Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase

Horton, J.R.; Liebert, Kirsten; Hattman, Stanley; Jeltsch, Albert; Cheng, Xiaodong

doi:10.1016/j.cell.2005.02.021

Cited by 93 publications

(130 citation statements)

References 53 publications

(62 reference statements)

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“…It has been found that proteins contact the DNA using approximately the same binding site and orientation in all complexes (10)(11)(12)(13)(14)(15)(16)(17)(18). In nonspecific complexes, the interface between the two molecules is stabilized by electrostatic interactions between charged protein side chains and the DNA backbone (1,(9)(10)(11)(12)(13)(14)(15)(16)(17).…”

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confidence: 99%

“…In nonspecific complexes, the interface between the two molecules is stabilized by electrostatic interactions between charged protein side chains and the DNA backbone (1,(9)(10)(11)(12)(13)(14)(15)(16)(17). In complexes with target DNA sites, there are also interactions between side chains and bases (10)(11)(12)(13)(14)(15)(16)(17). Strikingly, some so-called "dual-role residues" interact with the DNA backbone in nonspecific complexes and with DNA bases in specific complexes (14,15,17) or form different interactions with bases in nonspecific and specific complexes (13).…”

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confidence: 99%

“…In complexes with target DNA sites, there are also interactions between side chains and bases (10)(11)(12)(13)(14)(15)(16)(17). Strikingly, some so-called "dual-role residues" interact with the DNA backbone in nonspecific complexes and with DNA bases in specific complexes (14,15,17) or form different interactions with bases in nonspecific and specific complexes (13). These residues are postulated to form transient "nonnative" interactions.…”

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confidence: 99%

“…The structures of several proteins in complex with target DNA sites, variants thereof and random DNA sequences, have been solved and used as models for transient intermediates of specific recognition (10)(11)(12)(13)(14)(15)(16)(17). It has been found that proteins contact the DNA using approximately the same binding site and orientation in all complexes (10)(11)(12)(13)(14)(15)(16)(17)(18).…”

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confidence: 99%

“…The kinetics of DNA sequence recognition (3,4) often involve multistate kinetic routes with populated intermediates (4)(5)(6)(7)(8). The build up of molecular interactions along multistate routes has been deduced indirectly from structural and thermodynamic studies (1)(2)(3)(9)(10)(11)(12)(13)(14)(15)(16)(17), but kinetic characterization of intermediates and transition state ensembles is still scarce.…”

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Experimental snapshots of a protein-DNA binding landscape

Sánchez

Ferreiro

Dellarole

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Protein recognition of DNA sites is a primary event for gene function. Its ultimate mechanistic understanding requires an integrated structural, dynamic, kinetic, and thermodynamic dissection that is currently limited considering the hundreds of structures of protein-DNA complexes available. We describe a protein-DNA-binding pathway in which an initial, diffuse, transition state ensemble with some nonnative contacts is followed by formation of extensive nonnative interactions that drive the system into a kinetic trap. Finally, nonnative contacts are slowly rearranged into native-like interactions with the DNA backbone. Dissimilar protein-DNA interfaces that populate along the DNA-binding route are explained by a temporary degeneracy of protein-DNA interactions, centered on "dual-role" residues. The nonnative species slow down the reaction allowing for extended functionality.energy landscape | human papillomavirus E2 protein | kinetic trap | kinetics | protein-DNA interaction

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Experimental snapshots of a protein-DNA binding landscape

Sánchez

Ferreiro

Dellarole

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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DamIP: Using Mutant DNA Adenine Methyltransferase to Study DNA‐Protein Interactions In Vivo

Xiao

Moore

2011

CP Molecular Biology

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DamIP is a new method for studying DNA-protein interaction in vivo. A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis, e.g. real-time PCR, microarray or high-throughput sequencing. This method is simple and does not require either protein-DNA crosslinking or a specific antibody to the protein of interest. This unit describes the application of this method for the identification of DNA binding sites in vivo.

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Base Flipping

Cheng¹,

Roberts²

2010

Encyclopedia of Life Sciences

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Base flipping involves the rotation of backbone bonds in double‐stranded deoxyribonucleic acid (DNA) to expose an out‐of‐stack base, which can then be a substrate for an enzyme‐catalysed chemical reaction or for a specific protein‐binding interaction. The phenomenon is fully established structurally and experimentally for DNA methyltransferases , for several key DNA repair enzymes, and for a few nonenzymatic DNA‐binding proteins involved in the DNA methylation and repair pathways, and is likely to prove general for enzymes or proteins that require access to unpaired, mismatched, damaged or modified bases. Recent results suggest that it may also be involved in the initial opening of a DNA helix during the initiation of transcription. Key Concept: Base flipping is a key mechanism used by many DNA and RNA modifying enzymes, including DNA repair enzymes, to gain access to one or more bases in a double helix.

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Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase

Cited by 93 publications

References 53 publications

Experimental snapshots of a protein-DNA binding landscape

Experimental snapshots of a protein-DNA binding landscape

DamIP: Using Mutant DNA Adenine Methyltransferase to Study DNA‐Protein Interactions In Vivo

Base Flipping

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