Current Protein and Peptide Science - Volume 16, Issue 8, 2015

The study of protein-protein interactions (PPIs) can help researchers raise new hypotheses about an organism or disease and guide new experiments. Various methods for the identification and analysis of PPIs have been discussed in the literature. These methods are generally categorized as experimental or computational - each having its own advantages and disadvantages. Experimental methods provide insights into the real state of biological interactions but tend to be time-consuming and costly. Computational methods, on the other hand, can study thousands of PPIs at a very low cost and in much less time; however, the accuracy of such in silico prediction results heavily depends on the specific computational approach used. Furthermore, there is no gold standard for these computational methods; a method that works well for predicting one PPI may perform poorly (by generating false positives and false negatives) for a different PPI. Therefore, all such predictions must be carefully validated, preferably with experimental data. In this paper, we review the existing computational approaches and emphasize the use of biological data as inputs for accurate predictions of PPIs. We also discuss how such input datasets and approaches may influence the sensitivity and specificity of the predicted PPI networks.

The term “agrochemicals” is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A “drug” on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of understanding nanoenvironmental factors that guide recognition and interaction of target protein and its function modifier, an agrochemical or a drug. The repertoire of nanoenvironment descriptors is used for two selected and specific cases we have approached in order to offer a technological solution for some very important problems that needs special attention in agriculture: elimination of pathogenicity of a bacterium which is attacking citrus plants and formulation of a new fungicide. Finally, we also briefly describe a workflow which might be useful when research requires that model structures of target proteins are firstly generated (starting from genome sequences), followed by identification of ligand-target sites at the surface of those modeled structures, then application of procedures that adequately prepare both protein and ligand structures (the latter also involving filtration that satisfies acceptable adsorption/desorption/metabolism/excretion/toxicity [ADMET] parameters) for virtual high throughput screening (involving docking of ligands to indicated sites) and terminating by ranking of best pairs: target protein with selected ligand.

We compare the DNA-interactive properties of bacteriophage T4 gene 32 protein (gp32) with those of crotamine, a component of the venom of the South American rattlesnake. Gene 32 protein is a classical single-stranded DNA binding protein that has served as a model for this class of proteins. We discuss its biological functions, structure, binding specificities, and how it controls its own expression. In addition, we delineate the roles of the structural domains of gp32 and how they regulate the protein’s various activities. Crotamine, a component of the venom of the South American rattlesnake, is probably not a DNA binding protein in nature, but clearly shows significant DNA binding in vitro. Crotamine has been shown to selectively disrupt rapidly dividing cells and this specificity has been demonstrated for crotamine-facilitated delivery of plasmid DNA Thus, crotamine, or a variant of the protein, could have important clinical and/or diagnostic roles. Understanding its DNA binding properties may therefore lead to more effective drug delivery vehicles.

Cell viability is only possible due to a dynamic range of essential nucleic acid-protein complex formation. DNA replication and repair, gene expression, transcription and protein synthesis are well-known processes mediated by nucleic acids (DNA and RNA) - protein interactions. Novel nucleic acid- protein complexes have been identified in the past few years aided by the development of numerous new techniques such as RNA capture or Tandem RNA Affinity Purification (TRAP). However, the biophysical and biochemical details of these interactions are mostly unknown. Here, we present three techniques (Electrophoretic Mobility Shift Assays, Microscale Thermophoresis and Surface Plasmon Resonance) that are commonly used to quantify and characterize DNA-protein and RNA-protein interactions and discuss their main advantages and limitations.

Proteins participate in almost every cell physiological function, and to do so, they need to reach a state that allows its function by folding and/or exposing surfaces of interactions. Spontaneous folding in the cell is in general hindered by its crowded and viscous environment, which favors misfolding and nonspecific and deleterious self-interactions. To overcome this, cells have a system, in which Hsp70 and Hsp90 play a central role to aid protein folding and avoid misfolding. The topics of this review include the biophysical tools used for monitoring protein-ligand and protein-protein interactions and also some important results related to the study of molecular chaperones and heat shock proteins (Hsp), with a focus on the Hsp70/Hsp90 network. The biophysical tools and their use to probe the conformation and interaction of Hsp70 and Hsp90 are briefly reviewed.

Schizophrenia (SCZ) is a devastating chronic mental disease determined by genetic and environmental factors, which susceptibility may involve an impaired neural migration during the neurodevelopmental process. Several candidate risk genes potentially associated with SCZ were related to the formation of protein complexes that ultimately mediate alterations in the neuroplasticity. The most studied SCZ risk gene is the Disrupted-in-Schizophrenia 1 (DISC1) gene, which functions seem to depend on the binding with cytoskeleton proteins, as the Nuclear-distribution gene E homolog like-1 (Ndel1) protein among others. Interestingly, Ndel1 is the only binding partner of DISC1 proteins with oligopeptidase activity, besides playing roles in multiple processes, including cytoskeletal organization, cell signaling, neuron migration, and neurite outgrowth. It is still not clear if the protein-protein interaction between Ndel1 and DISC1 is enough to explain all cellular functions attributed to these proteins, but there are several lines of evidence suggesting the importance of the catalytic activity of Ndel1 for the neurite outgrowth and neuron migration during embryogenesis. Recent works of the group have demonstrated the modulation of Ndel1 activity by DISC1, which is hypothetically impaired in SCZ patients. In fact, more recently, we also showed a lower Ndel1 activity in the plasma of SCZ patients compared to control health subjects, but the physiopathological significance of this feature is still unknown. Here we discuss Ndel1 ligands involved in protein-protein complex formations related to neurodevelopmental diseases, as (1) lissencephaly or Miller-Dieker Syndrome (MDS), which is characterized by the typical craniofacial features and abnormal smooth cerebral surface, and as (2) SCZ, since they both seem to be determined by defects in neuronal migration. Although impaired lissencephaly protein Lis1 complex formation with Ndel1 is the leading cause of lissencephaly, this binding does not affect Ndel1 oligopeptidase activity. On the other hand, although MDS and SCZ may be both determined by an abnormal neuronal migration, DISC1 complex formation with Ndel1 was shown to inhibit Ndel1 activity. Also differently of MDS, SCZ needs inputs from environmental factors, while lissencephaly is not likely dependent or affected by the environment. Several other proteins and peptide ligands were described for Ndel1, Lis1 and DISC1, thanks to the employment of biochemical, immunochemical, and biological (using cells or living animals) assays, including heterologous expression and also simply by purification from nature of these proteins in the complex form. Effects of the post-translational modifications of these proteins are also discussed here. Taken together, the data presented here show in essence how protein-protein and proteinpeptide interactions can underlie fundamental processes as cell division, maturation and migration, necessary for adequate formation of a complex structured tissue as the brain. A special attention was given to Ndel1 as this protein binds to either proteins or peptides, besides having proteolytic activity. Moreover, Ndel1 seems to be the key protein underlying two seemingly unrelated diseases with highly complex etiology, as lissencephaly and SCZ.

Phospholipases D (PLDs), the major dermonecrotic factors from brown spider venoms, trigger a range of biological reactions both in vitro and in vivo. Despite their clinical relevance in loxoscelism, structural data is restricted to the apo-form of these enzymes, which has been instrumental in understanding the functional differences between the class I and II spider PLDs. The crystal structures of the native class II PLD from Loxosceles intermedia complexed with myo-inositol 1-phosphate and the inactive mutant H12A complexed with fatty acids indicate the existence of a strong ligand-dependent conformation change of the highly conserved aromatic residues, Tyr 223 and Trp225 indicating their roles in substrate binding. These results provided insights into the structural determinants for substrate recognition and binding by class II PLDs.

Ammonia lyase belongs to the family of enzymes that catalyzes the deamination of amino acids. Depending on the relative activity towards the substrates, L-tryptophan ammonia lyase converts L-tryptophan to indole 3-acrylic acid and ammonia. Here, we isolated, purified, and characterized an L-tryptophan ammonia lyase from phototrophic purple non-sulfur bacterium Rubrivivax benzoatilyticus JA2. The isolated L-tryptophan ammonia lyase found to catalyze the reaction of L-tryptophan to produce indole 3-acrylic acid and NH3. The enzyme is a heterotetramer and has the highest affinity to L-tryptophan. The optimum pH and temperature for the enzymatic action were 7.5 and 35°C, respectively and the Km and Vmax were 40.4 ± 23.1 nM and 0.964±0.2046 s-1, respectively. These results suggest that the isolated enzyme is highly bioactive and could be a new class. Further molecular analyses are required to confirm the novelty of the enzyme.

In the present study, the surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) techniques were employed to kinetically evaluate the binding affinity of a new recombinant chimeric protein (CP10) toward anti-Leishmania infantum antibodies for the immunodiagnostics of the visceral leishmaniasis (VL). This chimeric protein was formed by the union in a same artificial coding DNA of ten different peptides, which showed themselves reactive toward positive canine serum for VL. Using the CP10 in enzyme-linked immunosorbent assays (ELISA), it was possible to detect 80% of the asymptomatic infected dogs. After this, SPR and QCM immunosensors were constructed by the covalent immobilization of the CP10 on a self-assembled monolayer (SAM) formed by adsorption of alkanethiol on gold substrates. The thickness (6.80 nm) and the refractive index (1.475) of the protein on the SAM were simultaneously determined through SPR curves measured in different wavelengths (670 and 785 nm). Interactions between the CP10 and its specific IgGs (anti-CP10 antibodies) were characterized by the electrochemical impedance spectroscopy, SPR and QCM techniques. The equilibrium dissociation constant obtained by SPR (KD = 8.27 x 10-10 mol.L-1) and QCM (KD = 2.42 x 10- 10 mol.L-1) demonstrated high binding affinity of the CP10 toward anti-CP10 antibodies. In this sense, this work quantitatively proves the strong antigenic character of a new recombinant chimeric protein, giving evidence to potential contribution for the use of this protein in programs of control of the VL.