On the PES for the interaction of an H atom with an H chemisorbate on a graphenic platelet.

Motivated by the problem of H(2) formation in diffuse clouds of the interstellar medium (ISM), we study the effect of including van der Waals-type corrections in DFT calculations on the entrance PES of the Eley-Rideal reaction H(b) + H(a)-GR → H(b)-H(a) + GR for a graphenic surface GR. The present calculations make use of the PBE-D3 dispersion corrected functional of Grimme et al. (2010) and are carried out on cluster models of graphenic surfaces: C(24)H(12) and C(54)H(18). To assess the soundness of the chosen functional we start by revisiting the H-GR adsorption potential. We find a satisfactory on top physisorption well (43-48 meV) correctly located at an H-GR distance of 3 Å. We then revisit the H(b)-H(a)-GR system using both the PW91 and PBE functionals. Our calculations do not reproduce the tiny potential barrier reported earlier for large H(b)distances from the surface. The barrier in the calculations of Sidis et al. (2000) and Morisset et al. (2003, 2004) has been traced to their previous use of an LSDA + POSTSCF PW91 procedure rather than the genuine PW91 one. The new PBE-D3 PES for the H(b)-H(a)-GR system is reported as a function of the H(b) distance to the surface and its impact parameter relative to the H(a) chemisorbate for the so-called "fixed puckered" ("diabatic" or "sudden") approach. The results are discussed in relation to recent experimental and theoretical work.

OH formation from O and H atoms physisorbed on a graphitic surface through the Langmuir-Hinshelwood mechanism: a quasi-classical approach.

We study the quasi-classical dynamics of OH formation on a graphitic surface through the Langmuir-Hinshelwood (LH) mechanism when both O and H ground-state atoms are initially physisorbed on the surface. The model proceeds from previous theoretical work on the LH formation of the H 2 molecule on graphite [Morisset, S.; Aguillon, F.; Sizun, M.; Sidis, V. J. Chem. Phys. 2004, 121, 6493; ibid 2005, 122, 194704]. The H-graphite system is first revisited with a view to get a tractable DFT-GGA computational prescription for the determination of atom physisorption onto graphitic surfaces. The DZP-RPBE combination is found to perform well; it is thereafter used along with MP2 calculations to determine the physisorption characteristics of atomic oxygen on graphitic surfaces. We also deal with chemisorption. In accordance with previous work, we find that O chemisorbs on graphite in a singlet spin state epoxy-like conformation. In the triplet state we find only "metastable" chemisorption with an activation barrier of 0.2 eV. The physisorption results are then used in the LH dynamics calculation. We show that in the [0.15 meV, 12 meV] relative collision energy range of the reacting O and H atoms on the surface, the OH molecule is produced with a large amount of internal energy ( approximately = 4eV) and a significant translation energy (>or=100 meV) relative to the surface.

Human immunodeficiency virus type 1 Vpr localization: nuclear transport of a viral protein modulated by a putative amphipathic helical structure and its relevance to biological activity.

Protein import into the nucleus is generally considered to involve specific nuclear localization signals (NLS) though it is becoming increasingly clear that efficient and well controlled import of proteins which lack a canonical NLS also occurs in cells. Human immunodeficiency virus type 1 (HIV-1) Vpr is one such protein which does not have an identifiable canonical NLS and yet efficiently localizes to the nuclear compartment. Here, we use confocal microscopy to demonstrate that mutations in the putative central hydrophobic helix of Vpr result in the retention of the protein in highly localized ring-like structures around the nuclear periphery with striking impairment in their ability to enter the nuclear interior. By characterizing other biological activities associated with this protein, such as its ability to incorporate into budding virions and its ability to arrest cells in G2, we show that this helical domain is specific for the nuclear translocation of the protein with very little effect on these other functions. Interestingly, however, perturbation of this helical motif also perturbs the protein's ability to augment viral replication in primary human macrophages indicating that the integrity of this secondary structure is essential for optimal infection in these non-dividing cells.

Unrestricted study of the Eley-Rideal formation of H(2) on graphene using a new multidimensional graphene-H-H potential: role of the substrate.

The Brenner potential is adapted to handle chemical interactions and reactions of H atoms at a graphene surface. The adapted potential reproduces several important features of DFT computed data and reveals an extended puckering of the surface upon its adsorption of an H atom. This potential is used to investigate in a much more realistic way than has been done before, the Eley-Rideal abstraction reaction producing H(2) in H + H-graphene collisions at energies E(col)< or = 0.2 eV. The graphene surface is represented by a slab of 200 carbon atoms and the study is carried out using classical molecular dynamics for vertical incidences in a cylinder centered about the chemisorption axis. A highlight of the present study is that upon the arrival of the gas phase H atom, the adsorbent C atom is attracted and pulls out its surrounding surface atoms. The hillock thus formed remains puckered until the newly formed molecule is released. The range of impact parameters leading to reaction depends on the collision energy and is governed by the shape of the entrance channel potential; the reaction probability in this range is 100%. On average, in the studied E(col) range, the available energy (3.92 eV + E(col)) is shared as: 69-52% for the internal energy, 11-23% for the translation energy and 20-25% for the energy imparted to the surface. Also, the average vibration and rotation energy levels of the nascent H(2) molecule are, respectively, v = 5-4 and j = 2-4.

Planar study of H2O+Cl<-->HO+HCl reactions.

The first four dimensional (4D) quantum scattering calculations on the tetra-atomic H2O+Cl<-->HO+HCl reactions are reported. With respect to a full (6D) treatment, only the planar constraint and a fixed length for the HO spectator bond are imposed. This work explicitly accounts for the bending and local HO stretching vibrations in H2O, for the vibration of HCl and for the in-plane rotation of the H2O, HO and HCl molecules. The calculations are performed with the potential energy surface of Clary et al. and use a Born-Oppenheimer type separation between the motions of the light and the heavy nuclei. State-to-state cross sections are reported for a collision energy range 0-1.8 eV measured with respect to H2O+Cl. For the H2O+Cl reaction, present results agree with previous (3D) non planar calculations and confirm that excitation of the H2O stretching promotes more reactivity than excitation of the bending. New results are related to the rotation of the H2O molecule: the cross sections are maximal for planar rotational states corresponding to 10

HIV-1 Vpr-chloramphenicol acetyltransferase fusion proteins: sequence requirement for virion incorporation and analysis of antiviral effect.

The human immunodeficiency virus type 1 Vpr is a virion-associated protein that is incorporated in trans into viral particles, presumably via an interaction with the p6 domain of the Gag polyprotein precursor. Recently, several studies demonstrated that Vpr fusion proteins could be used as intravirion inactivating agents. In this study, we compared different Vpr-chloramphenicol acetyltransferase (CAT) fusion proteins for their virion incorporation ability and their effect on the infectivity of HIV viruses. Our deletion analysis indicates that both the N-terminal alpha-helical domain and the leucine/isoleucine-rich (LR) domain located in the middle region of Vpr are required for optimal virion incorporation of Vpr-CAT fusion proteins. The C-terminal basic region, associated with Vpr's ability to mediate cell cycle arrest in G2, was not required for virion incorporation, thus allowing the development of Vpr-based chimeric proteins devoid of any effect on cell growth. The fusion of Vpr at the N- or C-terminus of CAT targeted with equal efficiency the chimeric protein into virions. While the virion incorporation of most Vpr-CAT fusion proteins tested in this study was dependent on the presence of an intact p6 domain, fusion proteins containing only the N-terminal alpha-helical domain of Vpr (amino acid 1 to 42) were incorporated into virions in a p6-independent manner. Virion incorporation of Vpr-CAT fusion proteins was shown to decrease viral infectivity. Moreover, the insertion of HIV protease-cleavage sites between Vpr and CAT not only efficiently delivered and released the cleaved CAT product into HIV viral particles, but also greatly potentiated the inhibition of progeny virion infectivity. Overall, our study: (1) defines the Vpr sequence requirement and configuration necessary for the specific and optimal incorporation of Vpr fusion protein into HIV particles; (2) shows that Vpr fusion proteins have the ability to suppress HIV infectivity by targeting multiple steps of viral morphogenesis.

Incorporation of Vpr into human immunodeficiency virus type 1 requires a direct interaction with the p6 domain of the p55 gag precursor.

The 96-amino acid Vpr protein is the major virion-associated accessory protein of the human immunodeficiency virus type 1 (HIV-1). As Vpr is not part of the p55 Gag polyprotein precursor (Pr55(gag)), its incorporation requires an anchor to associate with the assembling viral particles. Although the molecular mechanism is presently unclear, the C-terminal region of the Pr55(gag) corresponding to the p6 domain appears to constitute such an anchor essential for the incorporation of the Vpr protein. In order to clarify the mechanism by which the Vpr accessory protein is trans-incorporated into progeny virion particles, we tested whether HIV-1 Vpr interacted with the Pr55(gag) using the yeast two-hybrid system and the maltose-binding protein pull-down assay. The present study provides genetic and biochemical evidence indicating that the Pr55(gag) can physically interact with the Vpr protein. Furthermore, point mutations affecting the integrity of the conserved L-X-S-L-F-G motif of p6(gag) completely abolish the interaction between Vpr and the Pr55(gag) and, as a consequence, prevent Vpr virion incorporation. In contrast to other studies, mutations affecting the integrity of the NCp7 zinc fingers impaired neither Vpr virion incorporation nor the binding between Vpr and the Pr55(gag). Conversely, amino acid substitutions in Vpr demonstrate that an intact N-terminal alpha-helical structure is essential for the Vpr-Pr55(gag) interaction. Vpr and the Pr55(gag) demonstrate a strong interaction in vitro as salt concentrations as high as 900 mM could not disrupt the interaction. Finally, the interaction is efficiently competed using anti-Vpr sera. Together, these results strongly suggest that Vpr trans-incorporation into HIV-1 particles requires a direct interaction between its N-terminal region and the C-terminal region of p6(gag). The development of Pr55(gag)-Vpr interaction assays may allow the screening of molecules that can prevent the incorporation of the Vpr accessory protein into HIV-1 virions, and thus inhibit its early functions.

Human immunodeficiency virus type 1 (HIV-1) Vpr functions as an immediate-early protein during HIV-1 infection.

Human immunodeficiency virus type 1 (HIV-1) Vpr is a virion-associated protein which facilitates HIV-1 infection of nondividing cells by contributing to the nuclear transport of the preintegration complex (PIC). Vpr was also shown to induce a cell cycle G2 arrest in infected proliferating cells that optimizes HIV-1 long terminal repeat (LTR)-directed gene expression and viral production. However, it is unclear whether this activity is mediated primarily early by virion-associated Vpr or alternatively late during infection when Vpr is de novo expressed. We report here that in the absence of de novo expression, virion-associated Vpr induces a transient G2 arrest that can subsequently lead to cell killing by apoptosis. Interestingly, the induction of both cell cycle G2 arrest and apoptosis by virion-associated Vpr requires viral entry but not viral replication, since reverse transcriptase and protease inhibitor treatments do not prevent these Vpr effects. These results raise the possibility that in vivo both infectious and noninfectious viruses contribute to the dysfunction and killing of CD4(+) cells. In addition, our results reveal that virion-associated Vpr stimulates viral replication in proliferating cells after establishing a cell cycle G2 arrest by increasing LTR-directed gene expression. Importantly, this Vpr-mediated LTR activation appears to be a requirement for subsequent optimal Tat transactivation. Taken together, these results strongly suggest that in addition to participating in the HIV PIC nuclear transport in nondividing cells, virion-associated Vpr activates HIV-1 LTR-directed gene expression by manipulating the host cell cycle. From this, we conclude that Vpr functions as an immediate-early protein during HIV-1 infection.

Mutagenic analysis of human immunodeficiency virus type 1 Vpr: role of a predicted N-terminal alpha-helical structure in Vpr nuclear localization and virion incorporation.

The Vpr gene product of human immunodeficiency virus type 1 is a virion-associated protein that is important for efficient viral replication in nondividing cells such as macrophages. At the cellular level, Vpr is primarily localized in the nucleus when expressed in the absence of other viral proteins. Incorporation of Vpr into viral particles requires a determinant within the p6 domain of the Gag precursor polyprotein Pr55gag. In the present study, we have used site-directed mutagenesis to identify a domain(s) of Vpr involved in virion incorporation and nuclear localization. Truncations of the carboxyl (C)-terminal domain, rich in basic residues, resulted in a less stable Vpr protein and in the impairment of both virion incorporation and nuclear localization. However, introduction of individual substitution mutations in this region did not impair Vpr nuclear localization and virion incorporation, suggesting that this region is necessary for the stability and/or optimal protein conformation relevant to these Vpr functions. In contrast, the substitution mutations within the amino (N)-terminal region of Vpr that is predicted to adopt an alpha-helical structure (extending from amino acids 16 to 34) impaired both virion incorporation and nuclear localization, suggesting that this structure may play a pivotal role in modulating both of these biological properties. These results are in agreement with a recent study showing that the introduction of proline residues in this predicted alpha-helical region abolished Vpr virion incorporation, presumably by disrupting this secondary structure (S. Mahalingam, S. A. Khan, R. Murali, M. A. Jabbar, C. E. Monken, R. G. Collman, and A. Srinivasan, Proc. Natl. Acad. Sci. USA 92:3794-3798, 1995). Interestingly, our results show that two Vpr mutants harboring single amino acid substitutions (L to F at position 23 [L23F] and A30F) on the hydrophobic face of the predicted helix coded for relatively stable proteins that retained their ability to translocate to the nucleus but exhibited dramatic reduction in Vpr incorporation, suggesting that this hydrophobic face might mediate protein-protein interactions required for Vpr virion incorporation but not nuclear localization. Furthermore, a single mutation (E25K) located on the hydrophilic face of this predicted alpha-helical structure affected not only virion incorporation but also nuclear localization of Vpr. The differential impairment of Vpr nuclear localization and virion incorporation by mutations in the predicted N-terminal alpha-helical region suggests that this region of Vpr plays a role in both of these biological functions of Vpr.

Vpr stimulates viral expression and induces cell killing in human immunodeficiency virus type 1-infected dividing Jurkat T cells.

In this study we investigated the effects of Vpr during human immunodeficiency virus (HIV) infection of proliferating Jurkat T cells by using a vesicular stomatitis virus envelope G glycoprotein pseudotyped HIV superinfection system. We observe that the expression of Vpr results in a severe reduction in the life span of HIV type 1 (HIV-1)-infected dividing T cells in culture. In agreement with a recent report (S. A. Stewart, B. Poon, J. B. M. Jowett, and I. S. Chen, J. Virol. 71:5579-5592, 1997), we show that events characteristic of apoptotic cell death are involved in the Vpr-mediated cytopathic effects. Our results also show that infection with viruses expressing the wild-type vpr gene results in an increase in viral gene expression and production. Interestingly, the effects of Vpr on cell viability and on viral gene expression both correlate with the ability of the protein to induce a cell cycle arrest in the G2/M phase. Mutagenesis analyses show that the C terminus of Vpr is essential for these biological activities. Although the role of Vpr is currently associated with the infection of nondividing cells, our results suggest that Vpr can also directly increase viral replication in vivo in infected dividing T cells. Furthermore, these in vitro observations suggest that Vpr-mediated cytotoxic effects could contribute to the CD4+ depletion associated with AIDS progression.

The putative alpha helix 2 of human immunodeficiency virus type 1 Vpr contains a determinant which is responsible for the nuclear translocation of proviral DNA in growth-arrested cells.

Several viral determinants were shown to play a role in the ability of human immunodeficiency virus type 1 (HIV-1) to infect nondividing cells. In particular, Vpr and Gag matrix (MA) were recognized to be involved in the nuclear transport of the viral preintegration complex. The goal of the present study was to evaluate the ability of isogenic HIV-1 viruses harboring different vpr and gag genes to infect nondividing cells. Surprisingly, our results reveal that the introduction of mutations in the MA nuclear localization signal marginally affected the ability of proviruses to establish infection in growth-arrested HeLa or MT4 cells. In contrast, we show that in our experimental system, the absence of Vpr expression leads to a reduction in viral infectivity and production which correlates with a decrease in the synthesis and nuclear transport of proviral DNA as determined by PCR analysis. Moreover, our data demonstrate that this reduction of viral replication is also observed with proviruses containing different mutated Vpr alleles. In particular, the Vpr Q65E mutant, which contains a substitution in the second predicted amphipathic alpha-helical structure located in the central region of the protein, is associated with an impairment of the protein nuclear localization and a concomitant reduction of the nuclear transport of proviral DNA. The results of this study provide evidence that a putative amphipathic alpha-helical structure in the central region of Vpr contains a determinant involved in the nuclear translocation of the preintegration complex in nondividing cells.