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Aromatic-aromatic interactions in structures of proteins and protein-DNA complexes: a study based on orientation and distance.

ABSTRACT: Interactions between the aromatic amino acid residues have a significant influence on the protein structures and protein-DNA complexes. These interactions individually provide little stability to the structure; however, together they contribute significantly to the conformational stability of the protein structure. In this study, we focus on the four aromatic amino acid residues and their interactions with one another and their individual interactions with the four nucleotide bases. These are analyzed in order to determine the extent to which their orientation and the number of interactions contribute to the protein and protein-DNA complex structures.

SUBMITTER: Anjana R

PROVIDER: S-EPMC3530875 | biostudies-other | 2012

REPOSITORIES: biostudies-other

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Aromatic-aromatic interactions in structures of proteins and protein-DNA complexes: a study based on orientation and distance.

Anjana Ramnath R Vaishnavi Marthandan Kirti MK Sherlin Durairaj D Kumar Surapaneni Pavan SP Naveen Kora K Kanth Pasam Sandeep PS Sekar Kanagaraj K

Bioinformation 20121208 24

Interactions between the aromatic amino acid residues have a significant influence on the protein structures and protein-DNA complexes. These interactions individually provide little stability to the structure; however, together they contribute significantly to the conformational stability of the protein structure. In this study, we focus on the four aromatic amino acid residues and their interactions with one another and their individual interactions with the four nucleotide bases. These are an ...[more]

PMID: 23275723

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Project description:DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions. Accurate prediction of such target sequences, often represented by position weight matrices (PWMs), is an important step to understand many biological processes. Recent studies have shown that knowledge-based potential functions can be applied on protein-DNA co-crystallized structures to generate PWMs that are considerably consistent with experimental data. However, this success has not been extended to DNA-binding proteins lacking co-crystallized structures. This study aims at investigating the possibility of predicting the DNA sequences bound by DNA-binding proteins from the proteins' unbound structures (structures of the unbound state). Given an unbound query protein and a template complex, the proposed method first employs structure alignment to generate synthetic protein-DNA complexes for the query protein. Once a complex is available, an atomic-level knowledge-based potential function is employed to predict PWMs characterizing the sequences to which the query protein can bind. The evaluation of the proposed method is based on seven DNA-binding proteins, which have structures of both DNA-bound and unbound forms for prediction as well as annotated PWMs for validation. Since this work is the first attempt to predict target sequences of DNA-binding proteins from their unbound structures, three types of structural variations that presumably influence the prediction accuracy were examined and discussed. Based on the analyses conducted in this study, the conformational change of proteins upon binding DNA was shown to be the key factor. This study sheds light on the challenge of predicting the target DNA sequences of a protein lacking co-crystallized structures, which encourages more efforts on the structure alignment-based approaches in addition to docking- and homology modeling-based approaches for generating synthetic complexes.

Dataset Information

Aromatic-aromatic interactions in structures of proteins and protein-DNA complexes: a study based on orientation and distance.

Publications

Aromatic-aromatic interactions in structures of proteins and protein-DNA complexes: a study based on orientation and distance.

Similar Datasets

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