Home About us Contact
|
Home About us Contact | ||
|
|
||
Persistence Length (persistence + length)
Selected AbstractsPersistence Length of Cartilage Aggrecan Macromolecules Measured via Atomic Force MicroscopyMACROMOLECULAR SYMPOSIA, Issue 1 2004Laurel Ng Abstract Tapping mode atomic force microscopy (TMAFM) was employed to directly calculate the persistence length of individual fetal bovine epiphyseal and mature nasal cartilage aggrecan monomers, as well as their constituent chondroitin sulfate glycosaminoglycan chains. [source] An in vitro model system for cytoskeletal confinementCYTOSKELETON, Issue 10 2009Sarah Köster Abstract The motility, shape, and functionality of the cell depend sensitively on cytoskeletal mechanics which in turn is governed by the properties of filamentous proteins - mainly actin, microtubules, and intermediate filaments. These biopolymers are confined in the dense cytoplasm and therefore experience strong geometric constraints on their equilibrium thermal fluctuations. To obtain a better understanding of the influence of confinement on cytoskeletal filaments we study the thermal fluctuations of individual actin filaments in a microfluidic in vitro system by fluorescence microscopy and determine the persistence length of the filaments by analyzing the radial distribution function. A unique feature of this method is that we obtain the persistence length without detailed knowledge of the complete contour of the filament which makes the technique applicable to a broad range of biological polymers, including those with a persistence length smaller than the optical resolution. Cell Motil. Cytoskeleton 2009. © 2009 Wiley-Liss, Inc. [source] Hierarchical structure of niobate nanosheets in aqueous solutionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2007Satoshi Koizumi The hierarchical structure of an aqueous dispersion of niobate nanosheets was explored by using a combined method of ultra-small-angle and small-angle scattering of neutrons and X-rays. The concentration of the sheets studied was in the range where the dispersion exhibits a liquid-crystal phase as evidenced by observation between crossed polarizers in a previous report. The scattering data covered a wide q scale of more than four orders of magnitude [3 × 10,4,q, 10,nm,1, where q = (4,/,)sin(,/2), , and , being the wavelength of the incident beam and the scattering angle, respectively], corresponding to the length scale l = 2,/q from ~1,nm to ~20,µm. The scattering analyses provided information on the hierarchical structural elements including: (i) single nanosheets as a structure element (hierarchy I), (ii) parallel stacks of the sheets (hierarchy II), and (iii) spatial arrangements of the stacks (hierarchy III), in order of increasing length scale. Hierarchy II is closely related to the liquid-crystal nature of the dispersion in which the spacing and the persistence length, normal and parallel to the stack surface, respectively, were disclosed. Hierarchy III gives rise to the low- q upturn in the scattering profile, which may be characterized by mass-fractal-like power-law scattering behavior. This finding is a surprise from the viewpoint of the liquid-crystal nature of the dispersion, a possible model of which is proposed in the text. [source] Physicochemical characterization of carrageenans,A critical reinvestigationJOURNAL OF APPLIED POLYMER SCIENCE, Issue 6 2008Gisela Berth Abstract Kappa-, iota-, and lambda-carrageenan (food grade) were analyzed by static light scattering (MALS in batch mode) in 0.1M NaNO3 at 25 and 60°C, earlier heated up to 90°C or not. At 25°C, there was a strong tendency for a concentration-dependent aggregation in the order lambda < kappa < iota. At 60°C, all samples were molecularly dispersed. The strongly temperature-dependent refractive index increments (equilibrium dialysis) differ. Data interpretation in terms of the wormlike chain model using the Skolnik-Odijk-Fixman approach led to an intrinsic persistence length around 3 to 4 nm and expansion factors as high as 1.5 and above in a thermodynamically good solvent for all three types. Triple-detector HPSEC (DRI, MALS, viscometry) on the three commercial samples plus a degraded (by acidic hydrolysis) kappa-carrageenan in the same solvent/eluant at 60°C yielded a uniform and slightly curved [,]- M relationship for 5 × 103 , M/(g mol) , 3 × 106 and a nearly identical molar mass dependence of the radius of gyration. HPSEC at 25°C on kappa-carrageenan confirmed formation of soluble aggregates. Special emphasis was put on analytical and methodological aspects. The reliability of the experimental data was demonstrated by analogous measurements on dextran calibration standards. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008 [source] Agarose Sols and Gels RevisitedMACROMOLECULAR SYMPOSIA, Issue 1 2006Jean-Michel Guenet Abstract Agarose sols have been seen for long as solutions of flexible chains that, on cooling, produce thermoreversible gels through double-helix formation. Investigations of the chain conformation in the sol state by small-angle neutron scattering reveals instead a rigid chain with a very large persistence length (lp,>,9 nm). The chain cross-section radius and mass per unit length correspond to characteristics of helices as those described by Foord and Atkins. These results lead one to a reappraisal of the occurrence of double helices in the gelation process, as they rather suggest a transition of the type loose-single helix,tight single helix. Studies of gels from agarose/water/cosolvent where the cosolvent is Dimethyl Sulfoxide (DMSO), Dimethyl Formamide (DMF), and Methyl Formamide (MF) have led one to conclude on the formation of agarose/water/ cosolvent ternary complexes. The contrast variation method by neutron scattering gives further support to this assumption. Finally, determination of the gel nanostructure allows one to account for the two regimes observed for the variation of the elastic modulus vs concentration. [source] Persistence Length of Cartilage Aggrecan Macromolecules Measured via Atomic Force MicroscopyMACROMOLECULAR SYMPOSIA, Issue 1 2004Laurel Ng Abstract Tapping mode atomic force microscopy (TMAFM) was employed to directly calculate the persistence length of individual fetal bovine epiphyseal and mature nasal cartilage aggrecan monomers, as well as their constituent chondroitin sulfate glycosaminoglycan chains. [source] 15N relaxation study of the amyloid ,-peptide: structural propensities and persistence lengthMAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2006Jens Danielsson Abstract The dynamics of monomeric Alzheimer A,(1,40) in aqueous solution was studied using heteronuclear NMR experiments. 15N NMR relaxation rates of amide groups report on the dynamics in the peptide chain and make it possible to estimate structural propensities from temperature-dependent relaxation data and chemical shifts change analysis. The persistence length of the polypeptide chain was determined using a model in which the influence of neighboring residue relaxation is assumed to decay exponentially as a function of distance. The persistence length of the A,(1,40) monomer was found to decrease from eight to three residues when temperature was increased from 3 to 18 °C. At 3 °C the peptide shows structural propensities that correlate well with the suggested secondary structure regions of the peptide to be present in the fibrils, and with the ,-helical structure in membrane-mimicking systems. Our data leads to a structural model for the monomeric soluble ,-peptide with six different regions of secondary structure propensities. The peptide has two regions with ,-strand propensity (residues 16,24 and 31,40), two regions with high PII-helix propensity (residues 1,4 and 11,15) and two unstructured regions with higher mobility (residues 5,10 and 25,30) connecting the structural elements. Copyright © 2006 John Wiley & Sons, Ltd. [source] An experimental study of GFP-based FRET, with application to intrinsically unstructured proteinsPROTEIN SCIENCE, Issue 7 2007Tomoo Ohashi Abstract We have experimentally studied the fluorescence resonance energy transfer (FRET) between green fluorescent protein (GFP) molecules by inserting folded or intrinsically unstructured proteins between CyPet and Ypet. We discovered that most of the enhanced FRET signal previously reported for this pair was due to enhanced dimerization, so we engineered a monomerizing mutation into each. An insert containing a single fibronectin type III domain (3.7 nm end-to-end) gave a moderate FRET signal while a two-domain insert (7.0 nm) gave no FRET. We then tested unstructured proteins of various lengths, including the charged-plus-PQ domain of ZipA, the tail domain of ,-adducin, and the C-terminal tail domain of FtsZ. The structures of these FRET constructs were also studied by electron microscopy and sedimentation. A 12 amino acid linker and the N-terminal 33 amino acids of the charged domain of the ZipA gave strong FRET signals. The C-terminal 33 amino acids of the PQ domain of the ZipA and several unstructured proteins with 66,68 amino acids gave moderate FRET signals. The 150 amino acid charged-plus-PQ construct gave a barely detectable FRET signal. FRET efficiency was calculated from the decreased donor emission to estimate the distance between donor and acceptor. The donor,acceptor distance varied for unstructured inserts of the same length, suggesting that they had variable stiffness (persistence length). We conclude that GFP-based FRET can be useful for studying intrinsically unstructured proteins, and we present a range of calibrated protein inserts to experimentally determine the distances that can be studied. [source] Rational shape engineering of the filamentous protein , prefoldin through incremental gene truncationBIOPOLYMERS, Issue 6 2009Timothy A. Whitehead Abstract An enticing possibility in nanotechnology is to use proteins as templates for the positioning of molecules in regular patterns with nanometer precision over large surface areas. However, the ability to redesign protein quaternary structure to construct new shapes remains underdeveloped. In the present work, we have engineered the dimensions of a filamentous protein, the , prefoldin (, PFD) from the hyperthermophile Methanocaldococcus jannaschii, and have achieved controllable attachment of filaments in a specific orientation on a carbon surface. Four different constructs of , PFD were generated in which the coiled coils extending from the association domain are progressively truncated. Three of the truncation constructs form well-defined filaments with predictable dimensions according to transmission electron microscopy. Two of these constructs had 2D persistence lengths similar to that of , PFD at 300,740 nm. In contrast, the 2D persistence length of the shortest truncation mutant was 3500 nm, indicating that the filament adsorbs along a different axis than the other constructs with its two rows of coiled coils facing out from the surface. The elastic moduli of the filaments range from 0.7,2.1 GPa, similar to rigid plastics and within the lower limit for proteins whose primary intermolecular interaction is hydrogen bonding. These results demonstrate a versatile approach for controlling the overall dimensions and surface orientation of protein filaments, and expand the toolbox by which to tune two overall dimensions in protein space for the creation of templated materials over a wide variety of conditions. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 496,503, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Chromatin dynamics of unfolding and refolding controlled by the nucleosome repeat length and the linker and core histonesBIOPOLYMERS, Issue 4 2007Toshiro Kobori Abstract Chromatin is composed of genomic DNA and histones, forming a hierarchical architecture in the nucleus. The chromatin hierarchy is common among eukaryotes despite different intrinsic properties of the genome. To investigate an effect of the differences in genome organization, chromatin unfolding processes were comparatively analyzed using Schizosaccaromyces pombe, Saccharomyces cerevisiae, and chicken erythrocyte. NaCl titration showed dynamic changes of the chromatin. 400,1000 mM NaCl facilitated beads with ,115 nm in diameter in S. pombe chromatin. A similar transition was also observed in S. cerevisiae chromatin. This process did not involve core histone dissociation from the chromatin, and the persistence length after the transition was ,26 nm for S. pombe and ,28 nm for S. cerevisiae, indicating a salt-induced unfolding to "beads-on-a-string" fibers. Reduced salt concentration recovered the original structure, suggesting that electrostatic interaction would regulate this discrete folding-unfolding process. On the other hand, the linker histone was extracted from chicken chromatin at 400 mM NaCl, and AFM observed the "beads-on-a-string" fibers around a nucleus. Unlike yeast chromatin, therefore, this unfolding was irreversible because of linker histone dissociation. These results indicate that the chromatin unfolding and refolding depend on the presence and absence of the linker histone, and the length of the linker DNA. © 2007 Wiley Periodicals, Inc. Biopolymers 85:295,307, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Biological consequences of tightly bent DNA: The other life of a macromolecular celebrityBIOPOLYMERS, Issue 2 2007Hernan G. Garcia Abstract The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA persistence length. Similarly, eukaryotic DNA is packed in DNA,protein complexes (nucleosomes), in which DNA is tightly bent around protein spools. DNA is also tightly bent by many proteins that regulate transcription, resulting in a variation in gene expression that is amenable to quantitative analysis. In these cases, DNA loops are formed with lengths that are comparable to or smaller than the DNA persistence length. The aim of this review is to describe the physical forces associated with tightly bent DNA in all of these settings and to explore the biological consequences of such bending, as increasingly accessible by single-molecule techniques. © 2006 Wiley Periodicals, Inc. Biopolymers 85:115,130, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Effects of excluded volume and polydispersity on solution properties of lentinan in 0.1 M NaOH solution,BIOPOLYMERS, Issue 4 2005Xufeng Zhang Abstract Seven lentinan fractions of various weight-average molecular weights (Mw), ranging from 1.45 × 105 to 1.13 × 106 g mol,1 were investigated by static light scattering and viscometry in 0.1M NaOH solution at 25°C. The intrinsic viscosity [,] , Mw and radius of gyration ,s2, , Mw relationships for lentinan in 0.1M NaOH solution were found to be represented by [,] = 5.1 × 10,3M cm3 g,1 and ,s2, = 2.3 × 10,1M nm, respectively. Focusing on the effects of the Mw polydispersity with the Schulz,Zimm distribution function, the data of Mw, ,s2,, and [,] was analyzed on the basis of the Yoshizaki,Nitta,Yamakawa theory for the unperturbed helical wormlike chain combined with the quasi-two-parameter (QTP) theory for excluded-volume effects. The persistence length, molecular weight per unit contour length, and the excluded-volume strength were determined roughly to be 6.2 nm, 980 nm,1, and 0.1, respectively. Compared with the theoretical value calculated by the Monte Carlo model, the persistence length is longer than that of the single (1 , 3)-,- D -glucan chain. The results revealed that lentinan exists as single-stranded flexible chains in 0.1M NaOH solution with a certain degree of expansion due to the electrostatic repulsion from the interaction between the OH, anions and lentinan molecules. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 187,196, 2005 [source] Chain stiffness of heteropolysaccharide from Aeromonas gum in dilute solution by dynamic light scatteringBIOPOLYMERS, Issue 6 2002Xiaojuan Xu Abstract Dynamic light scattering measurements have been made on 15 fractions of aeromonas (A) gum, an extracellular heteropolysaccharide produced by the strain Aeromonas nichidenii, with dimethylsulfoxide containing 0.2M lithium chloride as the solvent at 25°C. Data for the translational diffusion coefficient D covering a molecular weight range from 4.5 × 105 to 2.1 × 106 and ratios of the z -average radius of gyration ,s2,z1/2 to the hydrodynamic radius RH (calculated with previous ,s2,z data) suggest that the polymer behaves like a semiflexible chain in this solvent similar to the stiffness of cellulose derivatives. Thus the D data are analyzed on the basis of the Yamakawa,Fujii theory for the translational friction coefficient of a wormlike cylinder by coarse-graining the heteropolysaccharide molecule. Excluded-volume effects are taken into account in the quasi-two-parameter scheme, as was done previously for ,s2,z and [,] (the intrinsic viscosity) of A gum in the same solvent. The molecular weight dependence of RH is found to be explained by the perturbed wormlike chain with a persistence length of 10 nm, a linear mass density of 1350 nm,1, an excluded-volume strength parameter of 1.3 nm, and a chain diameter of 2.8 nm. These parameters are in substantial agreement with those estimated previously from ,s2,z and [,] data, demonstrating that the solution properties (D, ,s2,z, and [,]) of the heteropolysaccharide are almost quantitatively described by the current theories for wormlike chains in the molecular weight range studied. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 387,394, 2002 [source] Radius of gyration of plasmid DNA isoforms from static light scatteringBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2010David R. Latulippe Abstract Despite the extensive interest in applications of plasmid DNA, there have been few direct measurements of the root mean square radius of gyration, RG, of different plasmid isoforms over a broad range of plasmid size. Static light scattering data were obtained using supercoiled, open-circular, and linear isoforms of 5.76, 9.80, and 16.8,kbp plasmids. The results from this study extend the range of RG values available in the literature to plasmid sizes typically used for gene therapy and DNA vaccines. The experimental data were compared with available theoretical expressions based on the worm-like chain model, with the best-fit value of the apparent persistence length for both the linear and open-circular isoforms being statistically identical at 46,nm. A new expression was developed for the radius of gyration of the supercoiled plasmid based on a model for linear DNA using an effective contour length that is equal to a fraction of the total contour length. These results should facilitate the development of micro/nano-fluidic devices for DNA manipulation and size-based separation processes for plasmid DNA purification. Biotechnol. Bioeng. 2010;107: 134,142. © 2010 Wiley Periodicals, Inc. [source] Revisiting the neighbor exclusion model and its applicationsBIOPOLYMERS, Issue 1 2010Marcio S. Rocha Abstract We review the neighbor exclusion model and some of its applications to analyze the binding data of DNA-ligand complexes. We revisit the closed form of the model developed by McGhee and von Hippel in 1974, showing that this classic model can be used to help studying the behavior of DNA contour and persistence lengths when interacting with intercalating ligands. We present methods to quantitatively analyze the variation of these two quantities, allowing one to determine important parameters of the interaction such as the intrinsic binding constant and the exclusion number of the ligand. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 1,7, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Multiscale modeling of nucleic acids: Insights into DNA flexibilityBIOPOLYMERS, Issue 9 2008Yannick J. Bomble Abstract The elastic rod theory is used together with all-atom normal mode analysis in implicit solvent to characterize the mechanical flexibility of duplex DNA. The bending, twisting, stretching rigidities extracted from all-atom simulations (on linear duplexes from 60 to 150 base pairs in length and from 94-bp minicircles) are in reasonable agreement with experimental results. We focus on salt concentration and sequence effects on the overall flexibility. Bending persistence lengths are about 20% higher than most experimental estimates, but the transition from low-salt to high-salt behavior is reproduced well, as is the dependence of the stretching modulus on salt (which is opposite to that of bending). CTG and CGG trinucleotide repeats, responsible for several degenerative disorders, are found to be more flexible than random DNA, in agreement with several recent studies, whereas poly(dA).poly(dT) is the stiffest sequence we have encountered. The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 722,731, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||||||||