Protein and Peptide Letters - Volume 16, Issue 11, 2009

Dipeptide L-threonyl-L-methionine (Thr-Met) is characterized structurally by means of a solid-state linear polarized IR- spectroscopy (IR-LD) of oriented samples as a colloidal suspension in nematic liquid crystal and quantum chemical ab initio calculations. Vibrational analysis supports the experimental data as well. The role of intermolecular hydrogen bonding on conformational behavior and spectroscopic properties of the compound, studied in solid state is determined.

The cytotoxicity of hPrP[173-195] prion peptide against a neuroblastoma cell model was found independent of its tendency to aggregate over time. Cytosolic and nuclear inclusions of peptide were highlighted by confocal microscopy, suggesting a role as a transcription factor in activating signal transduction pathways involved in cell toxicity.

Intracellular delivery of synthetic oligopeptides has the potential to promote the occurrence of various cellular events such as cell death, proliferation, growth inhibition, metabolic changes, and morphological changes. However, the regulation of cellular differentiation by intracellular delivery of synthetic oligopeptides has been little studied. Von Hippel- Lindau protein (pVHL) is one of the proteins that functions to induce the differentiation of neural progenitor cells (NPCs). To function in these cells, pVHL forms a complex composed of itself, elongin BC, Clu-2, and Rbx-1. It is suggested that the binding site of elongin BC in pVHL plays a critical role in pVHL function, i.e., ubiquitination, which is related to neuronal differentiation. So, we synthesized an oligopeptide corresponding to the elongin BC binding site, and delivered the oligopeptide into NPCs by using a mixture of trifluoroacetylated lipopolyamine and diloeoyl phosphatidylethanolamine (BioPorter) to form a peptide-lipid complex. After intracellular delivery of the oligopeptide, induction of differentiation of NPCs was shown in terms of neurite outgrowth and by immunocytochemical and electrophysiological means. The intracellular delivery of the synthetic oligopeptide derived from pVHL may provide a safe and valuable approach for the neuronal differentiation of NPCs.

There are two classes of tandem repeats in proteins - globular and non-globular. There are two subclasses of non-globular repeats. The first, such as collagen, form stable helices. Members of the second are flexible and somewhat disordered both in vitro and in vivo. This review focuses on this second subclass.

Two cysteine endopeptidases from latex of Araujia angustifolia (araujiain aI and araujiain aIII) were purified and characterized by means of conventional and proteomics techniques (MALDI-TOF). N-terminal sequences showed a high percentage of identity with cysteine proteinases belonging to the papain family. The peptide mass fingerprint analysis demonstrated a close homology among both proteinases.

Japanese encephalitis virus (JEV) is a mosquito-borne viral zoonosis of public health importance. Global efforts have been made towards development of vaccine for prevention of Japanese encephalitis. The envelope protein of JEV is associated with viral binding to cellular receptors, membrane fusion, and the induction of protective neutralizing antibody response in hosts. Here we report that the antibodies raised against refolded domain III of envelope protein of JEV neutralize the JE virus and inhibit the JEV infection to Porcine Stable Kidney (PS) cells. A reverse transcriptase-PCR amplified gene encoding domain III of JEV envelope protein was cloned into pET28a+ vector and over expressed in E. coli. The recombinant JEV-DIII protein was purified by affinity chromatography under denaturing conditions. The rJEVDIII was refolded by oxido-redux shuffle and purified to homogeneity by ion-exchange chromatography. Refolded rJEVDIII was characterized using biochemical and biophysical methods. The polyclonal antibodies were raised against in vitro refolded rJEV-DIII protein in BALB/c mice with Freunds adjuvant. Ninety percent JEV is neutralized when the serum against refolded rJEV-DIII is used at a dilution of 1:80 as against 60.5% neutralization capacity with the same dilution of serum raised against denatured rJEV-DIII. The method of expression and purification of biologically functional rJEV-DIII protein described in this study may help in better understanding the biology of JE virus and the development of better vaccine candidate. Since the expression system uses E. coli as the heterologous host, the process is easy and amenable to inexpensive scale-up.

The MIR algorithm provides an ab initio prediction of a protein's core residues. An improved version, the MIR2, is presented and validated on 3203 proteins from PDB. Structures are decomposed in Closed Loops, their limits constituting the observed core residues. They are predicted by MIR2 with an accuracy approaching 80%.

Radioresistance represents a major obstacle to a successful outcome for the treatment of non-Hodgkin's lymphoma (NHL). Here we performed a global differential proteome analysis of the mitochondria in Raji cells exposed to radiation. The results showed that 23 differentially expressed proteins were identified. Furthermore, GAPDH, RECQL4, MKI67, and ATAD3B could serve as potential biomarkers of radioresistance.

The stability of biocatalysts is an important criterion for a sustainable industrial operation economically. T1 lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1 (T1 lipase) that was isolated from palm oil mill effluent (POME) in Malaysia. We report here the results of high temperatures molecular dynamics (MD) simulations of T1 lipase in explicit solvent. We found that the N-terminal moiety of this enzyme was accompanied by a large flexibility and dynamics during temperature-induced unfolding simulations which preceded and followed by clear structural changes in two specific regions; the small domain (consisting of helices α3 and α5, strands β1 and β2, and connecting loops) and the main catalytic domain or core domain (consisting of helices α6- α9 and connecting loops which located above the active site) of the enzyme. The results suggest that the small domain of model enzyme is a critical region to the thermostability of this organism.

In this work, we describe the original characterization of peptides and proteins present in the skin secretions of the Mexican amphibian Hyla eximia. To this purpose, a novel water/dark extraction method, as well as the classic electrical stimulation procedure, was applied in order to extract the skin secretion. Two novel antimicrobial peptides He-1 and He-2 were sequenced. In addition, a molecular mass fingerprint revealed more than one hundred different molecules. Eight peptides in homogeneous form were assayed against five species of bacteria. Thereafter, the peptide He-2 demonstrated high antiparasitic activity against ookinete forms of malaria parasites at low concentration.

A specific SPRI sensor for cathepsin determination based on the interaction between immobilized cystatin and cathepsins has been developed. All cathepsins form the same calibration curve. The sensor dynamic response range is between 0.5 and 2.0 ng ml-1 and the detection limit is equal to 0.1 ng ml-1.

We analyzed 27 antifungal peptides (AFPs) to understand their stability by various parameters like, stabilization centers, GROMOS, OPLS and FOLDEF force fields. Subsequently, we propose that AFP, NK-Lysin could be considered a potential candidate and also could act as a template for designing the therapeutic peptide drug against pathogenic fungi.

We have attempted finding common sequential patterns among protein antigens. For this, we have used Gibbs multiple motif sampler on the set of all non-redundant antigenic sequences available in curated databanks. Several sequential motifs are obtained on these sequences when the amino acids are represented according to their similarity clusters. Significantly high proportions of known B-cell epitope sites are found within or adjacent to these motifs, thus indicating a possibility of linear epitope signatures. These findings may offer important applications in synthesis of peptide vaccines. A predictive example in this regard is presented.

An antifungal protein with multiple stable biological activities unaffected by chemical modification of tyrosine and tryptophan, and a protein with N-terminal sequence and molecular mass resemblance to the antifungal protein but no identifiable activities were isolated from culture broth of Bacillus amyloliquefaciens. The findings are analogous to previous reports on thaumatin and thaumatin-like proteins.

The first attempt has been made to suggest a model of influenza A virus matrix M1 protein spatial structure and molecule orientation within a virion on the basis of tritium planigraphy data and theoretical prediction results. Limited in situ proteolysis of the intact virions with bromelain and surface plasmon resonance spectroscopy study of the M1 protein interaction with lipid coated surfaces were used for independent confirmation of the proposed model.

The interaction of calreticulin with native and denatured forms and polypeptides in proteolytic digests of proteins representing structural classes of all-α-helix (hemoglobin, serum albumin), all-β-sheet (IgG) and α-helix + β-sheets (lysozyme, ovalbumin) was investigated. The binding of calreticulin to denatured proteins was found to depend on conformation and structural class of the protein. No interaction was observed with the native proteins, whereas binding was seen for the denatured proteins, the order of interaction being lysozyme = IgG > ovalbumin ≫ hemoglobin = serum albumin. Moreover, the interaction between calreticulin and the heat-denatured proteins depended on the temperature and time used for denaturation and the degree of proteolytic fragmentation. Calreticulin bound well to peptides in proteolytic digests from protease K or chymotrypsin treatment of lysozyme, IgG and ovalbumin but weakly or not at all to peptides in proteolytic digests of hemoglobin and serum albumin. Synthetic peptides from lysozyme and ovalbumin confirmed binding to hydrophobic peptides from these proteins. These results show that calreticulin has the ability to interact with denatured and fragmented forms of proteins with a preference for β-strand structure and hydrophobicity.