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At least 631 records · Page 35Linked to original sources

PubMed2000

Deimination of myelin basic protein. 1. Effect of deimination of arginyl residues of myelin basic protein on its structure and susceptibility to digestion by cathepsin D.

The effect of deimination of arginyl residues in bovine myelin basic protein (MBP) on its susceptibility to digestion by cathepsin D has been studied. Using bovine component 1 (C-1) of MBP, the most unmodified of the components with all 18 arginyl residues intact, we have generated a number of citrullinated forms by treatment of the protein with purified peptidylarginine deiminase (PAD) in vitro. We obtained species containing 0-9.9 mol of citrulline/mol of MBP. These various species were digested with cathepsin D, a metalloproteinase which cleaves proteins at Phe-Phe linkages. The rate of digestion compared to component 1 was only slightly affected when 2.7 or 3.8 mol of citrulline/mol of MBP was present. With 7.0 mol of citrulline/mol of MBP, a large increase in the rate of digestion occurred. No further increase was observed with 9.9 mol of citrulline/mol of MBP. The immunodominant peptide 43-88 (bovine sequence) was released slowly when 2.7 and 3.8 mol of citrulline/mol of MBP was present, but it was released rapidly when 7.0 mol of citrulline/mol of MBP was present. The dramatic change in digestion with 7.0 mol of citrulline/mol of MBP or more could be explained by a change in three-dimensional structure. Molecular dynamics simulation showed that increasing the number of citrullinyl residues above 7 mol/mol of MBP generated a more open structure, consistent with experimental observations in the literature. We conclude that PAD, which deiminates arginyl residues in proteins, decreases both the charge and compact structure of MBP. This structural change allows better access of the Phe-Phe linkages to cathepsin D. This scheme represents an effective way of generating the immunodominant peptide which sensitizes T-cells for the autoimmune response in demyelinating disease.

Animals↗

PubMed2005

Compact double-grating coupler between vertically stacked silicon-on-insulator waveguides.

We analyze a compact double-grating coupler that provides coupling through radiation modes between two vertically stacked silicon-on-insulator waveguides. The grating is sufficiently strong to be considered a one-dimensional photonic bandgap structure that facilitates a short coupling length. Simulations suggest that a 29% coupling efficiency is achievable in coupling light from one waveguide to another with 12.9 microm long binary gratings. We found that the coupling efficiency is enhanced by Fabry-Perot resonance between two gratings. The coupling efficiency can be increased by use of a blazed grating. We use the eigenmode expansion method to design and optimize the binary grating coupler, and the results are verified by use of the finite-difference time-domain method.

Journal Article↗

PubMed1998

Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: effects of solution environment on helicity.

alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha3 beta2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha3 beta2 interface. Here we describe the three-dimensional solution structure of MII determined using 2D 1H NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 A for the backbone atoms and 0.34 A for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha3beta2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.

Amino Acid Sequence↗

PubMed1996

Hemolytic characteristics of a pivot bearing supported Gyro centrifugal pump (C1E3) simulating various clinical applications.

Centrifugal blood pumps are playing a key role in circulatory mechanical assist systems including cardiopulmonary bypass (CPB), right and left ventricular assist devices (RVAD and LVAD), percutaneous cardiopulmonary support (PCPS), and extracorporeal membrane oxygenation (ECMO). Each of these circulatory assist systems requires specific flow and pressure conditions. In vitro hemolysis tests were performed using five compact mock loops with flow and pressure set equivalent to clinical conditions. These studies determined the hemolytic characteristics and clinical applicability of the pivot bearing-supported Gyro centrifugal pump with an eccentric port (C1E3) compared with the Bio-Medicus pump (BP-80). Normalized index of hemolysis (NIH) values of the C1E3 were less than those of the BP-80 under all conditions; in particular, they were significantly less in the CPB, LVAD, and RVAD conditions. In addition, linear correlation was observed between NIH values, rotational pump speed (RPM), total pressure head (delta P), and flow rate (Q) with both the C1E3 and BP-80: NIH = a(RPM/Q) + b, NIH = c(delta P/Q) + d. However, the slopes (a and c) of these equations were smaller with the C1E3 than those with the BP-80, which suggests that the C1E3 has decreased hemolytic characteristics when increasing the RPM and delta P. In other words, the increase of RPM and delta P results in less shear stress with the C1E3 than with the BP-80. One cause of these decreased hemolytic characteristics of the C1E3 is thought to be less pump power loss against an increase of RPM and delta P than with the BP-80. Furthermore, the average exposure time is shorter with the C1E3 than with the BP-80 because the priming volume of the C1E3 (30 ml) is smaller than that of the BP-80 (80 ml). From the point of both shear stress and exposure time, the C1E3 has less hemolytic features than the BP-80.

Animals↗

PubMed1996

Factors governing the foldability of proteins.

We use a three-dimensional lattice model of proteins to investigate systematically the global properties of the polypeptide chains that determine the folding to the native conformation starting from an ensemble of denatured conformations. In the coarse-grained description, the polypeptide chain is modeled as a heteropolymer consisting of N beads confined to the vertices of a simple cubic lattice. The interactions between the beads are taken from a random gaussian distribution of energies, with a mean value B0 < 0 that corresponds to the overall average hydrophobic interaction energy. We studied 56 sequences all with a unique ground state (native conformation) covering two values of N (15 and 27) and two values of B0. The smaller value of magnitude of B0 was chosen so that the average fraction of hydrophobic residues corresponds to that found in natural proteins. The higher value of magnitude of B0 was selected with the expectation that only the fully compact conformations would contribute to the thermodynamic behavior. For N = 15 the entire conformation space (compact as well as noncompact structures) can be exhaustively enumerated so that the thermodynamic properties can be exactly computed at all temperatures. The thermodynamic properties for the 27-mer chain were calculated using the slow cooling technique together with standard Monte Carlo simulations. The kinetics of approach to the native state for all the sequences was obtained using Monte Carlo simulations. For all sequences we find that there are two intrinsic characteristic temperatures, namely, T theta and Tf. At the temperature T theta the polypeptide chain makes a transition to a collapsed structure, while at Tf the chain undergoes a transition to the native conformation. We show that foldability of sequences can be characterized entirely in terms of these two temperatures. It is shown that fast folding sequences have small values of sigma = (T theta - Tf)/T theta whereas slow folders have larger values of sigma (the range of sigma is 0 < sigma < 1). The calculated values of the folding times correlate extremely well with sigma. An increase in sigma from 0.1 to 0.7 can result in an increase of 5-6 orders of magnitudes in folding times. In contrast, we demonstrate that there is no useful correlation between folding times and the energy gap between the native conformation and the first excited state at any N for any value of B0. In particular, in the parameter space of the model, many sequences with varying energy gaps, all with roughly the same folding time, can be easily engineered. Folding sequences in this model, therefore, can be classified based solely on the value of sigma. Fast folders have small values of sigma (typically less than about 0.1), moderate folders have values of sigma in the approximate range between 0.1 and 0.6, while for slow folders sigma exceeds 0.6. The precise boundary between these categories depends crucially on N and on the model. The range of sigma for fast folders decreases with the length of the chain. At temperatures close to Tf fast folders reach the native conformation via a native conformation nucleation collapse mechanism without forming any detectable intermediates, whereas only a fraction of molecule phi (T) reaches the native conformation by this process for moderate folders. The remaining fraction reaches the native state via three-stage multipathway process. For slow folders phi (T) is close to zero at all temperatures. The simultaneous requirement of native state stability and kinetic accessibility can be achieved at high enough temperatures for those sequences with small values of sigma. The utility of these results for de novo design of proteins is briefly discussed.

Kinetics↗

PubMed2006

Equibiaxial strain stimulates fibroblastic phenotype shift in smooth muscle cells in an engineered tissue model of the aortic wall.

Many cells in the body reside in a complex three-dimensional (3D) environment stimulated by mechanical force. In vitro bioreactor systems have greatly improved our understanding of the mechanisms behind cell mechanotransduction. Current systems to impose strain in vitro are limited either by the lack of uniform strain profile or inability to strain 3D engineered tissues. In this study, we present a system capable of generating cyclic equibiaxial strain to an engineered vascular wall model. Type I collagen hydrogels populated with rat aortic smooth muscle cells (RASMCs) were created either as a compacting disk or constrained hemisphere. Both models were adhered to silicone membranes precoated with collagen I, fibronectin, or Cell-Tak and assayed for adhesion characteristics. The best performing model was then exposed to 48 h of 10% strain at 1Hz to simulate wall strain profiles found in vascular aneurysms, with static cultures serving as controls. The finite strain profile at the level of the membrane and the free surface of the construct was quantified using microbeads. The results indicate that the hemisphere model adhered with Cell-Tak had the most stable adhesion, followed by fibronectin and collagen I. Disk models did not adhere well under any coating condition. Uniform strain propagation was possible up to a maximum area strain of 20% with this system. RASMC responded to 10% equibiaxial strain by becoming less elongated, and immunohistochemistry suggested that stretched RASMC shifted to a more synthetic phenotype in comparison to static controls. These results suggest that equibiaxial strain may induce smooth muscle cell differentiation. We conclude that this system is effective in stimulating cells with cyclic equibiaxial strain in 3D cultures, and can be applied to a variety of biomaterial and tissue engineering applications.

Animals↗

PubMed2003

Sodium silicate gel as a precursor for the in vitro nucleation and growth of a bone-like apatite coating in compact and porous polymeric structures.

In the present work, a new methodology to produce bioactive coatings on the surface of starch-based biodegradable polymers or other polymeric biomaterials is proposed. A sodium silicate gel is employed as an alternative nucleating agent to the more typical bioactive glasses for inducing the formation of a calcium-phosphate (Ca-P) layer. The method has the advantage of being able to coat efficiently both compact materials and porous 3D architectures aimed at being used on tissue replacement applications and as tissue engineering scaffolds. By means of this treatment, it is possible to observe the formation of an apatite-like layer, only after 6 hours of simulated body fluid immersion. For the porous materials, this layer could also be observed inside the pores, clearly covering the cell walls. Furthermore, an increase of the surface hydrophilicity (higher amount of polar groups in the surface) might contribute to the formation of silanol groups that also act as apatite inductors. After 30 days of SBF immersion, the apatite-like films exhibit a partially amorphous nature and the Ca/P ratios became much closer to the value attributed to hydroxyapatite (1.67). The obtained results are very promising for the development of cancellous bone replacement materials and for pre-calcifying bone tissue engineering scaffolds.

Apatites↗

PubMedDate not supplied

Technical evaluation of oxygen transfer rates of fish gills and artificial gills.

An artificial gill, which takes oxygen from water, would enhance the ability of people to function under water for extended periods. Increasing oxygen transfer rate, however, would be essential to the realization of compact, commercially viable equipment. Fish have evolved a variety of techniques to enable them to breathe under water, and their mechanisms must be clarified before compact, high-performance artificial gills can be developed. A model of the secondary lamellae of fish gills, through which oxygen is taken up from water to the blood, was devised, and its structure and oxygen transfer rate were evaluated by computer simulation analysis for carp and dogfish. Oxygen transfer rates were also found for an outside-water-flow artificial gill using a hollow fiber membrane at various fiber packing ratios. The biologic membrane is rate-determining for oxygen transfer through the secondary lamellae. Blood and water side boundary film resistances are small for fish because the blood and water channels are very narrow and numerous. When the fiber packing ratio of the artificial gill is raised, the oxygen transfer rate increases because of lower water side boundary film resistance. An optimum fiber packing ratio should be selected so that there is no major increase in pressure drop and no channeling occurs.

Animals↗

PubMed2006

Statins and bone metabolism.

3-Hydroxy-3-methylglutaryl coenzyme A reductase inhibitors (statins) are potent inhibitors of cholesterol biosynthesis. Cholesterol-lowering therapy using statins significantly reduces the risk of coronary heart disease. However, extensive use of statins leads to increases of other undesirable as well as beneficial effects, so-called pleiotropic effects. With respect to these effects, statins augment the expression of bone morphogenetic protein-2, a potent simulator of osteoblast differentiation and its activity, and promote mineralization by cultured osteoblasts, indicating that statins have an anabolic effect on bone. Chronic administration of statins in ovariectomized (OVX) rats modestly increases bone mineral density (BMD) of cancellous bone but not of compact bone. In clinical studies, there are conflicting results regarding the clinical benefits of this therapy for the treatment of osteoporosis. Observational studies suggest an association between statin use and reduction in fracture risk. Clinical trials reported no effect of statin treatment on BMD in hip and spine, and on bone turnover. Statins also may influence oral osseous tissues. Administration of statins in combination with osteoporosis therapy appears to improve alveolar bone architecture in the mandibles of OVX rats with maxillary molar extraction. Statins continue to be considered as potential therapeutic agents for patients with osteoporosis and possibly with periodontal disease. Development of new statins that are more specific and potent for bone metabolism will greatly increase the usefulness of these drugs for the treatment of bone diseases.

Alveolar Process↗

PubMed2006

An efficient robotic tendon for gait assistance.

A robotic tendon is a spring based, linear actuator in which the stiffness of the spring is crucial for its successful use in a lightweight, energy efficient, powered ankle orthosis. Like its human analog, the robotic tendon uses its inherent elastic nature to reduce both peak power and energy requirements for its motor. In the ideal example, peak power required of the motor for ankle gait is reduced from 250 W to just 77 W. In addition, ideal energy requirements are reduced from nearly 36 J to just 21 J. Using this approach, an initial prototype has provided 100% of the power and energy necessary for ankle gait in a compact 0.95 kg package, seven times less than an equivalent motor/gearbox system.

Achilles Tendon↗

PubMed2000

Boundary conditions for light propagation in diffusive media with nonscattering regions

The diffusion approximation proves to be valid for light propagation in highly scattering media, but it breaks down in the presence of nonscattering regions. We present a compact expression of the boundary conditions for diffusive media with nonscattering regions, taking into account small-index mismatch. Results from an integral method based on the extinction theorem boundary condition are contrasted with both Monte Carlo and finite-element-method simulations, and a study of its limit of validity is presented. These procedures are illustrated by considering the case of the cerebro-spinal fluid in the brain, for which we demonstrate that for practical situations in light diffusion, these boundary conditions yield accurate results.

Journal Article↗

PubMed2006

Equation-free dynamic renormalization in a glassy compaction model.

Combining dynamic renormalization with equation-free computational tools, we study the apparently asymptotically self-similar evolution of void distribution dynamics in the diffusion-deposition problem proposed by Stinchcombe and Depken [Phys. Rev. Lett. 88, 125701 (2002)]. We illustrate fixed point and dynamic approaches, forward as well as backward in time; these can be used to accelerate simulators of glassy dynamic phenomena.

Journal Article↗

PubMed2006

Optical and mechanical shrinkage effects in dye-doped photonic bandgap structures based on organic materials.

In this work we study the effects of the optical shrinkage in polymer and liquid crystal (LC) mixtures optimized for their use as active media in compact plastic laser devices. These mixtures are characterized by the presence of the rhodamine 6G as an active dye. Modifications in the reflection properties of the gratings as a function of the active dye concentration have been determined experimentally and a detailed theoretical simulation of the optical transmittance properties of these devices is provided. Moreover, the comparison between two different experimental approaches clarifies the contribution to the optical shrinkage due to the presence of the active dye. In principle this approach allows determining the linear mechanical shrinkage by separating the contribution to optical shrinkage due to photochemical transformations from that due to mechanical effects.

Journal Article↗

PubMed2004

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.

We have studied the potential of mean force of two peptides, one known to adopt a beta-hairpin and the other an alpha-helical conformation in solution. These peptides are, respectively, residues 41-56 of the C-terminus (GEWTYDDATKTFTVTE) of the B1 domain of protein G and the 13 residue C-peptide (KETAAAKFERQHM) of ribonuclease A. Extensive canonical ensemble sampling has been performed using a parallel replica exchange method. The effective potential employed in this work consists of the OPLS all-atom force field (OPLS-AA) and an analytical generalized Born (AGB) implicit solvent model including a novel nonpolar solvation free energy estimator (NP). An additional dielectric screening parameter has been incorporated into the AGBNP model. In the case of the beta-hairpin, the nonpolar solvation free energy estimator provides the necessary effective interactions for the collapse of the hydrophobic core (W43, Y45, F52, and V54), which the more commonly used surface-area-dependent nonpolar model does not provide. For both the beta-hairpin and the alpha-helix, increased dielectric screening reduces the stability of incorrectly formed salt bridges, which tend to disrupt the formation of the hairpin and helix, respectively. The fraction of beta-hairpin and alpha-helix content we obtained using the AGBNP model agrees well with experimental results. The thermodynamic stability of the beta-hairpin from protein G and the alpha-helical C-peptide from ribonuclease A as modeled with the OPLS-AA/AGBNP effective potential reflects the balance between the nonpolar effective potential terms, which drive compaction, and the polar and hydrogen bonding terms, which promote secondary structure formation.

Amino Acid Sequence↗

PubMed2004

Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules.

It has been established that in a dilute solution individual giant DNA molecules undergo a large discrete transition between an elongated coil state and a folded compact state. On the other hand, in concentrated solutions, DNA molecules assemble into various characteristic states, including multichain aggregate, liquid crystalline, ionic crystal, etc. In this study, we compared single-chain and multiple-chain events by observing individual chains using fluorescence microscopy. We used spermidine, SPD(3+), as a condensing agent for giant DNA. When the concentration of DNA is below 1 microM in base-pair units, individual DNA molecules exhibit a transition from an elongated state to a compact state. When the concentration of DNA is increased to 10 microM, a thick fiberlike assembly of multiple chains appears. AFM measurements of this thick fiber revealed that more than tens of DNA molecules form a bundle structure with parallel ordering of the chains. The transition between single-chain compaction and bundle formation with multiple-chain assemblies was reproduced by a theoretical calculation.

Base Pairing↗

PubMed2005

Exploring the free-energy landscape of a short peptide using an average force.

The reversible folding of deca-alanine is chosen as a test case for characterizing a method that uses an adaptive biasing force (ABF) to escape from the minima and overcome the barriers of the free-energy landscape. This approach relies on the continuous estimation of a biasing force that yields a Hamiltonian in which no average force is exerted along the ordering parameter xi. Optimizing the parameters that control how the ABF is applied, the method is shown to be extremely effective when a nonequivocal ordering parameter can be defined to explore the folding pathway of the peptide. Starting from a beta-turn motif and restraining xi to a region of the conformational space that extends from the alpha-helical state to an ensemble of extended structures, the ABF scheme is successful in folding the peptide chain into a compact alpha helix. Sampling of this conformation is, however, marginal when the range of xi values embraces arrangements of greater compactness, hence demonstrating the inherent limitations of free-energy methods when ambiguous ordering parameters are utilized.

Alanine↗

PubMed2002

Molecular dynamics simulations of conformational behavior of linear RGD peptidomimetics and cyclic prodrugs in aqueous and octane solutions.

Conformations available to a class of cyclic prodrugs and corresponding linear RGD peptidomimetics were explored using 1 ns length molecular dynamics simulations performed with the program CHARMM. Water and octane, modeled explicitly, were used as solvents to mimic the change of the environment experienced by the solutes upon partition from water to membrane in the trans-cellular transport process. In water, the linear peptidomimetics tended to populate extended-like structures, characterized by strong favorable interactions with solvent and low intrinsic stability. In these extended conformations the charged termini are able to assume large distances, above 15 A for the longest systems. These linear peptidomimetics have been found to exhibit the highest potency in experimental studies, in accord with the trends experimentally observed for RGD peptides. In contrast, in octane compact conformers of the linear peptidomimetics were favored, with all charged groups aggregated and shielded from solvent, exhibiting high intrinsic stability and weak solute-solvent interactions. Our calculations predict a large unfavorable energy change for transferring the linear systems from water to octane, in agreement with experimental findings that these compounds are not transported via the trans-cellular pathway. The cyclic prodrugs did not exhibit major structural differences between the simulations in water and octane, adopting turn-like conformations in both solvents. The limited response of the cyclic structures to changes in the environment leads to energies of transfer from water to octane that are also unfavorable, but much less so than for the linear molecules. This effect is in accord with the observed enhanced passive trans-cellular transport of the cyclic prodrugs.

Amino Acid Sequence↗

PubMed1996

Monte Carlo simulation of multiple attack mechanism of alpha-amylase.

Porcine pancreatic alpha-amylase (EC 3.2.1.1) produces short maltooligosaccharides from a single enzyme-substrate complex without dissociation by multiple or repetitive attack. Multiple attack is caused by relative sliding of the enzyme along the product chain of the enzyme-product complex without dissociation to form another productive complex. The Monte Carlo method was applied to the multiple attack mechanism to predict product distribution from amylose and amylopectin molecules of arbitrary sizes. The position of the initial attack to make the enzyme-substrate complex and branched reaction paths from the enzyme-product complex were selected by random numbers and probabilities. A simulated product distribution from 100,000 samples of amylose of chain length greater than 80 agreed completely with experimental data at the early stage of hydrolysis of amylose of mean chain length 90. On the other hand, the simulated product distribution from amylopectin agreed with experimental data of potato amylopectin when the effective chain length of the A chain was 9. Since the mean chain length of the A chain of potato amylopectin is 15, it is possible that amylopectin is partially compact in solution, so that the enzyme can recognize and act only on the outer side of the A chain at the early stage of digestion.

Amylopectin↗