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Conformation-dependent restraints for polynucleotides: the sugar moiety.

ABSTRACT: Stereochemical restraints are commonly used to aid the refinement of macromolecular structures obtained by experimental methods at lower resolution. The standard restraint library for nucleic acids has not been updated for over two decades and needs revision. In this paper, geometrical restraints for nucleic acids sugars are derived using information from high-resolution crystal structures in the Cambridge Structural Database. In contrast to the existing restraints, this work shows that different parts of the sugar moiety form groups of covalent geometry dependent on various chemical and conformational factors, such as the type of ribose or the attached nucleobase, and ring puckering or rotamers of the glycosidic (?) or side-chain (?) torsion angles. Moreover, the geometry of the glycosidic link and the endocyclic ribose bond angles are functionally dependent on ? and sugar pucker amplitude (?m), respectively. The proposed restraints have been positively validated against data from the Nucleic Acid Database, compared with an ultrahigh-resolution Z-DNA structure in the Protein Data Bank, and tested by re-refining hundreds of crystal structures in the Protein Data Bank. The conformation-dependent sugar restraints presented in this work are publicly available in REFMAC, PHENIX and SHELXL format through a dedicated RestraintLib web server with an API function.

SUBMITTER: Kowiel M

PROVIDER: S-EPMC6954431 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Conformation-dependent restraints for polynucleotides: the sugar moiety.

Kowiel Marcin M Brzezinski Dariusz D Gilski Miroslaw M Jaskolski Mariusz M

Nucleic acids research 20200101 2

Stereochemical restraints are commonly used to aid the refinement of macromolecular structures obtained by experimental methods at lower resolution. The standard restraint library for nucleic acids has not been updated for over two decades and needs revision. In this paper, geometrical restraints for nucleic acids sugars are derived using information from high-resolution crystal structures in the Cambridge Structural Database. In contrast to the existing restraints, this work shows that differen ...[more]

PMID: 31799624

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Project description:A water-soluble glycopeptide (PGY), fractionated and purified from the aqueous extract of the fruiting bodies of Ganoderma lucidum via two-step dialysis, anion exchange, and gel permeation chromatography, was constituted of two moieties of carbohydrate and peptide. Carbohydrate characterization with component analysis, methylation analysis, periodate oxidation, Smith degradation, enzymic hydrolysis, and IR and NMR experiments demonstrated that the carbohydrate moiety possessed a backbone of approximately 33 (1-->3)-linked beta-d-glucopyranosyl residues and side chains, at positions 6, of single alpha-l-arabinofuranosyl residues for every three Glcp residues in the main chain. On the basis of the results of amino acid composition and trypsin digestion, the peptide moiety, shown to consist of Arg, Ser, Ala, and Gly in a ratio of 1:1:2:2, exhibited the sequence of Ser-Arg-[(Ala)2(Gly)2] and was O-attached to the carbohydrate moiety via Ser. To contribute toward our understanding of the structure-activity relationship, a series of expected derivatives generated from PGY by trypsin digestion, debranching, and NaIO4 oxidation following reduction experiments, including PTC, DB-PGY, and PPP, were obtained. All of them, as well as PGY and a reference compound (butylated hydroxytoluene, BHT), were evaluated with two conventional antioxidant testing systems of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and superoxide radical scavenging and found to have their respective antioxidant activities in a concentration-dependent manner. Comparable radical-scavenging activities observed between PTC and PGY demonstrated that the removal of Ala and Gly in a peptide moiety did not result in the variation of biological functions of PGY. However, it was very interesting to note that the scavenging activity of PPP was higher for DPPH radicals, with an SC(50) value of 116.4 +/- 5.1 microg/mL, and lower for superoxide radicals, with an SC(50) value of 205.2 +/- 14.4 microg/mL, than that of PGY with corresponding SC(50) values of 133.5 +/- 5.5 and 140.5 +/- 7.7 microg/mL, and, moreover, DB-PGY displayed the weakest scavenging potency in the tested samples, indicating that the carbohydrate moiety, in particular the side chain of nonreducing end units of Araf residues as the functional region, played a vital role in the structure and antioxidant activity. In addition, compared with the SC(50) value of BHT, PGY showed lower DPPH radical-scavenging activity but possessed higher superoxide radical-quenching potency, suggesting that it could be presented as a possible new source of natural antioxidants.

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Conformation-dependent restraints for polynucleotides: the sugar moiety.

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Conformation-dependent restraints for polynucleotides: the sugar moiety.

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