GOR V server for protein secondary structure prediction

We have created the GOR V web server for protein secondary structure prediction. The GOR V algorithm combines information theory, Bayesian statistics and evolutionary information. In its fifth version, the GOR method reached (with the full jack-knife procedure) an accuracy of prediction Q3 of 73.5%. Although GOR V has been among the most successful methods, its online unavailability has been a deterrent to its popularity. Here, we remedy this situation by creating the GOR V server

Modulation of domain–domain interaction and protein function by a charged linker: A case study of mycobacteriophage D29 endolysin

AbstractPhage-encoded cell wall peptidoglycan hydrolyzing enzymes, called endolysins, are essential for efficient release of virions from bacteria, and show species-specific killing of the host. We have demonstrated previously that the interaction between N-terminal catalytic and C-terminal cell wall binding domains of mycobacteriophage D29 endolysin makes the enzyme inactive in Escherichia coli. Here, we demonstrate that such interaction occurs intramolecularly and is facilitated by a charged linker that connects the two domains. We also show that linker composition is crucial for the inactivation of PG hydrolase in E. coli. Such knowledge will immensely help in bioengineering of endolysins with narrow or broad spectrum antimicrobial activity

Structural Characterization of the NodD Transcription Factor

Abstract Using computer analysis and modeling we studied NodD transcription factor which controls expression of nodulation genes of symbiotic nitrogen-fixing bacteria. On the basis of the amino acid sequences it was predicted that in the secondary structure of NodD protein it must be present ten alpha helices and three beta sheets which form two do mains after folding. Since NodD acts in oligo meric mode, it was analy zed all four known for other similar factors of transcription ways of assembly into dime rs. Using molecular docking the probable mechanism o f NodD act ivation by binding of low molecular weight inducer (on the model o f luteolin) was clarified

Complete regression and systemic protective immune responses obtained in B16 melanomas after treatment with LTX-315

A manuscript version of this article is part of Ketil André Camilio's doctoral thesis, which is available in Munin at http://hdl.handle.net/10037/5489</a

Structural characterization of a novel luciferase-like monooxygenase from bacteria Pseudomonas meliae

Luciferase is well known oxidative enzyme that produce bioluminescence. Since the discovery of luciferase, it has been used in many applications as emission of light during bioluminescent nature serves as a visual indicator for observation. In this study, the aim is to model and characterise a novelty of the luciferase-like monooxygenase protein/amino acid found in Pseudomonas meliae for its similarity to well established luciferase enzymes. The novel protein sequence was modelled and compared with established structures using bioinformatics methods. The Pseudomonas meliae, a plant pathogen that causes wood rot on nectarine, peach and Platanus spp. possess a luciferase-like monooxygenase that if activated, creates an intriguing prospect of using the pathogen’s bioluminescent as a visual indicator of diseased plants. If the pathogen’s own protein can be activated when the plant has been infected, its bioluminescent bacterial gall can be used to identify affected plants. In this study, the suitability of the luciferase like monooxygenase from P. meliae that infects chinaberry plants has to be modelled first, and then studied by comparing it with existing known luciferase. The sequence of Pseudomonas meliae (A0A0P9UTV8) was characterized and modelled using 3B9O as a template, using bioinformatics tools. Similarities between uncharacterized luciferase from Pseudomonas meliae and template from Geobacillus thermodenitrificans were analysed. The active site remains identical but with the exception of two amino acids; P.meliae Tyr138 instead of His138 and Leu311 instead of His311. All the other data 9on various properties of luciferase-like monooxygenase protein and its comparison between template alkane monooxygenase and model luciferase-like monooxygenase primary structure characteristics, similarities of amino acids sequences, binding sites, and predicted active sites of almost similar models. Both structures have similar key characteristics such as, high amino acid residue, Aspartic acid, and Glutamic acid. The results suggest that the absence of bioluminescence in P.meliae could be due to the evolutionary mutation in position 138 and 311. The Pseudomonas genera has been shown to react with light such as Pseudomonas fluorescens that emit luminescence under UV light as well as the application of bioluminescent Pseudomonas aeruginosa to assess the antimicrobial efficacy of wound dressings by monitoring light emission. Therefore, the P.meliae will have a potential future application, should the residues 138 and 311 be mutated to restore luciferase light emitting ability in future research. Suitability for further improvement, activation, and repurposing the luciferase from Pseudomonas meliae as a disease marker would depend on the outcome of this study

Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins

We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2–3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3–6 Å RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures. The protocol has been web enabled and is accessible at

Plasticity in the Oxidative Folding Pathway of the High Affinity Nerita Versicolor Carboxypeptidase Inhibitor (NvCI)

Nerita Versicolor carboxypeptidase inhibitor (NvCI) is the strongest inhibitor reported so far for the M14A subfamily of carboxypeptidases. It comprises 53 residues and a protein fold composed of a two-stranded antiparallel β sheet connected by three loops and stabilized by three disulfide bridges. Here we report the oxidative folding and reductive unfolding pathways of NvCI. Much debate has gone on whether protein conformational folding guides disulfide bond formation or instead they are disulfide bonds that favour the arrangement of local or global structural elements. We show here that for NvCI both possibilities apply. Under physiological conditions, this protein folds trough a funnelled pathway involving a network of kinetically connected native-like intermediates, all sharing the disulfide bond connecting the two β-strands. In contrast, under denaturing conditions, the folding of NvCI is under thermodynamic control and follows a "trial and error" mechanism, in which an initial quasi-stochastic population of intermediates rearrange their disulfide bonds to attain the stable native topology. Despite their striking mechanistic differences, the efficiency of both folding routes is similar. The present study illustrates thus a surprising plasticity in the folding of this extremely stable small disulfide-rich inhibitor and provides the basis for its redesign for biomedical applications

Immuno-informatics based approaches to design a novel multi epitope-based vaccine for immune response reinforcement against Leptospirosis

Leptospirosis is known as a zoonotic disease of global importance originated from infection with the spirochete bacterium Leptospira. Although several leptospirosis vaccines have been tested, the vaccination is relatively unsuccessful in clinical application despite decades of research. Therefore, this study was conducted to construct a novel multi-epitope based vaccine against leptospirosis by using Hap1, LigA, LAg42, SphH and HSP58 antigens. T cell and IFN gamma epitopes were predicted from these antigens. In addition, to induce strong CD4+ helper T lymphocytes (HTLs) responses, Pan HLA DR-binding epitope (PADRE) and helper epitopes selected from Tetanus toxin fragment C (TTFrC) were applied. Moreover, for boosting immune response, Heparin-Binding Hemagglutinin (HBHA), a novel TLR4 agonist was added to the construct as an adjuvant. Finally, selected epitopes were linked together using EAAAK, GPGPG, AAY and HEYGAEALERAG linkers. Based on the predicted epitopes, a multi-epitope vaccine was construct with 490 amino acids. Physico-chemical properties, secondary and tertiary structures, stability, intrinsic protein disorder, solubility, and allergenicity of this vaccine construct were assessed by applying immunoinformatics analyses. A soluble, and non-allergic protein with a molecular weight of 53.476 kDa was obtained. Further analyses validated the stability of the chimeric protein and the predicted epitopes in the chimeric vaccine indicated strong potential to induce B-cell and T-cell mediated immune response. Therefore, immunoinformatics analysis showed that the modeled multi-epitope vaccine can properly stimulate the both T and B cells immune responses and could potentially be used for prophylactic or therapeutic usages