In addition, we previously fused NH2-terminal Rossmann fold modules of human glyceraldehyde-3-phosphate dehydrogenase (GapDH) (amino acids 1-148) thethe N-terminus of full-length human Mb to prepare a 'modules(GapDH -fused Mb' protein [38].
Protein and RNA fold modules are highly conserved in evolution [ 21, 22].
The model has a conserved folding module in ZNFs, which is the most probable folding obtained.
Folded modules: IgG, immunoglobulin fold: TR, tandem repeats: EGF, epidermal growth factor-like module: CRD, carbohydrate recognition domain: CBP, complement binding protein-like module.
Other projects in the lab focus on the mechanism of protein misfolding, the structural and energetic mechanism of signaling, computational identification of folding modules, and the role of ligand binding.
Comparison of the folding mechanisms for CheY, T4 lysozyme, and interleukin-1β leads us to postulate that subdomain competition is a general feature of large single-domain proteins with multiple folding modules.
All that is known is that, for lattice models, mutationally robust "prototype" sequences are characterized by an overrepresentation of special sequence motifs that fold in a context-insensitive manner reminiscent of "folding modules" (Cui et al. 2002).
These RNA folding modules can also be used to create thermodynamic matchers for structural RNA motifs by writing motif-specific grammars, as recently reported from an RNA-seq study in S inor hizobium meliloti (Reinkensmeier et al., 2011 ).
First, we analyzed the performance of the fold recognition module of HMMerThread by testing its ability to find known conserved domains with a statistically significant HMMER2 E-value.
The template-based models resulting from the comparative modeling and fold recognition modules are scored with two procedures.
No matter the direction of the net flux between f9SS and f10SS, for instance, modules 2, 3, and 6, which do not contain the recycling pathway f2SS, always have a higher up-regulated activity of X1 (with an averaged value above 3 fold) than modules 1, 4, 5, and 7 (with averaged values ranging from just above 1 to less than 2 fold).
