PubMed Health⌕ Search

Biomedical subjects

S F Parker

Publications and source records attributed to S F Parker.

8 recordsLinked to original sources
PubMed2006

Phonon driven proton transfer in crystals with short strong hydrogen bonds.

Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dynamics of these systems as functions of temperature. The mechanism determined in a previous work on urea phosphoric acid of low frequency vibrations stabilizing average crystal structures, in which the potential energy well of the hydrogen bond has its minimum shifted towards the center of the bond, is found to be valid here. The new feature of the N-H...O hydrogen bonds studied in this work is that the proton is transferred from the donor atom to the acceptor atom. Molecular dynamics simulations show that in an intermediate temperature regime, in which the proton is not completely transferred, the proton is bistable, jumping from one side of the hydrogen bond to the other. In the case of 3,5-pyridine dicarboxylic acid, which has been studied in most detail, specific phonons are identified, which influence the potential energy surface of the proton in the short, strong hydrogen bond.

Journal Article↗
PubMed2002

Neutron spectroscopic study of hydrogen bonding dynamics in L-serine.

Inelastic incoherent neutron scattering (IINS) spectra were obtained at 10 K for normal and deuterated L-serine. The geometry of L-serine molecule was optimized for the zwitterion form using ab initio HF, MP2 and DFT (B3LYP) levels with 6-31G* and 6-311 + +G4** basis sets. The theoretical frequencies of normal and d4-L-serine were compared with IINS spectra. Normal coordinate analysis and band assignments based on ab initio calculations and experimental data were presented. IINS frequencies due to the out-of-plane gamma(N-H...O) hydrogen bond motions were observed and identified.

Hydrogen Bonding↗
PubMed2001

Neutron scattering, infra red, Raman spectroscopy and ab initio study of L-threonine.

Inelastic incoherent neutron scattering spectra (IINS) were obtained for normal and deuterated L-threonine. Raman and infrared spectra were also recorded. Geometries were optimized for the zwitterion form using ab initio Hartree-Fock (HF) levels with 6-31G*, 6-311G*, 6-311G** and 6-311 + + G** basis sets. Force fields and normal modes were calculated and used as basis for an assignment of the spectral features.

Crystallization↗
PubMed2000

The vibrational spectrum of methyltrioxorhenium(VII).

The inelastic neutron scattering and high-resolution FT-Raman spectra of methyltrioxorhenium are reported. Literature assignments of the modes below 1600 cm(-1) are largely confirmed with the exceptions of the methyl torsion and the ReO3 bending modes. The methyl torsion is observed for the first time at 200 cm(-1), while the band at 230 cm(-1) assigned previously to the torsion is shown to be a component of the factor group splitting of the solid. In the FT-Raman spectrum, the bands that derive from the E modes in the isolated molecule are split by the Cs site symmetry of the crystal. This allows an unambiguous assignment of these modes to be made. On this basis, the assignment of the ReO3 bending modes is reversed with the asymmetric mode at 325 cm(-1) and the symmetric mode at 276 cm(-1).

Fourier Analysis↗
PubMed1997

Distinct domains of adenovirus E1A interact with specific cellular factors to differentially modulate human immunodeficiency virus transcription.

Transcription of human immunodeficiency virus (HIV) type 1 and other viruses is regulated by the transcription factor NF-kappaB, which interacts with the multifunctional cellular protein p300. p300, originally identified by its ability to bind adenovirus early region 1A (E1A), has also been shown to regulate HIV transcription through its interaction with NF-kappaB. The 13S form of E1A activates HIV gene expression, while the 12S form represses its transcription. In this report, we have investigated whether these divergent effects of E1A are dependent upon common or distinct cellular cofactors, including p300, pRb, and the TATA box-binding protein (TBP). Unlike activation in the absence of E1A, cooperative stimulation of HIV gene expression by 13S E1A and RelA was independent of the ability of E1A to bind p300 but was critically dependent on the E1A CR3 region which associates with TBP. In contrast, inhibition of basal HIV gene expression by the 12S form of E1A was dependent on p300 but not pRb or TBP. Interestingly, mutation of the CR2 region of 12S E1A responsible for pRb binding abolished the repression of HIV transcription stimulated by tumor necrosis factor alpha, suggesting that repression of cytokine-activated transcription involves cofactors different from those used in unstimulated cells. Repression and activation of HIV transcription by different forms of E1A are mediated by distinct sets of cellular cofactors. These findings suggest that E1A has evolved to interact by alternative mechanisms with a transcriptional coactivator and its associated cofactors to differentially modulate cellular and viral gene expression.

Adenovirus E1A Proteins↗
PubMed1996

A cooperative interaction of human T-cell leukemia virus type 1 Tax with the p21 cyclin-dependent kinase inhibitor activates the human immunodeficiency virus type 1 enhancer.

Interactions between the Tax transactivator of human T-cell leukemia virus type 1 (HTLV-1) and a cell cycle regulatory protein have been examined. We report cooperative stimulation of human immunodeficiency virus type 1 gene expression by Tax and a regulator of cell cycle progression, the p21 cyclin-dependent kinase inhibitor (CKI). This cooperativity results from the effect of p21 on transcriptional coactivation by Tax-induced NF-kappaB. This effect was abrogated by a mutation in Tax which specifically eliminated NF-kappaB induction, was inhibitable by IkappaB-alpha, and was markedly reduced in human immunodeficiency virus reporter plasmids with mutant kappaB sites. These studies demonstrate that transcriptional activation by Tax is influenced by cell cycle regulatory proteins.

Cyclin-Dependent Kinase Inhibitor p21↗
PubMed1995

Vibrational neutron spectroscopy of collagen and model polypeptides.

A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views of the proton-dominated modes of a protein over a wide energy range from the low frequency phonon region to the rich spectrum of localized high frequency modes. Several bands show a level of fine structure approaching that of optical data. The principal features of the spectra are assigned. A difference spectrum is obtained for protein associated water, which displays an acoustic peak similar to pure ice and a librational band shifted to lower frequency by the influence of the protein. Hydrogen-weighted densities of states are extracted for collagen and the model polypeptides, and compared with published calculations. Proton mean-square displacements are calculated from Debye-Waller factors measured in parallel quasi-elastic neutron-scattering experiments. Combined with the collagen density of states function, these yield an effective mass of 14.5 a.m.u. for the low frequency harmonic oscillators, indicating that the extended atom approximation, which simplifies analyses of low frequency protein dynamics, is appropriate.

Amino Acid Sequence↗