Computational study of ligand binding in lipid transfer proteins: Structures,interfaces, and free energies of protein‐lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein‐ligand interactions. We present here a computational study of protein‐ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries in molecular dynamics calculations, we computed Poisson‐Boltzmann electrostatic potentials, solvation energies, properties of the protein‐ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein‐lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity. © 2012 Wiley Periodicals, Inc.     

Nonstoichiometric polymer-surfactant complexes obtained in a lamellar lyotropic medium

The addition of a polyelectrolyte to lamellar media formed by an oppositely charged surfactant often leads to the coexistence of several phases without macroscopic phase separation, which makes their characterization difficult. Here, the effect of the polydiallyldimethylammonium chloride (PD) on the lamellar liquid crystal formed by the anionic surfactant Aerosol OT (AOT) and water is investigated. Small-angle X-ray scattering results are discussed regarding the changes in the lamellar spacing as a function on the PD or AOT concentrations. In most of the samples, two lamellar phases, without macroscopic phase separation, are detected. One of them is a typical swollen phase, while the other is a collapsed phase, which corresponds to the polymer-surfactant complex. At concentrations of polymer up to 3?wt%, the two lamellar phases coexist; however, at a critical concentration higher than 3?wt%, the swollen phase becomes isotropic, and a macroscopic phase separation takes place. A simple model is proposed to calculate the composition of the phases when macroscopic phase separation does not occur. The results thus calculated show that generally the polymer-surfactant complexes are nonstoichiometric containing a lesser amount of polymer than ideally expected.     

Incorporation of substituted acrylamides to the lamellar mesophase of Aerosol OT

The structure and stability of the lamellar liquid crystal formed by the surfactant sodium bis-2ethylhexyl sulfosuccinate (AOT) in water is perturbed by small amounts of the substituted acrylamides N-isopropyl, N,N-diethyl, N-acryloylmorpholine, and N,N-dimethyl methacrylamide, as revealed by small angle X-ray scattering (SAXS), deuterium NMR, and microscopy. These molecules are water soluble and stay mostly in the water layers between lamellae, but a small fraction of them (5-19%) are incorporated into the AOT bilayers, thereby producing dramatic changes. Both, the degree of anisotropy in the water molecules hydrating AOT (quadrupolar splitting in (2)H NMR) and the long period spacing between lamellae (SAXS), decrease with addition of this molecules at low concentrations, which is attributed to the lower average headgroup density at the AOT/water interface when the acrylamide is incorporated. The strength of these perturbations depends on the acrylamide, and goes in parallel with the hydrophobic character of the alkyl side groups in its molecule, which suggests that the acrylamides incorporated to the bilayer enter into contact with the lipophilic tails of the AOT molecule. An interaction with the hydrated heads of AOT is also suggested in the particular case of N-isopropylacrylamide. On increasing the molecule concentration an incipient melting of the lamellar phase towards an isotropic solution takes place, first at the microscopic level, then macroscopic. Near this phase transition, the ordered domains lose the random orientation prevailing at lower acrylamide concentrations, and adopt a preferred orientation, perpendicular to the magnetic field.     

A conventional an 2DCOS infrared approach to the kinetics of protein misfolding

Cell viability depends on the correct folding of the proteins involved in metabolism. Proteins are synthesized on the endoplasmic reticulum and must follow a pathway to a correct, metastable, tridimensional structure. Changes in structure or in environmental conditions can drive an instability of the folding conditions and produce non-active aggregates that in principle are proteolysed by the cellular mechanisms. However, these aggregates can be even more stable than the native proteins, escaping the cellular control. They can be classified as amorphous, if there is not a well-organized structural pattern, or ordered if a repetitive pattern is produced. These ordered structures, known as fibrils, are involved in many diseases. Infrared spectroscopy is a method of choice to study its formation because it is not affected by turbidity or the formation of high molecular weight aggregates. Moreover, in both cases, two bands characteristic of intermolecular β-sheets allow the monitoring of the aggregate formation. In both cases, the appearance of these bands involves a non-reversible path in protein folding. It has been suggested that a difference in the ordered structures involves an increasing in band intensity. This change can be the origin in variations on the 2DCOS maps. The synchronous map gives an overall idea of the process involved. The asynchronous is more informative because reflects the kinetic changes produced. The outcome of both processes, amorphous or ordered is that 2DCOS can provide a further insight to the knowledge of the kinetic processes giving rise to aggregated structures. This outcome could consist on the order in which the different secondary structures are prone to form the aggregates.     

Fluorescence Study on the Structure of Ionic Liquid Aggregates in Aqueous Solutions

Although ionic liquids are a relatively novel class of materials, it is well documented that they form micelles through aggregation of cation aliphatic tails. However, anion self-assembly has not yet been reported. In this study, we analyzed the intrinsic fluorescence of p-toluenesulfonate groups (tosylate) as part of the ionic liquid 1-ethyl-3-methylimidazolium tosylate ([emim][TOS]) and p-toluenesulfonic acid (pTSA), in aqueous solution. pTSA was found to have overlapping monomer and excimer emissions for chromophore concentrations from 10⁻³ to 1 M, whereas [emim][TOS], in the same conditions, showed monomer emission slightly broadened by much weaker excimer emission. These different photophysical behaviors of the same chromophore in the two compounds are explained by the formation of ion pairs by [emim][TOS], which can also be inferred from the loss of vibrational structure of the absorption spectra with respect to pTSA. Despite this different behavior regarding ion pairing, anion aggregation was observed in the excitation spectra of both pTSA and [emim][TOS]. While the absorption spectra corresponded to single chromophores, the excitation spectra changed from those characteristic of a single chromophore (below 10⁻³ M) to red-shifted narrow bands (above 0.1 M) typical of J aggregates. Between those concentrations, the excitation spectra split into blue- and red-shifted bands with relative intensities that changed with concentration as the chromophores rearranged in their clusters from head-to-head to head-to-tail aggregates. Differences between the absorption and excitation spectra were ascribed to aggregation-induced fluorescence enhancement.     

Computational study of the process of hydrogen bond breaking: the case of the formamide-formic acid complex

MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) quantum calculations are used to study the formamide-formic acid complex (FFAC), a system bound by two hydrogen bonds, N--H...O and O--H...O, that forms a bond ring at equilibrium. When the intermolecular separation between monomers R increases, this ring opens at a distance for which the weaker N--H...O bond breaks remaining the stronger O--H...O bond. The computational study characterizes that process addressing changes of interaction energy DeltaE, structure and properties of the electron density rho(r) as well as spatial distributions of rho(r), the electrostatic potential U(r), and the electron localization function eta(r). It is shown that the spatial derivatives of DeltaE, the topology of rho(r), and qualitative changes noticed in U(r) = 0 isocontours allow to identify a precise distance R for which one can say the N--H...O hydrogen bond has broken. Both levels of theory predict essentially the same changes of structure and electron properties associated to the process of breaking and virtually identical distances at which it takes place.     

Variation of atomic charges on proton transfer in strong hydrogen bonds: the case of anionic and neutral imidazole-acetate complexes

The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided.     

Structures and thermodynamics of biphenyl dihydrodiol stereoisomers and their metabolites in the enzymatic degradation of arene xenobiotics

A key step in the metabolic degradation of biphenyl xenobiotics is catechol formation upon dehydrogenation of cis‐ and trans‐dihydrodiols in prokaryotic and eukaryotic pathways, respectively. Structure and thermodynamics of stereoisomers of cis‐, trans‐2,3‐biphenyl‐dihydrodiols ( I ) and their dehydrogenation products (hydroxyketones, II ), as well as final catechol (2,3‐biphenyldiol, III ) are studied by means of ab initio MP2/6‐311++G(2df,2p)//MP2/6‐311G(d,p) calculations. Formation of stereoisomers I and II is exothermic and endergonic, whereas III is enthalpically and entropically driven. Dehydrogenations are endothermic (ΔH ～ 1.5–4 kcal mol^?1) and exergonic (ΔG ～ ?5 to ?7.5 kcal mol^?1) without noticeable differences between cis and trans pathways, although the same keto stereoisomer II ‐(2S) is found to be the more favored product from both cis‐ and trans‐ I . The final II → III tautomerization is thermodynamically enhanced (ΔH ～ ?27, ΔG ～ ?28 kcal mol^?1) but the process is shown to have a large activation energy if it had to occur via unimolecular path. Although this tautomerization is generally assumed to be a nonenzymatic process as it involves rearomatization of an oxygenated ring, proton transfer with an anionic intermediate might be a more probable process. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Distinct molecular surfaces and hydrophobicity of amino acid residues in proteins

Hydrophobicity is a useful concept to rationalize the role played by amino acid residues in terms of buried or exposed conformation with regard to the aqueous environment in proteins. The relationship of this concept with distinct approaches to represent the molecular surface is analyzed by computing reliable surface areas for three definitions namely the van der Waals, solvent-accessible, and solvent-excluded molecular surfaces. The surface areas are obtained for all of the naturally occurring amino acids by first setting a proper reference standard state and then calculating their values for a database of proteins containing a total of 4297 residues. Despite the great differences in these molecular surfaces, proper indexes are here defined for handling the information of interest to study the hydrophobic behavior of amino acids provided by such surfaces.