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EXAFS simulation refinement based on broken-symmetry DFT geometries for the Mn(IV)-Fe(III) center of class I RNR from Chlamydia trachomatis.

ABSTRACT: Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides necessary for DNA biosynthesis. Unlike the conventional class Ia RNRs which use a diiron cofactor in their subunit R2, the active site of the RNR-R2 from Chlamydia trachomatis (Ct) contains a Mn/Fe cofactor. The detailed structure of the Mn/Fe core has yet to be established. In this paper we evaluate six different structural models of the Ct RNR active site in the Mn(iv)/Fe(iii) state by using Mössbauer parameter calculations and simulations of Mn/Fe extended X-ray absorption fine structure (EXAFS) spectroscopy, and we identify a structure similar to a previously proposed DFT-optimized model that shows quantitative agreement with both EXAFS and Mössbauer spectroscopic data.

SUBMITTER: Luber S

PROVIDER: S-EPMC3855085 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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EXAFS simulation refinement based on broken-symmetry DFT geometries for the Mn(IV)-Fe(III) center of class I RNR from Chlamydia trachomatis.

Luber Sandra S Leung Sophie S Herrmann Carmen C Du Wenge Han WH Noodleman Louis L Batista Victor S VS

Dalton transactions (Cambridge, England : 2003) 20140101 2

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides necessary for DNA biosynthesis. Unlike the conventional class Ia RNRs which use a diiron cofactor in their subunit R2, the active site of the RNR-R2 from Chlamydia trachomatis (Ct) contains a Mn/Fe cofactor. The detailed structure of the Mn/Fe core has yet to be established. In this paper we evaluate six different structural models of the Ct RNR active site in the Mn(iv)/Fe(iii) state by using Mö ...[more]

PMID: 24129440

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Project description:Introduction Chlamydia trachomatis (C. trachomatis) is a Gram-negative bacterium and a common human pathogen. The World Health Organization (WHO) estimates that over 130 million people are infected with C. trachomatis globally each year and with increasing incidence. C. trachomatis causes long-lasting and recurrent infections that over time induce severe tissue damage in the female genital tract that can lead to ectopic pregnancy and infertility. Thus, the human immune system fails to control and eradicate C. trachomatis during primary infection and fails to develop protective immunity against secondary infections. In vivo infection models, using complement knock out mice, suggest that the complement system is critically involved in both anti-chlamydial immunity and infection-induced pathology. To increase our understanding of complement-mediated immunity against C. trachomatis we analyzed global complement deposition on serum-incubated C. trachomatis by mass spectrometry. Methods Purified C. trachomatis was incubated in seronegative normal human serum (NHS) or heat-inactivated normal human serum (HI-NHS) for 30 min, thoroughly washed, and processed for mass spectrometry. All samples were lysed, reduced and alkylated and digested with trypsin. Some samples were chemically modified to acetylate free amino groups (N-terminal and lysine amino groups) before trypsin digestion. Peptides were analyzed on a UltimateTM 3500 RSLCnano coupled to a Q Exactive HF-X mass spectrometer. Raw data files were searched against the Uniprot human reference proteome using MaxQuant. Results We demonstrate that C. trachomatis elicits potent complement activation demonstrated by deposition of both early and late complement factors together with several complement regulators. We further demonstrate proteolytically processing of complement C3b to “inactive” C3 cleavage fragments. Conclusion We demonstrate the deposition of several novel complement-associated proteins and -cleavage fragments on the surface of C. trachomatis.

Dataset Information

EXAFS simulation refinement based on broken-symmetry DFT geometries for the Mn(IV)-Fe(III) center of class I RNR from Chlamydia trachomatis.

Publications

EXAFS simulation refinement based on broken-symmetry DFT geometries for the Mn(IV)-Fe(III) center of class I RNR from Chlamydia trachomatis.

Similar Datasets

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