Cross-linking studies

Baird, B.A., and Hammes, G.G. (1976) Chemical cross-linking studies of chloroplast coupling factor 1. J. Biol. Chem. 251, 6953-6962. 

Baskin, L.S., and Yang, C.S. (1980a) Cross-linking studies of cytochrome P-450 and reduced nicotinamide adenine dinucleotide phosphate-cytochrome P-450 reductase. Biochemistry 19, 2260-2264. 

Hillel, Z., and Wu, C.W. (1977) Subunit topography of RNA polymerase from Escherichia coli. A cross-linking study with bifunctional reagents. Biochemistry 16, 3334-3342. 

Ikai, A., and Yanagita, Y. (1980) A cross-linking study of apo-low density lipoprotein. /. Biochem. (Tokyo) 88, 1359-1364. 

Interactions in the-Intact Nucleosome—Cross-Linking Studies... 

Gohring F, Fackelmayer FO (1997) The scaffold/matrix attachment region binding protein hnRNP-U (SAF-A) is directly bound to chromosomal DNA in vivo a chemical cross-linking study. Biochemistry 36(27) 8276-8283... 

There are at least two assembly domains, namely the L20 domain and the L15 domain, in the 50 S assembly map (Fig. 15). Proteins within the L20 domain are essential for the assembly but not for the function of the 50 S subunit whereas those in the L15 domain are functionally important proteins whose assembly occurs at a late state. As with the 30 S subunit, the assembly map of the 50 S subunit (Rohl and Nierhaus, 1982) not only reflects the assembly dependence but also the topographical relationship of the proteins within the ribosomal particle. This conclusion is supported by a good correspondence between the assembly map on the one hand, and results from cross-linking studies and from the sequential removal of proteins from the particle by LiCl on the other hand. There is also a correlation between the interdependence of proteins during the assembly process and the arrangement of their genes on the E. coli chromosome (Rbhl et al., 1982). 

The spike protein complex of the alphaviruses appears to be assembled in the ER. Cross-linking studies of Triton X-lOO-solubilized viral proteins have shown that the p62 and El proteins are linked together to form a complex in the ER (Ziemiecki et al.. 1980). The topology of these complexes is the reverse of that in the viral particle the spikes are within the lumen of the ER and the internal domain of E2 is on the cytoplasmic side of the ER membrane. 

Several lines of evidence demonstrate that the active unit of integrase is a multimer. It is clear, as an isolated protein in solution, that integrase forms dimers [6,10-12], and it has been shown by sedimentation equilibrium studies that Rous sarcoma virus (RS V) integrase exists in reversible equilibrium between monomeric, dimeric, and tetrameric forms [13]. Protein-protein cross-linking studies of HIV-1 [14] and RSV [15] integrases confirm the existence of protein dimers and tetramers in solution, and in vivo, the yeast GAL4 two-hybrid system has demonstrated that HIV-1 integrase can interact with itself [16]. 

In summary, the inherent chemical susceptibility of the arenediazonium-based photoaffinity ligands does not make them a popular tool for routine photo-cross-linking studies. Examples of arenediazonium-based photophores that have been incoporated into peptides are given in Table 3. 

Reported applications of EGS include cross-linking studies of cytochrome P-450 (Baskin and Yang, 1980a), conjugation of tumor necrosis factor with lymphotoxin (Browning and Ribolini, 1989), the conversion of a gonadotropin-releasing hormone... 

In protein cross-linking studies, DMP has been used to examine the subunit structure of muscle pyruvate kinase (Davies and Kaplan, 1972), for the cross-linking of lactose synthetase (Brew et al., 1975), and to conjugate a fluorescent derivative of a-lactalbumin to glactosyltransferase (O Keefe et al., 1980). The reagent also has... 

Baskin, L. S., and Yang, C. S. (1982) Cross-linking studies of the protein topography of rat liver microsomes. Biochim. Biophys. Acta 684, 263—271. 

In the V-ATPase, the presence of at least two peripheral stators has been reported (Boekema et al., 1999 Domgall et al., 2002 Wilkens et al., 1999, 2004). Candidates for the stator proteins in the V-ATPase are subunits E and G, and support for this assignment comes from photochemical cross-linking studies that place these subunits on the outside of the Vi domain for much of its length (Arata et al., 2002a,b). Another subunit that probably plays the role of a stator in the V-ATPase is the a-subunit of the Vo- The Vo a-subunit has a large cytoplasmic domain, and it has been shown that this domain interacts with the A-subunit of the Vi (Landolt-Marticorena et al, 2000). 

Detailed crystallographic structures are available for ccp, and c, and a detailed st ctural proposal exists for the noncovalent ccp/cytc complex, as shown in figure 9. In this complex, the hemes are roughly parallel with a closest approach distance of ca 16 A, (24 A Fe-Fe). A wide variety of physical evidence, including.chemical cross linking studies, supports this proposed structure. 

Ossipov D, Gohil S, Chattopadhyaya J. Synthesis of the DNA-[Ru(tpy )(dppz)(CH3CN)]2+ and their photo cross-linking studies with the complementary DNA strands. J Am Chem Soc 2002 124 13416-33. 

In cross-linking studies it is sometimes useful to adopt an exactly opposite approach to cross-link ( vulcanize ) previously prepared linear chains. This process is applied in practice many different ways, mostly in the rubber industry. For study purposes, reversible cross-linking is most suitable because the network can subsequently be destroyed, for example by hydrolysis. Reactions of suitable macromolecules with chelating compounds are interesting from this point of view. 

Kumar, M. A., and Davidson, V. L., 1990, Chemical cross-linking study of complex formation between methylamine dehydrogenase and amicyanin from Paracoccus denitrificans. Biochemistry, 29 529995304. 

The amount of basic study of property-structure relationships seems to vary inversely with the degree of cross linking. Thermoplastics have been studied intensively by solution and x-ray techniques. Elastomers have been explored using swelling techniques in strong solvents which yield valuable data on the chain length between cross links. Studies on highly cross-linked systems have been limited mostly to measurements of how physical properties vary with the state of cure. 

In addition to the 420,000 MW species, cross-linking studies of the gyrase-DNA complex also identified protein species of MW 230,000 and 330,000, which were tentatively assigned as the A2 and A2B species, respectively (Kievan and Wang, 1980). Cross-linking of the purified A protein also yielded the 230,000 MW species, identifying this species as the A dimer, but the purified B protein gave no cross-linked products. 

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