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PubMed2006

Exo-zodi detection capability of the Ground-Based European Nulling Interferometry Experiment (GENIE) instrument.

The Ground-Based European Nulling Interferometry Experiment (GENIE) is intended as an Earth-based precursor for the European Darwin mission that will prepare the Darwin science program and demonstrate the required technology at system level. We propose a compact nulling interferometer design consisting of a two-telescope aperture configuration, an optional split-pupil add-on, and only four active control loops for counteracting environmentally induced disturbances. We show by simulation that the proposed instrument is able to detect, within a few minutes of observation time, exo-zodiacal dust clouds around Sunlike stars at 20 parsecs that are 20 times stronger than the local zodiacal dust cloud density.

Journal Article↗

PubMed2006

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of "chimera proteins." In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape.

Computer Simulation↗

PubMed2001

Computational modeling predicts the structure and dynamics of chromatin fiber.

BACKGROUND: The compact form of the chromatin fiber is a critical regulator of fundamental processes such as transcription and replication. These reactions can occur only when the fiber is unraveled and the DNA strands contained within are exposed to interact with nuclear proteins. While progress on identifying the biochemical mechanisms that control localized folding and hence govern access to genetic information continues, the internal structure of the chromatin fiber, let alone the structural pathways for folding and unfolding, remain unknown. RESULTS: To offer structural insights into how this nucleoprotein complex might be organized, we present a macroscopic computer model describing the mechanics of the chromatin fiber on the polymer level. We treat the core particles as electrostatically charged disks linked via charged elastic DNA segments and surrounded by a microionic hydrodynamic solution. Each nucleosome unit is represented by several hundred charges optimized so that the effective Debye-Hückel electrostatic field matches the field predicted by the nonlinear Poisson-Boltzmann equation. On the basis of Brownian dynamics simulations, we show that oligonucleosomes condense and unfold in a salt-dependent manner analogous to the chromatin fiber. CONCLUSIONS: Our predicted chromatin model shows good agreement with experimental diffusion coefficients and small-angle X-ray scattering data. A fiber of width 30 nm, organized in a compact helical zigzag pattern with about 4 nucleosomes per 10 nm, naturally emerges from a repeating nucleosome folding motif. This fiber has a cross-sectional radius of gyration of R(c) = 8.66 nm, in close agreement with corresponding values for rat thymus and chicken erythrocyte chromatin (8.82 and 8.5 nm, respectively).

Algorithms↗

PubMed2006

The elastic properties of morsellised cortico-cancellous bone graft are dependent on its prior loading.

Confined compression experiments were carried out on cortico-cancellous bone taken from bovine femoral condyles to assess the effect of prior loading on the elastic confined modulus, E(c) of morsellised cortico-cancellous bone (MCB). Measurements were taken to find the values of E(c) for MCB subjected to cyclic loading resulting in axial stresses in the range of 0.5-3.0 N mm(2). Two values of E(c) were considered: E(ic), the instantaneous modulus, and E(dc), the delayed modulus allowing for stress relaxation effects. It was found that the values of E(c) increased with increasing maximum axial stress. It was also found that for each stress level the values of E(c) increased as the number of load cycles increased. The dependence of E(c) on the maximum axial stress and the number of load cycles is seen to explain the wide range of values for the apparent modulus of MCB found in previous studies. Tests examining the stress relaxation behaviour of MCB are also discussed. The results indicate that a minimum of 10 compaction episodes are required for MCB to achieve around 90% of its predicted maximum stiffness for a given compaction force.

Animals↗

PubMed2005

Reflectance spectroscopy for diagnosis of epithelial precancer: model-based analysis of fiber-optic probe designs to resolve spectral information from epithelium and stroma.

Reflectance spectroscopy is a promising technology for detection of epithelial precancer. Fiber-optic probes that selectively collect scattered light from both the epithelium and the underlying stroma are likely to improve diagnostic performance of in vivo reflectance spectroscopy by revealing diagnostic features unique to each layer. We present Monte Carlo models with which to evaluate fiber-optic probe geometries with respect to sampling depth and depth resolution. We propose a probe design that utilizes half-ball lens coupled source and detector fibers to isolate epithelial scattering from stromal scattering and hence to resolve spectral information from the two layers. The probe is extremely compact and can provide easy access to different organ sites.

Computer Simulation↗

PubMedDate not supplied

Three-dimensional diffractive imaging for crystalline monolayers with one-dimensional compact support.

The use of a compact support constraint along the beam direction is considered as a solution to the phase problem for diffraction by two-dimensional protein crystals. Specifically we apply the iterative Gerchberg-Saxton-Fienup algorithm to simulated three-dimensional transmission electron diffraction data from monolayer organic crystals. We find that oversampling along the reciprocal-lattice rods (relrods) normal to the monolayer alone does not solve the phase problem in this geometry in general. However, based on simulations for a crystalline protein monolayer (lysozyme), we find that convergence is obtained in three dimensions if phases are supplied from a few high resolution electron microscope images recorded at small tilts to the beam direction. In the absence of noise, amplitude-weighted phase residuals of around 5 degrees, and a cross-correlation coefficient of 0.96 between the true and estimated potential are obtained if phases are included from images at tilts of up to 15 degrees. The performance is almost as good in the presence of noise at a level that is comparable to that commonly observed in electron crystallography of proteins. The method should greatly reduce the time and labor needed for data acquisition and analysis in cryo-electron microscopy of organic thin crystals by avoiding the need to record images at high tilt angles.

Algorithms↗

PubMed1999

Design and characterization of a surfactant-enriched tablet formulation for oral delivery of a poorly water-soluble immunosuppressive agent.

The feasibility of incorporating significant quantities of the anionic surfactant, sodium lauryl sulfate (SDS), into an immediate release tablet formulation of a poorly water-soluble immunosuppressive agent was investigated. Despite the extremely poor compressibility of SDS and poor chemical stability of the drug, a commercializable, direct-compression tablet formulation with satisfactory mechanical properties and acceptable chemical stability was achieved. Optimal in vitro release of the drug from the tablet formulation was achieved by establishing the minimum molar uptake ratio necessary to achieve complete micellar solubilization of the drug, after which formulation studies were conducted to determine the influence of formulation and process variables on the rate and extent of drug release. A model-independent analysis of dissolution results in a reduced volume (250 ml) of modified simulated gastric fluid demonstrated that the rate and extent of drug release was highly dependent on the mean particle size of the bulk drug, but independent of compression force above that required to achieve a compact of acceptable mechanical strength. Employing the Korsmeyer-Peppas model of Fickian and non-Fickian drug release, it was further shown that release of the drug from the dosage form was governed largely by surface erosion of the surfactant-enriched tablet matrix.

Administration, Oral↗

PubMed2000

Spectroscopic evidence of beta-turn in N-glycated peptidomimetics related to leucine-enkephalin.

The conformational differences caused by N-glycation of the amide bond in endogenous opioid pentapeptide leucine-enkephalin (Tyr-Gly-Gly-Phe-Leu) have been explored in solution using FTIR spectroscopy, NMR and molecular modelling. The compounds studied include protected and unprotected enkephalin analogues N-alkylated at the second (Gly2) amino acid residue with a 6-deoxy-D-galactose moiety (1-3). Comparison of the amide I component bands in the FTIR spectra, measured in trifluoroethanol (TFE), CHCl3 and DMSO, revealed significant differences in the intensity as well as shifts in component band frequencies for glycopeptides 1-3. We found that only the FTIR spectrum of the fully protected compound 1 indicated the presence of a higher population of beta-turns, while the spectra of the partially protected and unprotected glycopeptides 2 and 3 reflected the dominance of unordered or open structures, with some low population of turns. The observed NOE connectivities in CDCl3 for both isomers of the fully protected compound 1, the all-trans one and another with Tyr1-Gly2 peptide bond in cis conformation, indicate the presence of a beta-like turn conformation. Molecular dynamics simulations of the glycopeptide 1 obtained by unconstrained energy minimization of trans- and cis-1 shows that one of trans form conformations is consistent with beta-turn whereas cis isomer has revealed less-compact turn.

Enkephalins↗

PubMed1993

Kinetics and thermodynamics of folding in model proteins.

Monte Carlo simulations on a class of lattice models are used to probe the thermodynamics and kinetics of protein folding. We find two transition temperatures: one at T theta, when chains collapse from a coil to a compact phase, and the other at Tf (< T theta), when chains adopt a conformation corresponding to their native state. The kinetics are probed by several correlation functions and are interpreted in terms of the underlying energy landscape. The transition from the coil to the native state occurs in three distinct stages. The initial stage corresponds to a random collapse of the protein chain. At intermediate times tau c, during which much of the native structure is acquired, there are multiple pathways. For longer times tau r (>> tau c) the decay is exponential, suggestive of a late transition state. The folding time scale (approximately tau r) varies greatly depending on the model. Implications of our results for in vitro folding of proteins are discussed.

Kinetics↗

PubMed1995

Secondary structure of the HAV peptide which regulates cadherin-cadherin interaction.

Cadherins are calcium-binding proteins which are responsible for cell-cell adhesion in biological systems. Cadherins are involved in embryo compaction, neurite growth, cellular differentiation and formation of biological barriers (i.e., intestinal and blood brain barriers). A short linear peptide, LRAHAVDVNG-NH2 (Peptide 1), which contains His-Ala-Val sequence and is derived from the N-cadherin sequence has been shown to inhibit embryo compaction and neurite growth; this is caused by inhibition of the cadherin-cadherin interactions. Peptide 1 was synthesized and its solution conformation was determined by proton nuclear magnetic resonance, circular dichroism and molecular dynamics simulations. These studies indicated that the peptide has an extended structure from residue Leu1 to Asp7, possibly a beta-sheet structure, followed by a beta-turn from Asp7 to Gly10. The X-ray crystal structure of a sequence similar to that of peptide 1 in hemagglutinin indicated that it also has a beta-sheet structure around the HAV sequence, followed by a beta-turn.

Amino Acid Sequence↗

PubMed2001

Stimulated electromagnetic shock radiation: classical second-order calculations.

By performing classical, relativistic, second-order calculations we have shown that simulated electromagnetic shock radiation (SESR) is given out as an enormously amplified, exponentially growing, frequency upshifted, highly directional coherent electromagnetic radiation. We have derived expressions specifying the electric field components of SESR in the most compact and readable form. Hence we have calculated the field amplitudes of SESR for different sets of external controlling parameters and plotted some typical results in the most sensitive region, viz., very near the threshold of superphase motion. We have also shown the variation of SESR with respect to external parameters graphically. The results obtained are of importance in achieving a tunable source of coherent radiation in the frequency region not covered by existing sources.

Journal Article↗

PubMed1983

Classroom use of personal computers in medical education: a practical approach.

Classroom lectures in medical schools have traditionally employed a blackboard and slides. We have developed a compact, durable, and relatively low-priced system for computer-assisted instruction which introduces audiovisual material in a random-access manner. When this system was used in the classroom to provide flexible, clinical simulations, it promoted a high level of audience-instructor interaction and facilitated problem-based learning. The system has been used successfully in lectures in our medical school, at other medical schools, at community hospitals and at national scientific meetings.

Computer-Assisted Instruction↗

PubMed2004

Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.

Bovine pancreatic ribonuclease (RNase A) forms two three-dimensional (3D) domain swapped dimers. Crystallographic investigations have revealed that these dimers display completely different quaternary structures: one dimer (N-dimer), which presents the swapping of the N-terminal helix, is characterized by a compact structure, whereas the other (C-dimer), which is stabilized by the exchange of the C-terminal end, shows a rather loose assembly of the two subunits. The dynamic properties of monomeric RNase A and of the N-dimer have been extensively characterized. Here, we report a molecular dynamics investigation carried out on the C-dimer. This computational experiment indicates that the quaternary structure of the C-dimer undergoes large fluctuations. These motions do not perturb the proper folding of the two subunits, which retain the dynamic properties of RNase A and the N-dimer. Indeed, the individual subunits of the C-dimer display the breathing motion of the beta-sheet structure, which is important for the enzymatic activity of pancreatic-like ribonucleases. In contrast to what has been observed for the N-dimer, the breathing motion of the two subunits of the C-dimer is not coupled. This finding suggests that the intersubunit communications in a 3D domain swapped dimer strongly rely on the extent of the interchain interface. Furthermore, the observation that the C-dimer is endowed with a high intrinsic flexibility holds interesting implications for the specific properties of 3D domain swapped dimers. Indeed, a survey of the quaternary structures of the other 3D domain swapped dimers shows that large variations are often observed when the structural determinations are conducted in different experimental conditions. The 3D domain swapping phenomenon coupled with the high flexibility of the quaternary structure may be relevant for protein-protein recognition, and in particular for the pathological aggregations.

Binding Sites↗

PubMed2002

Probing the hirudin-thrombin interaction by incorporation of noncoded amino acids and molecular dynamics simulation.

Thrombin is a primary target for the development of novel anticoagulants, since it plays two important and opposite roles in hemostasis: procoagulant and anticoagulant. All thrombin functions are influenced by Na+ binding, which triggers the transition of this enzyme from an anticoagulant (slow) form to a procoagulant (fast) form. In previous studies, we have conveniently produced by chemical synthesis analogues of the N-terminal fragment 1-47 of hirudin HM2 containing noncoded amino acids and displaying up to approximately 2700-fold more potent antithrombin activity, comparable to that of full-length hirudin. In the work presented here, we have exploited the versatility of chemical synthesis to probe the structural and energetic properties of the S3 site of thrombin through perturbations introduced in the structure of hirudin fragment 1-47. In particular, we have investigated the effects of systematic replacement of Tyr3 with noncoded amino acids retaining the aromatic nucleus of Tyr, as well as similar hydrophobic and steric properties, but possessing different electronic (e.g., p-fluoro-, p-iodo-, or p-nitro-Phe), charge (p-aminomethyl-Phe), or conformational (homo-Phe) properties. Our results indicate that the affinity of fragment 1-47 for thrombin is proportional to the desolvation free energy change upon complex formation, and is inversely related to the electric dipole moment of the amino acid side chain at position 3 of hirudin. In this study, we have also identified the key features that are responsible for the preferential binding of hirudin to the procoagulant (fast) form of thrombin. Strikingly, shaving at position 3, by Tyr --> Ala exchange, abolishes the differences in the affinity for thrombin allosteric forms, whereas a bulkier side chain (e.g., beta-naphthylalanine) improves binding preferentially to the fast form. These results provide strong, albeit indirect, evidence that the procoagulant (fast) form of thrombin is in a more open and accessible conformation with respect to the less forgiving structure it acquires in the slow form. This view is also supported by the results of molecular dynamics simulations conducted for 18 ns on free thrombin in full explicit water, showing that after approximately 5 ns thrombin undergoes a significant conformational transition, from a more open conformation (which we propose can be related to the fast form) to a more compact and closed one (which we propose can be related to the slow form). This transition mainly involves the Trp148 and Trp60D loop, the S3 site, and the fibrinogen binding site, whereas the S1 site, the Na+-binding site, and the catalytic pocket remain essentially unchanged. In particular, our data indicate that the S3 site of the enzyme is less accessible to water in the putative slow form. This structural picture provides a reasonable molecular explanation for the fact that physiological substrates related to the procoagulant activity of thrombin (fibrinogen, thrombin receptor 1, and factor XIII) orient a bulky side chain into the S3 site of the enzyme. Taken together, our results can have important implications for the design of novel thrombin inhibitors, of practical utility in the treatment of coagulative disorders.

Amino Acids↗

PubMed2006

Full length Vpu from HIV-1: combining molecular dynamics simulations with NMR spectroscopy.

Based on structures made available by solution NMR, molecular models of the protein Vpu from HIV-1 were built and refined by 6 ns MD simulations in a fully hydrated lipid bilayer. Vpu is an 81 amino acid type I integral membrane protein encoded by the human immunodeficiency virus type-1 (HIV-1) and closely related simian immunodeficiency viruses (SIVs). Its role is to amplify viral release. Upon phosphorylation, the cytoplasmic domain adopts a more compact shape with helices 2 and 3 becoming almost parallel to each other. A loss of helicity for several residues belonging to the helices adjacent to both ends of the loop region containing serines 53 and 57 is observed. A fourth helix, present in one of the NMR-based structures of the cytoplasmic domain and located near the C-terminus, is lost upon phosphorylation.

Amino Acid Sequence↗

PubMed2001

Predicting every spike: a model for the responses of visual neurons.

In the early visual system, neuronal responses can be extremely precise. Under a wide range of stimuli, cells in the retina and thalamus fire spikes very reproducibly, often with millisecond precision on subsequent stimulus repeats. Here we develop a mathematical description of the firing process that, given the recent visual input, accurately predicts the timing of individual spikes. The formalism is successful in matching the spike trains from retinal ganglion cells in salamander, rabbit, and cat, as well as from lateral geniculate nucleus neurons in cat. It adapts to many different response types, from very precise to highly variable. The accuracy of the model allows a compact description of how these neurons encode the visual stimulus.

Action Potentials↗

PubMed2003

On the molecular basis of the recognition of angiotensin II (AII). NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131.

The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints. After final refinement in explicit water, a family of 13 structures was obtained with a backbone RMSD of 0.73 +/- 0.23 A. AII adopts a fairly compact folded structure, with its C-terminus and N-terminus approaching to within approximately 7.2 A of each other. The side chains of Arg2, Tyr4, Ile5 and His6 are oriented on one side of a plane defined by the peptide backbone, and the Val3 and Pro7 are pointing in opposite directions. The stabilization of the folded conformation can be explained by the stacking of the Val3 side chain with the Pro7 ring and by a hydrophobic cluster formed by the Tyr4, Ile5 and His6 side chains. Comparison between the NMR-derived structure of AII in aqueous solution and the refined crystal structure of the complex of AII with a high-affinity mAb (Fab131) [Garcia, K.C., Ronco, P.M., Verroust, P.J., Brunger, A.T., Amzel, L.M. (1992) Science257, 502-507] provides important quantitative information on two common structural features: (a) a U-shaped structure of the Tyr4-Ile5-His6-Pro7 sequence, which is the most immunogenic epitope of the peptide, with the Asp1 side chain oriented towards the interior of the turn approaching the C-terminus; (b) an Asx-turn-like motif with the side chain aspartate carboxyl group hydrogen-bonded to the main chain NH group of Arg2. It can be concluded that small rearrangements of the epitope 4-7 in the solution structure of AII are required by a mean value of 0.76 +/- 0.03 A for structure alignment and approximately 1.27 +/- 0.02 A for sequence alignment with the X-ray structure of AII bound to the mAb Fab131. These data are interpreted in terms of a biological "nucleus" conformation of the hormone in solution, which requires a limited number of structural rearrangements for receptor-antigen recognition and binding.

Angiotensin II↗

PubMed2004

Dynamical determination of the innermost stable circular orbit of binary neutron stars.

We determine the innermost stable circular orbit (ISCO) of binary neutron stars (BNSs) by performing dynamical simulations in full general relativity. Evolving quasiequilibrium (QE) binaries that begin at different separations, we bracket the location of the ISCO by distinguishing stable circular orbits from unstable plunges. We study Gamma=2 polytropes of varying compactions in both corotational and irrotational equal-mass binaries. For corotational binaries, we find an ISCO orbital angular frequency somewhat smaller than that determined by applying turning-point methods to QE initial data. For the irrotational binaries, the initial data sequences terminate before reaching a turning point, but we find that the ISCO frequency is reached prior to the termination point. Our findings suggest that the ISCO frequency varies with compaction but does not depend strongly on the stellar spin.

Journal Article↗