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Biomedical subjects

B Rost

Publications and source records attributed to B Rost.

At least 19 recordsLinked to original sources
PubMed2000

Cutaneous manifestations in anorexia nervosa.

Anorexia nervosa is an eating disorder among adolescent girls and young women which, though common, often goes undetected and untreated. Anorexia nervosa is a response for young people with psychological conflicts who try to win love by having a body corresponding to the present-day image, symbolising strength, beauty, attraction, power and success. Anorexia nervosa involves inadequate calorie intake leading to marked cachexia with metabolic and endocrinological disturbances. We investigated dermatological changes in 21 young female anorectics aged 19-24 in an attempt to find dermatological markers which mirror the dynamics of the disease and thus obtain helpful signs for early diagnosis with its important bearing on the outcome. Extensive histories were taken and whole-body examinations performed. Seven sex- and age-matched persons served as a control group. The most common dermatological findings were xerosis (71%, controls 29%), cheilitis (76%), bodily hypertrichosis (62%), alopecia (24%), dry scalp hair (48%), acral coldness (38%), acrocyanosis (33%), periungual erythema (48%), gingival changes (37%), nail changes (29%) and calluses on dorsum of hand due to self-induced vomiting (67%). Our study documented for the first time that a body mass index of < or = 16 (kg/m2) can be considered a critical value at which skin changes are more frequent. There are remarkable similarities between cutaneous manifestations in anorexia nervosa and in HIV infection. Patients with anorexia nervosa develop early stereotype skin changes which are cardinal diagnostic symptoms and pointers to the diagnosis of eating disorders. During training at the Department of Child and Adolescent Psychiatry in Solothurn one of us (C. H.) was once more able to observe most of the above-described cutaneous and mucocutaneous changes in anorexic adolescents. This paper is intended to stimulate further basic research on this topic. We hope our study will facilitate early diagnosis of anorexia nervosa by the family physician and enable him or her to institute immediate treatment for the eating disorder and thereby improve the prognosis.

Adolescent↗
PubMed1999

Effective use of sequence correlation and conservation in fold recognition.

Protein families are a rich source of information; sequence conservation and sequence correlation are two of the main properties that can be derived from the analysis of multiple sequence alignments. Sequence conservation is related to the direct evolutionary pressure to retain the chemical characteristics of some positions in order to maintain a given function. Sequence correlation is attributed to the small sequence adjustments needed to maintain protein stability against constant mutational drift. Here, we showed that sequence conservation and correlation were each frequently informative enough to detect incorrectly folded proteins. Furthermore, combining conservation, correlation, and polarity, we achieved an almost perfect discrimination between native and incorrectly folded proteins. Thus, we made use of this information for threading by evaluating the models suggested by a threading method according to the degree of proximity of the corresponding correlated, conserved, and apolar residues. The results showed that the fold recognition capacity of a given threading approach could be improved almost fourfold by selecting the alignments that score best under the three different sequence-based approaches.

Amino Acid Sequence↗
PubMed1999

Time-resolved FT-IR studies on the CO adduct of Paracoccus denitrificans cytochrome c oxidase: comparison of the fully reduced and the mixed valence form.

The rebinding of CO to cytochrome c oxidase from Paracoccus denitrificans in the fully reduced and in the half-reduced (mixed valence) form as a function of temperature was investigated using time-resolved rapid-scan FT-IR spectroscopy in the mid-IR (1200-2100 cm-1). For the fully reduced enzyme, rebinding was complete in approximately 2 s at 268 K and showed a biphasic reaction. At 84 K, nonreversible transfer of CO from heme a3 to CuB was observed. Both photolysis at 84 K and photolysis at 268 K result in FT-IR difference spectra which show similarities in the amide I, amide II, and heme modes. Both processes, however, differ in spectral features characteristic for amino acid side chain modes and may thus be indicative for the motional constraint of CO at low temperature. Rebinding of photodissociated CO for the mixed-valence enzyme at 268 K is also biphasic, but much slower as compared to the fully reduced enzyme. FT-IR difference spectra show band features similar to those for the fully reduced enzyme. Additional strong bands in the amide I and amide II range indicate local conformational changes induced by electron and coupled proton transfer. These signals disappear when the temperature is lowered to 84 K. At 268 K, a difference signal at 1746 cm-1 is observed which is shifted by 6 cm-1 to 1740 cm-1 in 2H2O. The absence of this signal for the mutant Glu 278 Gln allows assignment to the COOH stretching mode of Glu 278, and indicates changes of the conformation, proton position, or protonation of this residue upon electron transfer.

Carbon Monoxide↗
PubMed1999

A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment.

We present a measure for the evaluation of secondary structure prediction methods that is based on secondary structure segments rather than individual residues. The algorithm is an extension of the segment overlap measure Sov, originally defined by Rost et al. (J Mol Biol 1994;235:13-26). The new definition of Sov corrects the normalization procedure and improves Sov's ability to discriminate between similar and dissimilar segment distributions. The method has been comprehensively tested during the second Critical Assessment of Techniques for Protein Structure Prediction (CASP2). Here, we describe the underlying concepts, modifications to the original definition, and their significance.

Algorithms↗
PubMed1999

CAFASP-1: critical assessment of fully automated structure prediction methods.

The results of the first Critical Assessment of Fully Automated Structure Prediction (CAFASP-1) are presented. The objective was to evaluate the success rates of fully automatic web servers for fold recognition which are available to the community. This study was based on the targets used in the third meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP-3). However, unlike CASP-3, the study was not a blind trial, as it was held after the structures of the targets were known. The aim was to assess the performance of methods without the user intervention that several groups used in their CASP-3 submissions. Although it is clear that "human plus machine" predictions are superior to automated ones, this CAFASP-1 experiment is extremely valuable for users of our methods; it provides an indication of the performance of the methods alone, and not of the "human plus machine" performance assessed in CASP. This information may aid users in choosing which programs they wish to use and in evaluating the reliability of the programs when applied to their specific prediction targets. In addition, evaluation of fully automated methods is particularly important to assess their applicability at genomic scales. For each target, groups submitted the top-ranking folds generated from their servers. In CAFASP-1 we concentrated on fold-recognition web servers only and evaluated only recognition of the correct fold, and not, as in CASP-3, alignment accuracy. Although some performance differences appeared within each of the four target categories used here, overall, no single server has proved markedly superior to the others. The results showed that current fully automated fold recognition servers can often identify remote similarities when pairwise sequence search methods fail. Nevertheless, in only a few cases outside the family-level targets has the score of the top-ranking fold been significant enough to allow for a confident fully automated prediction. Because the goals, rules, and procedures of CAFASP-1 were different from those used at CASP-3, the results reported here are not comparable with those reported in CASP-3. Nevertheless, it is clear that current automated fold recognition methods can not yet compete with "human-expert plus machine" predictions. Finally, CAFASP-1 has been useful in identifying the requirements for a future blind trial of automated served-based protein structure prediction.

Algorithms↗
PubMed1999

Metabolic changes in the brain of patients with anorexia and bulimia nervosa as detected by proton magnetic resonance spectroscopy.

OBJECTIVE: To investigate the brain of patients with anorexia and bulimia nervosa by localized proton magnetic resonance spectroscopy (1H-MRS) and to look for metabolic alterations. METHOD: Twenty patients with anorexia and bulimia nervosa were investigated by magnetic resonance imaging (MRI) and 1H-MRS in three regions of the brain. Age and sex-matched healthy subjects were investigated as controls. RESULTS: 1H-MRS revealed metabolic changes, such as a significant decrease of both myo-inositol and lipid compounds within the frontal white matter. The concentration of these compounds was further reduced with decreasing body mass index. Reduced lipid signals were also found in the occipital gray matter. In the cerebellum, the concentration of all metabolites including water, except lipids, was increased. DISCUSSION: The metabolic changes found in this study seem to be a consequence of nutritional deficiency. It has to be further investigated whether these findings have any relevance for brain function. 1H-MRS might serve as a valuable investigative tool to observe eating disorders as anorexia and bulimia nervosa and to follow the success of therapy.

Adolescent↗
PubMed1999

Evaluation of a guinea pig model to assess interference in the immunogenicity of different components of a combination vaccine comprising diphtheria, tetanus and acellular pertussis (DTaP) vaccine and haemophilus influenzae type b capsular polysaccharide conjugate vaccine.

A guinea pig model to assess the immunogenicity of a combination vaccine containing diphtheria, tetanus and acellular pertussis (DTaP) vaccine and Haemophilus influenzae type b (Hib) capsular polysaccharide conjugated to tetanus toxoid (HibT) was evaluated comparatively with the mouse immunogenicity test to study the effect of combining these antigens on the immunogenicity of various components. The immunogenicity test in mice was performed by subcutaneous injection of groups of 10 animals twice at an interval of four weeks with 1/10 of a single human dose of various formulations of combination vaccines, DTaP or HibT vaccine. The animals were bled at 4 and 6 weeks and IgG or total antibodies to various components were determined by ELISA or RIA. The guinea pig immunogenicity model included groups of animals injected subcutaneously twice at an interval of six weeks with 1.5 times the single human dose of various formulations. The animals were bled at 4, 6 and 8 weeks and serum samples were tested for antibodies to various components by ELISA, RIA and/or neutralization tests. Additionally, potency of tetanus and diphtheria components was assessed as per the US Food and Drug Administration's regulations. Aluminium phosphate (AIPO(4)) adsorbed HibT vaccine or HibT as a combination with AIPO(4)adsorbed DTaP vaccine showed significant increases in IgG antibodies to tetanus toxin in mice as well increased tetanus antitoxin levels in guinea pigs as compared to soluble HibT vaccine. In general, combining DTaP and HibT vaccines did not affect the antibody levels to tetanus and diphtheria toxoids whereas DTaP-HibT combination vaccine elicited significantly lower IgG antibodies to pertussis toxin and filamentous haemagglutinin than DTaP vaccine alone, particularly after first injection. Mice showed similar Hib antibody responses for the combination and HibT alone whereas guinea pigs consistently showed lower anamnestic responses to Hib for combination formulations than for HibT alone. Reducing the amount of HibT and/or tetanus toxoid in the combination formulations reduced this suppression of Hib antibody response in guinea pigs. Suppression of Hib antibody response in combination vaccines has also been reported from recent clinical trials. Based on the results from this study, it appears that the guinea pig model may be able to predict the human response to various components of combination vaccines.

Animals↗
PubMed1999

Twilight zone of protein sequence alignments.

Sequence alignments unambiguously distinguish between protein pairs of similar and non-similar structure when the pairwise sequence identity is high (>40% for long alignments). The signal gets blurred in the twilight zone of 20-35% sequence identity. Here, more than a million sequence alignments were analysed between protein pairs of known structures to re-define a line distinguishing between true and false positives for low levels of similarity. Four results stood out. (i) The transition from the safe zone of sequence alignment into the twilight zone is described by an explosion of false negatives. More than 95% of all pairs detected in the twilight zone had different structures. More precisely, above a cut-off roughly corresponding to 30% sequence identity, 90% of the pairs were homologous; below 25% less than 10% were. (ii) Whether or not sequence homology implied structural identity depended crucially on the alignment length. For example, if 10 residues were similar in an alignment of length 16 (>60%), structural similarity could not be inferred. (iii) The 'more similar than identical' rule (discarding all pairs for which percentage similarity was lower than percentage identity) reduced false positives significantly. (iv) Using intermediate sequences for finding links between more distant families was almost as successful: pairs were predicted to be homologous when the respective sequence families had proteins in common. All findings are applicable to automatic database searches.

Computer Simulation↗
PubMed1999

MRS of the brain in patients with anorexia or bulimia nervosa.

Twenty patients with anorexia or bulimia nervosa were prospectively investigated by magnetic resonance spectroscopy (MRS) of the brain. Compared to healthy controls, MRS of those with eating disorders revealed metabolic changes, which seem to be a consequence of their nutritional deficiency.

Adolescent↗
PubMed1998

Adaptation of protein surfaces to subcellular location.

In vivo, proteins occur in widely different physio-chemical environments, and, from in vitro studies, we know that protein structure can be very sensitive to environment. However, theoretical studies of protein structure have tended to ignore this complexity. In this paper, we have approached this problem by grouping proteins by their subcellular location and looking at structural properties that are characteristic to each location. We hypothesize that, throughout evolution, each subcellular location has maintained a characteristic physio-chemical environment, and that proteins in each location have adapted to these environments. If so, we would expect that protein structures from different locations will show characteristic differences, particularly at the surface, which is directly exposed to the environment. To test this hypothesis, we have examined all eukaryotic proteins with known three-dimensional structure and for which the subcellular location is known to be either nuclear, cytoplasmic, or extracellular. In agreement with previous studies, we find that the total amino acid composition carries a signal that identifies the subcellular location. This signal was due almost entirely to the surface residues. The surface residue signal was often strong enough to accurately predict subcellular location, given only a knowledge of which residues are at the protein surface. The results suggest how the accuracy of prediction of location from sequence can be improved. We concluded that protein surfaces show adaptation to their subcellular location. The nature of these adaptations suggests several principles that proteins may have used in adapting to particular physio-chemical environments; these principles may be useful for protein design.

Amino Acids↗
PubMed1998

Role of transmembrane domains in the functions of B- and T-cell receptors.

The antigen receptors on the surface of B- and T-lymphocytes are complexes of several integral membrane proteins, essential for their proper expression and function. Recent studies demonstrated that transmembrane (TM) domains of the components of these receptors play a critical role in their association and function. It was specifically demonstrated that in many cases point mutations in the TM domains can partially or completely disrupt the receptor surface expression and function. Here we review studies of the TM domains of B- and T-cell receptors. Furthermore, we use a novel method, PHDtopology, to provide estimates of the exact locations and lengths of the TM domains of the subunit components of these receptors. Most previous studies used single residue hydrophobicity as a criterion for determining the position and length of the TM domains. In contrast, PHDtopology utilizes a system of neural networks and the evolutionary information contained in multiple alignments of related sequences to predict the location, length, and orientation of transmembrane helices. Present results significantly differ from most published estimates of the TM domains of the B- and T-cell receptor components, primarily in the length of the TM domains. These results may lead to modification of putative TM motifs and re-interpretation of the results of studies using mutated TM domains. The availability of PHDtopology on the Internet would make it a valuable tool in the future studies of the TM domains of integral membrane proteins.

Amino Acid Sequence↗
PubMed1997

Protein fold recognition by prediction-based threading.

In fold recognition by threading one takes the amino acid sequence of a protein and evaluates how well it fits into one of the known three-dimensional (3D) protein structures. The quality of sequence-structure fit is typically evaluated using inter-residue potentials of mean force or other statistical parameters. Here, we present an alternative approach to evaluating sequence-structure fitness. Starting from the amino acid sequence we first predict secondary structure and solvent accessibility for each residue. We then thread the resulting one-dimensional (1D) profile of predicted structure assignments into each of the known 3D structures. The optimal threading for each sequence-structure pair is obtained using dynamic programming. The overall best sequence-structure pair constitutes the predicted 3D structure for the input sequence. The method is fine-tuned by adding information from direct sequence-sequence comparison and applying a series of empirical filters. Although the method relies on reduction of 3D information into 1D structure profiles, its accuracy is, surprisingly, not clearly inferior to methods based on evaluation of residue interactions in 3D. We therefore hypothesise that existing 1D-3D threading methods essentially do not capture more than the fitness of an amino acid sequence for a particular 1D succession of secondary structure segments and residue solvent accessibility. The prediction-based threading method on average finds any structurally homologous region at first rank in 29% of the cases (including sequence information). For the 22% first hits detected at highest scores, the expected accuracy rose to 75%. However, the task of detecting entire folds rather than homologous fragments was managed much better; 45 to 75% of the first hits correctly recognised the fold.

Algorithms↗
PubMed1997

Better 1D predictions by experts with machines.

Accuracy of predicting protein secondary structure and solvent accessibility has been improved significantly by using evolutionary information contained in multiple sequence alignments. For the second Asilomar meeting, predictions were made automatically for all targets using the publicly available prediction service PredictProtein. Additionally, a semiautomatic procedure for generating more informative alignments was used in combination with the PHD prediction methods. Results confirmed the estimates for prediction accuracy. Furthermore, the more informative alignments yielded better predictions. The fairly accurate predictions of 1D structure were successfully used by various groups for the Asilomar meeting as first step toward predicting higher dimensions of protein structure.

Expert Systems↗
PubMed1997

Protein structures sustain evolutionary drift.

A protein sequence folds into a unique three-dimensional protein structure. Different sequences, though, can fold into similar structures. How stable is a protein structure with respect to sequence changes? What percentage of the sequence is 'anchor' residues, that is, residues crucial for protein structure and function? Here, answers to these questions are pursued by analyzing large numbers of structurally homologous protein pairs. Most pairs of similar structures have sequence identity as low as expected from randomly related sequences (8-9%). On average, only 3-4% of all residues are 'anchor' residues. The symmetric shape of the distribution at low sequence identity suggests that for most structures, four billion years of evolution was sufficient to reach an equilibrium. The mean identities for convergent (different ancestor) and divergent (same ancestor) evolution of proteins to similar structures are quite close and hence, in most cases, it is difficult to distinguish between the two effects. In particular, low levels of sequence identity appear not to be indicative of convergent evolution.

Bias↗
PubMed1997

Sisyphus and prediction of protein structure.

The problem of predicting protein structure from the sequence remains fundamentally unsolved despite more than three decades of intensive research effort. However, new and promising methods in three-dimensional (3D), 2D and 1D prediction have reopened the field. Mean-force-potentials derived from the protein databases can distinguish between correct and incorrect models (3D). Inter-residue contacts (2D) can be detected by analysis of correlated mutations, albeit with low accuracy. Secondary structure, solvent accessibility and transmembrane helices (1D) can be predicted with significantly improved accuracy using multiple sequence alignments. Some of these new prediction methods have proven accurate and reliable enough to be useful in genome analysis, and in experimental structure determination. Moreover, the new generation of theoretical methods is increasingly influencing experiments in molecular biology.

Computers↗
PubMed1996

Carboxyl group protonation upon reduction of the Paracoccus denitrificans cytochrome c oxidase: direct evidence by FTIR spectroscopy.

The redox reactions of the cytochrome c oxidase from Paracoccus denitrificans were investigated in a thin-layer cell designed for the combination of electrochemistry under anaerobic conditions with UV/VIS and IR spectroscopy. Quantitative and reversible electrochemical reactions were obtained at a surface-modified electrode for all cofactors as indicated by the optical signals in the 400-700 nm range. Fourier transform infrared (FTIR) difference spectra of reduction and oxidation (reduced-minus-oxidized and oxidized-minus-reduced, respectively) obtained in the 1800-1000 cm(-1) range reveal highly structured band features with major contributions in the amide I (1620-1680 cm(-1)) and amide II (1580-1520 cm(-1)) range which indicate structural rearrangements in the cofactor vicinity. However, the small amplitude of the IR difference signals indicates that these conformational changes are small and affect only individual peptide groups. In the spectral region above 1700 cm(-1), a positive peak in the reduced state (1733 cm(-1)) and negative peak in the oxidized st ate (1745 cm(-1)) are characteristic for the formation and decay of a COOH mode upon reduction. The most obvious interpretation of this difference signal is proton uptake by one Asp or Glu side chain carboxyl group in the reduced state and deprotonation of another Asp or Glu residue. Moreover, both residues could well be coupled as a donor-acceptor pair in the proton transfer chain. An alternative interpretation is in terms of a protonated carboxyl group which shifts to a different environment in the reduced state. The relevance of this first direct observation of protein protonation changes in the cytochrome c oxidase for vectorial proton transfer and the catalytic reaction is discussed.

Electron Transport Complex IV↗