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D Baker

Publications and source records attributed to D Baker.

At least 145 records · Page 8Linked to original sources
PubMed1998

Clustering of low-energy conformations near the native structures of small proteins.

Recent experimental studies of the denatured state and theoretical analyses of the folding landscape suggest that there are a large multiplicity of low-energy, partially folded conformations near the native state. In this report, we describe a strategy for predicting protein structure based on the working hypothesis that there are a greater number of low-energy conformations surrounding the correct fold than there are surrounding low-energy incorrect folds. To test this idea, 12 ensembles of 500 to 1,000 low-energy structures for 10 small proteins were analyzed by calculating the rms deviation of the Calpha coordinates between each conformation and every other conformation in the ensemble. In all 12 cases, the conformation with the greatest number of conformations within 4-A rms deviation was closer to the native structure than were the majority of conformations in the ensemble, and in most cases it was among the closest 1 to 5%. These results suggest that, to fold efficiently and retain robustness to changes in amino acid sequence, proteins may have evolved a native structure situated within a broad basin of low-energy conformations, a feature which could facilitate the prediction of protein structure at low resolution.

Computer Simulation↗
PubMed1998

Prediction of local structure in proteins using a library of sequence-structure motifs.

We describe a new method for local protein structure prediction based on a library of short sequence pattern that correlate strongly with protein three-dimensional structural elements. The library was generated using an automated method for finding correlations between protein sequence and local structure, and contains most previously described local sequence-structure correlations as well as new relationships, including a diverging type-II beta-turn, a frayed helix, and a proline-terminated helix. The query sequence is scanned for segments 7 to 19 residues in length that strongly match one of the 82 patterns in the library. Matching segments are assigned the three-dimensional structure characteristic of the corresponding sequence pattern, and backbone torsion angles for the entire query sequence are then predicted by piecing together mutually compatible segment predictions. In predictions of local structure in a test set of 55 proteins, about 50% of all residues, and 76% of residues covered by high-confidence predictions, were found in eight-residue segments within 1.4 A of their true structures. The predictions are complementary to traditional secondary structure predictions because they are considerably more specific in turn regions, and may contribute to ab initio tertiary structure prediction and fold recognition.

Algorithms↗
PubMed1998

Cytokine gene therapy in experimental allergic encephalomyelitis by injection of plasmid DNA-cationic liposome complex into the central nervous system.

Experimental allergic encephalomyelitis (EAE) is an autoimmune disease of the central nervous system with many similarities to multiple sclerosis. The main effector cells involved are CD4+ T cells, recognizing encephalitogenic epitopes within the central nervous system, and macrophages, both of which secrete proinflammatory cytokines, such as IFN-gamma and TNF. Studies have shown that immunomodulation of this inflammatory response by anti-inflammatory cytokines (IL-4, IL-10, IFN-beta, and TGF-beta) can reduce clinical severity in EAE. The importance of TNF in EAE has been demonstrated by using soluble TNF-receptor molecules to inhibit EAE. However, the limitation of this type of therapy is the necessity for frequent administration of cytokine proteins due to their short biologic half-life. This study demonstrates that EAE can be inhibited by a single injection of therapeutic cytokine (IL-4, IFN-beta, and TGF-beta) DNA-cationic liposome complex directly into the central nervous system. DNA coding for a novel, dimeric form of human p75 TNF receptor also ameliorated clinical EAE. Local administration of DNA-cationic liposome complex has identified gene targets that may be more efficiently exploited using vectors producing more stable expression for effective treatment of neuroimmunologic disease.

Animals↗
PubMed1998

The sequences of small proteins are not extensively optimized for rapid folding by natural selection.

The thermodynamic stabilities of small protein domains are clearly subject to natural selection, but it is less clear whether the rapid folding rates typically observed for such proteins are consequences of direct evolutionary optimization or reflect intrinsic physical properties of the polypeptide chain. This issue can be investigated by comparing the folding rates of laboratory-generated protein sequences to those of naturally occurring sequences provided that the method by which the sequences are generated has no kinetic bias. Herein we report the folding thermodynamics and kinetics of 12 heavily mutated variants of the small IgG binding domain of protein L retrieved from high-complexity combinatorial libraries by using a phage-display selection for proper folding that does not discriminate between rapidly and slowly folding proteins. Although the stabilities of all variants were decreased, many of the variants fold faster than wild type. Taken together with similar results for the src homology 3 domain, this observation suggests that the sequences of small proteins have not been extensively optimized for rapid folding; instead, rapid folding appears to be a consequence of selection for stability.

Bacterial Proteins↗
PubMed1998

Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water.

The contribution of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water was investigated by comparing the potential of mean force (PMF) between two methane molecules in TIP4P water to those in a series of related liquids in which the solvent-solvent interactions were progressively turned off while keeping the solvent-solute interactions unchanged. The magnitude of the attraction between methanes was not significantly changed when the hydrogen bonding interaction between solvent molecules was eliminated and the solvent was maintained in the liquid state by increasing either the pressure or the magnitude of the solvent-solvent van der Waals interaction. However, when solvent-solvent excluded volume interactions were eliminated, the methane molecules interacted no more strongly than in the gas phase. The results are consistent with the idea that the primary contribution of hydrogen bonding to the hydrophobic interaction is to keep water molecules in a liquid state; at constant density, packing interactions rather than hydrogen bonding appear to be critical as suggested by scaled particle theories of solvation. The overall shape of the PMF was, however, changed in the absence of hydrogen bonding, pointing to an influence of hydrogen bonding on the detailed form of the interactions between nonpolar solutes in water. The effects of correlations between the configurations sampled during the Monte Carlo procedure used in the free energy calculations on the estimation of errors was also characterized.

Hydrogen Bonding↗
PubMed1998

Contact order, transition state placement and the refolding rates of single domain proteins.

Theoretical studies have suggested relationships between the size, stability and topology of a protein fold and the rate and mechanisms by which it is achieved. The recent characterization of the refolding of a number of simple, single domain proteins has provided a means of testing these assertions. Our investigations have revealed statistically significant correlations between the average sequence separation between contacting residues in the native state and the rate and transition state placement of folding for a non-homologous set of simple, single domain proteins. These indicate that proteins featuring primarily sequence-local contacts tend to fold more rapidly and exhibit less compact folding transition states than those characterized by more non-local interactions. No significant relationship is apparent between protein length and folding rates, but a weak correlation is observed between length and the fraction of solvent-exposed surface area buried in the transition state. Anticipated strong relationships between equilibrium folding free energy and folding kinetics, or between chemical denaturant and temperature dependence-derived measures of transition state placement, are not apparent. The observed correlations are consistent with a model of protein folding in which the size and stability of the polypeptide segments organized in the transition state are largely independent of protein length, but are related to the topological complexity of the native state. The correlation between topological complexity and folding rates may reflect chain entropy contributions to the folding barrier.

Animals↗
PubMed1998

Optic neuritis in chronic relapsing experimental allergic encephalomyelitis in Biozzi ABH mice: demyelination and fast axonal transport changes in disease.

The encephalitogenicity of optic nerve tissue was demonstrated in Biozzi ABH (H-2(dq1)) mice. Acute experimental allergic encephalomyelitis (EAE) occurred in 11/14 animals and 4/5 exhibited relapse. The involvement of the optic nerve in spinal cord homogenate induced chronic relapsing EAE (CREAE) was demonstrated by mononuclear cell infiltration and myelin degradation in the optic nerve prior to and during clinical disease. During the relapse phase gross pathological assessment revealed swollen and translucent plaques on the optic nerves. Advanced lesions showed widespread demyelination, astrocytic gliosis and fibrotic changes of the blood vessels. Physiologically, the fast axonal transport of proteins from the retina to the optic nerve and superior colliculus was significantly decreased during relapse. The association of inflammation and demyelination with physiological deficit in the optic nerve highlights the usefulness of this model in the study of multiple sclerosis in which acute monosymptomatic unilateral optic neuritis is a common manifestation. Furthermore, the novel induction of CREAE with optic nerve homogenate suggests that optic neuritis is a common significant role in the pathophysiology and progression of neurological disease in CREAE which may be relevant to studies of optic neuritis in multiple sclerosis.

Animals↗
PubMed1998

Self-administered topical 5% imiquimod cream for external anogenital warts. HPV Study Group. Human PapillomaVirus.

OBJECTIVE: To compare the safety and effectiveness of 5% and 1% imiquimod cream with vehicle cream in the treatment of external anogenital warts. DESIGN: Randomized, double-blind, placebo-controlled comparison that evaluated patients for total clearance of their warts. Patients who experienced total clearance were evaluated for recurrence in a 12-week follow-up. SETTING: Eleven ambulatory offices, including both private physician offices and referral medical centers. PATIENTS: Three hundred eleven healthy men and women aged 18 years or older with 2 to 50 external anogenital warts were recruited from the practices of investigators, referring physicians, and advertisements. Eighty-two additional patients were screened but did not qualify. Four patients discontinued use of the medication because of adverse effects. INTERVENTIONS: Five percent imiquimod (Aldara) cream, 1% imiquimod cream, or vehicle cream was applied to all external warts overnight 3 times each week for 16 weeks, or until all treated warts disappeared, whichever occurred first. MAIN OUTCOME MEASUREMENTS: The number of patients experiencing the elimination of all baseline warts and the recurrence rate of these warts. In addition, the reduction in baseline wart area the duration of therapy required to eliminate warts, and the frequency and severity of adverse reactions were principal measurements. RESULTS: In the intent-to-treat analysis, 54 (50%) of 109 patients who received 5% imiquimod cream, 21 (21%) of 102 of those who received 1% imiquimod cream, and 11 (11%) of 100 patients treated with vehicle cream experienced eradication of all treated baseline warts. The difference between the effectiveness of 5% imiquimod cream and the vehicle cream was statistically significant (P < .001). Of those patients whose warts cleared during therapy, 13% of patients who received 5% imiquimod experienced a recurrence of at least 1 wart. Recurrences occurred in none of the patients who used 1% imiquimod cream and in 10% of patients who used the vehicle cream. Local erythema was the most common adverse reaction, but the majority of patients in each group experienced no or only mild local inflammatory reactions. There were no differences in incidences of flulike symptoms among treatment groups. CONCLUSIONS: Five percent imiquimod cream is an effective and safe self-administered therapy for external anogenital warts when applied 3 times a week overnight for up to 16 weeks. The recurrence rate is low.

Adjuvants, Immunologic↗
PubMed1998

Body image dissatisfaction and eating attitudes in visually impaired women.

OBJECTIVE: The high levels of body dissatisfaction and abnormal eating attitudes currently prevalent in Western societies have been attributed by many authors to the promotion of an unrealistically thin ideal for women. We investigated the role of the visual media by examining the relationship between body image dissatisfaction and eating attitudes in visually impaired women. METHOD: Questionnaires were administered to 60 women, 20 congenitally blind, 20 blinded later in life, and 20 sighted. RESULTS: Congenitally blind women had lower body dissatisfaction scores and more positive eating attitudes compared to women blinded later in life and sighted women, the latter having the highest body dissatisfaction scores and the most negative eating attitudes. Scores from sighted women were positively correlated with each other. DISCUSSION: The results suggest the importance of the visual media in promoting unrealistic images of thinness and beauty and are discussed from a sociocultural perspective.

Adult↗
PubMed1998

Local gene therapy with CTLA4-immunoglobulin fusion protein in experimental allergic encephalomyelitis.

It has been reported previously that the induction phase of experimental allergic encephalomyelitis (EAE) is highly sensitive to systemic blockade of stimulation via MHC class II molecules and co-stimulation via the CD28:CD80/CD86 pathways. In contrast, the effector phases of EAE were relatively unaffected by similar treatments using MHC class II antigen (Ag)-specific mAb and cytotoxic T lymphocyte antigen (CTLA)4-Ig fusion proteins in some studies. This has been attributed to different sensitivities of effector cell function or the poor penetrance of inhibitory proteins into the central nervous system (CNS). To examine this question further, MHC class II Ag-specific mAb and CTLA4-Ig were delivered directly into the CNS following EAE induction, and both were found to inhibit disease. While it was found that systemic administration of mouse CTLA4-Ig could also inhibit the progression of effector immune responses when administered shortly before or during clinical disease, these were significantly more active when delivered directly into the CNS, which probably involved an action on both CD28 ligands, CD80 and CD86. Although mouse CTLA4-human Ig was therapeutically less efficient than mouse CTLA4-mouse Ig protein, probably due to the enhanced immunogenicity and lower functional activity, gene delivery of CTLA4-human Ig into the CNS using a non-replicating adenoviral vector was more effective than a single injection of CTLA4-human Ig protein. Gene delivery significantly ameliorated the development of EAE, without necessarily inhibiting unrelated peripheral immune responsiveness. Local gene delivery of CTLA4-Ig may thus be an important target for immunotherapy of human autoimmune conditions such as multiple sclerosis.

Abatacept↗
PubMed1998

Prediction and structural characterization of an independently folding substructure in the src SH3 domain.

Previous studies of the conformations of peptides spanning the length of the alpha-spectrin SH3 domain suggested that SH3 domains lack independently folding substructures. Using a local structure prediction method based on the I-sites library of sequence-structure motifs, we identified a seven residue peptide in the src SH3 domain predicted to adopt a native-like structure, a type II beta-turn bridging unpaired beta-strands, that was not contained intact in any of the SH3 domain peptides studied earlier. NMR characterization confirmed that the isolated peptide, FKKGERL, adopts a structure similar to that adopted in the native protein: the NOE and 3JNHalpha coupling constant patterns were indicative of a type II beta-turn, and NOEs between the Phe and the Leu side-chains suggest that they are juxtaposed as in the prediction and the native structure. These results support the idea that high-confidence I-sites predictions identify protein segments that are likely to form native-like structures early in folding.

Amino Acid Sequence↗
PubMed1998

In vivo study of meshes implanted over the inguinal ring and external iliac vessels in uncastrated pigs.

BACKGROUND: The effects of placing a prosthesis directly on the internal inguinal ring and external iliac vessels in inguinal hernia repair are unknown. We compared tissue responses to five prostheses implanted in this position in uncastrated male pigs. METHODS: Three types of polypropylene and two types of expanded polytetrafluoroethylene (ePTFE) mesh were implanted in 20 pigs (n = 8 for each prosthesis type). Specimens of the implants and surrounding tissue were obtained 30 and 90 days after implantation and assessed histologically. RESULTS: The polypropylene implants had more adhesions, more surface area covered by adhesions, and more tenacious adhesions than did the ePTFE implants. Perivascular cuffing was observed in eight polypropylene and one ePTFE specimen; ossification, necrosis, and testicular venous congestion were seen in polypropylene specimens. CONCLUSIONS: Abnormal healing processes after implantation of polypropylene mesh may increase complications of the transabdominal preperitoneal and total extraperitoneal approaches in laparoscopic inguinal hernia repair, whereas the minimal response to ePTFE meshes may make them safer for use in the preperitoneal space.

Animals↗
PubMed1998

Relationship of indoor allergen exposure to skin test sensitivity in inner-city children with asthma.

BACKGROUND: It is important to understand the relationship between environmental allergen exposure dose and the risk of atopic individuals becoming sensitized to that allergen if we are to change the risk of sensitization and morbidity from allergic disease. OBJECTIVE: The objective of these studies was to determine whether there was a dose response between current exposure to mite, cockroach, and cat allergen in inner-city children and to determine the prevalence of sensitization to these allergens. METHODS: A sample of 500 children was selected from the 1528 children enrolled in the National Cooperative Inner City Asthma Study. Children were selected who had a sample of home dust and valid skin test responses performed with a MultiTest skin test device. The samples of home dust were collected from the floor and furniture in the kitchen, bedroom, and television/living room and were assayed for Der p 1, Der f 1, Bla g 1, and Fel d 1 allergens. RESULTS: Each allergen level correlated significantly between rooms in individual homes. Mite (Der p 1 and Der f 1) and cat (Fel d 1) allergen levels were frequently below the detection limit of the assay. Cockroach allergen (Bla g 1) concentrations in the child's bedroom were related to the prevalence of positive skin test responses to cockroach allergen extract among the children, with an odds ratio for sensitization of 1.45 (1.11-1.92). Positive skin test responses to cockroach allergen were seen in 15% of children exposed to bedroom dust with a Bla g 1 concentration below the level of detection compared with a rate of 32% in bedrooms with Bla g 1 levels of 1 to 2 U/g and 40% to 44% among those in rooms with 4 U/g or greater. The relationship between exposure and positive skin test responses was clearly stronger among atopic children with a greater number of positive skin test responses. CONCLUSIONS: Despite widespread exposure to household allergens, the strongest relationship between exposure and sensitization was seen in the bedroom. The dose response between exposure to cockroach allergen and sensitization suggested that exposure to low doses of allergen, 2 U/g or less, was a risk factor and that the risk plateaus above 4 U/g. Atopy modified the relationship of exposure to sensitization.

Air Pollution, Indoor↗
PubMed1998

Successful techniques for retention of study participants in an inner-city population.

The purpose of this work was to describe methods of retaining participants in studies of inner-city populations, including the timing and intensity of contacts; and to describe the characteristics of participants who did not complete all follow-up interviews and/or return all peak flow diaries in the National Cooperative Inner-City Asthma Study. A cohort study design was used involving hospital emergency rooms and community clinics in seven major urban areas. Participants included 1337 4- to 9-year-old asthmatic children and their caretakers. Nearly 89% of participants completed 3-, 6-, and 9-month follow-up interviews. The 15% of participants who completed a baseline interview on the weekends were significantly more likely to complete follow-up interviews on a weekend. The percent of follow-up interviews conducted in person increased over time from 5% to 8%. The percent of participants with complete follow-up increased as the number of contact names increased (86% with zero contacts, 91% with two contracts; p = 0.03, test for trend). Participants who required at least four phone calls to complete the 3- and 6-month assessment were significantly more likely to be black, have higher participant stress, and have a smoker in the household (p < 0.05). Multiple logistic regression suggests that higher social support and lower parental stress were both predictors of completed interviews. Within our study sample of inner-city minority participants with asthmatic children, only a small proportion of participants missed any follow-up interviews. Increased caretaker stress, decreased social support, and inability to provide several alternate contacts were all predictive of retention problems. Having a flexible staff, computer tracking, and face-to-face recruitment appear essential to achieving nearly complete follow-up within a population historically difficult to follow.

Asthma↗
PubMed1998

Simplified proteins: minimalist solutions to the 'protein folding problem'.

Recent research has suggested that stable, native proteins may be encoded by simple sequences of fewer than the full set of 20 proteogenic amino acids. Studies of the ability of simple amino acid sequences to encode stable, topologically complex, native conformations and to fold to these conformations in a biologically relevant time frame have provided insights into the sequence determinants of protein structure and folding kinetics. They may also have important implications for protein design and for theories of the origins of protein synthesis itself.

Amino Acid Sequence↗
PubMed1998

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain.

Experimental and theoretical studies on the folding of small proteins such as the chymotrypsin inhibitor 2 (CI-2) and the P22 Arc repressor suggest that the folding transition state is an expanded version of the native state with most interactions partially formed. Here we report that this picture does not hold generally: a hydrogen bond network involving two beta-turns and an adjacent hydrophobic cluster appear to be formed in the folding transition state of the src SH3 domain, while the remainder of the polypeptide chain is largely unstructured. Comparison with data on other small proteins suggests that this structural polarization is a consequence of the topology of the SH3 domain fold. The non-uniform distribution of structure in the folding transition state provides a challenging test for computational models of the folding process.

Flow Injection Analysis↗