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Results: 11 to 20 of 35

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Trimerization and triple helix stabilization of the collagen XIX NC2 domain.
Boudko SP, Engel J, B├Ąchinger HP
(2008) J Biol Chem 283: 34345-51
MeSH Terms: Amino Acid Sequence, Animals, Biophysics, Collagen, Dimerization, Disulfides, Fibril-Associated Collagens, Fibrillar Collagens, Humans, Mice, Molecular Sequence Data, Oxygen, Peptides, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Thermodynamics
Show Abstract · Added November 2, 2017
The mechanisms of chain selection and assembly of fibril-associated collagens with interrupted triple helices (FACITs) must differ from that of fibrillar collagens, since they lack the characteristic C-propeptide. We analyzed two carboxyl-terminal noncollagenous domains, NC2 and NC1, of collagen XIX as potential trimerization units and found that NC2 forms a stable trimer and substantially stabilizes a collagen triple helix attached to either end. In contrast, the NC1 domain requires formation of an adjacent collagen triple helix to form interchain disulfide bridges. The NC2 domain of collagen XIX and probably of other FACITs is responsible for chain selection and trimerization.
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16 MeSH Terms
Evaluation of 3D modality-independent elastography for breast imaging: a simulation study.
Ou JJ, Ong RE, Yankeelov TE, Miga MI
(2008) Phys Med Biol 53: 147-63
MeSH Terms: Algorithms, Biophysical Phenomena, Biophysics, Breast, Breast Neoplasms, Computer Simulation, Elasticity, Elasticity Imaging Techniques, Female, Humans, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Phantoms, Imaging, Tomography, X-Ray Computed, Ultrasonography, Mammary
Show Abstract · Added November 13, 2013
This paper reports on the development and preliminary testing of a three-dimensional implementation of an inverse problem technique for extracting soft-tissue elasticity information via non-rigid model-based image registration. The modality-independent elastography (MIE) algorithm adjusts the elastic properties of a biomechanical model to achieve maximal similarity between images acquired under different states of static loading. A series of simulation experiments with clinical image sets of human breasts were performed to test the ability of the method to identify and characterize a radiographically occult stiff lesion. Because boundary conditions are a critical input to the algorithm, a comparison of three methods for semi-automated surface point correspondence was conducted in the context of systematic and randomized noise processes. The results illustrate that 3D MIE was able to successfully reconstruct elasticity images using data obtained from both magnetic resonance and x-ray computed tomography systems. The lesion was localized correctly in all cases and its relative elasticity found to be reasonably close to the true values (3.5% with the use of spatial priors and 11.6% without). In addition, the inaccuracies of surface registration performed with thin-plate spline interpolation did not exceed empiric thresholds of unacceptable boundary condition error.
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15 MeSH Terms
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
Egli M, Pallan PS
(2007) Annu Rev Biophys Biomol Struct 36: 281-305
MeSH Terms: Biochemistry, Biophysics, Carbohydrates, Cations, Crystallography, X-Ray, DNA, Macromolecular Substances, Models, Chemical, Molecular Conformation, Nucleic Acids, Oligonucleotides, Oligonucleotides, Antisense, Peptide Nucleic Acids, RNA, RNA Interference
Show Abstract · Added March 5, 2014
Chemically modified nucleic acids function as model systems for native DNA and RNA; as chemical probes in diagnostics or the analysis of protein-nucleic acid interactions and in high-throughput genomics and drug target validation; as potential antigene-, antisense-, or RNAi-based drugs; and as tools for structure determination (i.e., crystallographic phasing), just to name a few. Biophysical and structural investigations of chemically modified DNAs and RNAs, particularly of nucleic acid analogs with more significant alterations to the well-known base-sugar-phosphate framework (i.e., peptide or hexopyranose nucleic acids), can also provide insights into the properties of the natural nucleic acids that are beyond the reach of studies focusing on DNA or RNA alone. In this review we summarize results from crystallographic analyses of chemically modified DNAs and RNAs that are primarily of interest in the context of the discovery and development of oligonucleotide-based therapeutics. In addition, we re-examine recent structural data on nucleic acid analogs that are investigated as part of a systematic effort to rationalize nature's choice of pentose in the genetic system.
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15 MeSH Terms
Dipolar coupling between nitroxide spin labels: the development and application of a tether-in-a-cone model.
Hustedt EJ, Stein RA, Sethaphong L, Brandon S, Zhou Z, Desensi SC
(2006) Biophys J 90: 340-56
MeSH Terms: Anisotropy, Bacteriophage T4, Biophysics, Computer Simulation, Cyclic N-Oxides, Electron Spin Resonance Spectroscopy, Fourier Analysis, Models, Statistical, Muramidase, Nitric Oxide, Nitrogen Oxides, Normal Distribution, Software, Spin Labels, Thermodynamics
Show Abstract · Added February 20, 2013
A tether-in-a-cone model is developed for the simulation of electron paramagnetic resonance spectra of dipolar coupled nitroxide spin labels attached to tethers statically disordered within cones of variable halfwidth. In this model, the nitroxides adopt a range of interprobe distances and orientations. The aim is to develop tools for determining both the distance distribution and the relative orientation of the labels from experimental spectra. Simulations demonstrate the sensitivity of electron paramagnetic resonance spectra to the orientation of the cones as a function of cone halfwidth and other parameters. For small cone halfwidths (< approximately 40 degrees ), simulated spectra are strongly dependent on the relative orientation of the cones. For larger cone halfwidths, spectra become independent of cone orientation. Tether-in-a-cone model simulations are analyzed using a convolution approach based on Fourier transforms. Spectra obtained by the Fourier convolution method more closely fit the tether-in-a-cone simulations as the halfwidth of the cone increases. The Fourier convolution method gives a reasonable estimate of the correct average distance, though the distance distribution obtained can be significantly distorted. Finally, the tether-in-a-cone model is successfully used to analyze experimental spectra from T4 lysozyme. These results demonstrate the utility of the model and highlight directions for further development.
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15 MeSH Terms
Fleeting glimpses of lipid rafts: how biophysics is being used to track them.
Kenworthy AK
(2005) J Investig Med 53: 312-7
MeSH Terms: Animals, Biophysical Phenomena, Biophysics, Cholesterol, Diffusion, Glycosylphosphatidylinositols, Humans, Membrane Lipids, Membrane Microdomains, Membrane Proteins, Models, Biological, ras Proteins
Show Abstract · Added December 10, 2013
Cell membranes are fluid but can exhibit local order that gives rise to lateral inhomogeneities, often referred to as membrane microdomains. Among the best studied yet least well understood of these microdomains are lipid rafts. Lipid rafts are hypothesized to participate in a variety of physiologic and pathologic pathways important to human health by causing the spatial segregation of proteins and lipids within the plane of the membrane. Despite the widespread implications of the raft model, major questions remain about raft size, composition, and life span. This article discusses how recent biophysical measurements of the dynamic properties of rafts and putative raft-associated proteins and lipids are being used to test the hypothesis that confinement of proteins in rafts slows and/or impairs their ability to sample their microenvironment by lateral diffusion.
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12 MeSH Terms
Mimicry of a host anion channel by a Helicobacter pylori pore-forming toxin.
Czajkowsky DM, Iwamoto H, Szabo G, Cover TL, Shao Z
(2005) Biophys J 89: 3093-101
MeSH Terms: Anions, Bacterial Proteins, Bacterial Toxins, Biological Transport, Biophysical Phenomena, Biophysics, Bromides, Calcium, Cell Membrane Permeability, Electrophysiology, Helicobacter pylori, Ion Channels, Ions, Lipid Bilayers, Peptides, Sodium Compounds, Toxins, Biological
Show Abstract · Added March 5, 2014
Bacterial pore-forming toxins have traditionally been thought to function either by causing an essentially unrestricted flux of ions and molecules across a membrane or by effecting the transmembrane transport of an enzymatically active bacterial peptide. However, the Helicobacter pylori pore-forming toxin, VacA, does not appear to function by either of these mechanisms, even though at least some of its effects in cells are dependent on its pore-forming ability. Here we show that the VacA channel exhibits two of the most characteristic electrophysiological properties of a specific family of cellular channels, the ClC channels: an open probability dependent on the molar ratio of permeable ions and single channel events resolvable as two independent, voltage-dependent transitions. The sharing of such peculiar properties by VacA and host ClC channels, together with their similar magnitudes of conductance, ion selectivities, and localization within eukaryotic cells, suggests a novel mechanism of toxin action in which the VacA pore largely mimics the electrophysiological behavior of a host channel, differing only in the membrane potential at which it closes. As a result, VacA can perturb, but not necessarily abolish, the homeostatic ionic imbalance across a membrane and so change cellular physiology without necessarily jeopardizing vitality.
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17 MeSH Terms
Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2'-O-ribonucleic acid modifications.
Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M
(2005) Biochemistry 44: 9045-57
MeSH Terms: Base Sequence, Biophysical Phenomena, Biophysics, Crystallization, Crystallography, X-Ray, DNA, Enzyme Stability, Exonucleases, Models, Molecular, Nucleic Acid Conformation, Nucleic Acid Denaturation, Oligonucleotides, RNA, Ribonucleases, Static Electricity, Temperature
Show Abstract · Added March 5, 2014
The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the development of RNAi therapeutics.
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16 MeSH Terms
Structure and dynamics of model pore insertion into a membrane.
Lopez CF, Nielsen SO, Ensing B, Moore PB, Klein ML
(2005) Biophys J 88: 3083-94
MeSH Terms: Binding Sites, Biophysics, Computer Simulation, Diffusion, Dimyristoylphosphatidylcholine, Lipid Bilayers, Lipids, Macromolecular Substances, Membranes, Models, Molecular, Models, Theoretical, Nanotubes, Carbon, Thermodynamics, Time Factors, Water
Show Abstract · Added March 10, 2014
A cylindrical transmembrane molecule is constructed by linking hydrophobic sites selected from a coarse grain model. The resulting hollow tube assembly serves as a representation of a transmembrane channel, pore, or a carbon nanotube. The interactions of a coarse grain di-myristoyl-phosphatidyl-choline hydrated bilayer with both a purely hydrophobic tube and a tube with hydrophilic caps are studied. The hydrophobic tube rotates in the membrane and becomes blocked by lipid tails after a few tens of nanoseconds. The hydrophilic sites of the capped tube stabilize it by anchoring the tube in the lipid headgroup/water interfacial region of each membrane leaflet. The capped tube remains free of lipid tails. The capped tube spontaneously conducts coarse grain water sites; the free-energy profile of this process is calculated using three different methods and is compared to the barrier for water permeation through the lipid bilayer. Spontaneous tube insertion into an undisturbed lipid bilayer is also studied, which we reported briefly in a previous publication. The hydrophobic tube submerges into the membrane core in a carpetlike manner. The capped tube laterally fuses with the closest leaflet, and then, after plunging into the membrane interior, rotates to assume a transbilayer orientation. Two lipids become trapped at the end of the tube as it penetrates the membrane. The hydrophilic headgroups of these lipids associate with the lower tube cap and assist the tube in crossing the interior of the membrane. When the rotation is complete these lipids detach from the tube caps and fuse with the lower leaflet lipids.
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15 MeSH Terms
Light scattering from intact cells reports oxidative-stress-induced mitochondrial swelling.
Wilson JD, Bigelow CE, Calkins DJ, Foster TH
(2005) Biophys J 88: 2929-38
MeSH Terms: Aminolevulinic Acid, Animals, Biophysics, Cell Line, Tumor, Culture Techniques, Light, Liver, Mice, Microscopy, Electron, Microscopy, Polarization, Mitochondria, Mitochondrial Swelling, Models, Statistical, Oxidative Stress, Oxygen Consumption, Protoporphyrins, Rabbits, Scattering, Radiation, Time Factors
Show Abstract · Added February 12, 2015
Angularly resolved light scattering measurements were performed on suspensions of EMT6 cells and on mitochondria isolated from rabbit liver. Mie theory analysis of the scattering from intact cells indicated that mitochondrial-sized organelles dominated scattering in the range 5-90 degrees . This interpretation was supported by the analysis of scattering from isolated mitochondria. Intact cells were subjected to oxidative stress by photodynamic insult. After 3 h of incubation in the heme precursor aminolevulinic acid hexylester, EMT6 cells accumulated abundant protoporphyrin IX, an endogenous photosensitizer formed in mitochondria. Irradiation of aminolevulinic acid/protoporphyrin IX-sensitized cells with 10 J cm(-2) of 514 nm light led to pronounced changes in angularly resolved light scattering consistent with mitochondrial swelling. Electron microscopy of similarly treated EMT6 cell monolayers showed significant changes in mitochondrial morphology, which included distension of the outer unit membrane and bloating of the internal mitochondrial compartment. Informed by these electron microscopy results, we implemented a coated sphere model to interpret the scattering from intact cells subjected to oxidative stress. The coated sphere interpretation was compatible with the scattering measurements from these cells, whereas simpler Mie theory models based on homogenous swelling were dramatically unsuccessful. Thus, in this system, angularly resolved light scattering reports oxidative-stress-induced changes in mitochondrial morphology.
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19 MeSH Terms
Theoretical and computational methods for the noninvasive detection of gastric electrical source coupling.
Irimia A, Bradshaw LA
(2004) Phys Rev E Stat Nonlin Soft Matter Phys 69: 051920
MeSH Terms: Algorithms, Animals, Biophysics, Electrophysiology, Humans, Magnetics, Models, Anatomic, Models, Biological, Models, Statistical, Muscle, Smooth, Software, Stomach
Show Abstract · Added May 29, 2014
The ability to study the pathology of the stomach noninvasively from magnetic field measurements is important due to the significant practical advantages offered by noninvasive methods over other techniques of investigation. The inverse biomagnetic problem can play a central role in this process due to the information that inverse solutions can yield concerning the characteristics of the gastric electrical activity (GEA). To analyze gastrointestinal (GI) magnetic fields noninvasively, we have developed a computer implementation of a least-squares minimization algorithm that obtains numerical solutions to the biomagnetic inverse problem for the stomach. In this paper, we show how electric current propagation and the mechanical coupling of gastric smooth muscle cells during electrical control activity can be studied using such solutions. To validate our model, two types of numerical simulations of the GEA were developed and successfully used to demonstrate the ability of our computer algorithm to detect and accurately analyze these two phenomena. We also describe our analysis of experimental, noninvasively acquired gastric biomagnetic data as well as the information of interest that our numerical method can yield in clinical studies. Most importantly, we present experimental evidence that the coupling of gastric electrical sources can be observed using noninvasive techniques of measurement, in our case with the use of a superconducting quantum interference device magnetometer. We discuss the relevance and implications of our achievement to the future of GI research.
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12 MeSH Terms