[Photoaptamer heterodimeric constructs as a new approach to enhance the efficiency of formation of photocrosslinking with a target protein]

Using two DNA aptamers selectively recognizing anion-binding exosites 1 and 2 of thrombin as a model, it has been demonstrated that their conjugation by a poly-(dT)-linker (ranging from 5 to 65 nt in length) to produce aptamer heterodimeric constructs results into affinity enhancement. The apparent dissociation constant (Kd(app)) measured at the optical biosensor Biacore-3000 for complexes of thrombin with the heterodimeric constructs reached minimum values (Kd(app) = 0.2-0.4 nM) which were approximately 30-fold less than for the complexes with the primary aptamers. A photoaptamer heterodimeric construct was designed connecting photoaptamer and aptamer sequences with the poly-(dT)-linker of 35 nt long. The photoaptamer used could form photo-induced cross-links with the exosite 2 of thrombin and the aptamer used could bind to the exosite 1. The measured value of Kd(app) for the photoaptamer construct was approximately 40-fold less than that for the primary photoaptamer (5.3 and 190 nM, respectively). Upon exposure to the UV radiation at 308 nm of the equimolar mixtures of thrombin with the photoaptamer construct, the equal yield of the crosslinked complexes was observed at concentrations which were lower by two orders of magnitude than in the case of the primary photoaptamer. It was found that concurrently with crosslinking to thrombin a photo-induced inactivation of the photoaptamer occurs presumably due to formation of the intermolecular crosslinking.

Zinc-induced dimerization of the amyloid-β metal-binding domain 1-16 is mediated by residues 11-14

Analysis of complex formation between amyloid-β fragments using surface plasmon resonance biosensing and electrospray mass spectrometry reveals that region 11-14 mediates zinc-induced dimerization of amyloid-β and may serve as a potential drug target for preventing development and progression of Alzheimer's disease.

FMN binding site of yeast NADPH-cytochrome P450 reductase exposed at the surface is highly specific

NADPH-cytochrome P450 reductase (CPR) transfers two reducing equivalents derived from NADPH via FAD and FMN to microsomal P450 monooxygenases in one-electron transfer steps. The crystal structure of yeast CPR (yCPR) contains a surface-exposed FMN binding site (FMN2 site) at the interface of the FMN binding and connecting domains, in addition to the single buried site that has been observed in rat CPR. This finding provides a testable hypothesis of how intramolecular (between FAD and FMN) and intermolecular (between FMN and P450) electron transfer may occur in CPR. To verify that occupancy of the FMN2 site is not an artifact of crystallization, a surface plasmon resonance (SPR) biosensor technique has been applied to probe the selectivity of this site under functional conditions. A series of kinetic and equilibrium binding experiments involving yCPR immobilized on different sensor chip surfaces was performed using FMN and FAD, as well as FMN-derived compounds, including riboflavin, dimethylalloxazine, and alloxazine, and other molecules that resemble the planar isoalloxazine ring structure. Only FMN and FAD showed stoichiometric binding responses. Binding affinity for FMN was in the submicromolar range, 30 times higher than that for FAD. Association kinetic rates for the yCPR/FMN complex were up to 60-fold higher than for the yCPR/FAD complex. Taken together, these data indicate that (i) the surface-exposed site in yCPR is highly selective toward binding flavins, (ii) binding of FMN in this site is notably favored, and finally, (iii) both the phosphate group and the isoalloxazine ring of FMN are essential for binding.

[Comparative thermodynamic analysis of thrombin interaction with anti-thrombin aptamers and their heterodimeric construct]

Aptamers interacting selectively with the anion-binding exosites 1 and 2 of thrombin were merged into dimeric oligonucleotide constructs with use of a poly-(dT)-linker of 35 nucleotides (nt) long. Complexes of thrombin with the aptamers and their hetero- and homodimeric constructs were measured using the optical biosensor Biacore-3000. K(D) values measured for the hetero- and homodimeric constructs were correspondingly 25-30- and 2-3-fold lower than those for the primary aptamers. Analysis of temperature dependencies of K(D) values within the temperature interval of 10 degrees C-40 degrees C has shown that the values of enthalpy change deltaH upon formation of complexes of thrombin with the aptamers and the hetrodimeric construct are close. The value of the entropy change deltaS upon complex formation of thrombin with the aptamer heterodimeric construct was 1.5-2-fold higher than deltaS values for the complexes with the aptamers. The complex formation and dissociation rates increased with the elevation of temperature from 10 degrees C to 37 degrees C. However, the dissociation rate for the complex of thrombin with the heterodimeric construct was evidently lower that that for the complexes with the aptamers.

[Direct results of endovascular prosthetics of aneurysms of the infrarenal part of the aorta in patients with a severe concomitant pathology]

From May 2007 to March 2009 under observation there were 58 patients aged from 52 to 79 years (mean age 68) with the diagnosis of abdominal aortic aneurysm (AAA). Selection of patients for endoprosthesis was performed by the data of spiral computed aortography. The endovascular exclusion ofAAA from blood flow was performed in 15 patients. All the patients had high risk of surgery because of multiple concomitant pathologies. In 14 (93%) patients bifurcational and in 1 patient aortofemoral unilateral prostheses of AAA were made with the application of femoro-femoral bypass. All implantations were technically successful without complications. Shorter time of operation, less intraoperative blood loss, shorter tine of staying in hospital and time of rehabilitation were found to be 1.5-3 times as compared with classical surgical intervention. Implantation of bifurcational stent-graph seems to be the method of choice in treatment of AAA patients with severe concomitant pathology.

[Biosensor analysis of interaction of potential dimerization inhibitors with HIV-1 protease]

Currently inhibitors of protein-protein interactions are considered as perspective prototypes of new generation of drugs. The most attractive targets for such inhibitors are the oligomeric enzymes which active sites are formed by amino acid residues from different subunits. The classic example of such enzyme is HIV protease (HIVp), active only in the homodimeric form. We have developed a new approach for experimental screening of HIVp dimerization inhibitors. It is based on the original biosensoric test-system for differential analysis of interaction of tested substances with HIVp dimers and monomers. Using this test-system we have analyzed the most perspective candidate substances predicted by method of virtual screening, and some derivatives of glycyrrhizin, triterpenic and steroid glycosides. As a result we found one compound, which mainly interacts with HIVp monomers and inhibits in vitro activity of this enzyme with IC50 of about 10(-6) M.

[The endovascular approach to the open arterial duct surgery]

There are different ways of the open arterial duct treatment, based on its anatomical form. Endovascular occlusion is considered to be the safest. The morphometric protocol was developed for the adequate choice of the occluder. The first-stand results of the endovascular occlusion of the open arterial duct with the use of two types of guided occluders (Flipper and Amplatzer ductus occluder) are presented in the article.

[Use of Amplatzer septal occluder system for atrial septal defect closure]

Short-term results of minimally invasive transcatheter closure of atrial septal defect using Amplatzer septal occluder system (AGA Medical Corporation, USA) at 72 patients are analyzed. Technique of surgical procedure is described in detail. Morphometric protocol used for determination of indications and contraindication for endoscopic closure is also described. The causes of impossibility of endovascular procedures are established. The rate of transoccluder blood bypasses in postoperative period is demonstrated.

[Basic principles of molecular conformation analysis for medical biologists]

The main principles of the analysis and optimization of molecular conformation, which is the bases for molecular modeling methods in the field of bioinformatics, are briefly described. The basic approaches to molecular models energy minimization are considered. The given lecture is included into a theoretical cycle "Bioinformatics and computer aided drug design" for students of Medical and biologic faculty RGMU (biochemists, biophysics and medical cybernetics). It can be also recommended for other medical and biological students, as well as for PhD students.

Polarized-neutron study of spin dynamics in the Kondo insulator YbB12

Inelastic neutron scattering experiments have been performed on the archetype compound YbB(12), using neutron polarization analysis to separate the magnetic signal from the phonon background. With decreasing temperature, components characteristic for a single-site spin-fluctuation dynamics are suppressed, giving place to specific, strongly Q-dependent, low-energy excitations near the spin-gap edge. This crossover is discussed in terms of a simple crystal-field description of the incoherent high-temperature state and a predominantly local mechanism for the formation of the low-temperature singlet ground state.

[Late repeated operations after correction of heart isolated septal defects]

Overall 812 patients with heart isolated septal defects have been operated. Repeated operations were performed at 23 patients. The follow-up ranged 6 months to 15 years. The causes of repeated surgeries and structure of complications are analyzed in details.

[Oligomerization of L-asparaginase from Erwinia carotovora]

Bacterial L-asparaginases catalyzing hydrolysis of L-asparagine up to L-aspartate and ammonia, are used in medical practice for treatment of acute lymphoblastic leukemia. The long-term therapy with these preparations is accompanied by a number of side effects, which are attributed to glutaminase activity of L-asparaginase. Substrate specificity and activity of L-asparaginases are directly associated with the process of enzyme oligomerization. It is active only in the tetrameric form as the active sites are located in contact areas between monomers. The present work is devoted to homology modeling of spatial structure of L-asparaginase from Erwinia carotovora, the comparative molecular-graphic analysis of subunits interfaces, as well as development of experimental approach for enzyme oligomerization study. L-asparaginase was immobilized on a CM5 chip surface of optical biosensor Biacore 3000 based on the surface plasmon resonance technology. The dissociation process of enzyme tetrameric complexes up to monomers and subsequent oligomerization process have been registered.

[Valve-preserving reconstructive surgical procedures on pulmonary artery root in Fallot's tetralogy]

Original surgical method of dilated valvuloplasty is described. In moderate isolated hypoplasia of the fibrous ring of the pulmonary artery this method permits one to perform organ-preserving reconstruction of this zone without transannular plastic operation. Schemes of the surgery, experimental data and clinical experience based on surgical treatment of 31 patients with Fallot's tetrad in combination with hypoplasia of the fibrous ring of the pulmonary artery are presented. Short- and long-term results of the defect correction are reported.

Bioinformatics platform development: from gene to lead compound

In the past 10 yr, the field of bioinformatics has been characterized by the mapping of many genomes. These efforts have stimulated explosive development of novel bioinformatics and experimental approaches to predict the functions and metabolic role of the new proteins. The main application of the work is to search, validate, and prioritize new targets for designing a new generation of drugs. Modern computer and experimental methods for discovery of new lead compounds have also expanded and integrated into the process referred to as rational drug design. They are directed to accelerate and optimize the drug discovery process using experimental and virtual (computer-aided drug discovery) methods. Recently, these methods and approaches have merged into a "from gene to lead" platform that includes the processes from new target discovery through obtaining highly effective lead compounds. This chapter describes the strategies as employed by the "From Gene to Lead" platform, including the major computer and experimental approaches and their interrelationship. The latter part of the chapter contains some examples of the steps required for implementing this platform.

[Short- and long-term results of balloon dilatation of aorta coarctation]

Balloon dilatation is an alternative method of aorta coarctation (AC) treatment, and it may be effective in 80 - 90% cases with appropriate indications. Arterial hypertension is one of the symptoms of AC and frequent complication of short- and long-term postoperative period. Surgical correction does not guarantee regress of pathological symptoms in all the cases, and method of surgery does not influence the rate of postoperative arterial hypertension. The study reviews CA balloon dilatation experience and analyses cases of late arterial hypertension rate in long-term period after balloon dilatation procedure.

[Endovascular balloon valvuloplasty of pulmonary artery valvular stenosis]

Summarized experience of balloon valvuloplasty in isolated stenosis of pulmonary artery valve is analyzed. This procedure was performed in Russian Research Center of Surgery in 53 patients from 1980 to 2006. The technique of balloon valvuloplasty is described; short- and long-term results are analyzed. Complications and unsatisfactory results of this surgery are outlined.

[Optical biosensor study and molecular modeling of interactions between cytochrome P450cam and cytochrome b5]

The formation of complexes of cytochrome P450cam (P450cam) with full-length cytochrome b5 (d-b5) and its tryptic water-soluble fragment (t-b5) was analyzed using a two-channel IAsys+ optical biosensor. It was found that t-b5 can form complexes with P450cam, while d-b5 does not interact with P450cam. The involvement of amine groups of P450cam in the complex formation was demonstrated. The temperature dependence of t-b5(im)/P450cam complex formation was measured. The association rate constant (k(on)) increased with temperature, while the dissociation rate constant (k(off)) practically remained unchanged. It was concluded that hydrophobic interactions play a key role in the complex formation, while electrostatic interactions are significant for complex stabilization. Based on temperature dependence the activation energy, enthalpy and entropy of complex formation were calculated. It was shown that the entropy component plays a key role in t-b5(im)/P450cam interaction. Computer modeling of P450cam/t-b5 and P450cam/d-b5 interactions was carried out. Using the method of molecular docking some hypotheses of protein-protein complexes were advanced and the best ones were selected based on geometric complementarity, calculated binding energy and probability of electron tunneling between proteins. The computer modeling has shown that only P450cam and t-b5 can form the stable complex. These results are in good agreement with the experimental data obtained with the optical biosensor.

[Basic principles of computational chemistry for medical biologists]

The lecture describes the basic principles of computational chemistry underlying the methods of molecular modelling used in bioinformatics area. The basic positions, methods of molecular and quantum mechanics and combined approaches are considered. This lecture is from theoretical cycle "Bioinformatics and Computer-Aided Drug Design" for fourth year students of Medico-Biological Department of Russian State Medical University (specialty--biochemistry, biophysics and medical cybernetics). It can also be advised for all students and post-graduate students of medico-biological specialties.

[Methods of experimental validation of potential target proteins for creation of new drugs]

Review is devoted to the description of the main existing and developing technologies for experimental validation of potential targets predicted in silico by comparative genomics and bioinformatics methods. Since this problem has not been solved yet, the description of a wide set of methods, suitable for the validation of potential targets, is given. The following questions have been considered: (1) applications of proteomic technologies (control of potential targets expression and their variability, analysis of protein-protein interactions); (2) use of genomics technologies in experimental validation of targets (inactivation of the target genes, suppression of transcription, inactivation of the target mRNA, suppression of translation); (3) methods of direct inactivation of target proteins (monoclonal antibodies, light-inactivation, one-chain antibodies, intrabodies, aptamers); (4) high-throughput technologies; (5) targets validations in vivo.

[Anomalous origin of left coronary artery from pulmonary trunk: symptoms, diagnosis and surgical treatment]

Anomalous origin of left coronary artery from pulmonary artery is a rare congenital pathology causing death of most patients because of various arrhythmia and heart failure. The authors present 4 cases of this anomaly with description of clinical course, diagnosis and surgical procedures. The first patient was operated upon in 12 years after mitral valve replacement. Ligation of anterior interventricular and circumflex arteries at their origin in this patient was combined with anastomosis between mammary and anterior interventricular coronary arteries. Reimplantation of the left coronary artery into the aortic root was used in other 3 patients with good immediate postoperative effect. Restoration of left ventricular pump function occurred in all 3 patients.