Multiple helices

Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T (2004) Crystal structure of phenylalanine ammonia lyase multiple helix dipoles implicated in catalysis. Biochemistry 43(36) 11403-11416... 

Fig. 2. Principal configurations of elements used in bimetal thermometers (a) flat spiral, (b) single helix, (c) multiple helix...

What distinguishes coiled coils from multiple-helix bundles is that coiled coils contain a narrow hydrophobic face on the surface of each a-helix from the 3-4 hydrophobic repeat, whereas in multiple-helix bundles the hydrophobic interface can contain a wider hydro-phobic surface involving hydrophobes additional to the 3-4 repeat (Scheme 1 for a review, see retf22 ). The wider hydrophobic surface will change the hydrophobic packing and relative orientation of the a-helical chains with respect to each other in bundles as opposed to coiled coils.[17 ... 

J C Calabrese, D B Jordan, A Boodhoo, S Sariaslani, T Vannelli (2004) Crystal Structure of Phenylalanine Ammonia-Lyase Multiple Helix Dipoles Implicated in Catalysis Biochemistry 43(36) 11403-11416... 

J. G. Withers, Tube Side Heat Transfer and Pressure Drop for Tubes Having Helical Internal Ridging with Turbulent/Transitional Flow of Single-Phase Fluid. Pt. 2. Multiple-Helix Ridging, Heat Transfer Eng. (2/2) 43-50,1980. 

Unassociated helices remain in the networks in the single-helix case while there are no isolated helices in the multiple-helix case. In the former the helix content is not necessarily proportional to the elastic modulus of the network. 

In the single-helix case, two neighboring helices on the same chain may merge into one when they grow while in the multiple-helix case they collide and never merge. 

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further stmctural...

Attempts have also been made at predicting the secondary stmcture of proteins from the propensities for residues to occur in the a-helix or the P-sheet (23). However, the assignment of secondary stmcture for a residue only has an average accuracy of about 60%. A better success rate (70%) is achieved when multiple-aligned sequences having high sequence similarity are available. 

Fairman, R., et al. Multiple oligomeric states regulate the DNA binding of helix-loop-helix peptides. Proc. Natl. Acad. Sci. USA 90 10429-10433, 1993. 

A number of approaches have been followed in attempts to create even more potent and durable inhibitory peptides including various rational approaches to increase peptide binding affinities, stability, and half-life (Dwyer et al. 2007), and the use of peptides such as 5-helix bearing multiple HR domains (Dimitrov et al. 2005). 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

Structural analysis of the two pectate lyases PelC and PelE (5, 6), demonstrated that these proteins fold in a large heHx of parallel P strands. A stack of asparagine residues parallel to the helix probably plays a role in the stabUity of this structure. Identification of the structurally conserved amino adds lead to a reaHgnment of the protein sequences (7). In addition to Erwinia extracellular pectate lyases, the multiple aHgnment indudes the Bacillus subtilis pectate lyase, Aspergillus tdger and E. carotovora pectin lyases and plant proteins. 

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