Protein folding limitations

The examples of modelling discussed in section C2.5.2 and section C2.5.3 are meant to illustrate tlie ideas behind tlie tlieoretical and computational approaches to protein folding. It should be borne in mind tliat we have discussed only a very limited aspect of tlie rich field of protein folding. The computations described in section C2.5.3 can be carried out easily on a desktop computer. Such an exercise is, perhaps, tlie best of way of appreciating tlie simple approach to get at tlie principles tliat govern tlie folding of proteins. 

The method has severe limitations for systems where gradients on near-atomic scale are important (as in the protein folding process or in bilayer membranes that contain only two molecules in a separated phase), but is extremely powerful for (co)polymer mixtures and solutions [147, 148, 149]. As an example Fig. 6 gives a snapshot in the process of self-organisation of a polypropylene oxide-ethylene oxide copolymer PL64 in aqueous solution on its way from a completely homogeneous initial distribution to a hexagonal structure. 

Despite their contribution to the understanding of protein folding, the correspondence between lattice models and real proteins is still very limited. The first step toward making such models more realistic is to remove the lattice and study off-lattice minimalist models. Simple off-lattice models of proteins can have proteinlike shapes with well-defined sec-... 

Isomerization of proline residues can he a rate-limiting step in protein folding... 

Enzymes assist formation of proper disulfide bonds during folding Isomerization of proline residues can be a rate-limiting step in protein folding Proteins can fold or unfold inside chaperonins GroEL is a cylindrical structure with a... 

The RNA structures and protein folds mentioned in Section 4.11 are limited in number and most of the basic varieties, but not all, are maintained throughout evolution (see Sections 7.8 and 8.10). 

How well has Dill s prediction held up In 2000, the first ever microsecond-long molecular dynamics simulation of protein folding was reported. It required 750,000 node hours (equal to the product of the number of hours times the number of processors) of computer time on a Cray T3 supercomputer. According to Dill s prediction, this length of simulation was not to be expected until around 2010. However, as noted above, Dill s analysis does not take into account large-scale parallelization—which, unless the computation is communications-limited, will effectively increase the speed of a computation in proportion to the number of processors available. 

The steps leading to the formation of the intrinsic chro-mophore have recently been investigated kinetically with S65T-GFP. The process of chromophore formation is an ordered sequence of three distinct steps (1) slow protein folding (kf = 2.44 X 10 s ) that precedes chromophore modification (2) an intermediate step occurs that includes, but may not be necessarily limited to, cycli-zation of the tripeptide chromophore motif (kc = 3.8 X 10 s ) and (3) rate-limiting oxidation of the cyclized chromophore (kox = 1 51 X s ). Reid and Flynn also reasoned that because chromophore forms de novo from purified denatured protein and is a first-order process, GFP chromophore formation is likely to be an autocatalytic process. 

The ligand binding or catalytic sites are the most relevant parts of a protein domain for the development of small molecules as modulators of protein function. There is evidence that proteins with conserved folds often also have their functional sites on the same topological location. In some cases a remarkable conservatism in functional sites can be observed. This is true for the example described later in this review on similarity of Cdc25A phosphatase, acetylcholinesterase (AChE) and 1 Ifl-hydroxysteroid dehydrogenases (1 l HSD) (Fig. 9). Nevertheless, it should be stressed that the correlation patterns of amino acid sequence, protein fold and protein function remain a matter of debate. Moreover, a vast number of specific functions can be carried out by the limited number of protein domains due to the high amino acid diversity of proteins with similar folds. " ... 

The potential utility of peptides as therapeutics with clinical applications is limited by its metabolic instability or poor transmembrane mobility. Consequently, the preparation of metabolically stable peptide analogs that can either mimic or block the function of natural peptides or enzymes is an important area of medicinal chemistry research. Synthesis of fluoroolefin amide isosteres, its incorporation in peptidomimetics, and the influence of that isosteric substitution on the inhibition of several enzymes such as peptidyl prolyl isomerases, dipeptidyl peptidase IV, and thermolysin is described. Moreover, protein folding and activity... 

---