Studies on the solution conformation of human thioredoxin using heteronuclear nitrogen-15-proton nuclear magnetic resonance spectroscopy

Forman-Kay, Julie D.; Gronenborn, Angela M.; Kay, Lewis E.; Wingfield, Paul T.; Clore, G. Marius

doi:10.1021/bi00458a030

Cited by 85 publications

(27 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The acquisition and processing details for these experiments were given by Feng et al (1995). The backbone 3 JNHa coupling constants extracted from a 2D 1 H-15 N HMQC-J spectrum Forman-Kay et al, 1990) were also reported earlier (Feng et al, 1995). A 3D simultaneously 13 C, 15 N-edited ROESY-HSQC spectrum was recorded using similar acquisition parameters as for the corresponding NOESY-HSQC experiment in order to confirm that certain cross-peaks were due to cross-relaxation and not to chemical or conformational exchange.…”

Section: Methodsmentioning

confidence: 99%

Three-dimensional Solution Structure and Backbone Dynamics of a Variant of Human Interleukin-3

Feng¹,

Klein²,

McWherter³

1996

Journal of Molecular Biology

View full text Add to dashboard Cite

The three-dimensional structure and backbone dynamics of a truncated G.D. Searle and Companyand multiply substituted recombinant human interleukin-3 (IL-3) variant 700 Chesterfield (SC-65369) have been determined from multidimensional heteronuclear Parkway North, St. Louis MO 63198, USA nuclear magnetic resonance spectroscopic data. Sequential application of distance geometry and restrained molecular dynamics calculations produced a family of 25 convergent structures which satisfy a total of 1812 experimental constraints (1659 proton-proton NOEs, 75 backbone dihedral angle constraints, and 39 pairs of hydrogen bond constraints) with an average root-mean-square deviation from the mean coordinate positions of 0.88(20.15) Å and 1.37(20.13) Å for the backbone and all heavy atoms, respectively, of all residues except 28 to 39. The structure is a left-handed four-helix bundle (comprised of helices A through D) with two long overhand loops (designated as loops AB and CD). Loop AB contains a short fifth helix (helix A') which is closely packed against helix D in an approximately parallel fashion and which has multiple contacts with loop CD. The overall molecular tumbling time (6.5 ns) determined from the 15 N relaxation data was consistent with a monomeric protein under the conditions of the experiment (1 mM protein, pH 4.6, 30°C). The 15 N relaxation data indicate that the helical regions of SC-65369 are quite rigid, while portions of loop AB, loop CD, and the C terminus undergo significant internal motions. Among the structurally related four-helical bundle cytokines, the structure of SC-65369 is most similar to those of granulocyte-macrophage colony stimulating factor (GM-CSF) and the single structural domain of interleukin-5 (IL-5), all of which share a common receptor subunit required for signal transduction and activation of their hematopoietic target cells. Indeed, the C a atoms in the four-helix core of these three proteins can be superimposed to 1.71 Å (SC-65369 and GM-CSF, 62 C a atoms) and 1.96 Å (SC-65369 and IL-5 single structural domain, 58 C a atoms), respectively. When the structures of the IL-3 variant, GM-CSF, and IL-5 were aligned, the conserved and conservatively substituted residues were found to be hydrophobic and buried, with the single exception of Glu-22 (IL-3 numbering), which is strictly conserved but nonetheless fully exposed to solvent. The most remarkable differences between the SC-65369 structure and that of GM-CSF occur in loop AB. This loop in GM-CSF crosses over the top of helix D and passes underneath loop CD on its way to helix B. In contrast, loop AB of SC-65369 passes in front of helix D, similar to the first crossover loop in human growth hormone and granulocyte colony-stimulating factor. In addition, helix A', which is interdigitated into the helical bundle in a manner similar to the helices in the CD loop of interferon-b and interferon-g, exists in a region where short *Corresponding authors stretches of b-structure are found at analogous positions in GM-CSF and Abbreviations use...

show abstract

Section: Methodsmentioning

confidence: 99%

Three-dimensional Solution Structure and Backbone Dynamics of a Variant of Human Interleukin-3

Feng¹,

Klein²,

McWherter³

1996

Journal of Molecular Biology

View full text Add to dashboard Cite

show abstract

“…The present structure is based on the following series of spectra: 2D HMQC-J (Kay & Bax, 1990;Forman-Kay et al, 1990), 3D 15N- (Marionet al, 1989b;Zuiderweg & Fesik, 1989) and 13C-editedNOESY (Ikura et al, 1990a;Zuiderweg et al, 1990), 3D lH-15N HMQC-NOE-HMQC (Ikura et al, 1990b), 3D 15N-(Cloreet al, 1990a) and 13C-edited ROESY , 3D 15N-edited HOHAHA (Marion et Biochemistry, Vol. 32, No.…”

Section: Methodsmentioning

confidence: 99%

The high-resolution, three-dimensional solution structure of human interleukin-4 determined by multidimensional heteronuclear magnetic resonance spectroscopy

Powers¹,

Ds²,

Cj³

et al. 1993

Biochemistry

Self Cite

138

106

View full text Add to dashboard Cite

The high-resolution three-dimensional solution structure of recombinant human interleukin-4 (IL-4), a protein of ~15 kDa which plays a key role in the regulation of B and T lymphocytes, has been determined using threeand four-dimensional heteronuclear NMR spectroscopy. The structure is based on a total of 2973 experimental NMR restraints, comprising 2515 approximate interproton distance restraints, 102 distance restraints for 51 backbone hydrogen bonds, and 356 torsion angle restraints. A total of 30 structures was calculated by means of hybrid distance geometry-simulated annealing, and the atomic rms distribution about the mean coordinate positions for residues 8-129 is 0.44 ± 0.03 A for the backbone atoms, 0.83 ± 0.03 A for all atoms, and 0.51 ± 0.04 A for all atoms excluding disordered side chains. The Nand C-terminal residues (1-7 and 130-133, respectively) appear to be disordered. The structure of IL-4 is dominated by a left-handed four-helix bundle with an unusual topology comprising two overhand connections. The linker elements between the helices are formed by either long loops, small helical turns, or short strands.

show abstract

“…The 3JHN_Hc ~ coupling constants were measured through the use of an HMQC-J experiment (Kay et al 1989;Forman-Kay et al 1990;Kay and Bax 1990). The data were collected with 1024 complex points in T 1 and T 2 by using TPPI (Marion and Wfithrich 1983).…”

Section: Nmr Spectroscopymentioning

confidence: 99%

Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy.

Phillips¹,

Vershon²,

Johnson³

et al. 1991

Genes Dev.

View full text Add to dashboard Cite

The yeast a2 protein is a regulator of cell type in Saccharomyces cerevisiae. It represses transcription of a set of target genes by binding to an operator located upstream of each of these genes. The c~2 protein shares weak sequence similarity with members of the homeo domain family; the homeo domain is a 60-amino-acid segment found in many eukaryotic transcriptional regulators. In this paper we address the question of whether ~2 is structurally related to prototypical members of the homeo domain family. We used solution ~H and lSN nuclear magnetic resonance (NMR) spectroscopy to determine the secondary structure of an 83-amino-acid residue fragment of ~2 that contains the homeo domain homology. We have obtained resonance assignments for the backbone protons and nitrogens of the entire 60-residue region of the putative homeo domain and for most of the remainder of the ,Y2 fragment. The secondary structure was determined by using NOE connectivities between backbone protons, 3J~N_H. coupling constants, and dynamical information from the hydrogen exchange kinetics of the backbone amides. Three helical segments exist in the c~2 fragment consisting of residues 11-23, 32-42, and 46-60 (corresponding to residues 138-150, 159-169, and 173-187 of the intact protein). The positions of these three helices correspond extremely well to those of the Drosophila Antennapedia (Antp) and engrailed (en) homeo domains, whose three-dimensional structures have recently been determined by NMR spectroscopy and X-ray crystallography, respectively. This study reveals that in spite of low sequence similarity between the homeo domain of a2 and that of higher eukaryotes, the secondary structures of these proteins are well conserved.

show abstract

Studies on the solution conformation of human thioredoxin using heteronuclear nitrogen-15-proton nuclear magnetic resonance spectroscopy

Cited by 85 publications

References 21 publications

Three-dimensional Solution Structure and Backbone Dynamics of a Variant of Human Interleukin-3

Three-dimensional Solution Structure and Backbone Dynamics of a Variant of Human Interleukin-3

The high-resolution, three-dimensional solution structure of human interleukin-4 determined by multidimensional heteronuclear magnetic resonance spectroscopy

Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy.

Contact Info

Product

Resources

About