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Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H.

ABSTRACT: Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, (13)C(?/?), in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on ?s-ms time scales upon binding of Mg(2+) ions. Two groups of catalytic residues exhibit differential line broadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the "mobile metal ion" hypothesis, which was inferred from structural studies of RNase H.

SUBMITTER: Stafford KA

PROVIDER: S-EPMC3918730 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H.

Stafford Kate A KA Ferrage Fabien F Cho Jae-Hyun JH Palmer Arthur G AG

Journal of the American Chemical Society 20131120 48

Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, (13)C(γ/δ), in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. ...[more]

PMID: 24219366

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Project description:Helices are the most extensively studied secondary structures formed by ?-peptide foldamers. Among the five known ?-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of ?-peptide helices (?-helix and 3(10)-helix). The ?-peptide 12-helix is defined by i, i+3 C?O···H-N backbone hydrogen bonds and promoted by ?-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate ?-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical ?-peptides have previously been reported, both for homooligomers of trans-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical ?-peptides, all containing residues that bear side chains. Four of the crystallized ?-peptides include trans-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (dm-ACPC) residues, and the fifth contains a ?(3)-hPhe residue. These five ?-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of ?-residues and helical parameters are derived. These structural parameters are found to be similar to those for i, i+3 C?O···H-N hydrogen-bonded helices formed by other peptide backbones generated from ?- and/or ?-amino acids. The similarity between the conformational behavior of dm-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a ?(3)-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of ?-amino acids.

Dataset Information

Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H.

Publications

Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H.

Similar Datasets

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