Molecular Basis of the Recognition Process:  Hydrogen-Bonding Patterns in the Guanine Primary Recognition Site of Ribonuclease T1

Gu, Jiande; Wang, Jing; Leszczyński, Jerzy

doi:10.1021/jp061360x

Cited by 12 publications

(12 citation statements)

References 43 publications

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“…Table II demonstrates the geometrical changes of adenine during the complex process. The NPA charge distributions on adenine are calculated for its relationship with the recognition between bases and proteins 58 and also listed in Table II as well as the hydrogen bonding energies.…”

Section: Resultsmentioning

confidence: 99%

Retinal cone topography of artiodactyl mammals: Influence of body height and habitat

Schiviz

Ruf

Kuebber–Heiss

et al. 2008

J of Comparative Neurology

130

103

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This study addresses the correlation of retinal topography with factors such as the visual environment, life style, and behavior for a major mammalian group, the artiodactyls. To provide a broader basis for semiquantitative comparison, short-wavelength-sensitive (S)- and middle-to-long-wavelength-sensitive (M)-opsin cone receptor populations from 25 species from five artiodactyl families and of the African elephant were labeled and sampled. The resulting topographic maps were analyzed with respect to the position and extension of high-density regions. For better parameter differentiation, systematic relationships were statistically normalized. In all species examined, two classes of cones have been detected. In most species, the S-cone maxima were located in the temporodorsal retina, but there are exceptions such as the roe deer with accumulation in the ventral retina. For M-cones, as a consequence of their role in terrain/food assessment and predator detection, the standard topography is L-shaped: a horizontal visual streak including a temporal area centralis is extended by a temporal rim. Its extension is correlated with the animal's body height (P = 0.0017): small species (pudu, mouse deer) tend to have a visual streak only, whereas the giraffe shows a complete dorsal arch of elevated densities. Furthermore, a size-independent habitat correlation was revealed for a similar M-cone pattern (P < 0.0001): mountainous species show a striking specialization around the dorsal retina, pointing to the importance of the inferior visual field in precipitous terrain.

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Section: Resultsmentioning

confidence: 99%

Retinal cone topography of artiodactyl mammals: Influence of body height and habitat

Schiviz

Ruf

Kuebber–Heiss

et al. 2008

J of Comparative Neurology

130

103

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“…These observations are entirely consistent with methylation of G1405 by Sgm. The introduction of the methyl group on G1405 would render this position resistant to RNase T1 cleavage (35), resulting in a composite fragment for nts 1402–1415. This sequence from 16S rRNA has three methyl groups originating from ‘house-keeping’ MTs that are located on C1402 (dimethylated) and C1407 (36) (Figure 1C).…”

Section: Resultsmentioning

confidence: 99%

Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics

Savic

Lovrić

Tomić

et al. 2009

Nucleic Acids Research

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The 16S ribosomal RNA methyltransferase enzymes that modify nucleosides in the drug binding site to provide self-resistance in aminoglycoside-producing micro-organisms have been proposed to comprise two distinct groups of S-adenosyl-l-methionine (SAM)-dependent RNA enzymes, namely the Kgm and Kam families. Here, the nucleoside methylation sites for three Kgm family methyltransferases, Sgm from Micromonospora zionensis, GrmA from Micromonospora echinospora and Krm from Frankia sp. Ccl3, were experimentally determined as G1405 by MALDI-ToF mass spectrometry. These results significantly extend the list of securely characterized G1405 modifying enzymes and experimentally validate their grouping into a single enzyme family. Heterologous expression of the KamB methyltransferase from Streptoalloteichus tenebrarius experimentally confirmed the requirement for an additional 60 amino acids on the deduced KamB N-terminus to produce an active methyltransferase acting at A1408, as previously suggested by an in silico analysis. Finally, the modifications at G1405 and A1408, were shown to confer partially overlapping but distinct resistance profiles in Escherichia coli. Collectively, these data provide a more secure and systematic basis for classification of new aminoglycoside resistance methyltransferases from producers and pathogenic bacteria on the basis of their sequences and resistance profiles.

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“…Cherstvy [21] 考察了 DNA-蛋白质复合物界面上的电荷分布, 发现在 DNA-蛋白质复合物中带正电荷的氨基酸沿着 DNA 双链的分布是不均匀的. Gu 等 [22] 研究了鸟嘌呤与核糖核酸酶 T1 识别片段的氢键作用, 发现侧链氢键在二者结合中起重要作用且侧链氢键与主链氢键相互加强. 这些研究工作加深了我们对生物体系中氢键作用的认识.…”

Section: 引言unclassified

Site Preferences of Nucleic Acid Bases Hydrogen Bonding to Glycine Dipeptide

Liu¹,

Yu²,

Huang³

et al. 2015

Acta Chim. Sinica

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The optimal structures of twenty-eight hydrogen-bonded complexes, containing one glycine dipeptide molecule and one of the nucleic acid base adenine, thymine, uracil, guanine and cytosine, were obtained at the B3LYP/6-31＋G(d,p) level. The binding energies of these complexes were further evaluated at the CP-corrected MP2/aug-cc-pVTZ level. The site-preferences of the five nucleic acid bases hydrogen bonding to glycine dipeptide are explored. The calculation results show that any of the five nucleic acid bases can hydrogen bond to glycine dipeptide through different binding site. The hydrogen-bonded complexes formed through site A3 of adenine, site T1 of thymine, site U1 of uracil, site C1 of cytosine and site G3 of guanine are the most stable. The stability of the hydrogen-bonded complexes is associated with the enthalpy change of the protonation/deprotonation reaction of the nucleic acid bases. The more negative the enthalpy change of the protonation reaction or the smaller the enthalpy change of the deprotonation reaction, the more stable the hydrogen-bonded complexes.

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Molecular Basis of the Recognition Process: Hydrogen-Bonding Patterns in the Guanine Primary Recognition Site of Ribonuclease T1

Cited by 12 publications

References 43 publications

Retinal cone topography of artiodactyl mammals: Influence of body height and habitat

Retinal cone topography of artiodactyl mammals: Influence of body height and habitat

Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics

Site Preferences of Nucleic Acid Bases Hydrogen Bonding to Glycine Dipeptide

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