Biochemistry (Moscow) (v.77, #5)

Blood-brain barrier unlocked by N. Goldstein; R. Goldstein; D. Terterov; A. A. Kamensky; G. I. Kovalev; Yu. A. Zolotarev; G. N. Avakyan; S. Terterov (419-424).
The brain is protected by a physiological blood-brain barrier (BBB) against toxins and some metabolites circulating in the blood. At the same time, the BBB limits penetration into the brain of many neuroactive drugs. Efficient ways to increase BBB permeability for delivery of drugs of different chemical nature into the brain are unknown. This work deals with delivery into the brain of 10−2 M dopamine, a substance that does not penetrate the BBB under normal circumstances. It was studied in two independent experiments: (i) penetration of 3H-labeled dopamine from its mixture with 10−5 M H2O2 into hypothalamus and striatum structures of intact rat brain, and (ii) effect of unlabeled dopamine from a mixture with H2O2 on the rat motor activity in a haloperidol catalepsy model. It was shown that (i) at the third minute after nasal application of the dopamine + H2O2 mixture, the dopamine level increases 45-fold in the hypothalamus and almost 30-fold in the striatum and (ii) motility of animals in the catalepsy haloperidol model is recovered 90 sec after intranasal introduction of dopamine. No such effects were observed after replacement of H2O2 by 0.9% NaCl solution. Thus, it was shown on the example of dopamine that its introduction into the nasal cavity simultaneously with H2O2 provides for rapid delivery of the drug into the brain. These results expand our knowledge concerning the biological role of exoROS in modulating BBB permeability and may contribute to the development of a new therapeutic strategy for neurological diseases.
Keywords: blood-brain barrier; reactive oxygen species; hydrogen peroxide; 3H-labeled dopamine; haloperidol induced catalepsy

Identification of new M23A mRNA of mouse aquaporin-4 expressed in brain, liver, and kidney by T. Yu. Alikina; N. B. Illarionova; S. M. Zelenin; A. A. Bondar (425-434).
Aquaporins (AQPs) belong to a transmembrane protein family of water channels that are permeable to water by the osmotic gradient. There are two isoforms of mouse AQP4 — M1 and M23. Their balance in the cell determines water permeability of the plasma membrane. These two isoforms are encoded by three mRNAs: M1 isoform is encoded by M1 mRNA and M23 isoform is encoded by M23 and M23X mRNAs. Here we found a new fourth mRNA of mouse AQP4 — M23A mRNA. The start of transcription is different for M23A mRNA from all the known AQP4 mRNAs. The 5′-untranslated region (5′-UTR) of M23A mRNA is encoded by four new exons (A, B, C, and D), which are located in the 5′ region from exon-0 of the AQP4 gene. Alternative splicing between the exons-A, -B, -C, and -D leads to formation of multiple variants of M23A mRNA. We cloned six of these variants, all of which code full length M23 isoform of AQP4. Using RT-PCR we detected tissue-specific expression of the new M23A and already known M23, M23X, and M1 mRNAs. The M23A mRNA is expressed mostly in kidney, liver, and brain. Analysis of mRNA 5′-UTR structure showed low translation efficacy for M1 mRNA in comparison with high translation efficacy for M23A, M23X, and M23 mRNAs. We propose that AQP4 expression is controlled tissue-specifically by independent promoters. Thus multiple AQP4 mRNAs may allow long-term regulation of the balance between M1 and M23 AQP4 isoforms in the cell and thus water permeability of the plasma membrane.
Keywords: aquaporin-4; mRNA; gene; exon; alternative splicing; mouse

Classification of rhodopsin structures by modern methods of structural bioinformatics by G. V. Novikov; V. S. Sivozhelezov; A. S. Shebanova; K. V. Shaitan (435-443).
We report a classification of the crystallographic structures of bovine and squid rhodopsins corresponding to different stages of their photocycles. Using the resource Protein (Structure) Comparison, Knowledge, Similarity, and Information server (ProCKSI, http://www.procksi.net/ ), selected spatial structures were compared on the basis of classification schemes (dendrograms). To compare the spatial structures of transmembrane proteins, optimal consensus was developed from methods implemented in ProCKSI. Structures were also clustered using principal component analysis, resulting in good agreement with the classification based on the ProCKSI consensus method. Analysis of the results revealed the basic movements of individual transmembrane domains of these proteins that we were able to relate to different stages of the photoactivation of rhodopsin. A combination of methods identified in this study can be used as an up-to-date analytical tool to study the conformational dynamics of membrane receptors.
Keywords: receptor; rhodopsin; activation; conformation; photocycle; classification

In this work, the influence of the crystallographic water on electron transfer between primary donor P and acceptor BA was studied in reaction centers (RCs) of the purple bacterium Rhodobacter sphaeroides and the green bacterium Chloroflexus aurantiacus. For this purpose, time constants and oscillations of charge separation kinetics are compared between dry film RCs and RCs in glycerol-water buffer at 90 K. A common result of the drying of Rba. sphaeroides and Cfx. aurantiacus RCs is slowing of the charge separation process, decrease in amplitude of the oscillatory components of the kinetics, and the depletion of its spectrum. Thus, the major time constant of stimulated emission decay of P* bacteriochlorophyll dimer at 940 nm is increased from 1.1 psec for water-containing Rba. sphaeroides RCs to 1.9 psec for dry films of Rba. sphaeroides RCs. An analogous increase from 3.5 to 4.2 psec takes place in Cfx. aurantiacus RCs. In dry films of Rba. sphaeroides RCs, the amplitude of coherent oscillations of the absorption band of monomeric bacteriochlorophyll B A at 1020 nm is 1.8 times less for the 130-cm−1 component and 2.3 times less for the 32-cm−1 component than the analogous amplitudes for water-containing RCs. Measurements in the analogous band of Cfx. aurantiacus RCs show that strong decrease (∼5-10 times) of the B A absorption band and strong slowing (from ∼0.8 to ∼3 psec) of B A accumulation together with ∼3-fold decrease in oscillation amplitude occurs on drying of these RCs. The overtones of the 32-cm−1 component disappeared from the oscillations of the kinetics at 940 and 1020–1028 nm after drying of the Rba. sphaeroides and Cfx. aurantiacus RCs. The results are in agreement with the results for GM203L mutant of Rba. sphaeroides, in which the HOH55 water molecule is sterically removed, and with the results for dry films of pheophytin-modified RCs of Rba. sphaeroides R-26 and for YM210W and YM210L Rba. sphaeroides mutant RCs. The data are discussed in terms of the influence (or participation) of the HOH55 water molecule on electron transfer along the chain of polar atomic groups N-Mg(PB)-N-C-N(HisM202)-HOH55-O=(BA) connecting PB and BA in Rba. sphaeroides RCs.
Keywords: photosynthesis; charge separation; reaction center; wave packet; electron transfer

Initiation of the 3′:5′-AMP-induced protein kinase A Iα regulatory subunit conformational transition. Part I. A202 and A326 are critical residues by O. N. Rogacheva; B. F. Shchegolev; V. E. Stefanov; G. A. Zakharov; E. V. Savvateeva-Popova (456-464).
Protein-ligand docking and molecular dynamics studies have shown that the key event initiated by 3′:5′-AMP binding to the A- and B-domains of protein kinase A Iα regulatory subunit is formation of a hydrogen bond between 3′:5′-AMP and A202(A326) (the residue in parentheses being from the B-domain). The A202(A326) amide group movement associated with the bond formation leads to reorganization of the phosphate binding cassette (PBC) (the short 310-helix becomes the long α-helix). This process results in L203(L327) displacement and finally causes hinge (B-helix) rotation. The L203(L327) displacement and packing into the hydrophobic pocket formed by the PBC and β2β3-loop also depends on the β2β3-loop conformation. The correct conformation is maintained by R, I, E, but not K at position 209(333) of the A- and B-domains. So, the R209K and R333K mutants have problems with reaching B-conformation. The apo-form of the 3′:5′-AMP-binding domain also undergoes transition from H- to B-conformation. In this case, the movement of A202(A326) amide group seems to be a result of reorganization of the PBC into a more stable α-helix.
Keywords: A- and B-domains of PKA Iα R-subunit; 3′:5′-AMP; A202(A326); molecular dynamics; β2β3-loop; phosphate binding cassette

Protein-ligand docking and ab initio calculations have shown that the 3′:5′-AMP phosphorothioate analog (Rp-3′:5′-AMPS) blocks the A326 amide group displacement typical of transition from the H- to B-conformation within the B-domain of protein kinase A Iα R-subunit. This behavior of Rp-3′:5′-AMPS leads to the inhibition of initial stages of hydrophobic relay operation. In accordance with the proposed hypothesis, Rp-3′:5′-AMPS similarly to 3′:5′-AMP forms a hydrogen bond with the amide group of A326; however, the properties of this bond together with the position of the sulfur atom prevent the movement of A326. Finally, the Rp-3′:5′-AMPS-bound domain appears to be locked in the H-conformation, which is in agreement with the X-ray data.
Keywords: B-domain of PKA Iα R-subunit; 3′:5′-AMP; Rp-3′:5′-AMPS; A326; protein-ligand docking; quantum chemical analysis

Correlation between biological activity and conformational dynamics properties of tetra- and pentapeptides derived from fetoplacental proteins by N. T. Moldogazieva; A. A. Terentiev; M. Yu. Antonov; A. N. Kazimirsky; K. V. Shaitan (469-484).
In this work, using molecular dynamics simulation, we study conformational and dynamic properties of biologically active penta- and tetrapeptides derived from fetoplacental proteins such as alpha-fetoprotein, pregnancy specific β1-glycoprotein, and carcinoembryonic antigen. Existence of correlation between flexibility of peptide backbone and biological activity of the investigated peptides was shown. It was also demonstrated that flexibility of peptide backbone depends not only on its length, but also on the presence of reactive functional groups in amino acid side chains that participate in intramolecular interactions. Peptides that demonstrate similar biological effects in regulation of proliferation of lymphocytes and expression of differentiation antigens on their surface (LDSYQCT, PYECE, YECE, and YVCE) are characterized by rigidity of their peptide backbone. Increased backbone flexibility in peptides PYQCE, YQCE, SYKCE, YQCT, YQCS, YVCS, YACS, and YACE is correlated with decreased biological activity. Conformational mobility of amino acid residues does not depend on physicochemical properties only, but also on intramolecular interactions. So, evolutionary restrictions should exist to maintain such interactions in the environment of functionally important sites.
Keywords: alpha-fetoprotein; PSG; CEA; tetra- and pentapeptides; analogs; molecular dynamics; biological activity; flexibility of the peptide backbone

The wheat seedling endonucleases WEN1 and WEN2 dependent on Mg2+, Ca2+, and S-adenosyl-L-methionine (SAM) and sensitive to the substrate DNA methylation status have an expressed processing action. The enzymes hydrolyze DNA at a few subsequent stages: first, they split λ phage DNA specifically at CNG-sites (WEN1) with liberation of large fragments; second, they hydrolyze these fragments to 120–140 bp oligonucleotides that finally are hydrolyzed to very short fragments and mononucleotides. Initial stages of DNA hydrolysis may proceed in the absence of Mg2+, but subsequent hydrolysis stages are very strongly stimulated by Mg2+. It cannot be ruled out that modulation of enzymatic activity with Mg2+ and probably with DNA fragments formed is associated with reorganization of the structure of eukaryotic (wheat) endonucleases with respective changes in their catalytic properties and site specificity of action. Michaelis constant value for WEN1 endonuclease on hydrolysis of methylated λ phage DNA containing Cm5CWGG and Gm6ATC sites is four-fold lower compared with that observed on hydrolysis of unmethylated λ phage DNA. This may indicate that affinity of WEN1 enzyme to methylated DNA is higher than that to unmethylated DNA. In the presence of SAM, the Michaelis constant for WEN2 on the DNA hydrolysis stage characterized by formation of 120–140 bp fragments is decreased, but for WEN1 it is increased by 1.5–2.0-fold. This means that SAM inhibits WEN1 but stimulates WEN2. Thus, wheat endonucleases WEN1 and WEN2 differ significantly in affinities to substrate DNAs with different methylation status, in velocities of DNA hydrolysis, and time of production of DNA fragments of similar length. It seems that the investigated plant endonucleases can hydrolyze DNA in the nucleus as well to both large and very short fragments including mononucleotides, that is, in particular, essential for utilization of cell nucleic acid material during apoptosis.
Keywords: apoptosis; endonuclease; plant; wheat; kinetics; DNA methylation; processing action; SAM

Isolation and properties of recombinant inulinases from Aspergillus sp. by P. V. Volkov; O. A. Sinitsyna; E. A. Fedorova; A. M. Rojkova; A. D. Satrutdinov; I. N. Zorov; O. N. Okunev; A. V. Gusakov; A. P. Sinitsyn (492-501).
The genes inuA and inu1, encoding two inulinases (32nd glycosyl hydrolase family) from filamentous fungi Aspergillus niger and A. awamori, were cloned into Penicillium canescens recombinant strain. Using chromatographic techniques, endoinulinase InuA (56 kDa, pI 3) and exoinulinase Inu1 (60 kDa, pI 4.3) were purified to homogeneity from the enzymatic complexes of P. canescens new transformants. The properties, such as substrate specificity, pH- and T-optima of activity, stability at different temperatures, influence of cations and anions on the catalytic activity, etc., of both recombinant inulinases were studied.
Keywords: inulin; endoinulinase; exoinulinase; Penicillium canescens ; Aspergillus niger ; Aspergillus awamori

Food protein fragments are regulatory oligopeptides by A. A. Zamyatnin; O. L. Voronina (502-510).
Until recently food proteins were considered to be an energy source and a source of essential and nonessential amino acids required for protein synthesis and precursors of many vital biomolecules. However, we assumed earlier that food protein fragments might perform some regulatory functions. The theoretical justification for this assumption is advanced in this work. In the present work, the primary structures of protein fragments were compared with amino acid sequences of known natural regulatory oligopeptides in silico. It is shown that fragments formed as a result of animal food protein cleavage by proteolytic enzymes can exist in the gastrointestinal tract for a long time. Many of them are enzyme inhibitors, regulators of nervous, endocrine, and immune system, and possess antimicrobial and other activities. It has also been shown that the lifetime of fragments before their cleavage in the gastrointestinal tract could be enough for performing corrective functions. Thus, as a result of food protein fragmentation a dynamic pool of exogenous regulatory oligopeptides with functions changing as shorter fragments are generated may form. The detection of an endogenous-exogenous pool of regulatory molecules expands the significance and content of the Ashmarin-Obukhova hypothesis on a functional continuum of natural oligopeptides. The possible practical importance of these results is noted.
Keywords: fragment; oligopeptide; food protein; regulation; EROP-Moscow database; computer analysis; continuum

Teichulosonic acid, an anionic polymer of a new class from the cell wall of Actinoplanes utahensis VKM Ac-674T by A. S. Shashkov; G. M. Streshinskaya; Yu. I. Kozlova; E. M. Tul’skaya; S. N. Senchenkova; N. P. Arbatskii; O. V. Bueva; L. I. Evtushenko (511-517).
The cell wall of Actinoplanes utahensis VKM Ac-674T contains two anionic polymers: teichoic acid 1,3-poly(glycerol phosphate) that is widespread in cell walls of Gram-positive bacteria; and a unique teichulosonic acid belonging to a new class of bioglycans described only in microorganisms of the Actinomycetales order. The latter polymer contains residues of di-N-acyl derivative of sialic acid-like monosaccharide — 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-β-L-manno-non-2-ulosonic or pseudaminic acid (Pse) which bears the N-(3,4-dihydroxybutanoyl) group (Dhb) at C7. This polymer has irregular structure and consists of fragments of two types, which differ in substitution of the Dhb residues at O4 either with β-D-glucopyranose or with β-Pse residues. Most of the β-Pse residues (∼80%) are glycosylated at position 4 with α-D-galactopyranose residues in both types of fragments. The glucose, galactose, and Dhb residues are partly O-acetylated. The structures of the polymers were established by chemical and NMR spectroscopy methods.
Keywords: Actinoplanes utahensis ; cell wall; anionic polysaccharides; teichoic acids; teichulosonic acids; NMR spectroscopy

The phenomenon of interspecific hybridization accompanied by transfer of the mitochondrial genome from the northern red-backed vole (Clethrionomys rutilus) to the bank vole (Cl. glareolus) in northeastern Europe is well known already for 25 years. However, the possibility of recombination between homologous segments of maternal and paternal mtDNAs of the voles during fertilization was not previously studied. Analysis of data on variability of nucleotide sequences of the mitochondrial gene for cytochrome b in populations of red-backed and bank voles in the area of their sympatry has shown that as a result of interspecific hybridization, the mitochondrial gene pool of bank voles contains not only mtDNA haplotypes of red-backed vole females, but also mtDNA haplotypes of bank voles bearing short nucleotide tracts of red-backed vole mtDNA. This finding supports the hypothesis that an incomplete elimination of red-backed vole paternal mtDNA during the interspecific hybridization between bank vole females and red-backed vole males leads to the gene conversion of bank vole maternal mtDNA tracts by homologous ones of mtDNA of red-backed vole males.
Keywords: mitochondrial genome; interspecific hybridization; gene conversion; voles

Interaction of nucleotide excision repair proteins with DNA containing bulky lesion and apurinic/apyrimidinic site by L. V. Skosareva; N. A. Lebedeva; N. I. Rechkunova; E. A. Maltseva; P. E. Pestryakov; O. I. Lavrik (524-531).
The interaction of nucleotide excision repair (NER) proteins (XPC-HR23b, RPA, and XPA) with 48-mer DNA duplexes containing the bulky lesion-mimicking fluorescein-substituted derivative of dUMP (5-{3-[6-(carboxyamidofluo-resceinyl)amidocapromoyl]allyl}-2′-deoxyuridine-5′-monophosphate) in a cluster with a lesion of another type (apurinic/apyrimidinic (AP) site) has been studied. It is shown that XPC-HR23b is modified to a greater extent by the DNA duplex containing an AP site opposite nucleotide adjacent to the fluorescein residue than by DNA containing an AP site shifted to the 3′-or 5′-end of the DNA strand. The efficiency of XPA modification by DNA duplexes containing both AP site and fluorescein residue is higher than that by DNA lacking the bulky lesion; the modification pattern in this case depends on the AP site position. In accordance with its major function, RPA interacts more efficiently with single-stranded DNA than with DNA duplexes, including those bearing bulky lesions. The observed interaction between the proteins involved in nucleotide excision repair and DNA structures containing a bulky lesion processed by NER and the AP site repaired via base excision repair may be significant for both these repair pathways in cells and requires the specific sequence of repair of clustered DNA lesions.
Keywords: protein factors of nucleotide excision repair; bulky lesion; apurinic/apyrimidinic site; affinity labeling; DNA-protein complexes

A new viral vector exploiting RNA polymerase I-mediated transcription by T. V. Komarova; A. M. Schwartz; A. A. Makarov; Yu. L. Dorokhov (532-538).
We have developed a new viral vector system exploiting RNA-polymerase I transcription. The vector is based on the crucifer-infecting tobacco mosaic virus (crTMV) cDNA inserted into the rRNA transcriptional cassette (promoter and terminator). To visualize reproduction of the vector, the coat protein gene was replaced with the gene encoding green fluorescent protein (GFP) resulting in a PrrRNA-crTMV-GFP construct. Our results showed that agroinjection of Nicotiana benthamiana leaves with this vector results in GFP production from uncapped crTMV-GFP RNA because RNA polymerase I mediates synthesis of rRNA lacking a cap. Coexpression of the crTMV 122 kDa capping protein gene and the silencing suppressor encoded by the tomato bushy stunt virus p19 gene stimulated virus-directed GFP production more than 100-fold. We conclude that the Pol I promoter can be used to drive transcription in a transient expression system.
Keywords: tobacco mosaic virus; viral vector; crTMV; agroinjection; protein superproduction; RNA polymerase I

To identify potential cancer related glycoproteins in breast cancer cells, we enriched N-linked glycoproteins by lentil lectin from the human breast cancer cell line Hs578T and the normal breast cell line Hs578BST for proteomic comparison. Glycoproteins were separated and compared by two-dimensional electrophoresis. Twenty-four glycoproteins were identified that expressed remarkably differently, among which nine were involved in the progress of collagen synthesis. Prolyl 4-hydroxylase alpha polypeptide II (P4HA2) expression and influence in breast cancer was further investigated. Immunohistochemistry revealed that P4HA2 was upregulated in breast tumor cells compared with its adjacent normal tissues. Moreover, overexpression and RNA interference of P4HA2 showed that P4HA2 expression suppressed cell proliferation and migration in Hs578T in vitro.
Keywords: glycoproteomics; lectin; breast cancer; P4HA2