Irena Ekiel - Academia.edu (original) (raw)

Papers by Irena Ekiel

Research paper thumbnail of NMR structure of the J-domain (residues 2-72) in the Escherichia coli CbpA

Research paper thumbnail of Crystal Structure of E.coli Dha kinase DhaK-DhaL complex

Research paper thumbnail of NMR solution structure of NapD in complex with NapA1-35 signal peptide

Research paper thumbnail of ChemInform Abstract: COUPLING CONSTANTS BETWEEN CISOIDAL PROTONS IN PENTOSE NUCLEOSIDES. LIMITATIONS OF RANGE OF APPLICATION OF KARPLUS RELATION, AND SOLUTION CONFORMATIONS OF β-ARABINOFURANOSYL AND β-XYLOFURANOSYL NUCLEOSIDES

Chemischer Informationsdienst, Oct 17, 1978

Research paper thumbnail of ChemInform Abstract: STRUCTURE AND CONFORMATION OF 8-BROMO-9-β-D-XYLOFURANOSYLADENINE IN THE SOLID STATE AND IN SOLUTION

Chemischer Informationsdienst, Oct 26, 1982

Research paper thumbnail of Crystal Structure of E.coli Dha kinase DhaK

Research paper thumbnail of 1H, 13C, and 15N Chemical Shift Assignments for the PPIase domain from E. coli trigger factor

Journal of Back and Musculoskeletal Rehabilitation, Jun 25, 2003

Research paper thumbnail of Crystal structure and conformation of 8-bromo-9-β-D-xylofuranosyladenine hydrate

Acta Crystallographica Section A Foundations of Crystallography, 1981

Structural studies have been performed on a series of hydroxylated derivatives of the carcinogens... more Structural studies have been performed on a series of hydroxylated derivatives of the carcinogens benzo[a]pyrene and benzo[a]anthracene. These compounds represent stages in the metabolic path\.;ays leading to ultimate carcinogenic species that may react ~tiith cellular DNA. The molecular structures have revealed the systematic conformational changes produced in the aromatic systems as they become progressiyelY de-aromatised and more reactive in succeeding stag~s 9~ metabolism.

Research paper thumbnail of Preparation and Characterization of Bacterial Protein Complexes for Structural Analysis

Advances in protein chemistry and structural biology, 2009

Bacteria mediate a large variety of biological processes using protein complexes. These complexes... more Bacteria mediate a large variety of biological processes using protein complexes. These complexes range from simple binary heterodimeric enzymes to more complex multi-subunit complexes that can be described as macromolecular machines. A key to understanding how these complexes function is obtaining structural information using methods that include electron microscopy, small-angle X-ray scattering, NMR spectroscopy, and X-ray crystallography. Here we describe a variety of approaches to the expression, purification, and biophysical characterization of bacterial protein complexes as a prerequisite to structural analysis. We also give several examples of the kinds of information these different biophysical approaches can provide and various experimental approaches to obtaining structure information for a given system. Further, we describe several examples of protein complexes where we have obtained structural data that have led to new biological insights.

Research paper thumbnail of Solution structure of the catalytic domain from rat CNP

Research paper thumbnail of Solution Structure of the Pabc Domain of Human Poly(A) Binding Protein

Research paper thumbnail of Solution Structure of the PDZ2 Domain from Human Phosphatase HPTP1E Complexed with a Peptide

Research paper thumbnail of Solution Structure of the Archaeal Translation Elongation Factor 1BETA from Methanobacterium Thermoautotrophicum

Research paper thumbnail of Solution Structure of the PPIase Domain from E. coli Trigger Factor

Research paper thumbnail of Structural characterization of the lipids of Methanococcus voltae, including a novel N-acetylglucosamine 1-phosphate diether

Journal of Biological Chemistry, Dec 1, 1986

The lipids of a moderately halophilic methanogen, Methanococcus voltae, accounted for 5.1% of the... more The lipids of a moderately halophilic methanogen, Methanococcus voltae, accounted for 5.1% of the cell dry weight and consisted of 91% polar lipids and 9% neutral lipids. Twelve polar lipids were detected, three of which, all derivatives of 2,3-di-O-phytanyl-sn-glycerol, were identified as: 2,3-di-O-phytanyl-1-O-[beta-D-glucopyranosyl-(1-6)-beta-D- glucopyranosyl]-sn-glycerol, 2,3-di-O-phytanyl-1-O-[beta-D-glucopyranosyl]-sn-glycerol and a novel NAc-glucosamine 1-phosphate diether, and 2,3-di-O-phytanyl-1-[phosphoryl-2-acetamido-2-deoxy-beta-D- glucopyranosyl]-sn-glycerol. The neutral lipids consisted mainly of squalenes: squalene, dihydrosqualene, tetrahydrosqualene, hexahydrosqualene, and unidentified squalenes.

Research paper thumbnail of Crystal Structure of E.coli Dha kinase DhaK (H56N) complex with Dha

Research paper thumbnail of Solution Structure of a 8.3 Kda Protein (Gene MTH1184) from Methanobacterium Thermoautotrophicum

Research paper thumbnail of Solution conformations of the antimetabolite 9-beta-D-xylofuranosyladenine and its 8-bromo analogue

PubMed, 1979

An analysis has been made, with the aid of 1H NMR spectroscopy, of the solution conformation of t... more An analysis has been made, with the aid of 1H NMR spectroscopy, of the solution conformation of the known antimetabolite, 9-beta-D-xylofuranosyladenine (xyloA), and of its 8-bromo analogue. For xyloA, the results point to a strong preference for the sugar ring of the conformation type N (C(3') endo), a relatively low population of the gauche-gauche rotamer of the exocyclic 5'-CH2OH, and a preference for the conformation anti about the glycosidic bond. For 8-bromo-xyloA, the preference for the type N conformation of the sugar ring is less marked, and the preferred conformation about the glycosidic bond is syn. The conformation of the sugar ring in the foregoing xylonucleosides consequently differs appreciably from that for the corresponding ribonucleosides, which adopt preferentially the type S (C(2')endo) and gauche-gauche conformations. Comparison with previously reported results for O'-methyl derivatives of xyloA points to the similarity in conformational properties of all of these. In contrast to arabinonucleosides with free 2' and 5' hydroxyls, the conformation of xyloA is relatively unaffected in strongly alkaline medium where the sugar hydroxyl(s) dissociate. Under these conditions, there is no formation of an intramolecular hydrogen bond such as might have been anticipated from X-ray diffraction studies in the solid state.

Research paper thumbnail of Solution Structure of human PRL-3

Research paper thumbnail of Solution Structure of MTH1692 Protein from Methanobacterium thermoautotrophicum

Research paper thumbnail of NMR structure of the J-domain (residues 2-72) in the Escherichia coli CbpA

Research paper thumbnail of Crystal Structure of E.coli Dha kinase DhaK-DhaL complex

Research paper thumbnail of NMR solution structure of NapD in complex with NapA1-35 signal peptide

Research paper thumbnail of ChemInform Abstract: COUPLING CONSTANTS BETWEEN CISOIDAL PROTONS IN PENTOSE NUCLEOSIDES. LIMITATIONS OF RANGE OF APPLICATION OF KARPLUS RELATION, AND SOLUTION CONFORMATIONS OF β-ARABINOFURANOSYL AND β-XYLOFURANOSYL NUCLEOSIDES

Chemischer Informationsdienst, Oct 17, 1978

Research paper thumbnail of ChemInform Abstract: STRUCTURE AND CONFORMATION OF 8-BROMO-9-β-D-XYLOFURANOSYLADENINE IN THE SOLID STATE AND IN SOLUTION

Chemischer Informationsdienst, Oct 26, 1982

Research paper thumbnail of Crystal Structure of E.coli Dha kinase DhaK

Research paper thumbnail of 1H, 13C, and 15N Chemical Shift Assignments for the PPIase domain from E. coli trigger factor

Journal of Back and Musculoskeletal Rehabilitation, Jun 25, 2003

Research paper thumbnail of Crystal structure and conformation of 8-bromo-9-β-D-xylofuranosyladenine hydrate

Acta Crystallographica Section A Foundations of Crystallography, 1981

Structural studies have been performed on a series of hydroxylated derivatives of the carcinogens... more Structural studies have been performed on a series of hydroxylated derivatives of the carcinogens benzo[a]pyrene and benzo[a]anthracene. These compounds represent stages in the metabolic path\.;ays leading to ultimate carcinogenic species that may react ~tiith cellular DNA. The molecular structures have revealed the systematic conformational changes produced in the aromatic systems as they become progressiyelY de-aromatised and more reactive in succeeding stag~s 9~ metabolism.

Research paper thumbnail of Preparation and Characterization of Bacterial Protein Complexes for Structural Analysis

Advances in protein chemistry and structural biology, 2009

Bacteria mediate a large variety of biological processes using protein complexes. These complexes... more Bacteria mediate a large variety of biological processes using protein complexes. These complexes range from simple binary heterodimeric enzymes to more complex multi-subunit complexes that can be described as macromolecular machines. A key to understanding how these complexes function is obtaining structural information using methods that include electron microscopy, small-angle X-ray scattering, NMR spectroscopy, and X-ray crystallography. Here we describe a variety of approaches to the expression, purification, and biophysical characterization of bacterial protein complexes as a prerequisite to structural analysis. We also give several examples of the kinds of information these different biophysical approaches can provide and various experimental approaches to obtaining structure information for a given system. Further, we describe several examples of protein complexes where we have obtained structural data that have led to new biological insights.

Research paper thumbnail of Solution structure of the catalytic domain from rat CNP

Research paper thumbnail of Solution Structure of the Pabc Domain of Human Poly(A) Binding Protein

Research paper thumbnail of Solution Structure of the PDZ2 Domain from Human Phosphatase HPTP1E Complexed with a Peptide

Research paper thumbnail of Solution Structure of the Archaeal Translation Elongation Factor 1BETA from Methanobacterium Thermoautotrophicum

Research paper thumbnail of Solution Structure of the PPIase Domain from E. coli Trigger Factor

Research paper thumbnail of Structural characterization of the lipids of Methanococcus voltae, including a novel N-acetylglucosamine 1-phosphate diether

Journal of Biological Chemistry, Dec 1, 1986

The lipids of a moderately halophilic methanogen, Methanococcus voltae, accounted for 5.1% of the... more The lipids of a moderately halophilic methanogen, Methanococcus voltae, accounted for 5.1% of the cell dry weight and consisted of 91% polar lipids and 9% neutral lipids. Twelve polar lipids were detected, three of which, all derivatives of 2,3-di-O-phytanyl-sn-glycerol, were identified as: 2,3-di-O-phytanyl-1-O-[beta-D-glucopyranosyl-(1-6)-beta-D- glucopyranosyl]-sn-glycerol, 2,3-di-O-phytanyl-1-O-[beta-D-glucopyranosyl]-sn-glycerol and a novel NAc-glucosamine 1-phosphate diether, and 2,3-di-O-phytanyl-1-[phosphoryl-2-acetamido-2-deoxy-beta-D- glucopyranosyl]-sn-glycerol. The neutral lipids consisted mainly of squalenes: squalene, dihydrosqualene, tetrahydrosqualene, hexahydrosqualene, and unidentified squalenes.

Research paper thumbnail of Crystal Structure of E.coli Dha kinase DhaK (H56N) complex with Dha

Research paper thumbnail of Solution Structure of a 8.3 Kda Protein (Gene MTH1184) from Methanobacterium Thermoautotrophicum

Research paper thumbnail of Solution conformations of the antimetabolite 9-beta-D-xylofuranosyladenine and its 8-bromo analogue

PubMed, 1979

An analysis has been made, with the aid of 1H NMR spectroscopy, of the solution conformation of t... more An analysis has been made, with the aid of 1H NMR spectroscopy, of the solution conformation of the known antimetabolite, 9-beta-D-xylofuranosyladenine (xyloA), and of its 8-bromo analogue. For xyloA, the results point to a strong preference for the sugar ring of the conformation type N (C(3') endo), a relatively low population of the gauche-gauche rotamer of the exocyclic 5'-CH2OH, and a preference for the conformation anti about the glycosidic bond. For 8-bromo-xyloA, the preference for the type N conformation of the sugar ring is less marked, and the preferred conformation about the glycosidic bond is syn. The conformation of the sugar ring in the foregoing xylonucleosides consequently differs appreciably from that for the corresponding ribonucleosides, which adopt preferentially the type S (C(2')endo) and gauche-gauche conformations. Comparison with previously reported results for O'-methyl derivatives of xyloA points to the similarity in conformational properties of all of these. In contrast to arabinonucleosides with free 2' and 5' hydroxyls, the conformation of xyloA is relatively unaffected in strongly alkaline medium where the sugar hydroxyl(s) dissociate. Under these conditions, there is no formation of an intramolecular hydrogen bond such as might have been anticipated from X-ray diffraction studies in the solid state.

Research paper thumbnail of Solution Structure of human PRL-3

Research paper thumbnail of Solution Structure of MTH1692 Protein from Methanobacterium thermoautotrophicum