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. XV. Crystalline polyglycine II

A force field has been refined for the 3₁-helix structure of polyglycine II, using the polyglycine I force field plus previous C^αH^α…?O force constants as a starting point. Besides force constants associated with the hydrogen bonds, which must change since the hydrogen-bond characteristics are different in the two structures, we have had to modify only 10 force constants from the polyglycine I force field to make it suitable for reproducing the polyglycine II frequencies. Most involve the NC^α bond, which is the torsion angle that changes from the I to the II structure. Calculations were done for parallel chain and antiparallel chain crystal structures of polyglycine II, the observed spectra being found to agree best with the latter structure. Since this provides strong evidence for the loss of strict threefold symmetry in the chain, our analysis strengthens the support for the existence of C^αH^α…?O hydrogen bonds in the structure of polyglycine II.     

Normal vibrations of crystalline polyglycine I

A valence force field has been refined for crystalline polyglycine I using its known antiparallel chain pleated-sheet structure and without replacing the CH₂ group by a point mass. Polyglycine I and four of its isotopic derivatives were used in the refinement. The calculated frequencies are in good agreement with the observed, except for the amide I modes. It is shown that this is a consequence of the fact that no reasonable force field predicts a large D₁₀ term of the Miyazawa perturbation treatment. The amide I splittings can, however, be satisfactorily accounted for by introducing a direct interaction force constant between adjacent C?O groups in neighboring chains. This can reasonably arise from transition dipole coupling and corresponds to the heretofore neglected D₁₁ term.     

Structure of polyglycine I: a comparison of the antiparallel pleated and antiparallel rippled sheets

Packing energy calculations are made for two possible sheet structures of polyglycine I, i.e. the antiparallel pleated and rippled sheets. They indicate that the rippled sheet is the more stable structure and that its calculated lattice parameters are close to those experimentally determined. Furthermore, the results on the packing of pleated sheets of polyglycine improve understanding of the well-known model of silk fibroin structure of Marsh et al. (1955). They also suggest that the sheet structures of l-polypeptides with short side-chains should pack in monoclinic unit cells rather than the orthorhombic ones which are observed. A possible origin of this discrepancy is discussed.     

Crystal structure of polyglycine I

An electron diffraction study has been made of oriented polyglycine I (the β modification of polyglycine) and of single crystals grown from solution. The unit cell is very similar to that postulated by Astbu?y (1949). It is monoclinic with parameters a = 9.54 Å, b(chainaxis) = 7.044 Å, c = 3.67 Å and β = 113°. Examination of the possible structures suggests that polyglycine I does not have the familiar antiparallel pleated sheet, but rather the closely related antiparallel rippled sheet structure first described by Pauling &; Corey (1953a).     

Determination of the secondary structure of proteins from the amide I band of the laser Raman spectrum

The amide I band in the laser Raman spectrum of proteins has been resolved into six components, each representing residues in a different type of secondary structure. These structure types are ordered or bihydrogen-bonded helix (believed to be located in the center of helical segments), disordered or monohydrogen-bonded helix (believed to be located at the ends of helical segments), antiparallel beta sheet, parallel beta sheet, reverse turn, and undefined. The Raman spectrum representing 100% of each type of residue conformation has been computed from the solvent-subtracted Raman spectra of ten proteins with known secondary structure, plus poly-l-lysine using a least-squares solution of the overdetermined system of equations. Linear combinations of these reference spectra were then fitted to the experimental amide I spectra of these and other proteins to estimate the fractions of residues in these conformations. Statistical tests suggest that the discrimination between bihydrogen-bonded helix and monohydrogen-bonded helix is significant as is the discrimination between parallel and antiparallel β-sheet. However, the discrimination between random structure and turns has not yet been accomplished by these studies. The absolute difference between X-ray and Raman estimates of structure for 17 protein samples is generally less than 6%. We conclude that detailed and reasonably accurate estimates of secondary structure can be derived from the amide I spectra of proteins.     

Normal vibrations of polyglycine II

A valence force field has been refined for single-chain polyglycine II using the known structure and four isotopic derivatives. The calculated frequencies are in good agreement with the observed. The force field is compared with that derived from polyglycine I and for the nylons.     

Normal mode spectrum of the parallel-chain β-sheet

Normal mode calculations have been carried out for parallel-chain β-sheet structures. These include the parallel-chain pleated sheet of poly(L -alanine) and the parallel-chain rippled sheet of polyglycine. Dipole derivative coupling has been included for amide I and II modes, and the effects of parallel-sheet and antiparallel-sheet arrangements of varying separation have been examined for the poly(L -alanine) case. Some amide and nonamide modes are distinctly different from their antiparallel-chain counterparts, thus providing a basis for distinguishing between such structures from their ir and Raman spectra. As in our previous studies, these results emphasize the need for both kinds of spectral data in order to draw definitive conclusions about conformation.     

Vibrational analysis of the structure of gramicidin A. I. Normal mode analysis.

Normal mode frequencies have been calculated for single-stranded beta 4.4 and beta 6.3 and for double-stranded increases decreases beta 5.6, increases decreases beta 7.2, increases increases beta 5.6, and increases increases beta 7.2 helices that are possible models for the structure of gramicidin A. The force field used in the calculations is one that reproduces the frequencies of model polypeptide chain structures to about +/- 5 cm-1, and is therefore expected to provide meaningful distinctions between these conformations. The calculations predict significant differences in the infrared and Raman spectra of these beta-helices, suggesting that they should be identifiable from their spectra (which is shown in the following paper to be the case). The most sensitive region is that of the amide I frequencies, where the predicted patterns of intense infrared mode, infrared splittings, and intense Raman mode provide a characteristic identification of each of the above structures.     

Infrared spectra of the Gramicidin A transmembrane channel: the single-stranded-beta 6-helix

IR spectra are reported for preparations of Gramicidin A and malonyl Gramicidin A incorporated as the channel state in phospholipid structures. In this preparation Gramicidin A has already been shown to be unequivocally in the single-stranded beta-helical conformation. The result is an amide I frequency of 1633 +/- 1 cm-1. This demonstrates that the single-stranded beta-helix has an amide I frequency that has previously been considered to be diagnostic of antiparallel double-stranded beta-helix and of beta-sheet structures.     

Infrared and Raman study in the solid state of fully protected,monodispersed homooligopeptides of L-valine,L-isoleucine,and L-phenylalanine

An ir-absorption and Raman-scattering study, in the solid state, has been carried out on monodispersed, N- and C-protected homooligopeptides (number of residues, n, from 2 to 7) of L -valine, L -isoleucine, and L -phenylalanine. The amide I, II, III, V, and vNH regions have been examined. Some deuterated (ND) samples have been examined to complete the assignments. L -Phenylalanine dipeptide displays spectral characteristics compatible with the parallel β-structure; L -isoleucine and L -valine dipeptides are probably in a distorted structure. A mixture of parallel and antiparallel extended chains cannot be excluded for the peptides with n = 3. In the amide I region the spectra of peptides with n ≥ 4 show the existence of the β-conformation. The problem of chain orientation within the pleated-sheet structure is discussed on the basis of a recent theoretical treatment of vibrational interactions of the amide I mode.     

External reflection FTIR of peptide monolayer films in situ at the air/water interface: experimental design, spectra-structure correlations, and effects of hydrogen-deuterium exchange.

A Fourier transform infrared spectrometer has been interfaced with a surface balance and a new external reflection infrared sampling accessory, which permits the acquisition of spectra from protein monolayers in situ at the air/water interface. The accessory, a sample shuttle that permits the collection of spectra in alternating fashion from sample and background troughs, reduces interference from water vapor rotation-vibration bands in the amide I and amide II regions of protein spectra (1520-1690 cm-1) by nearly an order of magnitude. Residual interference from water vapor absorbance ranges from 50 to 200 microabsorbance units. The performance of the device is demonstrated through spectra of synthetic peptides designed to adopt alpha-helical, antiparallel beta-sheet, mixed beta-sheet/beta-turn, and unordered conformations at the air/water interface. The extent of exchange on the surface can be monitored from the relative intensities of the amide II and amide I modes. Hydrogen-deuterium exchange may lower the amide I frequency by as much as 11-12 cm-1 for helical secondary structures. This shifts the vibrational mode into a region normally associated with unordered structures and leads to uncertainties in the application of algorithms commonly used for determination of secondary structure from amide I contours of proteins in D2O solution.     

Properties of an aldose reductase from pig lens. Comparative studies of an aldehyde reductase from pig lens

THe characteristic feature of the crystal structure of erabutoxin b, a short neurotoxin from Laticauda semifasciata, and alpha-cobratoxin, a long neurotoxin from Naja naja siamensis, is the presence of a triple-stranded antiparallel pleated beta-sheet structure formed by the central and the third peptide loops. In the present study, we have studied the assignment of slowly exchangeable amide protons of Laticauda semifasciata III from L. semifasciata, using nuclear Overhauser effects (NOE) and spin-decoupling methods. The results show that nearly all of the slowly exchangeable amide protons are to be assigned to the back-bone amide protons, involved in the triple-stranded antiparallel pleated beta-sheet structure, indicating that this sheet is stable in 2H2O solution. In contrast, the amide protons in short neurotoxins are readily exchangeable under the same experimental condition, suggesting that long neurotoxins have a more rigid sheet structure than short ones. This rigidity may come from the hydrophobic and hydrogen bond interaction between the central loop and the tail, which is not present in short neurotoxins. Since the functionally important residues are located on this beta-sheet, the different kinetic properties of the neurotoxins are well correlated with the difference in the rigidity of the beta-sheet.     

Amide I band of IR spectrum and structure of collagen and related polypeptides

The infrared amide I band of collagens (rat and cod skin) and related compounds (polyproline, polyglycine, and polytripeptides) was studied. Assignment of amide I-band components for polyproline II and polytripeptides (Gly-Pro-Pro)_n and (Gly-Pro-Gly)_n in the solid state and water solution was made. Three amide I components observed in the polypeptide spectra were attributed to three different peptide CO groups in each triplet. On the basis of this assignment, the interpretation of the amide I multicomponent structure in collagen and isomorphous oligo- and polypeptides was attempted. The ordering of intra- and intermolecular hydrogen bonds involving peptide CO groups in collagen and related compounds was discussed.     

Conformation of tachyplesin I from Tachypleus tridentatus when interacting with lipid matrices.

The mode of action of tachyplesin I, an antimicrobial cationic heptadecapeptide amide isolated from the hemocyte debris of a horseshoe crab, Tachypleus tridentatus, toward lipid matrices was studied with synthetic tachyplesin I, its analogs with Phe in place of Trp or Tyr, a linear analog with no disulfide bonds, and two linear short fragments. Circular dichroism spectra showed that tachyplesin I took an antiparallel beta-structure in buffer solution and a certain less ordered structure in acidic liposomes composed of egg phosphatidylcholine and egg phosphatidylglycerol (3:1). Spectrophotometric titration of the peptides with laurylphosphorylcholine revealed that both Trp and Tyr residues orient toward the inside of lipid matrices, suggesting that they are on the same side of the peptide backbone. The carboxyfluorescein leakage experiment and fluorescence data indicated that tachyplesin I interacted strongly with neutral and acidic lipid bilayers and an aromaticity-rich hydrophobic part of the peptide was embedded in lipid membranes. All the peptides except for the short fragments were almost equally active in lipopolysaccharide binding. The energy-transfer experiment showed that a conformational change occurred such that the Tyr and Trp residues are positioned more closely to each other in acidic liposomes than in buffer solution. The present study strongly suggested that amphipathic lipid bilayers induced a conformational change of tachyplesin I from an energetically stable beta-structure to a less ordered, probably more amphipathic structure.     

The orientation of beta-sheets in porin. A polarized Fourier transform infrared spectroscopic investigation.

The orientation of the protein secondary structures in porin is investigated by Fourier transform infrared (FTIR) linear dichroism of oriented multilayers of porin reconstituted in lipid vesicles. The FTIR absorbance spectrum shows the amide I band at 1,631 cm-1 and several shoulders around 1,675 cm-1 and at 1,696 cm-1 indicative of antiparallel beta-sheets. The amide II is centered around 1,530 cm-1. The main dichroic signals peak at 1,738, 1,698, 1,660, 1,634, and 1,531 cm-1. The small magnitude of the 1,634 cm-1 and 1,531 cm-1 positive dichroism bands demonstrates that the transition moments of the amide I and amide II vibrations are on the average tilted at 47 degrees +/- 3 degrees from the membrane normal. This indicates that the plane of the beta-sheets is approximately perpendicular to the bilayer. From these IR dichroism results and previously reported diffuse x-ray data which revealed that a substantial number of beta-strands are nearly perpendicular to the membrane, a model for the packing of beta-strands in porin is proposed which satisfies both IR and x-ray requirements. In this model, the porin monomer consists of at least two beta-sheet domains, both with their plane perpendicular to the membrane. One sheet has its strands direction lying nearly parallel to the membrane normal while the other sheet has its strands inclined at a small angle away from the membrane plane.     

Vibrational spectrum of the unordered polypeptide chain: A Raman study of feather keratin

Raman spectra of native and solubilized feather keratin have been obtained, and the amide I and amide III regions have been analyzed by band resolution techniques. The amide I region of the native form indicates that at least 64% of the protein has an antiparallel chain pleated sheet structure, the remainder being unordered. For the solubilized keratin all of the protein is in an unordered state. The amide III region is not as easily analyzed into component contributions. Normal vibration analyses on N-acetyl-L -alanine-N-methylamide support the conclusion that the amide III region is not as satisfactory as the amide I region in characterizing unordered structures. Even in the latter case caution must be used, since the observed amide I band is an average over the conformational distribution in the particular unordered system.     

L-alanyl-L-alanyl-L-alanine: parallel pleated sheet arrangement in unhydrated crystal structure, and comparisons with the antiparallel sheet structure

The tripeptide L-alanyl-L-alanyl-L-alanine has been crystallized from a water/dimethylformamide solution in an unhydrated form, with cell dimensions a = 11.849, b = 10.004, c = 9.862 A, beta = 101.30 degrees, monoclinic space group P21 with 4 molecules per cell (2 independent molecules in the asymmetric unit). The structure was determined by direct methods and refined to a discrepancy index R = 0.057. The tri-L-alanine molecules are packed in a parallel pleated sheet arrangement with unusually long amide nitrogen-carbonyl oxygen contacts within sheets. Comparisons are made with the antiparallel pleated sheet structure of tri-L-alanine hemihydrate, previously crystallized from the same solvent system.     

Estimation of protein secondary structure from the laser Raman amide I spectrum

A new method for estimating protein secondary structure from the laser Raman spectrum has been developed whereby the amide I Raman band of a protein is analyzed directly as a linear combination of amide I bands of proteins whose secondary structures are known. For 14 proteins, analyzed by removing each one from the reference set and analyzing its structure in terms of the remaining proteins, the average correlation coefficients between the Raman and X-ray diffraction estimates of helix, beta-strand, turn, and undefined were 0.98, 0.98, 0.82 and 0.35, respectively. Significant correlations were also observed for distinctions between alpha-helix (0.98) and disordered helix (0.82), and between parallel (0.82) and antiparallel (0.97) beta-sheets. The average standard deviation of these Raman estimates from the X-ray values is less than 4%. In addition, a singular value analysis of 20 Raman amide I spectra indicates that there may be as many as nine significant independent pieces of information present in the amide I region.     

Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: constrained MD simulation studies

Using the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., alpha-helix, 3(10)-helix, pi-helix, antiparallel and parallel beta-sheets, and polyproline II (P(II)), are considered, and the vibrational characteristic features in their linear and nonlinear spectra in the amide I band region are discussed. Isotope-labeling effects on IR and VCD spectra are notable only for alpha- and pi-helical peptides due to the strong vibrational couplings between two nearest neighboring amide I local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure.