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PubMed2002

Discriminative ability with respect to amino acid types: assessing the performance of knowledge-based potentials without threading.

We present a novel method designed to analyze the discriminative ability of knowledge-based potentials with respect to the 20 residue types. The method is based on the preference of amino acids for specific types of protein environment, and uses a virtual mutagenesis experiment to estimate how much information a given potential can provide about environments of each amino acid type. This allows one to test and optimize the performance of real potentials at the level of individual amino acids, using actual data on residue environments from a dataset of known protein structures. We have applied our method to long-range and medium-range pairwise distance-dependent potentials. The results of our study indicate that these potentials are only able to discriminate between a very limited number of residue types, and that discriminative ability is extremely sensitive to the choice of parameters used to construct the potentials, and even to the size of the training dataset. We also show that different types of pairwise distance potentials are dominated by different types of interactions. These dominant interactions strongly depend on the type of approximation used to define residue position. For each potential, our methodology is able to identify a potential-specific amino acid distance matrix and a reduced amino acid alphabet of any specified size, which may have implications for sequence alignment and multibody models.

Amino Acid Substitution↗
PubMed2005

ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis.

The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only approximately 1.9% and approximately 0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an alpha-helix or a beta-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins.

Binding Sites↗
PubMed2005

Binding MOAD (Mother Of All Databases).

Binding MOAD (Mother of All Databases) is the largest collection of high-quality, protein-ligand complexes available from the Protein Data Bank. At this time, Binding MOAD contains 5331 protein-ligand complexes comprised of 1780 unique protein families and 2630 unique ligands. We have searched the crystallography papers for all 5000+ structures and compiled binding data for 1375 (26%) of the protein-ligand complexes. The binding-affinity data ranges 13 orders of magnitude. This is the largest collection of binding data reported to date in the literature. We have also addressed the issue of redundancy in the data. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 "best" complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This significant collection of protein-ligand complexes will be very useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques. The dataset can be accessed at http://www.BindingMOAD.org.

Biophysics↗
PubMed2006

Similarity networks of protein binding sites.

An increasing attention has been dedicated to the characterization of complex networks within the protein world. This work is reporting how we uncovered networked structures that reflected the structural similarities among protein binding sites. First, a 211 binding sites dataset has been compiled by removing the redundant proteins in the Protein Ligand Database (PLD) (http://www-mitchell.ch.cam.ac.uk/pld/). Using a clique detection algorithm we have performed all-against-all binding site comparisons among the 211 available ones. Within the set of nodes representing each binding site an edge was added whenever a pair of binding sites had a similarity higher than a threshold value. The generated similarity networks revealed that many nodes had few links and only few were highly connected, but due to the limited data available it was not possible to definitively prove a scale-free architecture. Within the same dataset, the binding site similarity networks were compared with the networks of sequence and fold similarity networks. In the protein world, indications were found that structure is better conserved than sequence, but on its own, sequence was better conserved than the subset of functional residues forming the binding site. Because a binding site is strongly linked with protein function, the identification of protein binding site similarity networks could accelerate the functional annotation of newly identified genes. In view of this we have discussed several potential applications of binding site similarity networks, such as the construction of novel binding site classification databases, as well as the implications for protein molecular design in general and computational chemogenomics in particular.

Animals↗
PubMed2006

Will my protein crystallize? A sequence-based predictor.

We propose a machine-learning approach to sequence-based prediction of protein crystallizability in which we exploit subtle differences between proteins whose structures were solved by X-ray analysis [or by both X-ray and nuclear magnetic resonance (NMR) spectroscopy] and those proteins whose structures were solved by NMR spectroscopy alone. Because the NMR technique is usually applied on relatively small proteins, sequence length distributions of the X-ray and NMR datasets were adjusted to avoid predictions biased by protein size. As feature space for classification, we used frequencies of mono-, di-, and tripeptides represented by the original 20-letter amino acid alphabet as well as by several reduced alphabets in which amino acids were grouped by their physicochemical and structural properties. The classification algorithm was constructed as a two-layered structure in which the output of primary support vector machine classifiers operating on peptide frequencies was combined by a second-level Naive Bayes classifier. Due to the application of metamethods for cost sensitivity, our method is able to handle real datasets with unbalanced class representation. An overall prediction accuracy of 67% [65% on the positive (crystallizable) and 69% on the negative (noncrystallizable) class] was achieved in a 10-fold cross-validation experiment, indicating that the proposed algorithm may be a valuable tool for more efficient target selection in structural genomics. A Web server for protein crystallizability prediction called SECRET is available at http://webclu.bio.wzw.tum.de:8080/secret.

Amino Acid Sequence↗
PubMed2006

Prediction of protein stability changes for single-site mutations using support vector machines.

Accurate prediction of protein stability changes resulting from single amino acid mutations is important for understanding protein structures and designing new proteins. We use support vector machines to predict protein stability changes for single amino acid mutations leveraging both sequence and structural information. We evaluate our approach using cross-validation methods on a large dataset of single amino acid mutations. When only the sign of the stability changes is considered, the predictive method achieves 84% accuracy-a significant improvement over previously published results. Moreover, the experimental results show that the prediction accuracy obtained using sequence alone is close to the accuracy obtained using tertiary structure information. Because our method can accurately predict protein stability changes using primary sequence information only, it is applicable to many situations where the tertiary structure is unknown, overcoming a major limitation of previous methods which require tertiary information. The web server for predictions of protein stability changes upon mutations (MUpro), software, and datasets are available at http://www.igb.uci.edu/servers/servers.html.

Binding Sites↗
PubMed2006

Predicting protease types by hybridizing gene ontology and pseudo amino acid composition.

Proteases play a vitally important role in regulating most physiological processes. Different types of proteases perform different functions with different biological processes. Therefore, it is highly desired to develop a fast and reliable means to identify the types of proteases according to their sequences, or even just identify whether they are proteases or nonproteases. The avalanche of protein sequences generated in the postgenomic era has made such a challenge become even more critical and urgent. By hybridizing the gene ontology approach and pseudo amino acid composition approach, a powerful predictor called GO-PseAA predictor was introduced to address the problems. To avoid redundancy and bias, demonstrations were performed on a dataset where none of proteins has >/= 25% sequence identity to any other. The overall success rates thus obtained by the jackknife cross-validation test in identifying protease and nonprotease was 91.82%, and that in identifying the protease type was 85.49% among the following five types: (1) aspartic, (2) cysteine, (3) metallo, (4) serine, and (5) threonine. The high jackknife success rates yielded for such a stringent dataset indicate the GO-PseAA predictor is very powerful and might become a useful tool in bioinformatics and proteomics.

Amino Acids↗
PubMed2006

YASSPP: better kernels and coding schemes lead to improvements in protein secondary structure prediction.

The accurate prediction of a protein's secondary structure plays an increasingly critical role in predicting its function and tertiary structure, as it is utilized by many of the current state-of-the-art methods for remote homology, fold recognition, and ab initio structure prediction. We developed a new secondary structure prediction algorithm called YASSPP, which uses a pair of cascaded models constructed from two sets of binary SVM-based models. YASSPP uses an input coding scheme that combines both position-specific and nonposition-specific information, utilizes a kernel function designed to capture the sequence conservation signals around the local window of each residue, and constructs a second-level model by incorporating both the three-state predictions produced by the first-level model and information about the original sequence. Experiments on three standard datasets (RS126, CB513, and EVA common subset 4) show that YASSPP is capable of producing the highest Q3 and SOV scores than that achieved by existing widely used schemes such as PSIPRED, SSPro 4.0, SAM-T99sec, as well as previously developed SVM-based schemes. On the EVA dataset it achieves a Q3 and SOV score of 79.34 and 78.65%, which are considerably higher than the best reported scores of 77.64 and 76.05%, respectively.

Algorithms↗
PubMed2007

Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility.

Analyzing the factors behind protein stability is a key research topic in molecular biology, and has direct implications on protein structure prediction and protein-protein interactions. We have analyzed protein stability upon point mutations using a distance-dependant pair potential representing mainly through-space interactions, and torsion angle potential representing mainly neighboring effects as a basic statistical mechanical setup for the analysis. The synergetic effect of accessible surface area and secondary structure preferences was used as a classifier for the potentials. In addition, short-, medium-, and long-range interactions of the protein environment were also analyzed. Two datasets of point mutations were taken for the comparison of theoretically predicted stabilizing energy values with experimental DeltaDeltaG and DeltaDeltaGH(2)O from thermal and chemical denaturation experiments. These include 1538 and 1603 mutations, respectively, and contain 101 proteins that share a wide range of sequence identity. The resulting force fields were carefully evaluated with different statistical tests. Results show a maximum correlation of 0.87 with a standard error of 0.71 kcal/mol between predicted and measured DeltaDeltaG values and a prediction accuracy of 85.3% (stabilizing or destabilizing) for all mutations together. A correlation of 0.77 (more than 80% prediction accuracy with a standard error of 0.95 kcal/mol) each for the test dataset of split-sample validation and fivefold crossvalidation was obtained and a correlation of 0.70 (77.4% prediction accuracy with a standard error of 1.17 kcal/mol) was shown by the jackknife test. The same model was implemented, and the results were analyzed for mutations with DeltaDeltaGH(2)O. A correlation of 0.78 (standard error 0.96 kcal/mol) was observed with a prediction efficiency of 84.65%. This model can be used for the future prediction of protein structural stability together with various experimental techniques.

Databases, Protein↗
PubMed1995

Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic archaeon Pyrococcus woesei.

The thermostable amylopullulanase from Pyrococcus woesei was crystallized. Crystals, suitable for a crystallographic analysis up to a size of 0.6 mm in their longest dimension, have been obtained by the vapor diffusion method in a solution containing polyethyleneglycol 4000 (PEG 4000), isopropanol, and Tris/Cl- buffer pH 7.5. Crystals grown under these conditions form hexagonal rods and diffract to a maximum resolution of 3 A. The crystals belong to the trigonal lattice type with the spacegroup P3(1)21 or P3(2)21, respectively, have the cell dimensions a = b = 96.8 A, c = 196.2 A, alpha = beta = 90 degrees, gamma = 120 degrees. The crystals have a theoretical packing density of 2.7 A3/Da, assuming one molecule with a molecule weight of 88.8 kDa in the asymmetric unit. Furthermore the self-rotation analysis of the dataset revealed only crystallographic symmetries. The merged native data of two crystals resulted in a 88% complete dataset.

Archaea↗
PubMed2005

Stable hydrogen and oxygen isotope ratios of bottled waters of the world.

Bottled and packaged waters are an increasingly significant component of the human diet. These products are regulated at the regional, national, and international levels, and determining the authenticity of marketing and labeling claims represents a challenge to regulatory agencies. Here, we present a dataset of stable isotope ratios for bottled waters sampled worldwide, and consider potential applications of such data for regulatory, forensic and geochemical standardization applications. The hydrogen and oxygen isotope ratios of 234 samples of bottled water range from -147 per thousand to +15 per thousand and from -19.1 per thousand to +3.0 per thousand, respectively. These values fall within and span most of the normal range for meteoric waters, indicating that these commercially available products represent a source of waters for use as laboratory working standards in applications requiring standardization over a large range of isotope ratios. The measured values of bottled water samples cluster along the global meteoric water line, suggesting that bottled water isotope ratios preserve information about the water sources from which they were derived. Using the dataset, we demonstrate how bottled water isotope ratios provide evidence for substantial evaporative enrichment of water sources prior to bottling and for the marketing of waters derived from mountain and lowland sources under the same name. Comparison of bottled water isotope ratios with natural environmental water isotope ratios demonstrates that on average the isotopic composition of bottled water tends to be similar to the composition of naturally available local water sources, suggesting that in many cases bottled water need not be considered as an isotopically distinct component of the human diet. Our findings suggest that stable isotope ratios of bottled water have the power to distinguish ultimate (e.g., recharge) and proximal (e.g., reservoir) sources of bottled water and constitute a potential tool for use in the regulatory monitoring of water products.

Beverages↗
PubMed1991

Multivariate analysis of spect images with illustrations in Alzheimer's disease.

Modern neuroimaging techniques such as positron emission tomography and single photon emission computed tomography (SPECT) often generate datasets consisting of a large number of variables measured on a small number of subjects. In addition, the data contain large 'subject effects' which must be adjusted for in any statistical analysis. This paper illustrates the dangers inherent in naive univariate analysis and proceeds to demonstrate the application of multivariate methods such as Hotellings T2-test, canonical correlation analysis and discriminant analysis. The issues and statistical methods are illustrated using a dataset from a SPECT study of groups of normal control subjects and subjects with a clinical diagnosis of Alzheimer's disease.

Alzheimer Disease↗
PubMed2004

The interobserver reliability of three-dimensional power Doppler data acquisition within the female pelvis.

OBJECTIVES: To examine the interobserver reliability of three-dimensional (3D) power Doppler data acquisition from the uterus and ovary. METHODS: 3D power Doppler angiography was used to acquire endometrial data from 20 patients and ovarian data from a further 20 different patients at various stages of in vitro fertilization. Two different observers each acquired two datasets from all 40 patients resulting in 80 endometrial and 80 ovarian datasets in total. Virtual Organ Computer-aided AnaLysis was used to define the object of interest and semiquantify the power Doppler signal within it. The reliability of measurements of volume and vascularity was assessed by calculating interclass correlation coefficients (ICCs) and limits of agreement between the two observers. RESULTS: Whilst volumetric data proved more reliably acquirable than power Doppler data, the interobserver reliability of data acquisition was high overall for both the endometrium and ovary with all measurements obtaining a lower ICC of above 0.9. Limits of agreement revealed minimal disagreement between the two observers for measurements of volume and vascularity within both the ovary and endometrium. The 'indices of vascularity' within the endometrium were less than those derived from the ovary and subendometrium, which were comparable. CONCLUSIONS: 3D ultrasound can be reliably used between observers to acquire power Doppler information from the ovary and endometrium thus supporting the current use and further development of this technique in clinical practice.

Data Collection↗
PubMed2005

Three- and four-dimensional freehand fetal echocardiography: a feasibility study using a hand-held Doppler probe for cardiac gating.

OBJECTIVE: To evaluate the clinical feasibility of the signal from a hand-held Doppler probe as a real-time tracking signal for dynamic three-dimensional (3D) (so-called four-dimensional (4D)) fetal echocardiography in a random patient cohort. METHODS: Seventy fetuses, with and without congenital heart disease, at various gestational ages (mean, 25 weeks; range, 18-38 weeks) were investigated using freehand 3D echocardiography. Time gating was achieved concurrently by obtaining a Doppler signal of the fetal heart without further signal averaging. In 10 fetuses, Doppler gating was compared to cardiotocogram (CTG)-gated 3D echo using signal averaging. Gray-scale and color Doppler dynamic 3D displays and multiplanar views were assessed according to their ability to accurately depict cardiac gating and cardiac morphology. RESULTS: In 68/70 fetuses, valid Doppler-based trigger signals were obtained. Correct cardiac gating was achieved in 231/275 (84%) 4D datasets. Doppler tracing of the fetal heart allowed beat-to-beat triggering without the necessity for signal averaging. Doppler gating detected rapid changes in the fetal heart rate more reliably than CTG gating, but was more sensitive to acoustic interference between the gating and echo-transducer when color-coded Doppler imaging was used. Image quality was highly dependent on random motion and the acoustic window. A total of 171/231 (74%) correctly gated datasets successfully demonstrated clinically useful 4D images of the fetal heart. The reconstruction of 3D and multiplanar views provided additional views not obtainable by two-dimensional imaging. CONCLUSION: These results show that a hand-held Doppler probe can be used as a reliable online gating source for 4D fetal echocardiography.

Adult↗
PubMed2005

The fetal cerebellar vermis: anatomy and biometric assessment using volume contrast imaging in the C-plane (VCI-C).

OBJECTIVES: To describe the normal appearance and study the biometry of the fetal cerebellar vermis by three-dimensional (3D) volume contrast imaging in the coronal (C-) plane (VCI-C). METHODS: A total of 203 normally developed fetuses were examined prospectively at 18-33 weeks' gestation. At the level of the view used to measure the transverse cerebellar diameter (TCD), a VCI-C plane was displayed to examine, using a transabdominal probe, the fetal mid-saggital vermis. The volumes acquired were stored for later review and measurement of the anteroposterior (AP) diameter, craniocaudal (CC) diameter and surface area of the cerebellar vermis. Each dataset was evaluated by two independent observers. Measurements as a function of gestational age (GA), biparietal diameter (BPD), head circumference (HC) and TCD were expressed by regression equations. Interobserver variability was evaluated. Nomograms were produced. In order to validate the use of VCI in fetal biometry, datasets from 57 patients were selected arbitrarily for comparison of their VCI-C measurements with those from mid-sagittal sections of a stored 3D multiplanar examination. Intraclass correlation was used to evaluate the agreement between these measurements. RESULTS: The mean maternal age was 32 years. We were able to measure mid-sagittal CC diameter, mid-sagittal AP diameter and cerebellar vermis surface area in all fetuses. Interobserver variability analysis showed no significant differences between the two observers (P > 0.05). Measurements of the cerebellar vermis (AP diameter, CC diameter and surface area) correlated linearly with GA, BPD, HC and TCD (r > or = 0.82, P < 0.0001). CC and AP diameters estimated from the mid-sagittal section of the multiplanar measurements were significantly correlated with VCI-C measurements (r = 0.96, P < 0.00001 and r = 0.95, P < 0.00001, respectively). CONCLUSIONS: VCI-C is a valuable tool, allowing intrauterine assessment of the normal appearance of the fetal cerebellar vermis. The nomograms developed in this study should enable accurate evaluation of the cerebellar vermis.

Adolescent↗
PubMed2007

The interobserver reliability of off-line antral follicle counts made from stored three-dimensional ultrasound data: a comparative study of different measurement techniques.

OBJECTIVE: To assess the interobserver reliability of antral follicle counts (AFCs) made from stored three-dimensional (3D) ultrasound data using conventional two-dimensional (2D) images, 3D multiplanar view and 3D-rendered 'inversion mode'. METHODS: 3D transvaginal ultrasound was performed in the early follicular phase (days 2-5) of the menstrual cycle in 41 subjects aged < 40 years, undergoing investigation for subfertility. From the stored 3D ultrasound datasets, the number of antral follicles of 2-10 mm in diameter in each ovary was independently measured, using all three methods by three investigators, each with a different level of experience. The image quality of each dataset was subjectively categorized into one of three groups, based on the proportion of the ovarian contour that could be seen clearly. RESULTS: There was no significant difference in the mean AFC between the observers for any of the three different techniques. The intraclass correlation coefficient (ICC) for the 2D-equivalent mode, the 3D multiplanar mode, and the 3D-rendered inversion mode were indicative of good interobserver reliability for each method. The interobserver reliability for the 3D-rendered inversion mode was better with Grade 1 image quality than with Grade 3 image quality. There were no equivalent differences, however, between the three different grades of image quality with the 2D-equivalent and 3D multiplanar modes. The time taken for AFC measurement using 3D-rendered inversion mode was significantly longer than with the 2D equivalent and 3D multiplanar methods. CONCLUSIONS: 3D image displays and rendering techniques do not appear to offer any advantage over a conventional 2D display in terms of AFC measurement reliability. AFC measurement using the 3D-rendered inversion mode has an adequate interobserver reproducibility but is dependent on image quality.

Adolescent↗
PubMed2003

Dynamic free-hand three-dimensional fetal echocardiography gated by cardiotocography.

OBJECTIVE: To evaluate the clinical feasibility of conventional cardiotocography (CTG) as a cardiac cycle triggering signal for three-dimensional (3D) fetal echocardiography. METHOD: Free-hand 3D echocardiography was performed on a total of 25 fetuses with and without congenital heart disease at various gestational ages (mean, 29 weeks; range, 19-35 weeks). Simultaneously, online CTG was used for time gating. Gray-scale and color Doppler dynamic 3D displays, as well as multiplanar views, were assessed for their ability to depict the cardiac morphology and correct cardiac gating. RESULTS: Valid CTG-based trigger signals could be obtained in 24 of the 25 fetuses. Correct cardiac gating was achieved in 101 of the 111 (91%) 3D datasets. Color Doppler imaging of blood flow in four dimensions was possible in 34 of 36 (94%) datasets. Reconstructed 3D and multiplanar views provided additional views not available in two-dimensional (2D) imaging. Acoustic interference between the CTG transducer and echotransducer could be reduced by the use of a high-frequency echotransducer, second-harmonic frequency imaging and appropriate positioning of the two transducers. Imaging quality was highly dependent on the quality of 2D images and random motion artifacts. CONCLUSIONS: CTG can be used as an online gating source for dynamic 3D fetal echocardiography.

Blood Flow Velocity↗
PubMed2006

The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast.

The last two years have seen the publication of three genome-wide gene expression studies of the fission yeast cell cycle. While these microarray papers largely agree on the main patterns of cell cycle-regulated transcription and its control, there are discrepancies with regard to the identity and numbers of periodically expressed genes. We present benchmark and reproducibility analyses showing that the main discrepancies do not reflect differences in the data themselves (microarray or synchronization methods seem to lead only to minor biases) but rather in the interpretation of the data. Our reanalysis of the three datasets reveals that combining all independent information leads to an improved identification of periodically expressed genes. These evaluations suggest that the available microarray data do not allow reliable identification of more than about 500 cell cycle-regulated genes. The temporal expression pattern of the top 500 periodically expressed genes is generally consistent across experiments and the three studies, together with our integrated analysis, provide a coherent and rich source of information on cell cycle-regulated gene expression in Schizosaccharomyces pombe. The reanalysed datasets and other supplementary information are available from an accompanying website: http://www.cbs.dtu.dk/cellcycle/. We hope that this paper will resolve the apparent discrepancies between the previous studies and be useful both for wet-lab biologists and for theoretical scientists who wish to take advantage of the data for follow-up work.

Cell Cycle↗