Protein and Peptide Letters - Volume 23, Issue 2, 2016

Nucleoside diphosphate kinases (NDK; EC 2.7.4.6) are enzymes required for maintaining intracellular levels of nucleosides triphosphates (NTP) through transfer the γ-phosphoryl group from a NTP to a NDP. The enzyme is associated with several biological functions including prevention of host ATP-mediated cytolysis during pathogenic infections. Here we present the biophysical characterization of NDK from Leishmania major and the effect of a mutation on the protein structure in solution. The structural stability was analyzed since this secreted protein may act in different microenvironments at various stages of the parasite life cycle. LmNDK and P95S mutant were subjected to denaturation with pH and guanidine. Structural transitions were monitored by circular dichroism and intrinsic fluorescence tryptophan emission. Our results showed that the LmNDK is more structurally stable than other described NDKs and that the catalytically active P95S mutant in the Kpn loop presented a decrease in protein stability, indicating the importance of this proline for maintenance of the LmNDK structure.

Solvent perturbation was used to study variations in structure of Arisaema helliborifolium lectin (AHL) with the help of circular dichroism (CD), intrinsic fluorescence (IF), extrinsic fluorescence, quenching and dynamic light scattering (DLS). AHL was studied under acidic, alkaline and 6 M guanidine hydrochloride (GuHCl) equilibrium states. Three structural states were identified for AHL at different conditions, that are native (N; pH 7.0), molten globule (MG; pH 2.0) and unfolded (U; pH 12.0). CD analysis revealed that 50% of secondary structure of AHL was β-sheet component. A complete loss of secondary structure was observed at GuHCl treatment. The tertiary structural changes as studied by changes in microenvironment of trp residues also suggested a pH induced MG state as in case of CD. Parameter-A analysis pointed at the multi-step unfolding process of lectin under varying pH (pH 1-13). A comparision of CD and IF data further indicated that different pathways were followed for secondary and tertiary structure unfolding. Tryptophans of native AHL were only partially exposed to solvent belonging to Class II. Hydrodynamic diameter (Dh ) measurements of AHL via DLS also confirmed of a pH induced molten globule. A thermally induced molten globule was identified for AHL between 54-60 °C as monitored by DLS. An irreversible thermal denaturation was observed with the formation of a large aggregate. The Dh of AHL at neutral pH was confirmed by transmission electron microscopy (TEM).

Ice nucleation proteins (INPs) form oligomeric structures by self-assembly and aggregation. We looked for the presence of potential aggregating sequences inside the INP from Pseudomonas syringae by a computational approach with the AGGRESCAN, FOMDAMYLOID and TANGO softwares. A total of 38 hot spots of aggregation were predicted in the INP sequence: 7 localized in the Nterminal domain, 2 in the C-terminal region, 28 in the highly repetitive central (HRC) region and 1 shared between the HRC and the Carboxyl-terminus regions of the protein. All the hot spots of aggregation identified in the HRC domain overlapped a 8-residue low fidelity repeat including a LIAGYrelated sequence. We confirmed the predictions by an experimental approach using synthetic peptides corresponding to different parts of the INP central sequence, absorbance spectroscopy and fluorescence spectroscopy in the presence of Congo red (CR) or Thioflavin T (ThT), respectively. Peptide 620-SFIIAGYG-627 predicted to aggregate by the three softwares induced an increase in fluorescence of ThT. Peptide 729-GFKSILTAGY-738 predicted to aggregate by AGGRESCAN and FOLDAMYLOID induced a shift in the maximum of absorbance of CR. Peptide 1124-SVLTAGA-1130 predicted to aggregate only by TANGO did not interfere with CR absorbance or ThT fluorescence. In conclusion, the use of three aggregation prediction algorithms and two biochemical assays showed that the hexapeptide repeated segment LIAGY, previously shown to form a hairpin loop may be involved in the aggregation of the P. syringae INP.

To identify proteins involved in the molecular mechanisms of pressure overload-induced heart failure, we quantitatively analyzed the left ventricular proteomic profile in a transverse aortic constriction (TAC) mouse model, a well-established model of cardiac hypertrophy and dysfunction. Multidimensional LC-MS/MS in combination with Isobaric Tags for Relative and Absolute Quantification (iTRAQ) labeling were used to analyze cardiac tissue samples and identify proteins that are differentially expressed in the left ventricle of mice that were challenged by TAC through 14 and 28 days. In this study, 1,748 high-quality reference proteins were identified compared with control mice, which showed 64 proteins up-regulated and 68 proteins down-regulated in the left ventricle of TAC mice through 14 days. Meanwhile, 46 proteins were upregulated and 40 proteins were down-regulated in the left ventricle of TAC mice through 28 days. Of all the differentially expressed proteins, we performed GO, pathway analysis and their interactions to the differentially expressed proteins and found that most of the proteins are related to cardiac muscle contraction, energy metabolism, occurrence of diseases and signal transduction. These proteins represent potential novel diagnostic and therapeutic targets for the treatment of pressure overload-induced heart failure.

B-cell epitope is a group of residues which is on the surface of an antigen. It invokes humoral responses. Locating B-cell epitope is important for effective vaccine design, and the development of diagnostic reagents. Mimotope-based B-cell epitope prediction method is a kind of conformational B-cell epitope prediction, and the core idea of the method is mapping the mimotope sequences which are obtained from a random phage display library. However, current mimotope-based B-cell epitope prediction methods cannot maintain a high degree of satisfaction in the circumstances of employing only mimotope sequences. In this study, we did a multi-perspective analysis on parameters for conformational B-cell epitopes and characteristics between epitope and mimotope on a benchmark datasets which contains 67 mimotope sets, corresponding to 40 unique complex structures. In these 67 cases, there are 25 antigen-antibody complexes and 42 protein-protein interactions. We analyzed the two parts separately. The results showed the mimotope sequences do have some epitope features, but there are also some epitope properties that mimotope sequences do not contain. In addition, the numbers of epitope segments with different lengths were obviously different between the antigen-antibody complexes and the protein-protein interactions. This study reflects how similar do mimotope sequence and genuine epitopes have; and evaluates existing mimotope-based B-cell epitope prediction methods from a novel viewpoint.

Polymorphonuclear neutrophils are the main cells of the innate immunity inflammatory response. Several factors can activate or stimulate neutrophils, including platelet-activating factor (PAF), a lipid mediator. Some authors consider the activation induced by PAF priming because it triggers limited production of reactive oxygen species (ROS) and it amplifies the response of the cell to a subsequent activator. The stimulation is reversible, which is critical for modulating the inflammatory response. Exacerbated inflammatory responses lead to serious diseases, such as systemic inflammatory response syndrome (SIRS), among others. Characterizing the stimulation of neutrophils during the possible reversion or prevention of an exaggerated inflammatory response is critical for the development of control strategies. In this study, a proteomic approach was used to identify 36 proteins that differ in abundance between quiescent neutrophils and PAFstimulated neutrophils. The identified proteins were associated with increased DNA repair processes, calcium flux, protein transcription, cytoskeleton alterations that facilitate migration and degranulation, and the release of proinflammatory cytokines and proteins that modulate the inflammatory response. Some of the identified proteins have not been previously reported in neutrophils.

An intracellular aliphatic amide degrading inducible amidase produced by Rhodococcus rhodochrous PA-34 was characterized and acrylic acid synthesis from acrylamide was carried out using whole cell amidase. A bioprocess was developed at 50 ml fed batch reaction using 400 mM acrylamide feeding at an interval of 30 min resulted in the production of 4 g acrylic acid with volumetric and catalytic productivity of 80 g/l and 19 g/g/h respectively. The amidase of this organism had molecular weight of 40 kDa and was purified to 8.5 fold with 8% yield. This enzyme was active within the temperature range of 30 to 60 °C, with optimum temperature 45 °C and pH 7.5. The Vmax, Km, and kcat of purified amidase were calculated as 250 U/mg protein, 4.5 mM, and 166 sec-1 for acrylamide. The enzyme showed tolerance to metal chelating agent (EDTA) and was strongly inhibited by heavy metal ions Hg2+, Ag2+, Cu2+ and Co2+. R. rhodochrous PA-34 amidase preferentially hydrolyzed small aliphatic toxic amide such as acrylamide. Thus, the amidase of R. rhodochrous PA-34 is promising biocatalyst for the synthesis of industrially important acids and biodegradation of toxic amides.

Constructing a vaccine against HIV-1, able to induce production of broadly neutralizing antibodies, is crucial. We report here the selection and characterization of RDWSFDRWSLSEFWL peptide mimotope that binds specifically to bNAbs 2F5. The peptide mimotope was selected from 15-mer phage-displayed peptide library by using Mab 2F5 as the selecting agent. The most abundant RDWSFDRWSLSEFWL peptide was inserted into a carrier, an artificial polyepitope immunogen - TBI (T- and B-cell immunogen). TBI-2F5 polyepitope immunogen that includes the mimotope of 2F5 epitope was constructed. It was shown that sera of mice immunized with TBI-2F5 protein recognized TBI protein as well as RDWSFDRWSLSEFWL peptide. The capacity of sera of immunized mice to neutralize HIV-1 was demonstrated using subtype B env-pseudoviruses of HIV-1 QH0692.42 and PVO.4. Based on these results, we conclude that peptide mimotope of 2F5 epitope RDWSFDRWSLSEFWL can be an essential component for a successful HIV-vaccine.

Cell penetrating peptides can be used as therapeutic agents via modulation of selective cell functions. Nitric oxide (NO) generated by vascular endothelial NO synthase (eNOS) plays a critical role in the NO/ cyclic guanosine 5’-monophosphate (cGMP)-mediated pulmonary vascular function. Here we examined whether internalization of a fifteen amino acid (KRFNSISCSSWRRKR) synthetic peptide (P3) enhances the catalytic activity of eNOS via caveolae/eNOS dissociation leading to NO release and increased cGMP production in pulmonary artery endothelial cells (EC). ECs were treated with varying concentrations of P3 and used to monitor internalization, isolation of caveolae-enriched fraction, the catalytic activity of eNOS, NO/cGMP production, and intracellular Ca2+ release. Confocal images show timedependent internalization of P3 in EC. Treatment of EC with P3, but not scrambled P3, increased the catalytic activity of eNOS in a dose-dependent manner without change in eNOS expression or phosphorylation. Treatment of EC with P3 stimulated intracellular Ca2+ release, increased the catalytic activity of phospatidylinsositide 3 kinase (PI3K) and resulted in eNOS/caveolae-1 (Cav-1) dissociation leading to translocation of eNOS to intracellular compartment in EC. P3- mediated activation of eNOS was abolished by intracellular Ca2+ chelator 1,2-bis(2-aminophenooxy)ethane-N,N,N’,N’- tertraacetic acid-AM (BAPTA-AM), PI3K inhibition, or by siRNA-mediated Cav-1 suppression. These results demonstrate that exogenous peptide consisting of cationic amino acids can internalize and enhance the catalytic activity of eNOS via modulation of caveolar signaling and intracellular Ca2+ release in EC.

In this study, we have used an approach that allows us to determine in what region of the polypeptide chain of protein it is required to insert a disulphide bond in order to stabilize it. In our previous paper [Melnik et al., JBSD. 2012] it was proposed that to search for a “weak” site in the protein, it is possible to use programs (for example, PONDR-FIT and IsUnstruct) finding intrinsic disorder protein regions. We suggested that in structured globular proteins, such programs predict not protein regions in the polypeptide chain disordered under native conditions, but “weakened”, feebly stabilized ones. Accordingly, an artificial introduction of SS-bridges using mutations in such regions would reliably result in the protein stabilization. We have taken advantage of this approach to stabilize protein Gαo from Drosophila melanogaster. The designed SS-bridge increased by 4 degrees the melting temperature of one domain of protein Gαo.

Polo-like kinases (PLKs) belong to the serine/threonine kinase subfamily, characterized by the presence of the signature motif called Polo-box domain. PLK members studied so far have emerged as the conserved regulator of cell cycle and cell division in eukaryotes. The Polo-box domain adds diversity to PLK functions by targeting the enzyme to an array of substrates found at different sub-cellular structures for exquisite regulation of cell cycle. More than a dozen members of PLK subfamily have been identified in the eukaryotic world except in the higher plants. Despite the similarities in governing cell division, PLKs have diverse and unique functions in different organisms. This review summarizes the plethora of functions of PLK in yeast to humans. Along with its classical functions, this review also emphasizes on the role of PLKs in regulating DNA replication, repair, genome integrity, development, and morphogenesis pathways. Perturbations in PLK functions have disease implications, such as cancer in humans, and thus human PLK1 is targeted for cancer therapeutics. PLKs also play a vital role in regulating several stages of meiotic cell division. Thus, PLKs are emerging as a unique class of proteins with multiple and diverse functions in different organisms.