Core particles

In the MS approximation, for hard core particles of diameter a, one approximates the direct correlation fiinction by... 

Page 1171 (Figure 28 7) is adapted from crystallograpliic coordinates deposited with The Protein Data Bank PDB ID lAOl Luger A Mader W Richmond R K Sargent D F Richmond T J Crystal Structure of the Nucleosome Core Particle at 2 8 A Resolution Nature 1997 V 389 251... 

Antimicrobial agents are used where there is a need to inhibit bacterial and fungal growth. The additives can consist of copper, germanium, zinc and zinc compounds, metal oxides or sulfides, metal zeofltes, as well as silver and copper oxide-coated inorganic core particles (154—159) (see Industrial ANTIMICROBIAL AGENTS). 

Fig. 3.18 Nucleosome core particle (NCP)-polyamide co-crystal structures (PDB codes 1M18 and 1M19). (Top) Partial structure, viewed down the superhelical axis. Base pairs 58-145 (shown in white) and associated proteins (H3, blue H4, green H2A, yellow H2B, red) are shown for each complex. Superhelix locations (SHLs) are labeled as each major...

C.L. White, C. Melander, J.M. Gotteseeld, P. B. Dervan, and K. Luger Crystal stmctures of nucleosome core particles in complex with minor groove DNA-binding ligands. J. Mol. Biol. 2003, 326, 371-380. 

Another method to synthesize hollow nanocapsules involves the use of nanoparticle templates as the core, growing a shell around them, then subsequently removing the core by dissolution [30-32]. Although this approach is reminiscent of the sacrificial core method, the nanoparticles are first trapped and aligned in membrane pores by vacuum filtration rather than coated while in aqueous solution. The nanoparticles are employed as templates for polymer nucleation and growth Polymerization of a conducting polymer around the nanoparticles results in polymer-coated particles and, following dissolution of the core particles, hollow polymer nanocapsules are obtained. 

The next two chapters concern nanostructured core particles. Chapter 13 provides examples of nano-fabrication of cored colloidal particles and hollow capsules. These systems and the synthetic methods used to prepare them are exceptionally adaptable for applications in physical and biological fields. Chapter 14, discusses reversed micelles from the theoretical viewpoint, as well as their use as nano-hosts for solvents and drugs and as carriers and reactors. 

Luger L et al Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997 398 251. 

Using long-chain alkylsulfobetaines as the stabilizer, a number of highly water soluble nanometal colloids have been isolated in excellent yields (see Figure 8). The core particle size can be tailored between 1 and 10 nm. TEM examinations have shown that the resulting materials are generally mono-disperse. Further, a combination of spectroscopic methods confirmed the zerovalent nature of the metal cores [200]. 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

Fig. 10 Charge transport is observed in a variety of nucleic acid assemblies over a wide distance regime (3.4-200 A). Shown are examples of nucleic acid structures through which charge transport has been examined a B-form DNA b DNA-RNA hybrids c cross-over junctions and d nucleosome core particles. In all assemblies, the charge transport chemistry is extremely sensitive to the structure of the -stacked nucleic acid bases...

Our first example of an application of the potential distribution formula [Eq. (5)] is in the calculation of the excess chemical potential of a simple hydrophobic solute dissolved in water (Hummer et al., 1998a, 2000), which we consider to be a hard-core particle that excludes all water molecules from its molecular volume. We note that these purely... 

SADP or sulfo-SADP also have been used to study the phenylalanine-methionine-arginine-phenylalanine-amide-activated sodium channel (Coscoy et al., 1998), various apolipoprotein E isoforms (Mann et al., 1995), the high-affinity phenylalkylamine Ca2+ antagonist binding protein from guinea pig (Moebius et al., 1994), the interaction of non-histone proteins with nucleosome core particles (Reeves and Nissen, 1993), and the interactions among cytochromes P-450 in the endoplasmic reticulum (Alston et al., 1991). See Chapter 28 for methods of using photoreactive heterobifunctional crosslinkers to study protein interactions. 

Wash the resultant core particles twice with the ethanol/ammonia solution using centrifugation. 

Figure 14.25 The preparation of highly controlled fluorescent silica nanoparticles can be done by first polymerizing APTS that has been covalently modified with an amine-reactive dye to form fluorescent core particles. The core then is capped by a shell of silica by polymerization of TEOS. The shell layer can be further derivatized with silane coupling agents to provide functional groups for conjugation.

Reeves, R., and Nissen, M.S. (1993) Interaction of high mobility group-I (Y) nonhistone proteins with nucleosome core particles./. Biol. Chem. 268, 21137-21146. 

Figure 6.8 Illustration of colloid-templated nanoparticle assemblies. The process involves the layer-by-layer adsorption of charged polymers and oppositely charged nanoparticles onto the surfaces of the colloidal template. The colloidal core particles may then be removed to generate a hollow sphere of nanoparticles, held together by electrostatic interactions with the linear polymer glue ...

Coat proteins that make up the inner virus (core) particle. The virus gene that specifies these protein is called the gag gene. The gag gene codes for p 24, p 17 (p 18), p 9, and p 7. 

Graft polymerization of monomers such as acrylic acid on core particles consisting of magnetic iron oxide embedded in cross-linked poly (vinyl alcohol) (PVA) has been described previously (2). 

Time-dependent fluorescence measurements have been made on tyrosine in calf thymus nucleosome core particles by Ashikawa et al. S7) Based on the salt dependence of the decay data, the tyrosines were divided into two classes. At 20 to 400 mM salt, about half of the tyrosine residues appear to be partially quenched, possibly by resonance energy transfer to DNA bases. The other half are thought to be statically quenched, possibly by hydrogen bonds this quenching is partially eliminated at about 2 M salt. In view of the number of tyrosines per nucleosome core particle (estimated at 30), it is impossible to make a more detailed analysis of the decay data. 

The fluorescence of purified histones has been studied by several different groups, 90 95) with the most detailed studies being on calf thymus histone HI. Histone HI, which binds to the outside of core particles, contains one tyrosine and no tryptophan. This protein exhibits a substantial increase in fluorescence intensity in going from a denatured to a folded state.<90) Collisional quenching studies indicate that the tyrosine of the folded HI is in a buried environ-ment.(91) Libertini and Small(94) have identified three emissions from this residue when in the unfolded state with peaks near 300, 340, and 400 nm. The 340-nm peak was ascribed to tyrosinate (vide infra), and several possibilities were considered for the 400-nm component, including room temperature phosphorescence, emission of a charge transfer complex, or dityrosine. Dityrosine has the appropriate spectral characteristics, but would require... 

L. J. Libertini and E. W. Small, Salt induced transitions of chromatin core particles studied by tyrosine fluorescence anisotropy, Nucleic Acids Res. 8, 3517-3534 (1980). 

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