Accessory helix

Schug, A. Herges, T. Wenzel, W., All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method, Proteins-Struct. Funct. Bioinform. 2004, 57, 792-798... 

Fig. 9. Accessory helices in core histone structures, (a) Accessory H3 helix, shown in a ribbon Ca model, interacts with the DNA entering and leave the nucleosome. A short helix in the tail of H2A is seen between the accessory and medial helix of H3. (b) Solvent accessible surface representation of the C-terminal residues of H2A showing the contribution of these residues to the ventral surface of the NCP.

Summary. We recently developed an all-atom free energy force field (PFFOl) for protein structure prediction with stochastic optimization methods. We demonstrated that PFFOl correctly predicts the native conformation of several proteins as the global optimum of the free energy surface. Here we review recent folding studies, which permitted the reproducible all-atom folding of the 20 amino-acid trp-cage protein, the 40-amino acid three-helix HIV accessory protein and the sixty amino acid bacterial ribosomal protein L20 with a variety of stochastic optimization methods. These results demonstrate that all-atom protein folding can be achieved with present day computational resources for proteins of moderate size. 

The sequences of RCs from five different bacteria and of PS2 from different organisms are currently available. Only very few clusters of amino acids are common to all the sequenced L and D1 (M and D2) subunits. In most cases, the conserved amino acids in PS2 and the bacterial reaction centers are isolated within variable sequences so that it appears difficult to locate their possible homologues in the PS1 subunits. Only two helices out of the five present in bacterial RC and in PS2 exhibit sequence homologies that can be looked for in the PS1 heavy subunits the B and D helices of the L and M subunits of bacterial RCs (helices II and IV from the D1 and D2 subunits of PS2) (see figures 1 and 2). In bacterial RCs. the B helices run along the primary electron acceptor Bpheo (helix B of the L subunit) and along the accessory Bpheo (helix B of the M subunit) (5). The D helices are Involved in the ligation of the central Mg atoms of the BChl of the primary electron donor. 

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