Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

Jakubec, Dávid; Laskowski, Roman A.; Vondrášek, Jiřı́

doi:10.1371/journal.pone.0158704

Cited by 12 publications

(25 citation statements)

References 67 publications

(85 reference statements)

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“…Explore the relationship between binding affinity and structural/sequence-based features of proteins and nucleic acids to understand the molecular mechanism of protein–nucleic acid interactions ( 25 , 26 ). ProNAB provides a wealth of data for the binding affinities of protein–nucleic acid complexes, which can be used to elucidate the important features based on structure and function, which governs the affinities.…”

Section: Applicationsmentioning

confidence: 99%

ProNAB: database for binding affinities of protein–nucleic acid complexes and their mutants

Harini

Srivastava

Kulandaisamy

et al. 2021

Nucleic Acids Research

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Protein–nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation and packaging. The binding affinities of protein–DNA and protein–RNA complexes are important for elucidating the mechanism of protein–nucleic acid recognition. Although experimental data on binding affinity are reported abundantly in the literature, no well-curated database is currently available for protein–nucleic acid binding affinity. We have developed a database, ProNAB, which contains more than 20 000 experimental data for the binding affinities of protein–DNA and protein–RNA complexes. Each entry provides comprehensive information on sequence and structural features of a protein, nucleic acid and its complex, experimental conditions, thermodynamic parameters such as dissociation constant (Kd), binding free energy (ΔG) and change in binding free energy upon mutation (ΔΔG), and literature information. ProNAB is cross-linked with GenBank, UniProt, PDB, ProThermDB, PROSITE, DisProt and Pubmed. It provides a user-friendly web interface with options for search, display, sorting, visualization, download and upload the data. ProNAB is freely available at https://web.iitm.ac.in/bioinfo2/pronab/ and it has potential applications such as understanding the factors influencing the affinity, development of prediction tools, binding affinity change upon mutation and design complexes with the desired affinity.

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Section: Applicationsmentioning

confidence: 99%

ProNAB: database for binding affinities of protein–nucleic acid complexes and their mutants

Harini

Srivastava

Kulandaisamy

et al. 2021

Nucleic Acids Research

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“…The IE calculations were performed using parameters derived from AMBER parm94 (DNA) ( 15 ) and parm99 (protein) ( 9 , 16 ) classical molecular mechanical force fields and, where applicable, a GB/SA implicit solvent and their technical details were described in detail elsewhere ( 17 , 18 ). The amino acid–deoxyribonucleotide interaction analysis part of the web server allows the user to view the interaction energies of the amino acid–DNA base or amino acid–deoxyribonucleoside monophosphate (dNMP) pairs.…”

Section: Amino Acid–nucleotide Interaction Analysis Toolmentioning

confidence: 99%

“…The amino acid–deoxyribonucleotide interaction analysis part of the web server allows the user to view the interaction energies of the amino acid–DNA base or amino acid–deoxyribonucleoside monophosphate (dNMP) pairs. These pairs were extracted from the structures of 1584 protein–DNA complexes solved by X-ray crystallography to a resolution better than 2.5 A deposited in the RCSB PDB ( 17 , 19 ). As such, they cover the configurational variability of amino acid–deoxyribonucleotide contacts under the constraining requirements of the protein–DNA interface.…”

Section: Amino Acid–nucleotide Interaction Analysis Toolmentioning

confidence: 99%

“…Up to six such clusters were identified in each distribution as described in our previous works ( 17 , 18 ). In each amino acid cluster within each distribution, a single amino acid–DNA residue pair, called cluster representative, can be defined as the pair containing the amino acid which has the lowest RMSD of the atomic positions from all the other members of that cluster ( 17 , 18 , 20 ). The amino acid–deoxyribonucleotide interaction analysis web server interface is shown in Figure 2 .…”

Section: Amino Acid–nucleotide Interaction Analysis Toolmentioning

confidence: 99%

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Amino Acid Interaction (INTAA) web server

Galgonek

Vymětal

Jakubec

et al. 2017

Nucleic Acids Research

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Large biomolecules—proteins and nucleic acids—are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein–DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein–DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid–deoxyribonucleotide pairs found at the protein–DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations.

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“…Moreover, they cannot be applied to the entire genome efficiently. With the development of gene sequence project and gene expression profile, much efforts turn to recognize the TFBSs by computing-based methods [8][9][10].…”

Section: Introductionmentioning

confidence: 99%

Discovery of DNA Motif Utilising an Integrated Strategy Based on Random Projection and Particle Swarm Optimization

Sun

et al. 2019

Mathematical Problems in Engineering

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During the process of gene expression and regulation, the DNA genetic information can be transferred to protein by means of transcription. The recognition of transcription factor binding sites can help to understand the evolutionary relations among different sequences. Thus, the problem of recognition of transcription factor binding sites, i.e., motif recognition, plays an important role for understanding the biological functions or meanings of sequences. However, when the established search space processes much noise subsequences, many optimization algorithms tend to be trapped into local optimum. In order to solve this problem, a particle swarm optimization and random projection-based algorithm (PSORPS) is proposed for recognizing DNA motifs. First, a random projection strategy is employed to filter the noise subsequences for constructing the objective space. Moreover, the sequence segments distributed in the majority of DNA sequences can be obtained and used for the population initialization of PSO. Then, the motifs of DNA sequences can be automatically searched by using a designed PSO algorithm in the constructed l-mer objective space. Finally, to alleviate the base deviation and further improve the recognition accuracy, the two operators of associated drift and independent drift are performed on the optimization results obtained by PSO. The experiments are conducted on real-world biological datasets, and the experimental results verify the effectiveness of the proposed algorithm.

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Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

Cited by 12 publications

References 67 publications

ProNAB: database for binding affinities of protein–nucleic acid complexes and their mutants

ProNAB: database for binding affinities of protein–nucleic acid complexes and their mutants

Amino Acid Interaction (INTAA) web server

Discovery of DNA Motif Utilising an Integrated Strategy Based on Random Projection and Particle Swarm Optimization

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