scholarly journals Probing serpin reactive-loop conformations by proteolytic cleavage

1996 ◽  
Vol 314 (2) ◽  
pp. 647-653 ◽  
Author(s):  
Wun-Shaing W. CHANG ◽  
Mark R. WARDELL ◽  
David A. LOMAS ◽  
Robin W. CARRELL
Keyword(s):  
Complex Formation ◽  
Conformational Changes ◽  
Limited Proteolysis ◽  
Serine Proteinase ◽  
Hinge Region ◽  
Helical Conformation ◽  
Binary Complex ◽  
Native Form ◽  
Binary Complexes ◽  
Loop Conformations

Several crystal structures of intact members of the serine proteinase inhibitor (or serpin) superfamily have recently been solved but the relationship of their reactive-loop conformations to those of circulating forms remains unclear. Here we examine reactive-loop conformational changes of anti-trypsin and anti-thrombin by using limited proteolysis and binary complex formation with synthetic homologous reactive-loop peptides. Proteolysis at the P10–P9, P8–P7 and P7–P6 of anti-trypsin was distorted by binary complex formation. The P1´–P2´ bond in anti-thrombin was more accessible to proteolysis after binary complex formation, whereas cleavage at the P4–P3 bond was variably altered by synthetic peptide insertion. The proteolytic accessibility of the reactive-site P1–P1´ bond of anti-trypsin and anti-thrombin binary complexes was identical with that of the native form and no cleavage was observed in the hinge region (P15–P10) of either protein, whether native or as binary complexes. These results fit with the proposal that the hydrophobic reactive loop of serpins adopts a modified helical conformation in the circulation, with the hinge region being partly incorporated into the A β-pleated sheet. This loop can be displaced by peptides and induced to adopt a new conformation similar to the three-turn helix of ovalbumin. Both the native and binary complexed forms of anti-thrombin showed a greatly increased proteolytic sensitivity in the presence of heparin, indicating that heparin either induces a conformational change in the local structure of the helical reactive loop or facilitates the approximation of enzyme and inhibitor.

scholarly journals Binding characteristics of pro-insulin-like growth factor-II from cancer patients: binary and ternary complex formation with IGF binding proteins-1 to -6

2000 ◽  
Vol 165 (2) ◽  
pp. 253-260 ◽  
Author(s):  
JJ Bond ◽  
S Meka ◽  
RC Baxter
Keyword(s):  
Complex Formation ◽  
Ternary Complex ◽  
Binding Proteins ◽  
Ternary Complexes ◽  
Binary Complex ◽  
Igf Binding Proteins ◽  
Ternary Complex Formation ◽  
Binary Complexes ◽  
Igf Binding ◽  
Igfbp 3

Many tumours secrete IGF-II in incompletely processed precursor forms. The ability of these pro-IGF-II forms to complex with the six IGF binding proteins (IGFBPs) is poorly understood. In this study, pro-IGF-II has been extracted from the serum and tumour tissue of two patients with non-islet cell tumour hypoglycaemia. These samples were used to study binary complex formation with IGFBPs-1 to -6 using competitive IGF-II binding assays and ternary complex formation with IGFBP-3 and IGFBP-5. In each case, IGFBPs-1 to -6 showed little difference in their ability to form binary complexes with recombinant IGF-II or tumour-derived pro-IGF-II forms, when the preparations were standardised according to IGF-II immunoreactivity. As previously described, ternary complex formation by acid-labile subunit (ALS) with IGFBP-3 and pro-IGF-II was greatly decreased compared with complex formation with mature IGF-II. In contrast, ALS bound similarly to IGFBP-5 in the presence of pro-IGF-II and mature IGF-II. These studies suggest that pro-IGF-II preferentially forms binary complexes with IGFBPs, and ternary complexes with IGFBP-5, rather than ternary complexes with IGFBP-3 as seen predominantly in normal serum. This may increase the tissue availability of serum pro-IGF-II, allowing its insulin-like potential to be realised.

Determination of the native form of FadD, the Escherichia coli fatty acyl-CoA synthetase, and characterization of limited proteolysis by outer membrane protease OmpT

2001 ◽  
Vol 360 (3) ◽  
pp. 699-706 ◽  
Author(s):  
Jae-Ho YOO ◽  
Oscar H. CHENG ◽  
Gerhard E. GERBER
Keyword(s):  
Escherichia Coli ◽  
Outer Membrane ◽  
Conformational Changes ◽  
Limited Proteolysis ◽  
Fatty Acyl ◽  
Native Form ◽  
Terminal Fragment ◽  
Sequencing And Expression

Several studies have described FadD, the Escherichia coli fatty acyl-CoA synthetase [also known as fatty acid:CoA ligase (AMP-forming); EC 6.2.1.3], as a 42–50kDa enzyme. Based on sequencing and expression data from the fadD gene, other reports have suggested that FadD is a 62kDa protein and represents the sole fatty acyl-CoA synthetase in E. coli. We report that the 62kDa FadD enzyme is a substrate for the outer membrane protease OmpT in vitro, producing a 43kDa C-terminal fragment and a 19kDa N-terminal fragment. Immunoblotting with a FadD antibody revealed that only the 62kDa form of the enzyme is present in vivo, but we utilized the proteolytic sensitivity of FadD to investigate its structure. Photoaffinity labelling experiments revealed that both intact FadD and the 43kDa fragment bound a long-chain fatty acid. Intact and cleaved FadD were also purified to determine the effect of cleavage on function. When using oleate as a substrate, cleaved FadD displayed 2-fold higher Km and Vmax values compared with intact FadD, but the catalytic efficiencies (kcat/Km) of the two forms were similar. This indicated that cleavage did not adversely affect enzyme activity. Proteolysis of FadD by OmpT was altered by the presence of oleate or ATP, both of which are ligands for the fatty acyl-CoA synthetase. This suggested that FadD undergoes ligand-induced conformational changes and implies that the region surrounding the cleavage site is mobile, a common characteristic of linker domains.

scholarly journals Palmitoylation of the 25-kDa synaptosomal protein (SNAP-25) in vitro occurs in the absence of an enzyme, but is stimulated by binding to syntaxin

1999 ◽  
Vol 345 (1) ◽  
pp. 145-151 ◽  
Author(s):  
Michael VEIT
Keyword(s):  
Conformational Changes ◽  
Disulfide Bonds ◽  
Snare Complex ◽  
Helical Conformation ◽  
Cysteine Residues ◽  
Binary Complex ◽  
Protein Receptor ◽  
Protein Palmitoylation

The neuronal N-ethylmaleimide-sensitive-factor-attachment-protein receptor (SNARE) proteins 25-kDa synaptosomal protein (SNAP-25), syntaxin 1 and synaptobrevin 2 interact to form the intermembrane SNARE complex, which mediates docking and fusion of synaptic vesicles with the plasma membrane. Assembly of the SNARE complex is accompanied by conformational changes, especially in SNAP-25. SNAP-25 is palmitoylated in vivo at cysteine residues located in the middle of the molecule. Acylation is required for membrane binding or membrane targeting of this intrinsically hydrophilic protein. Palmitoylation of recombinant SNAP-25 was studied in vitro in the absence of an enzyme source with [3H]palmitoyl-CoA as the lipid donor. [3H]Palmitate incorporation into unbound SNAP-25 was negligible, but was stimulated 100-fold when SNAP-25 was present in the SNARE complex. SNAP-25 in a binary complex with syntaxin 1 was palmitoylated with almost the same efficiency. A mutant of SNAP-25, which was not acylated in vivo, did not incorporate [3H]palmitate in this assay. [3H]Palmitate incorporation into wild-type SNAP-25 was blocked by chemical blocking of free SH groups, but slightly stimulated by reduction of disulfide-bonds. This shows that palmitoylation of SNAP-25 in vitro occurs at the same cysteine residues that are palmitoylated in vivo. This demonstrates that efficient palmitoylation of SNAP-25 depends on an interaction with a physiological binding partner. It suggests further that palmitoylation of SNAP-25 requires the α-helical conformation of the protein, which is induced by binding to syntaxin 1.

scholarly journals Limited proteolysis of complement components C2 and factor B. Structural analogy and limited sequence homology

1979 ◽  
Vol 183 (3) ◽  
pp. 615-622 ◽  
Author(s):  
M A Kerr
Keyword(s):  
Sequence Homology ◽  
Polyacrylamide Gel Electrophoresis ◽  
Limited Proteolysis ◽  
Gel Filtration ◽  
Serine Proteinase ◽  
Terminal Sequence ◽  
Complement Components ◽  
Factor B ◽  
Terminal Residue ◽  
Covalently Linked

A method is described for the simultaneous purification of milligram quantities of complement components C2 and Factor B. Both products are homogeneous by the criteria of polyacrylamide-gel electrophoresis and N-terminal sequence analysis. Component C2 is cleaved by serine proteinase C1s at an X-Lys bond to give fragment C2a (approx. mol.wt. 74000) and fragment C2b (approx. mol.wt. 34000). The two fragments can be separated by gel filtration without the need for reducing or denaturing agents. Fragment C2b represents the N-terminal end of the molecule. Similar results were seen on cleavage of Factor B by Factor D in the presence of component C3. Again two non-covalently linked fragments are formed. The smaller, fragment Ba (approx. mol.wt. 36,000),) has threonine as the N-terminal residue, as does Factor B; the larger, fragment Bb (approx. mol. wt. 58000), has lysine as the N-terminal residue. A similar cleavage pattern is obtained on limited proteolysis of Factor B by trypsin, suggesting an Arg-Lys-or Lys-Lys bond at the point of cleavage. Although component C2 and Factor B show no apparent N-terminal sequence homology, a limited degree of sequence homology is seen around the sites of proteolytic cleavage.

scholarly journals New Insights into the Spring-Loaded Conformational Change of Influenza Virus Hemagglutinin

2002 ◽  
Vol 76 (9) ◽  
pp. 4456-4466 ◽  
Author(s):  
Jennifer A. Gruenke ◽  
R. Todd Armstrong ◽  
William W. Newcomb ◽  
Jay C. Brown ◽  
Judith M. White
Keyword(s):  
Influenza Virus ◽  
Conformational Change ◽  
Conformational Changes ◽  
Limited Proteolysis ◽  
Coiled Coil ◽  
Fusion Peptide ◽  
Wild Type ◽  
Influenza Virus Hemagglutinin ◽  
Target Membrane ◽  
Mutant Forms

ABSTRACT Influenza virus hemagglutinin undergoes a conformational change in which a loop-to-helix “spring-loaded” conformational change forms a coiled coil that positions the fusion peptide for interaction with the target bilayer. Previous work has shown that two proline mutations designed to disrupt this change disrupt fusion but did not determine the basis for the fusion defect. In this work, we made six additional mutants with single proline substitutions in the region that undergoes the spring-loaded conformational change and two additional mutants with double proline substitutions in this region. All double mutants were fusion inactive. We analyzed one double mutant, F63P/F70P, as an example. We observed that F63P/F70P undergoes key low-pH-induced conformational changes and binds tightly to target membranes. However, limited proteolysis and electron microscopy observations showed that the mutant forms a coiled coil that is only ∼50% the length of the wild type, suggesting that it is splayed in its N-terminal half. This work further supports the hypothesis that the spring-loaded conformational change is necessary for fusion. Our data also indicate that the spring-loaded conformational change has another role beyond presenting the fusion peptide to the target membrane.

scholarly journals The Oxazolidinone Linezolid Inhibits Initiation of Protein Synthesis in Bacteria

1998 ◽  
Vol 42 (12) ◽  
pp. 3251-3255 ◽  
Author(s):  
Steve M. Swaney ◽  
Hiroyuki Aoki ◽  
M. Clelia Ganoza ◽  
Dean L. Shinabarger
Keyword(s):  
Protein Synthesis ◽  
Complex Formation ◽  
Antimicrobial Agents ◽  
Ribosomal Subunit ◽  
Multidrug Resistant ◽  
Binary Complex ◽  
Initiation Complex ◽  
Ribosomal Subunits ◽  
Bacterial Translation

ABSTRACT The oxazolidinones represent a new class of antimicrobial agents which are active against multidrug-resistant staphylococci, streptococci, and enterococci. Previous studies have demonstrated that oxazolidinones inhibit bacterial translation in vitro at a step preceding elongation but after the charging ofN-formylmethionine to the initiator tRNA molecule. The event that occurs between these two steps is termed initiation. Initiation of protein synthesis requires the simultaneous presence of N-formylmethionine-tRNA, the 30S ribosomal subunit, mRNA, GTP, and the initiation factors IF1, IF2, and IF3. An initiation complex assay measuring the binding of [3H]N-formylmethionyl-tRNA to ribosomes in response to mRNA binding was used in order to investigate the mechanism of oxazolidinone action. Linezolid inhibited initiation complex formation with either the 30S or the 70S ribosomal subunits fromEscherichia coli. In addition, complex formation withStaphylococcus aureus 70S tight-couple ribosomes was inhibited by linezolid. Linezolid did not inhibit the independent binding of either mRNA or N-formylmethionyl-tRNA toE. coli 30S ribosomal subunits, nor did it prevent the formation of the IF2–N-formylmethionyl-tRNA binary complex. The results demonstrate that oxazolidinones inhibit the formation of the initiation complex in bacterial translation systems by preventing formation of theN-formylmethionyl-tRNA–ribosome–mRNA ternary complex.

Conformational Changes in ι- and κ-Carrageenans Induced by Complex Formation with Bovine β-Casein

2007 ◽  
Vol 8 (2) ◽  
pp. 368-375 ◽  
Author(s):  
Tatiana V. Burova ◽  
Natalia V. Grinberg ◽  
Valerij Ya. Grinberg ◽  
Anatoly I. Usov ◽  
Vladimir B. Tolstoguzov ◽  
...  
Keyword(s):  
Complex Formation ◽  
Conformational Changes

scholarly journals Structural Basis of Complex Formation Between Mitochondrial Anion Channel VDAC1 and Hexokinase-II

2020 ◽  
Author(s):  
Nandan Haloi ◽  
Po-Chao Wen ◽  
Qunlii Cheng ◽  
Meiying Yang ◽  
Gayathri Natarajan ◽  
...  
Keyword(s):  
Complex Formation ◽  
Hybrid Approach ◽  
Md Simulations ◽  
Structural Basis ◽  
Stable Complex ◽  
Binary Complex ◽  
Hexokinase Ii ◽  
Insertion Depth ◽  
Form Complex ◽  
Membrane Bound

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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