Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:Q86TM3 (cage)
 29,987 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Two types of isopentenyl diphosphate:dimethylallyl diphosphate isomerases (IDI) have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. Here, we report the first structure of an IDI-2 from Bacillus subtilis at 1.9A resolution in the ligand-free form and of the FMN-bound form at 2.8A resolution. The enzyme is an octamer that forms a D4 symmetrical open, cage-like structure. The monomers of 45 kDa display a classical TIM barrel fold. FMN is bound only with very moderate affinity and is therefore completely lost during purification. However, the enzyme can be reconstituted in the crystals by soaking with FMN. Three glycine-rich sequence stretches that are characteristic for IDI-2 participate in FMN binding within the interior of the cage. Regions harboring strictly conserved residues that are implicated in substrate binding or catalysis remain largely disordered even in the presence of FMN.
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PMID:Crystal structure of the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Bacillus subtilis. 1279 87

The La2@C72 metallofullerene having the so-called "missing" C72 fullerene cage was structurally elucidated by using 13C NMR and 139La NMR spectroscopy. The obtained structure of La2@C72 does not satisfy fullerene's structural golden rule, that is, the isolated-pentagon rule. The structure is consistent with a non-IPR D2-C72 (#10611) cage structure where each La atom is situated close to one of the two-fused pentagons.
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PMID:Structure of a missing-caged metallofullerene: La2@C72. 1282 79

Owing to the unique feature of the non-IPR D3 (isomer 6140) C68 cage (IPR=isolated pentagon rule), Sc3N@C68 has been attracting great interest in the fullerene community. Herein we report the first high-yield synthesis of Sc3N@C68 by the "reactive gas atmosphere" method and its facile isolation by single-step HPLC to a high purity (>or=99 %). Thus, Sc3N@C68 is isolated in sufficient quantities for its further spectroscopic characterization, while the high purity of the sample ensures the reliability of the spectroscopic data obtained. In particular, the electronic and vibrational structures of Sc3N@C68 were studied in detail experimentally and by theoretical computations. The assignment of the observed absorption bands to particular electronic transitions is given in detail on the basis of time-dependent DFT computations. Vibrational spectroscopy of Sc3N@C68 reveals good agreement between the measured spectra and the theoretically calculated spectra. A detailed assignment of the vibrational modes, including the Sc3N cluster modes, cage modes, and vibrations of the adjacent pentagons are discussed. This study reveals that the effect of Sc3N encapsulation in the cage is much more complicated than just a formal transfer of six electrons. Consequently the electronic and vibrational spectra of the carbon cage in Sc3N@C68 cannot be adequately understood on the basis of a C68 (6-) cage alone.
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PMID:A facile route to the non-IPR fullerene Sc3N@C68: synthesis, spectroscopic characterization, and density functional theory computations (IPR=isolated pentagon rule). 1693 46

The structure of isomer 2 of Tb3N@C84 has been determined through single-crystal X-ray diffraction on Tb3N@C84.NiII(OEP).2(C6H6). The carbon cage has a distinct egg shape due to the presence of a single pair of fused pentagons at one apex of the molecule. Thus, although 24 IPR structures are available to the C84 cage, Nature utilizes one of the 51 568 isomeric structures that do not conform to the IPR for this unusual molecule. The Tb3N portion of isomer 2 of Tb3N@C84 is strictly planar. One Tb atom is nestled within the fold of the fused pentagons, while the other Tb atoms are disordered over four pairs of sites.
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PMID:Tb3N@C84: an improbable, egg-shaped endohedral fullerene that violates the isolated pentagon rule. 1693 48

We show here that La@C72 has a non-IPR cage, unique electronic properties, and high reactivity by the spectroscopic and X-ray crystallographic analysis and the theoretical study. The isolation of La@C72 as a stable derivative might constitute an important stepping-stone on the way to isolation of these unknown metallofullerenes and open new material science of metallofullerenes.
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PMID:La@C72 having a non-IPR carbon cage. 1707 75

The recent finding that isomer 2 of Tb(3)N@C(84) uses one of the 51,568 possible nonisolated pentagon rule (non-IPR) structures for the C(84) cage rather than one of the 24 cage isomers that do obey the IPR suggests that further experimental work on the structure of larger endohedrals is needed to observe the utility of the IPR rule in this uncharted territory. The structures of the newly synthesized endohedral fullerenes--Tb(3)N@C(88), Tb(3)N@C(86), and the Ih and D(5)(h) isomers of Tb(3)N@C(80)--have been determined by single-crystal X-ray diffraction on samples cocrystallized with NiII(octaethylporphyrin). In contrast to the situation for isomer 2 of Tb(3)N@C(84), the structures of Tb(3)N@C(88) and Tb(3)N@C(86) do conform to the IPR. Both Tb(3)N@C(88) and Tb(3)N@C(86) have chiral structures with D(2) symmetry for Tb(3)N@C(880 and D(3) symmetry for Tb(3)N@C(86). Within this group of endohedrals, the size of the carbon cage affects the Tb-N and Tb-C distances, the orientations of the carbon cage with respect to the porphyrin plane, the locations of the metal ions and their orientations relative to the porphyrin plane, and the degree of pyramidalization of the Tb(3)N unit.
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PMID:Isolation and structural characterization of a family of endohedral fullerenes including the large, chiral cage fullerenes Tb(3)N@C(88) and Tb(3)N@C(86) as well as the I(h) and D(5)(h) isomers of Tb(3)N@C(80). 1725 57

Molecular structures of Dy(3)N@C(78) and Tm(3)N@C(78) clusterfullerenes are addressed by the IR and Raman vibrational spectroscopic studies and density functional theory (DFT) computations. First, extensive semiempirical calculations of 2927 isomers of C(78) hexaanions followed by DFT optimization were applied to establish their relative stability. Then, DFT calculations of a series of M(3)N@C(78) (M = Sc, Y, Lu, La) isomers were performed which have shown that the stability order of the isomers depends on the cluster size. While the Sc(3)N cluster is planar in the earlier reported Sc(3)N@C(78) (D(3)h: 24,109) clusterfullerenes, relatively large Y(3)N and Lu(3)N clusters would be forced to be pyramidal inside this cage, which would result in their destabilization. Instead, these clusters remain planar in the nonisolated pentagon rule (non-IPR) C(2): 22,010 isomer making Y(3)N@C(78) and Lu(3)N@C(78) clusterfullerenes with this cage structure the most stable ones. Finally, on the basis of a detailed analysis of their IR and Raman spectra supplemented with DFT vibrational calculations, the recently isolated Tm(3)N@C(78) and the major isomer of Dy(3)N@C(78) are assigned to the non-IPR C(2): 22,010 cage structure. A detailed assignment of their experimental and computed IR and Raman spectra is provided to support this conclusion and to exclude other cage isomers.
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PMID:C78 cage isomerism defined by trimetallic nitride cluster size: a computational and vibrational spectroscopic study. 1738 9

Extensive semiempirical calculations of the hexaanions of IPR (isolated pentagon rule) and non-IPR isomers of C(68)-C(88) and IPR isomers of C(90)-C(98) followed by DFT calculations of the lowest energy structures were performed to find the carbon cages that can provide the most stable isomers of M(3)N@C(2n) clusterfullerenes (M = Sc, Y) with Y as a model for rare earth ions. DFT calculations of isomers of M(3)N@C(2n) (M = Sc, Y; 2n = 68-98) based on the most stable C(2n)(6-) cages were also performed. The lowest energy isomers found by this methodology for Sc(3)N@C(68), Sc(3)N@C(78), Sc(3)N@C(80), Y(3)N@C(78), Y(3)N@C(80), Y(3)N@C(84), Y(3)N@C(86), and Y(3)N@C(88) are those that have been shown to exist by single-crystal X-ray studies as Sc(3)N@C(2n) (2n = 68, 78, 80), Dy(3)N@C(80), and Tb(3)N@C(2n) (2n = 80, 84, 86, 88) clusterfullerenes. Reassignment of the carbon cage of Sc(2)@C(76) to the non-IPR Cs: 17490 isomer is also proposed. The stability of nitride clusterfullerenes was found to correlate well with the stability of the empty 6-fold charged cages. However, the dimensions of the cage in terms of its ability to encapsulate M(3)N clusters were also found to be an important factor, especially for the medium size cages and the large Y(3)N cluster. In some cases the most stable structures are based on the different cage isomers for Sc(3)N and Y(3)N clusters. Up to the cage size of C(84), non-IPR isomers of C(2n)(6-) and M(3)N@C(2n) were found to compete with or to be even more stable than IPR isomers. However, the number of adjacent pentagon pairs in the most stable non-IPR isomers decreases as cage size increases: the most stable M(3)N@C(2n) isomers have three such pairs for 2n = 68-72, two pairs for n = 74-80, and only one pair for n = 82, 84. For C(86) and C(88) the lowest energy IPR isomers are much more stable than any non-IPR isomer. The trends in the stability of the fullerene isomers and the cluster-cage binding energies are discussed, and general rules for stability of clusterfullerenes are established. Finally, the high yield of M(3)N@C(80) (Ih) clusterfullerenes for any metal is explained by the exceptional stability of the C(80)(6-) (Ih: 31924) cage, rationalized by the optimum distribution of the pentagons leading to the minimization of the steric strain, and structural similarities of C(80) (Ih: 31924) with the lowest energy non-IPR isomers of C(760(6-), C(78)(6-), C(82)(6-), and C(84)(6-) pointed out.
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PMID:Structure, stability, and cluster-cage interactions in nitride clusterfullerenes M3N@C2n (M = Sc, Y; 2n = 68-98): a density functional theory study. 1776 Apr 44

The first non-IPR C(76) cage based on a mixed metal nitride cluster, DySc(2)N@C(76), was successfully synthesized and isolated. DySc(2)N@C(76) is a stable fullerene with a small band gap of 0.96 eV. According to the FTIR spectroscopic study in combination with extensive DFT calculations, the cage structure of DySc(2)N@C(76) has been assigned to the non-IPR C(s): 17490-I isomer having two pairs of the adjacent pentagons. DySc(2)N@C(76)provides the first example of stabilization of the non-IPR C(76) cage by encapsulation of an asymmetric DySc(2)N mixed cluster, revealing the role of the cluster structure on the stability of the fullerene cage. As the asymmetric DySc(2)N cluster has a more suitable geometry for the inner space of the C(76) cage compared to that of the homogeneous clusters like Sc(3)N or Dy(3)N, the highest yield for C(76)-based cluster fullerenes with the Dy(x)Sc(3)-(x)N mixed nitride cluster is achieved for the DySc(2)N@C(76)
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PMID:The role of an asymmetric nitride cluster on a fullerene cage: the non-IPR endohedral DySc2N@C76. 1800 40

Although there are 51 568 non-IPR and 24 IPR structures for C84, the egg-shaped endohedral fullerenes Tm3N@C(s)(51 365)-C84 and Gd3N@C(s)(51 365)-C84 utilize the same non-IPR cage structure as found initially for Tb3N@C(s)(51 365)-C84.
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PMID:New egg-shaped fullerenes: non-isolated pentagon structures of Tm3N@C(s)(51 365)-C84 and Gd3N@C(s)(51 365)-C84. 1829 92


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