Restrained least-squares refinement of Themiste dyscritum methydroxohemerythrin at 2.0 Å resolution

Stenkamp, Ronald E.; Sieker, L.C.; Jensen, L. H.

doi:10.1107/s0567740882004087

Cited by 25 publications

(19 citation statements)

References 10 publications

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“…Eliminating true structural differences in extracting errors There are real differences between multiple molecules in the asymmetric unit due to differences in the packing environment "The four-letter code refers to the PDB designation for each structure, for which the references are: lTHB (Waller & Liddington, 1990); 2CCY (Finzel et al, 1985); 4CHA (Tsukada & Blow, 1985); 4DFR (Bolin et al, 1982); ZHHB (Fermi et al, 1984); 3CYT (Takano & Dickerson, 1980); ZAZA (Baker, 1988); l G D l (Skarzynski et al, 1987); lAZA (Norris et al, 1983);lGPl (Epp et al, 1983); 1HMQ (Stenkamp et al, 1982);2pKA (Bodeetal., 1983); 2PFK (Rypniewski Evans, 1989); 1FCB (Xia & Mathews, 1990); 4MDH (Birktoft et al, 1989); 4ATc (Ke et al, 1984); ~F C I (Deisenhofer, 1981); IHBS (Padlan & Love, 1985). of the independent molecules.…”

Section: Deriving the Empirical Error Curve Ex(b)mentioning

confidence: 99%

Significance of structural changes in proteins: Expected errors in refined protein structures

Stroud

Fauman

1995

Protein Science

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A quantitative expression key to evaluating significant structural differences or induced shifts between any two protein structures is derived. Because crystallography leads to reports of a single (or sometimes dual) position for each atom, the significance of any structural change based on comparison of two structures depends critically on knowing the expected precision of each median atomic position reported, and on extracting it for each atom, from the information provided in the Protein Data Bank and in the publication. The differences between structures of protein molecules that should be identical, and that are normally distributed, indicating that they are not affected by crystal contacts, were analyzed with respect to many potential indicators of structure precision, so as to extract, essentially by "machine learning" principles, a generally applicable expression involving the highest correlates. Eighteen refined crystal structures from the Protein Data Bank, in which there are multiple molecules in the crystallographic asymmetric unit, were selected and compared. The thermal E factor, the connectivity of the atom, and the ratio of the number of reflections to the number of atoms used in refinement correlate best with the magnitude of the positional differences between regions of the structures that otherwise would be expected to be the same. These results are embodied in a six-parameter equation that can be applied to any crystallographically refined structure to estimate the expected uncertainty in position of each atom. Structure change in a macromolecule can thus be referenced to the expected uncertainty in atomic position as reflected in the variance between otherwise identical structures with the observed values of correlated parameters.

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Section: Deriving the Empirical Error Curve Ex(b)mentioning

confidence: 99%

Significance of structural changes in proteins: Expected errors in refined protein structures

Stroud

Fauman

1995

Protein Science

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“…As a first step the idealized length of the four helices and terminally connecting loops were replaced by those of hemerythrin (from sipunculid worm (Stenkamp et al, 1982)). However, the distribution of hydrophobic amino acid residues was maintained according to that of the idealized hydrophobic wheel (Figure 1) and without correspondence to the hemerythrin primary structure.…”

Section: (D) Folding Of Non-idealized Four-helix Bundlesmentioning

confidence: 99%

“…The following Brookhaven files were utilized: I HMD (hemerythrin from sipunculid worm (Stenkamp et al , 1982)); 256B (cytochrome b S62 from Escherichia coli (Lederer et al , 1981)); 2CCY (cytochrome c' from Rhodospirillum molischianum (Finzel et al, 1985)) ; and ICRN (crambin from Abyssinian cabbage (Hendrickson & Teeter, 1981)). Structures resulting from the simulation as well as those experimentally verified were visualized with the protein characterization system of Chelvanayagam & McKeaig (1991).…”

Section: (B) Model Representationmentioning

confidence: 99%

Folding the Main Chain of Small Proteins with the Genetic Algorithm

Dandekar

Argos

1994

Journal of Molecular Biology

133

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Grid-free protein folding simulations were effected using the genetic algorithm, a backbone representation and standard dihedral angular conformations. The topological folding of idealized four-helix bundles was investigated in detail to differentiate among the important protein folding forces used as fitness criteria. Hydrophobic interactions were the most significant while local forces and hydrogen bonds were far less effective in promoting folding. Stable secondary structural regions were also important as nucleating centers. Using the fitness parameters optimized in idealized simulations together with standard secondary structure predictions derived from the amino acid sequence alone, the proper main-chain folding of the four-helix bundle proteins cytochrome b 562 , cytochrome c' and hemerythrin was achieved. In addition the backbone topology as predicted by the genetic algorithm for cram bin, a mixed helix/strand protein with known structure, is presented and discussed.

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“…1 Left). In the met form [formerly identified as aquomet (3) or hydroxomet (4)], one of the iron atoms, designated Fe2, is pentacoordinate ( Fig. 1 Right).…”

mentioning

confidence: 99%

“…Both reflections of each Friedel pair were measured by the step-scan technique (16). Empirical absorption (17) and deterioration corrections (18) were applied, and the Friedel mates were averaged to eliminate the effects of anomalous scattering as described elsewhere (18,19). The data set comprised 5686 reflections of which 4184 were observed with I > 2o(I).…”

mentioning

confidence: 99%

Active site structures of deoxyhemerythrin and oxyhemerythrin.

Stenkamp¹,

Sieker²,

Jensen³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

136

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The physiologically active forms of the nonheme-iron, oxygen-transport protein hemerythrin have been studied by x-ray crystallographic techniques. At 3.9-A resolution, a difference electron-density map between the deoxy form and met form (methemerythrin) of the protein suggests only small differences in the binuclear iron complexes. The coordination of the iron atoms appears to be the same in both the deoxy and met forms, one iron of the complexes being pentacoordinate, the other iron being hexacoordinate. The iron atoms appear to be somewhat farther apart in the deoxy form. A 2.2-A resolution study of oxyhemerythrin shows that dioxygen binds to one iron atom-the pentacoordinate one in the met form of the protein, the same binding site found for azide in azidomethemerythrin.The initial objective of the crystallographic structure determinations of hemerythrin was to structurally characterize this nonheme-iron, oxygen-transport protein to provide a basis for understanding the chemical differences between its derivatives. The early studies focused on the structure of the oxidized form, or methemerythrins (1, 2), primarily because they are more stable than are the physiologically more interesting deoxy and oxy forms. The active center is a binuclear iron complex bound to the protein by amino acid side chains. In azidomethemerythrin, the iron atoms are both hexacoordinate ( Fig. 1 Left). In the met form [formerly identified as aquomet (3) or hydroxomet (4)], one of the iron atoms, designated Fe2, is pentacoordinate ( Fig. 1 (11), and x-ray absorption spectroscopy (12) indicate that the metal complex in oxyhemerythrin is similar to that in azidomethemerythrin, where the two Fe(III) atoms are bridged by a A-oxygen atom, and the exogenous ligand binds only to one Fe atom. The x-ray crystallographic results reported here support this description for oxyhemerythrin and, in addition, suggest some rearrangement in the binuclear iron complex upon conversion from deoxy to oxy. The 2.2-A resolution crystallographic investigations provide important structural information bearing on the functional properties of the protein and limiting the mechanisms to be considered in explaining the biological action of the molecule. EXPERIMENTALThe sipunculid T. dyscrita was obtained from the Oregon Institute of Marine Biology (Charleston, OR). Hemerythrin was extracted and crystallized from the coelomic fluid as described (13, 14). The crystals were dissolved in 0.2 M Tris sulfate (pH 8.0) and concentrated to -30 mg of protein per ml by ultrafiltration (XM-50 filter; Amicon). The hemerythrin solution was depleted of oxygen by anaerobic dialysis against nitrogen-purged buffer. A 4-fold molar excess (per hemerythrin monomer) of solid sodium dithionite was added to the dialysis buffer. After 25 hr the protein solution displayed the pale yellow color characteristic of reduced hemerythrin. Crystals of deoxyhemerythrin were obtained by slow dialysis of the concentrated solution against 0.02 M Tris sulfate (pH 7.2) under anaerobic condition...

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Restrained least-squares refinement of Themiste dyscritum methydroxohemerythrin at 2.0 Å resolution

Cited by 25 publications

References 10 publications

Significance of structural changes in proteins: Expected errors in refined protein structures

Significance of structural changes in proteins: Expected errors in refined protein structures

Folding the Main Chain of Small Proteins with the Genetic Algorithm

Active site structures of deoxyhemerythrin and oxyhemerythrin.

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