An infrared study of unordered poly-L-proline in CaCl 2 solutions

Evaluation of IR and Raman spectroscopic markers of human collagens: Insides for indicating colorectal carcinogenesis

Vibrational spectroscopic methods are widely used in the molecular diagnostics of carcinogenesis. Collagen, a component of connective tissue, plays a special role as a biochemical marker of pathological changes in tissues. The vibrational bands of collagens are very promising to distinguish between normal colon tissue, benign and malignant colon polyps. Differences in these bands indicate changes in the amount, structure, conformation and the ratio between the individual structural forms (subtypes) of this protein. The screening of specific collagen markers of colorectal carcinogenesis was carried out based on the FTIR and Raman (λ_ex 785 nm) spectra of colon tissue samples and purified human collagens. It was found that individual types of human collagens showed significant differences in their vibrational spectra, and specific spectral markers were found for them. These collagen bands were assigned to specific vibrations in the polypeptide backbone, amino acid side chains and carbohydrate moieties. The corresponding spectral regions for colon tissues and colon polyps were investigated for the contribution of collagen vibrations. Mentioned spectral differences in collagen spectroscopic markers could be of interest for early ex vivo diagnosis of colorectal carcinoma if combine vibrational spectroscopy and colonoscopy.

Self-Assembly and Rearrangement of a Polyproline II Helix Peptide on Gold

Polyproline peptide sequences have gained popularity as anchors for peptide-based self-assembled monolayers (SAMs) due to their attractive properties. In this work, peptides containing the polyproline II helix (PPII) conformation were designed and assembled on gold (Au). A quartz crystal microbalance with dissipation was used to characterize SAM formation kinetics and related properties. Peptides were designed with the sequence (GPPPPPG)₂C. It was discovered that a biexponential adsorption and rearrangement model describes the binding kinetics of the PPII-containing peptide on Au. In this model, an initial reversible binding step is followed by an irreversible rearrangement step, given by parameter k_t. This study found k_t to be approximately 0.00064 s^-1 for the PPII-containing peptides. Similarly, we found that the adsorption of the PPII-containing peptide on Au, given by ΔG_ads, was thermodynamically favorable (-7.8 kcal mol^-1) and comparable to other common thiol terminated SAMs on Au. Furthermore, we characterized SAM properties via QCM-D, Fourier-transform infrared (FTIR) spectroscopy, and electrochemical techniques to reveal high molecular density SAMs consisting of PPII helices. In addition, these SAMs were found to have high antifouling properties. Overall, this study characterizes the fundamental assembly mechanisms, particularly, rearrangement of PPII-containing peptides for the first time, which will be useful in the designing of future peptide-based SAMs with high surface coverage and antifouling properties.

Protein Phosphorylation and Mineral Binding Affect the Secondary Structure of the Leucine-Rich Amelogenin Peptide

Previously, we have shown that serine-16 phosphorylation in native full-length porcine amelogenin (P173) and the Leucine-Rich Amelogenin Peptide (LRAP(+P)), an alternative amelogenin splice product, affects protein assembly and mineralization in vitro. Notably, P173 and LRAP(+P) stabilize amorphous calcium phosphate (ACP) and inhibit hydroxyapatite (HA) formation, while non-phosphorylated counterparts (rP172, LRAP(-P)) guide the growth of ordered bundles of HA crystals. Based on these findings, we hypothesize that the phosphorylation of full-length amelogenin and LRAP induces conformational changes that critically affect its capacity to interact with forming calcium phosphate mineral phases. To test this hypothesis, we have utilized Fourier transform infrared spectroscopy (FTIR) to determine the secondary structure of LRAP(-P) and LRAP(+P) in the absence/presence of calcium and selected mineral phases relevant to amelogenesis; i.e., hydroxyapatite (HA: an enamel crystal prototype) and (ACP: an enamel crystal precursor phase). Aqueous solutions of LRAP(-P) or LRAP(+P) were prepared with or without 7.5 mM of CaCl₂ at pH 7.4. FTIR spectra of each solution were obtained using attenuated total reflectance, and amide-I peaks were analyzed to provide secondary structure information. Secondary structures of LRAP(+P) and LRAP(-P) were similarly assessed following incubation with suspensions of HA and pyrophosphate-stabilized ACP. Amide I spectra of LRAP(-P) and LRAP(+P) were found to be distinct from each other in all cases. Spectra analyses showed that LRAP(-P) is comprised mostly of random coil and β-sheet, while LRAP(+P) exhibits more β-sheet and α-helix with little random coil. With added Ca, the random coil content increased in LRAP(-P), while LRAP(+P) exhibited a decrease in α-helix components. Incubation of LRAP(-P) with HA or ACP resulted in comparable increases in β-sheet structure. Notably, however, LRAP(+P) secondary structure was more affected by ACP, primarily showing an increase in β-sheet structure, compared to that observed with added HA. These collective findings indicate that phosphorylation induces unique secondary structural changes that may enhance the functional capacity of native phosphorylated amelogenins like LRAP to stabilize an ACP precursor phase during early stages of enamel mineral formation.

Unraveling the aggregation propensity of human insulin C-peptide

Over the last 20 years, proinsulin C-peptide emerged as an important player in various biological events. Much time and effort has been spent in exploring all functional features of C-peptide and recording its implications in Diabetes mellitus. Only a few studies, though, have addressed C-peptide oligomerization and link this procedure with Diabetes. The aim of our work was to examine the aggregation propensity of C-peptide, utilizing Transmission Electron Microscopy, Congo Red staining, ATR-FTIR, and X-ray fiber diffraction at a 10 mg ml^-1 concentration. Our experimental work clearly shows that C-peptide self-assembles into amyloid-like fibrils and therefore, the aggregation propensity of C-peptide is a characteristic novel feature that should be related to physiological and also pathological conditions. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 108: 1-8, 2017.

Formation process and solvent-dependent structure of a polyproline self-assembled monolayer on a gold surface

The formation process and structure of a self-assembled monolayer (SAM) of lipoic-acid-terminated polyproline on a gold surface in aqueous solution were investigated by several techniques. The amount of polyproline molecules on the gold surface was determined from the area of the reductive desorption peak, and orientation and thickness of the polyproline SAM were determined in situ by attenuated total reflection infrared (ATR-IR) spectroscopy and ellipsometry. The kinetics of the polyproline SAM formation process were discussed on the basis of these results. The in situ IR study confirmed that the conformation of the polyproline SAM was changed by changing the solvent from water to methanol and methanol to water, as is the case for polyproline dissolved in solution.

Biominerals--hierarchical nanocomposites: the example of bone

Many organisms incorporate inorganic solids in their tissues to enhance their functional, primarily mechanical, properties. These mineralized tissues, also called biominerals, are unique organo-mineral nanocomposites, organized at several hierarchical levels, from nano- to macroscale. Unlike man-made composite materials, which often are simple physical blends of their components, the organic and inorganic phases in biominerals interface at the molecular level. Although these tissues are made of relatively weak components under ambient conditions, their hierarchical structural organization and intimate interactions between different elements lead to superior mechanical properties. Understanding basic principles of formation, structure, and functional properties of these tissues might lead to novel bioinspired strategies for material design and better treatments for diseases of the mineralized tissues. This review focuses on general principles of structural organization, formation, and functional properties of biominerals on the example the bone tissues.

Dependence of the AmII'p proline Raman band on peptide conformation

We utilized UV resonance Raman (UVRR) measurements and density functional theory (DFT) calculations to relate the AmII'p frequency to the psi angle. The AmII'p frequency shifts by approximately 25 cm(-1) as the psi angle is varied over allowed angles of the Pro peptide bond. The AmII'p frequency does not show any significant dependence on the phi dihedral angle. The conformation sensitivity of the AmII'p frequency derives from conformation-induced changes in the planarity of the Pro peptide bond; psi angle changes push the amide nitrogen out of the peptide bond plane. We use this AmII'p frequency dependence on the psi angle to track temperature-induced conformation changes in a polyproline peptide. The temperature-induced 7 cm(-1) downshift in the AmII'p frequency of the polyproline peptide results from an approximately 45 degrees rotation of the psi dihedral angle from psi = 145 degrees (ideal PPII conformation) to psi = 100 degrees (collapsed PPII conformation).

Collagen-DNA complex

Previously presented models of collagen-DNA (7) and collagen-siRNA (8) complexes point to a general description of delivery systems and indicate to what specific topology that system should be equipped with to effectively deliver the gene into the living body via in vivo and in vitro injection. We focused our interest on the nature of collagen-DNA complex structure and the molecular and environmental determinants of the self-association processes of collagen with the presence of DNA. In this aspect, the self-association of collagen-DNA complex offers an opportunity to characterize a unique system, which may be related to the general mechanisms of self-association of fiber macromolecules by water bridges. For characterizing the collagen-DNA interaction, we used FTIR-ATR, NMR, and AFM experiments done on a separate collagen film, DNA film, and on the peptide-DNA aqueous solution. We demonstrate that collagen-DNA spontaneously forms self-assembling complex systems in aqueous solution. Such self-association of the complex could be induced by electrostatic interactions between neutral collagen cylinders, having strong dipole moment, and negatively charged DNA cylinders. A final complex could be formed by hydrogen bonds between specified donor groups of collagen and phosphate acceptor groups of DNA. According to FTIR measurements, a collagen triple helix should not change global conformation during collagen-DNA complex formation.

Conformational changes in salivary proline-rich protein 1 upon adsorption to calcium phosphate crystals

Conformational analyses of PRP1, a proline-rich acidic salivary protein and major component of the acquired enamel pellicle, have been carried out in solution and upon binding to two enamel prototypes, hydroxyapatite (HA) and carbonated hydroxyapatite (CHA), using Fourier transform infrared spectroscopy (FTIR) in attenuated total reflection (ATR) mode. We have shown for the first time that, in solution, large portions of PRP1 adopt the hydrated polyproline type II (PPII) helical structure in addition to the random coil structure, with the maximum absorbance of the amide I band around 1620 cm(-1). Upon binding to HA or CHA, the protein undergoes significant conformational changes, loosing a considerable portion of hydrated PPII and random coil domains with a shift in the maximum absorbance to 1666 cm(-1), indicating that a large fraction of the protein is composed of beta turns. A small fraction of PPII in a calcium-bound or anhydrous form (approximately 1642 cm(-1)) was also observed in the HA- and CHA-bound proteins, which could play a role in protein-mineral interactions. The conformational changes in PRP1 adsorbed on CHA and HA were similar in nature; however, these changes were greater in the protein bound to HA. Interestingly, these results are in agreement with protein adsorption data that show that less protein is adsorbed onto CHA than onto HA. Our results demonstrate that binding to apatitic mineral surfaces leads to major conformational changes in PRP1, which might reflect the expulsion of water and the formation of protein-mineral and/or protein-protein interactions in the adsorbed layer.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

The infrared absorption of amino acid side chains

Amino acid side chains play fundamental roles in stabilising protein structures and in catalysing enzymatic reactions. These fields are increasingly investigated by infrared spectroscopy at the molecular level. To help the interpretation of the spectra, a review of the infrared absorption of amino acid side chains in H(2)O and 2H(2)O is given. The spectral region of 2600-900cm(-1) is covered.

Reassessment of the random coil conformation: vibrational CD study of proline oligopeptides and related polypeptides

The "random coil" conformational problem is examined by comparison of vibrational CD (VCD) spectra of various polypeptide model systems with that of proline oligomers [(Pro)n] and poly(L-proline). VCD, ir and uv CD spectra of blocked L-proline oligopeptides [(Pro)n, n = 2-12] in different solvents are reported and compared to the spectra of poly(L-proline) II, poly(L-glutamic acid), and unblocked proline oligomers. Based on the chain-length dependence of the VCD and electronic CD (ECD) spectra of proline oligomers, it is established that VCD spectra are dominated by short-range interactions. The VCD of random coil model polypeptides is shown to be identical in shape but smaller in magnitude than poly(L-proline) II and of similar magnitude to that of (Pro)n (n = 3, 4). Based on the spectral evidence, it is concluded that the "random coil" conformation has a large fraction of helical regions, conformationally similar to the left-handed, 3(1) polyproline II helix, as was previously suggested by Krimm and co-workers. This conclusion is further supported by studies of effects of salt (CaCl2, LiBr, LiClO4), temperature (5-75 degrees C), and pH on the VCD spectra of L-proline oligomers, poly(L-proline) II, and poly(L-glutamic acid). These show that, after each of these perturbations, a significant local ordering remains in the oligomers and polymers studied, and that charged polypeptides such as poly(L-glutamic acid) are more flexible than are polyproline or even L-proline oligomers.

Vibrational circular dichroism spectra of unblocked proline oligomers

Vibrational Circular Dichroism (VCD) spectra of unblocked L-proline oligopeptides, (Pro)n n = 3 to 7, dissolved in D2O are reported. For these oligomers, the VCD spectra can be attributed to a conformational dominance of the trans amide conformation with subunits interrelated by a left-handed twist, particularly for the longer oligomers. As a function of oligomer length, formation of this conformation starts at n = 3; and by n = 5 a spectrum closely resembling that of the poly-L-proline II helix in shape and magnitude is seen. The VCD data are compared with previous (Pro)n results using IR, CD, Raman and NMR spectroscopies, and reasons for the variations in interpretation are discussed.

Transformation of the structure of collagen. A time-resolved analysis of mechanochemical processes using synchrotron radiation

Mechanochemically induced molecular transformations of collagen fibres were analysed using time-resolved small-angle diffraction spectra and histomechanical measurements. In particular, the influence of aqueous and methanolic perchlorate solutions was examined. According to a transformation continuing from the periphery towards the centre, the macroscopic contraction that is completed less than five minutes after incubation with perchlorate is caused by peripherally transformed fibrils only, whereas the centrally situated fibrils first undergo an accordion-like folding, but after more than 20 minutes are transformed similarly. The triple-helical transformation is preceded by a structure-breaking effect on structural water that can be monitored in time-resolved diffraction spectra. The combined loss of meridional low-angle reflections and cross-striated fibrils in micrographs is irreversible. By dialysis of colloidally dissolved collagen against a solution of ATP, however, segment-long spacing aggregates are obtained. Under isometric conditions, an instantaneous transformation of intermittent regions leads to an increase in the long period of adjacent, still structured regions of the same fibril that is correlated with a delayed increase in tension in the fibre. Increase of tension under isometric conditions as well as the flow-properties of a fibre relaxed in perchlorate are interpreted in terms of the parallel sliding of subunits of varying lengths, which has been demonstrated by diffraction analysis.

Spectroscopic study of the conformations of proline-containing oligopeptides in the crystalline state and in solution

A conformational study has been carried out on a series of linear proline-containing oligopeptides (ZGP, ZGPL, ZGPLG and ZGPLGP) in both the crystalline state and in DMSO-d6 solution, using Raman and n.m.r. spectroscopy. The amide I and III bands in the Raman spectra of the crystalline forms indicate the presence of the type I beta-bend conformation in ZGPLG and ZGPLGP, but not in ZGP and ZGPL. This result is in agreement with X-ray data on these molecules. The Raman spectra of these peptides in solution indicate that more than one conformation is present, i.e. that the beta-bend structure of the solid form of ZGPLG and ZGPLGP is destabilized by DMSO-d6. 13C and 1H n.m.r. data also demonstrate the presence of more than one conformation in ZGP, ZGPL, ZGPLG and ZGPLGP in DMSO-d6 solution. These isomers differ in their conformation (cis and trans) about their Gly-Pro peptide bonds and possibly about the c alpha-C' bond of the C-terminal proline in ZGPLGP. For ZGP, ZGPL, ZGPLG and ZGPLGP, the ensemble of conformations in DMSO-d6 includes C5 and C7 hydrogen-bonded rings; in addition, ZGPLGP may contain a small percentage of a beta-bend conformation (at Pro2-Leu3) with trans peptides in both Gly-Pro moieties.