Tosiyuki Noguti

INSECT PROTHORACICOTROPIC HORMONE : A NEW MEMBER OF THE VERTEBRATE GROWTH FACTOR SUPERFAMILY

Prothoracicotropic hormone (PTTH) is a brain neurosecretory protein that controls insect development. PTTH of the silkmoth Bombyx mori is a homodimeric protein, the subunit of which consists of 109 amino acids. Clear‐cut sequence similarity to any other proteins has not been observed. By disulfide‐bond pattern analysis and modeling of the PTTH structure based on the known three‐dimensional (3D) structures of growth factor family with cystine‐knot motif, we propose that the PTTH protomer adopts the fold unique to the structural superfamily of the growth factors, β‐nerve growth factor (β‐NGF), transforming growth factor‐β2 (TGF‐β2), and platelet‐derived growth factor‐BB (PDGF‐BB). The insect neurohormone PTTH appears to be a member of the growth factor superfamily, sharing a common ancestral gene with the three vertebrate growth factors, β‐NGF, TGF‐β2 and PDGF‐BB.

Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility

In comparative modeling, the quality of amino acid sequence alignment still constitutes a major bottleneck in the generation of high quality models of protein three‐dimensional (3D) structures. Substantial efforts have been made to improve alignment quality by revising the substitution matrix, introducing multiple sequences, replacing dynamic programming with hidden Markov models, and incorporating 3D structure information. Improvements in the gap penalty have not been a major focus, however, following the development of the affine gap penalty and of the secondary structure dependent gap penalty. We revisited the correlation between protein 3D structure and gap location in a large protein 3D structure data set, and found that the frequency of gap locations approximated to an exponential function of the solvent accessibility of the inserted residues. The nonlinearity of the gap frequency as a function of accessibility corresponded well to the relationship between residue mutation pattern and residue accessibility. By introducing this relationship into the gap penalty calculation for pairwise alignment between template and target amino acid sequences, we were able to obtain a sequence alignment much closer to the structural alignment. The quality of the alignments was substantially improved on a pair of sequences with identity in the “twilight zone” between 20 and 40%. The relocation of gaps by our new method made a significant improvement in comparative modeling, exemplified here by the Bacillus subtilis yitF protein. The method was implemented in a computer program, ALAdeGAP (ALignment with Accessibility dependent GAp Penalty), which is available at http://cib.cf.ocha.ac.jp/target_protein/. Proteins 2011;

Hydrogen bond network of cytochrome P-450cam: a network connecting the heme group with helix K

During investigations of the structural character of a mutant P-450cam where Glu-286 is replaced with lysine, we obtained evidence of a hydrogen bond network between helix K and the heme group via helix L of P-450cam. This mutant protein loses the ability to maintain the heme group in a proper position, possibly due to a break in the hydrogen bond network.

Mechanical stability of compact modules of barnase

© 1997 Federation of European Biochemical Societies.

Conformational characterization of designed minibarnase.

We have designed a minibarnase by removing one module from barnase, a bacterial RNase from Bacillus amyloliquefaciens. Barnase, consisting of 110 amino acid residues, is decomposed into six modules, M1-M6. Module is defined as a peptide segment consisting of contiguous amino acid residues that makes a small compact conformation within a globular domain. To understand the role of module in protein architecture, we analyzed NMR and CD spectra of a minibarnase, which lacked 26 amino acid residues corresponding to module M2. We demonstrated the formation of hydrophobic cores in the minibarnase similar to those of barnase. Although its conformational stability against acids and heat was reduced in comparison with barnase, the minibarnase retained cooperative folding character (two-state folding). Therefore, the folding of the minibarnase consisting of modules M1 and M3-M6 is independent to some extent of module M2. This finding may be useful for future module-based protein design.