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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
Abstrakt
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein–DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation.
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Informacje szczegółowe
- Kategoria:
- Publikacja w czasopiśmie
- Typ:
- artykuł w czasopiśmie wyróżnionym w JCR
- Opublikowano w:
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NUCLEIC ACIDS RESEARCH
nr 45,
wydanie 13,
strony 7643 - 7654,
ISSN: 0305-1048 - Język:
- angielski
- Rok wydania:
- 2017
- Opis bibliograficzny:
- Wieczór M., Czub J.: How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1// NUCLEIC ACIDS RESEARCH. -Vol. 45, iss. 13 (2017), s.7643-7654
- DOI:
- Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1093/nar/gkx534
- Weryfikacja:
- Politechnika Gdańska
wyświetlono 172 razy