Protein structure prediction by threading. Why it works and why it does not

We developed a novel Monte Carlo threading algorithm which allows gaps and insertions both in the template structure and threaded sequence. The algorithm is able to find the optimal sequence-structure alignment and sample suboptimal alignments. Using our algorithm we performed sequence-structure alignments for a number of examples for three protein folds (ubiquitin, immunoglobulin and globin) using both "ideal" set of potentials (optimized to provide the best Z-score for a given protein) and more realistic knowledge-based potentials. Two physically different scenarios emerged. If a template structure is similar to the native one (within 2 A RMS), then (i) the optimal threading alignment is correct and robust with respect to deviations of the potential from the "ideal" one; (ii) suboptimal alignments are very similar to the optimal one; (iii) as Monte Carlo temperature decreases a sharp cooperative transition to the optimal alignment is observed. In contrast, if the template structure is only moderately close to the native structure (RMS greater than 3.5 A), then (i) the optimal alignment changes dramatically when an "ideal" potential is substituted by the real one; (ii) the structures of suboptimal alignments are very different from the optimal one, reducing the reliability of the alignment; (iii) the transition to the apparently optimal alignment is non-cooperative. In the intermediate cases when the RMS between the template and the native conformations is in the range between 2 A and 3.5 A, the success of threading alignment may depend on the quality of potentials used. These results are rationalized in terms of a threading free energy landscape. Possible ways to overcome the fundamental limitations of threading are discussed briefly.     

EEG-based communication: evaluation of alternative signal prediction methods

Individuals can learn to control the amplitude of EEG activity in specific frequency bands over sensorimotor cortex and use it to move a cursor to a target on a computer screen. For one-dimensional (i.e., vertical) cursor movement, a linear equation translates the EEG activity into cursor movement. To translate an individual's EEG control into cursor control as effectively as possible, the intercept in this equation, which determines whether upward or downward movement occurs, should be set so that top and bottom targets are equally accessible. The present study compares alternative methods for using an individual's previous performance to select the intercept for subsequent trials. In offline analyses, five different intercept selection methods were applied to EEG data collected while trained subjects were moving the cursor to targets at the top or bottom edge of the screen. In the first two methods-moving average, and weighted sum-a single intercept was selected for the entire 1-2 sec period of each trial. In the other three methods-blocked moving average, blocked weighted sum, and blocked recursive sum (a variation of the weighted sum)-an intercept was selected for each 200-ms segment of the trial. The results from these methods were compared in regard to their balance between upward and downward movements and their consistency of performance across trials. For all subjects combined, the five methods performed similarly. However, performance across subjects was more consistent for the moving average, blocked moving average, and blocked recursive sum methods than for the weighted sum and blocked weighted sum methods. Due to its consistent performance and its computational simplicity, the moving average method, using the five most recent pairs of top and bottom trials, appears to be the method of choice.     

Protein secondary structure prediction using two-level case-based reasoning

We have developed a two-level case-based reasoning architecture for predicting protein secondary structure. The central idea is to break the problem into two levels: (i) reasoning at the object (protein) level and using the global information from this level to focus on a more restricted problem space; (ii) decomposing objects into pieces (segments) and reasoning at the level of internal structures. As a last step to the procedure, inferences from the parts of the internal structure are synthesized into predictions about global structure. The architecture has been developed and tested on a commonly used data set with 69.5% predictive accuracy. It was then tested on a new data set with 68.2% accuracy. With additional tuning, over 70% accuracy was achieved. In addition, a series of experiments were conducted to test various aspects of the method and the results are informative.     

Adult intussusception: demonstration by current MR techniques

We describe magnetic resonance findings in three patients with small bowel intussusception from different etiologies including idiopathic, adenomatous polyps, and hamartomatous polyps. Magnetic resonance findings showed a bowel-within-bowel appearance in two patients and a coiled-spring appearance in one patient. These findings were best shown on T2-weighted images, and clear definition was present on breathing independent T2-weighted images using half fourier acquisition snap shot turbo spin echo T2-weighted images.     

Ampullary carcinoma: demonstration by current MR techniques

Rheumatoid arthritis (RA) is characterised by chronic inflammation of synovial tissue with aggressive proliferation of synovial cells causing destruction of cartilage and bone. Immunopathological mechanisms, infectious causes and genetic factors have been discussed, but the etiology of the disease has not been understood until now. Especially, the mechanisms driving tumourlike growth and invasive behaviour of fibroblastoid synovial cells have not been identified yet. Our aim is to find cellular factors which are mediators for such pathways. One possibility to approach this, is searching for disease-relevant genes. We applied the mRNA-differential display technique to compare mRNA expression patterns of normal and rheumatic synovial fibroblasts. We identified an upregulation of the human semaphorin E gene in rheumatoid synovial fibroblastoid cells. Interestingly semaphorin E is a member of a protein-family described to play an immunosuppressive role via inhibition cytokines. A relevance of this finding towards the pathogenesis of RA is discussed.     

Protein secondary structure prediction by the analysis of variation and conservation in multiple alignments

A number of methods exist for the prediction of protein secondary structure from primary sequence. One method identifies variable charged and conserved hydrophobic residues within large multiple alignments as a means of indicating outside and inside sites respectively in the protein structure. These sites are then manually fitted to secondary structure templates to generate a secondary structure prediction. Using the existing theoretical bases of this method, we present an algorithm (STAMA) which automatically carries out the initial variation/conservation analysis of the alignment. We also test the accuracy of complete predictions carried out by manual fitting of the STAMA-derived assignments to structure templates, using five large multiple alignments each including a protein of known structure. The method was found on average to predict only 57% of residues in the correct secondary structure, and was only as accurate as predictions carried out using the established and automated method of Garnier, Osguthorpe and Robson (1978) applied to a single sequence. When used in conjunction with other secondary structure prediction methods, however, the resulting consensus predictions were found to be very accurate, with 78% of the elements (alpha helices or beta strands) for which a consensus could be obtained being predicted correctly. The algorithm presented here, plus the assessment of the accuracy of prediction generated by this method, should enable this predictive approach to receive informed general use.     

Assisted conception: current techniques and outcome

PURPOSE: To determine whether ingestion of a tooth whitener containing 6% hydrogen peroxide as bleaching agent affected the gastric mucosa of adult, female laboratory rats. MATERIALS AND METHODS: Thirty-six fasting rats were intubated with a single bolus (5 g/kg body weight) of the tooth whitener Natural White which contains 6% hydrogen peroxide. Thirty-two control rats received deionized water. Rats were necropsied 15 minutes, 2 hours, 1 and 2 weeks after whitener ingestion. The gastric mucosa was examined histologically and blood hematocrit, glucose, BUN, and bilirubin measured. RESULTS: Six of the 36 rats died within 2 hours of receiving whitener. Within 15 minutes of whitener ingestion, stomachs were grossly bloated with gas. Histological observation showed that gastric mucosal cells were vacuolated and gastric glands dilated. After 2 hours, gastric epithelial and glandular cells had sloughed off into the gastric lumen. Mean blood glucose and hematocrit were significantly (P < 0.05) elevated (233 +/- 41 mg/ml and 50.5 +/- 0.9%) over mean control values (129 +/- 8 mg/ml and 42.8 +/- 2.4%). Within 1 week, the stomachs of experimental rats were no longer bloated, the gastric mucosa appeared normal histologically, but mean blood hematocrit was significantly (P < 0.05) decreased (38.0 +/- 1.5%) from mean control value (43.3 +/- 0.5%). There were no significant differences in mean blood values 2 weeks after whitener ingestion.     

White cell-reduced red cells prepared by filtration: a critical evaluation of current filters and methods for counting residual white cells

Atrial natriuretic peptide (ANP) is reported to dilate a major coronary artery in both experimental animals and humans. Spasm of a major coronary artery is the cause of variant angina pectoris and can be induced by hyperventilation. The effect of the ANP infusion on anginal attack induced by hyperventilation was studied in patients with variant angina pectoris. The study was performed in the early morning on 3 consecutive days in 11 patients with variant angina pectoris in whom the attacks were reproducibly induced by hyperventilation. On days 1 and 3 (saline solution infusion), and day 2 (ANP infusion), hyperventilation was started 14 minutes after beginning infusion of ANP (0.1 microgram/kg/min) or saline solution for 6 minutes. The attacks were induced in all 11 patients by hyperventilation on days 1 and 3. However, the attacks were not induced in any patient on day 2 of the ANP infusion. The plasma ANP level increased from 33 +/- 7 pg/ml to the peak level of 2,973 +/- 479 pg/ml (p < 0.01) at the end of the ANP infusion, and the plasma level of cyclic guanosine monophosphate (cGMP) increased from 5 +/- 1 pmol/ml to the peak level of 58 +/- 6 pmol/ml (p < 0.01) 5 minutes after the ANP infusion. The plasma levels of ANP and cGMP did not change after hyperventilation on days 1 and 3. It is concluded that the ANP infusion suppresses the attacks induced by hyperventilation in patients with variant angina pectoris, and cGMP is related to the mechanisms of suppression of the attacks.     

Protein annotation: detective work for function prediction

Agranulocytosis induced by metamizole is uncommon, with a frequency of less than one case per million treatments. We describe such a case in a patient requiring emergency surgery. An 85-year-old man with a history of infantile paralysis with mental retardation and Paget's disease and X-ray signs of the right femur came to the emergency room with a diaphysial fracture. He received 1 g metamizole i.v. every 8 hours for analgesia. Ten hours after admission a routine blood cell count showed a rapid fall in the number of leukocytes; at 24 hours the count was 600 x 10(9)/l. The diagnosis was agranulocytosis induced by metamizole. Postponement of surgery was advisable and treatment with granulocyte colony stimulating factor (GCSF) at a dose of 5 micrograms/kg/day. Agranulocytosis resolved after 3 days of treatment, after which time the bone was set with a straight femoral plate under subarachnoid anesthesia. Two packs of red blood cells were required during the immediate postoperative period. Twelve days after surgery the patient was released. We review the anesthetic approach to agranulocytosis and its treatment.     

A new approach to secondary structure evaluation: secondary structure prediction of porcine adenylate kinase and yeast guanylate kinase by CD spectroscopy of overlapping synthetic peptide segments

A new approach for evaluating the secondary structure of proteins by CD spectroscopy of overlapping peptide segments is applied to porcine adenylate kinase (AK1) and yeast guanylate kinase (GK3). One hundred seventy-six peptide segments of a length of 15 residues, overlapping by 13 residues and covering the complete sequences of AK1 and GK3, were synthesized in order to evaluate their secondary structure composition by CD spectroscopy. The peptides were prepared by solid phase multiple peptide synthesis method using the 9-fluorenylmethoxycarbonyl/tert-butyl strategy. The individual peptide secondary structures were studied with CD spectroscopy in a mixture of 30% trifluoroethanol in phosphate buffer (pH 7) and subsequently compared with x-ray data of AK1 and GK3. Peptide segments that cover alpha-helical regions of the AK1 or GK3 sequence mainly showed CD spectra with increasing and decreasing Cotton effects that were typical for appearing and disappearing alpha-helical structures. For segments with dominating beta-sheet conformation, however, the application of this method is limited due to the stability and clustering of beta-sheet segments in solution and due to the difficult interpretation of random-coiled superimposed beta-sheet CD signals. Nevertheless, the results of this method especially for alpha-helical segments are very impressive. All alpha-helical and 71% of the beta-sheet containing regions of the AK1 and GK3 could be identified. Moreover, it was shown that CD spectra of consecutive peptide content reveal the appearance and disappearance of alpha-helical secondary structure elements and help localizing them on the sequence string.     

Protein structure in KBr pellets by infrared spectroscopy

The S14 ribosomal protein from the thermophilic organism Thermus thermophilus, which contains a zinc-finger-like motif, namely -C-X2-C-X12-C-X2-C- [Tsiboli, P. & Choli, T. (1995) Biol. Chem. Hoppe-Seyler 376, 127-130], has been overproduced, purified and investigated for its zinc content. According to atomic absorption experiments, the protein contains zinc at a molar ratio of one. Denaturation experiments with simultaneous use of denaturing and chelating agents (guanidine hydrochloride and EDTA), as well as renaturation experiments, have shown both that Zn is strongly bound to the protein and with 1:1 Zn/protein stoicheiometry. These findings provide very strong evidence in support of the participation of the zinc-finger motif and the Zn in the formation of a zinc-finger domain.     

Sex-selection of human spermatozoa: evolution of current techniques and applications

The present paper examines the occurrence of matters relating to the ending of life, including active euthanasia, which is, technically speaking, illegal worldwide. Interest in this most controversial area is drawn from many varied sources, from legal and medical practitioners to religious and moral ethicists. In some countries, public interest has been mobilized into organizations that attempt to influence legislation relating to euthanasia. Despite the obvious international importance of euthanasia, very little is known about the extent of its practice, whether passive or active, voluntary or involuntary. This examination is based on questionnaires completed by 49 national representatives of the International Association for Suicide Prevention (IASP), dealing with legal and religious aspects of euthanasia and physician-assisted suicide, as well as suicide. A dichotomy between the law and medical practices relating to the end of life was uncovered by the results of the survey. In 12 of the 49 countries active euthanasia is said to occur while a general acceptance of passive euthanasia was reported to be widespread. Clearly, definition is crucial in making the distinction between active and passive euthanasia; otherwise, the entire concept may become distorted, and legal acceptance may become more widespread with the effect of broadening the category of individuals to whom euthanasia becomes an available option. The "slippery slope" argument is briefly considered.     

Cholangiocarcinoma: spectrum of appearances on MR images using current techniques

This study describes the spectrum of appearances of cholangiocarcinoma on magnetic resonance (MR) sequences, including gadolinium-enhanced, fat-suppressed spoiled gradient echo images and MR cholangiography. Fifteen patients were included in the study. Histologic diagnosis was established in 11 patients by surgical resection (6 patients), percutaneous biopsy (4 patients), and open liver biopsy (1 patient). The final diagnosis was determined by correlation of the MR findings with cholangiographic studies and laboratory studies in 4 patients. MR studies were performed at 1.5 T, and the following sequences were obtained: T1-weighted spoiled gradient echo (SGE), T1-weighted fat-suppressed spin echo or SGE, T2-weighted fat-suppressed conventional or turbo spin echo, MR cholangiography, and gadolinium-enhanced T1-weighted fat-suppressed SGE images. The following determinations were made: tumor location, tumor extent, ductal dilatation, ductal wall thickness, signal intensity, enhancement pattern, and associated findings. Mass-like neoplasms were peripheral (6 patients), hilar (1 patient), and extrahepatic (2 patients). Circumferential tumors were hilar (2 patients) and extrahepatic (4 patients). All peripheral tumors were multifocal. Mass-like tumors were well-defined, rounded, and ranged from 1 to 14 cm in diameter. Circumferential tumors had less well-defined margins and measured from 3 to 15 mm in thickness. All mass-like tumors were moderately hypointense on T1-weighted images and mildly to moderately hyperintense on T2-weighted images. The circumferential tumors were iso- to moderately hypointense on T1-weighted images and iso- to mildly hyperintense on T2-weighted images. Mass-like tumors were generally well shown on non-contrast and immediate gadolinium-enhanced images, whereas circumferential tumors were poorly seen on non-contrast images and best shown on gadolinium-enhanced T1-weighted fat-suppressed images. The degree of enhancement ranged from minimal to intense on immediate gadolinium-enhanced images, with all tumors becoming more homogeneous in signal intensity on images obtained between 1 and 5 min following contrast administration. Tumor-containing lymph nodes greater than or equal to 1 cm in diameter were demonstrated in 11 out of 15 patients (73.3%). These were best shown on T2-weighted fat-suppressed images and gadolinium-enhanced fat-suppressed SGE images. MR cholangiography demonstrated the level of obstruction and degree of dilatation of the proximal biliary system in 5 out of 6 patients who underwent MR cholangiography. The spectrum of appearances of cholangiocarcinoma is demonstrable on MR images. Mass-like tumors are well shown on both pre- and post-gadolinium sequences. Circumferential tumors may cause minimally increased duct wall thickness and are most clearly shown on gadolinium-enhanced fat-suppressed SGE images obtained 1 to 5 min following gadolinium administration.     

JPred: a consensus secondary structure prediction server

An interactive protein secondary structure prediction Internet server is presented. The server allows a single sequence or multiple alignment to be submitted, and returns predictions from six secondary structure prediction algorithms that exploit evolutionary information from multiple sequences. A consensus prediction is also returned which improves the average Q3 accuracy of prediction by 1% to 72.9%. The server simplifies the use of current prediction algorithms and allows conservation patterns important to structure and function to be identified. AVAILABILITY: http://barton.ebi.ac.uk/servers/jpred.h tml CONTACT: geoff@ebi.ac.uk     

Protein sidechain conformer prediction: a test of the energy function

BACKGROUND: Homology modeling is an important technique for making use of the rapidly increasing number of protein sequences in the absence of structural information. The major problems in such modeling, once the alignment has been made, concern the positions of loops and the orientations of sidechains. Although progress has been made in recent years for sidechain prediction, current methods appear to have a limit on the order of 70% in their accuracy. It is important to have an understanding of this limitation, which for energy-based methods could arise from inaccuracies of the potential function. RESULTS: A test of the CHARMM function for sidechain prediction was performed. To eliminate the multiple-residue search problem, the minimum energy positions of individual sidechains in ten proteins were calculated in the presence of all other sidechains in their crystal orientations. This test provides a necessary condition that any energy function useful for sidechain placement must satisfy. For chi1 x chi2 rotations, the accuracies were 77.4% and 89.5%, respectively, and in the presence of crystal waters were 86.5% and 94.9%, respectively. If there was an error, the crystal structure usually corresponded to an alternative local minimum on the calculated energy map. Prediction accuracy correlated with the size of the energy gap between primary and secondary minima. CONCLUSIONS: The results indicate that the errors in current sidechain prediction schemes cannot be attributed to the potential energy function per se. The test used here establishes a necessary condition that any proposed energy-based sidechain prediction method, as well as many statistically based methods, must satisfy.     

Antigen retrieval techniques in immunohistochemistry: comparison of different methods

Routine sections of normal and pathological samples fixed in 10 per cent buffered formalin or B5, including EDTA-decalcified bone-marrow biopsies, were tested with 61 antibodies following heating in three different fluids: 0.01 M citrate buffer (pH 6.0), 0.1 M Tris-HCl (pH 8.0), and 1 mM EDTA-NaOH solution (pH 8.0). The sections underwent either three cycles of microwave treatment (5 min each) or pressure cooking for 1-2 min. The alkaline phosphatase/anti-alkaline phosphatase (APAAP) technique was used as the standard detection method; with 16 antibodies a slightly modified streptavidin-biotin complex (SABC)-immunoperoxidase technique was applied in parallel. The results obtained were compared with those observed without any antigen retrieval (AR), or following section digestion with 0.05 per cent protease XIV at 37 degrees C for 5 min. Chess-board titration tests showed that all antibodies but one profited by AR. Protease XIV digestion represented the gold standard for five antibodies, while 55 produced optimal results following the application of heat-based AR. By comparison with the other fluids, EDTA appeared to be superior in terms of both staining intensity and the number of marked cells. These results were independent of tissue processing, immunohistochemical approach, and heating device. Pressure cooking was found to be more convenient on practical grounds, as it allowed the simultaneous handling of a large number of slides and a time saving of 1 min 30 s, representing the proper time for the treatment.     

alpha-Amylases from Thermoactinomyces vulgaris: characteristics, primary structure and structure prediction

Two amylolytic active protein fractions (named alpha-amylase 1 and alpha-amylase 2) were isolated from the bacterium Thermoactinomyces vulgaris strain 94-2A. alpha-Amylase 1 had a molecular mass of 51.6 kDa, whereas alpha-amylase 2 consists of two fragments which have molecular masses of 17.0 and 34.6 kDa, respectively. These two fragments are products from a proteolytic cleavage of alpha-amylase 1 at amino acid position 303 (tryptophan) by a serine protease (thermitase) which is also produced by T. vulgaris. The purified alpha-amylase 1 and 2 follow the Michaelis-Menten kinetics in the presence of starch as substrate with Km values of 1.37 +/- 0.07 and 1.29 +/- 0.18 mg/mL, respectively. In effect they differ in their stability characteristics. The amino acid sequence of alpha-amylase from T. vulgaris derived from DNA sequence (1) was compared with those of other alpha-amylases. It reveals high homologies to alpha-amylases from other microorganisms (e.g. B. polymyxa, A. oryzae, S. occidentalis and S. fibuligera). A three-dimensional structure model for alpha-amylase 1 on the basis of the 3 A X-ray structure of Taka-amylase was constructed.