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).     

Conformational energy studies of beta-sheets of model silk fibroin peptides. I. Sheets of poly(Ala-Gly) chains

A new model structure is proposed for the silk I form of the crystalline domains of Bombyx mori silk fibroin and the corresponding crystal form of poly(L-Ala-Gly). It was deduced from conformational energy computations on stacked sheet structures of poly(L-Ala-Gly). The novel sheet structure contains interstrand hydrogen bonds but is composed of anti-parallel polypeptide chains whose conformation differs from that of the antiparallel beta-sheets that constitute the silk II structure. The strands of the new sheet have a two-residue repeat, in which the Ala residues adopt a right-handed and the Gly residues a left-handed sheet-like conformation. The computed unit cell is orthorhombic, with cell dimensions a = 8.94 A, b = 6.46 A, and c = 11.26 A. The model accounts for most spacings in the observed fiber x-ray diffraction patterns of silk I and of the silk-I-like form of poly(L-Ala-Gly), and it is consistent with nmr and ir spectroscopic data. As a test of the computations, the well-established beta-sheet structure of silk II and the corresponding form of poly(L-Ala-Gly) have been reproduced. The computed energies for the two forms of poly(L-Ala-Gly) indicate that the silk-II-like form is more stable, by about 1.0 kcal/mol per residue. The main difference between the two structures is the orientation of the Ala side chains of neighboring strands in each sheet. In the Pauling-Corey beta-sheet and in the silk II form, referred to as an "in-register" structure, the Ala side chains of every strand point to the same side of a sheet. In the silk I structure, referred to as "out-of-register," the side chains of Ala residues in adjacent strands point to opposite sides of the sheet.     

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.     

Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH

The homotetramer of transthyretin (TTR) dissociates into a monomeric amyloidogenic intermediate that self-assembles into amyloid fibrils at low pH. We have performed molecular dynamics simulations of monomeric TTR at neutral and low pH at physiological (310 K) and very elevated temperature (498 K). In the low-pH simulations at both temperatures, one of the two beta-sheets (strands CBEF) becomes disrupted, and alpha-sheet structure forms in the other sheet (strands DAGH). alpha-sheet is formed by alternating alphaL and alphaR residues, and it was first proposed by Pauling and Corey. Overall, the simulations are in agreement with the available experimental observations, including solid-state NMR results for a TTR-peptide amyloid. In addition, they provide a unique explanation for the results of hydrogen exchange experiments of the amyloidogenic intermediate-results that are difficult to explain with beta-structure. We propose that alpha-sheet may represent a key pathological conformation during amyloidogenesis.     

Molecular and crystal structure of the regenerated form of (1----3)-alpha-D-mannan.

The crystal structure of the hydrated form of (1----3)-alpha-D-mannan, obtained by solid-state deacetylation of the partially O-acetylated mannan, was analyzed by combined X-ray diffraction and stereochemical-model refinement techniques. The structure crystallizes in a four-chain, monoclinic unit cell with parameters a = 11.33 A, b = 18.36 A, c (fiber repeat) = 8.25 A, and gamma = 101.75 degrees, and the most probable space group is P2(1). In the most probable structure the chain-backbone conformation is a two-fold helix, but with all four O-6 rotational positions nonequivalent. The chains pack with antiparallel polarity and are connected by pairs of intermolecular hydrogen bonds that form an infinite, zig-zag sheet. There are 16 water molecules in the unit cell, generally embedded between the sheets in crystallographic positions, providing additional hydrogen bonding and establishing a three-dimensional hydrogen-bond network in the crystal structure. The reliability of the structure analysis is indicated by the X-ray residual R" = 0.281, based on 98 hkl reflection intensities.     

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover.

Guanine rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosidic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanine tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanines along a strand and different possible orientations of guanine strands in a G-tetraplex structure. It is found that for an oligo G stretch per se, a parallel four stranded structure with all guanines in anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanines along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosidic conformation and the inverted stacking arrangement arising from base flipover, in antiparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.     

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 reorganization of molecular sheets derived from cellulose II by molecular dynamics simulations

We investigated structural reorganization of two different kinds of molecular sheets derived from the cellulose II crystal using molecular dynamics (MD) simulations, in order to identify the initial structure of the cellulose crystal in the course of its regeneration process from solution. After a one-nanosecond simulation, the molecular sheet formed by van der Waals forces along the () crystal plane did not change its structure in an aqueous environment, while the other one formed by hydrogen bonds along the (1 1 0) crystal plane changed into a van der Waals-associated molecular sheet, such as the former. The two structures that were calculated showed substantial similarities such as the high occupancy of intramolecular hydrogen bonds between O3^H and O5 of over 0.75, few intermolecular hydrogen bonds, and the high occurrence of hydrogen bonding with water. The convergence of the two structures into one denotes that the van der Waals-associated molecular sheet can be the initial structure of the cellulose crystal formed in solution. The main chain conformations were almost the same as those in the cellulose II crystal except for a −16° shift of φ (dihedral angle of O5-C1-O1-C4) and the gauche-gauche conformation of the hydroxymethyl side group appears probably due to its hydrogen bonding with water. These results suggest that the van der Waals-associated molecular sheet becomes stable in an aqueous environment with its hydrophobic inside and hydrophilic periphery. Contrary to this, a benzene environment preferred a hydrogen-bonded molecular sheet, which is expected to be the initial structure formed in benzene.     

Conformational and geometrical properties of idealized beta-barrels in proteins

An equation for calculating the distances between the atoms involved in forming an idealized hydrogen bond in a parallel or antiparallel beta-barrel has been derived by adjusting the corresponding data given by Pauling and Corey for a beta-sheet. Based on these distances, a geometrical optimization method was developed, by which one can generate various idealized beta-barrels: parallel or antiparallel, tilted or non-tilted, right-tilted or left-tilted. For each type of idealized beta-barrel thus obtained, the corresponding conformation and characteristic geometric parameters as well as their relationship are analyzed and discussed. Since the strand in a tilted beta-barrel traces a curve rather than a straight line on a cylinder-like surface, a regular chain in which the dihedral angles of each residue are the same cannot form a tilted beta-barrel but only a non-tilted beta-barrel. As observed, the strands of a right-tilted beta-barrel possess a very strong right-handed twist. The radii of the idealized tilted parallel and antiparallel beta-barrels are greater than those of the corresponding non-tilted ones by approximately 1 A and approximately 1.5 A, respectively. Consequently, there is relatively more room for a tilted beta-barrel to accommodate the internal side-chains, suggesting that a conformational change from a non-tilted beta-barrel to a tilted one would ease the repulsion among the crowded internal side-chains so as to make the structure more stable. The values of root-mean-square fits indicate that the idealized right-tilted beta-barrels coincide quite well with the observed beta-barrels in both parallel and antiparallel cases.     

Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family

Magainin 2 and PGLa are among the best-studied cationic antimicrobial peptides. They bind preferentially to negatively charged membranes and apparently cause their disruption by the formation of transmembrane pores, whose detailed structure is still unclear. Here we report the results of 5–9 μs all-atom molecular dynamics simulations starting from tetrameric transmembrane helical bundles of these two peptides, as well as their stoichiometric mixture, and the analog MG-H2 in DMPC or 3:1 DMPC/DMPG membranes. The simulations produce pore structures that appear converged, although some effect of the starting peptide arrangement (parallel vs. antiparallel) is still observed on this timescale. The peptides remain mostly helical and adopt tilted orientations. The calculated tilt angles for PGLa are in excellent agreement with recent solid state NMR experiments. The antiparallel dimer structure in the magainin 2 simulations resembles previously determined NMR and crystal structures. More transmembrane orientations and a larger and more ordered pore are seen in the 1:1 heterotetramer with an antiparallel helix arrangement. Insights into the mechanism of synergy between these two peptides are obtained via implicit solvent modeling of homo- and heterodimers and analysis of interactions in the atomistic simulations. This analysis suggests stronger pairwise interactions in the heterodimer than in the two homodimers.     

Mechanical Response of Silk Crystalline Units from Force-Distribution Analysis

The outstanding mechanical toughness of silk fibers is thought to be caused by embedded crystalline units acting as cross links of silk proteins in the fiber. Here, we examine the robustness of these highly ordered β-sheet structures by molecular dynamics simulations and finite element analysis. Structural parameters and stress-strain relationships of four different models, from spider and Bombyx mori silk peptides, in antiparallel and parallel arrangement, were determined and found to be in good agreement with x-ray diffraction data. Rupture forces exceed those of any previously examined globular protein many times over, with spider silk (poly-alanine) slightly outperforming Bombyx mori silk ((Gly-Ala)_n). All-atom force distribution analysis reveals both intrasheet hydrogen-bonding and intersheet side-chain interactions to contribute to stability to similar extent. In combination with finite element analysis of simplified β-sheet skeletons, we could ascribe the distinct force distribution pattern of the antiparallel and parallel silk crystalline units to the difference in hydrogen-bond geometry, featuring an in-line or zigzag arrangement, respectively. Hydrogen-bond strength was higher in antiparallel models, and ultimately resulted in higher stiffness of the crystal, compensating the effect of the mechanically disadvantageous in-line hydrogen-bond geometry. Atomistic and coarse-grained force distribution patterns can thus explain differences in mechanical response of silk crystals, opening up the road to predict full fiber mechanics.     

Antiparallel beta-sheets in the crystal structure of the heptapeptide Met-Glu-His-Phe-Arg-Trp-Gly (ACTH 4-10)

The conformation of the molecules in ACTH 4-10 has been determined as part of a study of the conformations of the biologically active N-terminal fragments of the adrenocorticotropic hormone (ACTH). ACTH 4-10 crystallizes in two different superstructures. The substructure considered in the present work, is monoclinic, space group C2, a = 25.75(1) A, b = 27.78(1) A, c = 20.35(1) A, beta = 114.0(1) degrees, Z = 8 molecules ACTH 4-10 plus 22 weight per cent solvent. The crystals contain antiparallel beta-sheets, the orientations of the side groups are not found, because of disorder. The present crystal structure and those of other linear oligopeptides emphasize that antiparallel beta-sheets are energetically favourable. It is very unlikely, however, that the ACTH 4-10 crystals contain the molecules in their biologically active form.     

Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology

The self-assembly of beta(2)-microglobulin into fibrils leads to dialysis-related amyloidosis. pH-mediated partial unfolding is required for the formation of the amyloidogenic intermediate that then self-assembles into amyloid fibrils. Two partially folded intermediates of beta(2)-microglobulin have been identified experimentally and linked to the formation of fibrils of distinct morphology, yet it remains difficult to characterize these partially unfolded states at high resolution using experimental approaches. Consequently, we have performed molecular dynamics simulations at neutral and low pH to determine the structures of these partially unfolded amyloidogenic intermediates. In the low-pH simulations, we observed the formation of alpha-sheet structure, which was first proposed by Pauling and Corey. Multiple simulations were performed, and two distinct intermediate state ensembles were identified that may account for the different fibril morphologies. The predominant early unfolding intermediate was nativelike in structure, in agreement with previous NMR studies. The late unfolding intermediate was significantly disordered, but it maintained an extended elongated structure, with hydrophobic clusters and residual alpha-extended chain strands in specific regions of the sequence that map to amyloidogenic peptides. We propose that the formation of alpha-sheet facilitates self-assembly into partially unfolded prefibrillar amyloidogenic intermediates.     

Determination of intermolecular distance for a model peptide of Bombyx mori silk fibroin, GAGAG, with rotational echo double resonance

Rotational echo double resonance NMR spectroscopy is applied for the determination of the distance of intermolecular chains of pentapeptide, GAGAG (G: Gly, A: Ala), a model typical of the crystalline domain in Bombyx mori silk fibroin. 1:4 mixture of G[1-(13)C]AGAG and GAG[(15)N]AG with antiparallel beta-sheet structure was used to determine the distance of intermolecular hydrogen bonding between adjacent molecules within pleated sheet and the (13)C-(15)N interatomic distance was determined to be 4.3 A. On the other hand, 1:4 mixture of GAG[1-(13)C]AG and GAG[(15)N]AG gave information on the interpleated sheet arrangement. When we assumed the same distances between two interpleated sheets, the distance was calculated to be 5.3 A and the angle (15)N-(13)C-(15)N was 180 degrees.     

Cooperative effects in hydrogen-bonding of protein secondary structure elements: a systematic analysis of crystal data using Secbase

A systematic analysis of the hydrogen-bonding geometry in helices and beta sheets has been performed. The distances and angles between the backbone carbonyl O and amide N atoms were correlated considering more than 1500 protein chains in crystal structures determined to a resolution better than 1.5 A. They reveal statistically significant trends in the H-bond geometry across the different secondary structural elements. The analysis has been performed using Secbase, a modular extension of Relibase (Receptor Ligand Database) which integrates information about secondary structural elements assigned to individual protein structures with the various search facilities implemented into Relibase. A comparison of the mean hydrogen-bond distances in alpha helices and 3(10) helices of increasing length shows opposing trends. Whereas in alpha helices the mean H-bond distance shrinks with increasing helix length and turn number, the corresponding mean dimension in 3(10) helices expands in a comparable series. Comparing similarly the hydrogen-bond lengths in beta sheets there is no difference to be found between the mean H-bond length in antiparallel and parallel beta sheets along the strand direction. In contrast, an interesting systematic trend appears to be given for the hydrogen bonds perpendicular to the strands bridging across an extended sheet. With increasing number of accumulated strands, which results in a growing number of back-to-back piling hydrogen bonds across the strands, a slight decrease of the mean H-bond distance is apparent in parallel beta sheets whereas such trends are obviously not given in antiparallel beta sheets. This observation suggests that cooperative effects mutually polarizing spatially well-aligned hydrogen bonds are present either in alpha helices and parallel beta sheets whereas such influences seem to be lacking in 3(10) helices and antiparallel beta sheets.     

Effect of external electrostatic field on the stability of β sheet structures

To explore the effect of an external electrostatic field (EEF) on the stability of protein conformations, the molecular dynamic modeling approach was applied to evaluate the effect of an EEF along the x or y direction on a water cluster containing a parallel or antiparallel β sheet structure. The β sheet structure contained two strands with a (Gly)₃ sequence separated by a distance d along the x direction. The mean forces between the two strands along the x direction were computed from the trajectories of molecular dynamics simulations. In the absence of the EEF, the forces between the two strands in vacuum were repulsive and attractive in the parallel and antiparallel β sheet structures, respectively. In contrast, the mean forces between the two strands in water were attractive in both the parallel and antiparallel β sheet structures. This is because the electric interactions between the two strands were shielded by water, and the hydrophobic effect dominated the interaction between the two strands. When an EEF >50 MV/cm was applied to the water cluster, the attractive force between the two strands in the parallel and antiparallel β sheet structures decreased and increased, respectively. Further, the binding affinity between the two strands in the parallel and antiparallel β sheet structures also decreased and increased, respectively. This is because the large EEF leads to dielectric saturation, and consequently reduces the effects of the dielectric shielding and hydrophobic interactions. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 861–870, 2014.     

Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding

An amino-terminal fragment of human apolipoprotein E3 (residues 1-165) has been expressed and crystallized in three different crystal forms under similar crystallization conditions. One crystal form has nearly identical cell dimensions to the previously reported orthorhombic (P2(1)2(1)2(1)) crystal form of the amino-terminal 22 kDa fragment of apolipoprotein E (residues 1-191). A second orthorhombic crystal form (P2(1)2(1)2(1) with cell dimensions differing from the first form) and a trigonal (P3(1)21) crystal form were also characterized. The structures of the first orthorhombic and the trigonal form were determined by seleno-methionine multiwavelength anomalous dispersion, and the structure of the second orthorhombic form was determined by molecular replacement using the structure from the trigonal form as a search model. A combination of modern experimental and computational techniques provided high-quality electron-density maps, which revealed new features of the apolipoprotein E structure, including an unambiguously traced loop connecting helices 2 and 3 in the four-helix bundle and a number of multiconformation side chains. The three crystal forms contain a common intermolecular, antiparallel packing arrangement. The electrostatic complimentarity observed in this antiparallel packing resembles the interaction of apolipoprotein E with the monoclonal antibody 2E8 and the low density lipoprotein receptor. Superposition of the model structures from all three crystal forms reveals flexibility and pronounced kinks in helices near one end of the four-helix bundle. This mobility at one end of the molecule provides new insights into the structural changes in apolipoprotein E that occur with lipid association.     

Crystal structure of an extended-conformation leucine-enkephalin dimer monohydrate

The structure of a new crystal form of leucine-enkephalin has been determined by X-ray diffraction. There are two independent molecules in the asymmetric unit and both have extended peptide backbone conformations with side-chains arranged alternately above and below the backbone planes. The two pentapeptides are hydrogen-bonded to each other and to other molecules forming an extended antiparallel beta-pleated sheet. The structure differs from that in similar crystals of methionine enkephalin primarily in side-chain orientations and inter-sheet interactions.     

The crystal structure of Bombyx mori silk fibroin at the air–water interface

A new crystalline polymorph of Bombyx mori silk, which forms at the air–water interface, has been characterized. A previous study found this structure to be trigonal, and to be distinctly different than the two previously observed silk crystal structures, silk I and silk II. This new structure was named silk III. Identification of this new silk polymorph was based on evidence from transmission electron microscopy and electron diffraction, coupled with molecular modeling. In the current paper, additional data enables us to refine our model of the silk III structure. Some single crystal electron diffraction patterns indicate a deviation in symmetry away from a perfect trigonal unit cell to monoclinic unit cell. The detailed shape of the powder diffraction peaks also supports a monoclinic cell. The monoclinic crystal structure has an nonprimitive unit cell incorporating a slightly distorted hexagonal packing of silk molecular helices. The chains each assume a threefold helical conformation, resulting in a crystal structure similar to that observed for polyglycine II, but with some additional sheet-like packing features common to the threefold helical crystalline forms of many glycine-rich polypeptides. © 1997 John Wiley & Sons, Inc. Biopoly 42: 705–717, 1997     

Crystal and molecular structure of the dehydropeptide Ac-delta Phe-Val-delta Phe-NH-Me.

The dehydropeptide Ac-delta Phe-L-Val-delta Phe-NH-Me, containing two dehydrophenylalanine (delta Phe) residues, crystallizes from methanol/water in space group P212121, with a = 12.622 (1), b = 12.979 (1), and c = 15.733 (1) A. In the solid state, the molecular structure is characterized by the presence of two intramolecular hydrogen bonds which form two consecutive beta-bends. The (phi, psi) torsion angles of the three residues are very similar and close to the standard values of type III beta-bends, so the molecular conformation corresponds to an incipient right-handed 3(10)-helix, only slightly distorted. In the crystal, the molecules are linked by head-to-tail hydrogen bonds, thus forming continuous helical columns packed in antiparallel mode. There are no lateral hydrogen bonds; the only interactions are hydrophobic contacts between the apolar side chains of neighboring helical columns.