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1.
In this work, by applying a non-deterministic, randomly-oriented minimal force to the dissociated CO ligand of the MauG-CO system, the molecular-dynamics (MD) behavior of this system could be quickly unraveled. It turned out that CO has no marked directional egress from the high-spin c-heme iron distal pocket. Rather, CO is able to exploit all interstices created during the protein fluctuations. Nonetheless, no steady route toward the surrounding solvent was ever observed: CO jumped first into other binding pockets before being able to escape the protein. In a few cases, on hitting the surrounding H(2) O molecules, CO was observed to reverse direction, re-entering the protein. A contention that conformational inversion of the P107 ring provides a gate to the iron ion is not supported by the present simulations.  相似文献   

2.
The iron‐sulfur protein 1 (Isu1) and the J‐type co‐chaperone Jac1 from yeast are part of a huge ATP‐dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron‐sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1–Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I‐TASSER server and YASARA software and thereafter tested for stability in the all‐atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1–Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse‐grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the Γ‐shaped Jac1 molecule by the β‐sheet section of Isu1. Residues L105, L109, and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J Mol Biol 2012; 417:1–12). These residues were also found, by UNRES/molecular dynamics simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N95, T98, P102, H112, V159, L167, and A170 of Jac1, not yet tested experimentally, were also found to be important in binding. Proteins 2015; 83:1414–1426. © 2015 Wiley Periodicals, Inc.  相似文献   

3.
Iron deficiency leads to abnormal expression and function of band 3 protein in erythrocytes, but the underlying mechanisms remain elusive. The mRNA of erythroid‐specific 5‐aminolevulinate synthase (eALAS) contains an iron response element and the eALAS protein is an important mediator of iron utilization by erythrocytes. In this study, we investigated the effect of short hairpin RNA (shRNA) mediated silencing of eALAS on the expression of band 3 protein induced by iron. By real‐time RT‐PCR and Western blot we showed that at mRNA and protein level iron‐induced expression of band 3 protein was lower in eALAS‐shRNA transfected K562 cells than in control cells. Of note, the lowest expression was detected in K562 cells cultured in iron deficiency condition (p < 0.01). Thus either iron deficiency or depletion of eALAS could suppress the expression of erythroid band 3 protein. These results demonstrated for the first time that iron and the iron‐regulatory system regulate the expression of the erythrocyte membrane proteins. Copyright © 2010 John Wiley & Sons, Ltd.  相似文献   

4.
The aim of this investigation was to test the hypothesis that elevation of intracellular pH would inhibit iron uptake by reticulocytes. The experiments were performed with rabbit reticulocytes and iron bound to rabbit transferrin. Incubation of the cells with NH4Cl, (NH4)2CO3, CH3NH2 and (CH3)2NH was used in an attempt to increase intracellular pH. These substances were all found to inhibit iron uptake by reticulocytes. The mechanism of action of NH4Cl and CH3NH2 was investigated in detail. Similar results were found with both reagents. They inhibited iron uptake in a concentration-dependent manner, but produced a small increase in the cellular uptake of transferrin. The onset of action was rapid and the effect was reversible. There was no decrease in the number of transferrin-binding sites per cell and their apparent affinity for transferrin increased slightly, while the efficiency of iron removal from transferrin per binding site diminished greatly. The rate of transferrin release from reticulocytes was unaffected. NH4Cl did not affect the rate of iron release from transferrin in a cell-free system. Incubation of reticulocytes with 10 mM NH4Cl or CH3NH2 was found to produce an increase in intracellular pH of 0.05—0.15 pH units. The intracellular pH determined by used of the weak acid 5,5-dimethyl-oxazolidine-2,4-dione was significantly higher than that obtained with the weak base (CH3)2NH. By transmission electron microscopy it was shown that reticulocytes treated with NH4Cl or CH3NH2 have enlarged intracellular vesicles. The results are considered to support the hypothesis that iron release from transferrin in reticulocytes occurs as a result of protonation of the transferrin within intracellular vesicles. According to this hypothesis, weak bases such as NH3 and CH3NH2 inhibit iron release by neutralizing H+ within the vesicles.  相似文献   

5.
The backbone NH groups of proteins can form N1N3‐bridges to δ‐ve or anionic acceptor atoms when the tripeptide in which they occur orients them appropriately, as in the RL and LR nest motifs, which have dihedral angles 1,2‐αRαL and 1,2‐αLαR, respectively. We searched a protein database for structures with backbone N1N3‐bridging to anionic atoms of the polypeptide chain and found that RL and LR nests together accounted for 92% of examples found (88% RL nests, 4% LR nests). Almost all the remaining 8% of N1N3‐bridges were found within a third tripeptide motif which has not been described previously. We term this a “crown,” because of the disposition of the tripeptide CO groups relative to the three NH groups and the acceptor oxygen anion, and the crown together with its bridged anion we term a “crown bridge.” At position 2 of these structures the dihedral angles have a tight αR distribution, but at position 1 they have a wider distribution, with ? and ψ values generally being lower than those at position 1. Over half of crown bridges involve the backbone CO group three residues N‐terminal to the tripeptide, the remainder being to other main‐chain or side‐chain carbonyl groups. As with nests, bridging of crowns to oxygen atoms within ligands was observed, as was bridging to the sulfur atom of an iron‐sulfur cluster. This latter property may be of significance for protein evolution. Proteins 2015; 83:2067–2076. © 2015 Wiley Periodicals, Inc.  相似文献   

6.
Iron is a member of a small group of nutrients that limits aquatic primary production. Mechanisms for utilizing iron have to be efficient and adapted according to the ecological niche. In respect to iron acquisition cyanobacteria, prokaryotic oxygen evolving photosynthetic organisms can be divided into siderophore‐ and non‐siderophore‐producing strains. The results presented in this paper suggest that the situation is far more complex. To understand the bioavailability of different iron substrates and the advantages of various uptake strategies, we examined iron uptake mechanisms in the siderophore‐producing cyanobacterium Anabaena sp. PCC 7120. Comparison of the uptake of iron complexed with exogenous (desferrioxamine B, DFB) or to self‐secreted (schizokinen) siderophores by Anabaena sp. revealed that uptake of the endogenous produced siderophore complexed to iron is more efficient. In addition, Anabaena sp. is able to take up dissolved, ferric iron hydroxide species (Fe′) via a reductive mechanism. Thus, Anabaena sp. exhibits both, siderophore‐ and non‐siderophore‐mediated iron uptake. While assimilation of Fe′ and FeDFB are not induced by iron starvation, FeSchizokinen uptake rates increase with increasing iron starvation. Consequently, we suggest that Fe′ reduction and uptake is advantageous for low‐density cultures, while at higher densities siderophore uptake is preferred.  相似文献   

7.
Seagrass ecosystems are expected to benefit from the global increase in CO 2 in the ocean because the photosynthetic rate of these plants may be Ci‐limited at the current CO 2 level. As well, it is expected that lower external pH will facilitate the nitrate uptake of seagrasses if nitrate is cotransported with H+ across the membrane as in terrestrial plants. Here, we investigate the effects of CO 2 enrichment on both carbon and nitrogen metabolism of the seagrass Zostera noltii in a mesocosm experiment where plants were exposed for 5 months to two experimental CO 2 concentrations (360 and 700 ppm). Both the maximum photosynthetic rate (Pm) and photosynthetic efficiency (α) were higher (1.3‐ and 4.1‐fold, respectively) in plants exposed to CO 2‐enriched conditions. On the other hand, no significant effects of CO 2 enrichment on leaf growth rates were observed, probably due to nitrogen limitation as revealed by the low nitrogen content of leaves. The leaf ammonium uptake rate and glutamine synthetase activity were not significantly affected by increased CO 2 concentrations. On the other hand, the leaf nitrate uptake rate of plants exposed to CO 2‐enriched conditions was fourfold lower than the uptake of plants exposed to current CO 2 level, suggesting that in the seagrass Z. noltii nitrate is not cotransported with H+ as in terrestrial plants. In contrast, the activity of nitrate reductase was threefold higher in plant leaves grown at high‐CO 2 concentrations. Our results suggest that the global effects of CO 2 on seagrass production may be spatially heterogeneous and depend on the specific nitrogen availability of each system. Under a CO 2 increase scenario, the natural levels of nutrients will probably become limiting for Z. noltii. This potential limitation becomes more relevant because the expected positive effect of CO 2 increase on nitrate uptake rate was not confirmed.  相似文献   

8.
A functional proteomic technology using protein chip and molecular simulation was used to demonstrate a novel biomolecular interaction between P11, a peptide containing the Ser‐Asp‐Val (SDV) sequence and integrin αvβ3. P11 (HSDVHK) is a novel antagonistic peptide of integrin αvβ3 screened from hexapeptide library through protein chip system. An in silico docking study and competitive protein chip assay revealed that the SDV sequence of P11 is able to create a stable inhibitory complex onto the vitronectin‐binding site of integrin αvβ3. The Arg‐Gly‐Asp (RGD)‐binding site recognition by P11 was site specific because the P11 was inactive for the complex formation of a denatured form of integrin–vitronectin. P11 showed a strong antagonism against αvβ3‐GRGDSP interaction with an IC50 value of 25.72±3.34 nM, whereas the value of GRGDSP peptide was 1968.73±444.32 nM. The binding‐free energies calculated from the docking simulations for each P11 and RGD peptide were ?3.99 and ?3.10 kcal/mol, respectively. The free energy difference between P11 and RGD corresponds to approximately a 4.5‐fold lower Ki value for the P11 than the RGD peptide. The binding orientation of the docked P11 was similar to the crystal structure of the RGD in αvβ3. The analyzed docked poses suggest that a divalent metal–ion coordination was a common driving force for the formation of both SDV/αvβ3 and RGD/αvβ3 complexes. This is the first report on the specific recognition of the RGD‐binding site of αvβ3 by a non‐RGD containing peptide using a computer‐assisted proteomic approach.  相似文献   

9.
10.
Iron acquisition by iron‐limited cyanobacteria is typically considered to be mediated mainly by siderophores, iron‐chelating molecules released by iron‐limited cyanobacteria into the environment. In this set of experiments, iron uptake by iron‐limited cells of the cyanobacterium Anabaena flos‐aquae (L.) Bory was investigated in cells resuspended in siderophore‐free medium. Removal of siderophores decreased iron‐uptake rates by ~60% compared to siderophore‐replete conditions; however, substantial rates of iron uptake remained. In the absence of siderophores, Fe(III) uptake was much more rapid from a weaker synthetic chelator [N‐(2‐hydroxyethyl)ethylenediamine‐N,N′,N′‐triacetic acid (HEDTA); log Kcond = 28.64 for Fe(III)HEDTA(OH)?] than from a very strong chelator [N,N′‐bis(2‐hydroxybenzyl)‐ethylenediamine‐N,N′‐diacetic acid (HBED); log Kcond = 31.40 for Fe(III)HBED?], and increasing chelator:Fe(III) ratios decreased the Fe(III)‐uptake rate; these results were evident in both short‐term (4 h; absence of siderophores) and long‐term (116 h; presence of siderophores) experiments. However, free (nonchelated) Fe(III) provided the most rapid iron uptake in siderophore‐free conditions. The results of the short‐term experiments are consistent with an Fe(III)‐binding/uptake mechanism associated with the cyanobacterial outer membrane that operates independently of extracellular siderophores. Iron uptake was inhibited by temperature‐shock treatments of the cells and by metabolically compromising the cells with diphenyleneiodonium; this finding indicates that the process is dependent on active metabolism to operate and is not simply a passive Fe(III)‐binding mechanism. Overall, these results point to an important, siderophore‐independent iron‐acquisition mechanism by iron‐limited cyanobacterial cells.  相似文献   

11.
Colorectal cancer is a commonly diagnosed cancer in the world. Monoclonal antibody (mAb) CO17‐1A recognizes the tumor‐associated antigen GA733, a cell surface glycoprotein highly expressed in colorectal carcinoma cell, which is considered to be applicable for diagnosis and therapeutic treatment against colorectal cancer. In addition antibodies are glycoproteins, efficiently recognize and eliminate specific pathogenic and disease antigens. We have currently established baculovirus insect cell expression system to produce anti‐colorectal cancer mAb CO17‐1A. In this study, mAb CO17‐1A was expressed in the transgenic insect cell line SfSWT4, in which glycosylation processing pathway has been humanized. Immunoblot confirmed that mAb CO17‐1A properly expressed in SfSWT4 insect cells. mAb CO17‐1A was purified using protein G affinity column. In addition, MALDI‐TOF verified that the mAb CO17‐1A fused to KDEL, endoplasmic reticulum (ER) retention signal (mAb CO17‐1AK) had high mannose type of glycan structure. Migration assay showed that insect cell‐derived mAb CO17‐1AK (mAbI CO17‐1AK) with high mannose type of glycan structure was effective as mammalian‐derived mAb CO17‐1A (mAbM CO17‐1A) in inhibition of metastasis. Kinetic analysis of antigen‐antibody interaction using Surface Plasmon Resonance (SPR) confirmed that mAbI CO17‐1AK is efficient to interact with antigen GA733 as mAbM CO17‐1A. These results suggest that the insect cell expression system with the SfSWT4 possibly can be used as a useful alternative way to produce full‐size mAb for cancer immunotherapy.  相似文献   

12.
Oligodendrocytes stain more strongly for iron than any other cell in the CNS, and they require iron for the production of myelin. For most cell types transferrin is the major iron delivery protein, yet neither transferrin receptor protein nor mRNA are detectable in mature oligodendrocytes. Thus an alternative iron delivery mechanism must exist. Given the significant long term consequences of developmental iron deficiency and the iron requirements for normal myelination, identification of the iron delivery mechanism for oligodendrocytes is important. Previously we have reported that oligodendrocytes bind H‐ferritin and that H‐ferritin binds to white matter tracts in vivo. Recently, T cell immunoglobulin and mucin domain‐containing protein‐2 (Tim‐2) was shown to bind and internalize H‐ferritin. In the present study we show that Tim‐2 is expressed on oligodendrocytes both in vivo and in vitro. Further, the onset of saturable H‐ferritin binding in CG4 oligodendrocyte cell line is accompanied by Tim‐2 expression. Application of a blocking antibody to the extracellular domain of Tim‐2 significantly reduces H‐ferritin binding to the differentiated CG4 cells and primary oligodendrocytes. Tim‐2 expression on CG4 cells is responsive to iron; decreasing with iron loading and increasing with iron chelation. Taken together, these data provide compelling evidence that Tim‐2 is the H‐ferritin receptor on oligodendrocytes suggesting it is the primary mechanism for iron acquisition by these cells.  相似文献   

13.
Makino M  Sawai H  Shiro Y  Sugimoto H 《Proteins》2011,79(4):1143-1153
Cytoglobin (Cgb) is a vertebrate heme‐containing globin‐protein expressed in a broad range of mammalian tissues. Unlike myoglobin, Cgb displays a hexa‐coordinated (bis‐hystidyl) heme iron atom, having the heme distal His81(E7) residue as the endogenous sixth ligand. In the present study, we crystallized human Cgb in the presence of a reductant Na2S2O4 under a carbon monoxide (CO) atmosphere, and determined the crystal structure at 2.6 Å resolution. The CO ligand occupies the sixth axial position of the heme ferrous iron. Eventually, the imidazole group of His81(E7) is expelled from the sixth position and swings out of the distal heme pocket. The flipping motion of the His81 imidazole group accompanies structural readjustments of some residues (Gln62, Phe63, Gln72, and Ser75) in both the CD‐corner and D‐helix regions of Cgb. On the other hand, no significant structural changes were observed in other Cgb regions, for example, on the proximal side. These structural alterations that occurred as a result of exogenous ligand (CO) binding are clearly different from those observed in other vertebrate hexa‐coordinated globins (mouse neuroglobin, Drosophila melanogaster hemoglobin) and penta‐coordinated sperm whale myoglobin. The present study provides the structural basis for further discussion of the unique ligand‐binding properties of Cgb. Proteins 2011. © 2011 Wiley‐Liss, Inc.  相似文献   

14.
This work describes an investigation of pathways and binging pockets (BPs) for dioxygen (O2) through the cofactorless oxygenase 3‐hydroxy‐2‐methylquinolin‐4‐one 2,4‐dioxygenase in complex with its natural substrate, 3‐hydroxy‐2‐methylquinolin‐4(1H)‐one, in aqueous solution. The investigation tool was random‐acceleration molecular dynamics (RAMD), whereby a tiny, randomly oriented external force is applied to O2 in order to accelerate its movements. In doing that, care was taken that the external force only continues, if O2 moves along a direction for a given period of time, otherwise the force changed direction randomly. Gates for expulsion of O2 from the protein, which can also be taken as gates for O2 uptake, were found throughout almost the whole external surface of the protein, alongside a variety of BPs for O2. The most exploited gates and BPs were not found to correspond to the single gate and BP proposed previously from the examination of the static model from X‐ray diffraction analysis of this system. Therefore, experimental investigations of this system that go beyond the static model are urgently needed.  相似文献   

15.
High‐risk human papillomaviruses (HPVs) cause cervical cancer, and while there are good prophylactic vaccines on the market, these are ineffective against established infections, creating a clear need for therapeutic vaccines. The HPV E7 protein is one of the essential oncoproteins for the onset and maintenance of malignancy and is therefore an ideal therapeutic vaccine target. We fused the HPV‐16 E7 protein to the Limulus polyphemus antilipopolysaccharide factor (LALF32‐51), a small hydrophobic peptide that can penetrate cell membranes and that has immunomodulatory properties. LALF32‐51‐E7 was transiently expressed in Nicotiana benthamiana, and we previously determined that it accumulated better when targeted to chloroplasts compared to being localized in the cytoplasm. Subsequently, we aimed to prove whether LALF32‐51‐E7 was indeed associated with the chloroplasts by determining its subcellular localization. The LALF32‐51‐E7 gene was fused to one encoding enhanced GFP to generate a LG fusion protein, and localization was determined by confocal laser scanning microscopy and transmission electron microscopy (TEM). The fluorescence observed from chloroplast‐targeted LG was distinctively different from that of the cytoplasmic LG. Small spherical structures resembling protein bodies (PBs) were seen that clearly localized with the chloroplasts. Larger but less abundant PB‐like structures were also seen for the cytoplasmic LG. PB‐like structure formation was confirmed for both LG and LALF32‐51‐E7 by TEM. LALF32‐51‐E7 was indeed targeted to the chloroplasts by the chloroplast transit peptide used in this study, and it formed aggregated PB‐like structures. This study could open a new avenue for the use of LALF32‐51 as a PB‐inducing peptide.  相似文献   

16.
Electrochemical reduction of CO2 provides an opportunity to reach a carbon‐neutral energy recycling regime, in which CO2 emissions from fuel use are collected and converted back to fuels. The reduction of CO2 to CO is the first step toward the synthesis of more complex carbon‐based fuels and chemicals. Therefore, understanding this step is crucial for the development of high‐performance electrocatalyst for CO2 conversion to higher order products such as hydrocarbons. Here, atomic iron dispersed on nitrogen‐doped graphene (Fe/NG) is synthesized as an efficient electrocatalyst for CO2 reduction to CO. Fe/NG has a low reduction overpotential with high Faradic efficiency up to 80%. The existence of nitrogen‐confined atomic Fe moieties on the nitrogen‐doped graphene layer is confirmed by aberration‐corrected high‐angle annular dark‐field scanning transmission electron microscopy and X‐ray absorption fine structure analysis. The Fe/NG catalysts provide an ideal platform for comparative studies of the effect of the catalytic center on the electrocatalytic performance. The CO2 reduction reaction mechanism on atomic Fe surrounded by four N atoms (Fe–N4) embedded in nitrogen‐doped graphene is further investigated through density functional theory calculations, revealing a possible promotional effect of nitrogen doping on graphene.  相似文献   

17.
18.
19.
(?)‐Epicatechin (EPI) has beneficial effects on the cardiovascular disease. The human ether‐a‐go‐go‐related gene (HERG) potassium channel is crucial for repolarization of cardiac action potential. Dysfunction of the HERG channel can cause long QT syndrome type 2 (LQT2). Arsenic trioxide (As2O3) has shown efficacy in the treatment of acute promyelocytic leukemia. However, As2O3 can induce the deficiency of HERG channel and cause LQT2. In this study, we examined whether EPI could rescue the As2O3‐induced HERG channel deficiency. We found that 3 μM EPI obviously increased protein expression and current of HERG channel. EPI was able to recover the protein expression and current of HERG channel disrupted by As2O3. EPI was able to increase the expression of SP1 protein and recover the expression of SP1 protein disrupted by As2O3. In addition, EPI significantly shortened action potential duration prolonged by As2O3. Our data suggest that EPI rescues As2O3‐induced HERG channel deficiency through upregulating SP1 expression.  相似文献   

20.
The monoclonal antibody (mAb) CO17‐1A specifically binds to the tumor‐associated cell surface glycoprotein GA733 in colorectal cancer cells. Thus, mAb CO17‐1A has the potential to act as an immune therapeutic protein against colorectal cancer. Recently, it was shown that the baculovirus insect cell expression system produces anti‐colorectal cancer mAb CO17‐1A. In this study, the colorectal cancer antibody mAb CO17‐1A fused to the endoplasmic reticulum (ER) retention signal sequence (KDEL), and the (mAb CO17‐1AK) was expressed in Spodoptera frugiperda Sf9 insect cells. The yield, cell cytotoxicity, and in vitro anti‐tumor activity of mAb CO17‐1AK were verified. Western blotting was performed to confirm that both heavy and light chains of mAb CO17‐1A were expressed in Sf9 insect cells. The insect‐derived mAb (mAbI) CO17‐1A was purified using a protein G affinity column. An in vitro wound healing assay was conducted to determine the inhibition activity of mAb CO17‐1A during tumor cell migration, showing that mAbI CO17‐1AK was effective as mammalian‐derived mAb CO17‐1A (mAbM CO17‐1A). These results suggest that the insect cell expression system can produce and properly assemble mAbs that inhibit tumor cell migration.  相似文献   

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