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PubMed2000

The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.

The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross-linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure.

Base Sequence↗

PubMed2005

Intelligent initialization of resource allocating RBF networks.

In any neural network system, proper parameter initialization reduces training time and effort, and generally leads to compact modeling of the process under examination, i.e. less complex network structures and better generalization. However, in cases of multi-dimensional data, parameter initialization is both difficult and time consuming. In the proposed scheme a novel, multi-dimensional, unsupervised clustering method is used to properly initialize neural network architectures, focusing on resource allocating networks (RAN); both the hidden and output layer parameters are determined by the output of the clustering process, without the need for any user interference. The main contribution of this work is that the proposed approach leads to network structures that are compact, efficient and achieve best classification results, without the need for manual selection of suitable initial network parameters. The efficiency of the proposed method has been tested on several classes of publicly available data, such as iris, Wisconsin and ionosphere data.

Algorithms↗

PubMed1993

A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors.

Based on the similarity in primary structure between the newly characterized ligand for CD40 (CD40L) and the tumor necrosis factors (TNFs), we have modeled a detailed 3-D structure for CD40L. We used the known structure of TNF alpha as a template for the generation of the CD40L model. The soundness of the model-building algorithms was verified by constructing a 3-D model of TNF beta and comparing it to its crystallographically determined structure. The CD40L sequence is entirely compatible with the 'jelly-roll' beta-strand structure characteristic of the TNFs. Like the TNFs, CD40L is predicted to form a compact trimer, although the interactions between monomers are distinct from those found in the TNFs. The model predicts which regions of CD40L could interact with its receptor(s) and which amino acids are essential for the maintenance of its trimeric structure.

Amino Acid Sequence↗

PubMed2006

Geometry of proteins: hydrogen bonding, sterics, and marginally compact tubes.

The functionality of proteins is governed by their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for understanding the common character of globular proteins. We argue that a recent critique of the tube idea is not well founded.

Computer Simulation↗

PubMed2004

A simplified model for V-ATPase H+ extrusion.

An analytical model of V-type H+-translocating ATPase (V-ATPase) was developed based on an approximation to the mechanochemical model of Grabe et al. (Biophys. J., pp. 2798-2813, vol. 78, 2000). Grabe's work utilizes structural information and physiological assumptions to construct a detailed mechanochemical model of the V-ATPase. Due to the complexity of their model, it does not give a readily usable mathematical expression for the V-ATPase current. Based on their analysis of the structure of the proton pump, we develop a two-compartment model of the V-ATPase, which contains a membrane "half-channel" for proton translocation separated by a hydrophilic strip and a hydrophobic wall from the cytoplasm. Using the Langevin equation to describe proton transport across the membrane, we simplify the model based on their assumptions on the molecular structure of the pump and arrive at a general form of solution to the proton pump flux driven by ATP hydrolysis based on assumptions on the physiological properties of the strip and the wall, as well as the two fluid compartments. In this process of simplification, we explicitly relate V-ATPase structure, stoichiometry, pump efficiency, and ATP hydrolysis energy to the active pump current. The simplified model is used to provide model-generated approximations to measured data from a variety of laboratories. In addition, it provides a very compact characterization of V-ATPase, which can be used as a proton extruder in a variety of different cell membranes, as well as in the membranes of intracellular organelles. Index Terms-Electrophysiology, mechanochemstry, molecular motors, proton extrusion

Biological Transport, Active↗

PubMed2004

Calculations of protein circular dichroism from first principles.

Understanding the relationship between the amino acid sequence of a protein and its unique, compact 3D structure is one of the grand challenges in molecular biophysics. One particularly exciting approach is time-resolved electronic circular dichroism (CD) spectroscopy, which offers resolution on a nanosecond (or faster) time scale, although it does not provide the spatial resolution of techniques like X-ray crystallography or NMR. The thrust of our work is to underpin fast time scale spectroscopic studies of protein folding with a stronger theoretical foundation. Ultimately, we seek to use molecular dynamics simulations to study the influence of conformational dynamics and conformational transitions on the electronic CD spectra of proteins. We discuss how improved quantum chemical models of individual chromophores, including aromatic sidechains, can be incorporated into calculations of the electronic structure of proteins and their CD.

Bacterial Proteins↗

PubMed2003

Generation and stability of bentonite colloids at the bentonite/granite interface of a deep geological radioactive waste repository.

The possible mechanisms of colloid generation at the near field/far field interface of a radioactive repository have been investigated by means of novel column experiments simulating the granite/bentonite boundary, both in dynamic and in quasi-static water flow conditions. It has been shown that solid particles and colloids can be detached from the bulk and mobilised by the water flow. The higher the flow rate, the higher the concentration of particles found in the water, according to an erosion process. However, the gel formation and the intrinsic tactoid structure of the clay play an important role in the submicron particle generation even in the compacted clay and in a confined system. In fact, once a bentonite gel is formed, in the regions where the clay is contacted with water, clay colloids can be formed even in quasi-static flow conditions. The potential relevance of these colloids in radionuclide transport has been studied by evaluating their stability in different chemical environments. The coagulation kinetics of natural bentonite colloids was experimentally studied as a function of the ionic strength and pH, by means of time-resolved light scattering techniques. It has been shown that these colloids are very stable in low saline (approximately 1 x 10(-3) M) and alkaline (pH > or = 8) waters.

Aluminum Silicates↗

PubMed1994

Cardiotoxin II from Taiwan cobra venom, Naja naja atra. Structure in solution and comparison among homologous cardiotoxins.

The three-dimensional structure in solution of cardiotoxin II, a membrane toxin from the venom of Taiwan cobra, Naja naja atra, was determined using 1H nuclear magnetic resonance spectroscopy and molecular modeling based on the hybrid distance geometry/dynamic simulated annealing technique. A complete sequence-specific proton assignment was obtained, and the secondary structures of the protein were determined from information on nuclear Overhauser effect connectivities, coupling constants, and hydrogen exchange were confirmed using the main-chain-directed strategy. Twelve simulated annealing structures found to be within a single family were selected based on the condition of distance constraint violation less than 0.02 nm and the dihedral angle violation less than 4 degrees. The average atomic root mean square deviation between the selected structures and their geometric average are 0.079 nm for the backbone atoms and 0.137 nm for all heavy atoms; they are 0.044 nm and 0.117 nm, respectively, when considering the secondary structural residues only. The molecule adopts a compact structure consisting of three major loops emerging from a globular head. These loops contain five strands to form double- and a triple-stranded antiparallel beta sheets. Comparisons are made between this structure and those of its homologous cardiotoxins in order to derive further information on their structural variations.

Amino Acid Sequence↗

PubMed2006

Developmental and cross-linguistic variation in the infant vowel space: the case of Canadian English and Canadian French.

This article describes the results of two experiments. Experiment 1 was a cross-sectional study designed to explore developmental and cross-linguistic variation in the vowel space of 10- to 18-month-old infants, exposed to either Canadian English or Canadian French. Acoustic parameters of the infant vowel space were described (specifically the mean and standard deviation of the first and second formant frequencies) and then used to derive the grave, acute, compact, and diffuse features of the vowel space across age. A decline in mean F1 with age for French-learning infants and a decline in mean F2 with age for English-learning infants was observed. A developmental expansion of the vowel space into the high-front and high-back regions was also evident. In experiment 2, the Variable Linear Articulatory Model was used to model the infant vowel space taking into consideration vocal tract size and morphology. Two simulations were performed, one with full range of movement for all articulatory paramenters, and the other for movement of jaw and lip parameters only. These simulated vowel spaces were used to aid in the interpretation of the developmental changes and cross-linguistic influences on vowel production in experiment 1.

Child Language↗

PubMed1999

Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins.

The temperature dependences of the unfolding-refolding reaction of a shorter version of the alpha-spectrin SH3 domain (PWT) used as a reference and of two circular permutants (with different poly-Gly loop lengths at the newly created fused loop) have been measured by differential scanning microcalorimetry and stopped-flow kinetics, to characterize the thermodynamic nature of the transition and native states. Differential scanning calorimetry results show that all these species do not belong to the same temperature dependency of heat effect. The family of the N47-D48s circular permutant (with 0-6 Gly inserted at the fused-loop) shows a higher enthalpy as happens with the PWT domain. The wild type (WT) and the S19-P20s permutant family have a more similar behavior although the second is far less stable. The crystallographic structure of the PWT shows a hairpin formation in the region corresponding to the unstructured N-terminus tail of the WT, explaining the enthalpic difference. There is a very good correlation between the calorimetric changes and the structural differences between the WT, PWT, and two circular permutants that suggests that their unfolded state cannot be too different. Elongation of the fused loop in the two permutants, taking as a reference the protein with one inserted Gly, results in a small Gibbs energy change of entropic origin as theoretically expected. Eyring plots of the unfolding and refolding semireactions show different behaviors for PWT, S19-P20s, and N47-D48s in agreement with previous studies indicating that they have different transition states. The SH3 transition state is relatively close to the native state with regard to changes in heat capacity and entropy, indicating a high degree of compactness and order. Regarding the differences in thermodynamic parameters, it seems that rapid folding could be achieved in proteins by decreasing the entropic barrier.

Amino Acid Sequence↗

PubMed2001

Miniaturized tests for computer-assisted identification of motile Aeromonas species with an improved probability matrix.

AIMS: To develop miniaturized tests for the phenotypic identification of motile Aeromonas species using an improved probability matrix. METHODS AND RESULTS: Conventional tests were miniaturized for use in 96-well plates, and their performance assessed using 60 aeromonads comprising type and reference strains as well as clinical, fish and water isolates. A revised probability matrix for Aeromonas hybridization groups 1-14, including A. allosaccharophila, A. bestiarum, A. encheleia and A. popoffii, was developed. Using 26 tests, all the reference strains were correctly identified with the revised probability matrix, and 80% of the isolates were correctly identified at a Willcox probability level of 95%. CONCLUSION: The compact test format, coupled with a robust identification matrix, provides a convenient basis for identifying motile aeromonads. SIGNIFICANCE AND IMPACT OF THE STUDY: The identification system for identifying aeromonads will be of use to medical and veterinary laboratories undertaking disease diagnosis.

Aeromonas↗

PubMed2007

Wear of composite resin veneering materials and enamel in a chewing simulator.

OBJECTIVES: The purpose of this in vitro study was to evaluate the wear of six composite resins for the veneering of crowns compared with the wear of human and bovine enamel, tested in a dual-axis chewing simulator. METHODS: Eight specimens of six different composite resins (Targis I+II, Solidex, BelleglassHP, Estenia, Solidex) and of human and bovine enamel were prepared. Steatite ceramic balls served as antagonistic specimens. Specimens were dynamically loaded in a dual-axis chewing simulator with 49 N up to 1,200,000 loading cycles with additional thermal cycling between 5 and 55 degrees C. After 120,000, 240,000, 480,000, 840,000 and 1,200,000 loading cycles, an impression of the specimens' surface and the antagonistic specimen was taken using a polyvinylsiloxane impression material. The substance loss at the surface was measured with computer-aided laser profilometry. Data were analyzed using ANOVA and the Tukey test. RESULTS: The wear of the ultra fine compact filled composite resins Solidex and BelleglassHP was not statistically significantly different from that of human enamel. The other composite resins and bovine enamel showed a wear statistically significantly higher than human enamel. SIGNIFICANCE: Comparing six composite resins for the veneering of crowns, ultra fine compact filled composite resins BelleGlassHP and Solidex showed a wear not significantly different from the wear of human and bovine enamel.

Animals↗

PubMed1998

The structural basis of ankyrin-like repeat function as revealed by the solution structure of myotrophin.

BACKGROUND: Myotrophin is a 12.5 kDa protein that appears to have a key role in the initiation of cardiac hypertrophy, a central process in many heart diseases. Myotrophin primarily comprises ankyrin-like (ANK) repeats, the 33 amino acid motifs involved in a wide range of protein-protein interactions. As a first step in the structure-based search for cardiac hypertrophy antagonists and in order to gain insight into the molecular basis of action of the ubiquitous and multifunctional ANK repeat motif, we have determined the solution structure of myotrophin using multidimensional heteronuclear NMR spectroscopy. RESULTS: The myotrophin structure determination was based on 2786 experimental NMR restraints, and the precision of the coordinates for the final 45 simulated-annealing structures is 0.43 A for the backbone atoms and 0.87 A for all atoms. The structure of myotrophin is well defined and is ellipsoidal: approximately 46 A long and 21 A wide. The ANK repeats, which constitute the main part of the myotrophin structure, are characteristic of a hairpin-like protruding tip followed by a helix-turn-helix motif. The V-shaped helix-turn-helix of the ANK repeats stack sequentially in bundles and are stabilized by compact hydrophobic cores, whereas the protruding tips are less ordered. This arrangement is quite different to the continuous beta-sheet topology observed in the corresponding regions of another ANK protein, 53BP2, the structure of which was determined in complex with p53. CONCLUSIONS: The solution structure of myotrophin provides important insights into the structural and dynamic features of the ANK motif, and suggests that the protruding tips with highly variable sequences may be critical to facilitate diverse protein-protein recognition. The present structure also provides a molecular basis for the further functional characterization of myotrophin and the development of therapeutics for hypertrophy-related heart diseases.

Amino Acid Sequence↗

PubMed1995

Three-dimensional structure in solution of the polypeptide cardiac stimulant anthopleurin-A.

The three-dimensional structure in aqueous solution of the 49-residue polypeptide anthopleurin-A (AP-A), from the sea anemone Anthopleura xanthogrammica, has been determined from 1H NMR data. A restraint set consisting of 411 interproton distance restraints inferred from NOEs and 19 backbone and 13 side chain dihedral angle restraints from spin-spin coupling constants, as well as 15 lower bound restraints based on the absence of NOEs in the spectra, was used as input for distance geometry calculations in DIANA and simulated annealing and restrained energy minimization in X-PLOR. Stereospecific assignments for 12 beta-methylene pairs were also included. The final set of 20 structures had mean pairwise rms differences over the whole molecule of 2.04 A for the backbone heavy atoms (N, C alpha, and C) and 2.59 A for all heavy atoms. For the well-defined region encompassing residues 2-7 and 17-49, the corresponding values were 0.82 and 1.27 A, respectively. AP-A adopts a compact structure consisting of four short strands of antiparallel beta-sheet (residues 2-4, 20-23, 34-37, and 45-48) connected by three loops. The first loop commences with a type I beta-turn which includes two important Asp residues; this loop is the least well-defined region of the protein, although a beta-turn involving residues 13-16 is observed in nearly half the structures. The loop linking the second and third strands is constrained by the 29-47 disulfide bond and contains two well-defined beta-turns, while the third loop contains the Gly40-Pro41 sequence, which has been identified previously as the site of cis-trans isomerism. The carboxylate group of Asp7 is close to the epsilon-ammonium group of Lys37, suggesting that they may form a salt bridge. A pH titration monitored by 2D NMR supports this by showing that Asp7 has a low pKa. It is proposed that this region of the molecule and the nearby residues Asp9 and His39 form part of the molecular surface which interacts with the mammalian cardiac sodium channel.

Animals↗

PubMed1998

On the realization of an analytic high-resolution EEG.

The analytic solution of the harmonic downward continuation of the scalp potential field in an N-shell heterogeneous, but isotropic, spherical volume conductor model has been derived. The objective of this paper was to investigate the realization of a so-called "high-resolution electroencephalogram (EEG)": by enhancing the poor spatial resolution of EEG recordings. To this end, the forward problem for a dipolar source arbitrarily located at the source point Q = Q(rs, phi s, theta s) has been determined in a compact matrix notation. It is possible to transfer the potential field given on the outer surface of a spherically shaped volume conductor to an arbitrary inner surface (e.g., to the cortical surface) under consideration of the electrical and geometrical properties of the model. For the application of the proposed method to real-world problems, the coefficients of the series expansion describing the cortical potential distribution are determined by minimizing the squared curvature of the scalp potential field integrated over the scalp surface. Simulation results for distributed sources show that the proposed method is superior to the surface Laplacian method for interelectrode distances below 2.5 cm.

Electrodes↗

PubMed1992

Modeling the effects of mutations on the denatured states of proteins.

We develop a model for the reversible denaturation of proteins and for the effects of single-site mutations on the denatured states. The model is based on short chains of sequences of H (hydrophobic) and P (other) monomers configured as self-avoiding walks on the two-dimensional square lattice. The N (native) state is defined as the unique conformation of lowest contact energy, whereas the D (denatured) state is defined as the collection of all other conformations. With this model we are able to determine the exact partition function, and thus the exact native-denatured equilibrium for various solvent conditions, using the computer to exhaustively enumerate every possible configuration. Previous studies confirm that this model shows many aspects of protein-like behavior. The present study attempts to model how the denatured state (1) depends on the amino acid sequence, and (2) is changed by single-site mutations. The model accounts for two puzzling experimental results: (1) the replacement of a polar residue by a hydrophobic amino acid on the surface of a protein can destabilize a native protein, and (2) the "denaturant slope," m = partial delta G/partial c (where c is the concentration of denaturant--urea, guanidine hydrochloride), can sometimes change by as much as 30% due to a single mutation. The principal conclusion of the present study is that, under strong folding conditions, the denatured conformations that are in equilibrium with the native state are not open random configurations. Instead, they are an ensemble of highly compact conformations with a distribution that depends on the residue sequence and that can be substantially altered by single mutations. Most importantly, we conclude that mutations can exert their dominant effects on protein stability by changing the entropy of folding.

Amino Acid Sequence↗

PubMed1996

Comparison of the size and morphology of UHMWPE wear debris produced by a hip joint simulator under serum and water lubricated conditions.

This paper investigates the effect of lubricant on the size and morphology of ultra-high molecular weight polyethylene (UHMWPE) wear debris produced by a hip joint simulator. Bovine serum and water were chosen as the lubricants for comparison. When bovine serum was used as lubricant, the majority of the wear debris produced was submicron sized and equiaxed or elongated in shape; no transfer film was found on the femoral heads. When water was used as lubricant, large pieces of thin UHMWPE flakes about 2-3 mm across were produced and patches of transfer films were observed on the femoral heads. These large flakes were comprised of numerous smaller thin flakes compacted together. While the size and shape of the wear debris produced with serum lubrication are similar to those reported from clinical studies in total hip replacement, the debris produced with water lubrication bears no resemblance to what has been seen clinically.

Animals↗

PubMed2003

Refolding of a high molecular weight protein: salt effect on collapse.

Small-angle neutron scattering experiments were performed on dilute solutions of a high molecular weight protein (fibronectin, M = 580 kg/mol) in four cases: native conditions; unfolded state obtained by a denaturing agent (urea); and two badly refolded (or collapsed) states obtained by progressive elimination of the denaturing agent in salt-containing or salt-free solutions. Our main result is concerned by the conformation of the protein as the attempt for refolding is driven with or without salt. In salt-containing solution, we observe unambiguously that the protein chain collapses at large length scales but still obeys to a Gaussian statistics at short length scales. In other words, the globule embodies a large quantity of solvent compared to the compact situation. In salt-free solutions, the badly refolded protein is not globular but displays both a coil-like and an open conformation at large length scales and a local high density area. This behavior is discussed with respect to the scaling theories for polymers and polyampholytes.

Computer Simulation↗