Interaction between Nbp35 and Cfd1 Proteins of Cytosolic Fe-S Cluster Assembly Reveals a Stable Complex Formation in Entamoeba histolytica

ABSTRACTComplex formation between hexokinase-II (HKII) and the mitochondrial channel VDAC1 plays a crucial role in regulating cell growth and survival; however, structural details of this complex remain elusive. We hypothesize that a conserved, hydrophobic helix (H-anchor) of HKII first inserts into the outer membrane of mitochondria (OMM) and then interacts with VDAC1 on the cytosolic leaflet of OMM to form a binary complex. To systematically investigate this process, we adopted a hybrid approach: 1) the membrane binding of HKII was first described with molecular dynamics (MD) simulations employing a membrane mimetic model with enhanced lipid diffusion, then 2) the resulting membrane-bound HKII was used to form complex with VDAC1 in millisecond-scale Brownian dynamics (BD) simulations. We show that H-anchor inserts its first 10 residues into the membrane, substantiating previous experimental findings. The insertion depth of the H-anchor was used to derive positional restraints in subsequent BD simulations to preserve the membrane-bound pose of HKII during the formation of the HKII/VDAC1 binary complex. Multiple BD-derived structural models were further refined with MD simulations, resulting in one stable complex. A major feature in the complex is the partial (not complete) blockade of VDAC1’s permeation pathway by HKII, a result supported by our comparative electrophysiological measurements of the channel in the presence and absence of HKII. Additionally, we showed how VDAC1 phosphorylation disrupts HKII binding, a feature that is verified by our electrophysiology recordings and have implications in mitochondria-mediated cell death.

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Stable complex formation with boric acid in pyrolysis of levoglucosan in acidic media

Journal of Analytical and Applied Pyrolysis ◽

10.1016/j.jaap.2007.12.008 ◽

2008 ◽

Vol 82 (1) ◽

pp. 78-82 ◽

Cited By ~ 8

Author(s):

H. Kawamoto ◽

S. Saito ◽

S. Saka

Keyword(s):

Complex Formation ◽

Boric Acid ◽

Stable Complex ◽

Acidic Media

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Transcription factor binding is limited by the 5'-flanking regions of a Drosophila tRNAHis gene and a tRNAHis pseudogene

Molecular and Cellular Biology ◽

10.1128/mcb.4.12.2714-2722.1984 ◽

1984 ◽

Vol 4 (12) ◽

pp. 2714-2722

Author(s):

L Cooley ◽

J Schaack ◽

D J Burke ◽

B Thomas ◽

D Söll

Keyword(s):

Complex Formation ◽

Hela Cell ◽

Cell Extract ◽

Deletion Analysis ◽

Stable Complex ◽

Flanking Sequence ◽

Factor Binding ◽

Real Gene ◽

Hela Cell Extract ◽

Flanking Regions

We determined the sequence of a Drosophila tRNA gene cluster containing a tRNAHis gene and a tRNAHis pseudogene in close proximity on the same DNA strand. The pseudogene contains eight consecutive base pairs different from the region of the bona fide gene which codes for the 3' portion of the anticodon stem of tRNAHis. The tRNAHis gene is transcribed efficiently in Drosophila Kc cell extract, whereas the pseudogene is not. The pseudogene is also a much poorer competitor than the real gene in a stable transcription complex formation assay, even though the sequence alteration in the pseudogene does not affect the sequence or spacing of the putative internal transcription control regions. Recombinant clones were constructed in which the 5'-flanking regions are exchanged. The transcription efficiencies and competitive abilities of the recombinant clones resemble those of the genes from which the 5' flank was derived; for example, the tRNAHis pseudogene with the 5'-flanking sequence of the tRNAHis gene is now efficiently transcribed. Deletion analysis of the pseudogene 5' flank failed to uncover an inhibitory element. Deletion analysis of the real gene showed very high dependence on the presence of the wild-type 5'-flanking sequence for factor binding to the internal control regions and stable complex formation. The 5'-flanking sequence of a Drosophila tRNAArg gene active in the Drosophila Kc cell extract does not restore transcriptional activity or stable complex formation. The tRNAHis gene and pseudogene behave atypically in HeLa cell extract. Both genes compete for HeLa transcription factors, but neither of them is efficiently transcribed. Removal of the 5'-flanking sequences of each gene and replacement with various sequences, including the tRNAArg gene 5' flank, does not allow increased transcription in HeLa cell extract.

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Interactions of plasma kallikrein and C1-s with normal and dysfunctional C1(-)-inhibitor proteins from patients with hereditary angioneurotic edema: analytic gel studies

Blood ◽

10.1182/blood.v69.4.1096.1096 ◽

1987 ◽

Vol 69 (4) ◽

pp. 1096-1101 ◽

Cited By ~ 2

Author(s):

VH Donaldson ◽

CJ Wagner ◽

B Tsuei ◽

G Kindness ◽

DH Bing ◽

...

Keyword(s):

Complex Formation ◽

Gel Electrophoresis ◽

Sodium Dodecyl ◽

Original Position ◽

Stable Complex ◽

Plasma Kallikrein ◽

Type Ii ◽

C1 Inhibitor ◽

Angioneurotic Edema ◽

Hereditary Angioneurotic Edema

Abstract Purified preparations of normal C1(-)-inhibitor (C1(-)-INH) formed high mol wt complexes with plasma kallikrein that were stable during sodium dodecyl sulfate (SDS)-gel electrophoresis, but most of the dysfunctional C1(-)-INH proteins isolated from plasma of patients with type II hereditary angioneurotic edema (HANE) did not. Two of eight dysfunctional C1(-)-INH proteins were cleaved to lower mol wt forms that were not seen following the reaction of normal C1(-)-INH with equimolar amounts, or less, of plasma kallikrein. Only the higher mol wt component of normal C1(-)-INH (106,000 mol wt) appeared to form a stable complex with the plasma kallikrein, whereas both the 106,000 and 96,000 mol wt forms made stable complexes with C1-s. When a preparation of normal C1(-)-INH containing a homogeneous single band of C1(-)-INH was exposed to C1-s or kallikrein, a “doublet” form evolved in which the heaviest band was in the original position of native C1(-)-INH; C1- s cleavage provided a second band of 96,000; and cleavage by kallikrein, a second band of 94,000 mol wt. We conclude that dysfunctional C1(-)-INH proteins from plasma of persons with type II hereditary angioneurotic edema have impaired interactions with plasma kallikrein and are heterogeneous with respect to these interactions. Moreover, the requirements for the formation of stable complexes between normal C1(-)-INH and plasma kallikrein differed from those for stable complex formation with C1-s. The doublet form of C1(-)-INH, which purified preparations frequently demonstrate, may be due to prior cleavage by C1-s or kallikrein.

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Computer simulation of complex of lysine dendrigraft with molecules of therapeutic KED peptide

ITM Web of Conferences ◽

10.1051/itmconf/20192402008 ◽

2019 ◽

Vol 24 ◽

pp. 02008

Author(s):

Igor Neelov ◽

Valerii Bezrodnyi ◽

Anna Marchenko ◽

Emil Fatullaev ◽

Sofia Miktaniuk

Keyword(s):

Molecular Dynamics ◽

Computer Simulation ◽

Molecular Dynamics Simulation ◽

Complex Formation ◽

Simulation Method ◽

Dynamics Simulation ◽

Stable Complex ◽

Target Organs ◽

Therapeutic Peptides ◽

Drug And Gene Delivery

Lysine dendrimers and dendrigrafts are often used in biomedicine for drug and gene delivery to different target organs or cells. In present paper the possibility of complex formation by lysine dendrigraft and 16 molecules of therapeutic KED peptide was investigated using molecular dynamics simulation method. A system containing of one dendrigraftt and 16 KED peptides in water were studied. It was shown that stable complex consisting of the dendrigraft and the peptide molecules formed and structure of this complex was studied. Similar complexes could be used in future for delivery of other therapeutic peptides to target organs.

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The effect of complex-formation with polyanions on the redox properties of cytochrome c

Biochemical Journal ◽

10.1042/bj1920687 ◽

1980 ◽

Vol 192 (2) ◽

pp. 687-693 ◽

Cited By ~ 32

Author(s):

L C Petersen ◽

R P Cox

Keyword(s):

Cytochrome C ◽

Complex Formation ◽

Reaction Rates ◽

Reduced Form ◽

Stable Complex ◽

Phase System ◽

Two Phase ◽

The Difference ◽

Low Ionic Strength ◽

Positively Charged

1. The stable complex formed between mammalian cytochrome c and phosvitin at low ionic strength was studied by partition in an aqueous two-phase system. Oxidized cytochrome c binds to phosvitin with a higher affinity than reduced cytochrome c. The difference was equivalent to a decrease of the redox potential by 22 mV on binding. 2. Complex-formation with phosvitin strongly inhibited the reaction of cytochrome c with reagents that react as negatively charged species, such as ascorbate, dithionite, ferricyanide and tetrachlorobenzoquinol. Reaction with uncharged reagents such as NNN‘N’-tetramethylphenylenediamine and the reduced form of the N-methylphenazonium ion (present as the methylsulphate) was little affected by complex-formation, whereas oxidation of the reduced cytochrome by the positively charged tris-(phenanthroline)cobalt(III) ion was greatly stimulated. 3. A similar pattern of inhibition and stimulation of reaction rates was observed when phosvitin was replaced by other macromolecular polyanions such as dextran sulphate and heparin, indicating that the results were a general property of complex-formation with polyanions. A weaker but qualitatively similar effect was observed on addition of inositol hexaphosphate and ATP. 4. It is suggested that the effects of complex-formation with polyanions on the reactivity of cytochrome c with redox reagents are mainly the result of replacing the positive charge on the free cytochrome by a net negative charge. Any steric effects on polyanion binding are small in comparison with such electrostatic effects.

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