Protein and Peptide Letters - Volume 18, Issue 7, 2011

β-1,3-glucanases are found in organisms as diverse as plants, animals, bacteria and fungi. In plants, such enzymes are not only associated with defense mechanisms against pathogens, but also play critical roles in physiological and developmental processes. Here we identified a new β-1,3-glucanase in maize seeds, and named it ZmGlucA. Sequence analysis revealed that ZmGlucA belongs to the class A of β-1,3-glucanase, a class related to defense and physiological processes in plants. mRNA and protein assays showed that zmGlucA is expressed exclusively in seeds, and it is differentially regulated during seed development. Additionally, zmGlucA expression is strongly induced in seeds of the mutant dek 827Kpro1, which is defective for embryo and endosperm development. Our data support the idea that ZmGlucA protein is relevant to seed development.

Glutamine (GLN), which is the most abundant free amino acid of the human body, is an important cellular fuel and an essential precursor for the antioxidant glutathione (GSH). GLN plays a regulatory role in several cell specific processes, such as metabolism, protein synthesis and degradation, and respiratory burst. Severe GLN deficiencies usually occur rapidly in critical illness. GLN has regulatory capacity in immune and cell modulation, and GLN reduces morbidity and mortality in critical illness. The expression of heat shock proteins (HSP) is vital to cellular and tissue protection in stress or injury. GLN can function as a metabolic fuel and stress-signaling molecule in illness and injury via HSP. GLN has the ability to enhance HSP expression in injury, regulate the expression of some genes related to metabolism, signal transduction, cell defense and repair, and activate intracellular signaling pathways. The focus of this review is to describe how GLN participates in the regulation of illness and health and regulates the expression of HSP.

Hydantoinases are industrial enzymes with varying degree of activities on variable substrates to form different products. Although, few of the hydantoinase structures were known recently, the functional details and active site mechanism were not clearly understood yet. In a structure determination effort we reported that Bacillus sp. AR9 hydantoinase contains uncarboxylated lysine in the active site, whereas all the other hydantoinases have a carboxylated active site lysine. Here we describe the importance of carboxylated lysine for differential activities by making lysine mutations as well as carboxylating the lysine in a D-hydantoinase from Bacillus sp. AR9. The lysine to alanine and lysine to arginine mutations showed reduced activities whereas carboxylation of the lysine has enhanced the activity. Theoretical studies involving the calculation of electrostatic potentials for the hydroxide ion between the two metal ions present in the active site suggest that the presence of carboxylated lysine increases the nucleophilicity of the hydroxide.

On the basis of Bayesian probabilistic inference, Gaussian process (GP) is a powerful machine learning method for nonlinear classification and regression, but has only very limited applications in the new areas of computational vaccinology and immunoinformatics. In the current work, we present a paradigmatic study of using GP regression technique to quantitatively model and predict the binding affinities of over 7000 immunodominant peptide epitopes to six types of human major histocompatibility complex (MHC) proteins. In this procedure, the sequence patterns of diverse peptides are characterized quantitatively and the resulting variables are then correlated with the experimentally measured affinities between different MHC and their peptide ligands, by using a linearity- and nonlinearity-hybrid GP approach. We also make systematical comparisons between the GP and two sophisticated modeling methods as partial least square (PLS) regression and support vector machine (SVM) with respect to their fitting ability, predictive power and generalization capability. The results suggest that GP could be a new and effective tool for the modeling and prediction of MHC-peptide interactions and would be promising in the field of computer-aided vaccine design (CAVD).

Mono-, di- and trisaccharide representing the reducing terminal of the core structure of N-glycans were incorporated into Leu-Lys-Asn-Gly-Gly-Pro hexapeptide that is a partial structure of the Trp-cage mini-protein by linear assembly. These studies provide evidence that the used combination of Fmoc and Boc strategy and mild conditions result in glycopeptides in high purity and reasonable yield.

Prediction of thermophilic and mesophilic protein plays a crucial role in both biochemistry and bioengineering. In this study, a different mode of pseudo amino acid composition (PseAAC) was proposed to formulate the protein samples by integrating the amino acid composition, the physic chemical features, as well as the composition transition and distribution features, where each of the protein samples was represented by a numerical vector through the sequencebased approach. Using the support vector machine algorithm, an accurate and reliable classifier was constructed to predict the thermophilic and mesophilic proteins. Moreover, three feature reduction algorithms were obtained for locating the most vital features and reducing the size of feature space. Among the three feature reduction algorithms, the genetic algorithm performed best. Finally, with the reduced features extracted from the genetic algorithm, it was observed that for the selected dataset the new classifier achieved a high accuracy of 95.93% with the Matthews correlation coefficient of 0.9187.

The human leukemia inhibitory factor (hLIF) is one of the most important cytokines in the interleukin-6 (IL-6) cytokine family. Numerous studies have demonstrated that hLIF is a pleiotropic cytokine with multiple effects on different types of cells and tissues. The optimal chemical synthesis of the hLIF gene has been previously reported to increase the expression of the recombinant inclusion body protein in E. coli. However, the required refolding step limits the recovery rate. In this report, a novel strategy was designed to produce a soluble recombinant human LIF (rhLIF) in the prokaryotic system in order to obtain higher yields of the bioactive protein with simpler steps. This optimal hLIF gene was cloned, and it successfully expressed the soluble recombinant protein in E. coli using the thioredoxin (Trx) protein as a fusion partner. A simple purification procedure is established to purify the recombinant fusion protein from the soluble supernatant of the lysed culture cells. This procedure yields up to 5 mg/L rhLIF with above 95% purity. The strategy allows the protease to release target cytokines without additional N-terminus amino acids, which is an important consideration for maintaining its bioactivity. Functional analysis of the purified rhLIF by murine myeloblastic leukemia M1 cell proliferation assay demonstrates biological activity that is similar and comparable to that of hLIF. These results present a sound strategy for the soluble production of rhLIF and other homologous tertiary structure cytokines consisting of four ..-helices in a bundle for basic research, as well as clinical applications.

Recombinant antihypertensive peptide multimer (AHPM-2, 8kDa/68AA), a new designed polypeptide with potential antihypertensive effect in vivo, is composed of 15 low-molecular-weight antihypertensive peptides tandemly linked up according to the restriction sites of gastrointestinal proteases. After gene optimization, the DNA fragment encoding AHPM-2 was chemically synthesized, cloned into the pET32a, and successfully expressed in E.coli, above 90% in a soluble form. After chromatographic purification, the expressed fusion protein Trx-AHPM-2 was subject to the simulated gastrointestinal digestion, and the hydrolysate showed potent ACE inhibitory activity with an IC50 value of 4.5±0.3 ìg ml-1. The active fragments from the AHPM-2 were identified by UPLC-MS/MS. This method will be useful in obtaining an appreciable quantity of recombinant AHP at low cost, and the intact AHPM-2 is expected to be developed into functional food for preventing hypertension as well as for therapeutic.

Discriminating thermophilic lipases from their similar thermostable counterparts is a challenging task and it would help to design stable proteins. In this study, the distributions of N (N=2, 3) neighboring amino acids and the nonadjacent di-residue coupling patterns in the sequences of 65 thermostable and 77 thermophilic lipases had been systematically analyzed. It was found that the hydrophobic residues Leu, Pro, Met, Phe, Trp, as well as the polar residue Tyr had higher occurrence in thermophilic lipases than thermostable ones. The occurrence frequencies of KC, EE, KE, RE, VE, YI, EK, VK, EV, YV, EY, KY, VY and YY in thermophilic proteins were significantly higher, while the occurrence frequencies of QC, QH, QN, HQ, MQ, NQ, QQ, TQ, QS and QT were significantly lower. CXP or CPX showed significantly positive to lipase thermostability, while XXQ or QXX showed significantly negative to lipase thermostability. Nonadjacent di-residue coupling patterns of PR14, RY32, YR47, LE53, LE64, PP64, RP70 and PP101 were significantly different in thermophilic lipases and their thermostable counterparts. The composition of dipeptide, tripeptide and nonadjacent di-residue patterns contained more information than amino acid composition. A statistical method based on support vector machines (SVMs) was developed for discriminating thermophilic and thermostable lipases. The accuracy of this method for the training dataset was 97.17%. Furthermore, the highest accuracy of the method for testing datasets was 98.41%. The influence of some specific patterns on lipase thermostability was also discussed.

The protein translocations across mitochondrial membranes are carried out by specialized complexes, the Translocase of Outer Membrane (TOM) and Translocase of Inner Membrane (TIM). TIM23 translocon is responsible for translocating the mitochondrial matrix proteins across the mitochondrial inner membrane. Tim44 is an essential, peripheral membrane protein in TIM23 complex. Tim44 is tightly associated with the inner mitochondrial membrane on the matrix side. The Tim44 C-Terminal Domain (CTD) functions as an Inner Mitochondrial Membrane (IMM) anchor that recruits the Presequence protein Associated Motor (PAM) to the TIM23 channel. Using X-ray crystallographic and biochemical data, we show that the N-terminal helices A1 and A2 of Tim44 - CTD are crucial for its membrane tethering function. Based on our data, we propose a model showing how the N-terminal A1 and A2 amphipathic helices can either expose their hydrophobic face during membrane binding or conceal it in the soluble form. Therefore, the A1 and A2 helices of Tim44 may function as a membrane sensor.

Superoxide dismutase (SOD, EC 1.15.1.1) plays an important antioxidant defense role in organisms exposed to oxygen. Copper- and zinc-containing SOD (Cu/Zn-SOD) catalysis and the change in folding behavior of this enzyme in response to inactivators are therefore of interest. We studied the inhibitory effects of trifluoroethanol (TFE) on the activity and conformation of a Cu/Zn-SOD from Bos taurus. We found that TFE inactivated the enzyme and disrupted the tertiary and secondary structures of Cu/Zn-SOD. Kinetic studies showed that TFE-induced inactivation of Cu/Zn-SOD follows first-order reaction kinetics and that TFE binding sites are distinct from the copper- and zinc-containing active site. These structural changes occurred prior to enzyme activity loss. A computational docking simulation of Cu/Zn-SOD and TFE (binding energy of Dock 6.3: -11.52 kcal/mol) suggested that THR37, ASP40, and GLU119, which are located near the active site, interact with TFE. Evaluation of the ligand binding kinetics of Cu/Zn-SOD during unfolding in the presence of TFE combined with computational prediction allowed us to gain insight into the inactivation of Cu/Zn-SOD.

Human heat shock protein 60 (hHSP60) and apolipoprotein B-100 (ApoB-100) in oxidized low density lipoproteins are considered pro-atherosclerotic factors by inducing autoimmunity response, and immunization with peptides from these two proteins can inhibit atherosclerosis in animal models. In this study, we constructed chimeric proteins containing ApoB-100 and/or hHSP60 peptides by human intestinal trefoil factor (ITF) as a scaffold and then fused with glutathionine- S transferase (GST) for expression in Escherichia coli. These purified chimeric proteins were used for immunizing apolipoprotein E (ApoE)-null mice fed on Western diet, and then the immune response and anti-atherosclerotic effect was assayed. Unexpectedly, neither anti-ApoB-100 nor anti-hHSP60 antibodies could be detected in serum. Histological analysis demonstrated the mice immunized with a chimeric protein containing both ApoB-100 and hHSP60 peptides showed the most significant reduction of atherosclerotic lesions (65.9%), and the mice immunized with the chimeric protein only containing ApoB-100 or hHSP60 peptide also showed a 26.7% (p<0.01) or 61.5% (p<0.001) reduction of atherosclerotic lesions when compared to GST control. The chimeric protein containing hHSP60 peptide was more efficient than that containing apoB-100 peptide for inhibiting atherosclerosis. This result was further supported by the in vitro assay that hHSP60 peptide could induce DCs and CD4+ T cells to produce more TGF-beta (p<0.01) and less IFN-gamma (p<0.001) than ApoB-100 peptide. This result highlights a way for developing anti-atherosclerotic agents by construction of chimeric proteins containing hHSP60 and/or ApoB-100 peptides in the future.

We investigated the delivery of calcium-alginate encapsulated peptidase (Flavourzyme®, Aspergillus oryzae) on proteolysis of Cheddar cheese. Physical and chemical characteristics such as moisture, pH and fat content were measured, and no differences were found between control and experimental cheese at day 0. SDS-PAGE analysis clearly showed that proteolysis of α and k casein was significantly accelerated after three months of maturity in the experimental cheese. A large number of low molecular weight peptides were found in the water soluble fraction of the experimental cheeses and some of these peptides were new. N-terminal amino acid sequence analysis identified these as P1, Leu-Thu- Glu; P3, Asp-Val-Pro-Ser-Glu and relatively abundant stable peptides P2, P4, Arg-Pro-Lys-His-Pro-Ile; P5, Arg-Pro-Lys- His-Pro-Ile-Lys and P6. These peptides were mainly originated from αs1-CN and β-CN. Four of the identified peptides (P1, P2, P3 and P4) are known to be biologically active and P1 and P3 were only present in experimental cheese suggesting that experimental cheese has improved health benefits.

Cyclotides are macrocyclic knotted peptides originating from plants. They are extremely stable and have a range of bioactivities including anti-HIV and insecticidal activity. Given the stability of the cyclotide framework, there is interest in using these peptides as scaffolds in drug design. In the current study, we have shown that nano-LC Fourier transform mass spectrometry (FTMS) is an effective method of analyzing cyclotides in plants. In addition, we have used this technique to find cyclotides in a novel species, Viola ignobilis (Violaceae plant family), which was collected from the East Azerbaijan province of Iran. Varv peptide A, cycloviolacin B2, and cycloviolacin O8 were found in this species. This study provides a novel method for directly analyzing cyclotide sequences without enzymatic digestion and further information regarding the distribution of cyclotides in plant species.