Hydrogen bonds in protein–DNA complexes: Where geometry meets plasticity

Coulocheri, Stavroula A.; Pigis, Diomidis G.; Papavassiliou, Kostas A.; Papavassiliou, Athanasios G.

doi:10.1016/j.biochi.2007.07.020

Cited by 81 publications

(65 citation statements)

References 63 publications

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“…However, Gln-48 recognizes bases with lower specificity only through a hydrogen bond. Previous studies indicate that a single hydrogen bond usually does not contribute to base specificity (1,31). Consistent with our interpretation, our mutation experiments indicated that Lys-47, but not Gln-48, is essential for DNA binding specificity of Ms6564.…”

Section: Discussionsupporting

confidence: 92%

Structural Basis for Interaction between Mycobacterium smegmatis Ms6564, a TetR Family Master Regulator, and Its Target DNA

Yang

Gao

et al. 2013

Journal of Biological Chemistry

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Background:The structural basis for interaction between a master regulator and DNA remains unclear. Results: We solved the crystal structures of a broad regulator Ms6564 and its protein-operator complex. Conclusion: Ms6564 binds DNA with strong affinity but makes flexible contacts with DNA. Significance: Ms6564 might slide more easily along the genomic DNA and extensively regulate the expression of diverse genes.

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Section: Discussionsupporting

confidence: 92%

Structural Basis for Interaction between Mycobacterium smegmatis Ms6564, a TetR Family Master Regulator, and Its Target DNA

Yang

Gao

et al. 2013

Journal of Biological Chemistry

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“…Those protein-DNA residues that have a distance of less than 3.5 Å are assumed to be realistic for hydrogen bond formation (Si et al, 2011). The studies of hydrogen bond formation are significant because these hydrogen bonds confer stability and specificity in the protein-DNA complexes (Coulocheri et al, 2007).…”

Section: Evaluation Of Docking Resultsmentioning

confidence: 99%

Identification and analysis of regulatory elements in the germin and germin-like proteins family promoters in rice

Ali¹,

Mahmood²

2015

Turk J Bot

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IntroductionGermins and germin-like proteins (GLPs) belong to the cupin superfamily of proteins, identified in several plants, including monocot, dicot, gymnosperms, Physarum polycephalum, and myxomycete (slime mold), after initial discovery of a protein marker germin in the germination of wheat seeds. Germin relatives have also been recognized in animals, prokaryotes, and fern spores (Lu et al., 2010).Germins and GLPs present major problems in classification due to their high sequence conservation in multiple plant species (Dunwell and Gane, 1998). A strong classification system is established by structural characteristics of these proteins due to the clustering of proteins with conserved functions (Agarwal et al., 2009). The proteins that have oxalate oxidase (OXO) enzymes activity, exclusively found within cereal plant species, are placed in a well-conserved homogeneous group called true germins (Carrillo et al., 2009;Davidson et al., 2009), while the germin-motif comprising proteins with an average of 50% amino acid sequence identity that either do not have OXO action or have not yet been allotted an enzymatic function are placed in a heterogeneous group called germinlike protein (Dunwell et al., 2008;Breen and Bellgard, 2010).To date, major research on germins and GLPs has been conducted on cereal plants, especially wheat, maize, barley, and rice. On the basis of various enzymatic activities, six germin subfamilies (GER1-6) have been described. GER1 (true germin proteins) has been shown to possess OXO activity, while GER2 has been shown to possess superoxide dismutase (SOD) action (Banerjee and Maiti, 2010). It has also been shown that the GER1 subfamily is important for early plant development and germination in plants (Federico et al., 2006). The GLPs with mostly unknown function in plant genomes have been classified into subfamilies Thornburg, 1999, 2000). In contrast to a true germin subfamily, both GLP1 and GLP2 subfamilies are limited to proteins of SOD action, while GLP3 is involved in phosphodiesterase activities. However, recently more subdivisions were suggested (Breen and Bellgard, 2010). A key feature of the germin and GLP subdivisions was the conservation of a motif derived from that of the cupin superfamily (Carter and Thornburg,

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“…Protein-nucleic acid recognition can be understood by atomic interactions between amino acids and nucleotides (Rhodes and Stephen, 2000;Lavery, 2005;Coulocheri et al, 2007;Hé garat et al, 2008). These complexes have been analysed by several authors, for more than 30 years.…”

Section: Protein-dna Interactionsmentioning

confidence: 99%

Amino acids–nucleotides biomolecular recognition: from biological occurrence to affinity chromatography

Sousa

Cruz

Queiroz

2010

J of Molecular Recognition

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aIn this review, the protein-DNA interactions are discussed considering different perspectives, and the biological occurrence of this interaction is explained at atomic level. The evaluation of the amino acid-nucleotide recognition has been investigated analysing datasets for predicting the association preferences and the geometry that favours the interaction.Based on this knowledge, an affinity chromatographic method was developed also exploiting this biological favoured contact. In fact, the implementation of this technique brings the possibility to apply the concept of molecular interactions to the development of new purification methodologies. In addition, the integration of the information recovered by all the different perspectives can bring new insights about some biological mechanisms, though not totally clarified.

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Hydrogen bonds in protein–DNA complexes: Where geometry meets plasticity

Cited by 81 publications

References 63 publications

Structural Basis for Interaction between Mycobacterium smegmatis Ms6564, a TetR Family Master Regulator, and Its Target DNA

Structural Basis for Interaction between Mycobacterium smegmatis Ms6564, a TetR Family Master Regulator, and Its Target DNA

Identification and analysis of regulatory elements in the germin and germin-like proteins family promoters in rice

Amino acids–nucleotides biomolecular recognition: from biological occurrence to affinity chromatography

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