Lipid intermolecular hydrogen bonding: influence on structural organization and membrane function

The great variety of different lipids in membranes, with modifications to the hydrocarbon chains, polar groups and backbone structure suggests that many of these lipids may have unique roles in membrane structure and function. Acidic groups on lipids are clearly important, since they allow interaction with basic groups on proteins and with divalent cations. Another important property of certain lipids is their ability to interact intermolecularly with other lipids via hydrogen bonds. This interaction occurs through acidic and basic moieties in the polar head groups of phospholipids, and the amide moiety and hydroxyl groups on the acyl chain, sphingosine base and sugar groups of sphingo- and glycolipids. The putative ability of different classes of lipids to interact by intermolecular hydrogen bonding, the molecular groups which may participate and the effect of these interactions on some of their physical properties are summarized in Table IX. It is frequently questioned whether intermolecular hydrogen bonding could occur between lipids in the presence of water. Correlations of their properties with their molecular structures, however, suggest that it can. Participation in intermolecular hydrogen bonding increases the lipid phase transition temperature by approx. 8-16 Cdeg relative to the electrostatically shielded state and by 20-30 Cdeg relative to the repulsively charged state, while having variable effects on the enthalpy. It increases the packing density in monolayers, possibly also in the liquid-crystalline phase in bilayers, and decreases the lipid hydration. These effects can probably be accounted for by transient, fluctuating hydrogen bonds involving only a small percentage of the lipid at any one time. Thus, rotational and lateral diffusion of the lipids may take place but at a slower rate, and the lateral expansion is limited. Intermolecular hydrogen bonding between lipids in bilayers may be significantly stabilized, despite the presence of water, by the fact that the lipids are already intermolecularly associated as a result of the hydrophobic effect and the Van der Waals' interactions between their chains. The tendency of certain lipids to self-associate, their asymmetric distribution in SUVs, their preferential association with cholesterol in non-cocrystallizing mixtures, their temperature-induced transitions to the hexagonal phase and their inhibitory effect on penetration of hydrophobic residues of proteins partway into the bilayer can all be explained by their participation in intermolecular hydrogen bonding interactions.(ABSTRACT TRUNCATED AT 400 WORDS)     

Interaction of myelin basic protein with different ionization states of phosphatidic acid and phosphatidylserine

Myelin basic protein (BP) has a perturbing effect on some lipids, causing, among other effects, a decrease in the temperature and enthalpy of the phase transition. This is believed to be a result of penetration of some hydrophobic residues of the protein partway into the lipid bilayer. Variations in the perturbing effect of BP on different acidic lipids has been attributed to the ability of the lipids to participate in intermolecular hydrogen bonding which inhibits penetration of the protein. Participation in intermolecular hydrogen bonding depends on the ionization state of the lipid as well as the type of lipid. In order to further test the dependence of the degree of penetration of BP on the intermolecular hydrogen bonding properties of lipids, the effect of BP on the phase transition of lipids in different ionization states was studied using differential scanning calorimetry. Dipalmitoylphosphatidic acid (DPPA) and dimyristoylphosphatidylserine (DMPS) were studied at different pH-values from 4 to 9.5. The results were compared to data obtained earlier with phosphatidylglycerol (PG), which is in the same ionization state at pH-values above 4, in order to distinguish the effects of pH on the protein from effects on the lipids. The perturbing effect of BP on PG increases with increase in pH. This is probably a result of the increasing hydrophobicity of the protein as the histidines become deprotonated, which allows greater penetration of the protein into the bilayer. In contrast, the effect on DPPA was greatest at low pH, where the state of ionization of the lipid is less than 1 and protein binding utilizes all of the hydrogen bond accepting sites (P-O-) on the lipid. BP had no perturbing effect on DPPA at higher pH where the state of ionization is between 1 and 1.5, and hydrogen bond accepting and donating sites (P-OH) are still available even after binding of the protein. Thus hydrogen bonding occurs at high pH and penetration of hydrophobic residues of the protein into DPPA is inhibited. BP had a large perturbing effect on DMPS at all pH values above 4 suggesting that lipid intermolecular hydrogen bonding does not occur in the presence of the protein and its hydrophobic residues consequently can penetrate into the bilayer. The protein may inhibit hydrogen bonding by binding electrostatically to the anionic hydrogen bond accepting group of PS.     

The nucleation of monomeric parallel beta-sheet-like structures and their self-assembly in aqueous solution

The aromatic diacid residue 4,6-dibenzofuranbispropionic acid (1) was designed to nucleate a parallel beta-sheet-like structure in small peptides in aqueous solution via a hydrogen-bonded hydrophobic cluster. Even though a 14-membered ring hydrogen bond necessary for parallel beta-sheet formation is favored in simple amides composed of 1, this hydrogen bonding interaction does not appear to be sufficient to nucleate parallel beta-sheet formation in the absence of hydrophobic clustering between the dibenzofuran portion of 1 and the hydrophobic side chains of the flanking alpha-amino acids. The subsequence --hydrophobic residue-1-hydrophobic residue-- is required for folding in the context of a nucleated two-stranded parallel beta-sheet structure. In all cases where the peptidomimetics can fold into two diastereomeric parallel beta-sheet structures having different hydrogen bonding networks, these conformations appear to exchange rapidly. The majority of the parallel beta-sheet structures evaluated herein undergo linked intramolecular folding and self-assembly, affording a fibrillar beta-sheet quaternary structure. To unlink folding and assembly, asymmetric parallel beta-sheet structures incorporating N-methylated alpha-amino acid residues have been synthesized using a new solid phase approach. Residue 1 facilitates the folding of several peptides described within affording a monomeric parallel beta-sheet-like structure in aqueous solution, as ascertained by a variety of spectroscopic and biophysical methods, increasing our understanding of parallel beta-sheet structure.     

Effects of temperature and concentration on the structure of ethylene oxide–propylene oxide–ethylene oxide triblock copolymer (Pluronic P65) in aqueous solution: a molecular dynamics simulation study

The effects of temperature and solution concentration on the structure of triblock polymeric surfactant (ethylene oxide)₁₉(propylene oxide)₂₉(ethylene oxide)₁₉ (Pluronic P65) have been investigated by fully atomistic molecular dynamics simulations. The Flory–Huggins interaction parameter χ, hydrogen bonding and molecular mobility in the aqueous solution of P65 were investigated covering a composition range of 0.1–0.73 (water weight fraction) and a temperature range of 273–373 K. The Flory–Huggins parameters indicated that propylene oxide (PO) segments became hydrophobic with the increase in temperature, whereas ethylene oxide (EO) segments remained hydrophilic, which caused the increase in repulsion between EO and PO segments. The intermolecular hydrogen bonds in P65 solution including water–water hydrogen bonds and water–P65 hydrogen bonds increased with the increase in solution concentration and decreased with the increase in temperature. The critical micellar temperature of Pluronic P65 predicted by Flory–Huggins interaction parameter χ and hydrogen bonding was in good agreement with experimental data.     

On the Occurrence of Three-Center Hydrogen Bonds in Cyclodextrins in Crystalline Form and in Aqueous Solution: Comparison of Neutron Diffraction and Molecular Dynamics Results

Abstract

Three-center (bifurcated) hydrogen bonds may play a role by serving as an intermediate state between different dynamically changing hydrogen bonding patterns. Hydrogen bonding configurations can be studied experimentally by neutron diffraction and theoretically by computer simulation techniques. Here, both methods are used to analyse the occurrence of three-center hydrogen bonds in crystals of cyclodextrins.

Almost all experimentally observed three-center hydrogen bonds in the crystal are reproduced in the molecular dynamics (MD) simulations, even as far as the detailed asymmetric geometry is concerned. On the basis of this result a MD simulation of cyclodextrin in aqueous solution is searched for the occurrence of three-center hydrogen bonds. Significant differences are found. In solution more different three-center hydrogen bonds per α-cyclodextrin molecule are observed than in the crystal but the population (existence as percent of the simulation period) of each three-center hydrogen bond is lower in solution than in crystal. These may indeed serve as intermediate states in the process of changing one hydrogen bonding pattern into another.     

The structure and dynamics of ACTH (1-10) on the surface of a sodium dodecylsulfate (SDS) micelle: a molecular dynamics simulation study

ACTH (1-10), an adrenocorticotropin hormone fragment, was studied by molecular dynamics (MD) simulation in the NPT ensemble in an explicit sodium dodecylsulfate (SDS) micelle. Initially, distance restraints derived from NMR nuclear Overhauser enhancements were incorporated during the equilibration stage of the simulation. The analyses of the trajectories from the subsequent unrestrained MD showed that ACTH (1-10) does not conform to a helical structure at the micelle-water interface; however, the structure is amphipathic. The loss of the helical structure is due to decreased intramolecular hydrogen bonding accompanied by an increase of hydrogen bonding between the amide hydrogens of the peptide and the micelle head-groups. ACTH (1-10) was found to lie on the surface of the SDS micelle. Most of the hydrophobic interactions came from the side-chains of Met-4, Phe-7 and Trp-9. The peptide bonds were either hydrated or involved in intramolecular hydrogen bonding. Decreased hydration for the backbone of His-6 and Phe-7 was due to intermolecular hydrogen bonding with the SDS head-groups. The time correlation functions of the N-H bonds of the peptide in water and in the micelle showed that the motions of the peptide, except for the N- and C-termini, are significantly reduced when partitioned in the micelle.     

π-Facial hydrogen bonding in the chiral resolving agent 2,2,2-trifluoro-1-(9-anthryl)-ethanol and its racemic modification

2,2,2-Trifluoro-(9-anthryl)-ethanol (TFAE) has been extensively used, in its pure enantiomeric forms, as a chiral solvating agent in nuclear magnetic resonance spectroscopy (NMR). It has also played an important role in the development of chiral stationary phases in liquid chromatography (LC). X-ray crystallography of the enantiomeric and racemic crystals shows, in both cases, the formation of an intermolecular hydrogen bond between the O? H and the π-face of one of the rings of the anthracene aromatic system.¹ Few examples of such hydrogen bonding have been published previously, and those that have are not as clear cut as in this case. An explanation for the hydrogen bonding is sought using molecular modelling via the PM3 analytically derived molecular electrostatic potentials. Using NMR and dynamic lineshape analysis, the barrier to rotation about the aryl-carbon bond is estimated, indicating the C? CF₃ bond to be perpendicular to the anthracene axis in nonpolar solution. This conformation is identical to the conformation in the crystal. Evidence is also presented to support the formation of intermolecular π-facial hydrogen bonding in TFAE solutions. It is thought that such hydrogen bonding may be implicated in chiral recognition using this compound. © 1994 Wiley-Liss, Inc.     

Elimination of self-association as the source of the thermodynamic nonideality in aqueous proline solutions

The effect of high concentrations of proline on the diffusion coefficient of water has been examined to assess the extent to which the resulting thermodynamic nonideality could be explained on the statistical-mechanical basis of excluded volume. In fact, such a space-filling role not only accounts for the proline concentration-dependence of the diffusion coefficient of water but it also accounts for the nonideality of proline in freezing point depression and isopiestic measurements. These findings refute the conclusion (Schobert, B. and Tschesche, H. (1978) Biochim. Biophys. Acta 541, 270–277) that the stabilization of enzyme structure by high concentrations of proline stems from self-association of the imino acid via intermolecular hydrogen bonding; and thereby support the concept that the protective effect of proline on enzyme stability must reside mainly in its action as an inert, space-filling solute.     

Heat capacity of hydrogen-bonded networks: an alternative view of protein folding thermodynamics

Large changes in heat capacity (deltaCp) have long been regarded as the characteristic thermodynamic signature of hydrophobic interactions. However, similar effects arise quite generally in order-disorder transitions in homogeneous systems, particularly those comprising hydrogen-bonded networks, and this may have significance for our understanding of protein folding and other biomolecular processes. The positive deltaCp associated with unfolding of globular proteins in water, thought to be due to hydrophobic interactions, is also typical of the values found for the melting of crystalline solids, where the effect is greatest for the melting of polar compounds, including pure water. This suggests an alternative model of protein folding based on the thermodynamics of phase transitions in hydrogen-bonded networks. Folded proteins may be viewed as islands of cooperatively-ordered hydrogen-bonded structure, floating in an aqueous network of less-well-ordered H-bonds in which the degree of hydrogen bonding decreases with increasing temperature. The enthalpy of melting of the protein consequently increases with temperature. A simple algebraic model, based on the overall number of protein and solvent hydrogen bonds in folded and unfolded states, shows how deltaCp from this source could match the hydrophobic contribution. This confirms the growing view that the thermodynamics of protein folding, and other interactions in aqueous systems, are best described in terms of a mixture of polar and non-polar effects in which no one contribution is necessarily dominant.     

Hydrophobic interactions affect hydrogen bond strengths in complexes between peptides and vancomycin or ristocetin

A study on complexes of the glycopeptide antibiotics vancomycin and ristocetin with various dipeptides and tripeptides shows that the intermolecular hydrogen bond strengths of the complexes are reasonably well correlated with their free energy of formation. Such correlation is not anticipated on the basis of a purely hydrophobic interaction of the peptide side-chains with the antibiotics. It is also shown that the free energy changes observed are very different from those expected as a result of hydrophobic forces. These facts suggest that addition of a hydrophobic group not only allows hydrophobic bonding but also strengthens existing hydrogen bonds. The increased hydrogen bond strength can be an important factor in determining the overall binding energy.     

Design and synthesis of AB(3)-type (A = 1,3,5-benzenetricarbonyl unit; B = Glu diOME or Glu(7) octa OMe) peptide dendrimers: crystal structure of the first generation

The first generation molecule of glutamic acid-based dendrons on a 1, 3,5-benzenetricarbonyl core leads to a cylindrical assembly as demonstrated by single crystal x-ray diffraction. The benzene pi-pi stack (A) is stabilized by vertical NH...O===C hydrogen bonding with each subunit participating in three intermolecular hydrogen bonds related by three-fold rotation symmetry.     

Is there an osmotic regulatory mechanism in algae and higher plants?

Under water-stress conditions the amounts of various polyols and also of the imino acid proline are found to increase significantly in different algae and higher plants. These substances have been interpreted until now to act osmotically by increasing the concentration in the cell, thus causing water reflux and balancing osmotic pressure difference from outside the cell to inside.A new concept is described, which proposes that the regulatory function of these accumulating substances is conducted by two mechanisms quite different from osmotic regulation. It is assumed that these regulatory pathways are connected with the hydrophobic groups of biopolymers in the cell cytoplasm. (1) Polyols can replace water molecules by means of their water like OH-groups and thus participate in the hydrophobically enforced water structure. (2) Proline is postulated to associate via its hydrophobic phot with hydrophobic side chains, thereby converting them into hydrophilic groups by exposure the carboxylic and imino group versus water molecules. The advantage is due to the fact that water associated with hydrophilic groups is bound via hydrogen bonding forces, in contrary to hydrophobic groups. In addition, the number of water molecules adjoining hydrophilic groups is far less than those involved with hydrophobic residues. By means of these two alternative mechanisms complete hydration of the biopolymers is maintained, even with a reduced number of available water molecules.     

The structures of the horseradish peroxidase C-ferulic acid complex and the ternary complex with cyanide suggest how peroxidases oxidize small phenolic substrates

We have solved the x-ray structures of the binary horseradish peroxidase C-ferulic acid complex and the ternary horseradish peroxidase C-cyanide-ferulic acid complex to 2.0 and 1.45 A, respectively. Ferulic acid is a naturally occurring phenolic compound found in the plant cell wall and is an in vivo substrate for plant peroxidases. The x-ray structures demonstrate the flexibility and dynamic character of the aromatic donor binding site in horseradish peroxidase and emphasize the role of the distal arginine (Arg(38)) in both substrate oxidation and ligand binding. Arg(38) hydrogen bonds to bound cyanide, thereby contributing to the stabilization of the horseradish peroxidase-cyanide complex and suggesting that the distal arginine will be able to contribute with a similar interaction during stabilization of a bound peroxy transition state and subsequent O-O bond cleavage. The catalytic arginine is additionally engaged in an extensive hydrogen bonding network, which also includes the catalytic distal histidine, a water molecule and Pro(139), a proline residue conserved within the plant peroxidase superfamily. Based on the observed hydrogen bonding network and previous spectroscopic and kinetic work, a general mechanism of peroxidase substrate oxidation is proposed.     

NMR spectroscopic and theoretical study of the complexation of the inhibitor allosamidin in the binding pocket of the plant chitinase hevamine

Based on NMR spectroscopic information about the allosamidin-hevamine complex, ab initio MO calculations of the ring current effect of the aromatic moieties of Trp255, Tyr183 and Tyr6 of hevamine were carried out to investigate the role of these amino acid residues in binding interactions with allosamidin in solution. In addition, the intermolecular steric compression effect on the 13C chemical shifts of the allosamizoline carbon atoms and the hydrogen bonding to Glu127 was identified. It can be inferred that the binding forces are strongest in the allosamizoline moiety of allosamidin.     

Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation

Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer's disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side-chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions.     

Excited state intermolecular hydrogen bond’s effect on the luminescent behaviour of the 2D covalent organic framework (PPy-COF): A TDDFT insight

The theoretical investigation of electronically excited stated intermolecular hydrogen bonding dynamics of the 2D luminescent polypyrene covalent organic framework and methanol molecule (PPy-COF-MeOH) was performed using the density functional theory (DFT) and time-dependent (TD-DFT) method. The strengthening of Hydrogen bonds C-H---O-H and B-O---H-O upon photoexcitation was confirmed via comparison of geometric structures, electronic transition energies, ¹H-NMR, binding energies, UV-Vis and infrared spectra in S0 and S1 states. Frontier molecular orbitals (MOs) analysis, electronic configuration, Mulliken charge analysis; and the charge density variation in hydrogen bonding proximity demonstrated that the strengthened hydrogen bonds facilitate the nonradiative path which may consequently proceed the luminescence quenching. Hence, the molecular material property prediction package (MOMAP) programme verified the fluorescence quenching because PPy-COF-MeOH complex showed a lower fluorescent rate constant compared to isolated PPy-COF fragment. The S1-T1 energy gap analysis also revealed the possibility of the Intersystem crossing (ISC). Above results significantly highlighted the role of the hydrogen bonding dynamics on luminescence property of the PPy-COF.     

Conformation and dynamics of the chemotactic peptide formyl-L-methionyl-L-leucyl-L-phenylalanine in solution

Several conformational and dynamic features of the chemotactic peptide formyl-L-methionyl-L-leucyl-L-phenylalanine in solution have been delineated by investigations of NMR and IR spectroscopic parameters. Both 1D and 2D NMR experiments have been performed for detection of scalar and dipolar proton-proton connectivities, whereas 13C and 1H relaxation parameters have been interpreted in terms of molecular dynamics. The main conformation appeared to be unfolded with the three hydrophobic side chains extending in divergent directions with respect to the backbone. The existence of relatively weak intermolecular hydrogen bonds was demonstrated, involving the formamide end group, with increase in the hydrophobicity of the external surface.     

Compartmentalization of amino acids in surfactant aggregates

Cationic amino acids, arginine and lysine partition differentially from water into aqueous micellar sodium dodecanoate. Conversely, partitioning of serine, glycine, aspartic acid, glutamic acid, threonine, alanine, proline, valine, leucine, phenylalanine and isoleucine do not vary appreciably. Partitioning from neat hexane into dodecylammonium propionate trapped water in hexane is, however, dependent upon both electrostatic and hydrophobic interactions. These results imply that the interior of dedecylammonium propionate aggregates is negatively charged and is capable of hydrogen bonding in addition to providing a hydrophobic enviroment. The solubilities of amino acids in neat hexane substantiate the previously derived amino acid hydrophobicity scale. Relevance of partitioning in these systems to the postulated selective amino acid compartmentalization is discussed.     

Characterization and intermolecular interactions of hydroxypropyl guar solutions

Aqueous solutions of guar galactomannan and hydroxypropyl guars (HPG) with different molar substitution (MS) levels were studied using dilute solution viscometry and gel permeation chromatography. When guar is modified to HPG, the added hydroxypropyl groups sterically block the hydrogen bonding sites on the guar backbone and reduce the hydrogen bonding attractions between guar molecules. The effects of molar substitution on the intermolecular interactions are inferred from measurements of the Huggins coefficients, which measure intermolecular interactions in dilute solution, and molecular volumes, which reflect intrachain associations. The behavior can be divided into three regimes: (1) at low MS levels (0 < MS < approximately 0.4), there is a sharp decrease in intermolecular interactions as a function of MS; (2) in the intermediate range ( approximately 0.4 < MS < approximately 1.0), interactions become independent of MS; (3) at high substitution levels (MS > approximately 1.0), the temperature dependence of inter- and intramolecular hydrophobic interactions produces a temperature dependence in the Huggins coefficient and molecular volumes that is not seen at lower substitutions. By acid hydrolysis, HPG samples with a range of molecular weights and consistent polydispersities were obtained. On the basis of these samples, the Mark-Houwink-Sakurada parameters and "characteristic ratio" C(infinity) were evaluated for HPG (MS approximately 0.6) and compared to the values for guar. The HPG chain stiffens as the degree of substitution increases.