Vibrational circular dichroism in amino acids and peptides. 7. Amide stretching vibrations in polypeptides

Vibrational circular dichroism (VCD) spectra for the principal amide stretching vibrations, amide A (N? H stretch) and amide I (predominantly C?O stretch), are presented and analyzed for a variety of polypeptides dissolved in chloroform, as well as for two examples in D₂O. Our results for poly(γ-benzyl-L -glutamate) confirm the first and only previous report of VCD in polypeptides carried out by Singh and Keiderling [(1981) Biopolymers 20 , 237–240]. Collectively, our spectra show that the sense of the bisignate VCD in these two regions depends on the sense of α-helicity and not on the absolute configuration of the constituent amino acids. This conclusion is established by obtaining VCD for the two polypeptides, poly(β-benzyl-L -asparate) and poly(im-benzyl-L -histidine), that form left-handed as opposed to right-handed α-helices. A new amide band having significant VCD intensity owing to its Fermi resonance interaction with the N? H stretching mode has been identified as a weak shoulder on the low-frequency side of the amide A band near 3200 cm^?1 and is assigned as a combination band of the amide I and amide II vibrations. VCD spectra of polypeptides in D₂O solution, although weak, have been successfully measured in the amide I region, where spectra appear to be more complicated due to the presence of solvated and internally hydrogen-bonded amide groups. Strong monosignate contributions to the VCD in the amide A and amide I regions for some of the polypeptides indicate coupling of an electronic nature between these two regions and is deduced by an application of the concept of local sum rules of rotational strength. It appears that a detailed understanding of the VCD obtained for polypeptides will not only be diagnostic of secondary structure, but also of more subtle structural and vibrational effects that give rise to local, intrinsic chirality in the amide vibrations.     

Vibrational analysis of peptides,polypeptides, and proteins. II. β-Poly(L-alanine) and β-poly(L-alanylglycine)

The normal vibration frequencies of poly(L -alanine) and poly(L -alanylglycine) in the antiparallel chain-pleated sheet structure have been calculated, using the force field for polyglycine I from the previous paper (Biopolymers 15 , 2439–2464) plus additional force constants for the methyl group. The agreement with observed ir and Raman bands is very good. This substantiates the excellent transferability of the force field, since polyglycine I was shown to have a rippled-sheet structure. The amide I and amide II mode splittings are very well accounted for by transition dipole coupling, showing that subtle structural differences are sensitively manifested through this mechanism.     

Vibrational analysis of peptides,polypeptides, and proteins. XVIII. Conformational sensitivity of the α-helix spectrum: αI- and αII-Poly(L-alanine)

The α_II-helix (? = ?70.47°, ψ = ?35.75°) is a structure having the same n and h as the (standard) α_I-helix (? = ?57.37°, ψ = ?47.49°). Its conformational angles are commonly found in proteins. Using an improved α-helix force field, we have compared the vibrational frequencies of these two structures. Despite the small conformational differences, there are significant predicted differences in frequencies, particularly in the amide A, amide I, and amide II bands, and in the conformation-sensitive region below 900 cm^?1. This analysis indicates that α_II-helices are likely to be present in bacteriorhodopsin [Krimm, S. & Dwivedi, A. M. (1982) Science 216 , 407–408].     

Ab initio-based vibrational analysis of α-poly(L-alanine)

Polarized ir and Raman spectra have been obtained on oriented films of α-helical poly(L -alanine) (α-PLA) and its N-deuterated derivative. These improved spectra permit a more complete assignment of observed bands to A-, E₁-, and E₂-species modes. A new empirical force field has been refined, based on ab initio force fields of N-methylacetamide and L -alanyl-L -alanine, which reproduces observed frequencies above 200 cm⁻¹ to less than 5 cm⁻¹. A new transition dipole coupling treatment avoids the weak coupling and perturbation approximations, and can now account for the newly observed and reassigned amide I (E₂) mode. As a result of this improved force field, several other observed bands have also been reassigned. © 1998 John Wiley & Sons, Inc. Biopoly 46: 283–317, 1998     

Comparative analysis of the amino- and carboxy-terminal domains of calmodulin by Fourier transform infrared spectroscopy

Fourier transform infrared spectra were obtained for mammalian calmodulin and two of its fragments produced by limited proteolysis with trypsin TR₁C (1–77) and TR₂C (78–148). Experiments were done in H₂O, D₂O and D₂O/trifluoroethanol (TFE) mixtures. Information about secondary structure was obtained from analysis of the amide I and II bands; while characteristic absorbances for tyrosine, phenylalanine and carboxylate groups were analyzed for changes in tertiary structure. Our data indicate that the secondary and tertiary structure is preserved in the two half molecules of CaM, both in the apo- and Ca²⁺-saturated state. Addition of the structure-inducing solvent TFE causes marked changes only in the apo-TR₁C domain. The maximum wavenumber for the amide I band of the two domains of CaM in D20 was markedly different (1642 cm^–1 for TR₁C versus 1646/1648 cm^–1 for Ca ²⁺ and apo-TR₂C). This renders the amide I band for the intact protein very broad in comparison to that in other proteins and is indicative of a distribution of -helices with slightly different hydrogen bonding patterns.     

Origin of enhanced VCD in amyloid fibril spectra: Effect of deuteriation and pH

Supramolecular chirality of amyloid fibrils, protein aggregates related to many neurodegenerative diseases, is a remarkable property associated with fibril structure and polymorphism. Since its discovery almost 10 years ago there is still little understanding of this phenomenon, including the cause of the highly enhanced vibrational circular dichroism (VCD) intensity arising from fibril supramolecular chirality. In this study, VCD spectra, enhanced by filament supramolecular chirality, are presented for lysozyme and insulin fibrils above and below pH 2 and after deuterium exchange, above and below pD 2. Supramolecular chirality (observed by VCD) and fibril morphology (documented by atomic force microscopy) are not affected by protein deuteriation. In D₂O the fibril VCD sign pattern changes to fewer bands, with implications for the amide I/II origin of enhanced VCD intensity. Separation of amide I and II signals will facilitate calculations of enhanced VCD spectra of amyloid fibrils and enable a better understanding of the origin of the VCD sign pattern.     

Predicting ecosystem carbon balance in a warming Arctic: the importance of long‐term thermal acclimation potential and inhibitory effects of light on respiration

The carbon balance of Arctic ecosystems is particularly sensitive to global environmental change. Leaf respiration (R), a temperature‐dependent key process in determining the carbon balance, is not well‐understood in Arctic plants. The potential for plants to acclimate to warmer conditions could strongly impact future global carbon balance. Two key unanswered questions are (1) whether short‐term temperature responses can predict long‐term respiratory responses to growth in elevated temperatures and (2) to what extent the constant daylight conditions of the Arctic growing season inhibit leaf respiration. In two dominant Arctic species E riophorum vaginatum (tussock grass) and B etula nana (woody shrub), we assessed the extent of respiratory inhibition in the light (R _L/R _D), respiratory response to short‐term temperature change, and respiratory acclimation to long‐term warming treatments. We found that R of both species is strongly inhibited by light (averaging 35% across all measurement temperatures). In E . vaginatum both R _L and R _D acclimated to the long‐term warming treatment, reducing the magnitude of respiratory response relative to the short‐term response to temperature increase. In B . nana, both R _L and R _D responded to short‐term temperature increase but showed no acclimation to the long‐term warming. The ability to predict plant respiratory response to global warming with short‐term temperature responses will depend on species‐specific acclimation potential and the differential response of R _L and R _D to temperature. With projected woody shrub encroachment in Arctic tundra and continued warming, changing species dominance between these two functional groups, may impact ecosystem respiratory response and carbon balance.     

FTIR-monitored thermal titration reveals different mechanisms for the alkaline isomerization of tuna compared to horse and bovine cytochromes c

 Fourier transform infrared (FTIR) spectroscopy is used to compare the thermally induced conformational changes in horse, bovine and tuna ferricytochromes c in 50 mM phosphate/0.2 M KCl. Thermal titration in D₂O at pD 7.0 of the amide II intensity of the buried peptide NH protons reveals tertiary structural transitions at 54  °C in horse and at 57  °C in bovine c. These transitions, which occur well before loss of secondary structure, are associated with the alkaline isomerization involving Met80 heme-ligand exchange. In tuna c, the amide-II-monitored alkaline isomerization occurs at 35  °C, followed by a second amide II transition at 50  °C revealing a hitherto unreported conformational change in this cytochrome. Amide II transitions at 50  °C (tuna) and 54  °C (horse) are also observed during the thermal titration of the CN^–-ligated cytochromes (where CN^– displaces the Met80 ligand), but a well-defined 35  °C amide II transition is absent from the titration curve of the CN^–adduct of tuna c. The different mechanisms suggested by the FTIR data for the alkaline isomerization of tuna and the mammalian cytochromes c are discussed. After the alkaline isomerization, loss of secondary structure and protein aggregation occur within a 5  °C range with T _m values at 74  °C (bovine c), 70  °C (horse c) and 65  °C (tuna c), as monitored by changes in the amide I′ bands. The FTIR spectra were also used to compare the secondary structures of the ferricytochromes c at 25  °C. Curve fitting of the amide I (H₂O) and amide I′ (D₂O) bands reveals essentially identical secondary structure in horse and bovine c, whereas splitting of the α-helical absorption of tuna c indicates the presence of less-stable helical structures. CN^– adduct formation results in no FTIR-detectable changes in the secondary structures of either tuna or horse c, indicating that Met80 ligation does not influence the secondary structural elements in these cytochromes. The data provided here demonstrate for the first time that the selective thermal titration of the amide II intensity of buried peptide NH protons in D₂O is a powerful tool in protein conformational analysis. Received: 1 April 1999 / Accepted: 24 August 1999     

Purification,characterization, gene cloning and nucleotide sequencing of D-stereospecific amino acid amidase from soil bacterium: Delftia acidovorans

The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40°C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45°C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd²⁺, Ag⁺, Zn²⁺, Hg²⁺ and As³⁺ . The NH₂ terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.

     

Conformational study of linear alternating and mixed D- and L-proline oligomers using electronic and vibrational CD and fourier transform IR

Vibrational CD (VCD) spectra of a series of blocked linear, alternating D - and L -proline containing oligopeptides, dissolved in D₂O and in CDCl₃. are reported. For the Boc-LDL -Pro₃ to Boc-DLDLDLDL-Pro₈ oligomers. The VCD spectra in the amide I band is a positive couplet, opposite in sense to that obtained for (L -Pro)_n oligomers. While this admits the possibility of their favoring a right-handed helical chain conformation, the amide I ir spectra for these dl oligomers in D₂O indicate a mixed, apparently alternate, cis-trans conformation that prevents a simple conclusion. Their VCD in D₂O evidence no narrowing and has a progressive loss in intensity (measured as Δ /A,) with an increase in chain length. In CDCl₃a similar pattern of positive VCD couplets decreasing in intensity with length was seen, but their spectra are narrower. Their electronic CD (ECD) in the uv, also indicates a loss in intensity with increasing length. Oligomers with odd or even numbers of Pro residues have different ECD patterns, indicating that those spectra are strongly influenced by local contributions arising in the N-terminal groups. The VCD arises from dipolar and vibrational coupling of the amides in the helical structure. All the spectra are consistent with the chiral end groups leading to formation of an excess of one helical handedness. With an increase in length, the influence of this selectiveness is less and the overall CD measured decreases. © 1995 John Wiley & Sons, Inc.     

Reductive methylation andpKa determination of the lysine side chains in calbindin D9k

The Lys residues in the 75-residue Ca²⁺-binding protein calbindin D_9k were reductively methylated with¹³C-enriched formaldehyde. The possible structural effects resulting from the chemical modification were critically investigated by comparing two-dimensional NMR spectra and the exchange rates of some of the amide protons of the native and the modified protein. Our results show that the protein retains its structure even though 10 Lys out of a total of 75 amino acid residues were modified. In the Ca²⁺- and apo-forms of the protein, the¹³C-methylated Lys residues can be detected with high sensitivity and resolution using two-dimensional (¹H,¹³C)-heteronuclear multiple quantum coherence (HMQC) NMR spectroscopy. ThepKa values of the individual Lys residues in Ca²⁺-calbindin D_9k and apo-calbindin D_9k were obtained by combiningpH titration experiments and (¹H,¹³C)-HMQC NMR spectroscopy. Each Lys residue in the Ca²⁺- and apo-forms of calbindin D_9k has a uniquepKa value. The LyspKa values in the calcium protein range from 9.3 to 10.9, while those in the apo-protein vary between 9.7 and 10.7. Although apo-calbindin D_9k has a very similar structure compared to Ca²⁺-calbindin D_9k, the removal of two Ca²⁺ ions from the protein leads to an increase of thepKa values of the Lys residues.     

Quasielastic light scattering from solutions of lollipop-shaped particles

An expression is derived for the field correlation function of the light scattered from a solution of lollipop-shaped particles. Such particles are a tractable model of certain bacteriophages. They are assumed to consist of an ellipsoidal head containing optically anisotropic scattering material and a tail which does not scatter. Because of the tail, Brownian rotational movement occurs around a center of rotational friction which is at a distance r₀ from the center of the head. The dependence of the field correlation function C(τ) on the rotational diffusion coefficient D_R is given by the factor Σ_lB_l exp[?l(l + 1)D_Rτ]. It is shown that the tail causes the coefficients B_l to be different from zero for all values of l. Therefore, C(τ) contains a term proportional to exp(?2D_Rτ), which is not present when r₀ = 0. We give plots of B_l for various combinations of parameters. It turns out that dynamic light scattering may be used to measure r₀.     

Proton magnetic resonance studies on dermorphin and its peptide fragments

Dermorphin (Tyr? D-Ala? Phe? Gly? Tyr? Pro? Ser? NH₂), a potent natural peptide opioid, its synthetic L-Ala² analog, and all the N fragments from the tripeptide (Tyr? D -Ala? Phe? NH₂) to the parent hexapeptide amide were characterized for the first time by means of proton nmr spectroscopy at 11.74 T. Assignments of most protons of dermorphin were facilitated by the study of the N-terminal fragments. Comparison of spectroscopic parameters with relative pharmacological activity is proposed as a possible means of studying flexible agonists in solution.     

Structure of the O-polysaccharide from the lipopolysaccharide of Providencia alcalifaciens O60

An O-polysaccharide (O-antigen) was isolated by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O60 and studied by sugar and methylation analyses as well as ¹H and ¹³C NMR spectroscopy, including 2D ROESY and ¹H,¹³C HMBC experiments in D₂O and a ROESY experiment in a 9:1 H₂O–D₂O mixture to reveal correlations for NH protons. It was found that the polysaccharide is built up of linear pentasaccharide repeating units containing an amide of d-glucuronic acid with l-serine and has the following structure:The O-antigen studied is structurally and serologically closely related to the O-antigen of Proteus vulgaris O44.     

Raman study of crystalline peptides containing beta turns

The Raman spectra of crystalline H-ProLeuGlyNH₂ which has a type II β turn, crystalline S-benzylCysProLeuGlyNH₂ which has a type I β-turn, and crystalline gramicidin S which has two β turns and β-sheet structure in its conformation, were investigated. The amide I and amide III bands of the peptides with β turns were generally different from those which are diagnostic for α-helix and β-sheet conformations. The patterns of the amide I and amide III bands, when examined together, indicate that Raman spectra can provide diagnostic evidence for β-turn structure in peptides.     

Quantification of heparin's antimetastatic effect by single‐cell force spectroscopy

In circulation, cancer cells induce platelet activation, leading to the formation of a cancer cell‐encircling platelet cloak which facilitates each step of the metastatic cascade. Since cancer patients treated with the anticoagulant heparin showed reduced metastasis rates and improved survival, it is supposed that heparin suppresses the cloak's formation by inhibiting the interaction between platelet's adhesion molecule P‐selectin with its ligands on cancer cells. To quantify this heparin effect, we developed a single‐cell force spectroscopy approach and quantified the adhesion (maximum adhesion force [F_A] and detachment work [W_D]) between platelets and human non‐small cell lung cancer cells (A549). A configuration was used in which A549 cells were glued to tipless cantilevers and force‐distance (F‐D) curves were recorded on a layer of activated platelets. The concentration‐response relationship was determined for heparin at concentrations between 1 and 100 U/mL. Sigmoid dose‐response fit revealed half‐maximal inhibitory concentration (IC₅₀) values of 8.01 U/mL (F_A) and 6.46 U/mL (W_D) and a maximum decrease of the adhesion by 37.5% (F_A) and 38.42% (W_D). The effect of heparin on P‐selectin was tested using anti‐P‐selectin antibodies alone and in combination with heparin. Adding heparin after antibody treatment resulted in an additional reduction of 9.52% (F_A) and 7.12% (W_D). Together, we quantified heparin's antimetastatic effect and proved that it predominantly is related to the blockage of P‐selectin. Our approach represents a valuable method to investigate the adhesion of platelets to cancer cells and the efficiency of substances to block this interaction.     

Laser Raman studies of conformational variations of poly-L-lysine

The frequencies and intensities of the laser Raman spectra of poly-L -lysine (PLL) have been observed in the following studies: (1) the thermally induced α-to-β transition which occurs with increasing temperature at high pH; (2) the ionized form to α transition at 10°C by increasing pH; and (3) the ionized form to α transition by ionic strength at low pH. The frequency-dependent bands which have been observed are the amide I (in H₂O), amide I′ (in D₂O), amide III, and C–C stretch. It has been found possible to assign an unique set of frequencies and intensities to each conformation of PLL of α, β, and ionized form. In this way the nature of the conformations intermediate in the transitions can be determined. The frequencies of the amide III and amide III′ are very weak in the α-helix and somewhat higher than usual in the β form. Hence it appears the amide III and amide III′ bands may differ from one type of polypeptide to another with the same backbone conformation.     

VCD Robustness of the Amide‐I and Amide‐II Vibrational Modes of Small Peptide Models

The rotational strengths and the robustness values of amide‐I and amide‐II vibrational modes of For(AA)_nNHMe (where AA is Val, Asn, Asp, or Cys, n = 1–5 for Val and Asn; n = 1 for Asp and Cys) model peptides with α‐helix and β‐sheet backbone conformations were computed by density functional methods. The robustness results verify empirical rules drawn from experiments and from computed rotational strengths linking amide‐I and amide‐II patterns in the vibrational circular dichroism (VCD) spectra of peptides with their backbone structures. For peptides with at least three residues (n ≥ 3) these characteristic patterns from coupled amide vibrational modes have robust signatures. For shorter peptide models many vibrational modes are nonrobust, and the robust modes can be dependent on the residues or on their side chain conformations in addition to backbone conformations. These robust VCD bands, however, provide information for the detailed structural analysis of these smaller systems. Chirality 27:625–634, 2015 © 2015 Wiley Periodicals, Inc.     

A simple model of the relationship between asymmetry and developmental stability

The relationship between developmental stability and morphological asymmetry is derived under the standard view that structures on each side of an individual develop independently and are normally distributed. I use developmental variance of sizes of parts, V_D, as the converse of developmental stability, and assume that V_D follows a gamma distribution. Repeatability of asymmetry, a measure of how informative asymmetry is about V_D, is quite insensitive to the variance in V_D, for example only reaching 20% when the coefficient of variation of V_D is 100%. The coefficient of variation of asymmetry, CV_FA, also increases very slowly with increasing population variation in V_D. CV_FA values from empirical data are sometimes over 100%, implying that developmental stability is sometimes more variable than any previously studied type of trait. This result suggests that alternatives to this model may be needed.