Conversion of the amino acid sequence Gly-Pro-Pro in protein to Gly-Pro-Hyp by collagen proline hydroxylase

The amino acid sequence Gly-Pro-Hyp is unique to and recurs in collagen. In contrast, the sequence Gly-Pro-Pro recurs in the experimentally produced collagenase degradable protein which serves as substrate for the enzyme, collagen proline hydroxylase. The primary structure of substrate reappears to be identical with the primary structure of collagen except for the replacement of hydroxyprolyl by prolyl residues. The quantity of the two tripeptides has been determined in collagenase digests of hydroxylase substrate before and after incubation in an enzyme-dependent, proline hydroxylating system. During incubation, Gly-Pro-Pro sequences of substrate are stoichiometrically converted to the Gly-Pro-Hyp sequences characteristic of natural collagen. Approximately 37% of the total hydroxyproline synthesized in vitro is located in Gly-Pro-Hyp sequences. The hydroxyproline formed is 4-hydroxyproline.     

Conformational analysis of polytripeptides (Gly-Pro-Ala)n, (Gly-Ala-Hyp)n,and (Gly-Ala-Ala)n in connection with the problem of collagen structure

Conformational analysis of triple helics of a type of collagen was performed with typical collagen tripeptide sequences based on Gly-Pro-Ala, Gly-Ala-Hyp, and Gly-Ala-Ala. During energy minimization, the possibility of continual deformation of the pyrrolidine cycle was taken into account in order to achieve better accuracy in the resulting structure. The (Gly-Pro-Ala)_n structure is almost isomorphic to the (Gly-Pro-Hyp)_n structure obtained in the previous work [Tumanyan, V. G. & Esipova, N.G. (1982) Biopolymers 21 , 475–497]. For a collagen-type structure, the optimal conformation of (Gly-Ala-Hyp)_n tends to have a decreased unit twist (t = 15°), although the energy advantage with respect to the conformation with t = 45° is not so significant. A similar situation is observed for (Gly-Ala-Ala)_n. In this case, the energy decrease during unwinding to t = 15° from t = 45° is quite small. The conformations of (Gly-Ala-Hyp)_n and (Gly-Ala-Ala)_n with t = 15° exhibit a similarity with a triple complex of polyproline II helices—a noncoiled coil such as (Gly-Pro-Hyp)_n and (Gly-Pro-Ala)_n. A similar structure may be postulated for subcomponent cq1 of the first component of a human complement containing substantial Gly-X-Pro and Gly-X-Y tripeptide derivatives in the primary structure (X, Y = any amino acid). The results suggest that the observed helical symmetry of collagen (t = 36°) is a consequence of superposition of diffraction patterns (for sufficiently long segments) from various helices (t varies from ～15° for Gly-X-Hyp and Gly-X-Y to ～56° for Gly-Pro-Ala). For short alternating segments, some unification of different helical structures is possible.     

Interactions between poly(Gly-Pro-Pro) triple helices: a model for molecular packing in collagen

Potential-energy calculations are reported on the interaction between two collagenlike triple-stranded poly(Gly-L-Pro-L-Pro) helices. Short helices can pack in a variety of orientations, but there is a unique parallel packing arrangement of the two helices for longer polypeptide chains.     

The association reaction of collagen model polypeptides (Pro-Pro-Gly)n

The characterization of recently synthesized (Pro-Pro-Gly)_n, n = 7, 8 is described, along with melting profile studies of its association equilibrium, and thermal quenching studies of the kinetics of its association reaction. The order of the kinetic reaction is about 3, implying that three peptide chains are involved in the activated state of the rate-limiting step. The reaction rate was found to exhibit a negative temperature coefficient. With the (Pro-Pro-Gly)₇ peptide, the concentration dependence of the (Pro-Pro-Gly)_n association equilibrium was observed for the first time. Detailed thermodynamic analysis for these n = 7, 8 data, together with literature data for n = 10, 15, 20 were carried out for both the simple “all-or-none” binding model and for a series of complex equilibrium models. For the latter, all of the (Pro-Pro-Gly)_n data (in 10% acetic acid) are fit best with a maximally cooperative near-neighbor model with a standard enthalpy change ΔH = ?650 cal/mole of residues, and a standard entropy change ΔS = ?14.63 ?10/n cal/deg-mole of residues, wherein the ?10 eu represents an end-effect contribution to the binding free energy. With regard to optical rotatory properties and thermodynamic parameters, the data for the new n = 7, 8 peptides match rather well with the literature data for the n = 10, 15, and 20 peptides. The enthalpic stabilization per residue of the triple-helical form of (Pro-Pro-Gly)_n was nearly an order of magnitude smaller than the enthalpic stabilization per additional proline obtained from direct calorimetric measurements on native collagens of different (and much lower) proline contents by Privalov and Tiktopulo. [Biopolymers (1970) 9 , 127–139.] Possible explanations for this phenomenon are discussed.     

Polypeptide models of collagen: Properties of (Pro-Pro-betaAla)n.

We have synthesized (Pro-Pro-βAla)_n as a model for collagen. The synthetic polytripeptide, mol wt 6500, exhibits a large negative optical rotation with a very strong negative Cotton effect centered at 216 nm. The optical rotatory dispersion of (Pro-Pro-βAla)_n followed a single-term Drude equation and the λ_c was 195 nm. The rotation decreased markedly on heating with the midpoint of the broad transition at 55°C. Preliminary studies also showed loss of structure in guadinine HCl. The circular dichroism spectrum of the polymer exhibited a deep trough at 190 nm. The marked similarities of solution properties of (Pro-Pro-βAla)_n to (Pro-Pro-Gly)_n suggest that β-alanine can replace glycine in generating collagen-like helix in solution.     

Two types of tripeptide conformation in collagen. Calculation of the structure of (Gly-Pro-Ser)n and (Gly-Val-Hyp)n polytripeptides

Conformational analysis of polypeptides (Gly-Pro-Ser)n and (Gly-Val-Hyp)n was carried out for collagen-like triple helical complexes (coiled coils with screw symmetry). The lowest energy structure of the first polymer (helical parameters t 52,8, h 0,282 nm) is very close to that of (Gly-Pro-Hyp)n. The hydroxyl group of a serine residue does not form any intramolecular hydrogen bonds in this structure. (Gly-Val-Hyp)n triple complex is shown to unwind to t 7,7, h 0,297 nm as a result of optimization procedure. These findings confirm the assumption, made earlier on the basis of conformational analysis of (Gly-Pro-Hyp)n, (Gly-Pro-Ala)n, (Gly-Ala-Hyp)n, (Gly-Ala-Ala)n, that the collagen triple helix contains stable wound triplets with proline in the second position, while the absence of imino acid in the 2nd position facilitates the unwinding of the triple helix. Thus, a collagen helix appears to have different parameters for the sites differing in the amino acid sequence. The values measured in the X-ray experiments (h 0,29 nm, t' 36) should be considered as a result of averaging. The model allows to reconcile the X-ray data for collagen and crystalline (Gly-Pro-Pro)10 oligomer.     

Polyamine-induced B-DNA to Z-DNA conformational transition of a plasmid DNA with (dG-dC)n insert.

We investigated the ability of natural polyamines putrescine, spermidine, and spermine to provoke a left-handed Z-DNA conformation in a recombinant plasmid (pDHg16) with a 23-base pair insert of (dG-dC)n.(dG-dC)n sequences. Using a monoclonal anti-Z-DNA antibody (Z22) and an enzyme-linked immunosorbent assay protocol, we found that spermidine and spermine were capable of converting pDHg16 to the Z-DNA form. The concentrations of spermidine and spermine at the midpoint of the B-DNA to Z-DNA transition were 280 and 5 microM, respectively, in buffer containing 50 mM NaCl, 1 mM sodium cacodylate, and 0.15 mM EDTA, pH 7.4. A plot of ln[Na+] versus ln [spermine4+], where [Na+] is the bulk NaCl concentration and [spermine4+] is the spermine concentration at the midpoint of the B-DNA to Z-DNA transition, gave a straight line with a slope of 1.2. Structural specificity was clearly evident in the efficacy of three spermidine homologs to induce the Z-DNA conformation in pDHg16. Putrescine and acetylspermidines had no effect on the conformation of the plasmid DNA up to a 3 mM concentration. Control experiments with the parental plasmid (pDPL6) showed no binding of the plasmid DNA with Z22. These results indicate that spermidine and spermine are capable of provoking the left-handed Z-DNA conformation in small blocks of (dG-dC)n sequences embedded in a right-handed B-DNA matrix. Since blocks of (dG-dC)n sequences are found in certain native DNAs, conformational alterations of these regions to the Z-DNA form in the presence of polyamines may have important gene regulatory effects.     

Experimental and theoretical conformational studies on polypeptide models of collagen. Poly(Gly-Pro-Ile) and poly(Gly-Ile-Pro)

The synthetic polytripeptides poly(Gly-Pro-Ile) and poly(Gly-Ile-Pro) were studied both experimentally (mainly by circular dichroism spectroscopy) and theoretically by quantum mechanical methods. Poly(Gly-Ile-Pro) adopts a collagen-like structure under favourable conditions while the isomeric poly(Gly-Pro-Ile) does not. Theoretical studies emphasize severe intrastrand interactions which limit the main chain conformations in the case of poly(Gly-Ile-Pro). On the other hand, both the side cahin and the backbone in poly(Gly-Pro-Ile) can take up many different local conformations. Therefore, it seems that the conformational behaviour of synthetic polytripeptides can be at least partially explained in terms of local interactions.     

NMR studies of pH-dependent conformational polymorphism of alternating (C-T)n sequences.

Alternating (C-T)n sequences are involved in the H-DNA structure associated with (GA)n.(CT)n sequences. Low pH values facilitate H-DNA formation. We have undertaken a detailed analysis of the structural consequences of the (C-T)n sequence as a function of pH. The structures of three DNA oligonucleotides, d(CT)4, d(TC)4 and d(TC)15, have been studied by NMR. We found that their conformations are polymorphic and pH dependent. There are at least three major conformational species: an antiparallel-stranded (APS) duplex with entirely C:T base pairs at pH 7, an antiparallel-stranded (APS) duplex with entirely C+:T base pairs at pH 3, and a possible parallel-stranded (PS) duplex with C+:C and T:T base pairs near pH 5. In the intermediate pH range, the APS duplex may have varying numbers of C+:T and C:T base pairs, and there may be a fast exchange going on between APS duplex species involving these two kinds of base pairs. However, the transition between the APS and PS duplexes is slow. Structural refinement of the two octamers, d(TC)4 and d(CT)4, at pH = 6.9 and pH = 3 using 2D-NOE data suggests that the molecules are likely in the duplex form at 5 degrees C. We lack evidence that the structure at pH 3 is a PS structure with T nucleotides residing in the exterior of the helix. Titration of the longer oligonucleotide, d(TC)15, showed a prominent pKa of approximately 6, approaching the value of 7.0 obtained from the titration of poly-(dC).     

Theoretical conformational analysis on Cyclo(prolyl-phenylalanyl) peptides

Empirical energy calculations on cyclo(L -Pro-L -Phe) and cyclo(L -Pro-D-Phe) indicate that different conformations are possible for each molecule. The theoretical results are compared to ir, nmr, and crystallographic data. The interdependence between diketopiperazine ring and side-chain conformations is also discussed.     

Polypeptide models of collagen. II. Solution properties of (Pro-Gly-Phe)n

The conformation of (Pro-Gly-Phe)_n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro-Gly-Phe)_n can exist in a partially triple-helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly-R₂-R₃, in collagen.     

Murine responses to (Tyr-Glu-Ala-Gly)n

A series of known sequential polypeptides is being synthesized and used in our laboratory to study the contribution of antigen structure, i. e., amino acid sequence and conformation in antigen recognition and specificity of the immune response. The capacity to respond to one such -helical polypeptide (T-G-A-Gly)_n, is T-cell dependent and restricted to mice of theH- 2^b haplotype. The response is controlled by anIr gene mapping to theK region and/or theIA subregion which allows the animal to make both a T-cell mediated response, as well as a humoral response to the polypeptide. The response of three mutant strains at theK end of the major histocompatibility locus (MHC) need not differ from that of the responder parental haplotype.PETLES obtained from mice possessing a responder haplotype proliferate when cultured in vitro with (T-G-A-Gly)_n. The antibody level of individual inbred mice of a given strain at a given time differs significantly (from 80% binding to less than 10% antigen bound in 3 out of 57 mice). There is also great individual variability in time of appearance of the antibody response and where peak optimal levels are seen. Possible explanations for the variation in the antibody expression include: (a) the polymer is a weak immunogen, (b) the presence of modifier gene(s) outside of the major histocompatibility complex controlling the magnitude of the antibody level, (c) the possible effect of the polymer which is a B cell mitogen as a generator of suppressor T cells and, (d) a feedback mechanism effect on B cells controlling the antibody level.This work was supported in part by the following grants: The National Institute of Allergy and Infectious Diseases A107825; American Cancer Society Grant IM-5F; National Foundation-March of Dimes 1-492.     

Frontier molecular orbital analysis of Cu(n)-O(2) reactivity

Frontier molecular orbital (FMO) theory coupled with density functional calculations has been applied to investigate the chemical reactivity of three key bioinorganic Cu(n)-O(2) complexes, the mononuclear end-on hydroperoxo-Cu(II), the side-on bridged mu-eta(2):eta(2)-O(2)(2-) Cu(II)(2) dimer and the bis-mu-oxo Cu(III)(2) dimer. Two acceptor orbitals (sigma* and pi*) of each complex and two types of donating substrates (sigma-substrate, phosphine; pi-substrate, alkylbenzene) are considered in the electrophilic attack mechanism. The angular dependences of different reaction pathways are determined using FMO theory and the angular overlap model. Including steric effects, the sigma*/sigma and pi*/pi pathways are found more reactive than the corresponding cross sigma*/pi and pi*/sigma pathways which have poor donor-acceptor orbital overlaps in the sterically constrained substrate access region.     

Contribution of tertiary amides to the conformational stability of collagen triple helices

The collagen triple helix is composed of three polypeptide strands, each with a sequence of repeating (Xaa-Yaa-Gly) triplets. In these triplets, Xaa and Yaa are often tertiary amides: L-proline (Pro) and 4(R)-hydroxy-L-proline (Hyp). To determine the contribution of tertiary amides to triple-helical stability, Pro and Hyp were replaced in synthetic collagen mimics with a non-natural acyclic tertiary amide: N-methyl-L-alanine (meAla). Replacing a Pro or Hyp residue with meAla decreases triple-helical stability. Ramachandran analysis indicates that meAla residues prefer to adopt straight phi and psi angles that are dissimilar from those of the Pro and Hyp residues in the collagen triple helix. Replacement with meAla decreases triple-helical stability more than does replacement with Ala. All of the peptide bonds in triple-helical collagen are in the trans conformation. Although an Ala residue greatly prefers the trans conformation, a meAla residue exists as a nearly equimolar mixture of trans and cis conformers. These findings indicate that the favorable contribution of Pro and Hyp to the conformational stability of collagen triple helices arises from factors other than their being tertiary amides.     

Synthesis of heterotrimeric collagen models containing Arg residues in Y-positions and analysis of their conformational stability

An Arg residue incorporated into the Y-position of collagenous host-guest peptide Ac-(Gly-Pro-Hyp)(3)-Gly-Pro-Y-(Gly-Pro-Hyp)(4)-Gly-Gly-NH(2) is reported to stabilize the triple helical structure as well as a 4(R)-hydroxyproline (Hyp) residue. Here, we synthesized heterotrimeric collagen models containing Arg in Y-positions utilizing the cystine knot strategy. Analysis of their thermal transition temperatures using circular dichroism spectrometry demonstrated unexpected decrease in the triple helical stability as the number of Arg increased. The obtained results indicated that an Arg residue in a Y-position is not always an equivalent of a Hyp residue, and that it possesses a potential helix destabilizing effect.