Protein and Peptide Letters - Volume 13, Issue 7, 2006

Over the past two decades, research scientists have been involved in the investigation of thermophilic and hyperthermophilic microorganisms owing to the unique features of their enzymic systems. Such in-depth investigations are now on their way to mastering the cloning and industrial exploitation of a broad variety of genes encoding enzymes involved in starch hydrolysis, amino acid biosynthesis, protein hydrolysis, etc. In this work, we review the state of the art and future perspectives of industrial applications of enzymes from hyperthermophilic and extreme thermophilic microorganisms, special attention being paid to the biotechnological methods involved in their industrial exploitation.

We report the isolation and characterization of a cDNA sequence (Mec1) coding for a glutamic acid-rich protein (Pt2L4) from cassava storage roots. Comparative sequence analysis showed a high identity of Pt2L4 with cassava protein C54, which is expressed in vascular tissues of storage roots. Northern blot analysis showed that the Mec1 transcript expression pattern might be related to the maturation of the storage parenchyma cells.

The selective toxicity of depressant scorpion neurotoxins to insects is useful in studying the insect sodium channel gating, as well as being relevant to several other applications. In order to carry out structure/activity studies, the functional expression of such polypeptides is required. In the work reported here, the cDNA of a new peptide from the venom of the scorpion Buthotus saulcyi was cloned and sequenced. It codes for a 64 residues peptide (BsaulI) with 8 highly-conserved cysteines. This peptide shares high sequence similarity with depressant insect toxins of other scorpion species. Large amounts of insoluble BsaulI protein were expressed in Escherichia coli. Purification of this peptide was carried out under denaturing conditions. Renaturation was performed by pulsed dilution of the denatured BsaulI in the refolding buffer. Production of refolded Bsaul1, however, is approximately an order of magnitude higher than that obtained with similar scorpion depressant toxins. Intrinsic fluorescence, far-UV circular dichroism spectra and biological activity assays indicate that the peptide adopts a folded structure.

Purified glucoamylase from Arachniotus citrinus was immobilized on polyacrylamide gel with 70% yield of immobilization. The immobilization improved the pH optima, temperature optima, values of Km, Vmax, and activation energy. Irreversible thermal denaturation studies of soluble and immobilized glucoamylase indicated that immobilization decreased the entropy and enthalpy of deactivation by magnitudes and made the immobilized glucoamylase thermodynamically more stable.

Pancreatic ribonuclease A (RNase A) has been shown to aggregate moderately and gradually at 65°C. Antibodies raised against the dodecapeptide KETAAAKFERQG corresponding to the N-terminal 1-12 amino acid residues of RNase A (Npep) as well as native RNase A were effective in lowering RNase A aggregation at 65°C. The antiRNase A antibodies were, however, more protective. The binding of antiNpep antibodies to the N-terminal region of RNase A may interfere with initiation of oligomerization of the enzyme and consequently its aggregation. The antiRNase A antibodies were presumably more effective in protecting RNase A against aggregation by binding to multiple epitopes of the enzyme including the N-terminal region and hence restricting the interaction of the monomers.

Neuronal tau, through its proline-rich domain and the microtubule binding domain, binds to RNA nonsequence- specifically via electrostatic interaction. This binding inhibits the activity of tau. Tau and RNA were also found to co-localize in SH-SY5Y cells suggesting that RNA has opportunities to interact with tau in cells.

Human multisynthetase complex auxiliary component, protein p43 is an endothelial monocyte-activating polypeptide II precursor. In this study, comprehensive sequence analysis of N-terminus has been performed to identify structural domains, motifs, sites of post-translation modification and other functionally important parameters. The spatial structure model of full-chain protein p43 is obtained.

Hsp70 proteins assist refolding of polypeptides in an ATP dependent manner. Crystal structure of intact Hsp70 protein has not been determined yet however, structures of its two domains were solved separately. Allostery between ATPase domain and peptide-binding domain facilitates unfolded substrate processing. To elucidate function of key residues and affect of other factors involved in this allosteric mechanism, a biochemical study was undertaken.

Hsp70 is a universally conserved essential protein chaperone. In addition to its roles in many cellular process, Hsp70 protects cells from stress by binding partially unfolded proteins. Therefore, Hsp70 prevents protein aggregation and prion formation. Prions are infectious agents and are responsible for several fatal neurodegenerative diseases. Eukaryotic cells have several cytosolic Hsp70 isoforms, some constitutively expressed (Hsc70s), and others expressed only when cells are exposed to stress (Hsp70s). To determine which factors conferred functional specificity, we constructed hybrid Hsc/Hsp chaperones. All hybrids supported growth except those that contained the ATPase domain derived from inducible Hsp70. Thus, regulation of peptide binding by ATP hydrolysis must differ significantly between Hsc- and Hsp70 isoforms. In this work, nucleotide and peptide binding domain communication of Hsp70 proteins during their interaction with nucleotides and peptide substrates were investigated in vitro by using hybrid constructs.

A new PLA2 Bj-V from Bothrops jararacussu (14039.49 Da determined by MALDI-TOF mass spectrometry) was isolated in only one chromatographic step by HPLC ion-exchange and its purity was confirmed by reverse phase. Amino acid analysis showed a high content of hydrophobic and basic amino acids as well as 14 half-cysteine residues. The N-terminal sequence (DLWQFGQMIL KETGKIPFPY YGAYGCYCGW GGRGGKPKDG TDRCCYVHD . . .) showed a high degree of homology with basic D49 PLA2 myotoxins from other Bothrops venoms. Bj V showed discrete sigmoidal enzymatic behavior, with maximal activity at pH 8.4 and 35-40°C. Full PLA2 activity required Ca2+ (10 mM) and there was little catalytic activity in the presence of 1 mM Ca2+.The addition of Mn2+ or Mg2+ (10 mM) in the presence of low (1 mM) Ca2+ slightly increased the enzyme activity, whereas Zn2+ and Cu2+ (10 mM) diminished the activity. The substitution of Ca2+ for Mg2+ or Cu2+ also reduced the enzymatic activity. Bj V had PLA2 activity and produced cytotoxicity in murine C2C12 skeletal muscle myoblasts and myotubes. The isolation of these isoforms Bj-IV [1] and Bj-V (described herein) found in a fraction previously described as homogeneous shows us the importance of optimization in purification techniques in order to better understand their biological behavior.

An effective and simple strategy for preparing peptide crosslinkers is described. An MMP-13 degradable peptide QPQGLAK-NH2 was prepared on the solid-phase using Fmoc chemistry. The peptide crosslinker was synthesized onbead by the coupling reaction between acrylic acid and the amine groups of glutamine and lysine residues. The synthetic procedure employed the acid-labile Fmoc-Lys (Mtt)-OH and base-labile Fmoc-AA-OH derivatives. Selective deprotection, of -Mtt and -Fmoc groups on-bead, freed the amine end-groups on glutamine and lysine residues for coupling reaction with acrylic acid while maintaining the peptide attached to the resin. Subsequent cleavage from the resin yielded a peptide crosslinker with two unsaturated acrylate end-groups with high yield and purity. This method can be generally employed for the synthesis of a wide range of peptides with one or more reactive groups for grafting in the fabrication of biomimetic scaffolds in tissue engineering applications.

To design melittin (ME) analogues that are not cytotoxic against mammalian cells but which possessing potent antimicrobial activity, we synthesized a ME analogue (ME-w) in which the Trp-19 residue of ME was replaced by a Trppeptoid residue (Nhtrp). ME-w exhibited similar antimicrobial activity compared to ME against the tested six bacteria and C. albicans. However, it was much less cytotoxic against the hRBCs and HeLa and NIH-3T3 cells than ME. Tryptophan fluorescence and CD spectra revealed that the Trp-19 ® Nhtrp substitution in ME contributed to a much lower helical assembly in an aqueous environment and structural flexibility and exterior localization to zwitterionic membrane which modulates its selectivity toward bacterial cells.

Cyclophilins are an evolutionarily conserved family of peptidyl-prolyl cis-trans isomerases (PPIases). A cyclophilin B (cypB) gene from the anaerobic fungus Orpinomyces sp. strain PC-2 was cloned and overexpressed in Escherichia coli. It was expressed as an amino-terminal 6 x His-tagged recombinant protein to facilitate purification. Highly purified protein (26.5 kDa) was isolated by two chromatographic steps involving affinity and gel filtration for biochemical studies of the enzyme. The recombinant CypB displayed PPIase activity with a kcat/Km of 8.9 x 106 M-1 s-1 at 10°C and pH 7.8. It was inhibited by cyclosporin A (CsA) with an IC50 of 23.5 nM, similar to those of the native protein and other cyclophilin B enzymes from animals. Genomic DNA analysis of cypB revealed that it was present as a single copy in Orpinomyces PC-2 and contained two introns, indicating it has a eukaryotic origin. It is one of the most heavily interrupted genes with intron sequences found in anaerobic fungi. The three-dimensional model of Orpinomyces PC-2 CypB was predicted with a homology modeling approach using the Swiss-Model Protein Modeling Server and three dimensional structure of human CypB as a template. The overall architecture of the CypB molecule is very similar to that of human CypB.

The best way to introduce information about amino acid residues into calculations of protein bioinformatics was examined. That was done for predicting helical regions with a neural network. Several fundamental and instructive ways for information processing were developed and are described.

The protein population secreted from three wine-contaminant microorganisms was studied by two-dimensional electrophoresis and screened for proteases. Proteolytic enzymes were electrophoretically purified and their activity, optimum pH and temperature determined. The protease of Acetobacter aceti maintained its activity over the range of pHs 3.0- 5.0, thus being of potential biotechnological interest.

Structural-energetic analysis of peptide and protein antigens in the context of binding to antibody reveals fundamental differences between the cross-reactions of antipeptide antibody with protein and antiprotein antibody with peptide, providing a physicochemical basis for B-cell epitope prediction as applied to the development of peptide-based vaccines and immunodiagnostics.