PIER: protein interface recognition for structural proteomics

Recent advances in structural proteomics call for development of fast and reliable automatic methods for prediction of functional surfaces of proteins with known three-dimensional structure, including binding sites for known and unknown protein partners as well as oligomerization interfaces. Despite significant progress the problem is still far from being solved. Most existing methods rely, at least partially, on evolutionary information from multiple sequence alignments projected on protein surface. The common drawback of such methods is their limited applicability to the proteins with a sparse set of sequential homologs, as well as inability to detect interfaces in evolutionary variable regions. In this study, the authors developed an improved method for predicting interfaces from a single protein structure, which is based on local statistical properties of the protein surface derived at the level of atomic groups. The proposed Protein IntErface Recognition (PIER) method achieved the overall precision of 60% at the recall threshold of 50% at the residue level on a diverse benchmark of 490 homodimeric, 62 heterodimeric, and 196 transient interfaces (compared with 25% precision at 50% recall expected from random residue function assignment). For 70% of proteins in the benchmark, the binding patch residues were successfully detected with precision exceeding 50% at 50% recall. The calculation only took seconds for an average 300-residue protein. The authors demonstrated that adding the evolutionary conservation signal only marginally influenced the overall prediction performance on the benchmark; moreover, for certain classes of proteins, using this signal actually resulted in a deteriorated prediction. Thorough benchmarking using other datasets from literature showed that PIER yielded improved performance as compared with several alignment-free or alignment-dependent predictions. The accuracy, efficiency, and dependence on structure alone make PIER a suitable tool for automated high-throughput annotation of protein structures emerging from structural proteomics projects.     

Application of a sensitive near‐field microwave microprobe to the nondestructive characterization of microbial rhodopsin

We study the opto‐electrical properties of Natronomonas pharaonis sensory rhodopsin II (NpSRII) by using a near‐field microwave microprobe (NFMM) under external light illumination. To investigate the possibility of application of NFMM to biological macromolecules, we used time dependent properties of NPSRII before/after light activation which has three distinct states – ground‐state, M‐state, and O‐state. The diagnostic ability of NFMM is demonstrated by measuring the microwave reflection coefficient (S₁₁) spectrum of NpSRII under steady‐state illumination in the wavelength range of 350–650 nm. Moreover, we present microwave reflection coefficient S₁₁ spectra in the same wavelength range for two fast‐photocycling rhodopsins: green light‐absorbing proteorhodopsin (GPR) and Gloeobacter rhodopsin (GR). In addition the frequency sweep shift can be detected completely even for tiny amounts of sample (～10^–3 OD of rhodopsin). Based on these results NFMM shows both very high sensitivity for detecting conformational changes and produces a good time‐resolved spectrum. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Effects of beta-amyloid on behavioral and amino acids spectrum in rats’ brain and their modulation by embryonic proteins

One of the crucial events in the pathogenesis of neurodegenerative disorders linked with dementia-like Alzheimer’s Disease (AD) is the disturbance in neurotransmission based on progressive deficit of neuromediators that is manifested by marked decrease in cognitive behavior, loss of memory and inability to learn as a result of impairment in synaptic plasticity of neurons.In this study we have used a new complex of proteoglycans of embryonic genesis (PEG) created by Prof. L. Mkrtchyan, as a possible therapeutic approach that can rescue neurons from further degeneration caused by beta-amyloid (Aβ). We attempt to reveal the biochemical (determination of neuroactive amino acids such as glutamate, GABA, taurine, glycine and aspartate) changes and behavior on Y-maze and avoidance/exploratory activity on elevated plus-maze task in rats’ brain after modeling Alzheimer’s disease by i.c.v. injection of Aβ25–35. Furthermore, in this study we analyzed the neuroprotective properties of PEG.Under the influence of PEG the concentration of all investigated amino acids both in cerebral cortex and hippocampus (except striatum changes) increased. In the present study we demonstrated that bilateral i.c.v. injection of aggregated Aβ25–35 in dosage 30 nmol/rat resulted in impairment in spatial alternation behavior. Both preliminary (single) and double injection of PEG showed constant improvement of spatial memory after the first trial up to 90 days after i.c.v. injection of aggregated Aβ25–35.Our findings suggest that proteoglycans of embryonic genesis in neurodegenerative state show an expressed regulatory–protective effect.     

Survival of Trauma-Injured Neurons in Rat Brain by Treatment with Proline-Rich Peptide (PRP-1): An Immunohistochemical Study

The objective of this immunohistochemical research was to reveal the distribution of a proline-rich peptide-1 (PRP-1) in various brain structures of intact and trauma-injured rats and to identify the mechanisms of promotion of neuronal recovery processes following PRP-1 treatment. PRP-1, produced by bovine hypothalamic magnocellular cells and consisting of 15 amino acid residues, is a fragment of neurophysin vasopressin associated glycoprotein isolated from bovine neurohypophysis neurosecretory granules. PRP-1-immunoreactivity (PRP-1-IR) was detected in the brain of intact rats in the neurons of paraventricular (PVN) and supraoptic (SON) nuclei in the hypothalamus, in almost all cell groups in the medulla oblongata, in Purkinje and some cerebellar nuclei cells, and in nerve fibers. At 3 weeks after hemisection of the spinal cord (SC) an asymmetry of PRP-1 localization in the PVN and SON was observed: no PRP-1-IR was exhibited at the affected sides of both nuclei. Daily intramuscular administration of PRP-1 for 3 weeks significantly increased the number of PRP-1-immunoreactive (PRP-1-Ir) varicose nerve fibers, and cells in PVN and SON and in cell groups of the limbic system and brain stem. Tanycytes in the median eminence and covering ependyma also demonstrated strong PRP-1-IR. PRP-1 treatment also activated neuropeptide Y-IR (NPY-IR) in nerve fibers and immunophilin fragment-IR (IphF-IR) in lymphocytes and nerve cells. A strong increase of PRP-1-IR was observed in the PVN and SON of SC-injured rats following the treatment with another PRP (PRP-3). Preliminary physiological data demonstrate that PRP-3 is more "aggressive" in the recovery processes than PRP-1. Based on the findings regarding PRP action on neurons survival, axons regeneration, and the number of IphF-Ir lymphocytes and NPY-Ir nerve fibers, PRP is suggested to act as a neuroprotector, functioning as a putative neurotransmitter and immunomodulator.