Structure, three-dimensional chaperones

Proteins spontaneously fold into their native conformation, with the primary structure of the protein dictating its three-dimensional structure. Protein folding is driven primarily by hydrophobic forces and proceeds through an ordered set of pathways. Accessory proteins, including protein disulfide isomerases, peptidyl prolyl cis-trans isomerases, and molecular chaperones, assist proteins to fold correctly in the cell. 

The first basic tenet of protein-structure prediction is that the amino acid sequence, the primary structure, contains all of the information required for the correct folding of the polymer chain. This is a first approximation which clearly ignores the role of environment on the induction of structure or the action of chaperone proteins which assist the in vivo folding process. The wide variety of structural motifs that have been observed for proteins is derived from only twenty different monomers (amino acids), many of which are structurally quite similar (i.e., isoleucine and leucine vary only in branching of the butyl side chain). However, there are many cases in which the substitution of amino acids with structurally similar residues (so-called conservative substitution) will lead to a protein that will not properly fold. Studies involving deletion of even small portions of the termini of the protein sequence provide similar results. On the other hand there are proteins related through evolution with as little as 20% sequence identity which adopt similar three-dimensional structures. Therefore the information encoded in the primary sequence is specific for one protein fold, however, there are numerous other sequences, only remotely related at first glance, which will produce the same fold. 

The three-dimensional structure of the PapD periplasmic chaperone that forms transient complexes with pilus subunit proteins has been solved by Holmgren and Branden (1989). PapD consists of two globular domains oriented in the shape of a boomerang (Fig. 2). Each domain is a /3-barrel structure formed by two antiparallel /8-pleated sheets that have a topology similar to an immunoglobulin fold. The relationship between PapD and other immunoglobulin-like proteins is discussed in Section IV,C. 

Fig. 2. Ribbon model of the three-dimensional structure of the PapD chaperone. The consensus sequence for twelve members of the family was superimposed on the tertiary structure of PapD. The position of the invariant amino acid residues is shown in black, and that of the residues conserved in at least eight of the sequences, in gray.

Human phosphate binding protein (HPBP), an apolipoprotein that binds inorganic phosphate in blood, was serendipitously discovered. Its three-dimensional structure and complete amino acid sequence were solved (Morales et al, 2006 Diemer et al, 2008). The conditions found to separate HPBP and PONl in vitro indicated that HPBP is strongly associated with PONl (Renault et al, 2006). Moreover, the stabilization of the active form(s) of human PONl by HPBP suggests that HPBP could be a functional chaperone for PONl (Rochu et al, 2007b, c). 

AD. The physiological role of APP is as yet unknown. It can reduce Cu to Cu and the physiological and three-dimensional structure suggests a role as a copper chaperone. The binding of Cu to A/3 is toxic in neuronal cultures and this may contribute to the oxidative stress that is commonly observed in AD. 

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to form polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined three-dimensional (3D) structure. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins)... 

Once modified, do proteins always have the correct three-dimensional structure In theory, the primary structure of the protein determines its three-dimensional structure. However, in reality proteins often need the help of a chaperone to arrive at the correct structure. This is due to possible interactions with other proteins before the nascent protein chain is complete and also the possibility that a protein will begin to fold incorrectly in its early stages of translation before it is complete. 

In the text, Actin and Hsp-70 are shown to be homologous on the basis of their shared three-dimensional structures. Actin is found in essentially all eucaryotes, often as part of the contractile apparatus with myosin. Hsp-70 is found in eucaryotes, procaryotes, and archaea as a chaperone for protein folding. What can we deduce from this distribution ... 

C.B. Anfinsen, Principles that Govern the Folding of Protein Chains. Science, 181, 223-230, 1973. The Anfinsen principle is that the sequence of a protein dictates the full three-dimensional structure that it would form, that is, sequence dictates protein folding and assembly. The need for molecular chaperones suggests that the correctly folded protein, the lowest energy structure, is not always the result and that the problem arises out of improper hydrophobic associations. Interestingly, the... 

In the process of protein folding from the initial sequence to its three-dimensional structure, the cell needs protective molecules called ehaperones. Protein misfolding is due to the malfunctioning of chaperones in biological systems. 

---