinc-finger DNA-binding domain: Interaction with several nuclear receptors
    Masuda, N
    Yasumo, H
    Tamura, T
    Hashiguchi, N
    Furusawa, T
    Tsukamoto, T
    Sadano, H
    Osumi, T
    BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION, 1997, 1350 (01): : 27 - 32
  • [29] Cooperative dynamics of PARP-1 zinc-finger domains in the detection of DNA single-strand breaks
    Sarma, Parvathy A. P.
    Abbadie, Corinne
    Cleri, Fabrizio
    SCIENTIFIC REPORTS, 2024, 14 (01):
  • [30] An orphan nuclear receptor lacking a zinc-finger DNA-binding domain: interaction with several nuclear receptors
    Masuda, N.
    Yasumo, H.
    Tamura, T.
    Hashiguchi, N.
    B B A - Biomembranes, 1350 (01):
12345