The insulin A and B chains contain structural information for the formation of the native molecule. Studies with protein disulphide-isomerase.

It has been shown previously [Tang, Wang & Tsou (1988) Biochem. J. 255, 451-455] that, under appropriate conditions, native insulin can be obtained from scrambled insulin or the S-sulphonates of the chains with a yield of 25-30%, together with reaction products containing the separated A and B chains. The native hormone is by far the predominant product among the isomers containing both chains. It is now shown that the presence of added C peptide has no appreciable effect on the yield of native insulin. At higher temperatures the content of the native hormone decreases whereas those of the separated chains increase, and in no case was scrambled insulin containing both chains the predominant product in the absence of denaturants. Both the scrambling and the unscrambling reactions give similar h.p.l.c. profiles for the products. Under similar conditions cross-linked insulin with native disulphide linkages can be obtained from the scrambled molecule or from the S-sulphonate derivative with yields of 50% and 75% respectively at 4 degrees C, and with a dilute solution of the hexa-S-sulphonate yields better than 90% can be obtained. The regenerated product is shown to have the native disulphide bridges by treatment with CNBr to give insulin and by the identity of the h.p.l.c. profile of its peptic hydrolysate with that for cross-linked insulin. It appears that the insulin A and B chains contain sufficient information for the formation of the native molecule and that the role of the connecting C peptide is to bring and to keep the two chains together.     

Fibrillation of human insulin A and B chains

Human insulin, which consists of disulfide cross-linked A and B polypeptide chains, readily forms amyloid fibrils under slightly destabilizing conditions. We examined whether the isolated A and B chain peptides of human insulin would form fibrils at neutral and acidic pH. Although insulin exhibits a pH-dependent lag phase in fibrillation, the A chain formed fibrils without a lag at both pHs. In contrast, the B chain exhibited complex concentration-dependent fibrillation behavior at acidic pH. At higher concentrations, e.g., >0.2 mg/mL, the B chains preferentially and rapidly formed stable protofilaments rather than mature fibrils upon incubation at 37 degrees C. Surprisingly, these protofilaments did not convert into mature fibrils. At lower B chain concentrations, however, mature fibrils were formed. The explanation for the concentration dependence of B chain fibrillation is as follows. The B chains exist as soluble oligomers at acidic pH, have a beta-sheet rich conformation as determined by CD, and bind ANS strongly, and these oligomers rapidly form dead-end protofilaments. However, under conditions in which the B chain monomer is present, such as low B chain concentration (<0.2 mg/mL) or in the presence of low concentrations of GuHCl, which dissociates the soluble oligomers, mature fibrils were formed. Thus, both A and B chain peptides can form amyloid fibrils, and both are likely to be involved in the interactions leading to the fibrillation of intact insulin.     

Synergy between immunotoxins prepared with native ricin A chains and chemically-modified ricin B chains

Ricin B chains treated with chloramine-T in the presence or absence of NaI show a 100-fold to 200-fold reduction in their ability to bind to the galactose-containing protein asialofetuin. Such treated B chains do not form covalently associated homodimers with treated B chains or heterodimers with native ricin A chains. Furthermore, they cannot enhance the toxicity of a ricin A chain-containing rabbit anti-human immunoglobulin (RAHIg-A) for Daudi cells. However, when such B chains are coupled to goat anti-rabbit Ig (GARIg), they potentiate the killing of RAHIg-A-treated Daudi cells only slightly less effectively than GARIg coupled to native B chains. Furthermore, if GARIg-B chain conjugates are treated with chloramine-T after coupling, they fail to bind to asialofetuin but enhance the killing of Daudi cells treated with RAHIg-A. These results demonstrate that the ability of ricin B chains to bind to galactose and to enhance the toxicity of ricin A chains (in the form of an antibody-A chain) can be operationally separated. Thus, the two functions of the B chain may reside on separate domains of the molecule.     

Formation of native insulin from the scrambled molecule by protein disulphide-isomerase.

The formation of native insulin either from scrambled insulin or from the separated A chain and B chain S-sulphonates by protein disulphide-isomerase was demonstrated with yields of 20-30% as measured by h.p.l.c. analysis, receptor binding and stimulation of lipogenesis. The h.p.l.c. profile of the reaction products shows that, among all the possible isomers containing both chains, the native hormone is by far the predominating product and consequently the most stable under certain conditions.     

Interaction and reconstitution of carboxyl-terminal-shortened B chains with the intact A chain of insulin

With the S-(thiomethyl)-A chain and despentapeptide (26-30) and desoctapeptide (23-30) S-(thiomethyl)-B chains of insulin at pH 10.8 and a molar ratio of A/B = 1.5, difference spectra of the mixed against the separated chains with negative peaks at 245 and 295 nm and a weak positive peak at 278 nm indicate interaction of the chains leading to Tyr environmental changes as in the case for the intact chains. With the shortened B chains, freshly dissolved from lyophilized powders, it takes some 2 h for the difference spectra to approach completion whereas with the solutions of the shortened B chains left standing overnight at pH 10.8 and 4 degrees C the difference spectra, similar in shape to that described above, appear almost immediately after mixing. Solvent perturbation with 20% ethylene glycol suggests some ordered structure for the despentapeptide but not for the desoctapeptide B chain. The interactions of the A chain with the shortened B chains appear to be weaker as compared to that with the intact B chain as shown by decreasing reconstitution yields for the intact, despentapeptide, and desoctapeptide B chains respectively with the A chain. The above results indicate that the C-terminal portion of the B chain is important not only for the activity of insulin but also for the correct pairing of the chains.     

Resynthesis of insulin from its A and B chains in the presence of denaturants

Reoxidation of the reduced insulin A and B chains in 8 M urea leads to a recovery of native insulin of 2-7% whereas in 6 M guanidine or 0.5 mM dodecylsulfate very little, if any, resynthesis of insulin could be detected. Considering all the possibilities of different oligomeric forms containing one or both of the chains, the yield in 8 M urea is well over the yield as calculated from random joining of the chains and the yield in guanidine or dodecylsulfate is to be expected. It is concluded that some interaction and pairing of the chains occur even in the presence of 8 M urea.     

The pairing of the separated A and B chains of insulin and its derivatives, FTIR studies.

From the amide I bands of their deconvolved FTIR spectra, the S-thiomethyl derivatives of the insulin A, B, despentapeptide(26-30) B and desoctapeptide(23-30) B chains all contain significant amounts of ordered secondary structure. The intact B chain is considerably more ordered than either the A or the truncated B chains. Comparison of the spectra of the separated and mixed intact chains of insulin suggests further folding upon mixing of the chains leading to significant increases in ordered secondary structures, presumably because of stabilization by interaction of the chains. The interactions of the A chain with the DPI B chain appear to be weaker as compared to that with the intact B chain. The above results suggest that only the intact A and B chains contain sufficient structural information to recognize each other and interact to form a native-like structure which make the correct formation of the disulfide linkages possible.     

The N terminus of laminin A chain is homologous to the B chains

A major proteolytic fragment (E1/E1-4) of the basement membrane protein laminin, comprising the three short arms with some terminal globules missing, was isolated by elastase digestion, and partial protein sequence data were determined for several tryptic peptides. Sequences which corresponded to A-chain structures were used to synthesize oligonucleotides for the construction and screening of a primer-extended cDNA library from mouse PYS-2 cells. A clone of 1.1 kb was obtained and shown by sequencing to correspond to the 5' end of the 10-kb mRNA of the A chain of laminin. The clone contains 77 nucleotides of 5' untranslated sequence and a region coding for 334 amino acids, including a presumptive signal peptide of 24 amino acids. The sequence is 30% homologous to the corresponding N-terminal part of the B1 chain of laminin, suggesting the same structure for both domains. The data present further evidence for a recent structural model which postulates that each of the three laminin polypeptide chains forms a distinct short arm.     

A novel approach to structural alignment using realistic structural and environmental information

In the era of structural genomics, it is necessary to generate accurate structural alignments in order to build good templates for homology modeling. Although a great number of structural alignment algorithms have been developed, most of them ignore intermolecular interactions during the alignment procedure. Therefore, structures in different oligomeric states are barely distinguishable, and it is very challenging to find correct alignment in coil regions. Here we present a novel approach to structural alignment using a clique finding algorithm and environmental information (SAUCE). In this approach, we build the alignment based on not only structural coordinate information but also realistic environmental information extracted from biological unit files provided by the Protein Data Bank (PDB). At first, we eliminate all environmentally unfavorable pairings of residues. Then we identify alignments in core regions via a maximal clique finding algorithm. Two extreme value distribution (EVD) form statistics have been developed to evaluate core region alignments. With an optional extension step, global alignment can be derived based on environment-based dynamic programming linking. We show that our method is able to differentiate three-dimensional structures in different oligomeric states, and is able to find flexible alignments between multidomain structures without predetermined hinge regions. The overall performance is also evaluated on a large scale by comparisons to current structural classification databases as well as to other alignment methods.     

A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information

The insulin receptor (IR), the insulin-like growth factor 1 receptor (IGF1R) and the insulin receptor-related receptor (IRR) are covalently-linked homodimers made up of several structural domains. The molecular mechanism of ligand binding to the ectodomain of these receptors and the resulting activation of their tyrosine kinase domain is still not well understood. We have carried out an amino acid residue conservation analysis in order to reconstruct the phylogeny of the IR Family. We have confirmed the location of ligand binding site 1 of the IGF1R and IR. Importantly, we have also predicted the likely location of the insulin binding site 2 on the surface of the fibronectin type III domains of the IR. An evolutionary conserved surface on the second leucine-rich domain that may interact with the ligand could not be detected. We suggest a possible mechanical trigger of the activation of the IR that involves a slight 'twist' rotation of the last two fibronectin type III domains in order to face the likely location of insulin. Finally, a strong selective pressure was found amongst the IRR orthologous sequences, suggesting that this orphan receptor has a yet unknown physiological role which may be conserved from amphibians to mammals.     

Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins

We investigate the possibility that atomic burials, as measured by their distances from the structural geometrical center, contain sufficient information to determine the tertiary structure of globular proteins. We report Monte Carlo simulated annealing results of all-atom hard-sphere models in continuous space for four small proteins: the all-beta WW-domain 1E0L, the alpha/beta protein-G 1IGD, the all-alpha engrailed homeo-domain 1ENH, and the alpha + beta engineered monomeric form of the Cro protein 1ORC. We used as energy function the sum over all atoms, labeled by i, of |R(i) - R(i) (*)|, where R(i) is the atomic distance from the center of coordinates, or central distance, and R(i) (*) is the "ideal" central distance obtained from the native structure. Hydrogen bonds were taken into consideration by the assignment of two ideal distances for backbone atoms forming hydrogen bonds in the native structure depending on the formation of a geometrically defined bond, independently of bond partner. Lowest energy final conformations turned out to be very similar to the native structure for the four proteins under investigation and a strong correlation was observed between energy and distance root mean square deviation (DRMS) from the native in the case of all-beta 1E0L and alpha/beta 1IGD. For all alpha 1ENH and alpha + beta 1ORC the overall correlation between energy and DRMS among final conformations was not as high because some trajectories resulted in high DRMS but low energy final conformations in which alpha-helices adopted a non-native mutual orientation. Comparison between central distances and actual accessible surface areas corroborated the implicit assumption of correlation between these two quantities. The Z-score obtained with this native-centric potential in the discrimination of native 1ORC from a set of random compact structures confirmed that it contains a much smaller amount of native information when compared to a traditional contact Go potential but indicated that simple sequence-dependent burial potentials still need some improvement in order to attain a similar discriminability. Taken together, our results suggest that central distances, in conjunction to physically motivated hydrogen bond constraints, contain sufficient information to determine the native conformation of these small proteins and that a solution to the folding problem for globular proteins could arise from sufficiently accurate burial predictions from sequence followed by minimization of a burial-dependent energy function.     

Influence of imprinting with A and B chains of insulin on binding and functional changes in tetrahymena

Insulin and its A and B chain increased the quantity of intracellular PAS-positive material (glycogen) in tetrahymena, whereas the combined A+B chains decreased it. Imprinting—previous interaction—with insulin, its A and B chains in themselves and with the A+B chain increased the hormone binding capacity of tetrahymena, but the functional effect of imprinting (storage or breakdown of glycogen) showed a different tendency with insulin and A+B chain on the one hand, and A chain and B chain on the other. Since the imprinting potential of a molecule promotes the induction of receptor formation, the fact remains that both component chains of insulin were able to act as potential imprinters, although the A chain was superior to the B chain in this respect throughout, and combined treatment with the A+B chain ultimately induced the formation of a similar binding site as insulin itself.     

Interaction and combination of separate A and B chains of insulin effects of D-and L-tryptophan in position A1

The S-thiomethyl derivatives of insulin A chain with A1-Gly replaced by D- or L-Trp have been prepared and their respective interaction and combination with the S-thiomethyl B chain studied. The UV difference spectra of the mixed against the separated [Trp1]A chains with the B chain at pH 10.8 are similar to those obtained for the unmodified chains except that the 295-nm-negative peak for ionized Tyr residue appears to be less marked. Fluorescence studies show very little environmental changes at the A1-Trp residues when mixed with the B chain. The intact hormone with A1-Gly replaced by D-Trp is known to be considerably more active than the analog with L-Trp replacement. However, for both derivatives the resynthesis of the whole molecules correctly joined by disulfide bridges starting from the separated reduced chains, gives similar low yields as shown by HPLC analysis and by receptor-binding assay. The replacement of A1-Gly by D-Trp appears to affect the separated A chain more than the intact hormone and replacements at A1 by both D- and L-Trp probably lead to significant conformational changes of the A chain so as to prevent its correct pairing with the B chain.