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PubMed2001

Phage display of adenovirus type 5 fiber knob as a tool for specific ligand selection and validation.

Adenovirus (Ad) vectors are most potent for use as gene delivery vehicles to infect human cells in vitro and in vivo with high efficiency. The main limitation in utilization of Ad as a gene transfer vector is the lack of specificity. Genetic modifications of Ad capsid proteins resulting in incorporation of foreign polypeptide ligand sequences can redirect the vector towards target cells. However, in many cases the incorporated ligands lose specificity or lead to conformational changes influencing virion integrity. In order to select target-specific ligands a priori structurally compatible with Ad, we propose a system for displaying polypeptide sequences in the context of the Ad fiber knob on the surfaces of filamentous bacteriophages. To establish this concept, we displayed the wild-type Ad serotype 5 knob and knobs containing c-Myc epitopes and six-histidine sequences in the pJuFo phage system. The knobs remained trimeric and bound the coxsackievirus-Ad receptor, and the phage knob-displayed ligands recognized and bound their cognates in the phage-displayed knob context. Further development of this system may be useful for candidate ligand fidelity and Ad structural compatibility validation prior to Ad modification.

Adenoviruses, Human↗
PubMed2003

Pulse radiolysis, electron paramagnetic resonance spectroscopy and theoretical calculations of caffeic acid oligomer radicals.

Seven representative compounds isolated from Salvia officinalis, among them caffeic acid, the dimer rosmarinic acid and oligomers of caffeic acid, were investigated with regard to their antioxidant potential both expressed by the radical scavenging activity and the stability and structure of the intermediate radicals. Pulse-radiolytic investigation revealed very high rate constants with both hydroxyl and azide radicals. Evidence from kinetic modelling calculations suggested unusual complex behavior due to the presence of both O(4)- and O(3)-semiquinones and - in two cases - formation and decay of a hydroxyl radical adduct at the vinyl side chain. EPR spectroscopy studies, which included dihydrocaffeic acid as a model for the saturated side chains of the oligomers, confirmed that the radical structures after oxidation in slightly alkaline solutions are representing dissociated O(4)-semiquinones. While according to calculations based on hybrid density-functional theory the other radical structures are valid intermediates, they cannot be observed except by pulse radiolysis due to their fast decay.

Benzoquinones↗
PubMed2002

Prediction of biodegradability from structure: imidazoles.

A project for the development of Structure-Activity Relationship for Biodegradation is presented. The aim of the project is to assemble sets of structural rules governing the potential microbial degradability of (classes of) chemicals. These rules will provide tools to take into account the biodegradation aspects of a product--and all precursors in the production process--early in the product development. The modeling concept is to take all experimental biodegradation data available and combine structural trends in the data with mechanistical information from degradation pathways. The rules that are derived should give insight into the possibility of biodegradation for specific classes of chemicals, thereby revealing why a compound is biodegradable or not. For the class of imidazole derivatives such rules are derived, and a model degradation mechanism is proposed in analogy to the urocanate-hydratase mechanism from histidine metabolism. The model is validated using 12 imidazole-compounds, which are all predicted correctly to be poorly biodegradable. It is demonstrated that both data analysis and information on enzymatic reaction mechanisms are necessary to yield valid Structure-Biodegradation Relationship.

Bacteria↗
PubMed2004

Osteoporosis health belief scale: minor changes were required after telephone administration among women.

OBJECTIVE: The Osteoporosis Health Belief Scale (OHBS) is a 42-item scale designed to measure general health motivation, perceived susceptibility to and seriousness of osteoporosis, and beliefs about calcium intake and exercise in preventing and treating osteoporosis. The purpose of this study was to examine the psychometric properties of the OHBS by telephone administration among older women. STUDY DESIGN AND SETTING: A convenience sample of 425 women aged 61-93 years participating in a longitudinal arthritis study was recruited by telephone. Item clarity was evaluated and 22 additional items (6 reworded, 16 from other questionnaires) were considered to supplement or replace existing scale items. Multitrait scaling techniques and exploratory factor analysis were used to test scale structure. Construct validity was tested based on theoretical hypothesis between OHBS subscale scores and participant characteristics. RESULTS: A few modifications to the OHBS scale were suggested, reducing the scale by five items (two redundant, three did not load), rewording one item and moving on item to a different subscale. The modified 37-item OHBS had a seven-factor uncorrelated solution explaining 48% of the model variance with internal consistency ranging from 0.73 to 0.88. CONCLUSION: Relatively minor changes to the OHBS results in reduced redundancy and improved internal structure of the scale for telephone administration among women over 60 years of age. Further examination is recommended to confirm these findings.

Aged↗
PubMed1999

Mother and teacher reports of ADHD symptoms: DSM-IV Questionnaire data.

OBJECTIVE: Diagnosis of attention-deficit/hyperactivity disorder (ADHD) is thought to be best accomplished by a multimodal approach. In many research and clinical settings, such extensive procedures may not be feasible. A screening instrument that could identify children meeting necessary (but not sufficient) criteria would permit selection of subgroups for more resource-intensive diagnostic procedures. METHOD: The Diagnostic Rating Scale (DRS) was completed by the mothers and teachers of 124 children referred to hospital-based clinics and 225 nonreferred children. The authors performed principal components analysis (PCA) on the questionnaire, compared the scores obtained by children from the 2 samples, and examined age and gender effects. Diagnoses derived from the DRS were not validated against structured diagnostic interviews. RESULTS: PCAs replicated the DSM-IV symptom combinations. Children from the referred sample exhibited more symptoms (p < .001) than children from the community sample. Boys were overrepresented among the children who received DRS-derived ADHD diagnoses. Girls were more likely (92%) to receive a diagnosis of ADHD, predominantly inattentive subtype, than other ADHD diagnoses. CONCLUSIONS: The results of this study provide preliminary support for the validity of the parent and teacher DRS as time- and resource-efficient screening instruments for examining symptoms associated with ADHD.

Attention Deficit Disorder with Hyperactivity↗
PubMed2005

Determining the structure of an unliganded and fully glycosylated SIV gp120 envelope glycoprotein.

HIV/SIV envelope glycoproteins mediate the first steps in viral infection. They are trimers of a membrane-anchored polypeptide chain, cleaved into two fragments known as gp120 and gp41. The structure of HIV gp120 bound with receptor (CD4) has been known for some time. We have now determined the structure of a fully glycosylated SIV gp120 envelope glycoprotein in an unliganded conformation by X-ray crystallography at 4.0 A resolution. We describe here our experimental and computational approaches, which may be relevant to other resolution-limited crystallographic problems. Key issues were attention to details of beam geometry mandated by small, weakly diffracting crystals, and choice of strategies for phase improvement, starting with two isomorphous derivatives and including multicrystal averaging. We validated the structure by analyzing composite omit maps, averaged among three distinct crystal lattices, and by calculating model-based, SeMet anomalous difference maps. There are at least four ordered sugars on many of the thirteen oligosaccharides.

Animals↗
PubMed2002

The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR.

An interhelical distance has been precisely measured by REDOR solid-state NMR spectroscopy in the transmembrane tetrameric bundle of M2-TMP, from the M2 proton channel of the influenza A viral coat. The high-resolution structure of the helical backbone has been determined using orientational restraints from uniformly aligned peptide preparations in hydrated dimyristoylphosphatidylcholine bilayers. Here, the distance between (15)N(pi) labeled His37 and (13)C(gamma) labeled Trp41 is determined to be less than 3.9 A. Such a short distance, in combination with the known tilt and rotational orientation of the individual helices, permits not only a determination of which specific side chain pairings give rise to the interaction, but also the side chain torsion angles and restraints for the tetrameric bundle can also be characterized. The resulting proton channel structure is validated in a variety of ways. Both histidine and tryptophan side chains are oriented in toward the pore where they can play a significant functional role. The channel appears to be closed by the proximity of the four indoles consistent with electrophysiology and mutagenesis studies of the intact protein at pH 7.0 and above. The pore maintains its integrity to the N terminal side of the membrane, and at the same time, a cavity is generated that appears adequate for binding amantadine. Finally, the observation of a 2 kHz coupling in the PISEMA spectrum of (15)N(pi)His37 validates the orientation of the His37 side chain based on the observed REDOR distance.

Amino Acid Sequence↗
PubMed2024

Molecular basis for antibody recognition of multiple drug-peptide/MHC complexes.

The HapImmuneTM platform exploits covalent inhibitors as haptens for creating major histocompatibility complex (MHC)-presented tumor-specific neoantigens by design, combining targeted therapies with immunotherapy for the treatment of drug-resistant cancers. A HapImmune antibody, R023, recognizes multiple sotorasib-conjugated KRAS(G12C) peptides presented by different human leukocyte antigens (HLAs). This high specificity to sotorasib, coupled with broad HLA-binding capability, enables such antibodies, when reformatted as T cell engagers, to potently and selectively kill sotorasib-resistant KRAS(G12C) cancer cells expressing different HLAs upon sotorasib treatment. The loosening of HLA restriction could increase the patient population that can benefit from this therapeutic approach. To understand the molecular basis for its unconventional binding capability, we used single-particle cryogenic electron microscopy to determine the structures of R023 bound to multiple sotorasib-peptide conjugates presented by different HLAs. R023 forms a pocket for sotorasib between the VH and VL domains, binds HLAs in an unconventional, angled way, with VL making most contacts with them, and makes few contacts with the peptide moieties. This binding mode enables the antibody to accommodate different hapten-peptide conjugates and to adjust its conformation to different HLAs presenting hapten-peptides. Deep mutational scanning validated the structures and revealed distinct levels of mutation tolerance by sotorasib- and HLA-binding residues. Together, our structural information and sequence landscape analysis reveal key features for achieving MHC-restricted recognition of multiple hapten-peptide antigens, which will inform the development of next-generation therapeutic antibodies.

Humans↗
PubMed1994

Stabilization of beta-ribbon structures in peptides using disulfide bonds.

The effect of a disulfide crosslink between two peptide chains on the stability of beta-ribbon secondary structures formed by these peptides has been investigated. Based on structural principles, we hypothesized that introduction of an unstrained disulfide crosslink at appropriate locations on two peptide chains should have a stabilizing effect on the beta-ribbon structure formed by these two peptide chains. To test this hypothesis, we designed and synthesized two sets of 9-residue peptides incorporating cysteine in one and (S)-alpha-amino-epsilon-mercaptohexanoic acid in the other. Comparison of the CD data clearly show that the dimer containing a disulfide bond between the longer sidechains of (S)-alpha-amino-epsilon-mercaptohexanoic acid shows dramatically higher beta-ribbon character as compared to the dimer with cystine disulfide bond, thus validating our structural hypothesis.

Amino Acid Sequence↗
PubMed1991

Structure-activity relationships of chemical mutagens and carcinogens.

In recent years, octanol-water partition coefficients (P) have been used in toxicology studies to correlate chemical structure and biological activity. Generally, only limited attempts are made to show how a new correlation equation relates to those previously published, especially when different activities are involved. Evidence is presented to show that there is often a high degree of self-consistency between the dependence of activity on hydrophobicity (defined by log P) from different systems. Examples are drawn from nonspecific toxicity, mutagenicity and carcinogenicity. It is suggested that this kind of lateral correlation is an important means for validating structure-activity relationships.

Alcohols↗
PubMed1995

Accurate prediction of protein secondary structural class with fuzzy structural vectors.

The prerequisites for accurate prediction of protein secondary structural class (all-alpha, all-beta, alpha+beta, alpha/beta or multidomain) were studied, and a new similarity-based method is presented for the prediction of the secondary structural class of a protein from its sequence. The new method uses representatives of nuclear families as a learning set. For the sequence to be predicted, the method produces a vector of certainty factors called a fuzzy structural vector. Validation with independent test sets shows that the prediction accuracy of the proposed method has clear dependency on the representativity of the learning set. The representatives obtained from the nuclear families of the Brookhaven Protein Data Bank (PDB) were shown to give accurate predictions for PDB proteins, whilst the amino acid composition-based methods used previously achieve their maximum predictability with relatively limited learning sets, and they remain inaccurate even with highly representative learning sets. The usability of the new method is increased further by the fuzzy structural vectors, which substantially reduce the risk of misclassification and realistically describe vague secondary structural tendencies.

Algorithms↗
PubMed2026

Sperm subpopulations differing in mitochondrial abundance show divergent nuclear allele frequencies.

Mammalian ejaculates contain heterogeneous sperm subpopulations that differ in subcellular architecture and developmental history, despite appearing morphologically uniform. The extent to which this cellular heterogeneity reflects underlying nuclear genomic structure within a sire remains largely unexplored. Mitochondrial architecture in sperm is established during spermatogenesis, with final assembly and organization occurring during spermiogenesis under nuclear genomic control, positioning variation in mitochondrial abundance and organization as a potential phenomic indicator of within-sire allelic segregation. Here, we tested whether sperm subpopulations defined by differing mitochondrial abundance exhibit systematic differences in nuclear allele representation. Boar sperm were resolved into low and high mitochondrial subpopulations using fluorescence-activated cell sorting based on MitoTracker&#x2122; Green fluorescence while excluding debris, doublets, and non-viable cells. Epifluorescence microscopy confirmed that high MitoTracker&#x2122; Green fluorescence sperm possessed longer mitochondrial sheaths, validating a structural distinction between subpopulations. Whole-genome sequencing of paired mitochondrial subpopulations from three boars was performed, and allelic ratio distortion was evaluated relative to heterozygous baseline populations. Analyses across heterozygous loci genome-wide identified candidate allele frequency shifts between mitochondrial-defined subpopulations, suggesting non-random segregation of alleles within ejaculates. Using a minimum sequencing depth of 30 reads in both sorted fractions, 182 candidate SNPs were identified with evidence of allele-frequency differences between mitochondrial fluorescence-defined subpopulations. These findings suggest that sperm mitochondrial abundance can potentially serve as an indirect, high-throughput marker of nuclear genomic heterogeneity within sires. This proof-of-concept framework establishes a foundation for future studies integrating sperm phenotyping, genome-wide allele-frequency analysis and functional validation to better characterize gamete-level heterogeneity.

Male↗
PubMed2005

Psychometric properties of the 25-item National Eye Institute Visual Function Questionnaire (NEI VFQ-25), Japanese version.

BACKGROUND: The importance of evaluating the outcomes of health care from the standpoint of the patient is now widely recognized. The purpose of this study is to develop and test a Japanese version of the National Eye Institute Visual Function Questionnaire (NEI VFQ-25). METHODS: A Japanese version was developed with a previously standardized method. The questionnaire and optional items were completed by 245 patients with cataracts, glaucoma, or age-related macular degeneration, by 110 others before and after cataract surgery, and by a reference group (n = 31). We computed rates of missing data, measured reproducibility and internal consistency reliability, and tested for convergent and discriminant validity, concurrent validity, known-groups validity, factor structure, and responsiveness to change. RESULTS: Based on information from the participants, some items were changed to 2-step items (asking if an activity was done, and if it was done, then asking how difficult it was). The near-vision and distance-vision subscales each had 1 item that was endorsed by very few participants, so these items were replaced with items that were optional in the English version. For example, more than 60% of participants did not drive, so the driving question was excluded. Reliability and validity were adequate for all subscales except driving, ocular pain, color vision, and peripheral vision. With cataract surgery, most scores improved by at least 20 points. CONCLUSION: With minor modifications from the English version, the Japanese NEI VFQ-25 can give reliable, valid, responsive data on vision-related quality of life, for group-level comparisons or for tracking therapeutic outcomes.

Adult↗
PubMed2001

NMR structure of the Euplotes raikovi pheromone Er-23 and identification of its five disulfide bonds.

The NMR solution structure of the 51 residue pheromone Er-23 from the ciliated protozoan Euplotes raikovi (Er) was calculated with the torsion angle dynamics program DYANA from 582 nuclear Overhauser enhancement (NOE) upper limit distance constraints, 46 dihedral angle constraints and 30 disulfide bond constraints. The disulfide bridges had not been assigned by chemical methods, and initially were assigned tentatively on the basis of inspection of the positioning of the Cys sulfhydryl groups in a bundle of 20 conformers that was calculated without disulfide bond constraints. The assignment of disulfide bridges was then validated by structure calculations that assessed the compatibility of plausible alternative Cys-Cys disulfide combinations with the input of NOE upper distance constraints and dihedral angle constraints. For a group of 20 conformers used to characterize the solution structure, the average pairwise root-mean-square distances from the mean coordinates calculated for the backbone heavy atoms N, C(alpha) and C' of resideus 1-51 is 0.38 A. The molecular architecture consists of a three-dimensional arrangement of five helices comprised of residues 2-8, 14-17, 26-29, 34-36 and 38-47, with five disulfide bridges in the positions 3-24, 6-16, 13-47, 27-40, and 35-51, which has so far not been represented in the Protein Data Bank. Er-23 is unique among presently known Er-pheromones with respect to size, sequence, the number of disulfide bonds and the three-dimensional structure, thus providing a new structural basis for rationalizing the physiological functions of this protein family.

Amino Acid Sequence↗
PubMed2006

The psychometric properties of the Chinese version of the Fagerstrom Test for Nicotine Dependence.

This study examined the psychometric properties of the Chinese version of the Fagerstrom Test for Nicotine Dependence (FTND). Criterion validity, factorial structure, and construct reliability were conducted using PRELIS 2 and LISREL 8.7 software. Two hundred and forty-five adult smokers were recruited from April to August 2005 in Taiwan. Because some items of the FTND are dichotomous and ordinal, biserial and polyserial correlations between the items and saliva cotinine levels were utilized. Confirmatory factor analyses (CFA) were performed to compare the relative fit of three competing models. Computation of the construct reliability was necessitated by a lack of tau-equivalence. The results demonstrated that the Chinese version has satisfactory validity and reliability. One item, "Smoke more in the morning," had low correlations with saliva cotinine. CFA found the items of the Chinese version were best modeled as two correlated factors without a cross-loading. These findings differ from the previous research testing the English version. Studies addressing the specific features of cigarette dependence in different socio-cultural contexts are needed.

Adolescent↗
PubMed2001

Cross-cultural comparability of the Geriatric Depression Scale: comparison between older Koreans and older Americans.

It is becoming increasingly clear that, in order to better understand the implications of global aging, more cross-cultural research is needed. In the present study, the structure and validity of the Geriatric Depression Scale-Short Form (GDS-SF) was examined in Korean and US samples of older adults. The participants included 153 older adults living in Korea (mean age=65.9 years) and 459 older adults from Florida (mean age=72.4 years). All participants completed the original or translated versions of the GDS-SF, as well as additional demographic and health-related measures. The results indicated that the GDS-SF exhibited good reliability in both samples. However, the results of a principal components analysis indicated that the structure was not well replicated across the two samples. In general, the present study suggests that, despite great efforts to make the questionnaires equivalent in the two cultures, the concept of depression for older adults may vary greatly in Korea and the USA. Possible explanations for cross-cultural differences are discussed, as well as implications.

Aged↗
PubMed2002

A quick solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans and mechanistic implications.

Lysines 9 and 10 in Desulfuromonas acetoxidans cytochrome c7, which could be involved in the interaction mechanism with the redox partners, have been replaced by alanine residues using site-directed mutagenesis. The solution structure of the fully oxidized form of K9-10A cytochrome c7, which is paramagnetic with three paramagnetic centers, has been determined via 1H NMR. The assignment of the spectra has been performed through an automatic program whose algorithm and strategy are here described. The assignment of the NOESY spectra has been further extended by back calculating the NOESY maps. The final number of meaningful NOE-based upper distance limits was 1186. In the Restrained Energy Minimization calculations, 147 pseudocontact shift constraints were also included, which showed consistency with NOE-based constraints and therefore further contribute to validate the structure quality. A final family of 35 conformers was calculated with RMSD values with respect to the mean structure of 0.69 +/- 0.17 A and 1.05 +/- 0.14 A for the backbone and heavy atoms, respectively. The overall fold of the molecule is maintained with respect to the native protein. The loop present between heme III and heme IV results to be highly disordered also in the present structure although its overall shape mainly resembles that of the oxidized native protein, and the two strands which give rise to the short beta-sheet present at the N-terminus and connected by a turn containing the mutated residues, are less clearly defined. If this loop is neglected, the RMSD values are 0.52 +/- 0.07 A and 0.92 +/- 0.06 A for the backbone and heavy atoms, respectively, which represent a reasonable resolution. The relative distances and orientations of the three hemes are maintained, as well as the orientation of the imidazole rings of the axial histidine ligands, with the only exception of heme IV. Such difference probably reflects minor conformational changes due to the substitution of the vicinal Lys 10 with an Ala. The replacement of the two lysines does not affect the reduction potentials of the three hemes, consistently with the expectations on the basis of the structure and electrostatic calculations. However, the replacement of the two lysines affects the reactivity of the mutant cytochrome c7 with [Fe] hydrogenase, inducing a change in Km. This finding is in agreement with the identification of the protein area around heme IV as the interacting site.

Amino Acid Substitution↗
PubMed1999

Strategies toward predicting peptide cellular permeability from computed molecular descriptors.

The therapeutic efficacy of an orally administered drug is dictated not only by its pharmacological properties such as potency and selectivity, but also its pharmacokinetic properties such as its access to the site of activity. Thorough evaluation of the physicochemical and biological barriers to drug delivery is essential to the selection and successful development of drug candidates. We have demonstrated previously that cellular permeability, as a primary component of drug delivery, is principally dependent upon the desolvation potential of the polar functionalities in the molecule and, secondarily, upon the solute lipophilicity [Conradi, R.A., Hilgers, A.R., Ho, N.F.H., Burton, P.S. (1992). The influence of peptide structure on transport across Caco-2 cells. II. Peptide bond modification which results in improved permeability. Pharm. Res. 9, 473-479]. Increasingly sophisticated computational methods are becoming available for describing molecular structural features proposed to correlate with such molecular physicochemical determinants of permeability. Herein we examine the relationships of various computationally derived molecular geometric descriptors for a set of peptides and peptidomimetics, in the context of experimentally measured hydrogen-bond potentials and lipophilicities, with their cellular permeabilities. These descriptors include molecular volume, polar and non-polar surface areas and projected molecular cross-sectional areas. Particular attention is paid to the roles of solvation treatments and other computational factors in descriptor generation, deconvolution of cellular transport mechanisms and statistical analyses of the resulting data for the development of valid, structure-based and mechanistically meaningful models of cellular permeability. No significant correlation of cellular permeability with computed descriptors was found. This was primarily because of our inability to identify surrogates for hydrogen-bond desolvation potential for the solutes from among these descriptors.

Adenocarcinoma↗