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).     

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.     

A DFT study of structure and stability of pleated and rippled cross‐β sheets with hydrophobic sidechains

The rippled cross‐β sheet, a topography, in which mirror‐image peptides are arranged with alternating chirality into a periodic two‐dimensional network, is burgeoning as a new design principle for materials and biomedical applications. Experiments by the Schneider, Nilsson, and Raskatov labs have independently shown diverse racemic mixtures of aggregation‐prone peptide of different sizes to favor the rippled over the pleated topography. Yet, systematic ab initio studies are lacking, and the field is yet to develop rules that would enable the design of new rippled cross‐β frameworks from first principles. Here, DFT calculations were performed on a set of model systems, designed to begin understanding the impact that bulky, hydrophobic sidechains have upon the formation of pleated and rippled cross‐β frameworks. It is hoped that this study will help stimulate the development of a predictive, general framework to enable rational design of rippled cross‐β sheets in the future.     

Elastic Moduli of Helical Polypeptide Chain Structures

The elastic moduli of the α-helix, polyglycine II, and the parallel-chain and antiparallel-chain pleated sheet structures have been calculated. A Urey-Bradley type of potential was used, extended by the inclusion of hydrogen bond stretching terms where appropriate. In the one instance where a valid comparison with experimental data can be made, viz, α-keratin, the calculations indicate that the matrix component, rather than being amorphous, probably contains an ordered structure of higher modulus than the α-helix.     

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.     

Secondary structures of peptides: 5 · 15N n.m.r. CP/MAS spectroscopy of solid polypeptides and gramicidin-S

30.5 MHz ¹⁵N m.m.r. (CP/MAS) spectra of various solid polypeptides were measured using the cross-polarization/magic angle spinning technique. In order to obtain optimum signal-to-noise ratios, relatively short contact times (1 ± 0.5 ms) are required, because the cross-polarization times (T_NH) are short and because the proton rotating-frame relaxation times (T_1p) are in the order of 20 ms. The ¹⁵N n.m.r. signals of copolypeptides may be sensitive to sequence effects; yet they are in most cases more sensitive to the nature of the secondary structure. The signals of α-helices absorb ca. 8–10 ppm upfield of β-sheet structures, whereas the polyglycine II helix absorbs downfield. The natural abundance spectrum of crystalline gramicidin-S exhibits a signal at ?247 ppm, a characteristic chemical shift of the antiparallel pleated sheet structure.     

Far-infrared spectra of sequential copolymers of amino acids with alkyl group side chains

Far-infrared spectra were measured for the sequential copolymers of amino acids with alkyl group side chains. The analysis of the spectra showed that (L -Ala-L -Ala-Gly)_n, (L -Ala-Gly)_n, (L -Ala-Gly-Gly)_n, (L -Val-L -Ala-L -Ala)_n, and (L -Val-L -Ala)_n, have the antiparallel pleated sheet structures and that the backbone conformations of (L -Val-L -Val-L -Ala)_n and (L -Val-L -Val-Gly)_n are the same as that of poly-L -valine. The far-infrared bands characteristic of the antiparallel pleated sheet structure were assigned on the basis of the result of the normal coordinate analysis of poly-L -alanine with this structure. The intersheet and interchain spacings of the sequential copolymers with the antiparallel pleated sheet structure were determined from the x-ray powder-diffraction patterns of these samples.     

The colonization of squares of plastic suspended in midwater

(1) A flat substratum hung in midwater is colonized rapidly by a number of species normally found in vegetation. Some have been recorded consistently, a greater number occasionally, but only a few have not been recorded at all. Evidently most species are moving round frequently, even those, such as snails and case-building caddis-larvae, that cannot swim. (2) It seems likely from this that the identity of the plant cover has less influence on the structure of a community than some have thought. (3) A comparison of flat sheet, pleated sheet and artificial Littorella suspended in midwater makes possible certain statements and deductions. (i) Leptophlebia, Enallagma and chironomid larvae are more numerous on artificial Littorella; their natural habitat is within the vegetation cover. (ii) Cloeon, Cyrnus and Holocentropus are as numerous on the sheets or more numerous than in the artificial vegetation; they inhabit the surface of the plant cover where Cloeon is protected by its speed, and where the polycentropopids, protected by their nets, can trap both the true plankton and the Cladocera which feed in the vegetation. (iii) The foot of a snail and the suckers of a leech are most effective on a flat surface, which also provides a good feeding place for a snail. The higher numbers of Lymnaea and Erpobdella on the pleated compared with the flat sheets indicates the importance of cover for these two animals. (4) Flat plastic sheets hanging in the illuminated zone would improve the production of fish a little, pleating the sheets would improve it a little more, and best results would come from hanging something with a greater resemblance to natural vegetation.     

Molecular organization in molluscan operculae.

Operculin is a glycine-rich protein present as the major component of gastropod operculae. X-ray and infrared studies of operculins lead to the conclusion that operculae contain antiparallel-chain pleated sheets oriented so that the plane of the pleated sheet is parallel to the plane of the operculum, which is a flat ovoidal or circular sheet. Partial hydrolysis gives evidence of repeating Asp-Gly-Asp and Asp-Ala-Asp sequences as well as of regions rich in Gly.     

Strain-based estimation of time-dependent transmural myocardial architecture in the ovine heart

Left ventricular myofibers are connected by an extensive extracellular collagen matrix to form myolaminar sheets. Histological cardiac tissue studies have previously observed a pleated transmural distribution of sheets in the ovine heart, alternating sign of the sheet angle from epicardium to endocardium. The present study investigated temporal variations in myocardial fiber and sheet architecture during the cardiac cycle. End-diastolic histological measurements made at subepicardium, midwall, and subendocardium at an anterior-basal and a lateral-equatorial region of the ovine heart, combined with transmural myocardial Lagrangian strains, showed that the sheet angle but not the fiber angle varied temporally throughout the cardiac cycle. The magnitude of the sheet angle decreased during systole at all transmural depths at the anterior-basal site and at midwall and subendocardium depths at the lateral-equatorial site, making the sheets more parallel to the radial axis. These results support a previously suggested accordion-like wall-thickening mechanism of the myocardial sheets.     

Rapid determination and NMR assignments of antiparallel sheets and helices of a scorpion and a cobra toxin

An NMR method is described which should provide a rapid means for determining and assigning antiparallel sheets and helices in small proteins. It begins by locating apparent NOESY crosspeaks which suggest the presence of the secondary structure; this is followed by searches for MCD patterns (Englander & Wand (1987) Biochemistry 22, 5953) which are characteristic of these structures. As a result, only spin-systems of the amino acids within the secondary structure need to be defined. A triple-stranded, antiparallel sheet and a helix have been found and assigned for both alpha-cobratoxin and the scorpion toxin AaH III.     

Matrix formulation of the transition from a statistical coil to an intramolecular antiparallel beta sheet

A tractible matrix formulation is developed for the formation of intramolecular antiparallel β sheets in a homopolymer chain molecule. The formulation is applicable to chains with a finite degree of polymerization. It can readily be extended to treat specific-sequence heteropolymers. Individual sheets may contain any number of strands, the number of residues per strand can range upward from two, and there is no artificial constraint linking the numbers of residues in adjacent strands. The weighting scheme utilizes two end-effect parameters, denoted by τ and δ. The first parameter is associated with each residue that does not have a partner in a proceding strand, and the latter is associated with each β bend. A third parameter, t, is associated with every residue in the sheet. Conditions are described which lead to the formation of different types of sheets: (1) “sheets” comprised of isolated extended strands; (2) cross-β fibers in which a sheet contains a large number of very short strands; (3) fibers in which a few very long strands run parallel to the fiber axis; (4) sheets comprised of several strands in which the average strand contains five residues. The fourth type of sheet resembles those found in globular proteins. It is formed when τ and δ are both small, with the ratio, τ/δ, being slightly less than one.     

A crystal structure with features of an antiparallel α-pleated sheet

A single-crystal x-ray diffraction analysis of Boc-L -Ala-D -aIle-L -Ile-OMe has been carried out. The analysis has shown (a) that the tripeptide molecules have in part an α-extended conformation, the torsion angles of the L -Ala and D -aIle residues being φ₁ = ?75.1° and ψ₁ = ?25.8° and φ₂ = 67.3° and ψ₂ = 44.1°, respectively, and (b) that the molecules are organized in rippled planes where they occur in relative antiparallel orientation linked together side by side by H bonds. This molecular organization of the tripeptide corresponds closely to that of an antiparallel α-pleated sheet, and likely constitutes the first example of a structure of this kind for which a characterization at the atomic level has been achieved. A molecular dynamics study has shown that the molecular conformation of the tripeptide in the crystalline state is determined primarily by intermolecular interactions. © 1994 John Wiley & Sons, Inc.     

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.     

Conformational analysis of the beta sheet structure of poly-L-alanine and poly(L-alanine-glycine).

The β pleated sheet structures of poly-l-alanine and the polydipeptide (Ala-Gly)_n are analysed by conformational energy calculations, and the results are compared with the structures previously determined by X-ray methods. Structural parameters calculated for β poly-l-alanine using two different sets of potentials are in close agreement (within 5% or less) with the results of X-ray structure analysis (Arnott et al., 1967). For (Ala-Gly)_n, the alanyl and glycyl-glycyl intersheet distances calculated by assuming the model of Fraser et al. (1965) are comparable to those observed in the polydipeptide, but differ significantly from those of (Gly)_n and (Ala)_n. These calculations help establish the structural details of both the polydipeptide and the closely related Bombyx mori silk protein in their β form.     

Secondary structure of histones in solution

The secondary structure of histones H2B and H3 from calf thymus has been quantitatively studied in heavy water solutions in a wide range of histone concentrations, pD, and concentrations of sodium chloride by an infrared spectroscopy method. Also, the interactions between molecules of different histones in equimolar mixtures H2A-H2B, H2A-H3, H2A-H4, H2B-H3, H2B-H4, H3-H4, and H2A-H2B-H3-H4 have been investigated using the same method. For H2B and H3 conditions favourable for aggregation have been shown to induce the formation of pleated sheet structure. When the pD and concentration of NaCl are in a physiological range, the secondary structure of H2B and H3 contains about 15% of alpha-helix, 4% of parallel pleated sheet structure, 14% of antipatallel pleated sheet structure in H2B and 18% in H3. For mixtures in all cases, except H2A-H4, there is an interaction between molecules of different histones followed by a reduction of the antiparallel pleated sheet structure content. The data on the secondary structure of histones in different states (under self-association, in mixtures, in nucleosomes, and in chromatin) have been discussed and it is suggested that: 1) the secondary structure of histones in chromatin is essentially similar to that in the state of self-association; 2) in the core nucleosome particle the quantity of DNA (in nucleotide pairs), and the quantities of alpha-helix and antiparallel pleated sheet structure (in peptide groups) satisfy the relation 1 : 1 : 1.     

Logical analysis of the mechanism of protein folding II. The nucleation process

Regions of secondary structure are predicted, without using information about the conformation of the protein itself, and compared with crystallographic assignments for seven proteins of recently published sequence and conformation (Table 1). It is observed in Table 3 that the prediction of helices is good (78.7% for %cor.ass.3), except for proteins having large antiparallel pleated sheets, and the prediction of β-structure is quite good (51.2% for %cor.ass.3) except for helix-rich proteins.The prediction of secondary structure from sequence, and a survey of all protein structures analysed so far by X-ray crystallography, suggest that nuceleation starts in almost all cases from interactions in the medium range between the regions having helical potential (α-candidate) and β-structural potential (β-candidate), which are very close to each other but separated by at least three hydrophilic or neutral residues in four consecutive residues on the polypeptide chain. Predictability of loops or turns is enhanced to 71.3% (%cor.ass.2) from 64.4% by taking into account the contiguous α-β interactions. Such a medium-range interaction is called here a probable nucleus. There are a lot of nuclei in large proteins such as carboxypeptidase Aα, while there exists at least one in small proteins like the trypsin inhibitor, Moreover, such an interaction could be a transitionary state towards a helix-rich protein, and towards a helix-deficient protein having a large antiparallel pleated sheet β-structure as well.The analysis of the relation between probable nuclei with regard to their mutual spatial proximity strongly suggests that the topological pathway of the polypeptide chain in three-dimensional space might be decided by the long-range interactions between an α-candidate and a β-candidate. An empirical rule is observed that almost all parallel pleated sheets are accompanied by helices in their neighbourhood. An accumulation of chemical facts, such as complementation experiments, combinations of disulphide bonds, etc., seems also to be elucidated by the proposed mechanism of protein folding.     

Structural modeling of snow flea antifreeze protein

The glycine-rich antifreeze protein recently discovered in snow fleas exhibits strong freezing point depression activity without significantly changing the melting point of its solution (thermal hysteresis). BLAST searches did not detect any protein with significant similarity in current databases. Based on its circular dichroism spectrum, discontinuities in its tripeptide repeat pattern, and intramolecular disulfide bonding, a detailed theoretical model is proposed for the 6.5-kDa isoform. In the model, the 81-residue protein is organized into a bundle of six short polyproline type II helices connected (with one exception) by proline-containing turns. This structure forms two sheets of three parallel helices, oriented antiparallel to each other. The central helices are particularly rich in glycines that facilitate backbone carbonyl-amide hydrogen bonding to four neighboring helices. The modeled structure has similarities to polyglycine II proposed by Crick and Rich in 1955 and is a close match to the polyproline type II antiparallel sheet structure determined by Traub in 1969 for (Pro-Gly-Gly)_n. Whereas the latter two structures are formed by intermolecular interactions, the snow flea antifreeze is stabilized by intramolecular interactions between the helices facilitated by the regularly spaced turns and disulfide bonds. Like several other antifreeze proteins, this modeled protein is amphipathic with a putative hydrophobic ice-binding face.     

The pleated sheet: an unusual negative-staining method for transmission electron microscopy of biological macromolecules

A novel method for preparing negatively stained specimens is described which appears to improve the routine resolution of biological structure in direct images obtained by transmission electron microscopy. In the new method, which we term the pleated sheet technique, macromolecules are adsorbed to a carbon film by the Valentine procedure (R. Valentine, B. Shapiro, and E. Stadtman (1968) Biochemistry, 7, 2143-2152), and the film then carefully pleated while in contact with a 1% uranyl formate solution to trap stain within the folds of pleats. A grid is placed on the compressed film, and film plus grid retrieved with a Saran Wrap drum. Subsequent dehydration produces a filmed grid containing negatively stained macromolecules within the folds of pleated regions and positively stained macromolecules in single sheet regions. The effect of sandwiching sample and stain between carbon layers is to produce exceedingly uniform negative staining so that stain contours more accurately and more reproducibly reflect true molecular contours. Electron micrographs of IgG and IgA molecules prepared by these methods are exhibited that permit unambiguous comparison of structure imaged in the electron microscope against known structures solved by single-crystal X-ray diffraction. Correlation is excellent; the smallest resolvable element in micrographs is an immunoglobulin domain, whose molecular weight is 12 000.     

Vibrational analysis of peptides,polypeptides, and proteins. I. Polyglycine I

A force field has been refined for the antiparallel chain-rippled sheet structure of polyglycine I. Transition dipole coupling and hydrogen bonding are explicitly taken into account. Amide I and amide II mode splittings are well accounted for, the latter also providing a quantitative explanation of the amide A and amide B mode frequencies and intensities. In addition to predicting other features of the vibrational spectrum of polyglycine I, this force field is completely transferable to other β polypeptides, even though these have the antiparallel chainpleated sheet structure.