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Biomedical subjects

C Woodward

Publications and source records attributed to C Woodward.

At least 19 recordsLinked to original sources
PubMed2004

A link between mRNA turnover and RNA interference in Arabidopsis.

In RNA interference (RNAi), double-stranded RNA (dsRNA) triggers degradation of homologous messenger RNA. In many organisms, RNA-dependent RNA polymerase (RdRp) is required to initiate or amplify RNAi, but the substrate for dsRNA synthesis in vivo is not known. Here, we show that RdRp-dependent transgene silencing in Arabidopsis was caused by mutation of XRN4, which is a ribonuclease (RNase) implicated in mRNA turnover by means of decapping and 5'-3' exonucleolysis. When both XRN4 and the RdRp were mutated, the plants accumulated decapped transgene mRNA. We propose that mRNAs lacking a cap structure become exposed to RdRp to initiate or maintain RNAi.

Animals↗
PubMed2004

Comparison of selected analytical techniques for protein sizing, quantitation and molecular weight determination.

Protein analysis techniques are developing fast due to the growing number of proteins obtained by recombinant DNA techniques. In the present paper we compare selected techniques, which are used for protein sizing, quantitation and molecular weight determination: sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), lab-on-a-chip or microfluidics technology (LoaC), size exclusion chromatography (SEC) and mass spectrometry (MS). We compare advantages and limitations of each technique in respect to different application areas, analysis time, protein sizing and quantitation performance.

Chromatography↗
PubMed2003

Mg segregation at Al/Al3Sc heterophase interfaces on an atomic scale: experiments and computations.

Microscopic factors governing solute partitioning in ternary two-phase Al-Sc-Mg alloys are investigated combining three-dimensional-atom-probe (3DAP) microscopy measurements with first-principles computations. 3DAP is employed to measure composition profiles with subnanometer-scale resolution, leading to the identification of a large enhancement of Mg solute at the coherent alpha-Al/Al(3)Sc (fcc/L1(2)) heterophase interface. First-principles calculations establish an equilibrium driving force for this interfacial segregation reflecting the nature of the interatomic interactions.

Journal Article↗
PubMed2002

Flexible Ab initio boundary conditions: simulating isolated dislocations in bcc Mo and Ta.

We report the first ab initio density-functional study of the strain field and Peierls stress of isolated <111> screw dislocations in bcc Mo and Ta. The local dislocation strain field is self-consistently coupled to the long-range elastic field using a flexible boundary condition method. This reduces the mesoscopic atomistic calculation to one involving only degrees of freedom near the dislocation core. The predicted equilibrium core for Mo is significantly different from previous atomistic results and the Peierls stress shows significant non-Schmid behavior as expected for the bcc metals.

Journal Article↗
PubMed2001

NMR-detected order in core residues of denatured bovine pancreatic trypsin inhibitor.

The NMR characteristics of [14-38]Abu, a synthetic variant of BPTI that is partially folded in aqueous buffer near neutral pH, support a model of early folding events which begin with stabilization of the nativelike, slow exchange core [Barbar, E., Hare, M., Daragan, V., Barany, G., and Woodward, C. (1998) Biochemistry 37, 7822-7833 (1)]. In partially folded [14-38]Abu, urea denaturation profiles for representative amide protons show that global unfolding is non-two-state and that core residues require a higher concentration of urea to unfold. Dynamic properties of pH-denatured [14-38]Abu and fully reduced and unfolded BPTI analogue were determined from heteronuclear NMR relaxation measurements at similar solution conditions. Differences at various sites in the polypeptide chain were evaluated from spectral density functions determined from T1, T2, and steady-state heteronuclear NOE data. Although denatured [14-38]Abu contains no persistent secondary structure, its most ordered residues are those that, in native BPTI, fold into the slow exchange core. The fully reduced analogue is significantly more mobile and shows less heterogeneous dynamics, but at 1 degree C, restricted motion is observed for residues in the central segments of the polypeptide chain. These observations indicate that there is a developing core or cores even in highly unfolded species. Apparently the effect of 14-38 disulfide on unfolded

Animals↗
PubMed2001

Experimental approaches to protein folding based on the concept of a slow hydrogen exchange core.

In a review of protein hydrogen exchange, we concluded that the slow exchange core is the folding core. By this we mean that the elements of secondary structure carrying the slowest exchanging backbone amides will tend to be the elements of secondary structure to fold first, that partially folded proteins will tend to be most organized in the core, and that peptides made to mimic the slow exchange core will tend to show nativelike structure. These generalizations have led us to ask several experimental questions that will be examined here: (1) In partially folded and unfolded proteins, how do the dynamics and structure of core regions differ from noncore regions? (2) Can we make protein 'core modules' as peptides corresponding to the slow exchange core? Can core modules be covalently linked to make a native state in which one conformation is significantly more stable than all other accessible conformations? (3) In a mutant perturbed outside the core, what are the effects on hydrogen exchange and folding?

Amino Acid Sequence↗
PubMed2000

Synthesis and characterization of a beta-hairpin peptide that represents a 'core module' of bovine pancreatic trypsin inhibitor (BPTI).

A new strategy for the design and construction of peptide fragments that can achieve defined, nativelike secondary structure is presented. The strategy is based upon the hypothesis that 'core elements' of a protein, synthesized in a single polypeptide molecule, will favor nativelike structure, and that by incorporating a cross-link, nativelike core structure will dominate the ensemble as the more extended conformations are excluded. 'Core elements' are the elements of packed secondary structure that contain the slowest exchanging backbone amide protons in the native protein. The 'core elements' in bovine pancreatic trypsin inhibitor (BPTI) are the two long strands of antiparallel beta-sheet (residues 18-24 and 29-35) and the small beta-bridge (residues 43-44). To test the design strategy, we synthesized an 'oxidized core module', which contains the antiparallel strands connected by a modified reverse turn (A27 replaced by D), a natural disulfide cross-link at the open end of the hairpin, and N- and C-termini blocking groups. A peptide with identical sequence but lacking the disulfide cross-link at the open end was used as the 'reduced core module' control. The conformational behavior of both peptides was examined using (1)H NMR spectroscopy. Chemical shift dispersion, chemical shift deviation from random coil values, sequential and long-range NOEs, and H/D amide exchange rates were compared for the two peptides. We conclude that the ensemble of oxidized and reduced core module conformations samples both nativelike 4:4 and non-native 3:5 beta-hairpin structure, and that the oxidized module samples nativelike structure for a greater fraction of the time than the reduced module.

Amino Acid Sequence↗
PubMed2000

First principles simulation of a ceramic /Metal interface with misfit

The relaxed atomic structure of a model ceramic/metal interface, 222MgO/Cu, is simulated, including lattice constant mismatch, using first principles local-density functional theory plane wave pseudopotential methods. The 399-atom computational unit cell contains 36 O and 49 Cu atoms per layer in accordance with the 7/6 ratio of MgO to Cu lattice constants. The atomic layers on both sides of the interface warp to optimize the local bonding. The interface adhesive energy is calculated. The interface electronic structure is found to vary appreciably with the local environment.

Journal Article↗
PubMed2000

The relationship of disease severity, health beliefs and medication adherence among HIV patients.

The objective was to investigate the relationship of disease severity, health beliefs and medication adherence among HIV/AIDS patients. A survey was administered to 72 patients in three different stages of HIV/AIDS (CDC clinical categories A, B, C). Multivariate analyses revealed that there were no significant differences in patients' perceptions of the severity of HIV/AIDS or perceptions of the benefits and barriers for the treatment across three disease stages. However, the most severely ill patients (in stage C) perceived a higher risk of complications if they did not take their medicine as prescribed compared to asymptomatic patients (stage A) (p = 0.01). Also, patients in stages B and C were more adherent to their medications compared to patients in stage A (p = 0.007). Finally, perceived susceptibility-inaction was positively related to medication adherence (p = 0.005) and difficulty in following doctors' instructions was negatively related to patients' medication adherence (p = 0.009). In conclusion, patients' illness experiences are associated with their beliefs about the chances of developing complications if they do not adhere to their medications. Patients who have experienced more complications perceive a stronger relationship between medication non-adherence and AIDS-related complications, and are also more adherent to their medication regimen when compared to patients with no prior complications.

Acquired Immunodeficiency Syndrome↗
PubMed1999

Drug treatment of common STDs: Part II. Vaginal infections, pelvic inflammatory disease and genital warts.

The Centers for Disease Control and Prevention (CDC) released new guidelines for the treatment of sexually transmitted diseases (STDs) in 1998. Several treatment advances have been made since the previous guidelines were published. Part II of this two-part series on STDs describes recommendations for the treatment of diseases characterized by vaginal discharge, pelvic inflammatory disease, epididymitis, human papillomavirus infection, proctitis, proctocolitis, enteritis and ectoparasitic diseases. Single-dose therapies are recommended for the treatment of several of these diseases. A single 1-g dose of oral azithromycin is as effective as a seven-day course of oral doxycycline, 100 mg twice a day, for the treatment of chlamydial infection. Erythromycin and ofloxacin are alternative agents. Four single-dose therapies are now recommended for the management of uncomplicated gonococcal infections, including 400 mg of cefixime, 500 mg of ciprofloxacin, 125 mg of ceftriaxone or 400 mg of ofloxacin. Advances in the treatment of bacterial vaginosis also have been made. A seven-day course of oral metronidazole is still recommended for the treatment of bacterial vaginosis in pregnant women, but intravaginal clindamycin cream and metronidazole gel are now recommended in nonpregnant women. Single-dose therapy with 150 mg of oral fluconazole is a recommended treatment for vulvovaginal candidiasis. Two new topical treatments, podofilox and imiquimod, are available for patient self-administration to treat human papillomavirus infection. Permethrin cream is now the preferred agent for the treatment of pediculosis pubis and scabies.

Anti-Infective Agents↗
PubMed1999

Drug treatment of common STDs: part I. Herpes, syphilis, urethritis, chlamydia and gonorrhea.

In 1998, the Centers for Disease Control and Prevention released guidelines for the treatment of sexually transmitted diseases. Several treatment advances have been made since the previous guidelines were published. Part I of this two-part article describes current recommendations for the treatment of genital ulcer diseases, urethritis and cervicitis. Treatment advances include effective single-dose regimens for many sexually transmitted diseases and improved therapies for herpes infections. Two single-dose regimens, 1 g of oral azithromycin and 250 mg of intramuscular ceftriaxone, are effective for the treatment of chancroid. A three-day course of 500 mg of oral ciprofloxacin twice daily may be used to treat chancroid in patients who are not pregnant. Parenteral penicillin continues to be the drug of choice for treatment of all stages of syphilis. Three antiviral medications have been shown to provide clinical benefit in the treatment of genital herpes: acyclovir, valacyclovir and famciclovir. Valacyclovir and famciclovir are not yet recommended for use during pregnancy. Azithromycin in a single oral 1-g dose is now a recommended regimen for the treatment of nongonococcal urethritis.

Anti-Infective Agents↗
PubMed1999

The hydrogen exchange core and protein folding.

A database of hydrogen-deuterium exchange results has been compiled for proteins for which there are published rates of out-exchange in the native state, protection against exchange during folding, and out-exchange in partially folded forms. The question of whether the slow exchange core is the folding core (Woodward C, 1993, Trends Biochem Sci 18:359-360) is reexamined in a detailed comparison of the specific amide protons (NHs) and the elements of secondary structure on which they are located. For each pulsed exchange or competition experiment, probe NHs are shown explicitly; the large number and broad distribution of probe NHs support the validity of comparing out-exchange with pulsed-exchange/competition experiments. There is a strong tendency for the same elements of secondary structure to carry NHs most protected in the native state, NHs first protected during folding, and NHs most protected in partially folded species. There is not a one-to-one correspondence of individual NHs. Proteins for which there are published data for native state out-exchange and theta values are also reviewed. The elements of secondary structure containing the slowest exchanging NHs in native proteins tend to contain side chains with high theta values or be connected to a turn/loop with high theta values. A definition for a protein core is proposed, and the implications for protein folding are discussed. Apparently, during folding and in the native state, nonlocal interactions between core sequences are favored more than other possible nonlocal interactions. Other studies of partially folded bovine pancreatic trypsin inhibitor (Barbar E, Barany G, Woodward C, 1995, Biochemistry 34:11423-11434; Barber E, Hare M, Daragan V, Barany G, Woodward C, 1998, Biochemistry 37:7822-7833), suggest that developing cores have site-specific energy barriers between microstates, one disordered, and the other(s) more ordered.

Animals↗
PubMed1999

Influence of companion animals on the physical and psychological health of older people: an analysis of a one-year longitudinal study.

OBJECTIVE: To examine whether companion animals or attachment to a companion animal was associated with changes in physical and psychological health in older people and whether the relationships between physical and psychological health and human social networks were modified by the presence or absence of a companion animal. DESIGN: A 1-year longitudinal study with standardized telephone interview data collected at baseline and repeated at 1-year SETTING: Wellington County, Ontario, Canada PARTICIPANTS: An age- and sex stratified random sample (baseline n = 1054; follow-up n = 995) of noninstitutionalized adults aged 65 and older (mean age = 73, SD +/- 6.3) MEASUREMENTS: Social Network Activity was measured using a family and non-family social support scale, participation in an organized social group, involvement in the affairs of the social group, the practice of confiding in others, feelings of loneliness, and the perceived presence of support in a crisis situation. Chronic conditions were measured as the current number of selected health problems. Pet ownership was assessed by the report of owning a dog or a cat and the Lexington Attachment to Pets Scale score. Physical health was assessed as the ability to perform Activities of Daily Living (ADLs). Psychological health was measured as a summed score comprising the level of satisfaction regarding one's health, family and friend relationships, job, finances, life in general, overall happiness, and perceived mental health. Sociodemographic variables assessed include subject age, sex, marital status, living arrangements, education, household income, and major life events. RESULTS: Pet owners were younger, currently married or living with someone, and more physically active than non-pet owners. The ADL level of respondents who did not currently own pets deteriorated more on average (beta = -.270, P = .040) than that of respondents who currently owned pets after adjusting for other variables during the 1-year period. No statistically significant direct association was observed between pet ownership and change in psychological well-being (P > .100). However, pet ownership significantly modified the relationship between social support and the change in psychological well-being (P = .001) over a 1-year period. CONCLUSIONS: The results demonstrate the benefits of pet ownership in maintaining or slightly enhancing ADL levels of older people. However, a more complex relationship was observed between pet ownership and an older person's well-being.

Aged↗
PubMed1998

Dynamics of the conformational ensemble of partially folded bovine pancreatic trypsin inhibitor.

A single-disulfide variant of bovine pancreatic trypsin inhibitor (BPTI), [14-38]Abu, is a partially folded ensemble which includes two, and in one case three, conformations that interconvert slowly enough to exhibit separate cross-peaks in the amide region of homonuclear and heteronuclear NMR spectra. Each conformation is itself composed of many subconformations in rapid equilibrium. Partially folded BPTI undergoes local motions that are slow, noncooperative, independent fluctuations of short segments within the chain. Cooperative global unfolding of the ensemble is also observed. Heteronuclear NMR has been used to measure interconversion rate constants of partially folded conformational substates; the rate constants differ for each residue and vary over an order of magnitude. For local fluctuation, the forward rate constants for amide protons of the antiparallel beta-sheet are significantly smaller than the rest of the molecule, consistent with other indications that this is the most stable part of the partially folded protein. The reverse rate constants also vary; they are the highest for Ala 27 in the turn between the strands in the sheet and for Phe 33 in the antiparallel beta-sheet. Global unfolding interconversion rate constants vary over a 3-fold range, consistent with previously observed deviations from two-state behavior. Fast backbone dynamics, from T1, T2, and NOE relaxation parameters, are obtained for the slowly interchanging conformations in the partially folded ensemble. Clear differences are observed between the two conformations; one is more flexible and less compact than the other. In the more flexible and disordered partially folded conformation, intermediate exchange is detected for some backbone amides, namely, those in the central beta-sheet and the turn. These same sheet and turn residues are more ordered in the globally denatured ensemble as well. Our results suggest that the turn initiates formation of a partially folded ensemble in which the slow-exchange core is the most stable region and in which segmental fluctuations reflect multiple nuclei for folding of the rest of the molecule.

Animals↗
PubMed1998

Conformation, stability, and active-site cysteine titrations of Escherichia coli D26A thioredoxin probed by Raman spectroscopy.

The active-site cysteines (Cys 32 and Cys 35) of Escherichia coli thioredoxin are oxidized to a disulfide bridge when the protein mediates substrate reduction. In reduced thioredoxin, Cys 32 and Cys 35 are characterized by abnormally low pKa values. A conserved side chain, Asp 26, which is sterically accessible to the active site, is also essential to oxidoreductase activity. pKa values governing cysteine thiol-thiolate equilibria in the mutant thioredoxin, D26A, have been determined by direct Raman spectrophotometric measurement of sulfhydryl ionizations. The results indicate that, in D26A thioredoxin, both sulfhydryls titrate with apparent pKa values of 7.5+/-0.2, close to values measured previously for wild-type thioredoxin. Sulfhydryl Raman markers of D26A and wild-type thioredoxin also exhibit similar band shapes, consistent with minimal differences in respective cysteine side-chain conformations and sulfhydryl interactions. The results imply that neither the Cys 32 nor Cys 35 SH donor is hydrogen bonded directly to Asp 26 in the wild-type protein. Additionally, the thioredoxin main-chain conformation is largely conserved with D26A mutation. Conversely, the mutation perturbs Raman bands diagnostic of tryptophan (Trp 28 and Trp 31) orientations and leads to differences in their pH dependencies, implying local conformational differences near the active site. We conclude that, although the carboxyl side chain of Asp 26 neither interacts directly with active-site cysteines nor is responsible for their abnormally low pKa values, the aspartate side chain may play a role in determining the conformation of the enzyme active site.

Binding Sites↗
PubMed1998

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design.

Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structure-based ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings, as well as cavities. The program specifies the atoms lining pockets, pocket openings, and buried cavities; the volume and area of pockets and cavities; and the area and circumference of mouth openings. CAST analysis of over 100 proteins has been carried out; proteins examined include a set of 51 monomeric enzyme-ligand structures, several elastase-inhibitor complexes, the FK506 binding protein, 30 HIV-1 protease-inhibitor complexes, and a number of small and large protein inhibitors. Medium-sized globular proteins typically have 10-20 pockets/cavities. Most often, binding sites are pockets with 1-2 mouth openings; much less frequently they are cavities. Ligand binding pockets vary widely in size, most within the range 10(2)-10(3)A3. Statistical analysis reveals that the number of pockets and cavities is correlated with protein size, but there is no correlation between the size of the protein and the size of binding sites. Most frequently, the largest pocket/cavity is the active site, but there are a number of instructive exceptions. Ligand volume and binding site volume are somewhat correlated when binding site volume is < or =700 A3, but the ligand seldom occupies the entire site. Auxiliary pockets near the active site have been suggested as additional binding surface for designed ligands (Mattos C et al., 1994, Nat Struct Biol 1:55-58). Analysis of elastase-inhibitor complexes suggests that CAST can identify ancillary pockets suitable for recruitment in ligand design strategies. Analysis of the FK506 binding protein, and of compounds developed in SAR by NMR (Shuker SB et al., 1996, Science 274:1531-1534), indicates that CAST pocket computation may provide a priori identification of target proteins for linked-fragment design. CAST analysis of 30 HIV-1 protease-inhibitor complexes shows that the flexible active site pocket can vary over a range of 853-1,566 A3, and that there are two pockets near or adjoining the active site that may be recruited for ligand design.

Algorithms↗