Tritium Planigraphy Research Articles

Changes in the structure of potato virus A virions during limited proteolysis <i>in situ</i> according to tritium labeling data and computer simulation

The coat proteins (CP) of potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. A comparative analysis of the structures of coat proteins (CPs) in intact PVA virions and in virus particles lacking the N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using the atomic resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of CP PVA, the available CP surfaces in the PVY virion were calculated and the areas of intersubunit/ interhelix contacts were determined. For this purpose, the approach of Lee and Richards (Lee, B., and Richards, F. M. (1971) J. Mol. Biol., 55, 379-400) was used. Comparison of the incorporation profiles of the tritium label in intact and trypsin-degraded PVA∆32 revealed the position of the ΔN-peptide shielding the surface domain (a.a. 66-73, 141-146) and the interhelix zone (a.a. 161-175) of the PVA CP. The presence of channels/cavities was found in the virion, which turned out to be partially permeable to tritium atoms. Upon removal of the ∆N-peptide, a decrease in the label within the virion (a.a. 184-200) was also observed, indicating a possible structural transition leading to virion compactization. Based on the data obtained, we can conclude that part of the surface ∆N-peptide is located between the coils of the virion helix, which increases the helix pitch and provides greater flexibility of the virion, which is important for the intercellular transport of the viruses in the plants.

Changes in the Structure of Potato Virus A Virions after Limited in situ Proteolysis According to Tritium Labeling Data and Computer Simulation.

Coat proteins (CP) of the potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. Comparative analysis of the structures of coat proteins (CPs) in the intact PVA virions and in the virus particles lacking N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using atomic-resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of the CP PVA, the available CP surfaces in the PVY virion were calculated and the areas of intersubunit/interhelix contacts were determined. For this purpose, the approach of Lee and Richards [Lee, B., and Richards, F. M. (1971) J. Mol. Biol., 55, 379-400] was used. Comparison of incorporation profiles of the tritium label in the intact and trypsin-degraded PVAΔ32 revealed position of the ΔN-peptide shielding the surface domain (a.a. 66-73, 141-146) and the interhelix zone (a.a. 161-175) of the PVA CP. Presence of the channels/cavities was found in the virion, which turned out to be partially permeable to tritium atoms. Upon removal of the ΔN-peptide, decrease in the label incorporation within the virion (a.a. 184-200) was also observed, indicating possible structural transition leading to the virion compactization. Based on the obtained data, we can conclude that part of the surface ΔN-peptide is inserted between the coils of the virion helix thus increasing the helix pitch and providing greater flexibility of the virion, which is important for intercellular transport of the viruses in the plants.

Surface characterization of the thermal remodeling helical plant virus.

Previously, we have reported that spherical particles (SPs) are formed by the thermal remodeling of rigid helical virions of native tobacco mosaic virus (TMV) at 94°C. SPs have remarkable features: stability, unique adsorption properties and immunostimulation potential. Here we performed a comparative study of the amino acid composition of the SPs and virions surface to characterize their properties and take an important step to understanding the structure of SPs. The results of tritium planigraphy showed that thermal transformation of TMV leads to a significant increase in tritium label incorporation into the following sites of SPs protein: 41–71 а.a. and 93–122 a.a. At the same time, there was a decrease in tritium label incorporation into the N- and C- terminal region (1–15 a.a., 142–158 a.a). The use of complementary physico-chemical methods allowed us to carry out a detailed structural analysis of the surface and to determine the most likely surface areas of SPs. The obtained data make it possible to consider viral protein thermal rearrangements, and to open new opportunities for biologically active complex design using information about SPs surface amino acid composition and methods of non-specific adsorption and bioconjugation.

Self-organization of lysozyme—Ionic surfactant complexes at the aqueous-air interface as studied by tritium bombardment

The self-organization of lysozyme with cationic (dodecyltrimethylammonium bromide) and anionic (sodium dodecylsufate) surfactants at an aqueous-air interface was studied by means of tritium planigraphy. It was found that even if the surfactant concentration is too low to induce significant structural changes in the protein globule, the surfactant can bind with the protein via both electrostatic and hydrophobic interactions and can displace the protein from the interface. Different mechanisms of complex formation are suggested for lysozyme mixed with SDS or DTAB. SDS molecules screen positively charged groups of amino acid residues via electrostatic interactions and form hydrogen bonds with polar groups of amino acid residues. SDS also penetrates the protein globule via hydrophobic interactions. In contrast, DTAB interacts with hydrophobic amino acid residues, screening them from tritium atoms. For both surfactants, it was found that lysozyme maintains a longways-on orientation in the mixed adsorption layer.

Tritium planigraphy and nanosized biological particles

Advances in studies of protein and complex biological systems by tritium planigraphy are considered. Particular attention is paid to detailing the structural organization of the protein components of the influenza virus. The structure of the M1 protein in a solution, virion, and crystal is analyzed. The specific features of this protein identified using tritium planigraphy and computer simulation are indicative of significant changes in its conformation depending on the “phase” state. Models of the spatial structure of the M1 protein in solution and in the virion are proposed. Structural disorder is observed in one of the three domains of this protein. Ideas on the importance of this structure for the multifunctional properties of the protein, such as binding to the membrane and a ribonucleoprotein complex, as well as the transfer of genetic material during viral infection of healthy cells, were suggested.

Tritium planigraphy as a tool for studying the structural organization nanobiocomplexes

The tritium planigraphy method is based on the nonselective substitution of radioactive isotope tritium for hydrogen in hydrocarbon fragments of molecules by means of a chemical reaction involving hot tritium atoms. Data on the steric accessibility of the system components (macromolecules in the complex, amino acid residues, and even individual atomic groups of macromolecules) characterize the structure of the object. The method, applicable to substances in different phase states, has no restrictions on the molecular weight of the target. Tritium planigraphy, used equally successfully in both crystals and solutions, makes it possible to study fine changes in the structure. The main results of studies of the structure of nanosized biocompexes by tritium planigraphy are presented.

Tritium planigraphy: Differences in the spatial structures of the influenza virus M1 protein in crystal, solution, and virion

Spatial structure of the influenza virus A/Puerto Rico/8/34 (PR8, subtype H1N1) M1 protein in a solution and composition of the virion was studied by tritium planigraphy technique. The special algorithm for modeling of the spatial structure is used to simulate the experiment, as well as a set of algorithms predicting secondary structure and disordered regions in proteins. Tertiary structures were refined using the program Rosetta. To compare the structures in solution and in virion, also used the X-ray diffraction data for NM-domain. The main difference between protein structure in solution and crystal is observed in the contact region of N- and M-domains, which are more densely packed in the crystalline state. Locations include the maximum label is almost identical to the unstructured regions of proteins predicted by bioinformatics analysis. These areas are concentrated in the C-domain and in the loop regions between the M-, N-, and C-domains. Analytical centrifugation and dynamic laser light scattering confirm data of tritium planigraphy. Anomalous hydrodynamic size, and low structuring of the M1 protein in solution were found. The multifunctionality of protein in the cell appears to be associated with its plastic tertiary structure, which provides at the expense of unstructured regions of contact with various molecules-partners.

Modeling of protein spatial structure using tritium planigraphy

The results of proteins spatial structure modeling using the tritium planigraphy technique are presented. The knowledge of three-dimensional structure of macromolecules is extremely necessary to understand the basic mechanisms of interaction in biological systems and complex technological processes. Known limitations of the X-ray analysis (crystal state) and NMR (molecular weight) make it necessary to seek new approaches to modeling the spatial structure of proteins. Semiempirical tritium planigraphy technique is one of these approaches. The method is based on the bombardment of the object by beam of hot tritium atoms (E(at) > or = 0.3 eV) and a computer simulation experiment. On the example of proteins of the different structural classes we set that by using this integrated approach can be obtained by three-dimensional model of the structure, well consistent with the data of X-ray analysis. An important factor is a sequence search of contacts between secondary structure elements: the best fit model with the native structure is achieved by assembling the elements of a vector in the sequence from the N- to C-terminus of the polypeptide chain.

Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium

The structure of the C-terminal domain of the influenza virus A matrix M1 protein, for which X-ray diffraction data were still missing, was studied in acidic solution. Matrix M1 protein was bombarded with thermally-activated tritium atoms, and the resulting intramolecular distribution of the tritium label was analyzed to assess the steric accessibility of the amino acid residues in this protein. This technique revealed that interdomain loops and the C-terminal domain of the protein are the most accessible to labeling with tritium atoms. A model of the spatial arrangement of the C-terminal domain of matrix M1 protein was generated using rosetta software adjusted to the data obtained by tritium planigraphy experiments. This model suggests that the C-terminal domain is an almost flat layer with a three-α-helical structure. To explain the high level of tritium label incorporation into the C-terminal domain of the M1 protein in an acidic solution, we also used independent experimental approaches (CD spectroscopy, limited proteolysis and MALDI-TOF MS analysis of the proteolysis products, dynamic light scattering and analytical ultracentrifugation), as well as multiple computational algorithms, to analyse the intrinsic protein disorder. Taken together, the results obtained in the present study indicate that the C-terminal domain is weakly structured. We hypothesize that the specific 3D structural peculiarities of the M1 protein revealed in acidic pH solution allow the protein greater structural flexibility and enable it to interact effectively with the components of the host cell.

Intrinsically unstructured regions in the C domain of the influenza virus M1 protein

The M1 matrix protein of the influenza virus is one of the main structural components of the virion that performs several different functions in the infected cell. X-ray analysis (with 2.08 A resolution) has been performed for the N-terminal part of the M1 protein (residues 2–158) but not for its C-terminal domain (159–252). In the present study, we analyzed the structure of the M1 protein of the influenza virus A/Puerto Rico/8/34 (H1N1) strain in acidic solution using tritium planigraphy. The incorporation of tritium label into the domains of the M1 protein were studied; the C domain and the interdomain loops are preferentially accessible to tritium. Analytical centrifugation and dynamic laser light scattering demonstrated anomalous hydrodynamic parameters and low structuredness of the M1 protein, which has also been confirmed by circular dichroism data. Bioinformatic analysis of the M1 protein sequence revealed intrinsically unstructured segments that were concentrated in the C domain and interdomain loops between the N-, M-, and C domains. We suggest that the multifunctionality of the M1 protein in a cell is determined by the plasticity of its tertiary structure, which is caused by the presence of intrinsically unstructured segments.

Analysis of the role of the coat protein N-terminal segment in Potato virus X virion stability and functional activity.

Previously, we have reported that intact Potato virus X (PVX) virions cannot be translated in cell-free systems, but acquire this capacity by the binding of PVX-specific triple gene block protein 1 (TGBp1) or after phosphorylation of the exposed N-terminal segment of intravirus coat protein (CP) by protein kinases. With the help of in vitro mutagenesis, a nonphosphorylatable PVX mutant (denoted ST PVX) was prepared in which all 12 S and T residues in the 20-residue-long N-terminal CP segment were substituted by A or G. Contrary to expectations, ST PVX was infectious, produced normal progeny and was translated in vitro in the absence of any additional factors. We suggest that the N-terminal PVX CP segment somehow participates in virion assembly in vivo and that CP subunits in ST virions may differ in structure from those in the wild-type (UK3 strain). In the present work, to test this suggestion, we performed a comparative tritium planigraphy study of CP structure in UK3 and ST virions. It was found that the profile of tritium incorporation into ST mutant virions in some CP segments differed from that of normal UK3 virions and from UK3 complexed with the PVX movement protein TGBp1. It is proposed that amino acid substitutions in ST CP and the TGBp1-driven remodelling of UK3 virions induce structural alterations in intravirus CPs. These alterations affect the predicted RNA recognition motif of PVX CP, but in different ways: for ST PVX, labelling is increased in α-helices 6 and 7, whereas, in remodelled UK3, labelling is increased in the β-sheet strands β3, β4 and β5.

Tritium planigraphy study of structural alterations in the coat protein of Potato virus X induced by binding of its triple gene block 1 protein to virions

Alterations in Potato virus X (PVX) coat protein structure after binding of the protein, encoded by the first gene of PVX triple gene block (triple gene block 1 protein, TGBp1), to the virions were studied using tritium planigraphy. Previously, it has been shown that TGBp1 molecules interact with the PVX particle end, containing the 5'-terminus of PVX RNA, and that this interaction results in a strong decrease in virion stability and its transformation to a translationally active state. In this work, it has been shown that the interaction of TGBp1 with PVX virions leads to an increase of approximately 50% in tritium label incorporation into the 176-198 segment of the 236-residue-long PVX coat protein subunit, with some decrease in label incorporation into the N-terminal coat protein region. According to the new 'sandwich' variant of our recently proposed model of the three-dimensional structure of the intravirus PVX coat protein, the 176-198 segment is assigned to the beta-sheet region located at the subunit surface, presumably participating in coat protein interactions with the intravirus RNA and/or in protein-protein interactions, whereas the N-terminal coat protein region corresponds to the other part of the same beta-sheet. For the remaining segments of the PVX coat protein subunit, no significant difference between tritium incorporation into untreated and TGBp1-treated PVX was observed. A detailed description of the 'sandwich' version of the intravirus PVX coat protein model is presented.

The In Situ Structural Characterization of the Influenza A Virus Matrix M1 Protein within a Virion

The first attempt has been made to suggest a model of influenza A virus matrix M1 protein spatial structure and molecule orientation within a virion on the basis of tritium planigraphy data and theoretical prediction results. Limited in situ proteolysis of the intact virions with bromelain and surface plasmon resonance spectroscopy study of the M1 protein interaction with lipid coated surfaces were used for independent confirmation of the proposed model.

Potato virus X: structure, disassembly and reconstitution

SUMMARY This paper summarizes some structural characteristics of Potato virus X (PVX), the flexuous filamentous plant potexvirus. A model of PVX coat protein (CP) tertiary structure in the virion proposed on the basis of tritium planigraphy combined with predictions of the protein tertiary structure is described. A possible role of glycosylation and phosphorylation in the CP structure and function is discussed. Two forms of PVX virion disassembly are discussed: (i) the virion co-translational disassembly after PVX CP in situ phosphorylation and (ii) disassembly of PVX triggered by different factors after linear destabilization of the virion by binding of the PVX-coded movement protein (TGBp1) to one end of the polar CP-helix. Special emphasis was placed on a translational activation of encapsidated PVX RNA and rapid disassembly of TGBp1-PVX complexes into free RNA and CP. The results of experiments on the PVX CP repolymerization and PVX reconstitution are considered. In particular, the products assembled from PVX RNA, CP and TGBp1 were examined. Single-tailed particles were found with a helical, head-like structure consisting of helically arranged CP subunits located at the 5'-tail of RNA; the TGBp1 was bound to the end of the head. Translatable 'RNA-CP-TGBp1' complexes may represent the transport form of the PVX infection.

Structures of Helical Plant Virus Ribonucleoproteins as Assessed by Tritium Planigraphy and Theoretical Modeling

This review considers the results of probing the structure of ribonucleoprotein particles of helical plant viruses by tritium planigraphy (TP). This method works by exposing macromolecular targets to a beam of tritium atoms and analyzing the tritium label distribution along the macromolecule length. The TP data combined with theoretical predictions made it possible to propose a structural model of the coat protein for the virions of potato viruses X (the type representative of potexviruses) and A (a potyvirus), which eluded X-ray diffraction analysis so far. TP revealed fine structural differences between the wild-type tobacco mosaic virus (strain U1) and its temperature-sensitive mutant with an altered coat protein and host specificity. The possibilities of using TP for studying the RNA–protein interactions in helical virus particles are discussed.

Iceberg Model of the Structure of Globular Protein Adsorption Layers at the Air–Water Interface. Study by the Tritium Planigraphy Technique

The organization of the adsorption layers of insulin, pancreatic inhibitor of trypsin, ribonuclease S, lysozyme, myoglobin, carboxypeptidase A, subtilisin, and thermolysin at the air–water interface was studied by tritium planigraphy technique. The location of globular protein molecules relative to the interface was determined for solution concentrations corresponding to the formation of saturated adsorption layers (10–4 M, pH 6). It is established that the fraction of solution surface occupied by protein component is equal to 7–62%. Only a small part of globules with the height from 2 to 19% of their effective diameter is above the solution surface, whereas the main part of globules is submerged into water (the iceberg model).

Conformational differences between native and recombinant horseradish peroxidase revealed by tritium planigraphy.

Significant conformational differences between native and recombinant horseradish peroxidase have been shown by tritium planigraphy, which includes a method of thermal activation of tritium followed by amino acid analysis of the protein preparation. Comparison of radioactivity distribution among the amino acid residues with the theoretical (calculated) accessibility shows that the recombinant enzyme is characterized by high hydrophobicity and compactness of folding. The protective role of oligosaccharides in native enzyme has been confirmed. An unexpected result of the study is a finding on high accessibility of a catalytic histidine residue in solution. An effect of low dose (3 Gy) of irradiation on the accessibility of amino acid residues has been unequivocally demonstrated. The data can be interpreted as swelling of the compact folding and increase in the surface hydrophilicity of the recombinant enzyme. In the case of native enzyme, irradiation does not cause remarkable changes in the accessibility of amino acid residues indicating the possible extensive radical modification of the native enzyme in the life-course of the cell. The catalytic histidine is an exception. It becomes inaccessible after the enzyme irradiation, while its accessibility in the recombinant enzyme increases. An additional observation of a 5-fold decrease in the rate constant towards hydrogen peroxide points to the destructive effect of irradiation on the hydrogen bond network in the distal domain of the native enzyme molecule and partial collapse of the active site pocket.

Tritium planigraphy comparative structural study of tobacco mosaic virus and its mutant with altered host specificity

Spatial organization of wild-type (strain U1) tobacco mosaic virus (TMV) and of the temperature-sensitive TMV ts21-66 mutant was compared by tritium planigraphy. The ts21-66 mutant contains two substitutions in the coat protein (Ile21-->Thr and Asp66-->Gly) and, in contrast with U1, induces a hypersensitive response (formation of necroses) on the leaves of plants bearing a host resistance gene N' (for example Nicotiana sylvestris); TMV U1 induces systemic infection (mosaic) on the leaves of such plants. Tritium distribution along the coat protein (CP) polypeptide chain was determined after labelling of both isolated CP preparations and intact virions. In the case of the isolated low-order (3-4S) CP aggregates no reliable differences in tritium distribution between U1 and ts21-66 were found. But in labelling of the intact virions a significant difference between the wild-type and mutant CPs was observed: the N-terminal region of ts21-66 CP incorporated half the amount of tritium than the corresponding region of U1 CP. This means that in U1 virions the CP N-terminal segment is more exposed on the virion surface than in ts21-66 virions. The possibility of direct participation of the N-terminal tail of U1 CP subunits in the process of the N' hypersensitive response suppression is discussed.

Determination of Low Activity of Tritium-Labeled Amino Acids Using Simultaneously Flow Scintillation and Amino Acid Analyzers

The possibility of measuring a low activity of tritium-labeled amino acids in the eluate from Amino Acid Analyzer 835 (Hitachi, Japan) using a Radiomatic 150TR Flow Scintillation Analyzer (Packard Instrument Co., USA) was studied. Due to stepped variations of pH, ionic strength, and salt concentration in eluting solutions during amino acid separation and utilization of ninhydrin reagent in spectrophotometric measurements of amino acids, special selection of scintillation liquids was necessary. Six scintillation cocktails were tested: ZhS-8 (Reakhim, Ukraine), OptiPhase “HiSafe” 3 (Wallac Oy, EGGgr; Co., Finland), Hionic-Fluor, Ultima-Flo AP, Ultima-Flo M, and Ultima Gold (Packard Instrument Co., USA). It was found that Hionic-Fluor and Ultima-Flo AP cocktails are the most appropriate for flow measurements of tritium activity. Under optimal conditions the detection limit with Hionic-Fluor and Ultima-Flo AP was 150 and 100 decays min- 1 in the peak of amino acid, respectively. Such a high sensitivity allows utilization of the above analytical system for measurements of amino acid radioactivity to study the structure of proteins and protein complexes by tritium planigraphy.

Permeability of Lipid Membranes for Atomic Tritium or Atom “Slipping” Effect and Its Role in Tritium Planigraphy

The depth of penetration of tritium atoms capable of isotope substitution, generated by thermal dissociation on a tungsten wire (thermal activation of tritium), into a solid target is considered. On the basis of calculations used in the theory of recoil atom stopping, with a lipid bilayer as example, the possibility of penetration of reactive atoms to a depth of up to 5 nm was demonstrated. This result is nicely consistent with the available experimental data. The possibility of “slipping” of atomic tritium, without loss of its reactivity, into cavities with a decreased electron density was suggested. This phenomenon should be taken into account when interpreting the results of studying biological macromolecules and their complexes by tritium planigraphy.