Molecular structures for microbial polysaccharides: conformation of the Klebsiella serotype K25 capsular polysaccharide

Fibre type X-ray diffraction patterns have been obtained from oriented, semi-crystalline films prepared from the sodium salt of the capsular polysaccharide of Klebsiella serotype K25. This molecule has a tetrasaccharide repeating structure consisting of a disaccharide backbone and a disaccharide side chain. The backbone contains a di-equatorially 1,4 linked β-d-glucose residue followed by a di-equatorially 1,3 linked β-d-galactose residue. The side chain is attached to the axial O(4) position of the galactose residue and consists of a di-equaltorially 1,2 linked β-d-glucoronic acid with a β-d-glucose residue attached terminally. An interesting feature of the backbone linkage geometry of this polysaccharide is its similarity with those of the animal connective tissue polydisaccharides. Analysis of diffraction patterns gives rise to an extended three fold helical conformation with an axially projected advance per chemical repeat of 0.97 nm. Molecular models have been computer generated using least squares techniques to optimize interatomic contacts and simultaneously meet the observed helical parameters. A left handed helix with inter-residue stabilizing hydrogen bonds was found to be most favourable and comparison of this model with other relevant polysaccharide structures is male.     

Molecular structures for microbial polysaccharides: x-ray diffraction results from Klebsiella serotype K57 capsular polysaccharide

Fibre X-ray diffraction patterns have been obtained from oriented, semi-crystalline films of the Klebsiella capsular polysaccharide secrotype K57. K57 is a polytetrasaccharide that contains galactosyluronic acid, mannosyl, and galactosyl residues in the backbone, and an additional mannosyl group as a side-appendage. The simplest interpretation of the diffraction pattern is that the molecule crystallizes as a three-fold helix with an axially projected repeat of 1.143 nm which correlates directly with the chemical repeat. The chain is highly extended, even though it incorporates a 1,2-diaxial linkage in the main backbone. Molecular models have been built using least-squares techniques to minimise interatomic compression and simultaneously meet the observed helical parameters. These models have been compared with the experimental data by using cylindrically averaged, Fouriertransform calculations.     

Molecular structures for microbial polysaccharides. X-ray diffraction from the capsular polysaccharide of Klebsiella K-type 5

Fibre Type X-ray diffraction patterns have been obtained from oriented, semicrystalline films prepared from the sodium salt form of the capsular polysaccharide of K5. The molecule has a linear trisaccharide repeating sequence containing a 1,3 linked β-d-glucuronic acid and a 1,4 linked β-d-glucose residue, resulting in a backbone linkage geometry of Man(1 eq-4e1)-GIcUA (1-eg-4eg) Gle (1 eq-3 eq) Man. It also contains an O-acetyl group and two charged groups, namely a uronic acid and a pyruvate. Analysis of the diffraction results gives rise to an extended two-fold helical conformation with an axially projected advance of 1.35 nm which correlates directly with the covalent repeating sequence. X-ray diffraction patterns from preparations of deacetylated K5 polysaccharide showed similar conformations for the individual helices but the interchain packing arrangements are different. In each case, isolated helices have been computer generated using molecular model building procedures and the most favourable conformations for both preparations were those which contained three stabilizing interresidue hydrogen bonds, one across each of the glycosidic linkages.     

The crystal and molecular structure of the alpha-helical nonapeptide antibiotic leucinostatin A

The crystal and molecular structure of the nonapeptide antibiotic leucinostatin A, containing some uncommon amino acids and three Aib residues, has been determined by x-ray diffraction analysis. The molecule crystallizes in the orthorhombic space group P2(1)2(1)2(1), a = 10.924, b = 17.810, c = 40.50 A, C62H111N11O13, HCl.H2O, Z = 4. The peptide backbone folds in a regular right-handed alpha-helix conformation, with six intramolecular i----(i + 4) hydrogen bonds, forming C13 rings. The nonapeptide chain includes at the C end an unusual beta-Ala residue, which also adopts the helical structure of the other eight residues. In the crystal the helices are linked head to tail by electrostatic and hydrogen-bond interactions, forming continuous helical rods. The crystal packing is formed by adjacent parallel and antiparallel helical rods. Between adjacent parallel helical columns there are only van der Waals contacts, while between adjacent antiparallel helical columns hydrogen-bond interactions are formed.     

Structural studies on triacetates of mannan and glucomannan

Mannan triacetates prepared from material extracted from ivory nut and Tubera salep were studied by means of electron and X-ray diffraction. The former is uniquely constituted of acetylated d-mannopyranosyl units linked by a (1 → 4)-β-linkage whereas the latter contains acetylated (1 → 4)-β-d-glucopyranosyl randomly distributed in the backbone with a ratio of mannose to glucose of about 3:1. However, there seems to be no effect on crystallisation due to the presence of the glucosidic units on the conformation of the chain.Single crystals of ivory nut triacetate were prepared by slowly cooling a dilute solution of nitromethane and butanol. The crystals were long narrow laths which provide electron diffraction data after annealing at 190°C in a vacuum.Two different unit cells were derived from the acetylated Tubera salep X-ray data. A first unit cell with a = 1·18 nm, b = 1·54 nm and c = 1·60 nm contains eight sugar units, whereas the second unit cell with a = 0.369 nm, b = 0·96 nm and c = 1·58 nm would accommodate 16 residues. The latter agrees best with the base-plane parameters derived from electron diffraction of single crystals.The X-ray fibre diagram was interpreted in terms of a two-fold helix and an asymmetric unit composed of two triacetyl mannopyranosyl units. This means that two chemically identical mannose units would not be conformationally equivalent along the backbone.The presence of glucose units in the backbone does not seem to perturb the crystalline conformation. The ‘isomorphous replacement’ hypothesis was invoked to explain this observation. The helical parameters derived herein for Tubera salep mannan triacetate are different from those reported earlier for the same acetylated glucomannan but crystallised using a different technique. This is attributed to the occurrence of polymorphism in this material.     

Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy

The atomic resolution structure of Pf1 coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles in solution is compared to the structures previously determined by X-ray fiber and neutron diffraction, the structure of its membrane-bound form, and the structure of fd coat protein. These structural comparisons provide insights into several biological properties, differences between class I and class II filamentous bacteriophages, and the assembly process. The six N-terminal amino acid residues adopt an unusual "double hook" conformation on the outside of the bacteriophage particle. The solid-state NMR results indicate that at 30 degrees C, some of the coat protein subunits assume a single, fully structured conformation, and some have a few mobile residues that provide a break between two helical segments, in agreement with structural models from X-ray fiber and neutron diffraction, respectively. The atomic resolution structure determined by solid-state NMR for residues 7-14 and 18-46, which excludes the N-terminal double hook and the break between the helical segments, but encompasses more than 80% of the backbone including the distinct kink at residue 29, agrees with that determined by X-ray fiber diffraction with an RMSD value of 2.0 A. The symmetry and distance constraints determined by X-ray fiber and neutron diffraction enable the construction of an accurate model of the bacteriophage particle from the coordinates of the coat protein monomers.     

The peptide chain of tyrosyl tRNA synthetase: No evidence for a super-secondary structure of four α-helices

A detailed backbone model has been built for 274 residues of tyrosyl tRNA synthetase, based on an X-ray diffraction study. This includes eight helical sections and a six-stranded pleated sheet. The four helices near the carboxyl terminal end are not arranged like the helices of TMV disk protein and hemerythrin, and the structure gives no support to the idea that four antiparallel helices form a common structural unit in proteins.     

Tryptophan rich peptides: influence of indole rings on backbone conformation

Synthetic peptides with defined secondary structure scaffolds, namely hairpins and helices, containing tryptophan residues, have been investigated in this study to probe the influence of a large number of aromatic amino acids on backbone conformations. Solution NMR investigations of Boc-W-L-W-(D)P-G-W-L-W-OMe (peptide 1), designed to form a well-folded hairpin, clearly indicates the influence of flanking aromatic residues at the (D)Pro-Gly region on both turn nucleation and strand propagation. Indole-pyrrolidine interactions in this peptide lead to the formation of the less-frequent type I' turn at the (D)Pro-Gly segment and frayed strand regions, with the strand residues adopting local helical conformations. An analog of peptide 1 with an Aib-Gly turn-nucleated hairpin (Boc-W-L-W-U-G-W-L-W-OMe (peptide 2)) shows a preference for helical structures in solution, in both chloroform and methanol. Peptides with either one (Boc-W-L-W-U-W-L-W-OMe (peptide 3)) or two (Boc-U-W-L-W-U-W-L-W-OMe (peptide 4)) helix-nucleating Aib residues give rise to the well-folded helical conformations in the chloroform solution. The results are indicative of a preference for helical folding in peptides containing a large number of Trp residues. Investigation of a tetrapeptide analog of peptide 2, Boc-W-U-G-W-OMe (peptide 5), in solution and in the crystal state (by X-ray diffraction), also indicates a preference for a helical fold. Additionally, peptide 5 is stabilized in crystals by both aromatic interactions and an array of weak interactions. Examination of Trp-rich sequences in protein structures, however, reveals no secondary structure preference, suggesting that other stabilizing interactions in a well-folded protein may offset the influence of indole rings on backbone conformations.     

Sequential folding of transfer RNA: A nuclear magnetic resonance study of successively longer tRNA fragments with a common 5′ end

Most folding studies on proteins and nucleic acids have been addressed to the transition between the folded and unfolded states of an intact molecule, where an entire residue sequence is present during the folding event. However, since these polymers are synthesized sequentially from one terminus to the other in vivo, their folding pathways may be influenced greatly by the sequential appearance of the residues as a function of time.The three-dimensional structure of yeast tRNA^Phe in the crystalline state is correlated with 360 MHz proton nuclear magnetic resonances from three fragments plus an intact molecule of the tRNA that share a common 5′ end and are in a solution condition similar to that of the crystal structure. This has allowed identification of folded structures present in the fragments and presumably present in the growing tRNA molecule as it is being synthesized from the 5′ end. The experiments show that only the correct stems are formed in the fragments; no additional or competing helical region is produced. This suggests that in the biosynthesis of this tRNA, correct folding of helical stems occurs before the entire molecule is formed. Further, some of the tertiary interactions (hydrogen bonds) found in the crystal structure are also probably present before the synthesis is completed. These findings are generalized to consider the precursor of the tRNA as well as other tRNAs.     

The elusive π-helix

Central to protein architecture is the local arrangement or secondary structure of the polypeptide backbone. Thirty to forty percent of protein domains are α-helices with 3.6 residues per turn. π-Helices, in which the peptide chain is more loosely coiled (4.4 residues per turn), have also been proposed. However, such structures necessitate an energetically unfavorable ～1 Å central helical hole. We show that rather than being composed of idealized π-helices, helical regions formed from putative π-helices actually consist of a series of concatenated wide turns with unique elliptical configurations. These structures have a larger helical radius akin to that of a π-helix, but without the loss of favorable cross-core van der Waals interactions. This not only obviates the helical void, but also endows proteins with important functionalities, including metal ion coordination, enhanced flexibility and specific enzyme-substrate binding interactions.     

3D Structure of fish muscle myosin filaments

Myosin filaments isolated from goldfish (Carassius auratus) muscle under relaxing conditions and viewed in negative stain by electron microscopy have been subjected to 3D helical reconstruction to provide details of the myosin head arrangement in relaxed muscle. Previous X-ray diffraction studies of fish muscle (plaice) myosin filaments have suggested that the heads project a long way from the filament surface rather than lying down flat and that heads in a single myosin molecule tend to interact with each other rather than with heads from adjacent molecules. Evidence has also been presented that the head tilt is away from the M-band. Here we seek to confirm these conclusions using a totally independent method. By using 3D helical reconstruction of isolated myosin filaments the known perturbation of the head array in vertebrate muscles was inevitably averaged out. The 3D reconstruction was therefore compared with the X-ray model after it too had been helically averaged. The resulting images showed the same characteristic features: heads projecting out from the filament backbone to high radius and the motor domains at higher radius and further away from the M-band than the light-chain-binding neck domains (lever arms) of the heads.     

Structure of the dna binding cleft of the gene 5 protein from bacteriophage fd

The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3-Å resolution by X-ray diffraction techniques. The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface. The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft. Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place. The structure and binding mechanism as we visualize it appear to be fully consistent with evidence provided by physical-chemical studies of the protein in solution.     

Interpretation of the low-angle meridional neutron diffraction patterns from collagen fibres in terms of the amino acid sequence

Measurement of fully corrected, low angle meridional neutron diffraction intensities from native collagen fibres, in a full range of H₂O/D₂O contrasts, is described. The observed contrast dependence of the intensities of the first 12 orders of 670 A (D) axial periodicity is fitted to a general quadratic theory of contrast variation. The observed first order contrast dependence is compared to predictions based on the amino acid sequence, assuming different extents of chemical H/D exchange, and found to be consistent with complete non-carbon linked H/D exchange except for 1 to 1.6 hydrogen atoms per gly-X-Ytriplet involved in H-bonding. Both X-ray and neutron diffraction data in a variety of contrasts are consistent with a unique model for the axially projected structure of native collagen fibrils based on the amino acid sequence. This model if characterized by average axial residua translations in the NH₂ and COOH terminal, non-triple helical telopeptides, expressed as multiples of the triple helical residue translation, of 0.85 ± 0.05 and 0.7 ± 01 respectively, with D = 235 ± 1 residues.     

Branched arabino-oligosaccharides isolated from sugar beet arabinan

Sugar beet arabinan consists of an α-(1,5)-linked backbone of l-arabinosyl residues, which can be either single or double substituted with α-(1,2)- and/or α-(1,3)-linked l-arabinosyl residues. Neutral branched arabino-oligosaccharides were isolated from sugar beet arabinan by enzymatic degradation with mixtures of pure and well-defined arabinohydrolases from Chrysosporium lucknowense followed by fractionation based on size and analysis by MALDI-TOF MS and HPAEC. Using NMR analysis, two main series of branched arabino-oligosaccharides have been identified, both having an α-(1,5)-linked backbone of l-arabinosyl residues. One series carries single substituted α-(1,3)-linked l-arabinosyl residues at the backbone, whereas the other series consists of a double substituted α-(1,2,3,5)-linked arabinan structure within the molecule. The structures of eight such branched arabino-oligosaccharides were established.     

The structure of cytochrome c3 from Desulfovibrio vulgaris Miyazaki at 2.5 A resolution

The structure of tetraheme cytochrome c3 isolated from Desulfovibrio vulgaris Miyazaki has been determined at 2.5 A resolution by an X-ray diffraction method. Protein phases were computed by the multiple isomorphous replacement method using the native and four heavy atom derivatives, anomalous scattering measurements of the latter being considered. The mean figure of merit was 0.77. Four heme groups are exposed on the surface of the molecule. There are some short helical segments in the polypeptide chain, and hair-pin turns are often observed at glycine and alanine residues.     

Synthèse et structure de la poly-O-carbobenzoxy L- tyrosine et de copolymères de O-carbobenzoxy L-tyrosine et de glutamate de benzyle ou d'aspartate de benzyle

The optical rotatory dispersion of copolymers of O-carbobenzoxy-L -tyrosine and benzyl L (or D )-glutamate as well as benzyl L -aspartate, dissolved in nonpolar solvent, has been studied. Moffitt's equation permits the determination of b₀ coefficients whose variation, with varying composition in amino acid residues, suggests that the molecules of poly-O-carbobenzoxy-L -tyrosine have a helical structure similar to that of poly-(benzyl L -glutamate). Results obtained from infrared spectroscopy and x-ray diffraction show that the copolymers possess a helical conformation in the solid state, even when they are very rich in carbobenzoxy-L -tyrosine residues. The value of the b₀, coefficient for poly-O-carbobenzoxy-L -tyrosine may be explained by a regular stacking of the chromophore groups around the helical backbone. The ordering of the molecules of this polymer in a purely helical structure seems favored by the insertion of a small number of foreign residues in the polypeptide chain.     

The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of Arabidopsis thaliana

The interaction between xylan and cellulose microfibrils is important for secondary cell wall properties in vascular plants; however, the molecular arrangement of xylan in the cell wall and the nature of the molecular bonding between the polysaccharides are unknown. In dicots, the xylan backbone of β‐(1,4)‐linked xylosyl residues is decorated by occasional glucuronic acid, and approximately one‐half of the xylosyl residues are O‐acetylated at C‐2 or C‐3. We recently proposed that the even, periodic spacing of GlcA residues in the major domain of dicot xylan might allow the xylan backbone to fold as a twofold helical screw to facilitate alignment along, and stable interaction with, cellulose fibrils; however, such an interaction might be adversely impacted by random acetylation of the xylan backbone. Here, we investigated the arrangement of acetyl residues in Arabidopsis xylan using mass spectrometry and NMR. Alternate xylosyl residues along the backbone are acetylated. Using molecular dynamics simulation, we found that a twofold helical screw conformation of xylan is stable in interactions with both hydrophilic and hydrophobic cellulose faces. Tight docking of xylan on the hydrophilic faces is feasible only for xylan decorated on alternate residues and folded as a twofold helical screw. The findings suggest an explanation for the importance of acetylation for xylan–cellulose interactions, and also have implications for our understanding of cell wall molecular architecture and properties, and biological degradation by pathogens and fungi. They will also impact strategies to improve lignocellulose processing for biorefining and bioenergy.     

AlphaDL and piDL helices of alternating poly-gamma-benzyl-D-L-glutamate.

Poly-γ-benzyl-glutamate with strict alternation of l and d residues is shown to exist in α and possibly ω helical conformations, and in a new helical structure specific to poly-d-l-peptides, the π_DL helix. Infrared, X-ray and electron diffraction data on these structures are given. The transconformation mechanism from α_DL to π_DL, helices, which implies the formation of a new set of hydrogen bonds, is discussed. The multiplicity of conformations observed with this polymer (which can also exist in an unusual sheet structure) is discussed from the point of view of the sequence-structure relation.     

Tryptophan-containing peptide helices: interactions involving the indole side chain.

Two designed peptide sequences containing Trp residues at positions i and i + 5 (Boc-Leu-Trp-Val-Ala-Aib-Leu-Trp-Val-OMe, 1) as well as i and i + 6 (Boc-Leu-Trp-Val-Aib-Ala-Aib-Leu-Trp-Val-OMe, 2) containing one and two centrally positioned Aib residues, respectively, for helix nucleation, have been shown to form stable helices in chloroform solutions. Structures derived from nuclear magnetic resonance (NMR) data reveal six and seven intramolecularly hydrogen-bonded NH groups in peptides 1 and 2, respectively. The helical conformation of octapeptide 1 has also been established in the solid state by X-ray diffraction. The crystal structure reveals an interesting packing motif in which helical columns are stabilized by side chain-backbone hydrogen bonding involving the indole Nepsilon1H of Trp(2) as donor, and an acceptor C=O group from Leu(6) of a neighboring molecule. Helical columns also associate laterally, and strong interactions are observed between the Trp(2) and Trp(7) residues on neighboring molecules. The edge-to-face aromatic interactions between the indoles suggest a potential C-H...pi interaction involving the Czeta3H of Trp(2). Concentration dependence of NMR chemical shifts provides evidence for peptide association in solution involving the Trp(2) Nepsilon1H protons, presumably in a manner similar to that observed in the crystal.     

Some phytotoxic glycopeptides from Ceratocystis ulmi, the Dutch Elm Disease pathogen

Ceratocystis ulmi, the causal agent of Dutch Elm Disease, produces phytotoxic glycopeptides in culture. A mixture of phytotoxic glycopeptides has been prepared by affinity chromatography on a concanavalin A-Sepharose column and collectively they have been termed the toxin. The polydisperse component that makes up the majority of the toxin (80%) by weight has a molecular weight of about 2.7·10⁵. The large molecular weight component (<5%) elutes at the void volume of a Bio-Gel A50 m column. The other component (15%) appears as a trailing peak on the edge of the major component and has an approximate molecular weight of 7 · 10⁴. The toxin is composed of 38% sugar residues, primarily rhamnose and mannose, and 7% amino acid residues. Methylation analysis coupled with mild acid hydrolysis indicates that the backbone of the polysaccharide portion of the toxin is composed of α-1,6-linked mannosyl residues with a 3-linked terminal rhamnosyl residue linked to C-3 of almost every mannosyl residue. The carbohydrate portion of the molecule is linked to the peptide via O-glycosidic linkages to both threonyl and seryl residues. All three components of the toxin are capable of causing wilt in stem cuttings of American elm.