Optical activity of polypeptides in the infrared. Predicted CD of the amide I and amide II bands.

The Miyazawa-Blout-Krimm (M-B-K) treatment of polypeptide absorption in the infrared is extended to the calculation of circular dichroism (CD), linear dichroism, and oriented CD for the amide I and amide II transitions. Matrix methods are applied to the α helix and β structures using measured values for the strengths and directions of the transition dipole moments and empirical values from M-B-K for the coupling constants. Relatively small aggregates, a 36-residue helix, and 8-chain × 4-residue β sheets, are large enough to show calculated absorption agreeing with M-B-K results, which are based on infinite lattices. In all cases the predicted CD is an approximately conservative couple. The strongest CD should appear in the α helix, Δε/ε ?± 10^?3 for both transitions. The amide II transition should show moderate CD couples in both β structures, Δε/ε ? (+2 to ?1) × 10^?4. The amide I transitions in β structures should show weak CD couples, Δε/ε = (+3 to ?2) × 10^?5, except that the negative branch in the antiparallel structure may be detectable (Δε/ε ? ?2 × 10^?4) because absorption is very low at its wavelength peak. CD on oriented samples should be enhanced over the unoriented cases, giving values as large as Δε/ε = 3 × 10^?3 because particular directions of observation allow the light to avoid much of the absorption in the sample. If all three structures are considered as helices, then the larger distance of the transition dipoles from the axis in the α helix, and the orientations of the transitions in the different structures, are the factors that, in terms of our previous theoretical work [Snir and Schellman (1973) J. Phys. Chem. 77 , 1653] satisfactorily explain the calculated results. Simple dipole–dipole interaction is calculated to make a substantial contribution to the coupling between groups.     

Intensities and other spectral parameters of infrared amide bands of polypeptides in the alpha-helical form

Intensities and other spectral parameters of infrared amide I and II bands of α-helical polypeptides in solutions have been determined for poly(γ-benzylglutamate), poly(γ-ethylglutamate), and polymethionine in chloroform, polylysine, poly(glutamic acid), and fibrillar protein tropomyosin from rabbit muscles in heavy water. The majority of spectral parameters are characteristic. The half-width of the amide I band was found to vary in the range of 15–40 cm^?1 for different polypeptides in the different solutions. The correlation between this parameter of the amide I band and the stability of the α-helix was estimated. A new weak band near 1537 cm^?1 of unknown origin was observed for the hydrogen form of polypeptides in the α-helical state.     

Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods

A method for estimating protein secondary structure from infrared spectra has been developed. The infrared spectra of H2O solutions of 13 proteins of known crystal structure have been recorded and corrected for the spectral contribution of water in the amide I and II region by using the algorithm of Dousseau et al. [Dousseau, F., Therrien, M., & Pézolet, M. (1989) Appl. Spectrosc. 43, 538-542]. This calibration set of proteins has been analyzed by using either a classical least-squares (CLS) method or the partial least-squares (PLS) method. The pure-structure spectra calculated by the classical least-squares method are in good agreement with spectra of poly(L-lysine) in the alpha-helix, beta-sheet, and undefined conformations. The results show that the best agreement between the secondary structure determined by X-ray crystallography and that predicted by infrared spectroscopy is obtained when both the amide I and II bands are used to generate the calibration set, when the PLS method is used, and when it is assumed that the secondary structure of proteins is composed of only four types of structure: ordered and disordered alpha-helices, beta-sheet, and undefined conformation. Attempts to include turns in the secondary structure estimation have led to a loss of accuracy. The standard deviation of the difference between X-ray and infrared secondary structure estimates with this method is 4.8% for the alpha-helix, 3.7% for the beta-sheet, and 5.1% for the undefined structure, whereas the regression coefficients are 0.95, 0.96, and 0.56, respectively. The spectra of the calibration proteins were also recorded in 2H2O solution.(ABSTRACT TRUNCATED AT 250 WORDS)     

Intensities and other spectral parameters of infrared amide bands of polypeptides in the β- and random forms

The intensities and other spectral parameters of the main components of infrared amide bands for the random and anti-parallel pleated sheet forms have been determined for poly-S-carbobenzoxymethylcysteine, poly-S-carboxymethylcysteine, polylysine and silk fibroin of Bombyx mori in heavy water solutions and in organic solvents. Assuming that the optical spectra of these two types of structure are additive, the method was proposed for determining relative contents and molar absorption coefficients of amide I band. Integral intensity and maximum frequency values of the main components of the amide I band for all the samples in the β-form turned out to be specific. In contrast to this the integral intensity of the band of amide I in the random coil form varied within certain limits, while the main maximum frequency for all samples remained the same.     

Computer analyses of characteristic infrared bands of globular proteins.

Infrared spectra of myoglobin, ribonuclease, lysozyme, α-chymotrypsin, α-lactalbumin, and β-lactoglobulin A were obtained in deuterium oxide solution in units of absorbance versus wavenumber from 1340 to 1750 cm^?1. The spectra were resolved into Gaussian components by means of an iterative computer program. Resolved characteristic absorption peaks for the two infrared active amide I′ components of antiparallel chain-pleated sheets (β-structure) were obtained. The characteristic amide I′ peaks of α-helical regions and apparently unordered regions overlap in D₂O solution. Absorptivity values for the resolved β-structure peak around 1630 cm^?1 were estimated on the basis of the known structure of ribonuclease, lysozyme, and β-chymotrypsin. The β-structure content of β-lactoglobulin was estimated to be ca. 48% of α-lactalbumin ca. 18%, and of α_s-casein close to zero. The results are in general agreement with conclusions drawn from circular dichroism and optical rotatory dispersion studies.     

Infrared spectra of erythrocyte shadows in the region of the amide I and amide II bands following microwave irradiation]

No beta-structures of protein molecules were observed by IR-spectra of intact erythrocyte shadows. Ultra high frequency irradiation in the range of 1009 mHz intensity of 45 mW/cm3 results in small conformational reconstructions of molecules in the membrane, but it does not induce a notable transition of alpha-helix or coil into beta-structure. A decrease of the intensity of lipid band by 1740 cm-1 is shown up at the spectra. Deuterium exchange for 36--38 min shows that the transition of the band amide II near 1540 cm-1 into the band 1450 cm-1 proceeds faster under UHF irradiation than in the control. The effects observed are in a direct relation-ship with the intensity of UHF-field and disappear at the intensities of 5--8 mW/cm3 and lower.     

Protein secondary structures in water from second-derivative amide I infrared spectra

Infrared spectra have been obtained for 12 globular proteins in aqueous solution at 20 degrees C. The proteins studied, which vary widely in the relative amounts of different secondary structures present, include myoglobin, hemoglobin, immunoglobulin G, concanavalin A, lysozyme, cytochrome c, alpha-chymotrypsin, trypsin, ribonuclease A, alcohol dehydrogenase, beta 2-microglobulin, and human class I major histocompatibility complex antigen A2. Criteria for evaluating how successfully the spectra due to liquid and gaseous water are subtracted from the observed spectrum in the amide I region were developed. Comparisons of second-derivative amide I spectra with available crystal structure data provide both qualitative and quantitative support for assignments of infrared bands to secondary structures. Band frequency assignments assigned to alpha-helix, beta-sheet, unordered, and turn structures are highly consistent among all proteins and agree closely with predictions from theory. alpha-Helix and unordered structures can each be assigned to only one band whereas multiple bands are associated with beta-sheets and turns. These findings demonstrate a method of analysis of second-derivative amide I spectra whereby the frequencies of bands due to different secondary structures can be obtained. Furthermore, the band intensities obtained provide a useful method for estimating the relative amounts of different structures.     

Light-scattering and infrared-spectrophotometric studies of chitin and chitin derivatives

A sample of chitin isolated from the shell of the crab Scylla serrata had, when in lithium thiocyanate solution, an average, weight-average molecular weight (1) of 1.036 x 10⁶ daltons, an intrinsic dissymmetry (2) of 1.93, and a Z-average radius of gyration (3) of 64.14 nm. Carboxymethylchitin and glycol chitin, in 0.5M sodium chloride, had, respectively, (1) 1.896 and 1.819 x 10⁶ daltons, (2) 3.25 and 4.31. and (3) 143.49 and 251.57 nm. They had similar degrees of polymerization, they underwent dissociation as the concentration of sodium chloride was increased to 2.5M, and the molecular packing of the chains was essentially side-by-side. Chitin in 5.55M lithium thiocyanate and carboxymethylchitin in 2.5M sodium chloride had similar degrees of polymerization. It is concluded that a small but significient number of the amino groups in the chitin molecule are not acetylated.     

Electrostatic calculations for assignment of infrared difference bands to carboxyl groups getting protonated during protein reactions

Fourier transform infrared (FTIR) difference spectroscopy is predestined to monitor the protonation of carboxyl groups during protein reactions, making glutamic and aspartic amino acids unique to follow proton pathways. The absorption of the corresponding vibrations are clearly distinguishable from the absorption of other amino acids. However, the assignment to specific groups within the protein needs additional information, e.g., from induced spectral changes due to isotopic labeling or mutation. Here, the capability of electrostatic calculations to assign IR difference bands to specific carboxyl groups getting protonated is demonstrated by the ion pump mechanism of the sarcoplasmic reticulum Ca(2+)-ATPase. Active Ca(2+) transport is coupled to the hydrolysis of ATP. Two Ca(2+) ions are transported per ATP hydrolysed and two or three H(+) ions are countertransported. FTIR difference spectra show that during the Ca(2+) release step, carboxyl groups become protonated. Multiconformation continuum electrostatic calculations (MCCE) have been carried out to determine the equilibrium distribution of residue ionization and side chain conformation in dependence of pH. Available structural X-ray data from the calcium-bound and the calcium-free state allows us to simulate the transition between the two states monitored in the IR difference spectra. Exemplarily for Asp 800, ligand of both calcium ions, it is shown that MCCE calculations can identify this specific Asp to contribute to the IR bands and therefore to take part in the proton countertransport of the Ca(2+)-ATPase. In addition, an energy analysis can be performed to understand what interactions shift the pK(a).     

Shrimp chitin as substrate for fungal chitin deacetylase

The fungal chitin deacetylases (CDA) studied so far are able to perform heterogeneous enzymatic deacetylation on their solid substrate, but only to a limited extent. Kinetic data show that about 5-10% of the N-acetyl glucosamine residues are deacetylated rapidly. Thereafter enzymatic deacetylation is slow. In this study, chitin was exposed to various physical and chemical conditions such as heating, sonicating, grinding, derivatization and interaction with saccharides and presented as a substrate to the CDA of the fungus Absidia coerulea. None of these treatments of the substrate resulted in a more efficient enzymatic deacetylation. Dissolution of chitin in specific solvents followed by fast precipitation by changing the composition of the solvent was not successful either in making microparticles that would be more accessible to the enzyme. However, by treating chitin in this way, a decrystallized chitin with a very small particle size called superfine (SF) chitin could be obtained. This SF chitin, pretreated with 18% formic acid, appeared to be a good substrate for fungal deacetylase. This was confirmed both by enzyme-dependent deacetylation measured by acetate production as well as by isolation and assay for the degree of deacetylation (DD). In this way chitin (10% DD) was deacetylated by the enzyme into chitosan with DD of 90%. The formic acid treatment reduced the molecular weight of the polymeric chain from 2x10(5) in chitin to 1.2 x 10(4) in the chitosan product. It is concluded that nearly complete enzymatic deacetylation has been demonstrated for low-molecular chitin.     

TEMPO-mediated oxidation of chitin, regenerated chitin and N-acetylated chitosan

A commercial chitin, regenerated chitin prepared from chitin solutions in 6.8% NaOH and N-acetylated chitosans with degrees of N-acetylation (DNAc) of 77–93% were subjected to oxidization in water with NaClO and catalytic amounts of 2,2,6,6-tetramethylpiperidinyloxy radical (TEMPO) and NaBr. When regenerated chitin with DNAc of 87% and N-acetylated chitosan with DNAc of 93% were used as starting materials, water-soluble β-1,4-linked poly-N-acetylglucosaminuronic acid (chitouronic acid) Na salts with degrees of polymerization of ca. 300 were obtained quantitatively within 70 min. On the other hand, the original chitin and N-acetylated chitosan with DNAc of 77% did not give water-soluble products, owing to incomplete oxidation. The high crystallinity of the original chitin brought about low reactivity, and the high C2-amino group content of the N-acetylated chitosan with DNAc of 77% led to degradations rather than the selective oxidation at the C6 hydroxyls. The obtained chitouronic acid had low viscosities in water, and clear biodegradability by soil microorganisms.     

Studies on chitin. 2. Preparation and properties of chitin membranes

A chitin membrane was prepared by a new procedure involving coagulation of the chitin solution in N,N-dimethyl acetamide, N-methyl 2-pyrrolidone and lithium chloride (DMA-NMP-LiCl) with 2-propanol. The solute permeability, water sorption and mechanical properties were compared with membranes prepared by two previously reported methods (coagulation of a formic acid and dichloroacetic acid (FA-DCA) solution of chitin with 2-propanol; and coagulation of a trichloroacetic acid and dichloroethane (TCA-DCE) solution of chitin with acetone). The permeability coefficients of the three chitin membranes were higher than a regenerated cellulose membrane (Cuprophane®). The membrane prepared from DMA-NMP-LiCl solution had a higher tensile strength (3·3 Mpa) in the wet state than the others. The membrane obtained from TCA-DCE solution absorbed more water (360%) and the membrane prepared from FA-DCA solution was relatively weak (1·8 MPa) in the wet state. It was suggested that 2-propanol was a favourable coagulant for membrane production. In addition, the effect of the origin of chitin on molecular weight and tensile properties of the membranes was studied.     

Photoreduction of the quinone pool in the bacterial photosynthetic membrane: identification of infrared marker bands for quinol formation

The photoreduction of the quinone (Q) pool in the photosynthetic membrane of the purple bacterium Rhodobacter sphaeroides was investigated by steady-state and time-resolved Fourier transform infrared difference spectroscopy. The results are consistent with the existence of a homogeneous Q pool inside the chromatophore membrane, with a size of around 20 Q molecules per reaction center. IR marker bands for the quinone/quinol (Q/QH(2)) redox couple were recognized. QH(2) bands are identified at 1491, 1470, 1433 and 1388-1375 cm(-1). The 1491 cm(-1) band, which is sensitive to (1)H/(2)H exchange, is assigned to a C-C ring mode coupled to a C-OH mode. A feature at approximately 1743/1720 cm(-1) is tentatively related to a perturbation of the carbonyl modes of phospholipid head groups induced by QH(2) formation. Complex conformational changes of the protein in the amide I and II spectral ranges are also apparent during reduction and reoxidation of the Q pool.     

Generation of reactive oxygen species in water under exposure to visible or infrared irradiation at absorption bands of molecular oxygen

It is found that in bidistilled water saturated with oxygen, hydrogen peroxide and hydroxyl radicals are formed under the influence of visible and infrared radiation in the absorption bands of molecular oxygen. Formation of reactive oxygen species (ROS) occurs under the influence of both solar and artificial light sources, including the coherent laser irradiation. The oxygen effect, i.e. the impact of dissolved oxygen concentration on production of hydrogen peroxide induced by light, is detected. It is shown that the visible and infrared radiation in the absorption bands of molecular oxygen leads to the formation of 8-oxoguanine in DNA in vitro. Physicochemical mechanisms of ROS formation in water when exposed to visible and infrared light are studied, and the involvement of singlet oxygen and superoxide anion radicals in this process is shown.     

Effect of protein side chain amide group on the hydrogen-bond equilibrium in nucleobases studied by infrared and 13C-NMR spectroscopy

Infrared spectra of 1:1 hydrogen-bonded complexes formed by derivatives of adenine and model molecules bearing the protein side chain amide group have been measured in chloroform solution. From the temperature dependence of hydrogen-bond formation, thermodynamic data on these complexes are determined. On the basis of these data, it is shown that the complexes consist of cyclic heterodimers, those that use the adenine N(1)H bond being favoured. Similarly infrared and 13C-NMR spectroscopy reveals that uracil-amide cyclic heterodimers formed through the uracil 4-carbonyl group are predominant. All of these results predict that Watson-Crick hydrogen bonds in adenine-uracil base-pairs may be opened to some extent, as proved in this work. The possible biological importance of these observations is also discussed.