Groove large

Broaching/honing Typically used for inside diamet of tubes and otim cylindrical parts, or for grooves, large holes, and otiier cavities Surfaces must be accessible to tools and withstand the local pressure and heat buildup Avmd very thin cross sections/wall tiiickness... 

In free molecular flow, if gaseous conductance were not independent of the flow direction, a perpetual-motion machine could be constmcted by connecting two large volumes by a pair of identical ducts having a turbine in front of one of the ducts. A duct that has asymmetricaUy shaped grooves on its waU surface could alter the probabUity of molecular passage in such a way that for a tube of equal entrance and exit areas, the probabUity of passage would be made directional. 

Figure 7.5 Pits on a large-diameter austenitic stainless steel pipe. Note the grooves formed by leakage of pit contents down the pipe wall in the direction of gravity. (Pipe wall was vertical in service.)...

The binding site is located at the tip of the subunit within the jelly roll structure (Figure 5.23). The sialic acid moiety of the hemagglutinin inhibitors binds in the center of a broad pocket on the surface of the barrel (Figure 5.24). In addition to this groove there is a hydrophobic channel that can accomodate large hydrophobic substituents at the C2 position of sialic acid (Figures 5.22 and 5.24). 

Figure 5.24 Space-filling model (green) of the sialic acid binding domain of hemagglutinin with a bound inhibitor (red) Illustrating the different binding grooves. The sialic acid moiety of the Inhibitor binds in the central groove. A large hydrophobic substituent, Ri, at the Cz position of sialic acid binds in a hydrophobic channel that runs from the central groove to the bottom of the domain. (Adapted from S.J. Watowich et al.. Structure 2 719-731, 1994.)...

The polypeptide chain of the lac repressor subunit is arranged in four domains (Figure 8.21) an N-terminal DNA-hinding domain with a helix-turn-helix motif, a hinge helix which binds to the minor groove of DNA, a large core domain which binds the corepressor and has a structure very similar to the periplasmic arablnose-binding protein described in Chapter 4, and finally a C-terminal a helix which is involved in tetramerization. This a helix is absent in the PurR subunit structure otherwise their structures are very similar. 

TBP binds in the minor groove and induces large structural changes in DNA... 

In conclusion, one important factor that contributes to the strong affinity of TBP proteins to TATA boxes is the large hydrophobic interaction area between them. Major distortions of the B-DNA structure cause the DNA to present a wide and shallow minor groove surface that is sterically complementary to the underside of the saddle structure of the TBP protein. The complementarity of these surfaces, and in addition the six specific hydrogen bonds between four side chains from TBP and four hydrogen bond acceptors from bases in the minor groove, are the main factors responsible for causing TBP to bind to TATA boxes 100,000-fold more readily than to a random DNA sequence. 

Zheng, Z.-H., Catano, A. R., Segelke, B.W., Stura, E.A., Peterson, P.A., Wilson, l.A. Crystal stmcture of mouse CDl an MHC-like fold with a large hydrophobic binding groove. Science 277 339-345, 1997. 

TBP-TATA box complexes are known A p sheet in TBP forms the DNA-binding site TBP binds in the minor groove and induces large structural changes in DNA The interaction area between TBP and the TATA box is mainly hydrophobic Functional implications of the distortion of DNA by TBP... 

The initial development of a cellular structure from an originally flat interface has been at least partially understood [130]. Let us look only at the large-wavelength A limit (for more details see [122]). In the numerical calculations it was found [123] that for fixed cell-spacing A at increasing velocity a tail instability occurs. A side branch in the groove between two... 

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

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