Helical twists of collagen model peptides

Average helical twists were calculated by the method of Sugeta and Miyazawa (Biopolymers 1967, 5, 673-679) for all of the collagen model peptides analyzed to date. Calculation of the helical twists of all triplets in each peptide strand provided novel insights for several model peptides. In the (Pro-Pro-Gly)n (n = 9 and 10), the helical twists showed cyclic fluctuations between 40 and 65 degrees with a 20 A period, suggesting that their molecular conformations were close enough to the ideal 7/2-helix to show the helical repeat of 20 A. Rather small helical twists in the guest regions of IBP in complex and T3-785 were attributed to the interaction with Integrin I domain and a relaxed conformation caused by three consecutive triplets lacking imino acid residues, respectively. Although most of the triplets used in this study were imino acid-rich triplets, helical twists were scattered in a wide range from 30 to 70 degrees with an overall average of 52.6 degrees . This distribution of helical twists indicated a strong preference for the 7/2-helical conformation (51.4 degrees ) rather than the 10/3-helical model (36 degrees ).     

Conformational change of the triple-helical structure. I. Synthesis of model peptides of collagen by the solid-phase method

As model peptides of collagen, (Pro-Pro-Gly)_n (n = 10, 12, 14, and 15) and (Pro-Pro-Gly)_n(Ala-Pro-Gly)_m(Pro-Pro-Gly)_n (2n + m = 15; m = 1, 3, and 5) were synthesized by the solid-phase method. The final products were pure when checked by high-voltage paper electrophoresis and by amino acid analysis. Elemental composition was also examined.     

Activity of matrix metalloproteinase-9 against native collagen types I and III

Interstitial collagen types I, II and III are highly resistant to proteolytic attack, due to their triple helical structure, but can be cleaved by matrix metalloproteinase (MMP) collagenases at a specific site, approximately three-quarters of the length from the N-terminus of each chain. MMP-2 and -9 are closely related at the structural level, but MMP-2, and not MMP-9, has been previously described as a collagenase. This report investigates the ability of purified recombinant human MMP-9 produced in insect cells to degrade native collagen types I and III. Purified MMP-9 was able to cleave the soluble, monomeric forms of native collagen types I and III at 37 degrees C and 25 degrees C, respectively. Activity against collagens I and III was abolished by metalloproteinase inhibitors and was not present in the concentrated crude medium of mock-transfected cells, demonstrating that it was MMP-9-derived. Mutated, collagenase-resistant type I collagen was not digested by MMP-9, indicating that the three-quarters/one-quarter locus was the site of initial attack. Digestion of type III collagen generated a three-quarter fragment, as shown by comparison with MMP-1-mediated cleavage. These data demonstrate that MMP-9, like MMP-2, is able to cleave collagens I and III in their native form and in a manner that is characteristic of the unique collagenolytic activity of MMP collagenases.     

Cleavage of native type III collagen in the collagenase susceptible region by thermolysin.

Viscometric assays were used to demonstrate the activity of thermolysin (EC 3.4.24.4) on native type III collagen in solution. Analysis of the reaction products by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and electron microscopic visualisation of segment long spacing aggregates demonstrated localised cleavage of the collagen in the collagenase susceptible region.     

The chain register in heterotrimeric collagen peptides affects triple helix stability and folding kinetics

Collagen type IV is a highly specialized form of collagen found only in basement membranes, where it provides mechanical stability and structural integrity to tissues and organs, and binding sites for cell adhesion. In its ubiquitous form, collagen type IV consists of two alpha1 chains and one alpha2 chain, whose internal alignment within the triple helix seems to exert a strong influence on the binding affinity to alpha1beta1 integrin receptor. This has been assessed recently using two synthetic collagen peptides that contain the cell adhesion epitope of collagen type IV and are assembled into the most plausible alpha1alpha2alpha1' and alpha2alpha1alpha1' registers. In the present study, the effects of the chain register on the stability of the triple helix and the folding kinetics of these collagen peptides were investigated by CD spectroscopy and microcalorimetry. The results revealed a multi-domain structural organization for both trimers, with an unexpected strong effect of the chain alignment on the conformational stability. Molecular dynamics simulations served to rationalize more properly the experimental results.     

Sequence-specific liquid crystallinity of collagen model peptides. I. Transmission electron microscopy studies of interfacial collagen gels

The conformation, crystal structure and self-assembly behavior of three peptides with collagen-like repetitive sequences [(1) peptide GAPGPP: (Glu)(5)(Gly-Ala-Pro-Gly-Pro-Pro)(6)(Glu)(5); (2) peptide GVPGPP: (Glu)(5)(Gly-Val-Pro-Gly-Pro-Pro)(6)(Glu)(5); and (3) peptide GAPGPA: (Glu)(5)(Gly-Ala-Pro-Gly-Pro-Ala)(6)(Glu)(5)] were compared. The peptides were characterized using transmission electron microscopy, electron diffraction, environmental scanning electron microscopy, and Fourier transform ir spectroscopy in order to determine how the molecular geometry dictated by each sequence affects the spontaneous generation of long-range ordered structures. Samples of each peptide, at ambient temperature and at 5 degrees C, were examined as films dried from aqueous solution, air-water interfacial films, and chloroform-water interfacial films. Peptide GAPGPP prepared at 5 degrees C and dried from bulk solution was found to have a collagen-like triple-helical structure. A sinusoidally textured gel, suggestive of cholesteric behavior was observed for peptides GAPGPP and GVPGPP at the aqueous chloroform interface at 5 degrees C. Peptide GAPGPA also formed a gel, but less reproducibly and the sinusoidal texture was not as well defined. The periodicities of the sinusoidal textures were reproducibly 10 microm for peptide GAPGPP, 7 microm for peptide GVPGPP, and 6 microm for peptide GAPGPA. The differences in the periodicity of the banded structure and in the crystallization behavior of the three peptides is attributed to differences in the symmetry of the preferred packing arrangement for each peptide, as evidenced by electron diffraction from crystallites that coexist with the sinusoidal gel. These differences are believed to be a measure of the effective symmetry and shape of the molecular cross section.     

Identification of cyanogen bromide peptides involved in intermolecular cross-linking of bovine type III collagen.

Cyanogn bromide peptides derived from bovine type III collagen and containing reducible cross-links were isolated and identified. Two peptides, alpha 1 (III)CB7 and alpha 1 (III)CB9B, from within the helical portion of the molecule were shown to contain the 'amino donor' residues cross-linked to non-helical 'aldehyde donor' residues in the formation of cross-links. This information, in conjunction with previously published data for the order of the cyanogen bromide peptides [Fietzek, Allman, Rauterberg & Wachter (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 84-86], suggests that in type III collagen intermolecular cross-links are located in the end-overlap regions, so as to stabilize a quarter-stagger arrangement of molecules within the fibre in a similar manner to that proposed for type I and type II collagens.     

Synthesis of peptides by the solid-phase method. III. Bradykinin: fragments and analogs

The natural sequence of bradykinin (BK) and 55 fragments or analogs of this peptide were perpared via the solid-phase method. The peptides were purified using ion-exchange (O-carboxymethyl(CM) and partition (Sephadex G-25) chromatography. The purity of each peptide was established by paper and thin-layer chromatography, paper electrophoresis, amino acid analysis, and biological assays. The compounds were tested in anesthetized rats (tested in vivo) and in two smooth-muscle preparations (rabbit aorta strip, cat ileum strip) in which BK produces contraction by stimulating specific receptors of different types. Some of the new peptides are interesting in that they either resist pulmonary inactivation, or are more potent than BK itself, or antagonize the myotropic effect of BK in rabbit aorta strips.     

Purification and characterization of native type XIV collagen.

A new molecule, type XIV collagen, with domains homologous to type IX and XII collagens has been recently discovered in pepsin extracts of fetal bovine tissues (Dublet, B., and van der Rest, M. (1991) J. Biol. Chem. 266, 6853-6858). In the present study, we describe the purification and the characterization of the intact native form of this newly discovered collagen. By using only two chromatographic steps we were able to obtain pure type XIV collagen. Furthermore, minor modifications of the protocol allowed us to perform the simultaneous large scale purification of type XII and type XIV collagens from the same tissue. Intact type XIV collagen migrates on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) as two bands of 220 and 290 kDa (reducing conditions). After collagenase treatment, a single band of 190 kDa is observed, which represents the large non-collagenous domain of the molecule (NC3). Rotary shadowing electron micrographs of intact type XIV collagen show a cross-shaped structure formed by a thin tail attached through a central globule to three identical fingers. These properties are similar to those previously described for intact chicken type XII collagen (Dublet, B., Oh, S., Sugrue, S. P., Gordon, M. K., Gerecke, D. R., Olsen, B. R., and van der Rest, M. (1989) J. Biol. Chem. 264, 13150-13156), but the two molecules are different gene products and have charge and glycosylation differences. Finally, we show that the three chains of purified type XIV collagen have an apparent molecular mass of approximately 220 kDa and are not cross-linked to each other by bonds other than disulfide bridges. The same observation was made for type XII collagen. In both cases, the 290-kDa migrating band in SDS-PAGE is due to incomplete denaturation in electrophoresis sample buffer in the absence of urea.     

Molecular basis of co-operativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates.

The hierarchical partition function formalism for protein folding developed earlier has been extended through the use of three-dimensional polar and apolar contact plots. For each amino acid residue in the protein, these plots indicate the apolar and polar surfaces that are buried from the solvent, the identity of all amino acid residues that contribute to this shielding, and the magnitude of their contributions. These contact plots are then used to examine the distribution of the free energy of stabilization throughout the protein molecule. Analysis of these data allows identification of co-operative folding units and their hierarchical levels, and the identification of partially folded intermediates with a significant probability of being populated. The overall folding/unfolding thermodynamics of 12 globular proteins, for which crystallographic and experimental thermodynamics are available, is predicted within error. An energetic classification of partially folded intermediates is presented and the results compared to those cases for which structural and thermodynamic experimental information is available. Four different types of partially folded states and their structural energies are considered. (1) Local intermediates, in which only a local region of the protein loses secondary and tertiary interactions, while the rest of the protein remains intact. (2) Global intermediates, corresponding to the standard molten globule definition, in which significant secondary structure is maintained but native-like tertiary structure contacts are disrupted. (3) Extended intermediates characterized by the existence of secondary structure elements (e.g. alpha-helices) exposed to solvent. (4) Folding intermediates in proteins with two structural domains. The structure and energetics of folding intermediates of apo-myoglobin, alpha-lactalbumin, phosphoglycerate kinase and arabinose-binding protein are considered in detail.     

Lysine proximity significantly affects glycation of lysine-containing collagen model peptides

Advanced glycation end products (AGE) are known to cause diabetes complications in hyperglycemia patients. In this study we prepared hetero-trimers of collagen model peptides comprising Ac-(Pro-Hyp-Gly)(5)-Pro-Lys-Gly-(Pro-Hyp-Gly)(5)-Ala-NH(2) (4) and Ac-(Pro-Hyp-Gly)(11)-Ala-NH(2) (5) to investigate the clustering effect of lysine on AGE formation. The formation rate of carboxymethyllysine over several months was determined for the mixtures of peptides 4 and 5 at (3:0), (2:1) and (1:2) in the presence of glucose. The contents of carboxymethyllysine were significantly enhanced for (3:0) and (2:1) as compared with (1:2), suggesting that the proximity of lysine residues in the trimers accelerated formation of the AGE. Furthermore, a lysine dimerization moiety (GOLD) was identified for the first time from AGEs of glucose origin, which implied the significance of GOLD in oligomerization of collagens and other long-life proteins.     

Synthesis and characterization of a collagen model delta-O-phosphohydroxylysine-containing peptide

The existence of delta-O-phosphohydroxylysine (HylP) residues in collagen has been reported. However, such phosphorylated residues have not been isolated nor has their location within the protein sequence been identified. To develop the analytical chemistry necessary for the identification of HylP in proteins, a model HylP-containing peptide, Phe-dl-HylP-Gly-Gln-Pro-Ala-Ile-Gly-Phe (I), was synthesized. The peptide was assembled using 9-fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase synthesis; N(alpha)-Fmoc-dl-hydroxy-dl-Lys(N(epsilon)-tert-butyloxycarbonyl)-OH was used to incorporate Hyl, and global phosphitylation/oxidation was used to introduce the phosphate group. The pK(a2) of the phosphate group, as determined using 31P NMR, was 5.6. Phosphoamino acid analysis of I was performed using either dabsyl chloride or phenylisothiocyanate derivatization followed by microbore reversed-phase HPLC separation of N(alpha, epsilon)-didabsyl-HylP or N(alpha, epsilon)-diphenylthiocarbamyl-HylP. HylP was found to be relatively resistant to acid hydrolysis, allowing for its quantitation. Solid-phase Edman degradation of I was used for positive identification of N(alpha)-phenylthiohydantoin-N(epsilon)-phenylthiocarbamyl-HylP. The masses of the phenylthiohydantoin and dabsyl derivatives of HylP were confirmed by electrospray ionization triple-quadrupole (ESI-MS). Peptide I was positively identified as a phosphopeptide by ESI-MS/precursor-ion scanning. Low-energy ESI-MS/MS confirmed the position of HylP within the sequence of I. Phosphorylation of Hyl led to complete resistance of I to lysine-specific endopeptidases.     

The influence of peptidyl-prolyl cis-trans isomerase on the in vitro folding of type III collagen

Peptidyl-prolyl cis-trans isomerase was extracted from pig kidney cortex and partially purified. Enzyme activity was monitored against the cis-trans isomerization of succinyl-Ala-Ala-Pro-Phe-methylcoumaryl amide by means of a two-step process using chymotrypsin as the trans cleaving activity. The in vitro refolding of denatured type III collagen, which is rate-limited by the cis-trans isomerization of peptide bonds, was studied in the presence of peptidyl-prolyl cis-trans isomerase by optical rotatory dispersion and by resistance to tryptic digestion. A 3-fold increase in the initial rate of folding was observed compared to the uncatalyzed refolding. This rate increase is comparable to the rate increase found for the CT-phase in the refolding of urea-denatured ribonuclease A, but it is smaller than the increase in the rate of isomerization of succinyl-Ala-Ala-Pro-Phe-methylcoumarylamide.     

Digestion of native collagen, denatured collagen, and collagen fragments by extracts of rat liver lysosomes.

Extracts of highly purified lysosomes from rat liver were examined for their ability to degrade native collagen and thermally denatured collagen at pH values between 3.5 and 7.0. After a 24-h digestion at 36 degrees with the lysosomal extract at a pH of 5.5 or lower (collagen/lysosomal protein; 2/1 or 8/1), both native and denatured collagen were degraded to an extent equivalent to 60 to 70% of that observed upon total acid hydrolysis in 6 N HCl as measured by the ninhydrin reaction (570 nm). At a pH of 6.0, native collagen and denatured collagen were degraded by the mixture of lysosomal proteinases to 11% and 40% of total acid hydrolysis, respectively. At pH 6.5 AND 7.0, the corresponding values were 3% versus 33% and 0.3% versus 11%, respectively. Fragments of collagen (TCA and TCB) are produced when mammalian collagenase degrades native collagen at 25 degrees. These fragments were degraded by the lysosomal extract at 36 degrees to an extent equivalent to 28% and 8% of total acid hydrolysis at pH 6.5 and 7.0, respectively. The experiments at pH 6.5 and 7.0 were done using a collagen/lysosomal protein ratio of 2/1. At pH 5.0 (a pH which is found within secondary lysosomes), the lysosomal extracts degraded collagen to a mixture of free amino acids and small peptides. Amino acid analysis established that approximately 30% of the amino acid residues of the collagen appeared in the lysosomal hydrolysate as free amino acids. Hydroxyproline and perhaps hydroxylysine were the only amino acids found in collagen which did not appear at least to some extent as the free amino acid in this hydrolysate.     

The building block folding model and the kinetics of protein folding.

Here we show that qualitatively, the building blocks folding model accounts for three-state versus the two-state protein folding. Additionally, it is consistent with the faster versus slower folding rates of the two-state proteins. Specifically, we illustrate that the building blocks size, their mode of associations in the native structure, the number of ways they can combinatorially assemble, their population times and the way they are split in the iterative, step-by-step structural dissection which yields the anatomy trees, explain a broad range of folding rates. We further show that proteins with similar general topologies may have different folding pathways, and hence different folding rates. On the other hand, the effect of mutations resembles that of changes in conditions, shifting the population times and hence the energy landscapes. Hence, together with the secondary structure type and the extent of local versus non-local interactions, a coherent, consistent rationale for folding kinetics can be outlined, in agreement with experimental results. Given the native structure of a protein, these guidelines enable a qualitative prediction of the folding kinetics. We further describe these in the context of the protein folding energy landscape. Quantitatively, in principle, the diffusion-collision model for the building block association can be used. However, the folding rates of the building blocks and traps in their formation and association, need to be considered.     

Evolutionary Pareto-optimization of stably folding peptides

Background  

As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the question whether there may be more such peptides that are unknown as yet. These molecules could be helpful in basic research and medicine.     

Serum antibodies to native and denatured type I and III collagen in patients with periodontal disease

Serum IgG antibodies to collagen were investigated by using enzyme linked immunosorbent assay (ELISA) in patients with chronic periodontal disease. Patients with varying forms of periodontal disease including gingivitis, juvenile periodontitis, and adult periodontitis were compared with the normal subjects. The mean serum IgG levels of ELISA antibodies to native type I or III collagen in patients with juvenile periodontitis were significantly higher than those of the normal subjects, but no difference was found between the patients with either gingivitis or adult periodontitis and the normal subjects. In addition, the mean serum IgG levels of ELISA antibodies to denatured type I or III collagen in patients with juvenile or adult periodontitis were significantly higher than those of the normal subjects. These findings suggest that antibodies to native and denatured type I or III collagen may be associated with different forms or severities of periodontal disease, especially advanced periodontal destruction.     

Optimizing protein folding to the native state in bacteria.

A correctly folded protein is usually both active and soluble. This review focuses on novel ways to improve the folding of recombinant proteins during production in bacteria and includes a few tips for refolding proteins. Major results in correlating protein primary structure with proper folding and stability, and the production of viral antigens and antibodies in bacteria are also discussed.