Loop domains

Indeed, hydrophilic N- or C-terminal ends and loop domains of these membrane proteins exposed to aqueous phases are able to undergo rapid or intermediate motional fluctuations, respectively, as shown in the 3D pictures of transmembrane (TM) moieties of bacteriorhodopsin (bR) as a typical membrane protein in the purple membrane (PM) of Halobacterium salinarum.176 178 Structural information about protein surfaces, including the interhelical loops and N- and C-terminal ends, is completely missing from X-ray data. It is also conceivable that such pictures should be further modified, when membrane proteins in biologically active states are not always present as oligomers such as dimer or trimer as in 2D or 3D crystals but as monomers in lipid bilayers. 

The estimated correlation times for the loop domains of the order of 10 4 s are obtained for the suppressed peaks in the [l-13C]amino-acid-labelled bR, including Gly, Ala, and Leu residues as shown in Figure 24C. The loop dynamics can be also examined by measurements of the 13C-1H dipolar couplings by DIPSHIFT experiment in which fluctuations of the Co,-Cp vector result in additional motional averaging as order parameters, in addition to the rotation of Ala methyl groups which scales the dipolar... 

Seal, R. P. and Amara, S. G. (1998) A reentrant loop domain in the glutamate carrier EAAT1 participates in substrate binding and translocation. Neuron 21,1487-1498. 

Nusrat A, Brown GT, Tom J, Drake A, Bui TTT, Quan C, and Mrsny RJ [2005] Multiple protein interactions involving proposed extracellular loop domains of the tight junction protein occludin. Mol Biol Cell 16 1725-1734... 

The chapter is organized as follows. Section II is devoted to materials and methods. In Section III, we show [34, 35] that the GC content displays rather regular nonlinear oscillations with two main periods of 110 20 kbp and 400 50 kbp, which are well-recognized characteristic scales of chromatin loops and loop domains involved in the hierarchical folding of chromatin fibers. 

C. Demeret, Y. Vassetzky, and M. Mechali, Chromatin remodelling and DNA replication From nucleosomes to loop domains. Oncogene 20, 3086-3093 (2001). 

Bazett-Jones, D.P., Cote, J., Landel, C.C., Peterson, C.L., and Workman, J.L. (1999a) The SWI/ SNF complex creates loop domains in DNA and polynucleosome arrays and can disrupt DNA-histone contacts within these domains. Mol. Cell. Biol. 19(2), 1470-1478. 

Figure 27-5 (A, B) Two possible models of the 30-nm chromatin fiber.55 (A) Thoma et al.85 (B) Woodcock et al.6i 87 The fully compacted structure is seen at the top of each figure. The bottom parts of the figures illustrate proposed intermediate steps in the ionic strength-induced compaction. (C) Possible organization of the DNA within a metaphase chromosome. Six nucleosomes form each turn of a solenoid in the 30-nm filament as in (A). The 30-nm filament forms 30 kb-loop domains of DNA and some of these attach at the base to the nuclear matrix that contains topoisomerase II. About ten of the loops form a helical radial array of 250-nm diameter around the core of the chromosome. Further winding of this helix into a tight coil 700 nm in diameter, as at the top in (C), forms a metaphase chromatid. From Manuelidis91.

Silvanovich, A., Li, M-G., Serr, M., Mische, S., and Hays, T. S. (2003). The third P-loop domain in cytoplasmic dynein heavy chain is essential for dynein motor function and ATP-sensitive microtubule binding. Mol. Biol. Cell 14, 1355-1365. 

The detailed mechanisms of helicases are still under active investigation. However, the determination of the three-dimensional structures of several helicases has been a source of insight. For example, a bacterial helicase called PcrA comprises four domains, hereafter referred to as domains Al, A2, Bl, and B2 (Figure 27.16). Domain A1 contains a P-loop NTPase fold, as was expected from amino acid sequence analysis. This domain participates in ATP binding and hydrolysis. Domain Bl is homologous to domain Al but lacks a P-loop. Domains A2 and B2 have unique structures. 

SauraCA, Tomita T, Soriano S, Takahashi M, Leem JY, et al. 2000. The noncon-served hydrophilic loop domain of presenilin (PS) is not required for PS en-doproteolysis or enhanced A beta 42 production mediated by familial early onset Alzheimer s disease-linked PS variants. J. Biol. Chem. 275 17136-42... 

Transporters are integral membrane proteins that typically have 12 transmembrane domains (TMDs), althongh some have 6, 8, 10, 11, 13 or even 17 TMDs. The TMDs are folded in a-heUcal stractures within the membrane and linked at both sides by amino acid seqnences floating in the internal or external cell environment. The amino acids in the external loop domains are freqnently A/-glycosylated, while those of the intracellnlar loops of SLC, ABC and MATE proteins bear phosphorylation sites the ABCs also have one or two ATP-binding domains. The 3D stmcture of TMDs is a crown shape, and they look like a channel allowing communication between the two fluid spaces separated by the lipid bilayer (Figure 34.3). Many SLC and MATE transporters have 300-800 amino acid residues and a molecular... 

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