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Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: Implications for barnase catalysis
Author(s) -
Roca Maite,
De Maria Leonardo,
Wodak Shoshana J.,
Moliner Vicente,
Tuñón Iñaki,
Giraldo Jesús
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21573
Subject(s) - chemistry , glycosidic bond , guanosine , protonation , stereochemistry , crystallography , ribonucleotide , cleavage (geology) , bond cleavage , guanine , deprotonation , reaction coordinate , ionic bonding , computational chemistry , nucleotide , catalysis , ion , organic chemistry , biochemistry , geotechnical engineering , fracture (geology) , engineering , gene , enzyme
To examine the possible relationship of guanine‐dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O 2 ′ . Similar energetic profiles featuring two minima corresponding to the anti and syn Gχ regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of ∼4 kcal/mol were obtained for the anti → syn transition. Structural analysis showed a remarkable sensitivity of the phosphate moiety to the conformation of the Gχ angle, suggesting a possible connection between this conformation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O 2 ′ P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O 2′ . The simulations revealed that the O 2 ′ attack along the syn Gχ was more favorable than that along the anti Gχ: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the OP bond formation; structurally, a lesser O 2 ′ P initial distance, and a better suited orientation for an in‐line attack was observed in the syn relative to the anti conformation. These results are consistent with the catalytically competent conformation of barnase–ribonucleotide complex, which requires a guanine syn conformation of the substrate to enable abstraction of the ribose H 2 ′ proton by the general base Glu73, thereby suggesting a coupling between the reactive substrate conformation and enzyme structure and mechanism. Proteins 2008. © 2007 Wiley‐Liss, Inc.