Geometrical effects of phospholipid olefinic bonds on the structure and dynamics of membranes: A molecular dynamics study

The trans isomers of fatty acids are found in human adipose tissue. These isomers have been linked with deleterious health effects (e.g., coronary artery disease). In this study, we performed molecular dynamics simulations to investigate the structures and dynamic properties of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-elaidoyl sn-glycero-3-phosphatidylcholine (PEPC) lipid bilayers. The geometry of the olefinic bond and membrane packing effects significantly influenced the conformations and dynamics of the two CC single bonds adjacent to the olefinic bond. For the PEPC lipid, the two CC single bonds adjacent to the olefinic bond adopted mainly nonplanar skew–trans and planar cis–trans motifs; although the cis conformation featured relatively strong steric repulsion, it was stabilized through membrane packing because its planar structure is more suitable for membrane packing. Moreover, membrane packing effects stabilized the planar transition state for conformational conversion to a greater extent than they did with the nonplanar transition state, thereby affecting the dynamics of conformational conversion. The rotational motions of the first neighboring CC single bonds were much faster than those of typical saturated CC single bonds; in contrast, the rotational motions of the second neighboring CC single bonds were significantly slower than those of typical saturated torsion angles. The packing of PEPC lipids is superior to that of POPC lipids, leading to a smaller area per lipid, a higher order parameter and a smaller diffusion coefficient. The distinct properties of POPC and PEPC lipids result in PEPC lipids forming microdomains within a POPC matrix.     

Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins

The packing of α-helices and β-sheets in six $\text{α}\text{β}$ proteins (e.g. flavodoxin) has been analysed. The results provide the basis for a computer algorithm to predict the tertiary structure of an $\text{α}\text{β}$ protein from its amino acid sequence and actual assignment of secondary structure.The packing of an individual α-helix against a β-sheet generally involves two adjacent ± 4 rows of non-polar residues on the α-helix at the positions i, i + 4, i + 8, i + 1, i + 5, i + 9. The pattern of interacting β-sheet residues results from the twisted nature of the sheet surface and the attendant rotation of the side-chains. At a more detailed level, four of the α-helical residues (i + 1, i + 4, i + 5 and i + 8) form a diamond that surrounds one particular β-sheet residue, generally isoleucine, leucine or valine. In general, the α-helix sits 10 Å above the sheet and lies parallel to the strand direction.The prediction follows a combinational approach. First, a list of possible β-sheet structures (10⁶ to 10¹⁴) is constructed by the generation of all β-sheet topologies and β-strand alignments. This list is reduced by constraints on topology and the location of non-polar residues to mediate the sheet/helix packing, and then rank-ordered on the extent of hydrogen bonding. This algorithm was uniformly applied to 16 $\text{α}\text{β}$ domains in 13 proteins. For every structure, one member of the reduced list was close to the crystal structure; the root-mean-square deviation between equivalenced C^α atoms averaged 5.6 Å for 100 residues. For the $\text{α}\text{β}$ proteins with pure parallel β-sheets, the total number of structures comparable to or better than the native in terms of hydrogen bonds was between 1 and 148. For proteins with mixed β-sheets, the worst case is glyceraldehyde-3-phosphate dehydrogenase, where as many as 3800 structures would have to be sampled. The evolutionary significance of these results as well as the potential use of a combinatorial approach to the protein folding problem are discussed.     

Crystal structure of Turkey egg-white lysozyme: Results of the molecular replacement method at 5 Å resolution

Turkey egg-white lysozyme differs from hen egg-white lysozyme in its primary structure in 7 of the 129 residues. We have determined the rotational and translational parameters relating the known co-ordinates of hen egg-white lysozyme molecule to the turkey lysozyme. The rotational parameters were determined using the rotation function, the translational parameters were determined by placing the properly rotated molecule systematically at all positions within the unit cell and searching for those positions producing few intermolecular contacts between the α-carbon atoms of one molecule and all its neighbors. These parameters were refined by minimizing the conventional R factor between observed and calculated structure amplitudes. The final rotational and translational parameters give an R value of 46.7% for reflections with d spacings between 6 Å and 12 Å and have 7 intermolecular contacts closer than 5 Å between the a carbon atoms of one molecule and all its neighbors. An electron density map has been calculated at 5 Å resolution; the packing of the molecules in this form appears to present the entire length of the active cleft in the vicinity of the crystallographic 6-fold axis and does not appear to be blocked by neighboring molecules.     

De-novo modeling and ESR validation of a cyanobacterial FoF1-ATP synthase subunit bb′ left-handed coiled coil

The structure and functional role of the dimeric external stalk of F_oF₁-ATP synthases have been very actively researched over the last years. To understand the function, detailed knowledge of the structure and protein packing interactions in the dimer is required. In this paper we describe the application of structural prediction and molecular modeling approaches to elucidate the structural packing interaction of the cyanobacterial ATP synthase external stalk. In addition we present biophysical evidence derived from ESR spectroscopy and site directed spin labeling of stalk proteins that supports the proposed structural model. The use of the heterodimeric bb′ dimer from a cyanobacterial ATP synthase (Synechocystis sp. PCC 6803) allowed, by specific introduction of spin labels along each individual subunit, the evaluation of the overall tertiary structure of the subunits by calculating inter-spin distances. At defined positions in both b and b′ subunits, reporter groups were inserted to determine and confirm inter-subunit packing. The experiments showed that an approximately 100 residue long section of the cytoplasmic part of the bb′-dimer exists mostly as an elongated α-helix. The distant C-terminal end of the dimer, which is thought to interact with the δ-subunit, seemed to be disordered in experiments using soluble bb′ proteins. A left-handed coiled coil packing of the dimer suggested from structure prediction studies and shown to be feasible in molecular modeling experiments was used together with the measured inter-spin distances of the inserted reporter groups determined in ESR experiments to support the hypothesis that a significant portion of the bb′ structure exists as a left-handed coiled coil.     

The specificity of α-glucosidase from Saccharomyces cerevisiae differs depending on the type of reaction: hydrolysis versus transglucosylation

Our investigation of the catalytic properties of Saccharomyces cerevisiae α-glucosidase (AGL) using hydroxybenzyl alcohol (HBA) isomers as transglucosylation substrates and their glucosides in hydrolytic reactions demonstrated interesting findings pertaining to the aglycon specificity of this important enzyme. AGL specificity increased from the para(p)- to the ortho(o)-HBA isomer in transglucosylation, whereas such AGL aglycon specificity was not seen in hydrolysis, thus indicating that the second step of the reaction (i.e., binding of the glucosyl acceptor) is rate-determining. To study the influence of substitution pattern on AGL kinetics, we compared AGL specificity, inferred from kinetic constants, for HBA isomers and other aglycon substrates. The demonstrated inhibitory effects of HBA isomers and their corresponding glucosides on AGL-catalyzed hydrolysis of p-nitrophenyl α-glucoside (PNPG) suggest that HBA glucosides act as competitive, whereas HBA isomers are noncompetitive, inhibitors. As such, we postulate that aromatic moieties cannot bind to an active site unless an enzyme-glucosyl complex has already formed, but they can interact with other regions of the enzyme molecule resulting in inhibition.     

Temperature dependence of the Langmuir monolayer packing of mycolic acids from Mycobacterium tuberculosis

Phase diagrams of the Langmuir monolayer of dicyclopropyl alpha mycolic acid (α-MA), cyclopropyl methoxy mycolic acid (MeO-MA), and cyclopropyl ketomycolic acids (Keto-MA) from Mycobacterium tuberculosis were obtained by thermodynamic analysis of the surface pressure (π) vs. average molecular area (A) isotherms at temperatures in the range of 10-46 °C. The Langmuir monolayers of MAs were shown to exhibit various phases depending on the temperature (T) and the π values. In the Langmuir monolayer of Keto-MA, the carbonyl group in the meromycolate chain apparently touches the water surface to give the molecule a W-shape in all the temperatures and surface pressures studied. Keto-MA formed a rigid solid condensed film, with four hydrocarbon chains packing together, not observed in the others. In contrast, the monolayer films of α-and MeO-MAs having no such highly hydrophilic intra-chain groups in the meromycolate chain were mostly in liquid condensed phase. This novel insight into the packing of mycolic acids opens up new avenues for the study of the role of mycolic acids in the mycobacterial cell envelopes and pathogenic processes.     

Effect of pinene isomers on germination and growth of maize

Terpenes, secondary metabolites that are present in the essential oils of aromatic plants, are responsible for the biochemical interaction between plants, known as allelopathy. Monoterpenes are a major component of essential oils. Pinene is a monoterpene well-known for its phytotoxic action, but little is known about the allelopathic effect of its isomers. The aim of this study is to determine the effect of pinene's structural isomers and enantioisomers [(−)-α-pinene; (+)-α-pinene; (−)-β-pinene and (+)-β-pinene] at 0.16 mM, on certain physiological parameters (growth, dry weight, phenol, photosynthetic pigments and abscisic acid content) in both the germination and growth of maize (Zea mays L.). In germination bioassays, neither of the α-pinene stereoisomers showed change when compared to the control with respect to seed vigour; but root growth was increased, while β-pinene (racemic mixture) inhibited germination and plant length. In the growth bioassay, all of the pinene isomers decreased the plant length. In general, β-pinene terpene was more phytotoxic than α-pinene in both bioassays. Differences in germination and growth of maize treated with the pinene isomers can be attributed to different action mechanisms which depends both on the growth phases of maize and on the particular pinene isomers.     

Vibrational frequencies and modes of alpha-helix

Dichroic properties of the far-infrared absorption bands of the right-handed α-helix of poly-L -alanine were measured. The normal vibration frequencies of this structure were calculated. The assignments of bands were made and the vibrational modes dis-cussed. The frequencies of the α-helix vibrations with various phase differences were calculated. The frequencies of accordionlike vibrations and Young's modulus of the α-helix were estimated. The vibrational frequency for the right-handed α-helices of poly-D -alanine and poly(L -α-amino-n-butyric acid) were calculated, and the results were used for the interpretation of the spectra of copoly-D ,L -alanines and poly(L -α-amino-n-butyric acid). For the latter compound the existence of the rotational isomers in the side chain was strongly suggested. The vibrational modes of the bands characteristic of the α-helix were discussed with regard to the results of the normal coordinate treatment.     

The role of local tight packing of hydrophobic groups in β-structure

An analysis of the tendency of hydrophobic groups to tight packing on the surface of β-sheets based on well-known parameters of β-sheets and hydrophobic groups was conducted. This analysis shows the existence of very limited numbers and clearly outlined architecture families of regular parts for the majority of β-structure-containing domains. Each family of architecture strongly depends on the number of β-strands in the pure β-domains and on the existence and number of additional α-helixes and on the mutual arrangements β-strands and α-helixes along the chain in mixed α/β-domains. This paper demonstrates that the tendency of hydrophobic groups to the local tight packing on the surface of β-sheets is probably the main reason for the twist of β-sheets. © 1993 Wiley-Liss, Inc.     

Synthesis of α- and β-N-oxalyl-l-α,β-diaminopropionic acids and their isolation from seeds of Lathyrus sativus

The α- and β-N-oxalyl derivatives of l-α,β-diaminopropionic acid have been chemically synthesized and also isolated from seed extracts of Lathyrus sativus. Chemical and physical properties of the natural and synthetic isomers were in good agreement. The toxicity of the α-isomer to chicks was evaluated and compared with that of the β-isomer.     

Solid state properties of anomeric 1-O-n-octyl-d-glucopyranosides

The anomers of 1-O-n-octyl-D-glucopyranosides exhibit different crystal packing and thermodynamic properties. Crystallization either from solution or by epitaxy of the α-anomer resembles that of other amphiphiles, such as lysolecithin, and is isostructural to the decyl homologue. The β-anomer crystallizes into a unique form, independent of conditions, with the longest cyrstallographic axis parallel to the best developed crystal face. Both compounds exhibit two phase transitions, one near 70°C, the other above 100°C. The latter corresponds to melting to an isotropic liquid for both forms, but the former is distinctly different for the two anomers. Thus, birefringence is lost only with the β-anomer, while the enthalpy change is two-fold larger for the α-anomer. The crystal packing of the two compounds are thus clearly different.     

Sorbents with immobilized glycopeptide antibiotics for separating optical isomers by high-performance liquid chromatography

Chiral sorbents for HPLC separation of optical isomers carrying glycopeptide antibiotics (eremomycin or its eremosaminyl aglycon, ristomycin, or vancomycin) fixed onto the surface of silica gel have been synthesized. The patterns of the retention and separation of profen isomers and their dependence on the nature of the chiral selector and the eluant composition have been studied. The sorbents were shown to be highly enantiospecific in separating the isomers of α-amino-, α-hydroxy-, and α-methylphenylcarboxylic acids (profens)     

Refolding of cytochromeb 562 and its structural stabilization by introducing a disulfide bond

The packing mechanism of the secondary structures (4-α-helices and 3₁₀-helix) of cytochromeb ₅₆₂ is simulated by the “island model,” where the formation of protein structure is accomplished by the growth-type mechanism with the driving force of packing of the long-range and specific hydrophobic interactions. Packing proceeds through the formation of the structure at the nonhelical part, where a lot of hydrophobic pairs are distributed. Consequently, conformation, nearly similar to the native one, is successfully obtained. With the help of this result, the theoretical prediction of the possibility of forming this disulfide mutant (N22C/G82C) ofb ₅₆₂ can be performed prior to the experiments by our geometrical criterion (“lampshade”). This criterion is expected to be a significant principle for introducing possible disulfide bonds into a protein to be engineered.     

Attraction of newly hatched codling moth larvae (Laspeyresia pomonella) to synthetic stereo-isomers of farnesene

Newly hatched Laspeyresia pomonella larvae were attracted to only two of six synthetic stereo-isomers of the acyclic sesquiterpene farnesene. These were (E,E)-α-farnesene and (Z,E)-α-farnesene which together comprise a natural attractant for the insect. Two other α-isomers and two β-isomers had no influence on larval behaviour. The activity of isomers is correlated with their molecular shape.     

The symmetries of filamentous phage particles

The helical symmetries of two classes of filamentous bacteriophage particles are distinctly different. The symmetry of the class I particles is²C₅S_~2.0 (a 5-fold rotation axis combined with an approximately 2-fold screw axis). The symmetry of the class II particles is C₁S_5.4 (a one-start helix with 27 subunits equally spaced along five turns). The same basic α-helical interlocking arrangement of the largely α-helical coat protein subunits can be accommodated by the symmetry of the two classes of phage particles. The conservation of this structural pattern reflects intrinsic packing properties of α-helices. The difference between the symmetries of the class I and class II particles suggests that different assembly processes may have evolved to form these structures with very similar protein packing architectures.     

The protein-solvent glass transition

The protein dynamical transition and its connection with the liquid-glass transition (GT) of hydration water and aqueous solvents are reviewed. The protein solvation shell exhibits a regular glass transition, characterized by steps in the specific heat and the thermal expansion coefficient at the calorimetric glass temperature T_G ≈ 170 K. It implies that the time scale of the structural α-relaxation has reached the experimental time window of 1–100 s. The protein dynamical transition, identified from elastic neutron scattering experiments by enhanced amplitudes of molecular motions exceeding the vibrational level [1], probes the α-process on a shorter time scale. The corresponding liquid-glass transition occurs at higher temperatures, typically 240 K. The GT is generally associated with diverging viscosities, the freezing of long-range translational diffusion in the supercooled liquid. Due to mutual hydrogen bonding, both, protein- and solvent relaxational degrees of freedom slow down in paralled near the GT. However, the freezing of protein motions, where surface-coupled rotational and librational degrees of freedom are arrested, is better characterized as a rubber-glass transition. In contrast, internal protein modes such as the rotation of side chains are not affected. Moreover, ligand binding experiments with myoglobin in various glass-forming solvents show, that only ligand entry and exit rates depend on the local viscosity near the protein surface, but protein-internal ligand migration is not coupled to the solvent. The GT leads to structural arrest on a macroscopic scale due to the microscopic cage effect on the scale of the intermolecular distance. Mode coupling theory provides a theoretical framework to understand the microcopic nature of the GT even in complex systems. The role of the α- and β-process in the dynamics of protein hydration water is evaluated. The protein-solvent GT is triggered by hydrogen bond fluctuations, which give rise to fast β-processes. High-frequency neutron scattering spectra indicate increasing hydrogen bond braking above T_G.     

An amino acid packing code for α-helical structure and protein design

This work demonstrates that all packing in α-helices can be simplified to repetitive patterns of a single motif: the knob-socket. Using the precision of Voronoi Polyhedra/Delauney Tessellations to identify contacts, the knob-socket is a four-residue tetrahedral motif: a knob residue on one α-helix packs into the three-residue socket on another α-helix. The principle of the knob-socket model relates the packing between levels of protein structure: the intra-helical packing arrangements within secondary structure that permit inter-helix tertiary packing interactions. Within an α-helix, the three-residue sockets arrange residues into a uniform packing lattice. Inter-helix packing results from a definable pattern of interdigitated knob-socket motifs between two α-helices. Furthermore, the knob-socket model classifies three types of sockets: (1) free, favoring only intra-helical packing; (2) filled, favoring inter-helical interactions; and (3) non, disfavoring α-helical structure. The amino acid propensities in these three socket classes essentially represent an amino acid code for structure in α-helical packing. Using this code, we used a novel yet straightforward approach for the design of α-helical structure to validate the knob-socket model. Unique sequences for three peptides were created to produce a predicted amount of α-helical structure: mostly helical, some helical, and no helix. These three peptides were synthesized, and helical content was assessed using CD spectroscopy. The measured α-helicity of each peptide was consistent with the expected predictions. These results and analysis demonstrate that the knob-socket motif functions as the basic unit of packing and presents an intuitive tool to decipher the rules governing packing in protein structure.     

Sequence information within the lamB genes in required for proper routing of the bacteriophage lambda receptor protein to the outer membrane of Escherichia coli K-12

The structure of Satellite tobacco necrosis virus (STNV) has been determined to 3.0 Å resolution by X-ray crystallography. Electron density maps were obtained with phases based on one heavy-atom derivative and several cycles of phase refinement using the 60-fold non-crystallographic symmetry in the particle. A model for one protein subunit was built using a computer graphics display. The subunit is constructed mainly of a β-roll structure forming two β-sheets, each of four antiparallel strands. The N-termini of the subunits form bundles of three α-helices extending into the RNA region of the virus at the 3-fold axis. The topology of the polypeptide chain is the same as, and the conformation clearly similar to, that of the shell domains of the Tomato bushy stunt virus (TBSV) and Southern bean mosaic virus (SBMV) protein subunits. The subunit packing in the T = 1 STNV structure is, however, significantly different from the packing of these T = 3 viruses: parts of some of the structural elements facing the RNA in TBSV and SBMV are utilized for subunit-subunit contacts in STNV. No RNA structure is obvious in the present icosahedrally averaged electron density maps. The protein surface facing the RNA contains mainly hydrophilic residues, especially lysine and arginine.     

Tubular arrays of spheres: Geometry,continuous and discontinuous contraction,and the role of moving dislocations

Microtubules, bacterial flagella, viral capsids, and other biological structures are tubular packings of subunits. The subunits form helical rows or parastichies. Such arrays are modeled as tubular packings of spheres. Parastichies along which spheres are in contact provide a symbol for a particular tubule. A tubule with hexagonal packing and k-fold rotational symmetry about its axis has the symbol k(m; m + n; n) where km, k(m + n), and kn represent the three sets of contact parastichies. A tubule with rhombic packing has two sets of contact parastichies and the symbol k(m; n). The symbol determines the chirality. Two processes are described by which tubules can be interconverted: continuous contraction and discontinuous contraction. In continuous contraction of a hexagonally packed tubule, contacts along km-, k(m + n)-, or kn-parastichies are broken uniformly throughout the tubule. The tubule becomes rhombic and undergoes twisting and change of length and radius. Continuation of the process converts the intermediate rhombic packing into a new hexagonal packing. Any tubule can be converted to any other having the same rotational symmetry k, by one or more steps of continuous contraction, but not to a tubule with different k. With respect to change in length, continuous contraction from one hexagonal packing to another may be either monotonic or non-monotonic. A step of discontinuous contraction of a hexagonally packed tubule is mediated by passage of an edge dislocation through the tubule, by glide or climb. The presence of a single edge dislocation in a tubule divides it into two parts with two different packings. Passage of the dislocation to one end or the other of the tubule converts the entire tubule into one packing or the other. Any tubule may be converted to any other, regardless of k, by one or more steps of discontinuous contraction. Maps showing possible paths of continuous and discontinuous contraction summarize the relationships among tubules. The analysis will provide a useful basis for studying particular biological cases of contraction.