Helix capping

Tidor, B., Helix-capping interaction in A-Cro protein — a free-energy simulation analysis, Proteins Struct. Func. Genet. 1994,19, 310-323. 

The versatility of this template was demonstrated with the synthesis of very short unusually helical polyalanine sequences stabilized by chaotrophic anions [35] and host systems for evaluation of the C-terminal helix capping propensities for nonpolar natural amino acids [36]. As model sequences WK4lnp2,LG-Hel-Ag-NH2 for the primary C-terminal amide and WK4Inp2 LG-Hel-A8-X-Inp-NH2 for candidate amino acids X were selected. In these sequences, Hel is the previously mentioned N-terminal helix template, Inp is 4-carboxypiperidine and L is tert-leucine. In the N-terminal region tryptophan (W) provides a UV reporter, four lysines (K4) are solubilizers, and Inp2 L a spacer element. The C-capping test region of these peptides is G-Hel-Ag-X-Inp, and its helicity is taken as proportional to [6)222, the per-residue ellipticity derived from CD analysis [37]. 

Donnelly, D., Overington, J. P, Blundell, T. L. The prediction and orientation of a-helices from sequence alignments the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules Prot. Engng. 1994 7, 645-653. 

In the case if length of putative TMH remains equal or greater than 24 FILTER subroutine is applied. It shortens TMH on both ends until helix preference becomes too high. Helical preference is multiplied with number of residues reached from the cap residue position and resulting value compared with (TMH length -21)/2. The FILTER creates new helix cap positions closer to the middle of TMH. The shift in the new cap positions is greater for lower helical preference and for longer TMH. 

After ending the main filter routine the T conformation is assigned to four residues next to each predicted helix cap. Also peaks in helix preference higher than 4.0 are examined for the whole sequence. Additional (overlooked) TMH is assigned as 15 residue segment centered around such peak if a) less than three of K, P, D, R, E residues are present in such a segment, if b) such segment is at least 20 residues removed from sequence terminals, and if c) TMH was not previously predicted in that position. 

B. Tidoi Proteins, 19, 310 (1994). Helix-Capping Interaction in 1 Cro Protein A Free Energy Simulation Analysis. 

The specific arrangement of two a helices joined by a loop region in lambda Cro and repressor, as well as in CAP, constitute the helix-turn-helix DNA-binding motif (Figure 8.8), which also occurs in some eucaryotic transcription factors as discussed in Chapter 9. The orientation of the two helices and... 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

Harper, E., and Rose, G. D., 1993. Helix stop signals in proteins and peptides The capping box. Biochemistry 32 7605-7609. 

N-eap helix dipole salt bridge salt bridge extra helix helix dipole C-cap stabili ation stability stabiiization... 

The amino acid sequence of our first aPNA (which we termed backbone 1 or bl) was designed based on this amphipathic hehx sequence (Fig. 5.3 B). Specifically, this aPNA backbone included hydrophobic amino acids (Ala and Aib), internal salt bridges (Glu-(aa)3-Lys-(aa)3-Glu), a macrodipole (Asp-(aa)i5-Lys), and an N-ace-tyl cap to favor a-helix formation. The C-termini of these aPNA modules end in a carboxamide function to preclude any potential intramolecular end effects. Each aPNA module incorporates five nucleobases for Watson-Crick base pairing to a target nucleic acid sequence. 

Helix-turn-helix j Ecoli i Phage I Mammals lac repressor CAP Xcl, cro, and tryptophan and 434 repressors homeo box proteins Pit-1, Oct1,Oct2... 

---