Protein and Peptide Letters - Volume 18, Issue 1, 2011

The microphase adsorption-spectral correction (MPASC) technique was described and applied to the study of the interactions of sodium octanesulfonate (SOS) with human serum albumin (HSA). The aggregation SOS obeys the Langmuir monolayer adsorption. The results show the adsorption ratio of sodium octanesulfonate to HSA is SOS:HSA=18:1. The adsorption constant is KSOS-HSA=4.03×102. The detection limit is 0.036μmol/L. FT-IR spectra proved the binding changed the conformation of HSA.

Protein domain boundary prediction is critical for understanding protein structure and function. In this study, we present a novel method, an order profile domain linker propensity index (OPI), which uses the evolutionary information extracted from the protein sequence frequency profiles calculated from the multiple sequence alignments. A protein sequence is first converted into smooth and normalized numeric order profiles by OPI, from which the domain linkers can be predicted. By discriminating the different frequencies of the amino acids in the protein sequence frequency profiles, OPI clearly shows better performance than our previous method, a binary profile domain linker propensity index (PDLI). We tested our new method on two different datasets, SCOP-1 dataset and SCOP-2 dataset, and we were able to achieve a precision of 0.82 and 0.91 respectively. OPI also outperforms other residue-level, profile-level indexes as well as other state-of-the-art methods.

Calmodulin-binding protein-10 (CaMBP10) was isolated previously from Chinese cabbage and identified as a member of the lipid transfer protein family. In this study, we found that CaMBP10 was phosphorylated in a calcium( Ca2+)-dependent manner, and the phosphorylation was inhibited by calmodulin (CaM) antagonists. In-gel kinase assay revealed that the phosphorylation of CaMBP10 was catalyzed by a 45 kDa protein kinase, which underwent autophosphorylation in the presence of Ca2+. Immunoblotting assay further identified this kinase as a calcium-dependent protein kinase (CDPK). In addition, the phosphorylation site was mapped to the C-terminal region of CaMBP10, where the CaMbinding domain resides. These results provide novel insights into the molecular mechanisms that regulate CaMBP10 functions.

A Surface Plasmon Resonance Imaging (SPRI) sensor has been developed for specific determination of cystatin. The sensor contains immobilised papain, which binds cystatin from solution. Papain activated with N- Hydroxysuccinimide (NHS) and N-Ethyl-N'-(3-dimethyl aminopropyl)carbodiimide (EDC) was immobilized on an amine-modified gold surface. Cysteamine was used for modification of the gold surface. Papain concentration and the pH of interaction were optimised. A concentration of papain of 1.5 μg mL-1 and a pH of 6.5 were selected as optimal. The specificity of interaction was verified by the lack of interaction with human albumin. The sensor's dynamic response range is between 0 and 0.6 μg mL-1, and the detection limit is 0.09 μg mL-1. The results were validated by comparison with the PETIA (particle enhanced immunoturbidimetric assay) method showing good agreement. A calibration curve of chicken egg white cystatin or Cystatin C was used. In order to demonstrate the sensor's potential, cystatin C was determined in blood plasma, urine and saliva, showing good agreement with data reported in the literature. The results for cystatin concentration in the blood plasma of people suffering from leukaemia were found to be below the normal level of cystatin.

Plants defend themselves against biotic or abiotic stress by triggering intracellular signaling pathways that regulate gene expression and responses to the offending agent. Phosphorylation and dephosphorylation represent major mechanisms for the regulation of plant defense pathways. Therefore, MAP kinases and phosphatases have been the focus of many studies in this area. This study identified three phosphatase activities, namely RcPPase I, II and III. Wounding increased the activity levels of RcPPase III, while the activities of RcPPase I and II remained constant compared to the control. N-terminal partial amino acid sequence, biochemical characterization with use of specific substrates and inhibitors indicated that the RcPPase III belong to the family of tyrosine phosphatases (PTPs).

Hepcidin was first identified as an antimicrobial peptide expressed in the liver. It was later demonstrated that hepcidin is in fact the long sought hormone that regulates iron homeostasis in mammals. Hepcidin is encoded as an 84 amino acid prepropeptide that is successively cleaved to yield prohepcidin and the mature 25 amino acid hepcidin. Both the bioactive 25-aa hepcidin and the 35-aa proregion are secreted by liver hepatocytes. The aim of the present study was to assess the antibacterial activity of the proregion peptide from human hepcidin. Using a chemically synthesized peptide corresponding to the proregion, we show that it is bactericidal against Bacillus megaterium (25μM), and inhibits Bacillus subtilis growth at high concentration (200μM). No synergistic interaction of proregion and Hepc25 against Bacillus megaterium was seen. In a further step, the mode of action of proregion on Bacillus megaterium was studied. It caused a slow accumulation of the vital stain SYTOX in the bacteria, indicating that it did not destroy the microbial membranes through a detergent-like mechanism, even at concentrations (80μM) higher than those required to kill the bacteria. This result suggests that the target of proregion might be an intracellular component. Finally, gel retardation assay showed that the DNA binding ability of the hepcidin proregion was equivalent to that observed for magainin 2, an antimicrobial peptide which exerts its antimicrobial effect by interfering with intracellular nucleic acids. In conclusion, we speculate that the proregion of hepcidin may have bacteriostatic effects, and as such may contribute to the innate immune response.

Human mitochondrial aldehyde dehydrogenase is a member of superfamily of multisubunit enzymes, catalyzing the conversion of a broad range of aldehydes to corresponding acids via the NAD (P)+-dependent irreversible reaction. They play an important role in the detoxification of acetaldehyde, in the development of alcohol sensitivity and human alcohol- related disorders. The study aimed to understand the role of conserved residues by comparing similarities and differences between the two isoenzymes. A 3D model of the human ALDHX is constructed by molecular modeling based on the crystal structure of human ALDH2 by using MODELLER (8V1) program. Assessment of reliability of the 3D model is carried out by the programs PROCHECK and PROSAII. The ALDHX fold is similar to the previously described ALDH structures. Sequence and structural analyses have highlighted a close structural and functional relationship between the two isoenzymes of human origin. The interfacial residues that are involved in crucial interactions across the interface stabilize the dimer-tetramer interface in the enzyme. Stability factors like salt bonds and hydrogen bonds aid and maintain the tetrameric assembly of the enzyme.

The Golgi apparatus is an important eukaryotic organelle. Successful prediction of Golgi protein types can provide valuable information for elucidating protein functions involved in various biological processes. In this work, a method is proposed by combining a special mode of pseudo amino acid composition (increment of diversity) with the modified Mahalanobis discriminant for predicting Golgi protein types. The benchmark dataset used to train the predictor thus formed contains 95 Golgi proteins in which none of proteins included has ≥ 40% pairwise sequence identity to any other. The accuracy obtained by the jackknife test was 74.7%, with the ROC curve of 0.772 in identifying cis-Golgi proteins and trans-Golgi proteins. Subsequently, the method was extended to discriminate cis-Golgi network proteins from cis-Golgi network membrane proteins and trans-Golgi network proteins from trans-Golgi network membrane proteins, respectively. The accuracies thus obtained were 76.1% and 83.7%, respectively. These results indicate that our method may become a useful tool in the relevant areas. As a user-friendly web-server, the predictor is freely accessible at http://immunet.cn/SubGolgi/.

A new 15-kDa Bowman-Birk type trypsin inhibitor (termed VFTI-G1) was isolated from the seeds of Faba bean (Vicia faba cv. Giza 843) using cation exchange chromatography on an SP-Sepharose column, anion exchange chromatography on Q-Sepharose and Mono Q columns, and finally size exclusion chromatography on a Superdex 75 column. VFTI-G1 manifested significant antiproteolytic activity against trypsin (5761 BAEE units/mg, Ki 20.4×10-9 M), but only a slight chymotrypsin inhibitory activity (<<10 BTEE units/mg). The suitable environment to sustain its trypsin inhibitory activity was at temperatures below 60 °C and at pH 7. Its trypsin inhibitory activity was inhibited by the reducing agent dithiothreitol in a dose-dependent manner, indicating the significance of intact disulfide bonds to the trypsin inhibitory activity. It inhibited HIV-1 reverse transcriptase (RT) activity with an IC50 of about 0.76 μM. Furthermore, VFTI-G1 showed specific antiproliferative activity toward HepG2 hepatoma cells by inducing chromatin condensation and cell apoptosis. The HIV-1 RT inhibitory activity of VFTI-G1 and its specific antiproliferative activity toward Hep G2 cells may find medical applications.

The use of multi-epitopes has been considered as a promising strategy to overcome the obstacle of antigenic variation in malarial vaccine development. Previously, we constructed a multi-epitope artificial antigen, Malaria Random Constructed Antigen-1(M.RCAg-1), to optimize expression of the antigen, and we subcloned the gene into three prokaryotic expression vectors that contain different fusion tags at the N-terminus. Three recombinant proteins expressed by these vectors, named M.RCAg-1/Exp.V-1, V-2, and V-3, were purified after the cleavage of the fusion tag. All three recombinant proteins were able to induce similar levels of antigenicity in BALB/c murine models. However, the antibody responses against the individual epitope peptides of the recombinant products were dramatically different. Additionally, the different epitopes elicited various CD4+ T-cell responses, as shown by the resulting lymphocyte proliferation and varied IFN-γ and IL-4 levels determined by EILSPOT; however, each could be distinctly recognized by sera derived from malaria patients. Additionally, the rabbit antibody induced by these proteins showed diverse efficacy in malaria parasite growth inhibition assays in vitro. Furthermore, analysis via circular dichroism spectroscopy confirmed that the secondary structure was different among these recombinant proteins. These results suggest that the expressed multi-epitope artificial antigens originating from the different vector fusion peptides indeed affect the protein folding and, subsequently, the epitope exposure. Thus, these proteins are able to induce both distinct humoral and cellular immune responses in animal models, and they affect the efficacy of immune inhibition against the parasite. This work should lead to a further understanding of the impact of vector fusion peptides on the conformation and immune reactivity of recombinant proteins and could provide a useful reference for the development of artificial multi-epitope vaccines.

Coordination of cell growth and cell division is very important for living organisms in order for these to develop harmonically. The present research is concerned with the purification and characterization of a new peptide hormone, namely ZmIGF (Zea mays insulin-like growth factor), which regulates growth and cell division in maize tissues. ZmIGF is a peptide of 5.7 kDa, as determined by mass spectroscopy. It was isolated either from maize embryonic axes of 48-h germinated seeds or from embryogenic callus and purified through several chromatographic procedures to obtain a single peak as shown by Reverse Phase High-Performance Liquid Chromatography (RP-HPLC). This peptide exhibits a well defined α-helix structure by circular dichroism analysis, similar to that reported for Insulin or for Insulin-like growth factor (IGF-1). Further, ZmIGF seems to perform, in maize, a similar function to that reported for insulin or peptides from the IGF family in animals. Indeed, maize tissues stimulated either by ZmIGF or insulin showed to induce selective synthesis of ribosomal proteins as well as of DNA. Taken together, the previously mentioned data strongly suggest that plants contain a peptide hormone of the IGF family, highly conserved through evolution that regulates growth and development.

Protein thermodynamic structure theory is an integrated approach to the study of protein dynamics and the mechanisms of enzyme catalysis. In this paper, a hypothesis arising from this theory is examined. The timescale of an enzymatic reaction (TER) gives a key to characterizing enzyme conformational changes. The aspects of timescale important in our approach are: (i) it is logically related to internal motions of the main chain of a protein; (ii) it sets the upper limit on the size or scope of protein conformational changes. Feature (i) is linked to the dynamic properties of enzyme-reactant complexes. Feature (ii) is linked to the dynamic sites of the main chain (promoting motion) involved in enzyme activity. Our analysis shows that a comprehensive understanding of enzymology can be established on the basis of protein thermodynamic structure theory.