Protein folds changes

Spot No. Spot- name Accession Protein Fold change T-test Seq. pi Seq. MW (kDa)... 

The protein structural similarity is generally described in terms of folds. However, evolutionarily related proteins may contain different folds, and proteins sharing the same fold do not necessarily descend from a common ancestor. Structural similarity may occur due to the limited number of favorable arrangements for secondary structure elements in fold space. Four of the most common mechanisms for protein-fold change (Grishin, 2001 Lupas et al, 2001) include ... 

Figure 18.4 Common mechanisms for protein fold changes. TOPS representations for four of the most common mechanisms for protein fold changes involving secondary structures are illustrated with examples. They are (A) insertion/deletion/substitution between lactate dehydrogenase and NADH peroxidase, (B) circular permutation between phospholipase C5 and synaptotagmin, (C) P-strand invasion/withdrawal between ras protein and adenylate kinase, and (D) P-hairpin flip/swap between retinol-binding protein and thrombin inhibitor triabin...

One drawback to a molecular dynamics simulation is that the trajectory length calculated in a reasonable time is several orders of magnitude shorter than any chemical process and most physical processes, which occur in nanoseconds or longer. This allows yon to study properties that change w ithin shorter time periods (such as energy finctnations and atomic positions), but not long-term processes like protein folding. 

These results indicate that is it possible to change the fold of a protein by changing a restricted set of residues. They also confirm the validity of the rules for stability of helical folds that have been obtained by analysis of experimentally determined protein structures. One obvious impliction of this work is that it might be possible, by just changing a few residues in Janus, to design a mutant that flip-flops between a helical and p sheet structures. Such a polypeptide would be a very interesting model system for prions and other amyloid proteins. 

SUMOylation. Figure 1 SUMOylation is a reversible and regulated process. Target protein modification by SUMO can be initiated and terminated by different cues. Sumoylation leads to changes in the behavior of the modified protein, for example, different cellular localization, enhanced/reduced activity, or increased stability. These changes are due to alterations either in protein interactions or protein folding. 

Keywords Molecular dynamics, pAT. Protein folding, pH-dependent conformational change... 

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