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Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI.

Abstract：

:Sequence-specific interactions between proteins and DNA are essential for a variety of biological functions. The (cytosine-C5)-methyltransferase from HhaI (M.HhaI) specifically modifies the second base in GCGC sequences, employing a base flipping mechanism to access the target base being chemically modified. The mechanism of sequence-specific recognition of M.HhaI is not evident based on crystallographic structures, leading to the suggestion that recognition is linked to the flipping event itself, a process that may be referred to as energetic recognition. Using computational methods, it is shown that the free energy barriers to flipping are significantly higher in non-cognate versus the cognate sequence, supporting the energetic recognition mechanism. Energetic recognition is imparted by two protein "selectivity filters" that function via a "web" of protein-DNA interactions in short-lived, high energy states present along the base flipping pathway. Other sequence-specific DNA binding proteins whose function involves significant distortion of DNA's conformation may use a similar recognition mechanism.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Huang N,MacKerell AD Jr

doi

10.1016/j.jmb.2004.10.042

keywords:

subject

Has Abstract

pub_date

2005-01-14 00:00:00

pages

265-74

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(04)01334-8

journal_volume

345

pub_type

杂志文章

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