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排序方式: 共有409条查询结果,搜索用时 46 毫秒
321.
Tommaso Prosdocimi Luca De Gioia Giuseppe Zampella Luca Bertini 《Journal of biological inorganic chemistry》2016,21(2):197-212
According to different studies, the interaction between amyloid β-peptide (Aβ) and copper ions could yield radical oxygen species production, in particular the highly toxic hydroxyl radical OH· that is suspected to contribute to Alzheimer’s disease pathogenesis. Despite intensive experimental and computational studies, the nature of the interaction between copper and Aβ peptide, as well as the redox reactivity of the system, are still matter of debate. It was proposed that in Cu(II) → Cu(I) reduction the complex Cu(II)–Aβ could follow a multi-step conformational change with redox active intermediates that may be responsible for OH· radical production from H2O2 through a Fenton-like process. The purpose of this work is to evaluate, using ab initio Density Functional Theory computations, the reactivity of different Cu(I)–Aβ coordination modes proposed in the literature, in terms of OH· production. For each coordination model, we considered the corresponding H2O2 adduct and performed a potential energy surface scan along the reaction coordinate of O–O bond dissociation of the peroxide, resulting in the production of OH· radical, obtaining reaction profiles for the evaluation of the energetic of the process. This procedure allowed us to confirm the hypothesis according to which the most populated Cu(I)–Aβ two-histidine coordination is not able to perform efficiently H2O2 reduction, while a less populated three-coordinated form would be responsible for the OH· production. We show that coordination modes featuring a third nitrogen containing electron-donor ligand (an imidazole ring of an histidine residue is slightly favored over the N-terminal amine group) are more active towards H2O2 reduction. 相似文献
322.
van Dijk AD Ciofi-Baffoni S Banci L Bertini I Boelens R Bonvin AM 《Journal of proteome research》2007,6(4):1530-1539
Proper assembly and function of cytochrome c oxidase, which catalyzes the reduction of O2 and generates the proton gradient driving ATP synthesis, depend on correct copper delivery and incorporation. Structural details about the protein-protein complexes involved in this process are still missing. We describe here models of four complexes along this pathway obtained by combining bioinformatics interface predictions with information-driven docking and discuss their relevance with respect to known and pathogenic mutations. 相似文献
323.
Molecular size has limited solution NMR analyses of proteins. We report 13C–13C NOESY experiments on a 480 kDa protein, the multi-subunit ferritin nanocage with gated pores. By exploiting 13C-resonance-specific chemical shifts and spin diffusion effects, we identified 75% of the amino acids, with intraresidue C–C
connectivities between nuclei separated by 1–4 bonds. These results show the potential of 13C–13C NOESY for solution studies of molecular assemblies >100 kDa. 相似文献
324.
Banci L Bertini I Cantini F Ciofi-Baffoni S Cavet JS Dennison C Graham AI Harvie DR Robinson NJ 《The Journal of biological chemistry》2007,282(41):30181-30188
CmtR from Mycobacterium tuberculosis is a winged helical DNA-binding repressor of the ArsR-SmtB metal-sensing family that senses cadmium and lead. Cadmium-CmtR is a dimer with the metal bound to Cys-102 from the C-terminal region of one subunit and two Cys associated with helix alphaR from the other subunit, forming a symmetrical pair of cadmium-binding sites. This is a significant novelty in the ArsR-SmtB family. The structure of the dimer could be solved at 312 K. The apoprotein at the same temperature is still a dimer, but it experiences a large conformational exchange at the dimer interface and within each monomer. This is monitored by an overall decrease of the number of nuclear Overhauser effects and by an increase of H(2)O-D(2)O exchange rates, especially at the dimeric interface, in the apo form with respect to the cadmium-bound state. The C-terminal tail region is completely unstructured in both apo and cadmium forms but becomes less mobile in the cadmium-bound protein due to the recruitment of Cys-102 as a metal-ligand. DNA binds to the apo dimer with a ratio 1:3 at millimolar concentration. Addition of cadmium to the apo-CmtR-DNA complex causes DNA detachment, restoring the NMR spectrum of free cadmium-CmtR. Cadmium binding across the dimer interface impairs DNA association by excluding the apo-conformers suited to bind DNA. 相似文献
325.
Ivano Bertini Marco Fragai Claudio Luchinat Maxime Melikian Efstratios Mylonas Niko Sarti Dmitri I. Svergun 《The Journal of biological chemistry》2009,284(19):12821-12828
The presence of extensive reciprocal conformational freedom between the
catalytic and the hemopexin-like domains of full-length matrix
metalloproteinase-1 (MMP-1) is demonstrated by NMR and small angle x-ray
scattering experiments. This finding is discussed in relation to the
essentiality of the hemopexin-like domain for the collagenolytic activity of
MMP-1. The conformational freedom experienced by the present system, having
the shortest linker between the two domains, when compared with similar
findings on MMP-12 and MMP-9 having longer and the longest linker within the
family, respectively, suggests this type of conformational freedom to be a
general property of all MMPs.Matrix metalloproteinases
(MMP)2 are
extracellular hydrolytic enzymes involved in a variety of processes including
connective tissue cleavage and remodeling
(1–3).
All 23 members of the family are able to cleave simple peptides derived from
connective tissue components such as collagen, gelatin, elastin, etc. A subset
of MMPs is able to hydrolyze more resistant polymeric substrates, such as
cross-linked elastin, and partially degraded collagen forms, such as gelatin
and type IV collagens (4).
Intact triple helical type I–III collagen is only attacked by
collagenases MMP-1, MMP-8, and MMP-13 and by MMP-2 and MMP-14
(5–12).
Although the detailed mechanism of cleavage of single chain peptides by MMP
has been largely elucidated
(13–19),
little is known about the process of hydrolysis of triple helical collagen. In
fact, triple helical collagen cannot be accommodated in the substrate-binding
groove of the catalytic site of MMPs
(9).All MMPs (but MMP-7) in their active form are constituted by a catalytic
domain (CAT) and a hemopexin-like domain (HPX)
(20–22).
The CAT domain contains two zinc ions and one to three calcium ions. One zinc
ion is at the catalytic site and is responsible for the activity, whereas the
other metal ions have structural roles. The isolated CAT domains retain full
catalytic activity toward simple peptides and single chain polymeric
substrates such as elastin, whereas hydrolysis of triple helical collagen also
requires the presence of the HPX domain
(9,
23–25).
It has been shown that the isolated CAT domain regains a small fraction of the
activity of the full-length (FL) protein when high amounts of either
inactivated full-length proteins or isolated HPX domains are added to the
assay solution (9). Finally, it
has been shown that the presence of the HPX domain alone alters the CD
spectrum of triple helical collagen in a way that suggests its partial
unwinding (26,
27). It is tempting to
speculate that full-length collagenases attack collagen by first locally
unwinding the triple helical structure with the help of the HPX domain and
then cleaving the resulting, exposed, single filaments
(9,
28).Until 2007, three-dimensional structures of full-length MMPs had been
reported only for collagenase MMP-1
(29–31)
and gelatinase MMP-2 (32). The
structures of the two proteins are very similar and show a compact arrangement
of the two domains, which are connected by a short linker (14 and 20 amino
acids, respectively). It is difficult to envisage that rigid and compact
molecules of this type can interact with triple helical collagen in a way that
can lead to first unwinding and then cleavage of individual filaments. It has
been recently suggested that such concerted action could occur much more
easily if the two domains could enjoy at least a partial conformational
independence (9). Slight
differences in the reciprocal orientation of the CAT and HPX domains of MMP-1
in the presence (29) and
absence (30,
31) of the prodomain were
indeed taken as a hint that the two domains could experience relative mobility
(29).Two recent solution studies have shown that conformational independence is
indeed occurring in gelatinase MMP-9
(33) and elastase MMP-12
(34), whereas the x-ray
structure of the latter (34)
is only slightly less compact than those of MMP-1
(29–31)
and MMP-2 (32). Among MMPs,
MMP-9 features an exceptionally long linker (68 amino acid)
(33,
35), which in fact constitutes
a small domain by itself (the O-glycosylated domain)
(33), and therefore, this
inspiring observation can hardly be taken as evidence that conformational
freedom is a general characteristic of the two-domain MMPs. MMP-12 features a
much more normal 16-amino acid linker, thereby making more probable a general
functional role for this conformational freedom
(34). However, both MMP-9 and
MMP-12 retain their full catalytic activity against their substrates even when
deprived of the HPX domain (9).
Therefore, the question remains of whether conformational freedom is also a
required characteristic for those MMPs that are only active as full-length
proteins, i.e. collagenases. Interestingly, the three collagenases
(MMP-1, MMP-8, and MMP-13) have the shortest linker (14 amino acids) among all
MMPs. Demonstrating or negating the presence of conformational freedom in one
of these collagenases would therefore constitute a significant step forward to
formulate mechanistic hypotheses on their collagenolytic activity.Our recent studies on MMP-12 in solution
(34) have shown that a
combination of NMR relaxation studies and small angle x-ray scattering (SAXS)
is enough to show the presence and the extent of the relative conformational
freedom of the two domains of MMPs. Here we apply the same strategy to
full-length MMP-1 and show that sizable conformational freedom is indeed
experienced even by this prototypical collagenase, although somewhat less
pronounced than that observed for MMP-12. 相似文献
326.
327.
Bioinformatics is a central discipline in modern life sciences aimed at describing the complex properties of living organisms starting from large-scale data sets of cellular constituents such as genes and proteins. In order for this wealth of information to provide useful biological knowledge, databases and software tools for data collection, analysis and interpretation need to be developed. In this paper, we review recent advances in the design and implementation of bioinformatics resources devoted to the study of metals in biological systems, a research field traditionally at the heart of bioinorganic chemistry. We show how metalloproteomes can be extracted from genome sequences, how structural properties can be related to function, how databases can be implemented, and how hints on interactions can be obtained from bioinformatics. 相似文献
328.
1H NMR spectroscopic characterization of binary and ternary complexes of cobalt(II) carboxypeptidase A with inhibitors 总被引:1,自引:0,他引:1
The binding of L- and D-phenylalanine and carboxylate inhibitors to cobalt(II)-substituted carboxypeptidase A, Co(II)CPD (E), in the presence and absence of pseudohalogens (X = N3-, NCO-, and NCS-) has been studied by 1H NMR spectroscopy. This technique monitors the proton signals of histidine residues bound to cobalt(II) and is therefore sensitive to the interactions of inhibitors that perturb the coordination sphere of the metal. Enzyme-inhibitor complexes, E.I, E.I2, and E.I.X, each with characteristic NMR features, have been identified. Thus, for example, L-Phe binds close to the metal ion to form a 1:1 complex, whereas D-Phe binds stepwise, first to a nonmetal site and then to the metal ion to form a 2:1 complex. Both acetate and phenylacetate also form 2:1 adducts stepwise with the enzyme, but beta-phenylpropionate gives a 2:1 complex without any detectable 1:1 intermediate. N3-, NCO-, and NCS- generate E.I.X ternary complexes directly with Co(II)CPD.L-Phe and indirectly with the D-Phe and carboxylate inhibitor 2:1 complexes by displacing the second moiety from its metal binding site. The NMR data suggest that when the carboxylate group of a substrate or inhibitor binds at the active site, a conformational change occurs that allows a second ligand molecule to bind to the metal ion, altering its coordination sphere and thereby attenuating the bidentate behavior of Glu-72. The 1H NMR signals also reflect alterations in the histidine interactions with the metal upon inhibitor binding. Isotropic shifts in the signals for the C-4 (c) and N protons (a) of one of the histidine ligands are readily observed in all of these complexes.(ABSTRACT TRUNCATED AT 250 WORDS) 相似文献
329.
Interaction of anions with the active site of carboxypeptidase A 总被引:1,自引:0,他引:1
Studies of azide inhibition of peptide hydrolysis catalyzed by cobalt(II) carboxypeptidase A identify two anion binding sites. Azide binding to the first site (KI = 35 mM) inhibits peptide hydrolysis in a partial competitive mode while binding at the second site (KI = 1.5 M) results in competitive inhibition. The cobalt electronic absorption spectrum is insensitive to azide binding at the first site but shows marked changes upon azide binding to the second site. Thus, azide elicits a spectral change with new lambda max (epsilon M) values of 590 (330) and 540 nm (190) and a KD of 1.4 M, equal to the second kinetic KI value for the cobalt enzyme, indicating that anion binding at the weaker site involves an interaction with the active-site metal. Remarkably, in the presence of the C-terminal products of peptide or ester hydrolysis or carboxylate inhibitor analogues, anion (e.g., azide, cyanate, and thiocyanate) binding is strongly synergistic; thus, KD for azide decreases to 4 mM in the presence of L-phenylalanine. These ternary complexes have characteristic absorption, CD, MCD, and EPR spectra. The absorption spectra of azide/carboxylate inhibitor ternary complexes with Co(II)CPD display a near-UV band between 305 and 310 nm with epsilon M values around 900-1250 M-1 cm-1. The lambda max values are close to the those of the charge-transfer band of an aquo Co(II)-azide complex (310 nm), consistent with the presence of a metal azide bond in the enzyme complex.(ABSTRACT TRUNCATED AT 250 WORDS) 相似文献
330.
R Bicknell A Schaeffer D S Auld J F Riordan R Monnanni I Bertini 《Biochemical and biophysical research communications》1985,133(2):787-793
Proteases in preparations of carboxypeptidase A progressively inactivate solutions of the apoenzyme but not the metal-containing enzyme. Free amino acids generated by proteolysis interfere with spectral studies after reconstituting the apoenzyme with cobalt. Purification by affinity chromatography eliminates this effect. Affinity-purified apoenzyme is susceptible to digestion with chymotrypsin but the metalloenzyme is not. 相似文献