The hypermodified Y base electrostatic contribution to the energetics of the codon-anticodon pairing in tRNAPhe

Werneck, Araken S.; Neto, Marçal de Oliveira; Maia, Elaine Rose

doi:10.1016/s0166-1280(97)00198-x

Cited by 8 publications

(10 citation statements)

References 21 publications

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“…2b) is that O (23) interacts with HC(15) instead of O(22) as compared to PCILO most stable structure (Fig. 2a) which would be important feature during codon-anticodon interactions according to previous studies [31,32] and PM3 most stable structure (Fig. 1b).…”

Section: Conformational Preferences Of Wybutine (Yw) By Pcilo Methodsmentioning

confidence: 62%

“…1b). Hence, the atoms O (22) and O(23) may not be available to participate in bonding with codons if present at 3 side as shown in earlier study [31,32]. Another slightly higher energy (0.4 kcal/mol) alternative conformation (Fig.…”

Section: Conformational Preferences Of Wybutine (Yw) By Semi-empiricamentioning

confidence: 70%

“…(15). Hence, the carboxymethyl (-COOCH3) group of wybutine side chain may also have interactions with codons if present at 3 -end as found in PM3 most stable structure and as suggested by earlier theoretical studies [31,32].…”

Section: Methodsmentioning

confidence: 80%

“…1b) is stabilized by intramolecular hydrogen bonding (Table 1) (23). Hence, the carboxy methyl (-COOCH3) group of wybutine side chain may have certain interactions with codons if present at 3 -end and such interactions are also discussed by Neto and co-workers [31,32].…”

Section: Conformational Preferences Of Wybutine (Yw) By Semi-empiricamentioning

confidence: 94%

“…It has been demonstrated by using semi-empirical quantum chemical AM1 calculations that some noticeable conformational change occurs in the wybutine side chain at 37th position when first uracil of codon UUC binds to the A36 of anticodon GAA of tRNA Phe [31]. It has also been concluded that the hypermodified Y base may provide electrostatic interactions for the energetic of codon-anticodon pairing [32] which may consequently help in gene expression. Molecular dynamics simulation study of yeast tRNA Phe anticodon domain in the presence and absence of codon trinucleotides UUC and UUU also show that there are small but identifiable differences found near the Y37 base [33].…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37th position in anticodon loop of tRNAPhe

Kumbhar

Sonawane

2011

Journal of Molecular Graphics and Modelling

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Section: Conformational Preferences Of Wybutine (Yw) By Pcilo Methodsmentioning

confidence: 62%

Section: Conformational Preferences Of Wybutine (Yw) By Semi-empiricamentioning

confidence: 70%

Section: Methodsmentioning

confidence: 80%

Section: Conformational Preferences Of Wybutine (Yw) By Semi-empiricamentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37th position in anticodon loop of tRNAPhe

Kumbhar

Sonawane

2011

Journal of Molecular Graphics and Modelling

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Reassociation of fragments using multicentered multipolar expansions: peptide junction treatments to investigate electrostatic properties of proteins

Dardenne¹,

Werneck²,

Neto³

et al. 2001

J Comput Chem

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ABSTRACT:We report an analysis of three schemes for fragment reassociation using multicentered multipolar expansions derived from ab initio quantum wave functions at the Hartree-Fock/6-31G * LCAO level, two of them involving single-bond partitioning in the peptide bond region, and the third one using a partially overlapping procedure based on a methodology proposed by Vigné-Maeder 21 (OME-overlap of multipolar expansions-reassociation method). The effects of different peptide junction treatments in the derivation of molecular electrostatic potentials and molecular electric fields of three peptide sequences are discussed. The results show that the OME reassociation method gives a better and a more homogeneous description of both the potential and the electric field than the other two treatments. We conclude that the OME method is the most indicated for studies involving electrostatic properties of proteins. Our results also indicate that the use of multicentered multipolar expansions coupled to the OME treatment is the best choice in protein studies including solvent effects using, for example, a continuum boundary method to solve the linearized Poisson-Boltzmann equation.

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Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25 (؊) …His159 (؉) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG3(His159)-ND1 direction; (ii) the electrostatic profile has a saddlepoint character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E SG3 ND1 attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator. Proteins 2003;52:236 -253.

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The hypermodified Y base electrostatic contribution to the energetics of the codon-anticodon pairing in tRNAPhe

Cited by 8 publications

References 21 publications

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37th position in anticodon loop of tRNAPhe

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37th position in anticodon loop of tRNAPhe

Reassociation of fragments using multicentered multipolar expansions: peptide junction treatments to investigate electrostatic properties of proteins

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

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