bluuebunny/crossref_metadata_2025 huggingface dataset:
Epstein-Barr Virus Nuclear Antigen 3C Regulates Cyclin A/p27 Complexes and Enhances Cyclin A-Dependent Kinase Activity
Authors: Knight Jason S. , Robertson Erle S.
Published: January 2004

Epstein-Barr virus (EBV) nuclear antigen 3C (EBNA3C) is essential for primary B-cell transformation. In this report we show that cyclin A, an activator of S phase progression, bound tightly to EBNA3C. EBNA3C interacted with cyclin A in vitro and associated with cyclin A complexes in EBV-transformed lymphoblastoid cell lines. Importantly, EBNA3C stimulated cyclin A-dependent kinase activity and rescued p27-mediated inhibition of cyclin A/Cdk2 kinase activity by decreasing the molecular association between cyclin A and p27 in cells. Additionally, phosphorylation of the retinoblastoma protein, a major regulator of cell cycle progression, was enhanced both in vitro and in vivo in the presence of EBNA3C. Cyclin A interacted with a region of the carboxy terminus of EBNA3C, shown to be important both for stimulation of cyclin A-dependent kinase activity and for cell cycle progression. This provides the first evidence of an essential EBV latent antigen's directly targeting a cell cycle regulatory protein and suggests a novel mechanism by which EBV deregulates the mammalian cell cycle, which is of critical importance in B-cell transformation.
Members of a Novel Family of Mammalian Protein Kinases Complement the DNA-Negative Phenotype of a Vaccinia Virus
ts
Mutant Defective in the B1 Kinase
Authors: Boyle Kathleen A. , Traktman Paula
Published: January 2004

Temperature-sensitive (
ts
) mutants of vaccinia virus defective in the B1 kinase demonstrate a conditionally lethal defect in DNA synthesis. B1 is the prototypic member of a new family of protein kinases (vaccinia virus-related kinases, or VRK) that possess distinctive B1-like sequence features within their catalytic motifs (R. J. Nichols and P. Traktman, J. Biol. Chem., in press). Given the striking sequence similarity between B1 and the VRK enzymes, we proposed that they might share overlapping substrate specificity. We therefore sought to determine whether the human and mouse VRK1 enzymes (hVRK1 and mVRK1, respectively) could complement a B1 deficiency in vivo. Recombinant
ts2
viruses expressing hVRK1, mVRK1, or wild-type B1 were able to synthesize viral DNA at high temperature, but those expressing the more distantly related human casein kinase 1α2 could not. Complementation required the enzymatic activity of hVRK1, since a catalytically inactive allele of hVRK1 was unable to confer a temperature-insensitive phenotype. Interestingly, rescue of viral DNA synthesis was not coupled to the ability to phosphorylate H5, the only virus-encoded protein shown to be a B1 substrate in vivo. Expression of hVRK1 during nonpermissive
ts2
infections restored virus production and plaque formation, whereas expression of mVRK1 resulted in an intermediate level of rescue. Taken together, these observations indicate that enzymatically active cellular VRK1 kinases can perform the function(s) of B1 required for genome replication, most likely due to overlapping specificity for cellular and/or viral substrates.
Lv2, a Novel Postentry Restriction, Is Mediated by both Capsid and Envelope
Authors: Schmitz Christian , Marchant David , Neil Stuart J. D. , Aubin Keith , Reuter Sandra , Dittmar Matthias T. , McKnight Áine
Published: January 2004

The characterization of restrictions to lentivirus replication in cells identifies critical steps in the viral life cycle and potential therapeutic targets. We previously reported that a human immunodeficiency virus type 2 (HIV-2) isolate was restricted to infection in some human cells, which led us to identify a step in the life cycle of HIV-2 detected after reverse transcription but prior to nuclear entry. The block is bypassed with a vesicular stomatitis virus glycoprotein G (VSV-G) envelope (A. McKnight et al., J. Virol.
75:
6914-6922, 2001). We hypothesized that, although the restriction is apparent at a post-reverse transcription step, the lack of progress results from a failure of the virus to reach a cellular compartment with access to the nucleus. Here we analyzed molecular clones of the restricted virus, MCR, and an unrestricted virus, MCN. Using sequence analysis and gene swapping, we mapped the viral determinants to
gag
and
env
. Site-directed mutagenesis identified a single amino acid at position 207 in CA to be responsible for the
gag
restriction. Pseudotype experiments indicate that this step is also important for the infection of cells by HIV-1. The HIV-1 NL4.3 core is restricted if supplied with a restricted MCR envelope but not with VSV-G. Also the NL4.3 envelope rescues the restricted core of HIV-2 MCR. Abrogation experiments with MLV demonstrate that the restriction is distinct from Fv1/Ref1/Lv1. We propose that this represents a new lentiviral restriction, Lv2. Thus, the envelope and capsid of HIV act to ensure that the virus is delivered into an appropriate cellular compartment that allows postentry events in viral replication to proceed efficiently.
Generation of Recombinant Human Parainfluenza Virus Type 1 Vaccine Candidates by Importation of Temperature-Sensitive and Attenuating Mutations from Heterologous Paramyxoviruses
Authors: Newman Jason T. , Riggs Jeffrey M. , Surman Sonja R. , McAuliffe Josephine M. , Mulaikal Teresa A. , Collins Peter L. , Murphy Brian R. , Skiadopoulos Mario H.
Published: January 2004

Human parainfluenza virus type 1 (HPIV1) is a significant cause of respiratory tract disease in infants and young children for which a vaccine is needed. In the present study, we sought to attenuate HPIV1 by the importation of one or more known attenuating point mutations from heterologous paramyxoviruses into homologous sites in HPIV1. The introduced mutations were derived from three attenuated paramyxoviruses: (i) HPIV3
cp
45, a live-attenuated HPIV3 vaccine candidate containing multiple attenuating mutations; (ii) the respiratory syncytial virus
cpts
530 with an attenuating mutation in the L polymerase protein; and (iii) a murine PIV1 (MPIV1) attenuated by a mutation in the accessory C protein. Recombinant HPIV1 (rHPIV1) mutants bearing a single imported mutation in C, any of three different mutations in L, or a pair of mutations in F exhibited a 100-fold or greater reduction in replication in the upper or lower respiratory tract of hamsters. Both temperature-sensitive (
ts
) (mutations in the L and F proteins) and non-
ts
(the mutation in the C protein) attenuating mutations were identified. rHPIV1 mutants containing a combination of mutations in L were generated that were more attenuated than viruses bearing the individual mutations, showing that the systematic accretion of mutations can yield progressive increases in attenuation. Hamsters immunized with rHPIV1 mutants bearing one or two mutations developed neutralizing antibodies and were resistant to challenge with wild-type HPIV1. Thus, importation of attenuating mutations from heterologous viruses is an effective means for rapidly identifying mutations that attenuate HPIV1 and for generating live-attenuated HPIV1 vaccine candidates.
Codon Substitution Mutations at Two Positions in the L Polymerase Protein of Human Parainfluenza Virus Type 1 Yield Viruses with a Spectrum of Attenuation In Vivo and Increased Phenotypic Stability In Vitro
Authors: McAuliffe Josephine M. , Surman Sonja R. , Newman Jason T. , Riggs Jeffrey M. , Collins Peter L. , Murphy Brian R. , Skiadopoulos Mario H.
Published: January 2004

The Y942H and L992F temperature-sensitive (
ts
) and attenuating amino acid substitution mutations, previously identified in the L polymerase of the HPIV3
cp
45 vaccine candidate, were introduced into homologous positions of the L polymerase of recombinant human parainfluenza virus type 1 (rHPIV1). In rHPIV1, the Y942H mutation specified the
ts
phenotype in vitro and the attenuation (
att
) phenotype in hamsters, whereas the L992F mutation specified neither phenotype. Each of these codon mutations was generated by a single nucleotide substitution and therefore had the potential to readily revert to a codon specifying the wild-type amino acid residue. We introduced alternative amino acid assignments at codon 942 or 992 as a strategy to increase genetic stability and to generate mutants that exhibit a range of attenuation. Twenty-three recombinants with codon substitutions at position 942 or 992 of the L protein were viable. One highly
ts
and
att
mutant, the Y942A virus, which had a difference of three nucleotides from the codon encoding a wild-type tyrosine, also possessed a high level of genetic and phenotypic stability upon serial passage in vitro at restrictive temperatures compared to that of the parent Y942H virus, which possessed a single nucleotide substitution. We obtained mutants with substitutions at position 992 that, in contrast to the L992F virus, possessed the
ts
and
att
phenotypes. These findings identify the use of alternative codon substitution mutations as a method that can be used to generate candidate vaccine viruses with increased genetic stability and/or a modified level of attenuation.
Protection of
Penaeus monodon
against White Spot Syndrome Virus by Oral Vaccination
Authors: Witteveldt Jeroen , Cifuentes Carolina C. , Vlak Just M. , van Hulten Mariëlle C. W.
Published: January 2004

White spot syndrome virus (WSSV) occurs worldwide and causes high mortality and considerable economic damage to the shrimp farming industry. No adequate treatments against this virus are available. It is generally accepted that invertebrates such as shrimp do not have an adaptive immune response system such as that present in vertebrates. As it has been demonstrated that shrimp surviving a WSSV infection have higher survival rates upon subsequent rechallenge, we investigated the potential of oral vaccination of shrimp with subunit vaccines consisting of WSSV virion envelope proteins.
Penaeus monodon
shrimp were fed food pellets coated with inactivated bacteria overexpressing two WSSV envelope proteins, VP19 and VP28. Vaccination with VP28 showed a significant lower cumulative mortality compared to vaccination with bacteria expressing the empty vectors after challenge via immersion (relative survival, 61%), while vaccination with VP19 provided no protection. To determine the onset and duration of protection, challenges were subsequently performed 3, 7, and 21 days after vaccination. A significantly higher survival was observed both 3 and 7 days postvaccination (relative survival, 64% and 77%, respectively), but the protection was reduced 21 days after the vaccination (relative survival, 29%). This suggests that contrary to current assumptions that invertebrates do not have a true adaptive immune system, a specific immune response and protection can be induced in
P. monodon
. These experiments open up new ways to benefit the WSSV-hampered shrimp farming industry.
Development of a GB Virus B Marmoset Model and Its Validation with a Novel Series of Hepatitis C Virus NS3 Protease Inhibitors
Authors: Bright Helen , Carroll Anthony R. , Watts Paul A. , Fenton Robert J.
Published: January 2004

GB virus B (GBV-B), a flavivirus closely related to HCV, has previously been shown to infect and replicate to high titers in tamarins (
Saguinus
sp.). This study describes the use of GBV-B infection and replication in the common marmoset (
Callithrix jacchus
) for the successful development and validation of a surrogate animal model for hepatitis C virus (HCV). Infection of marmosets with GBV-B produced a viremia that peaked at 10
8
to 10
9
genome copies/ml for a period of 40 to 60 days followed by viral clearance at 60 to 80 days postinfection. Passage of the initial tamarin-derived GBV-B in marmosets produced an infectious stock that gave a more reproducible and consistent infection in the marmoset. Titration of the virus stocks in vivo indicated that they contained 1 infectious unit for every 1,000 genome copies. Cultures of primary marmoset hepatocytes were also successfully infected with GBV-B, with high levels of virus detected in supernatants and cells for up to 14 days postinfection. Treatment of GBV-B-infected hepatocyte cultures with a novel class of HCV protease inhibitor (pyrrolidine 5,5
trans
-lactams) reduced viral levels by more than 2 logs. Treatment of GBV-B-infected marmosets with one such inhibitor resulted in a 3-log drop in serum viral titer over 4 days of therapy. These studies provide the first demonstration of the in vivo efficacy of a small-molecule inhibitor for HCV in an animal model and illustrate the utility of GBV-B as a surrogate animal model system for HCV.
Influence of Primate Lentiviral Vif and Proteasome Inhibitors on Human Immunodeficiency Virus Type 1 Virion Packaging of APOBEC3G
Authors: Liu Bindong , Yu Xianghui , Luo Kun , Yu Yunkai , Yu Xiao-Fang
Published: January 2004

The Vif protein of human immunodeficiency virus type 1 (HIV-1) is essential for viral evasion of the host antiviral protein APOBEC3G, also known as CEM15. Vif mutant but not wild-type HIV-1 viruses produced in the presence of APOBEC3G have been shown to undergo hypermutations in newly synthesized viral DNA upon infection of target cells, presumably resulting from C-to-U modification during minus-strand viral DNA synthesis. We now report that HIV-1 Vif could induce rapid degradation of human APOBEC3G that was blocked by the proteasome inhibitor MG132. The efficiency of Vif-induced downregulation of APOBEC3G expression depended on the level of Vif expression. A single amino acid substitution in the conserved SLQXLA motif reduced Vif function. Vif proteins from distantly related primate lentiviruses such as SIVagm were unable to suppress the antiviral activity of human APOBEC3G or the packaging of APOBEC3G into HIV-1 Vif mutant virions, due to a lack of interaction with human APOBEC3G. In the presence of the proteasome inhibitor MG132, virion-associated Vif increased dramatically. However, increased virion packaging of Vif did not prevent virion packaging of APOBEC3G when proteasome function was impaired, and the infectivity of these virions was significantly reduced. These results suggest that Vif function is required during virus assembly to remove APOBEC3G from packaging into released virions. Once packaged, virion-associated Vif could not efficiently block the antiviral activity of APOBEC3G.
The Human Immunodeficiency Virus Type 1 Ribosomal Frameshifting Site Is an Invariant Sequence Determinant and an Important Target for Antiviral Therapy
Authors: Biswas Preetha , Jiang Xi , Pacchia Annmarie L. , Dougherty Joseph P. , Peltz Stuart W.
Published: January 2004

Human immunodeficiency virus type 1 (HIV-1) utilizes a distinctive form of gene regulation as part of its life cycle, termed programmed −1 ribosomal frameshifting, to produce the required ratio of the Gag and Gag-Pol polyproteins. We carried out a sequence comparison of 1,000 HIV-1 sequences at the slippery site (UUUUUUA) and found that the site is invariant, which is somewhat surprising for a virus known for its variability. This prompted us to prepare a series of mutations to examine their effect upon frameshifting and viral infectivity. Among the series of mutations were changes of the HIV-1 slippery site to those effectively utilized by other viruses, because such mutations would be anticipated to have a relatively mild effect upon frameshifting. The results demonstrate that any change to the slippery site reduced frameshifting levels and also dramatically inhibited infectivity. Because ribosomal frameshifting is essential for HIV-1 replication and it is surprisingly resistant to mutation, modulation of HIV-1 frameshifting efficiency potentially represents an important target for the development of novel antiviral therapeutics.
Mutant PrP
Sc
Conformers Induced by a Synthetic Peptide and Several Prion Strains
Authors: Tremblay Patrick , Ball Haydn L. , Kaneko Kiyotoshi , Groth Darlene , Hegde Ramanujan S. , Cohen Fred E. , DeArmond Stephen J. , Prusiner Stanley B. , Safar Jiri G.
Published: January 2004

Gerstmann-Sträussler-Scheinker (GSS) disease is a dominantly inherited, human prion disease caused by a mutation in the prion protein (PrP) gene. One mutation causing GSS is P102L, denoted P101L in mouse PrP (MoPrP). In a line of transgenic mice denoted Tg2866, the P101L mutation in MoPrP produced neurodegeneration when expressed at high levels. MoPrP
Sc
(P101L) was detected both by the conformation-dependent immunoassay and after protease digestion at 4°C. Transmission of prions from the brains of Tg2866 mice to those of Tg196 mice expressing low levels of MoPrP(P101L) was accompanied by accumulation of protease-resistant MoPrP
Sc
(P101L) that had previously escaped detection due to its low concentration. This conformer exhibited characteristics similar to those found in brain tissue from GSS patients. Earlier, we demonstrated that a synthetic peptide harboring the P101L mutation and folded into a β-rich conformation initiates GSS in Tg196 mice (29). Here we report that this peptide-induced disease can be serially passaged in Tg196 mice and that the PrP conformers accompanying disease progression are conformationally indistinguishable from MoPrP
Sc
(P101L) found in Tg2866 mice developing spontaneous prion disease. In contrast to GSS prions, the 301V, RML, and 139A prion strains produced large amounts of protease-resistant PrP
Sc
in the brains of Tg196 mice. Our results argue that MoPrP
Sc
(P101L) may exist in at least several different conformations, each of which is biologically active. Such conformations occurred spontaneously in Tg2866 mice expressing high levels of MoPrP
C
(P101L) as well as in Tg196 mice expressing low levels of MoPrP
C
(P101L) that were inoculated with brain extracts from ill Tg2866 mice, with a synthetic peptide with the P101L mutation and folded into a β-rich structure, or with prions recovered from sheep with scrapie or cattle with bovine spongiform encephalopathy.
Analysis of Chromatin Attachment and Partitioning Functions of Bovine Papillomavirus Type 1 E2 Protein
Authors: Abroi Aare , Ilves Ivar , Kivi Sirje , Ustav Mart
Published: January 2004

Recent studies have suggested that the tethering of viral genomes to host cell chromosomes could provide one of the ways to achieve their nuclear retention and partitioning during extrachromosomal maintenance in dividing cells. The data we present here provide firm evidence that the partitioning of the bovine papillomavirus type 1 (BPV1) genome is dependent on the chromatin attachment process mediated by viral E2 protein and its multiple binding sites. On the other hand, the attachment of E2 and the E2-mediated tethering of reporter plasmids to host chromosomes are not necessarily sufficient for efficient partitioning, suggesting that additional E2-dependent activities might be involved in the latter process. The activity of E2 protein in chromatin attachment and partitioning is more sensitive to the point mutations in the N-terminal domain than its transactivation and replication initiation functions. Therefore, at least part of the interactions of the E2 N-terminal domain with its targets during the chromatin attachment and partitioning processes are likely to involve specific receptors not involved in transactivation and replication activities of the protein. The mutational analysis also indicates that the binding of E2 to chromatin is not achieved through interaction of linear N-terminal subsequences of the E2 protein with putative receptors. Instead, the composite surface elements of the N-terminal domain build up the receptor-binding surface of E2. In this regard, the interaction of BPV1 E2 with its chromosomal targets clearly differs from the interactions of LANA1 protein from Kaposi's sarcoma-associated human herpesvirus and EBNA1 from Epstein-Barr virus with their specific receptors.
Evolutionary Potential of an RNA Virus
Authors: Makeyev Eugene V. , Bamford Dennis H.
Published: January 2004

RNA viruses are remarkably adaptable to changing environments. This is medically important because it enables pathogenic viruses to escape the immune response and chemotherapy and is of considerable theoretical interest since it allows the investigation of evolutionary processes within convenient time scales. A number of earlier studies have addressed the dynamics of adapting RNA virus populations. However, it has been difficult to monitor the trajectory of molecular changes in RNA genomes in response to selective pressures. To address the problem, we developed a novel in vitro evolution system based on a recombinant double-stranded RNA bacteriophage, φ6, containing a β-lactamase (
bla
) gene marker. Carrier-state bacterial cells are resistant to ampicillin, and after several passages, they become resistant to high concentrations of another β-lactam antibiotic, cefotaxime, due to mutations in the virus-borne
bla
gene. We monitored the changes in
bla
cDNAs induced by cefotaxime selection and observed an initial explosion in sequence variants with multiple mutations throughout the gene. After four passages, a stable, homogeneous population of
bla
sequences containing three specific nonsynonymous mutations was established. Of these, two mutations (E104K and G238S) have been previously reported for β-lactamases from cefotaxime-resistant bacterial isolates. These results extend our understanding of the molecular mechanisms of viral adaptation and also demonstrate the possibility of using an RNA virus as a vehicle for directed evolution of heterologous proteins.
Induction of Simian AIDS in Infant Rhesus Macaques Infected with CCR5- or CXCR4-Utilizing Simian-Human Immunodeficiency Viruses Is Associated with Distinct Lesions of the Thymus
Authors: Reyes R. A. , Canfield Don R. , Esser Ursula , Adamson Lourdes A. , Brown Charles R. , Cheng-Mayer Cecilia , Gardner Murray B. , Harouse Janet M. , Luciw Paul A.
Published: January 2004

Newborn rhesus macaques were infected with two chimeric simian-human immunodeficiency virus (SHIV) strains which contain unique human immunodeficiency virus type 1 (HIV-1)envgenes and exhibit distinct phenotypes. Infection with either the CCR5-specific SHIVSF162P3or the CXCR4-utilizing SHIVSF33Aresulted in clinical manifestations consistent with simian AIDS. Most prominent in this study was the detection of severe thymic involution in all SHIVSF33A-infected infants, which is very similar to HIV-1-induced thymic dysfunction in children who exhibit a rapid pattern of disease progression. In contrast, SHIVSF162P3induced only a minor disruption in thymic morphology. Consistent with the distribution of the coreceptors CXCR4 and CCR5 within the thymus, the expression of SHIVSF162P3was restricted to the thymic medulla, whereas SHIVSF33Awas preferentially detected in the cortex. This dichotomy of tissue tropism is similar to the differential tropism of HIV-1 isolates observed in the reconstituted human thymus in SCID-hu mice. Accordingly, our results show that the SHIV-monkey model can be used for the molecular dissection of cell and tissue tropisms controlled by the HIV-1envgene and for the analysis of mechanisms of viral immunopathogenesis in AIDS. Furthermore, these findings could help explain the rapid progression of disease observed in some HIV-1-infected children.
Distribution of Hydrophobic Residues Is Crucial for the Fusogenic Properties of the Ebola Virus GP2 Fusion Peptide
Authors: Adam B. , Lins L. , Stroobant V. , Thomas A. , Brasseur R.
Published: January 2004

The lipid-destabilizing properties of the N-terminal domain of the GP2 of Ebola virus were investigated. Our results suggest that the domain of Ebola virus needed for fusion is shorter than that previously reported. The fusogenic properties of this domain are related to its oblique orientation at the lipid/water interface owing to an asymmetric distribution of the hydrophobic residues when helical.
Antiviral Activity of Distamycin A against Vaccinia Virus Is the Result of Inhibition of Postreplicative mRNA Synthesis
Authors: Broyles Steven S. , Kremer Marcia , Knutson Bruce A.
Published: January 2004

Distamycin A has been described as an inhibitor of the cellular pathogenesis of vaccinia virus in culture. Distamycin is an antibiotic that specifically targets the minor groove of DNA. We show here that distamycin is a potent inhibitor of vaccinia virus replication. Pulse-labeling experiments showed that most major late proteins failed to accumulate in the presence of the antibiotic. We characterized the effect of distamycin on vaccinia virus nucleic acid biosynthesis with the goal of determining the inhibitor's target. Early gene transcription was unaffected. DNA synthesis proceeded at normal rates, but DNA accumulated in large masses in the cytoplasm with no evidence of virion assembly. Transcription from the intermediate class promoter for the I1L gene was partially reduced by distamycin; however, transcription from the intermediate promoters for the three late transcription factor genes was severely inhibited. The accumulation of the late transcripts for the viral F17R and A10L genes also was severely impaired and was shown to be a direct inhibition of late promoter activity. These results indicate that inhibition of postreplicative intermediate and late transcription is the basis for inhibition of vaccinia virus by distamycin and indicate that DNA minor-groove ligands hold promise for effective anti-poxvirus drugs.
The Viral E4 Protein Is Required for the Completion of the Cottontail Rabbit Papillomavirus Productive Cycle In Vivo
Authors: Peh Woei L. , Brandsma Janet L. , Christensen Neil D. , Cladel Nancy M. , Wu Xing , Doorbar John
Published: January 2004

Expression of the papillomavirus E4 protein correlates with the onset of viral DNA amplification. Using a mutant cottontail rabbit papillomavirus (CRPV) genome incapable of expressing the viral E4 protein, we have shown that E4 is required for the productive stage of the CRPV life cycle in New Zealand White and cottontail rabbits. In these lesions, E4 was not required for papilloma development, but the onset of viral DNA amplification and L1 expression were abolished. Viral genome amplification was partially restored when mutant genomes able to express longer forms of E4 were used. These findings suggest that efficient amplification of the CRPV genome is dependent on the expression of a full-length CRPV E4 protein.
Phylogenetic Analyses of Texas Isolates Indicate an Evolving Subtype of the Clade B Feline Immunodeficiency Viruses
Authors: Weaver Eric A. , Collisson Ellen W. , Slater Margaret , Zhu Guan
Published: January 2004

Rigorous phylogenetic analyses were used to compare the nucleotide sequences of feline immunodeficiency virus strains isolated from Texas and throughout the world. The envelope V3-V4 sequences and capsid gene of the Texas isolates formed a cluster between subtypes B and E. Statistical comparisons with other published sequences confirmed that the Texas group is a unique cluster, possibly a new subtype, arising from subtype B.
On the Structure and Physical Origin of the Weak Interaction Between H and CO
Authors: Lukeš Vladimír , Laurinc Viliam , Ilčin Michal , Biskupič Stanislav
Published: January 2004

The adiabatic potential energy surface of the H-CO complex in the van der Waals region, described by Jacobi coordinates (r = 1.128 Å, R, Θ), was investigated using the supermolecular coupled-clusters CCSD(T) method. Our calculations indicate a minimum for bent arrangements. It was found on the carbon side of CO molecule at R = 3.6 Å (Θ = 76°) with a well depth of De = -156.5 μEh. The saddle points are localised at linear conformations for R = 4.37 Å (Θ = 0°) and R = 3.91 Å (Θ = 180°). The physical origin of the studied interaction was analysed by the intermolecular perturbation theory based on the single-determinant unrestricted Hartree-Fock wave function. The separation of the interaction energies shows that the locations of the predicted stable bent structure is primarily determined by delicate balance between the repulsive Heitler-London and attractive dispersion and induction energy components.
Theoretical Study on the Mechanism of Reaction of Ground-State Fe Atoms with Carbon Dioxide
Authors: Pantazis Dimitrios A. , Tsipis Athanassios C. , Tsipis Constantinos A.
Published: January 2004

Density functional calculations at the B3LYP level of theory, using the 6-31G(d) and 6-311+G(3df) basis sets, provide a satisfactory description of the geometric and energetic reaction profile of the Fe + CO2 → FeO + CO reaction. The reaction is predicted to be endothermic by 23.24 kcal/mol at the B3LYP/6-311+G(3df)//B3LYP/6-31G(d) level of theory and to proceed by formation of either a Fe(η2-OCO) or a Fe(η3-OCO) intermediate. The Fe(η2-OCO) intermediate in the 5A' ground state is weakly bound with respect to Fe(5D) and CO2 dissociation products by 0.78 (2.88) kcal/mol at the B3LYP/6-31G(d) (B3LYP/6-311+ G(3df)//B3LYP/6-31G(d)) levels of theory. In contrast, the Fe(η3-OCO) intermediate in the 5A1 ground state is unbound with respect to Fe(5D) and CO2 dissociation products by 8.27 (11.15) kcal/mol at the same levels of theory. However, both intermediates are strongly bound relative to the separated Fe+(6D) and [CO2]- anion; the computed bond dissociation energies for the Fe(η2-OCO) and Fe(η3-OCO) intermediates are 207.33 and 198.28 kcal/mol in terms of ∆E0 at the B3LYP/6-31G(d), respectively. In the Fe(η2-OCO) and Fe(η3-OCO) intermediates, an intramolecular insertion reaction of the Fe atom to O-C bond takes place yielding the isomeric OFe(η1-CO) and OFe(η1-OC) products, respectively, with a relatively low activation barrier of 25.24 (21.69) and 26.36 (23.38) kcal/mol at the B3LYP/6-31G(d) (B3LYP/6-311+G(3df)//B3LYP/6-31G(d)) levels of theory, respectively. The calculated structures, relative stability and bonding properties of all stationary points are discussed with respect to computed electronic and spectroscopic properties, such as charge density distribution and harmonic vibrational frequencies.
Magnetic Linear Birefringence in Rare Earth Systems. II. Third-Order Approach
Authors: Smentek Lidia
Published: January 2004

The theory of linear magnetic birefringence of rare earth ions in crystals is extended here by the contributions that represent a direct perturbing influence of the crystal field potential surrounding the central ion. The basic assumptions of the theoretical model are the same as in the previous analysis of second-order terms. The third-order contributions introduced here break the free ionic system approximation, and they represent the impact due to configuration interaction. The effective operators include the perturbing influence of the excitations from the 4f shell to one-electron states of the same parity (as previously at the second order), and in addition, the excitations to states of opposite parity. All contributing terms are expressed by the effective operators that are defined within the perturbed function approach. The tensorial structure of these operators is discussed, and special attention is directed to newly defined radial integrals. The values of all radial integrals that are necessary for the third-order numerical analysis are presented in the case of all lanthanide ions.
Theoretical Study of the Substituent and Solvent Effects on the Molecular Structures, Absorption and Emission Spectra of Open-Form Spiropyrans
Authors: Sheng Yinghong , Leszczynski Jerzy
Published: January 2004

The effects of substituents and solvents on the molecular structures, excitation energies and emission energies of a series of donor-acceptor substituted spiropyrans were investigated using the density functional methods. Different donor-acceptor pairs lead to alternations of the molecular structures. A relationship between the strengths of donor-acceptor pairs and the structural parameter BLA (bond length alternation) was examined and discussed. The impact on geometrical parameters induced by the solvents is more significant than that caused by the substituents, as indicated by the larger BLA changes. The substituent and solvent effects on the UV absorption and emission spectra of open-form spiropyrans were studied by the TD-DFT method. The absorption maxima of open-form spiropyrans are expected to red shift, and the emission are expected to blue shift as the strengths of donor-acceptor pairs and the polarities of solvents increase. A simple model was adopted to mimic the substituent and solvent effects, in the framework of AM1, employing Sparkles to create an external electric field on the open-form spiropyran, in order to induce a systematical polarization of the molecular equilibrium geometry and the electronic configuration.
Molecular Structure and Bonding in Platinum-Picoline Anticancer Complex: Density Functional Study
Authors: Michalska Danuta , Wysokiński Rafał
Published: January 2004

Density functional study has been performed for a new anticancer agent, cis-[PtCl2(NH3)(2-picoline)] (1), AMD473, now clinically tested. The molecular structure, natural charges, orbital occupancies, vibrational frequencies and metal-ligand stretching force constants were calculated using the modified Perdew-Wang functional (mPW1PW) with the combined D95V(d,p) and LANL2DZ basis set. For comparison, analogous calculations were performed for: cis-[PtCl2(NH3)(3-picoline)] (2), cis-[PtCl2(NH3)(pyridine)] (3) and cisplatin. The interesting structural feature of 1 is almost perpendicular orientation of the 2-picoline ligand with respect to the molecular plane. In the remaining complexes, 2 and 3, the tilt of the pyridine ring is smaller. The position of the methyl group in 1 introduces steric hindrance to an axial approach of the Pt metal. The natural bond analysis (NBO) has provided detailed insight into the electronic donor-acceptor interactions within the platinum coordination sphere. The results clearly indicate that the Pt-N(py) bond is stronger than Pt-NH3 bond, and the Pt-Cl bond trans to 2-picoline is weaker than the cis Pt-Cl bond. Thus, both the trans effect of the 2-picoline ligand and a steric hindrance of Pt in 1 can be of key importance in the different mode of binding of this drug to DNA, in comparison with cisplatin.
The Infrared Spectrum of CN in Its Ground Electronic State
Authors: Horká Veronika , Civiš Svatopluk , Špirko Vladimír , Kawaguchi Kentarou
Published: January 2004

12C14N vibration-rotation bands for the sequences (1-0) through (9-8) were observed in the spectral region 1800-2200 cm-1 using a Bruker 120 HR Fourier transform spectrometer at an unapodized resolution of 0.027 cm-1. Of the 362 lines observed, the wavenumbers of 237 lines were least-squares fitted using the Dunham expansion coefficients with a root-mean-square deviation of 0.00093 cm-1. Together with most accurate data from the literature, the data were also fitted in the framework of the reduced potential curve (RPC) method. The global potential energy function resulting from this fit provides a fairly quantitative description of the experimental data, at least up to 30 000 cm-1. In addition to global fitting, the RPC approach was also used for fully quantitative fitting of the data pertaining to the lowest three vibrational states. The effective potential energy curves obtained in this way allow for very accurate predictions of highly excited rotational states.
Can We Avoid the Intruder-State Problems in the State-Universal Coupled-Cluster Approaches While Preserving Size Extensivity?
Authors: Paldus Josef , Li Xiangzhu
Published: January 2004

Following the analysis of principal bottlenecks in the extension of the single-reference (SR) coupled-cluster (CC) methodology to the multireference (MR) case, we review and discuss some recent developments that facilitate the use of general model spaces (GMSs) within the state universal (SU) or Hilbert space MR CC formalism. The use of a GMS improves our ability to avoid the intruder state problems. This feature is further enhanced by generalizing the idea of the externally corrected (ec) SR CC formalism to the MR situations. In this latter approach we employ the cluster analysis to extract the most important higher-than-pair cluster amplitudes from a suitable set of known wave functions. Similarly to the SR case, the most convenient external source is represented by wave functions that are obtained via a modest size MR configuration interaction (CI), which employs an N-dimensional reference space. The resulting higher-than-pair cluster amplitudes are subsequently used in the SU CCSD method that is based on an M-dimensional GMS avoiding intruders. We discuss general aspects of these developments from various viewpoints and provide selective illustrations of the key concepts and ideas.
Convergence Enhancement in Perturbation Theory
Authors: Surján Peter R. , Szabados Ágnes
Published: January 2004

The Frobenius norm of operator QW is minimized with respect to level shift parameters applied to the zero-order spectrum, where W is the perturbation while Q is the reduced resolvent of the zero-order Hamiltonian. The stationary condition leads to a simple formula for the level shifts which eliminates degeneracy-induced singularities. Such level shifts may increase the radius of convergence of the perturbation series, and may improve low-order perturbative estimations - as it is found in the cases of a simple matrix eigenvalue problem and the one-dimensional quartic anharmonic oscillator.
Oxygen Sites at Molybdena and Vanadia Surfaces: Energetics of the Re-Oxidation Process
Authors: Tokarz-Sobieraj Renata , Grybos Robert , Witko Małgorzata , Hermann Klaus
Published: January 2004

In oxidation reactions proceeding in accordance with the Mars-van Krevelen mechanism lattice oxygen plays the role of an oxidizing agent. Surface vacancies created by incorporation of lattice oxygen into reacting molecules are filled in a subsequent step by gaseous oxygen or, if not enough oxygen is present in the reaction environment, by oxygen diffusion from the bulk. During this process, a very active, electrophilic surface oxygen species may be formed. In effect, total combustion takes place decreasing the selectivity for partial oxidation products. The thermodynamic aspect of this effect (neglecting reaction barriers) is demonstrated for molybdenum trioxide and vanadium pentoxide. On the catalytically most interesting surfaces, MoO3(010) and V2O5(010), three structurally different types of oxygen sites are present which exhibit different properties with respect to vacancy creation and annihilation. Re-oxidation of the catalyst by gaseous oxygen leads to oxygen molecules adsorbed in vacancies, preferably in an orientation parallel to the surface. Adsorption of the oxygen molecule in the vacancy leads to its activation followed by easy release of a neutral oxygen atom, which can be identified as the electrophilic species responsible for total combustion.
Convergence Behavior of Symmetry-Adapted Perturbation Expansions for Excited States. A Model Study of Interactions Involving a Triplet Helium Atom
Authors: Przybytek Michał , Patkowski Konrad , Jeziorski Bogumił
Published: January 2004

The convergence behavior of symmetry-adapted perturbation theory (SAPT) expansions is investigated for an interacting system involving an excited, open-shell monomer. By performing large-order numerical calculations for the interaction of the lowest, 1s2s, triplet state of helium with the ground state of the hydrogen atom we show that the conventional polarization and symmetrized Rayleigh-Schrödinger expansions diverge in this case. This divergence is attributed to the continuum of intruder states appearing when the hydrogen electron is falling on the helium 1s orbital and the 2s electron is ejected from the interacting system. One of the dimer states resulting from the interaction becomes then a resonance, which presents a hard case to treat by a perturbation theory. We show that the SAPT expansions employing the strong symmetry-forcing procedure, such as the Eisenschitz-London- Hirschfelder-van der Avoird or the Amos-Musher theories, can cope with this situation and lead to convergent series when the permutational symmetry of the bound, quartet state is forced. However, these theories suffer from a wrong asymptotic behavior of the second- and higher-order energies when the interatomic distance R grows to infinity, which makes them unsuitable for practical applications. We show that by a suitable regularization of the Coulomb potential and by treating differently the regular, long-range and the singular, short-range parts of the interatomic electron-nucleus attraction terms in the Hamiltonian one obtains a perturbation expansion which has the correct asymptotic behavior in each order and which converges fast for a wide range of interatomic distances.
A Coupled Cluster Study of van der Waals Interactions of the He Atom with CN, NO and O2 Radicals
Authors: Raab Juraj , Antušek Andrej , Biskupič Stanislav , Urban Miroslav
Published: January 2004

The partially spin-adapted coupled cluster method with the restricted open-shell Hartree- Fock reference was applied to calculations of interaction energies between the helium atom and the three radicals, CN (2Σ), NO (2Π), and O2 (3Sg-). Basis set dependences with medium-augmented correlation consistent basis sets were alleviated by using extrapolations to the basis set limit which were based on aug-cc-pVTZ and aug-cc-pVQZ results. The two-dimensional potential energy surfaces were fitted by exponential and polynomial functions. Minima and transition states were located. Potential energy surfaces are very floppy, especially for HeCN. This complex exhibits the weakest van der Waals interaction, the electronic interaction energy being 92 μEh. Interaction energy in HeNO is 122 μEh, almost the same as was found for HeO2 (124 μEh). Considering zero-point-vibrational corrections, the dissociation energy of HeCN, HeNO, and HeO2 is 4.6, 6.6, and 7.3 cm-1, respectively. This sequence of the magnitude of interaction energies and the structural data for global and local minima and transition states were compared with available literature data. No simple link between the magnitude of intermolecular forces and dipole moments and dipole polarizabilities of CN, NO, and O2 was found. The low-order long-range model based on the induction and dispersion forces is completely useless in the assessment of the sequence of the size of intermolecular interactions of the HeCN, HeNO, and HeO2 complexes.
Synthesis and Electrochemical Reduction of Methyl 3-Halo-1-benzothiophene-2-carboxylates
Authors: Rejňák Michal , Klíma Jiří , Svoboda Jiří , Ludvík Jiří
Published: January 2004

A preparative method of synthesis of the new methyl 3-iodo-1-benzothiophene-2-carboxylate was elaborated. Electrochemical behavior of methyl 3-chloro-, bromo- and iodo-1-benzothiophene-2-carboxylates 1-3, and of their reduction and dimer products 4, 5 in anhydrous dimethylformamide has been investigated at mercury and platinum electrodes using polarography, cyclic voltammetry and voltammetry on a rotating platinum disk electrode. The reduction in divided cells follows the ECE mechanism (electron - chemical step - electron), where the primary radical anion is split into a halide anion and neutral heterocyclic radical, which is immediately reduced by the second electron and protonated. The only reduction product is the methyl 1-benzothiophene-2-carboxylate (5); whereas the EDim mechanism (electron - dimer formation) leading to the dimeric species 4 was not observed under the above conditions. Reduction of 1-3 on platinum causes formation of a blocking film on the electrode. Sonication during electrolysis successfully reactivates the electrode.
Formation of Ring A in the Biosynthesis of Hopanoids from Squalene. A Density Functional Study
Authors: Hess B. Andes
Published: January 2004

Density functional calculations were carried out on the ring closure of the 2,6-dimethyloct-6-en-2-yl cation to a chair conformer of the 1,2,3,3-tetramethylcyclohexyl cation as a model for the first step in the biosynthetic cyclization of squalene to the triterpene hopanoids. The concerted reaction was found to have an activation energy of 4.6 kcal/mol and to be exothermic by 11.5 kcal/mol.
The immunohistochemical localisation of somatostatin receptors 1, 2, 3, and 5 in acoustic neuromas
Authors: Stafford N D , Condon L T , Rogers M J C , Helboe L , Crooks D A , Atkin S L
Published: January 2004

Aims:Acoustic neuroma is a benign tumour, which develops through an overproliferation of Schwann cells along the vestibular nerve. Somatostatin is a naturally occurring peptide, which exerts antiproliferative and antiangiogenic effects via five membrane bound receptor subtypes. The aim of this study was to determine whether somatostatin receptor subtypes (SSTRs) 1, 2, 3, and 5 are present in acoustic neuromas.

Methods:The expression of SSTRs 1, 2, 3, and 5 was studied in both the Schwann cells and blood vessels of eight acoustic neuroma specimens, by means of immunohistochemistry using novel rabbit polyclonal antibodies raised against human SSTR 1, 2, and 5 subtype specific peptides, and a commercial anti-SSTR3 antibody.

Results:SSTR2 was the most prevalent subtype in Schwann cells (seven of eight), with intermediate expression of SSTR3 (six of eight), and lower expression of SSTRs 1 and 5 (four of eight and five of eight, respectively). There was ubiquitous vascular expression of SSTR2, with no evidence of SSTR 1, 3, or 5 expression in blood vessels.

Conclusion:SSTRs 1, 2, 3, and 5 are differentially expressed in acoustic neuromas. Somatostatin analogues may have a therapeutic role in the management of this rare and challenging condition.
Rapid, accurate genotyping of the common −α4.2thalassaemia deletion based on the use of denaturing HPLC
Authors: Ou-Yang H , Hua L , Mo Q H , Xu X M
Published: January 2004

Aims:To develop an alternative assay for specific genotyping of the −α4.2thalassaemia deletion based on the DNA sequence features surrounding the breakpoint.

Methods:The 5′ and 3′ ends of the breakpoint regions of the −α4.2allele and the normal homologous segments were sequenced in Chinese individuals. A sequence haplotype composed of four single nucleotide variations within the X2/X1 box of the −α4.2breakpoint region was found in all of the 10 Chinese −α4.2thalassaemia alleles studied. Based on these findings, a novel polymerase chain reaction (PCR)/denaturing high performance liquid chromatography (DHPLC) assay was developed for rapid genotyping of the −α4.2allele instead of traditional Southern blotting or Gap-PCR. This method involves amplification of the α globin target sequence encompassing these four polymorphic sites, followed by a partially denaturing HPLC analysis using the transgenomic WAVE DNA fragment analysis system.

Results:The three major genotypes (−α4.2/αα, −α4.2/--SEA, and αα/αα) could be distinguished through the characteristic chromatograms generated by the WAVE system. The accuracy of this technique was evaluated blindly, and the results were 100% (40 of 40) concordant with the genotypes previously characterised by Southern blotting or Gap-PCR.

Conclusions:This study validates the PCR/DHPLC approach as a simple, rapid, highly accurate, and cost effective method, potentially adaptable for use in epidemiological surveys, genetic screening, and diagnosis of silent α+thalassaemia and Hb H disease.