Understanding the role of stereoelectronic effects in determining collagen stability. 2. A quantum mechanical/molecular mechanical study of (Proline-Proline-Glycine)(n) polypeptides

The importance of vicinal and long-range interresidue effects in determining the stability of the collagen triple helix has been investigated by quantum mechanical (QM) and molecular mechanical (MM) computations on suitable model polypeptides, taking into account solvent effects by the polarizable continuum model (PCM). At the QM level, the PII conformation corresponds to an energy minimum for pentapeptide analogues incorporating the sequence Gly-Pro-Pro-Gly, irrespective of the down or up puckering of the pyrrolidine ring. However, our computations indicate that the alternation of down and up prolines characterizing collagen and collagen-like peptides is not due to an intrinsic preference of the Pro-Pro-Gly sequence. This result is confirmed by MM computations of longer polypeptides. Next, MM computations on model triple helices show that a better packing is obtained for specific values of backbone dihedrals, which, in turn, favor the alternation of down and up prolines along each chain.     

A hyperstable collagen mimic

BACKGROUND: Collagen is the most abundant protein in animals. Each polypeptide chain of collagen is composed of repeats of the sequence: Gly-X-Y, where X and Y are often L-proline (Pro) and 4(R)-hydroxy-L-proline (Hyp) residues, respectively. These chains are wound into tight triple helices of great stability. The hydroxyl group of Hyp residues contributes much to this conformational stability. The existing paradigm is that this stability arises from interstrand hydrogen bonds mediated by bridging water molecules. This model was tested using chemical synthesis to replace Hyp residues with 4(R)-fluoro-L-proline (Flp) residues. The fluorine atom in Flp residues does not form hydrogen bonds but does elicit strong inductive effects. RESULTS: Replacing the Hyp residues in collagen with Flp residues greatly increases triple-helical stability. The free energy contributed by the fluorine atom in Flp residues is twice that of the hydroxyl group in Hyp residues. The stability of the Flp-containing triple helix far exceeds that of any untemplated collagen mimic of similar size. CONCLUSIONS: Bridging water molecules contribute little to collagen stability. Rather, collagen stability relies on previously unappreciated inductive effects. Collagen mimics containing fluorine or other appropriate electron-withdrawing substituents could be the basis of new biomaterials for restorative therapies.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.     

Role of length-dependent stability of collagen-like peptides

Understanding the structure, folding, and stability of collagen is complex because of its length and variations in the amino acid (AA) sequence composition. It is well known that the basic constituent of the collagen helix is the triplet repeating sequence of the form Gly-X(AA)-Y(AA). On the basis of previous models and with the frequency of occurrence of the triplets, the ((Gly-Pro-Hyp)n)3 (where n is the number of triplets) sequence replicate has been chosen as the model for the most stable form of the collagen-like sequence. With a view to understand the role of sequence length (or the number of triplets) on the stability of collagen, molecular dynamics simulations have been carried out by varying the number of triplet units on the model collagen-like peptides. The results reveal that five triplets are required to form the stable triple helix. Further analysis shows that the intermolecular structural rigidity of the imino acid residues, hydrogen bonding, and water structure around the three chains of the triple helix play the dominant roles on its structure, folding, and stabilization.     

The close-packed triple helix as a possible new structural motif for collagen

The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of v _CP =?43.3°. Contrary to the conventional notion, we suggest that close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some of the difficulties for the current understanding of the structure of collagen are reviewed: The ambiguity in assigning crystal structures for collagen-like peptides, and the failure to satisfactorily calculate circular dichroism spectra. Further, the proposed new geometrical structure for collagen is better packed than both the 10/3 and the 7/2 structure. A feature of the suggested collagen structure is the existence of a central channel with negatively charged walls. We find support for this structural feature in some of the early x-ray diffraction data of collagen. The central channel of the structure suggests the possibility of a one-dimensional proton lattice. This geometry can explain the observed magic angle effect seen in NMR studies of collagen. The central channel also offers the possibility of ion transport and may cast new light on various biological and physical phenomena, including biomineralization.     

Collagen-like peptides and peptide–polymer conjugates in the design of assembled materials

Collagen is the most abundant protein in mammals, and there has been long-standing interest in understanding and controlling collagen assembly in the design of new materials. Collagen-like peptides (CLPs), also known as collagen-mimetic peptides (CMPs) or collagen-related peptides (CRPs), have thus been widely used to elucidate collagen triple helix structure as well as to produce higher-order structures that mimic natural collagen fibers. This mini-review provides an overview of recent progress on these topics, in three broad topical areas. The first focuses on reported developments in deciphering the chemical basis for collagen triple helix stabilization, which we review not with the intent of describing the basic structure and biological function of collagen, but to summarize different pathways for designing collagen-like peptides with high thermostability. Various approaches for producing higher-order structures via CLP self-assembly, via various types of intermolecular interaction, are then discussed. Finally, recent developments in a new area, the production of polymer–CLP bioconjugates, are summarized. Biological applications of collagen contained hydrogels are also included in this section. The topics may serve as a guide for the design of collagen-like peptides and their bioconjugates for targeted application in the biomedical arena.     

Impact of carbamylation on type I collagen conformational structure and its ability to activate human polymorphonuclear neutrophils

Carbamylation by urea-derived cyanate is a posttranslational modification of proteins increasing during chronic renal insufficiency, which alters structural and functional properties of proteins and modifies their interactions with cells. We report here the major structural alterations of type I collagen induced by carbamylation. Biophysical methods revealed that carbamylated collagen retained its triple-helical structure, but that slight changes destabilized some regions within the triple helix and decreased its ability to polymerize into normal fibrils. These changes were associated with the incapacity of carbamylated collagen to stimulate polymorphonuclear neutrophil oxidative functions. This process involved their interaction with LFA-1 integrin, but no subsequent p(125)FAK phosphorylation. Carbamylation of collagen might alter interactions between collagen and inflammatory cells in vivo and interfere with the normal remodeling of extracellular matrix, thus participating in the pathophysiological processes occurring during renal insufficiency.     

Self-assembled heterotrimeric collagen triple helices directed through electrostatic interactions

Collagen, a fibrous protein, is an essential structural component of all connective tissues such as cartilage, bones, ligaments, and skin. Type I collagen, the most abundant form, is a heterotrimer assembled from two identical alpha1 chains and one alpha2 chain. However, most synthetic systems have addressed homotrimeric triple helices. In this paper we examine the stability of several heterotrimeric collagen-like triple helices with an emphasis on electrostatic interactions between peptides. We synthesize seven 30 amino acid peptides with net charges ranging from -10 to +10. These peptides were mixed, and their ability to form heterotrimers was assessed. We successfully show the assembly of five different AAB heterotrimers and one ABC heterotrimer. The results from this study indicate that intermolecular electrostatic interactions can be utilized to direct heterotrimer formation. Furthermore, amino acids with poor stability in collagen triple helices can be "rescued" in heterotrimers containing amino acids with known high triple helical stability. This mechanism allows collagen triple helices to have greater chemical diversity than would otherwise be allowed.     

Synthetic collagen heterotrimers: structural mimics of wild-type and mutant collagen type I

Collagen type I is an AAB heterotrimer assembled from two alpha1 chains and one alpha2 chain. Missense mutations in either of these chains that substitute a glycine residue in the ubiquitous X-Y-Gly repeat with a bulky amino acid leads to osteogenesis imperfecta (OI) of varying severity. These mutations have been studied in the past using collagen-like peptide homotrimers as a model system. However, homotrimers, which by definition will contain glycine mutations in all the three chains, do not accurately mimic the mutations in their native form and result in an exaggerated effect on stability and folding. In this article, we report the design of a novel model system based upon collagen-like heterotrimers that can mimic the glycine mutations present in either the alpha1 or alpha2 chains of type I collagen. This design utilizes an electrostatic recognition motif in three chains that can force the interaction of any three peptides, including AAA (all same), AAB (two same and one different), or ABC (all different) triple helices. Therefore, the component peptides can be designed in such a way that glycine mutations are present in zero, one, two, or all three chains of the triple helix. With this design, we for the first time report collagen mutants containing one or two glycine substitutions with structures relevant to native forms of OI. Furthermore, we demonstrate the difference in thermal stability and refolding half-life times between triple helices that vary only in the frequency of glycine mutations at a particular position.     

Peptide bond isosteres: ester or (E)-alkene in the backbone of the collagen triple helix

[structure: see text] Collagen is the most abundant protein in animals. Interstrand N-H...O=C hydrogen bonds between backbone amide groups form a ladder in the middle of the collagen triple helix. Isosteric replacement of the hydrogen-bond-donating amide with an ester or (E)-alkene markedly decreases the conformational stability of the triple helix. Thus, this recurring hydrogen bond is critical to the structural integrity of collagen. In this context, an ester isostere confers more stability than does an (E)-alkene.     

2D Crystal Engineering of Nanosheets Assembled from Helical Peptide Building Blocks

The successful integration of 2D nanomaterials into functional devices hinges on developing fabrication methods that afford hierarchical control across length scales of the entire assembly. We demonstrate structural control over a class of crystalline 2D nanosheets assembled from collagen triple helices. By lengthening the triple helix unit through sequential additions of Pro‐Hyp‐Gly triads, we achieved sub‐angstrom tuning over the 2D lattice. These subtle changes influence the overall nanosheet size, which can be adjusted across the mesoscale size regime. The internal structure was observed by cryo‐TEM with direct electron detection, which provides real‐space high‐resolution images, in which individual triple helices comprising the lattice can be clearly discerned. These results establish a general strategy for tuning the structural hierarchy of 2D nanomaterials that employ rigid, cylindrical structural units.     

Macrocyclic scaffold for the collagen triple helix

[structure: see text] Three strands of natural collagen are linked by covalent bonds prior to their folding into a triple helix. We report on a synthetic collagen in which the strands are pendent on a rigid macrocyclic scaffold of C(3) symmetry. The scaffold confers substantial conformational stability upon the collagen triple helix and makes its folding independent of concentration, both desirable attributes for exploring and exploiting synthetic collagens.     

异氰酸苯酯诱导的类胶原多肽自组装

Synthetic matrices provide powerful tools for dissecting molecular interactions involved in the organization of the extracellular matrix (ECM), establishment of cell axis polarity, and suppression of neoplasticity in pre-cancerous endothelial cells. Collagen is the most abundant protein in extracellular matrix. A de novo approach is essential for the synthesis of collagen matrices which can have a broad impact on the understanding of matrix biology and our capacity to construct safe and medically useful biomaterials. Conventionally, the ECM has been studied by an analytical "top-down" approach, where the individual components of the matrix are first isolated and then characterized to explore their biochemical and functional properties. Since native collagen is difficult to modify and can engender pathogenic and immunological side effects, its application on tissue regeneration is limited. Therefore, we attempted to synthesize artificial collagen directly through small organic molecule recognition. The collagen-like peptides possess various benefits such as being clean, programmable, and easy to modify; therefore, in recent years, they have been used as ideal substrates for the synthesis of collagen nanomaterials. The self-assembly of collagen-like peptides is mainly driven by various non-covalent interactions such as electrostatic attraction, π-π stacking, and metal coordination. This renders a difficulty in the rational design of uniform nanostructures from short synthesized peptides and demands a novel strategy. To date, small organic molecules have been rarely used for the self-assembly of collagen-like peptides. In the present study, we attempted to use the small organic molecules for the combined supramolecular self-assembly of collagen-like peptides. Initially, the collagen-like peptides, (POG)₆ and (POG)₈, synthesized by the solid-phase synthesis technique, were both modified chemically using 4, 4'-methylene bis(phenyl isocyanate) to obtain the collagen-like hybrid peptides, AP₆ and AP₈, respectively. Phenyl isocyanate contributes to the formation of potential weak forces, such as hydrogen bonds and π-π stacking at the N-terminal regions of the collagen-like hybrid peptides. The purity and molecular weight of the collagen-like hybrid peptides were analyzed using analytical high-performance liquid chromatography (HPLC) and matrix-assisted laser desorption ionization time of flight (MALDI-TOF), respectively. The stability of AP₆ and AP₈ triple helices was analyzed by circular dichroism (CD) spectroscopy. The small organic molecule 4, 4'-methylene bis(phenyl isocyanate) promoted the unfolding of (POG)₆ and increased the melting temperature (T_m) of (POG)₈ from 37.7 to 58.8 ℃to form a triple helix. The hydrodynamic radii of collagen-like hybrid peptides were measured by dynamic light scattering (DLS). Atomic force microscopy (AFM) and transmission electron microscopy (TEM) were used to analyze the morphology of the aggregation states. AFM results showed that the collagen-like hybrid peptides, AP₆ and AP₈, formed nanofibers spontaneously. Consistent with the AFM results, TEM showed that the AP₆ and AP₈ collagen-like hybrid peptides also formed nanofiber structures. The formation of stable complexes was attributed to the presence of multiple weak interactions such as hydrogen bonding, π-π stacking, and hydrophobic interactions. In the present study, we demonstrated that the chemical modification of collagen-like polypeptides at the N-terminus via the small organic molecule, 4, 4'-methylene bis(phenyl isocyanate), promoted the intramolecular and intermolecular assembly of collagen-like peptides. A simple and effective strategy has been developed in this study to promote the self-assembly of collagen-like peptides.     

Thermosensitive gel formation of novel polypeptides containing a collagen‐derived Pro‐Hyp‐Gly sequence and an elastin‐derived Val‐Pro‐Gly‐Val‐Gly sequence

A triple‐helix‐forming collagen model peptide, (prolyl‐trans‐4‐hydroxyprolyl‐glycyl)₁₀ [(Pro‐Hyp‐Gly)₁₀], and a thermosensitive elastin‐derived pentapeptide, valyl‐prolyl‐glycyl‐valyl‐glycyl (Val‐Pro‐Gly‐Val‐Gly), were copolymerized in various mole ratios using 1‐ethyl‐3‐(3‐dimethylaminopropyl)‐carbodiimide hydrochloride and 1‐hydroxybenzotriazole in dimethyl sulfoxide at 20 °C. All of the obtained polypeptides have molecular weight higher than 10³ and contain a triple‐helical structure, and showed an inverse phase transition from transparent solution to turbid suspension in response to a rise in temperature. The lower critical solution temperature of the polypeptide solution decreased upon increasing the content of Val‐Pro‐Gly‐Val‐Gly. Furthermore, polypeptides containing 82–86 mol % of Val‐Pro‐Gly‐Val‐Gly in composition showed reversible gel formation, suggesting that (Pro‐Hyp‐Gly)₁₀ acts as a hydrated unit and Val‐Pro‐Gly‐Val‐Gly acts as a thermosensitive crosslinking point. These biodegradable thermosensitive polypeptides may be useful for biomedical applications, including, as a scaffold for tissue regeneration. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6048–6056, 2005     

Triple-Helix-Stabilizing Effects in Collagen Model Peptides Containing PPII-Helix-Preorganized Diproline Modules

Collagen model peptides (CMPs) serve as tools for understanding stability and function of the collagen triple helix and have a potential for biomedical applications. In the past, interstrand cross-linking or conformational preconditioning of proline units through stereoelectronic effects have been utilized in the design of stabilized CMPs. To further study the effects determining collagen triple helix stability we investigated a series of CMPs containing synthetic diproline-mimicking modules (ProMs), which were preorganized in a PPII-helix-type conformation by a functionalizable intrastrand C₂ bridge. Results of CD-based denaturation studies were correlated with calculated (DFT) conformational preferences of the ProM units, revealing that the relative helix stability is mainly governed by an interplay of main-chain preorganization, ring-flip preference, adaptability, and steric effects. Triple helix integrity was proven by crystal structure analysis and binding to HSP47.     

Triple‐Helix‐Stabilizing Effects in Collagen Model Peptides Containing PPII‐Helix‐Preorganized Diproline Modules

Collagen model peptides (CMPs) serve as tools for understanding stability and function of the collagen triple helix and have a potential for biomedical applications. In the past, interstrand cross‐linking or conformational preconditioning of proline units through stereoelectronic effects have been utilized in the design of stabilized CMPs. To further study the effects determining collagen triple helix stability we investigated a series of CMPs containing synthetic diproline‐mimicking modules (ProMs), which were preorganized in a PPII‐helix‐type conformation by a functionalizable intrastrand C₂ bridge. Results of CD‐based denaturation studies were correlated with calculated (DFT) conformational preferences of the ProM units, revealing that the relative helix stability is mainly governed by an interplay of main‐chain preorganization, ring‐flip preference, adaptability, and steric effects. Triple helix integrity was proven by crystal structure analysis and binding to HSP47.     

Surprisingly high stability of collagen ABC heterotrimer: evaluation of side chain charge pairs

Type I collagen is a major component of skin, tendon, and ligament and forms more than 90% of bone mass. It is an AAB heterotrimer assembled from two identical alpha1 and one alpha2 chains. However, the majority of studies on the effects of amino acid substitution on triple helix stability have been performed on collagen homotrimeric helices. In a homotrimer, it is impossible to determine whether the contribution to stability is from the polyproline II helix propensity of the amino acids or from interhelix amino acid interactions. The presence of amino acids in all three chains further exaggerates their contribution. In contrast, in a heterotrimer, the individual chains may be tailored in order to have the substitution in one, two, or all three chains. Therefore, a heterotrimer can divulge specific information about any interaction based upon the substitutions in individual chains. In this paper, we evaluate the contribution of electrostatic interactions between side chain charge pairs on the stability of heterotrimers. We synthesize and analyze the stability of four AAB and four ABC heterotrimers including a surprisingly stable ABC heterotrimer composed of (DOG)10, (PKG)10, and (POG)10 chains (O = hydroxyproline). This heterotrimer has a stability comparable to that of a (POG)10 homotrimer even though D and K occur 20 times in the heterotrimeric helix and have been previously shown to significantly destabilize the triple helix compared to the P and O imino acids. These results show that the stability of heterotrimers cannot be directly determined from the analysis of charge pairs in homotrimers. Because collagen heterotrimers can be designed to have substitution in one, two, or three chains, it gives us the ability to decode cross-strand interactions in collagen in a similar fashion to alpha-helical coiled-coil interactions and DNA duplex hydrogen bonding.     

The role of cystine knots in collagen folding and stability,part II. Conformational properties of (Pro-Hyp-Gly)n model trimers with N- and C-terminal collagen type III cystine knots

In mature collagen type III the homotrimer is C-terminally cross-linked by an interchain cystine knot consisting of three disulfide bridges of unknown connectivity. This cystine knot with two adjacent cysteine residues on each of the three alpha chains has recently been used for the synthesis and expression of model homotrimers. To investigate the origin of correct interchain cysteine pairings, (Pro-Hyp-Gly)(n) peptides of increasing triplet number and containing the biscysteinyl sequence C- and N-terminally were synthesised. The possibilities were that this origin may be thermodynamically coupled to the formation of the collagen triple helix as happens in the oxidative folding of proteins, or it could represent a post-folding event. Only with five triplets, which is known to represent the minimum number for self-association of collagenous peptides into a triple helix, air-oxidation produces the homotrimer in good yields (70 %), the rest being intrachain oxidised monomers. Increasing the number of triplets has no effect on yield suggesting the formation of kinetically trapped intermediates, which are not reshuffled by the glutathione redox buffer. N-terminal incorporation of the cystine knot is significantly less efficient in the homotrimerisation step and also in terms of triple-helix stabilisation. Compared to an artificial C-terminal cystine knot consisting of two interchain disulfide bridges, the collagen type III cystine knot produces collagenous homotrimers of remarkably high thermostability, although the concentration-independent refolding rates are not affected by the type of disulfide bridging. Since the natural cystine knot allows ready access to homotrimeric collagenous peptides of significantly enhanced triple-helix thermostability it may well represent a promising approach for the preparation of collagen-like innovative biomaterials. Conversely, the more laborious regioselectively formed artificial cystine knot still represents the only synthetic strategy for heterotrimeric collagenous peptides.     

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set of parameters that reproduces the correct pucker preference. Our molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen-like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation (and thus the right phi angle) in the Y position.     

Insights on the conformational stability of collagen

This review describes work on the conformational stability of the collagen triple helix. In 1994, the structure of collagen was determined at high resolution. Since then, much work has been done on synthetic mimics of collagen that contain host-guest peptides, tethers, peptoid residues, or analogs of the prevalent 4(R)-hydroxy-L-proline residues. This work has revealed much about the chemical basis for collagen stability, and could spawn useful new biomaterials. The literature from 1994 to mid 2001 is reviewed, and 116 references are cited.