Fractionation of xyloglucan fragments and their interaction with cellulose.

Tamarind seed xyloglucan was partially degraded with a purified endoglucanase (endoV) from Trichoderma viride. Analysis by high-performance anion-exchange chromatography showed that this digest was composed of fragments consisting of 1 to 10 repeating oligosaccharide units ([xg]1-[xg]10). To study the adsorption of xyloglucan fragments to cellulose in detail, this digest was fractionated on BioGel P-6. Fragments were separated satisfactorily up to 5 repeating oligosaccharide units ([xg]5). The galactose substitution of the fragments increased with increasing molecular weight. The BioGel P-6 pools, as well as polymeric xyloglucan ([xg] infinity), were tested for their ability to interact with Avicel crystalline cellulose. Quantitative binding to cellulose occurred for sequences consisting of (at least) 4 repeating units. The adsorption of [xg]4 to Avicel was very high relative to that of [xg] infinity. The dimensions of these fragments were such that they could also penetrate the smaller pores of cellulose. Apparently, the effective surface area for the polymers is much smaller. Adsorption isotherms of [xg] infinity and [xg]4 showed a pattern that is typical for polydisperse systems. However, the mechanisms underlying these patterns were different. At high xyloglucan concentrations, this polydispersity resulted in preferential adsorption of the larger molecules in the case of [xg] infinity and a more extensive colonization of the smaller pores of cellulose in the case of [xg]4. The pH influenced the interaction between xyloglucan (fragments) and cellulose to only a small extent.     

Cloning, expression, and protein interaction of human nebulin fragments composed of varying numbers of sequence modules.

Nebulin, a family of giant myofibrillar proteins of 600-900 kDa, contains a large number of highly conserved sequence repeats of 31-38 amino acids. To investigate the significance of this repeat, human skeletal muscle nebulin cDNA fragments encoding two, six, seven, eight, or fifteen repeat modules were expressed in high yield as nonfusion proteins in Escherichia coli with the pET3d plasmid vector. F-actin cosedimentation and solid phase binding assays demonstrated that all nebulin fragments, except the smallest two-module 67-mer, bound to muscle actin with high affinity under physiological ionic conditions. Solid phase binding assays also revealed that a six-module fragment, NB5, binds to myosin and C-terminal protein but fails to bind to tropomyosin, troponin, and tubulin. Furthermore, the binding of NB5 to actin was inhibited by both tropomyosin and troponin. Immunoelectron microscopic localization of NB5 indicated that this N-terminal region fragment is situated near the distal end of thin filaments in the sarcomere. These results indicate that nebulin is a giant protein with an unprecedently large number of actin-binding sites along its length and is anchored at the C terminus to the Z line in the sarcomere. Nebulin may function as a multifunctional template protein that regulates the length of thin filaments and participates in muscle activities by interacting with actin and myosin filaments in the sarcomere of skeletal muscles.     

Antibacterial activity of bactenecin 5 fragments and their interaction with phospholipid membranes.

Bactenecin 5 (Bac 5) is an antibacterial 43mer peptide isolated from bovine neutrophils. It consists of an Arg-rich N-terminal region and successive repeats of Arg-Pro-Pro-Ile (or Phe). We synthesized Bac 5(1-23) and several related peptides to clarify the roles these regions play in antibacterial activity. An assay of antibacterial activity revealed that such activity requires the presence of Arg residues at or near the N-terminus, as well as a chain length exceeding 15 residues. None of the peptides exhibited haemolytic activity. Polyproline II-like CD curves were observed for most of the peptides. Measurements of the membrane perturbation and fusion indicated that the perturbation and fusogenic activities of the peptides were, generally, parallel to their antibacterial activities. Amino acid substitution in the repeating region had some effect on antibacterial activity.     

Targeting of nebulin fragments to the cardiac sarcomere

Nebulin, a vertebrate skeletal muscle actin binding protein, plays an important role in thin filament architecture. Recently, a number of reports have indicated evidence for nebulin expression in vertebrate hearts. To investigate the ability of nebulin to interact with cardiac myofilaments, we have expressed nebulin cDNA fragments tagged with green fluorescent protein (GFP) in chicken cardiomyocytes and PtK2 cells. Nebulin fragments from both the superrepeats and single repeats were expressed minus and plus the nebulin linker. Nebulin fragment incorporation was monitored by fluorescent microscopy and compared with the distribution of actin, alpha-actinin and titin. Expression of nebulin N-terminal superrepeats displayed a punctate cytoplasmic distribution in PtK2 cells and cardiomyocytes. Addition of the nebulin linker to the superrepeats resulted in association of the punctate staining with the myofibrils. Nebulin C-terminal superrepeats plus and minus the linker localized with stress fibers of PtK2 cells and associated with the cardiac myofilaments at the level of the Z-line. Expression of the single repeats plus and minus the nebulin linker region resulted in both a Z-line distribution and an A-band distribution. These data suggest that N-terminal superrepeat nebulin modules are incapable of supporting interactions with the cardiac myofilaments; whereas the C-terminal nebulin modules can. The expression of the N-terminal or C-terminal superrepeats did not alter the distribution of actin, alpha-actinin or titin in either atrial or ventricular cultures.     

Phosphorylation of microtubule-associated proteins regulates their interaction with actin filaments

We have determined the absolute phosphate content of microtubule-associated proteins (MAPs) and established that phosphorylation inhibits the actin filament cross-linking activity of MAPs and both of the major MAP components, MAP-2 and tau. Similar results were obtained with actin from rabbit muscle, hog brain, and Acanthamoeba castellanii. We used the endogenous phosphatases and kinases in hog brain microtubule protein to modulate MAP phosphate level before isolating heat-stable MAPs. MAPs isolated directly from twice-cycled microtubule protein contain 7.1 +/- 0.1 (S.E.) mol of phosphate/300,000 g protein. After incubating microtubule protein without ATP, MAPs, had 4.9 +/- 0.6 phosphates. After incubating microtubule protein with 1 mM ATP and 5 microM cAMP in 2 mM EGTA, MAPs had 8.6 +/- 0.5 phosphates but there was also exchange of three more [32P]phosphates from gamma-labeled ATP for preexisting MAP phosphate. Incubation of microtubule protein with ATP and cAMP in 5 mM CaCl2 resulted in exchange but no net addition of phosphate to MAPs. We fractionated the MAP preparations by gel filtration and obtained MAP-2 with 4.3 to 7.5 and tau with 1.5 to 2.2 mol of phosphate/mol of protein depending on how we treated the microtubule protein prior to MAP isolation. The actin filament cross-linking activity of whole MAPs, MAP-2, and tau depended on the MAP-phosphate content. In all cases, phosphorylation of MAPs inhibited actin filament cross-linking activity. The concentration of high phosphate MAPs required to form a high viscosity solution with actin filaments was 2 to 4 times more than that of low phosphate. MAPs. During incubation of microtubule protein with [gamma-32P]ATP, only MAP peptides are labeled. Treatment of these MAPs with either acid or alkaline phosphatase removes phosphate mainly from MAP-2, with an increase in actin filament cross-linking activity. Thus, both MAP phosphorylation and the effect of phosphorylation on actin cross-linking activity of MAPs are reversible.     

A sialic acid-binding lectin from ovine placenta: purification,specificity and interaction with actin

A sialic-acid-specific lectin from ovine placental cotyledons was purified by affinity chromatography on bovine submaxillary mucin-agarose followed by gel filtration, and it showed a molecular weight of 65 000 by sodium dodecylsulfate-polyacrylamide gel electrophoresis. This lectin has the capacity to interact with actin, since in binds to actin-F in a cosedimentation assay and it acts as a mediator in the binding of action to the affinity column. The lectin agglutinated rabbit and rat erythrocytes, but not human A, B or O erythrocytes. Haemagglutination inhibition assays of different saccharides, glycoproteins and glycolipids indicate that this lectin has affinity for sialic acid, which is enhanced by its O-acetylation. The N-terminal sequence of the protein shows 92% identity with rabbit and porcine uterine calreticulin.     

Protein-protein interactions of proteolytic fragments of actin.

Proteolytic fragments of actin, prepared by removal of up to sixty-eight residues from the N-terminal end of the molecule, can form filamentous structures after denaturation in urea solution. The filaments have a diameter similar to F-actin filaments and interact with myosin and tropomyosin. A fragment comprising residues 1 to 207 of the actin sequence did not form filaments or interact with myosin after the urea treatment.     

Hydrophobic interaction chromatography of myosin fragments: Potential use in purification

Myosin fragments were fractionated on columns of the hydrophobic gel phenyl-Sepharose CL-4B. In the presence of high NaCl concentrations the fragments bound tightly to the columns; they could be eluted by decreasing the ionic strength, by increasing the pH, or by applying various concentrations of ethylene glycol. In myosin subfragment-1 (S-1), the light chains underwent partial dissociation from the heavy chain and bound separately to the column matrix. The order of strength of binding of the various species to the column was heavy chain > A1 light chain > A2 light chain > native S-1 > denatured heavy chain or S-1. Thus the hydrophobic gel appears to be able to differentiate between enzymatically active and inactive S-1. Under appropriate elution conditions it was possible to obtain S-1 preparations depleted from nicked heavy chains and with specific ATPase activities 34–130% higher than those of untreated S-1. When S-1(A2) was fractionated on phenyl-Sepharose a fivefold enrichment of the heavy chain with respect to the light chains was obtained, while the ATPase activity was equal or larger than that of the original S-1, implying that the light chains are not essential for ATPase activity. Thus, it seems that chromatography of S-1 on phenyl-Sepharose is a potentially useful method for obtaining a purified myosin heavy-chain fragment with a high ATPase specific activity.     

Myosin and actin from ascidian smooth muscle and their interaction

Myosin and actin were purified from ascidian smooth muscle. Ascidian myosin contained two classes of light chains and the pH dependence of Ca2+-activated ATPase and the KCl dependence of actin-activated ATPase of ascidian myosin differed from those of vertebrate skeletal myosin. Troponin-tropomyosin complex from ascidian increased the ATPase activity of ascidian reconstituted actomyosin in a Ca2+-dependent manner. Ascidian myosin provided the reconstituted actomyosin with the responsiveness to calcium ions. Two actin isoforms were present in ascidian, which were distinguished by isoelectric points.     

On the interaction of muscle actin with gadolinium.

The polymerization of G-actin is prevented by concentrations of gadolinium (GdIII) that exceed the ATP present. Since the susceptibility of G-actin to enzymatic proteolysis is slightly decreased upon addition of GdIII, and the digestibility of F-actin is markedly increased with the same treatment, it appears that actin undergoes GdIII-induced conformational changes. The altered states of actin formed inhibit the GdIII-ATPase activity of myosin, but in all cases, the effect of GdIII on actin is reversed by removal of the trivalent ion with ATP. The reversible changes in conformation induced by GdIII create a state of actin which has properties unlike those of G-actin, F-monomer or F-actin.     

Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin

Nuclear actin and actin-related proteins (Arps) are integral components of various chromatin-remodelling complexes. Actin in such nuclear assemblies does not form filaments but associates in defined complexes, for instance with Arp4 and Arp8 in the INO80 remodeller. To understand the relationship between nuclear actin and its associated Arps and to test the possibility that Arp4 and Arp8 help maintain actin in defined states, we structurally analysed Arp4 and Arp8 from Saccharomyces cerevisiae and tested their biochemical effects on actin assembly and disassembly. The solution structures of isolated Arp4 and Arp8 indicate them to be monomeric and the crystal structure of ATP-Arp4 reveals several differences to actin that explain why Arp4 does not form filaments itself. Remarkably, Arp4, assisted by Arp8, influences actin polymerization in vitro and is able to depolymerize actin filaments. Arp4 likely forms a complex with monomeric actin via the barbed end. Our data thus help explaining how nuclear actin is held in a discrete complex within the INO80 chromatin remodeller.     

Analysis of tetramethylrhodamine-labeled actin polymerization and interaction with actin regulatory proteins

The hydrolysis of ATP accompanying actin polymerization destabilizes the filament, controls actin assembly dynamics in motile processes, and allows the specific binding of regulatory proteins to ATP- or ADP-actin. However, the relationship between the structural changes linked to ATP hydrolysis and the functional properties of actin is not understood. Labeling of actin Cys374 by tetramethylrhodamine (TMR) has been reported to make actin non-polymerizable and enabled the crystal structures of ADP-actin and 5'-adenylyl beta,gamma-imidodiphosphate-actin to be solved. TMR-actin has also been used to solve the structure of actin in complex with the formin homology 2 domain of mammalian Dia1. To understand how the covalent modification of actin by TMR may affect the structural changes linked to ATP hydrolysis and to evaluate the functional relevance of crystal structures of TMR-actin in complex with actin-binding proteins, we have analyzed the assembly properties of TMR-actin and its interaction with regulatory proteins. We show that TMR-actin polymerized in very short filaments that were destabilized by ATP hydrolysis. The critical concentrations for assembly of TMR-actin in ATP and ADP were only an order of magnitude higher than those for unlabeled actin. The functional interactions of actin with capping proteins, formin, actin-depolymerizing factor/cofilin, and the VCA-Arp2/3 filament branching machinery were profoundly altered by TMR labeling. The data suggest that TMR labeling hinders the intramolecular movements of actin that allow its specific adaptative recognition by regulatory proteins and that determine its function in the ATP- or ADP-bound state.     

Quantitative electroelution of oligonucleotides and large DNA fragments from gels and purification by electrodialysis

We have designed a new device [Biotrap (Elutrap in the U.S.A. and Canada), available from Schleicher & Schuell] for electroelution, -concentration , and -dialysis of DNA and other charged macromolecules above 5 kDa. In an electric field, the DNA migrates in an open channel out of the gel slice through a microporous membrane, BT2, into the trap section, where it is retained by a very dense, non-adsorbant, and inert membrane BT1. Specifically designed for use in an electric field, the matrix of this new membrane is much denser than that of dialysis membranes. In contrast to dialysis membranes, BT1 will not adsorb large DNA fragments nor allow passage of small DNA fragments when subjected to an electric field. In the absence of an electric field, BT1 and BT2 effectively seal the trap, maintaining the final elution volume of the purified sample. The trap can contain from 200-600 microliter and is collected from above with a pipet. In the experiments described here, 85-95% of oligonucleotides (14-mer) and large (150 kb) DNA fragments were recovered, independent of fragment length. The purity of the eluted DNA was demonstrated by restriction enzyme digestion, nick-translation, primer extension, end-labeling with polynucleotide kinase, and ligation. Electrodialysis was successfully used for the complete removal of common contaminants inhibiting the polynucleotide kinase reaction and for the removal of CsCl from DNA samples.     

Identification of amino acid substitutions differentiating actin isoforms in their interaction with myosin

Various aspects of actin--myosin interaction were studied with actin preparations from two types of smooth muscle: bovine aorta and chicken gizzard, and from two types of sarcomeric muscle: bovine cardiac and rabbit skeletal. All four preparations activated the Mg2+-ATPase activity of skeletal muscle myosin to the same Vmax, but the Kapp for the smooth muscle preparations was higher. At low KCl, pH 8.0 and millimolar substrate concentrations the Kapp values differed by a factor of 2.5. This differential behaviour of the four actin preparations correlates with amino acid substitutions at positions 17 and 89 of actin polypeptide chain, differentiating the smooth-muscle-specific gamma and alpha isomers from cardiac and skeletal-muscle-specific alpha isomers. This correlation provides evidence for involvement of the NH2-terminal portion of the actin polypeptide chain in the interaction with myosin. The differences in the activation of myosin ATPase by various actins were sensitive to changes in the substrate and KCl concentration and pH of the assay medium. Addition of myosin subfragment-1 or heavy meromyosin in the absence of nucleotide produced similar changes in the fluorescence of a fluorescent reagent N-(1-pyrenyl)-iodoacetamide, attached at Cys-374, or 1,N6-ethenoadenosine 5'-diphosphate substituted for the bound ADP in actin protomers in gizzard and skeletal muscle F-actin. The results are consistent with an influence of the amino acid substitutions on ionic interactions leading to complex formation between actin and myosin intermediates in the ATPase cycle but not on the associated states.     

Molecular dissection of the interaction of desmin with the C-terminal region of nebulin

In vertebrate skeletal muscle, ultrastructural studies have suggested that the Z-line and extracellular intermediate filaments are linked, although a structural basis for this has remained elusive. We searched for potential novel ligands of the Z-line portion of nebulin by a yeast two-hybrid (Y2H) approach. This identified that the nebulin modules M160 to M170 interact with desmin. In desmin, deletion series experiments assigned a 19-kDa central coiled-coil domain as the nebulin-binding site. The specific interactions of nebulin and desmin were confirmed in vitro by GST pull-down experiments. In situ, the nebulin modules M176 to M181 colocalize with desmin in a Z-line-associated, striated pattern as shown by immunofluorescence studies. Our data are consistent with a model that desmin attaches directly to the Z-line through its interaction with the nebulin repeats M163-M170. This interaction may link myofibrillar Z-discs to the intermediate filament system, thereby forming a lateral linkage system which contributes to maintain adjacent Z-lines in register.     

Expression and purification strategies for the production of single-chain antibody and T-cell receptor fragments inE. coli

This work describes protocols for the production of single-chain antibody and T-cell receptor fragments inE. coli. A choice of methods is given for the purification of the recombinant fragments that rely on the use of either immunoaffinity or metal chelate affinity chromatography. The TCR fragments may have to be denatured and refolded before the fragments attain their proper conformation.     

Expression and purification of the C-terminal fragments of TRPV5/6 channels

The transient receptor potential vanniloid 5 and 6 (TRPV5 and TRPV6) Ca(2+)-ion channels are crucial for the regulation of minute-to-minute whole body calcium homeostasis. They act as the gatekeepers of active Ca(2+) reabsorption in kidney and intestine, respectively. In spite of the great progress in the TRP channels characterization, very little is known at the atomic level about their structure and interactions with other proteins. To the major extent it is caused by difficulties in obtaining suitable samples. Here, we report expression and purification of 36 intracellular C-terminal fragments of TRPV5 and TRPV6 channels, for which no structural information is reported thus far. We demonstrate that these proteins contain intrinsically disordered regions and identify fragments suitable for biophysical characterization. By combining bioinformatic predictions and experimental results, we propose several criteria that may aid in designing a scheme for large-scale production of difficult proteins.     

The interaction of actin with dystrophin

Proton NMR spectroscopy of synthetic peptides corresponding to defined regions of human dystrophin has been employed to study the interaction with F-actin. No evidence of interaction with a C-terminal region corresponding to amino acid residues 3429-3440 was obtained. F-actin restricted the mobility of residues 19-27 in a synthetic peptide corresponding to residues 10-32. This suggests that this is a site of F-actin interaction in the intact dystrophin molecule. Identical sequences to that of residues 19-22 in dystrophin, namely Lys-Thr-Phe-Thr are also present in the N-terminal regions of the alpha-actinins implying this is also a site of F-actin interaction with alpha-actinin.     

Molecular interaction of fenvalarate with actin

The structure of α-Cyano-3-phenoxybenzyl-2-(4-chlorophenyl)-3-methylbutyrate (Fenvalarate) has been established by X-ray crystallography to understand the structure-activity relationship, which is of paramount importance in the toxicological studies of the compound. Fenvalarate is stabilized by intermolecular C-H…O, C-H…Cl, C-H…π and C-H…N interactions which are responsible for the stability of the compound and its interaction with the Actin. The crystallographic coordinates of the compound was extrapolated to docking studies to elucidate the action of fenvalarate against neural cytoskeletal protein of insect and mammalian β-actin. A strong affinity was observed in binding of fenvalarate with insect β-actin (-7.71kcal/mol, Ki = 2.23μM) indicating it as a potent insecticide and moderate toxicity towards mammalian β-actin (-7.07kcal/mol, Ki=6.54μM).