Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism

BACKGROUND

CCR5 and CXCR4 are the two membrane-standing proteins that, along with CD4, facilitate entry of HIV particles into the host cell. HIV strains differ in their ability to utilize either CCR5 or CXCR4, and this specificity, also known as viral tropism, is largely determined by the sequence of the V3 loop of the viral envelope protein gp120.

RESULTS

With statistical and docking approaches we have computationally analyzed binding preferences of CCR5 and CXCR4 to both V3 loop sequences of virus strains of different tropism and endogenous ligands.

CONCLUSIONS

We conclude that the tropism cannot be satisfactorily explained by amino-acid interactions alone, and suggest a two-step mechanism, by which initial coreceptor selection and approach of the ligand to the binding pocket is dominated by charge and glycosylation pattern of the viral envelope.

[The natural triterpenoid miliacin prevents methotrexate-induced oxidative stress and normalizes the expression of genes encoding the cytochrome P-450 2E1 isoform and glutathione reductase in the liver]

We studied the role of the natural triterpenoid miliacin (3-3-methoxy-Al8-oleanene) in the regulation of oxidative stress in the liver of (CBAxC57B1(6))F1 mice exposed to methotrexate. Miliacin attenuated methotrexate-induced lipid peroxidation as determined by an attenuation of thiobarbituric acid-reacting products in the liver. Furthermore, miliacin normalized the expression of genes encoding the 2e1 isoform of cytochrome P-450 and glutathione reductase that were dramatically dysregulated by methotrexate. These results established the role of miliacin in modulation of redox genes, thereby providing evidence for a new mechanism of organ protection by this triterpenoid.

[Age peculiarities of the sebaceous glands in the temporal area of the scalp skin in men]

The changes of the sebaceous gland number, size and sebocyte proliferative activity were studied in the temporal area of the scalp skin in the male individuals aged 10 to 70 years (n=77, autopsy material). The minimal number of the sebaceous glands was observed in children. This index rapidly increased thereafter, reaching a peak at 20 years, then gradually decreased. These parameters correlated with the sebaceous gland size, sebocyte proliferative activity and total blood testosterone level. In older men the size of the sebaceous glands was increased.

[Low-manifest infections in children and adolescents with consequences of perinatal damage of nervous system]

AIM

Study the specter of low-manifest infections (LMI) and their role in children and adolescents with diseases of central nervous system (CNS) against the background of consequences of perinatal damage of nervous system (PDNS).

MATERIALS AND METHODS

Infectologic and neurologic examinations were carried out in 42 patients with consequences of PDNS (17 girls and 25 boys, 3 - 15 years). Detection of LMI resulted in etiotropic therapy with evaluation of clinical and laboratory data in dynamics.

RESULTS

In 93% (39/42) of patients causative agents of LMI were diagnosed in various combinations and in various biological materials. Among those: Chlamydia spp.--in 71% of patients, Mycoplasma spp.--in 31%, Ureaplasma urealyticum--in 14% (in total the listed microorganisms were diagnosed in 83% of patients); Herpesviridae family viruses--in 75% (HHV-6--in 67%, VEB--in 36%, CMV--in 11%, HSV-1,2--in 11%). Combination of Chlamydia spp. with HHV-6 (R tetr = +0.61) and with VEB (R tet = +0.74) (P < 0.05) was detected. None of the patients had typical signs of encephalitis clinically or based on MRT. MRT signs of gliosis-atrophic changes in the CNS were detected in all the patients. Reduction of a number of psycho-neurologic and neurologic syndromes was noted in all the patients during LMI therapy.

CONCLUSION

Most of the patients with consequences of PDNS had low-intensity inflammatory-degenerative process in the CNS determined by LMI, first of all by Chlamydia spp. as well as Mycoplasma spp.

Computational identification of novel amino-acid interactions in HIV Gag via correlated evolution

Pairs of amino acid positions that evolve in a correlated manner are proposed to play important roles in protein structure or function. Methods to detect them might fare better with families for which sequences of thousands of closely related homologs are available than families with only a few distant relatives. We applied co-evolution analysis to thousands of sequences of HIV Gag, finding that the most significantly co-evolving positions are proximal in the quaternary structures of the viral capsid. A reduction in infectivity caused by mutating one member of a significant pair could be rescued by a compensatory mutation of the other.

[The development of secondary immunodeficiency in body when exposed to the effect of xenobiotics with immunosuppressive activity]

The State Education Institution of Higher professional education "The Orenburg State Medical Academy of Federal Agency in Public Health and Social Development". In the experiment on mice (CBA x C57Bl6) F1 and Wistar rats is shown the protective effect of triterpenoid plant--miliatsina (3-beta-methoxy-delta18-oleanena) in relation to the humoral immune response and clearance macrophage function hepatic xenobiotic conditions of use--methotrexate. The results define the term as used miliatsina immunoprotector with adverse effects on the body of environmental and industrial chemical factors that form the secondary immunodeficiency.

ProtChemSI: a network of protein-chemical structural interactions

Progress in structure determination methods means that the set of experimentally determined 3D structures of proteins in complex with small molecules is growing exponentially. ProtChemSI exploits and extends this useful set of structures by both collecting and annotating the existing data as well as providing models of potential complexes inferred by protein or chemical structure similarity. The database currently includes 7704 proteins from 1803 organisms, 11 324 chemical compounds and 202 289 complexes including 178 974 predicted. It is publicly available at http://pcidb.russelllab.org.

[Low-manifest infections with CNS damage in patients in prolonged unconscious state of non-inflammatory etiology]

AIM

Study of specter of low-manifest infections (LMI) with central nervous system (CNS) damage and their role in patients in prolonged unconscious state (PUS) of noninflammatory etiology.

MATERIALS AND METHODS

32 patients (23 male, 9 female; age 14-58) in PUS of various etiology were examined. The main group (18 patients) received therapy against all infectious diseases including LMI; control group (14 patients)--only against common and nosocomial microflora. Patients were immunologically, infectologically and neurologically examined in dynamic. The data obtained were treated by using STATISTICA for Windows (version 5.5).

RESULTS

Significant differences in immune and infectologic status depending on the nature of primary CNS damage were not detected. Immunodeficiency was detected in all patients; 94% of patients had increased non-specific IgM and IgE. Among LMI agents Chlamydia spp. were predominant. Cultural and/or PCR methods detected this microorganism during the primary examination in cerebrospinal fluid samples in 56% patients and in blood samples in 56%; during the second diagnostics or autopsy--only in 13 and 25%, respectively. Detection of Bacteroides fragilis, Human Herpes Virus (HHV-6), Virus Epstein Barr (VEB), Cytomegalovirus (CMV) in cerebrospinal fluid, blood and on mucous membranes of nasopharynx and conjunctiva was grouped more frequently with the presence of Chlamydia spp. in the CNS (p < 0.05) than with other LMI agents. Sanation of CNS from LMI was significantly accompanied by regeneration of communicative activity in comparison with the control group.

CONCLUSION

In patients with PUS high frequency of CNS infection by various LMI agents and primarily Chlamydia spp. should be considered. Sanation from LMI can become a "window" for effective neuro-regenerative treatment.

Combinations of protein-chemical complex structures reveal new targets for established drugs

Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. Here we use this principle to suggest new protein-chemical interactions via the network derived from three-dimensional structures. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The method reproduces 84% of complexes in a benchmark, and we make many predictions that would not be possible using conventional modeling techniques. Within 19,578 novel predicted interactions are 7,793 involving 718 drugs, including filaminast, coumarin, alitretonin and erlotinib. The growth rate of confident predictions is twice that of experimental complexes, meaning that a complete structural drug-protein repertoire will be available at least ten years earlier than by X-ray and NMR techniques alone.

Predicting drug-target interactions is a hot topic, and many efforts have been undertaken to do this, many using large interaction networks. We take a novel approach using protein-chemical interactions derived from 3D structures. The basic premise is that two proteins sharing a common bound chemical will likely share others. We use protein and chemical superimpositions and physical tests of chemical-protein compatibility to identify the most likely candidates among the nearly one million potential interactions. We show for a benchmark that known protein-chemical structures are reconstructed with good accuracy and sometimes via very different proteins and chemicals. We make thousands of confident predictions, including structures for known protein-drug interactions lacking a structure (e.g. topoisomerase-2/radicicol) and many new interactions. The number of confident predictions grows faster than the number of known structures, suggesting that this approach will play a key role in completing the protein-chemical interaction repertoire.

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

Background

Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.

Results

We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server http://bioinf.fbb.msu.ru/SDPfoxWeb/ and a stand-alone Java application available from the website.

Conclusions

SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.

Impact of genome reduction on bacterial metabolism and its regulation

To understand basic principles of bacterial metabolism organization and regulation, but also the impact of genome size, we systematically studied one of the smallest bacteria, Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients. More than 1300 growth curves were recorded in the presence of various nutrient concentrations. Measurements of biomass indicators, metabolites, and 13C-glucose experiments provided information on directionality, fluxes, and energetics; integration with transcription profiling enabled the global analysis of metabolic regulation. Compared with more complex bacteria, the M. pneumoniae metabolic network has a more linear topology and contains a higher fraction of multifunctional enzymes; general features such as metabolite concentrations, cellular energetics, adaptability, and global gene expression responses are similar, however.

Combining specificity determining and conserved residues improves functional site prediction

Background

Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core). Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities.

Results

Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs), as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples.

Conclusion

The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

[Computational method for prediction of protein functional sites using specificity determinants]

The current available data on protein sequences largely exceeds the experimental capabilities to annotate their function. So annotation in silico, i.e. using computational methods becomes increasingly important. This annotation is inevitably a prediction, but it can be an important starting point for further experimental studies. Here we present a method for prediction of protein functional sites, SDPsite, based on the identification of protein specificity determinants. Taking as an input a protein sequence alignment and a phylogenetic tree, the algorithm predicts conserved positions and specificity determinants, maps them onto the protein's 3D structure, and searches for clusters of the predicted positions. Comparison of the obtained predictions with experimental data and data on performance of several other methods for prediction of functional sites reveals that SDPsite agrees well with the experiment and outperforms most of the previously available methods. SDPsite is publicly available under http://bioinf.fbb.msu.ru/SDPsite.

Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases

Isocitrate and isopropylmalalte dehydrogenases are homologous enzymes important for the cell metabolism. They oxidize their substrates using NAD or NADP as cofactors. Thus, they have two specificities, towards the substrate and the cofactor, appearing in three combinations. Although many three-dimensional (3D) structures are resolved, identification of amino acids determining these specificities remains a challenge. We present computational identification and analysis of specificity-determining positions (SDPs). Besides many experimentally proven SDPs, we predict new SDPs, for example, four substrate-specific positions (103Leu, 105Thr, 337Ala, and 341Thr in IDH from E. coli) that contact the cofactor and may play a role in the recognition process.

Comparative genomics of regulation of heavy metal resistance in Eubacteria

BACKGROUND

Heavy metal resistance (HMR) in Eubacteria is regulated by a variety of systems including transcription factors from the MerR family (COG0789). The HMR systems are characterized by the complex signal structure (strong palindrome within a 19 or 20 bp promoter spacer), and usually consist of transporter and regulator genes. Some HMR regulons also include detoxification systems. The number of sequenced bacterial genomes is constantly increasing and even though HMR resistance regulons of the COG0789 type usually consist of few genes per genome, the computational analysis may contribute to the understanding of the cellular systems of metal detoxification.

RESULTS

We studied the mercury (MerR), copper (CueR and HmrR), cadmium (CadR), lead (PbrR), and zinc (ZntR) resistance systems and demonstrated that combining protein sequence analysis and analysis of DNA regulatory signals it was possible to distinguish metal-dependent members of COG0789, assign specificity towards particular metals to uncharacterized loci, and find new genes involved in the metal resistance, in particular, multicopper oxidase and copper chaperones, candidate cytochromes from the copper regulon, new cadmium transporters and, possibly, glutathione-S-transferases.

CONCLUSION

Our data indicate that the specificity of the COG0789 systems can be determined combining phylogenetic analysis and identification of DNA regulatory sites. Taking into account signal structure, we can adequately identify genes that are activated using the DNA bending-unbending mechanism. In the case of regulon members that do not reside in single loci, analysis of potential regulatory sites could be crucial for the correct annotation and prediction of the specificity.

[Effects of different methods of physical therapy on the course of autonomic dysfunction syndrome]

A comparative randomized controlled trial was made of efficacy of vegetative disorders correction with drugs and physiotherapeutic factors. A total of 120 patients with vegetative vascular dystonia entered this trial. Its results demonstrated that addition of physiotherapy to the rehabilitation complex allows differential functional changes in the autonomic nervous system. This can be used for optimization of rehabilitation programs.

Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications

Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational method allowing identification of the specificity-determining positions (SDPs) in families composed of proteins with similar but not identical function. Fifteen SDPs were identified within the RF1/2 superdomain II/IV known to be implicated in stop codon decoding. Three of these SDPs had particularly high scores. Five residues invariant for RF1 and RF2 [invariant amino acid residues (IRs)] were spatially clustered with the highest-scoring SDPs that in turn were located in two zones within the SDP/IR area. Zone 1 (domain II) included PxT and SPF motifs identified earlier by others as ‘discriminator tripeptides’. We suggest that IRs in this zone take part in the recognition of U, the first base of all stop codons. Zone 2 (domain IV) possessed two SDPs with the highest scores not identified earlier. Presumably, they also take part in stop codon binding and discrimination. Elucidation of potential functional role(s) of the newly identified SDP/IR zones requires further experiments.

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families

The increasing volume of genomic data opens new possibilities for analysis of protein function. We introduce a method for automated selection of residues that determine the functional specificity of proteins with a common general function (the specificity-determining positions [SDP] prediction method). Such residues are assumed to be conserved within groups of orthologs (that may be assumed to have the same specificity) and to vary between paralogs. Thus, considering a multiple sequence alignment of a protein family divided into orthologous groups, one can select positions where the distribution of amino acids correlates with this division. Unlike previously published techniques, the introduced method directly takes into account nonuniformity of amino acid substitution frequencies. In addition, it does not require setting arbitrary thresholds. Instead, a formal procedure for threshold selection using the Bernoulli estimator is implemented. We tested the SDP prediction method on the LacI family of bacterial transcription factors and a sample of bacterial water and glycerol transporters belonging to the major intrinsic protein (MIP) family. In both cases, the comparison with available experimental and structural data strongly supported our predictions.

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins

SDPpred (Specificity Determining Position prediction) is a tool for prediction of residues in protein sequences that determine the proteins' functional specificity. It is designed for analysis of protein families whose members have biochemically similar but not identical interaction partners (e.g. different substrates for a family of transporters). SDPpred predicts residues that could be responsible for the proteins' choice of their correct interaction partners. The input of SDPpred is a multiple alignment of a protein family divided into a number of specificity groups, within which the interaction partner is believed to be the same. SDPpred does not require information about the secondary or three-dimensional structure of proteins. It produces a set of the alignment positions (specificity determining positions) that determine differences in functional specificity. SDPpred is available at http://math.genebee.msu.ru/~psn/.

The channel in transporters is formed by residues that are rare in transmembrane helices

Transmembrane transport is an essential component of the cell life. Many genes encoding known or putative transport proteins are found in bacterial genomes. In most cases their substrate specificity is not experimentally determined and only approximately predicted by comparative genomic analysis. Even less is known about the 3D structure of transporters. Nevertheless, the published experimental data demonstrate that channel-forming residues determine the substrate specificity of secondary transporters and analysis of these residues would provide better understanding of the transport mechanism. We developed a simple computational method for identification of channel-forming residues in transporter sequences. It is based on the analysis of amino acids frequencies in bacterial secondary transporters. We applied this method to a variety of transmembrane proteins with resolved 3D structure. The predictions are in sufficiently good agreement with the real protein structure.

[Infrared laser therapy in distal diabetic polyneuropathy]

A course of laser therapy was applied to 50 patients with diabetic polyneuropathy by laser irradiation of low intensiveness in the nearest infrared spectrum. 20 patients from the group were treated by monotherapy only by laser exposure. Control group consisted of 24 patients treated by conventional therapy without laser exposure. According to the changes of vibratory and algesic sensitivity and electromyographic data the efficiency of therapy was estimated. It was found that laser exposure resulted in more pronounced restoration of functional state of nervous fibers than conventional therapy. Application of laser irradiation of low intensiveness was effective while in combined therapy of distal diabetic polyneuropathy as well as monotherapy.