Analysis of the code relating sequence to conformation in globular proteins. An informational analysis of the role of the residue in determining the conformation of its neighbours in the primary sequence

Intrinsically disordered proteins: Chronology of a discovery

Intrinsic disorder is a new reality that appears to penetrate every corner of modern protein science. It is difficult to imagine that only 20 years ago the situation was completely different, and almost nobody had heard about 'structure-less' but functional proteins. As a matter of fact, for many at that time, this idea was completely heretical when viewed in light of the then dominating lock-and-key model describing the protein structure-function relationship, where a unique amino acid sequence defines a unique crystal-like 3D structure that serves as a prerequisite for a unique function of a protein. It seems like the entire field of protein intrinsic disorder has magically emerged at the turn of the century due to a revelation to a small group of researchers. Although this may very well be true, literature shows that the first observations contradicting the lock-and-key view of protein functionality started to appear almost immediately after this model was proposed. The goal of this article is to provide a brief chronology (though admittedly a subjective one) of the events in the field of protein science that eventually culminated in the discovery of the protein intrinsic disorder phenomenon. The entire process represents a good example of the "dwarf standing on the shoulders of giants" (Latin: nanos gigantum humeris insidentes) metaphor, where the truth is discovered by building on previous discoveries.

Chromodomain helicase binding protein 8 (Chd8) is a novel A-kinase anchoring protein expressed during rat cardiac development

A-kinase anchoring proteins (AKAPs) bind the regulatory subunits of protein kinase A (PKA) and localize the holoenzyme to discrete signaling microdomains in multiple subcellular compartments. Despite emerging evidence for a nuclear pool of PKA that rapidly responds to activation of the PKA signaling cascade, only a few AKAPs have been identified that localize to the nucleus. Here we show a PKA-binding domain in the amino terminus of Chd8, and demonstrate subcellular colocalization of Chd8 with RII. RII overlay and immunoprecipitation assays demonstrate binding between Chd8-S and RIIα. Binding is abrogated upon dephosphorylation of RIIα. By immunofluorescence, we identified nuclear and perinuclear pools of Chd8 in HeLa cells and rat neonatal cardiomyocytes. We also show high levels of Chd8 mRNA in RNA extracted from post-natal rat hearts. These data add Chd8 to the short list of known nuclear AKAPs, and implicate a function for Chd8 in post-natal rat cardiac development.

Redefining the goals of protein secondary structure prediction

Secondary structure prediction recently has surpassed the 70% level of average accuracy, evaluated on the single residue states helix, strand and loop (Q3). But the ultimate goal is reliable prediction of tertiary (three-dimensional, 3D) structure, not 100% single residue accuracy for secondary structure. A comparison of pairs of structurally homologous proteins with divergent sequences reveals that considerable variation in the position and length of secondary structure segments can be accommodated within the same 3D fold. It is therefore sufficient to predict the approximate location of helix, strand, turn and loop segments, provided they are compatible with the formation of 3D structure. Accordingly, we define here a measure of segment overlap (Sov) that is somewhat insensitive to small variations in secondary structure assignments. The new segment overlap measure ranges from an ignorance level of 37% (random protein pairs) via a current level of 72% for a prediction method based on sequence profile input to neural networks (PHD) to an average 90% level for homologous protein pairs. We conclude that the highest scores one can reasonably expect for secondary structure prediction are a single residue accuracy of Q3 > 85% and a fractional segment overlap of Sov > 90%.

Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin

Neural networks provide a basis for semiempirical studies of pattern matching between the primary and secondary structures of proteins. Networks of the perceptron class have been trained to classify the amino-acid residues into two categories for each of three types of secondary feature: alpha-helix or not, beta-sheet or not, and random coil or not. The explicit prediction for the helices in rhodopsin is compared with both electron microscopy results and those of the Chou-Fasman method. A new measure of homology between proteins is provided by the network approach, which thereby leads to quantification of the differences between the primary structures of proteins.

Physical and immunological analysis of the two domains isolated from a variant surface glycoprotein of Trypanosoma brucei

A specific surface glycoprotein of a variant of Trypanosoma brucei was cleaved with trypsin and the two major domains of the molecule have been purified. We have studied the chemical composition of each domain and compared the data to published results of the specific cDNA sequence. Circular dichroism measurements show that the amino-terminal domain includes preferentially alpha-helical or beta-sheet structure. The physicochemical analyses are supplemented by a prediction of secondary structure and a statistical pattern of hydrophilicity-hydrophobicity. The results are discussed in light of the internal limits that were described in the process of partial gene conversion occurring between the variant gene sequence and related members of the same gene family. Immunoblots with homologous antiserum indicate that the amino-terminal domain is implicated in antigenicity. In addition, immunoblotting with heterologous antiserum on native antigen, tryptic hydrolysates, or purified domains suggests a site of interaction supported by the two domains.

Trypanosome variant-specific glycoproteins: a polygene protein family with multiple folding patterns?

Infection with the African trypanosomes gives rise to relapsing waves of parasitemia in the host. A predominant population of trypanosomes is present in each wave, and such predominant populations are usually serologically distinct from each other. Trypanosomes are covered by an extramembranous, highly antigenic, variant-specific glycoprotein coat that is 15 nm thick. The primary structure of a large portion of the glycoprotein molecule is different in the predominant trypanosome populations of each parasitemic wave. Analysis of the secondary structure potential of five full-length and five partial amino acid sequences of variant-specific glycoproteins from members of the Trypanosoma brucei complex has been carried out. The potentials for alpha-helix, beta-turns, and beta-strand structure have been calculated. A high degree of alpha-helical structure potential is present in all the full-length or partial sequences examined. There is conservation of secondary structure potential in the COOH-terminal 100 amino acids, where both partial and complete conservation of primary amino acid sequence exists. The NH2-terminal regions are rich in alpha-helix potential. However, over large stretches of the middle of the VSG molecules there is wide diversity of secondary structure potential. This suggests that tertiary folding structures may also be different in this region. If these predictions are true, different regions of the variant-specific glycoprotein could be exposed to the solvent in different variant-specific trypanosome serotypes. The implication is that antigenic variation is mediated by a polygene family of glycoproteins containing highly polymorphic regions. These could fold differently and expose different surface regions of the protein to the solvent. This device might reduce immune crossreactivity among members of the variant-specific glycoprotein family.

Information contained in protein shapes

The sequence of local conformations at C alpha atoms of a protein has been considered as an informational message string. The total self information contents and self information per letter have been evaluated for 83 globular proteins whose structures are known from X-ray crystallography. The derived information contents provide a method of quantitating structural specificity of proteins. This method of analysis enables repeating, intricate structural features to be recognized. Among the globular proteins whose structures have been solved, high potential iron protein stands out with the largest three-letter dependence.

Protein folding

This review describes recent advances in studies on the stabilities of the three-dimensional structures of proteins and on the processes leading to the formation of these structures. The term ‘protein folding’ will be used here to denote the process of the conversion of an open polypeptide chain into the unique three-dimensional conformation of the native protein. Experimental and theoretical aspects of protein folding have been reviewed by anfinsen & Scheraga (1975). In the present article, we emphasize advances made since the writing of that review, together with a brief summary of the background of recent studies.

The mechanism of folding of globular proteins. Suitability of a penicillinase from Staphylococcus Aureus as a model for refolding studies

1. A homogeneous preparation of penicillinase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6) was isolated and purified from cultures of Staphylococcus aureus by a simple two-stage procedure. 2. The native protein contains 20-30% helix as determined by optical-rotatory-dispersion and circular-dichroism measurements. Some 54(+/-5)% of the 13 tyrosine residues are exposed to solvent molecules of diameter 0.44 and 0.94 nm. 3. Conditions that allow full recovery of enzymic activity and native conformation from the fully unfolded state in 4M-guanidinium chloride were defined. 4. Refolding of the protein was shown to be inhibited by intermolecular interaction, by small changes in ionization and by low concentrations (0.025 M) of phenol.

Analysis of the code relating sequence to conformation in globular proteins. Development of a stereochemical alphabet on the basis of intra-residue information

1. The relation of primary sequence to all residue backbone conformations was explored to test out starting conformations for protein folding. 2. Information theory was used to obtain measures of information which quantitate the role of each residue in determining its own conformation; i.e. intra-residue information. 3. The information measures are plotted as a function of varphi, psi peptide-backbone angles and varphi, psi contour maps obtained for each of the 20 amino acids. These show characteristic differences between residues. 4. To find practical ways of relating sequence to varphi, psi angles, several types of stereochemical alphabet were investigated. The value of these was tested by using them to predict the varphi, psi angles of nine different proteins. 5. A difference plot was constructed to show regions of the sequence that require little or no information extra to the intra-residue information in order to predict a correct conformation. These regions are suggested to be candidates for nucleating sites in the protein.