Protein and Peptide Letters - Volume 14, Issue 8, 2007

Ryanodine receptor 1 (RyR1) is a large homotetrameric calcium channel that plays a pivotal role in skeletal muscle contraction. Sequence comparison and mutagenesis studies indicate that the pore architecture of RyR1, including the last two transmembrane helices and the luminal loop linking them, is similar to that of the bacterial KcsA K+ channel. Here, we describe the overexpression and purification of the C-terminal polyhistidine-tagged RyR1 pore-forming region. The nonionic detergent lauryldimethylamine oxide (LDAO) was selected for solubilization of the protein based on its ability to extract the protein from the membrane and to maintain it in a monodisperse state. The protein was then purified using nickel-affinity chromatography and gel filtration. Gel filtration analysis confirmed that the RyR1 fragment containing the pore-forming region (amino acids 4829-5037) is sufficient to form a tetramer.

Studies of conformational features of fragments SNase(111-143) and SNase(118-143) and segment E122-K136 in 1-139 fragment (SNase139) suggest that the high intrinsic helical propensity can drive segment E122-K136 fold into a stable helix only when the segments V111-H121 and L137-D143 flanked on segment E122-K136 in staphylococcal nuclease (SNase) have stable folding.

The conditions were optimized for maximum soluble yield of biologically active recombinant p38α mitogen activated protein kinase (MAPK) vis-a-vis insoluble fraction (inclusion body formation). This study reports a rapid, economical and single step purification process for the overproduction of GST tagged p38α MAPK. A yield of 18 mg of highly purified and soluble protein per liter of bacterial culture within 6 h timeframe was achieved. The purified protein was found to be biologically suitable for phosphorylation by upstream kinases and was catalytically active. We further demonstrated that our in-house p38α MAPK is more potent (>30%) than a commercially available enzyme.

Data of this study showed that αD-αE helices and the conserved interdomain linker are two interfaces essential not only for the self-association but also for the functional properties of rat HSC70. Self-association which is a conserved property of HSP70 seems to be important for the activity of these proteins.

Lipopeptides are amphiphilic compounds which contain both hydrophobic fatty acid moieties and amphiphilic peptide moieties. From the cell-free broth of Bacillus subtilis HSO121, eight cyclic lipopeptides were isolated by reversed- phase high performance liquid chromatography (RP-HPLC). The peptide part of each lipopeptide was elucidated according to electrospray ionization quadruple-time-of-flight mass spectrometry (ESI Q-TOF MS) and the fatty acid part was analyzed by electroionization gas chromatography/mass spectrometry (EI GC/MS). It showed that fractions 1-8 had molecular masses of 1007, 1021, 1021, 1035, 1035, 1035, 1063, and 1049, respectively. Analysis of hydrolyzed lipopeptides revealed that they had invariant amino acid compositions. The differences in molecular weights represent changes in the number of methylene groups and different types of branched chains in fatty acids. Peptide sequences of two of the eight lipopeptides appeared to be N-Asp-Leu-Leu-Val-Glu-Leu-Leu-C, which was different from previously reported lipopeptides. The remaining six had an identical peptide sequence of N-Glu-Leu-Leu-Val-Asp-Leu-Leu-C. The fatty acid parts were found to be mixtures of iso C12, iso C13, anteiso C13, iso C14, n C14, iso C15, anteiso C15, n C15, anteiso C16 and anteiso C17 β-hydroxy fatty acids. The structure of each lipopeptide was determined to be the β-hydroxy fatty acid bonded to the peptide chain.

Enzymatic activity is dependent on temperature, although some proteins have evolved to retain activity at low temperatures at the expense of stability. Cold adapted enzymes are present in a variety of organisms and there is ample interest in their structure-function relationships. Lysozyme (E.C. 3.2.1.17) is one of the most studied enzymes due to its antibacterial activity against Gram positive bacteria and is also a cold adapted protein. In this work the characterization of lysozyme from the insect Manduca sexta and its activity at low temperatures is presented. Both M. sexta lysozymes natural and recombinant showed a higher content of α-helix secondary structure compared to that of hen egg white lysozyme and a higher specific enzymatic activity in the range of 5-30 °C. These results together with measured thermodynamic activation parameters support the designation of M. sexta lysozyme as a cold adapted enzyme. Therefore, the insect recombinant lysozyme is feasible as a model for structure-function studies for cold-adapted proteins.

Human endothelin B receptor and its domain-truncated forms were cloned and expressed in Pichia pastoris. Ligand binding studies with expressed proteins were carried out using biotinylated endothelins. Competitive binding and liposome incorporation studies showed that the extracellular region is essential for ligand binding and that longer peptides have higher affinity.

A strong correlation between baking quality and size distribution of wheat glutenin polymers exists, so we have utilized Circular Dichroism Spectroscopy in presence of some denaturant agents to study glutenin polymers. Spectra indicated that all the changes induced by urea and by sodium dodecyl sulphate followed a multi-step transition process.

For biophysical studies using heteronuclear NMR analysis of amyloid beta peptide, construction of an efficient and high yield expression system of uniformly isotopic labeled amyloid beta peptide is desirable. Here we succeeded in obtaining 15N-labeled amyloid beta 1-40 expressed by attachment to hen egg white lysozyme as a fusion protein.

Ha-AP10 is a basic antifungal peptide from sunflower seeds (Helianthus annuus antifungal peptide of 10 kDa) belonging to the family of plant lipid transfer proteins. We report here its expression in E. coli [Glutathione S-transferase (GST) system] and its phosphorylation by endogenous membrane-bound calcium-dependent protein kinases.

A lectin that induces hemagglutination activity in mouse and rabbit erythrocytes has been purified from the hemolymph of the marine hair crab Erimacrus isenbeckii. The results of SDS-PAGE, gel-filtration, affinity and anionexchange chromatography indicate that this lectin, designated EIL (E. isenbeckii lectin), was successfully purified as a single protein, and comprises a mixture of a major (90%) dimeric and a minor (10%) oligomeric protein with a molecular mass of 116 kDa, with covalent linking between two subunits of 62 and 54 kDa. The activity was maximal at pH 5.6-8.0 and at temperatures below 50°C. The N-terminal amino acid sequences were determined, and these differed greatly from those of other reported lectins from invertebrates, vertebrates, or plants. EIL binds with high specificities to both the O-acetylsialic acid and mannose that are present in bacterial pathogens, which suggests that EIL can act as a defense protein against infection in this crab.

The fusA gene encoding a thermophilic protein EF-G with multiple rare condons was cloned from Thermoanaerobacter tengcongensis (TteEF-G) and overexpressed in Escherichia coli by cotransfering a RIG plasmid to overcome the potential codon-bias problem originated from Arg, Ile and Gly. The recombinant protein was identified by MALDITOF- MS for molecular mass with approximation of 76 kDa and by trypsin digestion coupled LC-MS/MS for peptide sequence coverage of 61.3%. The in vivo complementary assay indicates that TteEF-G could significantly rescue the E. coli LJ14 (frrts) at the non-permission temperature of 42°C in the bi-transformant of TteRRF and TteEF-G. This study indicated that coexpression of rare codons' cognate tRNA is a useful method for protein overexpression in E. coli.

It is a critical challenge to develop automated methods for fast and accurately determining the structures of proteins because of the increasingly widening gap between the number of sequence-known proteins and that of structureknown proteins in the post-genomic age. The knowledge of protein structural class can provide useful information towards the determination of protein structure. Thus, it is highly desirable to develop computational methods for identifying the structural classes of newly found proteins based on their primary sequence. In this study, according to the concept of Chou's pseudo amino acid composition (PseAA), eight PseAA vectors are used to represent protein samples. Each of the PseAA vectors is a 40-D (dimensional) vector, which is constructed by the conventional amino acid composition (AA) and a series of sequence-order correlation factors as original introduced by Chou. The difference among the eight PseAA representations is that different physicochemical properties are used to incorporate the sequence-order effects for the protein samples. Based on such a framework, a dual-layer fuzzy support vector machine (FSVM) network is proposed to predict protein structural classes. In the first layer of the FSVM network, eight FSVM classifiers trained by different PseAA vectors are established. The 2nd layer FSVM classifier is applied to reclassify the outputs of the first layer. The results thus obtained are quite promising, indicating that the new method may become a useful tool for predicting not only the structural classification of proteins but also their other attributes.

A phage display library of exendin-4 mutants was screened with the extracellular domain of rat glucagon-like peptide 1 receptor as the target. A novel variant of exendin-4 with higher affinity for the receptor fraction than that of the wild type was identified. The increased affinity was attributed to the substitution of Glu16 by Val16. Although the substitution probably caused an increased entropic cost to the helix region, the linker around Val16 is more flexible resulting in the increase of affinity for the receptor.

3-isopropylmalate dehydrogenase (3IPMDH) is the third enzyme in leucine biosynthesis and a promising target for the development of broad-spectrum antibacterial agents. We report here the expression, purification and biochemical characterisation of Haemophilus influenzae 3-isopropylmalate dehydrogenase. The observed enzyme inhibition by the reaction product NADH could represent a regulatory mechanism for 3IPMDH.

Two 30-kDa proteins with N-terminal sequence homology to chitinases have been isolated from fruits of the emperor banana by using a protocol that involved (NH4)2SO4 precipitation, affinity chromatography on Affi-gel blue gel, ion exchange chromatography by fast protein liquid chromatography (FPLC) on Mono S and gel filtration by FPLC on Superdex 75. The proteins were adsorbed on Affi-gel blue gel and Mono S. They both inhibited mycelial growth in Fusarium oxysporum but not in Mycosphaerella arachidicola. The chitinase-like protein more strongly bound on Mono S was obtained with a slightly lower yield and exhibited a higher antifungal potency toward F. oxysporum when compared with the less strongly bound chitinase-like protein.

PEDF is an effective inhibitor of angiogenesis in the eye with neuronal differentiating activity. Here, we show that PEDF prevents the AGEs-elicited eNOS reduction through its anti-oxidative properties. Our present study suggests that PEDF may also play a protective role against atherosclerosis.

The thrC gene of Streptococcus mutans encodes threonine synthase, which is a potential target for drug design. To study the structure and function of the enzyme, the thrC gene was amplified from Streptococcus mutans genomic DNA and cloned into the expression vector pET28α. The protein was expressed in Escherichia coli in soluble form and purified to homogeneity. Crystals suitable for X-ray diffraction were obtained by hanging-drop vapor diffusion method. The crystal diffracted to 2.5 Å and belonged to space group P31 or P32, with unit cell parameters a=b=60.39 Å, c=118.62 Å.