3ß-Corner Stability by Comparative Molecular Dynamics Simulations.

This study explored the mechanisms by which the stability of super-secondary structures of the 3ß-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3ß-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3ß-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3ß-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or "ready-made" building block in protein folding. The 3ß-corner can also be considered as an independent object for study in field of structural biology.

Agonists in the Extended Conformation Stabilize the Active State of ß-Adrenoceptors.

In this study, we conducted a comparative analysis of the structure of agonists and antagonists of transmembrane (TM) ß-adrenoceptors (ß-ARs) and their interactions with the ß-ARs and proposed the mechanism of receptor activation. A characteristic feature of agonist and antagonist molecules is the presence of a hydrophobic head (most often, one or two aromatic rings) and a tail with a positively charged amino group. All ß-adrenergic agonists have two carbon atoms between the aromatic ring of the head and the nitrogen atom of the amino group. In antagonist molecules, this fragment can be either reduced or increased to four atoms due to the additional carbon and oxygen atoms. The agonist head, as a rule, has two H-bond donors or acceptors in the para- and meta-positions of the aromatic rings, while in the antagonist heads, these donors/acceptors are absent or located in other positions. Analysis of known three-dimensional structures of ß-AR complexes with agonists showed that the agonist head forms two H-bonds with the TM5 helix, and the tail forms an ionic bond with the D3.32 residue of the TM3 helix and one or two H-bonds with the TM7 helix. The tail of the antagonist can form similar bonds, but the interaction between the head and the TM5 helix is much weaker. As a result of these interactions, the agonist molecule acquires an extended "strained string" conformation, in contrast to the antagonist molecule, which has a longer, bended, and flexible tail. The "strained string" of the agonist interacts with the TM6 helix (primarily with the W6.48 residue) and turns it, which leads to the opening of the G protein-binding site on the intracellular side of the receptor, while flexible and larger antagonist molecules do not have the same effect on the receptor.

The effects of chronic diseases on plutonium urinary excretion in former workers of the Mayak Production Association.

The radiochemical analysis of plutonium activity in urine is the main method for indirect estimation of doses of internal exposure from plutonium incorporation in professional workers. It was previously shown that late-in-life acute diseases, particularly those that affect the liver, can promote accelerated rates of release of plutonium from the liver with enhanced excretion rates. This initial study examines the relationships of some chronic diseases on plutonium excretion as well as the terminal relative distribution of plutonium between the liver and skeleton. Fourteen cases from former workers at the Mayak Production Association (Mayak PA) who provided from 4-9 urine plutonium bioassays for plutonium, had an autopsy conducted after death, and had sufficient clinical records to document their health status were used in this study. Enhanced plutonium excretion was associated with more serious chronic diseases, including cardiovascular diseases and other diseases that involved the liver. These chronic diseases were also associated with relatively less plutonium found in the liver relative to the skeleton determined by analyses conducted after autopsy. These data further document health conditions that affect plutonium biokinetics and organ deposition and retention patterns and suggest that health status should be considered when conducting plutonium bioassays as these may alter subsequent dosimetry and risk models.

Left-handed ßαß-units: frequency of occurrence and arrangement in protein structure.

Communicated by Ramaswamy H. Sarma.

Handedness of structural units depends on their mutual arrangement in protein structure.

Communicated by Ramaswamy H. Sarma.

THE MAYAK WORKER DOSIMETRY SYSTEM (MWDS-2016): INTERNAL DOSIMETRY RESULTS AND COMPARISON WITH MWDS-2013.

Differences in results from the new Mayak Worker Dosimetry System (MWDS-2016) vs the previous MWDS-2013 are described. Statistical characteristics are shown for the distribution of accumulated absorbed doses to organs for 8340 workers with bioassay data. Differences in mean values of accumulated doses and their relative standard uncertainties calculated by MWDS-2016 and MWDS-2013 were analysed separately for various types of industrial compounds of plutonium, specifically nitrates, mixtures and oxides. Within the range of accumulated doses >1 mGy, lung doses for nitrates and mixtures decreased by 41 and 15%, respectively, and remained at the same level for oxides. Accumulated liver doses within the range >1 mGy increased for nitrates and mixtures by 13 and 8%, respectively, and decreased for oxides by 7%.

Cold Crystallization of Glassy Polylactide during Solvent Crazing.

Uniaxial tension accompanied by the orientation and crystallization of polymer chains is one of the powerful methods for the improvement of mechanical properties. Crystallization of amorphous isotropic polylactide (PLA) at room temperature is studied for the first time during the drawing of films in the presence of liquid adsorption-active media (ethanol, water-ethanol mixtures, and n-heptane) by the solvent crazing mechanism. The crystalline structure arises only under simultaneous actions of a liquid medium and a tensile stress and does not depend on the nature of the environment. The degree of polymer crystallinity increases nearly linearly with the growth in the fraction of the fibrillar material and reaches a maximum value of 42-45%. It has been stated that polymer crystallization happens in crazes involving nanofibrils with a diameter of about 10-20 nm without affecting the bulk polymer parts. Wide-angle X-ray scattering has been used to confirm that the crazing-induced crystallization is accompanied by the formation of the α'-crystalline phase with crystallite sizes (X-ray coherent scattering region) of 3-5 nm, depending on the nature of the liquid medium. After stretching in liquid media to a high tensile strain, the strength of a PLA film has increased to 200 MPa.

Structural motifs in which ß-strands are clipped together with the П-like module.

In this study, the structural motifs that can be represented as combinations of small motifs such as ß-hairpins, S-, and Z-like ß-sheets and ßαß-units, and the П-like module are described and analyzed. The П-module consists of connected elements of the ß-strand-loop-ß-strand type arranged in space so that its overall fold resembles a clip or the Greek letter П. In proteins, the П-module itself and the structural motifs containing it exhibit unique overall folds and have specific sequence patterns of the key hydrophobic, hydrophilic and glycine residues. All this together enables us to conclude that these structural motifs can fold independently of the remaining part of the molecule and can act as nuclei and/or "ready-made" building blocks in protein folding.

Use of in vivo counting measurements to estimate internal doses from (241)Am in workers from the Mayak production association.

Comparisons between results of in vivo counting measurements of americium burden and results from radiochemical analyses of organ samples taken at autopsy of 11 cases of former Mayak workers were made. The in vivo counting measurements were performed 3-8 y before death. The best agreement between in vivo counting measurements for americium and autopsy data was observed for the skull. For lungs and liver, the ratios of burden measured by in vivo counting to those obtained from radiochemical analyses data ranged from 0.7-3.8, while those for the skull were from 1.0-1.1. There was a good correlation between the estimates of americium burden in the entire skeleton obtained from in vivo counting with those obtained from autopsy data. Specifically, the skeletal burden ratio, in vivo counting/autopsy, averaged 0.9 ± 0.1. The prior human americium model, D-Am2010, used in vivo counting measurements for americium in the skeleton to estimate the contents of americium and plutonium at death. The results using this model indicate that in vivo counting measurements of the skull can be used to estimate internal doses from americium in the Mayak workers. Additionally, these measurements may also be used to provide a qualitative assessment of internal doses from plutonium.

A novel structural tree for wrap-proteins, a subclass of (α+ß)-proteins.

In this paper, a novel structural subclass of (α+ß)-proteins is presented. A characteristic feature of these proteins and domains is that they consist of strongly twisted and coiled ß-sheets wrapped around one or two α-helices, so they are referred to here as wrap-proteins. It is shown that overall folds of the wrap-proteins can be obtained by stepwise addition of α-helices and/or ß-strands to the strongly twisted and coiled ß-hairpin taken as the starting structure in modeling. As a result of modeling, a structural tree for the wrap-proteins was constructed that includes 201 folds of which 49 occur in known nonhomologous proteins.

Accumulation, organ distribution, and excretion kinetics of ²4¹Am in Mayak Production Association workers.

Americium-241 (²4¹Am) is the second most significant radiation hazard after ²³9Pu at some of the Mayak Production Association facilities. This study summarizes current data on the accumulation, distribution, and excretion of americium compared with plutonium in different organs from former Mayak PA workers. Americium and plutonium were measured in autopsy and bioassay samples and correlated with the presence or absence of chronic disease and with biological transportability of the aerosols encountered at different workplaces. The relative accumulation of ²4¹Am was found to be increasing in the workers over time. This is likely from ²4¹Pu that increases with time in reprocessed fuel and from the increased concentrations of ²4¹Am and ²4¹Pu in inhaled alpha-active aerosols. While differences were observed in lung retention with exposures to different industrial compounds with different transportabilities (i.e., dioxide and nitrates), there were no significant differences in lung retention between americium and plutonium within each transportability group. In the non-pulmonary organs, the highest ratios of ²4¹Am/²4¹Am + SPu were observed in the skeleton. The relative ratios of americium in the skeleton versus liver were significantly greater than for plutonium. The relative amounts of americium and plutonium found in the skeleton compared with the liver were even greater in workers with documented chronic liver diseases. Excretion rates of ²4¹Am in ''healthy'' workers were estimated using bioassay and autopsy data. The data suggest that impaired liver function leads to reduced hepatic ²4¹Am retention, leading to increased ²4¹Am excretion.

Super-secondary structures and modeling of protein folds.

A characteristic feature of the polypeptide chain is its ability to form a restricted set of commonly occurring folding units composed of two or more elements of secondary structure that are adjacent along the chain. Some of these super-secondary structures exhibit a unique handedness and a unique overall fold irrespective of whether they occur in homologous or nonhomologous proteins. Such super-secondary structures are of particular value since they can be used as starting structures in protein modeling. The larger protein folds can be obtained by stepwise addition of other secondary structural elements to the starting structures taking into account a set of simple rules inferred from known principles of protein structure.

Modeling of folds and folding pathways for some protein families of (α + ß)- and (α/ß)-classes.

In this paper, updated structural trees for α/ß-proteins containing five- and seven-segment (α/ß)-motifs are represented. Novel structural motifs occurring in some families of (α + ß)- and (α/ß)-proteins are also characterized. Databases of these proteins have been compiled from the Protein Data Bank (PDB) and Structural Classification of Proteins (SCOP) and the corresponding structural trees have been constructed. The classification of these proteins has been developed and organized as an extension of the PCBOST database, which is available at http://strees.protres.ru . In total, the updated Protein Classification Based on Structural Trees database contains 11 structural trees, 106 levels, 635 folds, 4911 proteins and domains, and 14,202 PDB entries.

Structural motifs are closed into cycles in proteins.

Beta-hairpins, triple-strand beta-sheets and betaalphabeta-units represent simple structural motifs closed into cycles by systems of hydrogen bonds. Secondary closing of these simple motifs into large cycles by means of different superhelices, split beta-hairpins or SS-bridges results in the formation of more complex structural motifs having unique overall folds and unique handedness such as abcd-units, phi-motifs, five- and seven-segment alpha/beta-motifs. Apparently, the complex structural motifs are more cooperative and stable and this may be one of the main reasons of high frequencies of occurrence of the motifs in proteins.

PCBOST: Protein classification based on structural trees.

In this paper, we present the protein classification based on structural trees (PCBOST). This is a novel hierarchical classification of proteins that is primarily based on similarity of overall folds of proteins as well as on the modeled folding pathways of proteins. Amino acid sequences, functions of proteins and their evolutionary relationship are not taken into account in this classification. To date the database includes 3847 proteins and domains grouped into six categories having structural similarity and forming six structural trees (total 10,547 PDB-entries). The work on extension of the database and construction of novel structural trees is in progress. The service is free for all users and available at the URL .

Domain organization of the N-terminal portion of hordeivirus movement protein TGBp1.

Three 'triple gene block' proteins known as TGBp1, TGBp2 and TGBp3 are required for cell-to-cell movement of plant viruses belonging to a number of genera including Hordeivirus. Hordeiviral TGBp1 interacts with viral genomic RNAs to form ribonucleoprotein (RNP) complexes competent for translocation between cells through plasmodesmata and over long distances via the phloem. Binding of hordeivirus TGBp1 to RNA involves two protein regions, the C-terminal NTPase/helicase domain and the N-terminal extension region. This study demonstrated that the extension region of hordeivirus TGBp1 consists of two structurally and functionally distinct domains called the N-terminal domain (NTD) and the internal domain (ID). In agreement with secondary structure predictions, analysis of circular dichroism spectra of the isolated NTD and ID demonstrated that the NTD represents a natively unfolded protein domain, whereas the ID has a pronounced secondary structure. Both the NTD and ID were able to bind ssRNA non-specifically. However, whilst the NTD interacted with ssRNA non-cooperatively, the ID bound ssRNA in a cooperative manner. Additionally, both domains bound dsRNA. The NTD and ID formed low-molecular-mass oligomers, whereas the ID also gave rise to high-molecular-mass complexes. The isolated ID was able to interact with both the NTD and the C-terminal NTPase/helicase domain in solution. These data demonstrate that the hordeivirus TGBp1 has three RNA-binding domains and that interaction between these structural units can provide a basis for remodelling of viral RNP complexes at different steps of cell-to-cell and long-distance transport of virus infection.

Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n).

The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

One more probable structural transition in potato virus X virions and a revised model of the virus coat protein structure.

We found that a 2-h incubation of potato virus X (PVX) virions in 10 mM Tris-HCl buffer pH 7.5 at -20 degrees C results in a strong but reversible drop in virion stability. Under these conditions, the PVX virions are completely disrupted by low (starting from 50 mM) concentrations of LiCl and CaCl(2) but not of NaCl. Incubation of PVX samples with 0.05-2 M LiCl at +4 degrees C did not result in virion disassembly and the virions were not disrupted upon incubation at -20 degrees C in 10 mM Tris-HCl buffer pH 7.5 without LiCl. We suggest that a 2-h incubation of the PVX virions at -20 degrees C in 10 mM Tris-HCl pH 7.5 results in a structural transition in the virus particles. A revised model of the three-dimensional organization of coat protein subunits in the PVX virions is proposed. This two-domain model explains better the high plasticity of the PVX CP structure.

pH-dependent substrate preference of pig heart lipoamide dehydrogenase varies with oligomeric state: response to mitochondrial matrix acidification.

Cycling of intracellular pH has recently been shown to play a critical role in ischemia-reperfusion injury. Ischemia-reperfusion also leads to mitochondrial matrix acidification and dysfunction. However, the mechanism by which matrix acidification contributes to mitochondrial dysfunction, oxidative stress, and the resultant cellular injury has not been elucidated. We observe pH-dependent equilibria between monomeric, dimeric, and a previously undescribed tetrameric form of pig heart lipoamide dehydrogenase (LADH), a mitochondrial matrix enzyme. Dynamic light scattering studies of native LADH in aqueous solution indicate that lowering pH favors a shift in average molecular mass from higher oligomeric states to monomer. Sedimentation velocity of LADH entrapped in reverse micelles reveals dimer and tetramer at both pH 5.8 and 7.5, but monomer was observed only at pH 5.8. Enzyme activity measurements in reverse Aerosol OT micelles in octane indicate that LADH dimer and tetramer possess lipoamide dehydrogenase and diaphorase activities at pH 7.5. Upon acidification to pH 5.8 only the LADH monomer is active and only the diaphorase activity is observed. These results indicate a correlation between pH-dependent changes in the LADH reaction specificity and its oligomeric state. The acidification of mitochondrial matrix that occurs during ischemia-reperfusion injury is sufficient to alter the structure and enzymatic specificity of LADH, thereby reducing mitochondrial defenses, increasing oxidative stress, and slowing the recovery of energy metabolism. Matrix acidification may also disrupt the quaternary structure of other mitochondrial protein complexes critical for cellular homeostasis and survival.

Relationship between intramolecular hydrogen bonding and solvent accessibility of side-chain donors and acceptors in proteins.

This study shows that intramolecular hydrogen bonding in proteins depends on the accessibility of donors and acceptors to water molecules. The frequency of occurrence of H-bonded side chains in proteins is inversely proportional to the solvent accessibility of their donors and acceptors. Estimates of the notional free energy of hydrogen bonding suggest that intramolecular hydrogen-bonding interactions of buried and half-buried donors and acceptors can contribute favorably to the stability of a protein, whereas those of solvent-exposed polar atoms become less favorable or unfavorable.