Molecular symmetry of Lumbricus erythrocruorin (original) (raw)
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Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1988
The molecular structure of erythrocruorin (hemoglobin) from Lumbricus terrestris has been studied by electron microscopy of negatively stained particles. Over 1000 molecular projections were selected from a number of electron micrographs and were then classified by multivariate statistical image-processing techniques. The two main groups of top and side views were each subdivided into smaller classes with significantly different features. About half of the top-view projections exhibit perfect hexagonal symmetry at the current resolution of about 2.0 nm, while the other top views lack this symmetry, probably as a result of tilting of the molecules relative to the carbon support film. The side views were separated into two 'families', each associated with the two different stable side-view positions the molecules can take. From these narrow stable side-views, the two families of projections are, again, generated by tilting. The symmetry properties of the three non-tilted projections show that Lmnbricus erythrocruorin has a pointgroup D6 (622) symmetry rather than I)3 (32).
Lumbricus Erythrocruorin at 3.5 Å Resolution: Architecture of a Megadalton Respiratory Complex
Structure, 2006
Annelid erythrocruorins are highly cooperative extracellular respiratory proteins with molecular masses on the order of 3.6 million Daltons. We report here the 3.5 Å crystal structure of erythrocruorin from the earthworm Lumbricus terrestris. This structure reveals details of symmetrical and quasi-symmetrical interactions that dictate the self-limited assembly of 144 hemoglobin and 36 linker subunits. The linker subunits assemble into a core complex with D 6 symmetry onto which 12 hemoglobin dodecamers bind to form the entire complex. Although the three unique linker subunits share structural similarity, their interactions with each other and the hemoglobin subunits display striking diversity. The observed diversity includes design features that have been incorporated into the linker subunits and may be critical for efficient assembly of large quantities of this complex respiratory protein.
Biophysical Journal, 1997
We have investigated the kinetics of geminate carbon monoxide binding to the monomeric component Ill of Chironomus thummi-thummi erythrocruorin, a protein that undergoes pH-induced conformational changes linked to a pronounced Bohr effect. Measurements were performed from cryogenic temperatures to room temperature in 75% glycerol and either 0.1 M potassium phosphate (pH 7) or 0.1 potassium borate (pH 9) after nanosecond laser photolysis. The distributions of the low temperature activation enthalpy g(H for geminate ligand binding derived from the kinetic traces are quite narrow and are influenced by temperature both below and above-170 K, the glass transition temperature. The thermal evolution of the CO binding kinetics between-50 K and-170 K indicates the presence of some degree of structural relaxation, even in this temperature range. Above-220 K the width of the g(H progressively decreases, and at 280 K geminate CO binding becomes exponential in time. Based on a comparison with analogous investigations of the homodimeric hemoglobin from Scapharca inaequivalvis, we propose a link between dynamic properties and functional complexity.
Small-angle X-ray study on the quaternary structure of erythrocruorin from Caenestheria inopinata
International Journal of Biological Macromolecules, 1991
The erythrocruorin from the aquatic snail Helisoma trivolvis was studied in sodium phosphate buffer at pH 6.7 by small angle X-ray scattering. The following molecular parameters were determined: radius of gyration 9.4 +_ 0.1 nm and maximum dimension 29+_1 nm. A model which fits the experimental data well is presented. The overall shape is best described by a slightly ellipsoidal shape with a hole in the centre. A model consisting of 12 subunits forming a slightly ellipsoidal shape fits very well all scattering data.
Structural hierarchy in erythrocruorin, the giant respiratory assemblage of annelids
Proceedings of the National Academy of Sciences, 2000
Many annelids, including the earthworm Lumbricus terrestris, have giant cooperative respiratory proteins (molecular masses greater than 3.5 million Da) freely dissolved in the blood, rather than packaged in cells. These complexes, termed either erythrocruorins or hemoglobins, are assembled from many copies of both hemoglobin subunits and nonhemoglobin or ''linker'' subunits. In this paper, we present the crystal structure of Lumbricus erythrocruorin at 5.5-Å resolution, which reveals a remarkable hierarchical organization of 144 oxygen-binding hemoglobin subunits and 36 nonhemoglobin linker subunits. The hemoglobin chains arrange in novel dodecameric substructures. Twelve trimeric linker complexes project triple-stranded helical coiled-coil ''spokes'' toward the center of the complex; interdigitation of these spokes appears crucial for stabilization. The resulting complex of linker chains forms a scaffold on which twelve hemoglobin dodecamers assemble. This structure specifies the unique, self-limited assemblage of a highly cooperative single molecule.
Subunit structure of earthworm erythrocruorin
Journal of molecular biology, 1974
The subunit structure of earthworm erythrocruorin was studied. The native protein was found to have a sedimentation coefficient of 01.1 S and a molecular weight, as determined by sedimentation equilibrium, of 3.84 x 106. Dissociation of the 60 S molecule was observed at acid and basic pH. Calcium ion was found to prevent dissociation in the basic range. Dissociated species of 10.1, 3.5 and 2.3 S were isolated and their molecular weights determined to be 163 x 103, 41 x lo3 and 22 x 103, respectively. On a molecular weight basis, the native molecule consists of twenty-four 10 S subunits, each of which is composed of four 3.6 S units, which are further divided into two 2.3 S units. The 2.3 S species contains a single heme per molecule. A model of the 60 S molecule, where the twenty-four 10 S subunits are arranged into four concentric layers of six subunits each, is proposed. Support for this arrangement is provided by the excellent agreement between the sedimentation coefficient of a 1/24th unit calculated by the application of Kirkwood's (1954) theory with the experimentally determined sedimentation coefficient of the 10 S subunit. An 88 S aggregate observed at the transition pH of acid dissociation is attributed to a side-by-side association dimer of the 60 S molecule.
Article Symmetry versus Asymmetry in the Molecules of Life: Homomeric Protein Assemblies
2010
The essay is dedicated to the relation of symmetry and asymmetry-chirality in Nature. The Introduction defines symmetry and its impact on basic definitions in science and human activities. The following section Chirality of molecules reveals breifly development of notion of chirality and its significance in living organisms and science. Homochirality is a characteristic hallmark of life and its significance is presented in the section Homochirality of Life. Proteins, important constituents of living cells performing versatile functions are chiral macromolecules composed of L-amino acids. In particular, the protein assemblies are of a great importance in functions of a cell. Therefore, they have attracted researches to examine them from different points of view. Among proteins of known three-dimensional structures about 50-80% of them exist as homomeric protein complexes. Protein monomers lack any intrinsic, underlying symmetry, i.e. enantiomorphic protein molecules involve left-handed amino acids but their asymmetry does not appear to extend to the level of quaternary structures (homomeric complexes) as observed by Chothia in 1991. In the section Homomeric assemblies we performed our analysis of very special cases of homomers revealing non-crystallographic symmetry in crystals. Homochiral proteins can crystallize only in enantiomorphic space groups. Among 230 existing space groups 65 are enantiomorphic containing limited symmetry elements that are rotation and screw-rotation axes. Any axis of rotation symmetry of a crystal lattice must be twofold , threefold , four-fold, or six-fold. Five-fold, seven-fold, and higher-fold rotation symmetry axes are incompatible with the symmetry under spatial displacement of the three-dimensional crystal lattice.
Molecular Symmetry of the Dodecamer Subunit ofLumbricus terrestrishemoglobin
Journal of Molecular Biology, 1996
The principal functional subunit of the 03500 kDa extracellular Lumbricus terrestris hemoglobin is a 213 kDa dodecamer of four chemically distinct Wayne State University globin chains, consisting of a non-covalent complex of three trimer submits School of Medicine, Detroit (disulfide-bonded chains a, b and c) and three monomer subunits (chain d). MI 48201, USA X-ray diffraction of crystals of the dodecamer grown at neutral pH, were 2 Department of Physiology found to be monoclinic, with the unit cell dimensions: a = 112.3 Å, Wayne State University b = 190.0 Å, c = 69.6 Å, b = 102.0°with h + k + l = 2n + 1 absent, character-School of Medicine, Detroit istic of space group I121. In addition, these crystals exhibit a pseudo MI 48201, USA trigonal P321 symmetry with unit cell dimensions a = 190.5 Å, b = 190.5 Å, c = 69.5 Å, g = 120.0°. Assuming that the assymetric unit contains an entire 3 Institute of Crystallography dodecamer, a model of the latter was constructed that satisfies the Russian Academy of Sciences symmetry of the trigonal pseudo cell and is consistent with the symmetry 117333, Moscow, Russia of the I121 crystallographic cell. The resulting model has strong implications concerning the hexagonal bilayer structure of the native hemoglobin.
The 8.5Å Projection Structure of the Core RC–LH1–PufX Dimer of Rhodobacter sphaeroides
Journal of Molecular Biology, 2005
2D crystals of dimeric photosynthetic reaction centre-LH1-PufX complexes have been analysed by cryoelectron microscopy. The 8.5 Å resolution projection map extends previous analyses of complexes within native membranes to reveal the a-helical structure of two reaction centres and 28 LH1 ab subunits within the dimer. For the first time, we have achieved sufficient resolution to suggest a possible location for the PufX transmembrane helix, the orientation of the RC and the arrangement of helices within the surrounding LH1 complex. Whereas low-resolution projections have shown an apparent break in the LH1, our current map reveals a diffuse density within this region, possibly reflecting high mobility. Within this region the separation between b14 of one monomer and b2 of the other monomer is w6 Å larger than the average b-b spacing within LH1; we propose that this is sufficient for exchange of quinol at the RC Q B site. We have determined the position and orientation of the RC within the dimer, placing its Q B site adjacent to the putative PufX, with access to the point in LH1 that appears most easily breached. PufX appears to occupy a strategic position between the mobile ab14 subunit and the Q B site, suggesting how the structure, possibly coupled with a flexible ring, plays a role in optimizing quinone exchange during photosynthesis.
The Journal of Physical Chemistry B, 1997
The X-ray crystal structures of synthetic and protein-bound metalloporphyrins are analyzed using a new normal structural decomposition method for classifying and quantifying their out-of-plane and in-plane distortions. These distortions are characterized in terms of equivalent displacements along the normal coordinates of the D 4h -symmetric porphyrin macrocycle (normal deformations) by using a computational procedure developed for this purpose. Often it turns out that the macrocyclic structure is, even in highly distorted porphyrins, accurately represented by displacements along only the lowest-frequency normal coordinates. Accordingly, the macrocyclic structure obtained from just the out-of-plane normal deformations of the saddling (sad, B 2u )-, ruffling (ruf, B 1u )-, doming (dom, A 2u )-, waving [waV(x), waV(y); E g ]-, and propellering (pro, A 1u )-type essentially simulates the out-of-plane distortion of the X-ray crystal structure. Similarly, the observed inplane distortions are decomposed into in-plane normal deformations corresponding to the lowest-frequency vibrational modes including macrocycle stretching in the direction of the meso-carbon atoms (meso-str, B 2g ), stretching in the direction of the nitrogen atoms (N-str, B 1g ), x and y pyrrole translations [trn(x), trn(y); E u ], macrocycle breathing (bre, A 1g ), and pyrrole rotation (rot, A 2g ). The finding that the displacements of the 24 atoms of the macrocycle primarily occur along the lowest-frequency normal coordinates is expected on physical grounds and is verified by structural decomposition of more than 100 synthetic and 150 protein-bound metalloporphyrin X-ray crystal structures. Because of the high resolution of the X-ray crystal structures of synthetic metalloporphyrins, the small displacements for other normal coordinates are also able to be discerned. However, for the heme groups in proteins, only the displacements along the lowest-frequency modes are detectable because of the large uncertainties in the atomic positions. The heme groups in the four X-ray crystal structures of deoxyhemoglobin are used to evaluate the structural decomposition method. We find that the corresponding heme groups in different X-ray crystal structures are similar. Furthermore, the outof-plane distortions for the heme groups in the R-and -chains are found to be inequivalent, that is, the two R-heme groups are mainly ruffled and domed whereas the two -heme groups are primarily saddled and domed. In the case of isozyme-1 ferrocytochrome c and its mutants, the heme distortion is not significantly influenced by the point mutations, and the strongly nonplanar structure is most likely the result of interactions of the heme group with a small protein segment, probably the linkage Cys-Leu-Gln-Cys-His. This conclusion is in agreement with previous findings that the heme distortion in cytochrome c is conserved for the proteins for which X-ray crystal structures exist and significant structural variation occurs only when an amino acid difference appears in Cys-X-Y-Cys-His segment. A similar conclusion is suggested by the structural decomposition results of the four heme groups in cytochromes c 3 . The analogous covalently linked peptide segments vary for each heme group, giving different distortions for the four hemes. Nevertheless, the distinctive distortion of each heme group is conserved for cytochromes c 3 from different species as long as the short peptide sequences between the cysteine linkages are homologous.