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The structural and dynamic changes introduced during antibody humanization continue to be a topic open to new contributions. For this reason, the study of structural and functional changes of a murine scFv (mu.scFv) anti-rhIFN-α2b after humanization was carried out. As it was shown by long molecular dynamics simulations and circular dichroism analysis, changes in primary sequence affected the tertiary structure of the humanized scFv (hz.scFv): the position of the variable domain of light chain (VL) respective to the variable domain of heavy chain (VH) in each scFv molecule was different. This change mainly impacted on conformation and dynamics of the complementarity-determining region 3 of VH (CDR-H3) which led to changes in the specificity and affinity of humanized scFv (hz.scFv). These observations agree with experimental results that showed a decrease in the antigen-binding strength of hz.scFv, and different capacities of these molecules to neutralize the in vitro rhIFN-α2b biological activity. Besides, experimental studies to characterize antigen-antibody binding showed that mu.scFv and hz.scFv bind to the same antigen area and recognize a conformational epitope, which is evidence of docking results. Finally, the differences between these molecules to neutralize the in vitro rhIFN-α2b biological activity were described as a consequence of the blockade of certain functionally relevant amino acids of the cytokine, after scFv binding. All these observations confirmed that humanization affected the affinity and specificity of hz.scFv and pointed out that two specific changes in the frameworks would be responsible.

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The Cys residues are almost perfectly conserved in all antibodies. They contribute significantly to the antibody fragment stability. The relevance of two natural contiguous Cys residues of an anti-recombinant human-follicle stimulation hormone (rhFSH) in a format of single-chain variable fragment (scFv) was studied. This scFv contains 5 Cys residues: VH22 and VH92 in the variable heavy chain (VH) and VL23, VL87 and VL88 in the variable light chain (VL). The influence of two unusual contiguous Cys at positions VL87 and VL88 was studied by considering the wild type fragment and mutant variants: VL-C88S, VL-C87S, VL-C87Y. The analysis was carried out using antigen-binding ability measurement by indirect specific ELISA and a detailed molecular modeling that comprises homology methods, long molecular dynamics simulations and docking. We found that VL-C87 affected the antibody fragment stability without interfering with the disulfide bond formation. The effect of mutating the VL-C87 by a usual residue at this position like Tyr caused distant structural changes at the VH region that confers a higher mobility to the VH-CDR2 and VH-CDR3 loops improving the scFv binding to the antigen.

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Atomistic molecular dynamic simulations were performed to study the structure of isolated VBT-VBA (vinylbenzylthymine-vinylbenzyltriethylammonium chloride) copolymer chains in water at different monomeric species ratios (1:1 and 1:4). The geometric parameters of the structure that the copolymers form in equilibrium together with the basic interactions that stabilize them were determined. Atomic force microscopy (AFM) measurements of dried diluted concentrations of the two copolymers onto highly oriented pyrolytic graphite (HOPG) substrates were carried out to study their aggregation arrangement. The experiments show that both copolymers arrange in fiber-like structures. Comparing the diameters predicted by the simulation results and those obtained by AFM, it can be concluded that individual copolymers arrange in bunches of two chains, stabilized by contra-ions-copolymer interactions for the 1:1 copolymerization ratio at the ionic strength of our samples. In contrast, for the 1:4 system the individual copolymer chains do not aggregate in bunches. These results remark the relevance of the copolymerization ratio and ionic strength of the solvent in the mesoscopic structure of these materials.

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Detergents are essential tools to study biological membranes, and they are frequently used to solubilize lipids and integral membrane proteins. Particularly the nondenaturing zwitterionic detergent usually named CHAPS was designed for membrane biochemistry and integrates the characteristics of the sulfobetaine-type detergents and bile salts. Despite the available experimental data little is known about the molecular structure of its micelles. In this work, molecular dynamics simulations were performed to study the aggregation in micelles of several numbers of CHAPS (≤ 18) starting from a homogeneous water dilution. The force field parameters to describe the interactions of the molecule were developed and validated. After 50 ns of simulation almost all the systems result in the formation of stable micelles. The molecular shape (gyration radii, volume, surface) and the molecular structure (RDF, salt bridges, H-bonds, SAS) of the micelles were characterized. It was found that the main interactions that lead to the stability of the micelles are the electrostatic ones among the polar groups of the tails and the OH's from the ring moiety. Unlike micelles of other compounds, CHAPS show a grainlike heterogeneity with hydrophobic micropockets. The results are in complete agreement with the available experimental information from NMR, TEM, and SAXS studies, allowing the modeling of the molecular structure of CHAPS micelles. Finally, we hope that the new force field parameters for this detergent will be a significant contribution to the knowledge of such an interesting molecule.

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Amoebiasis is an intestinal infection caused by the human pathogen Entamoeba histolytica and representing the third leading cause of death by parasites in the world. Host-parasite interactions mainly involve anchored glycoconjugates localized in the surface of the parasitic cell. In protozoa, synthesis of structural oligo- and polysaccharides occurs via UDP-glucose, generated in a reaction catalyzed by UDP-glucose pyrophosphorylase. We report the molecular cloning of the gene coding for this enzyme from genomic DNA of E. histolytica and its recombinant expression in Escherichia coli cells. The purified enzyme was kinetically characterized, catalyzing UDP-glucose synthesis and pyrophosphorolysis with V(max) values of 95 U/mg and 3 U/mg, respectively, and affinity for substrates comparable to those found for the enzyme from other sources. Enzyme activity was affected by redox modification of thiol groups. Different oxidants, including diamide, hydrogen peroxide and sodium nitroprusside inactivated the enzyme. The process was completely reverted by reducing agents, mainly cysteine, dithiothreitol, and thioredoxin. Characterization of the enzyme mutants C94S, C108S, C191S, C354S, C378S, C108/378S, M106S and M106C supported a molecular mechanism for the redox regulation. Molecular modeling confirmed the role of specific cysteine and methionine residues as targets for redox modification in the entamoebic enzyme. Our results suggest that UDP-glucose pyrophosphorylase is a regulated enzyme in E. histolytica. Interestingly, results strongly agree with the occurrence of a physiological redox mechanism modulating enzyme activity, which would critically affect carbohydrate metabolism in the protozoon.

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We have studied the effect of the insertion of spin-labeled molecules n-doxyl-stearic acid (n-SASL, n = 5, 12, 16) on the structure and dynamics of a model lipid bilayer in gel-like phases using molecular dynamics simulations. We have studied the atomic density depth profiles and configurations of the labeled molecules in a host hydrated stearic acid bilayer system. We have found that the 5-SASL label positions its paramagnetic group at the water-lipid interface, and its polar head builds H bonds to neighboring lipids and to the solvent. 16-SASL positions its paramagnetic group at the lipid-lipid interface. The 12-SASL label presents two configurations at high lateral pressure. In one configuration, the doxyl ring lays at the lipid-lipid interface, shifting its polar head toward the bilayer center. The other equilibrium configuration of 12-SASL presents its paramagnetic group laying in the center of the compact hydrophobic region of the layer (erected configuration). It was determined that the coexistence of these two configurations is governed by the polar head-water interaction. We have found that the insertion of the labeled molecules at the concentrations used in the present work (0.36 mol %) do not perturb global properties like area per lipid, tilt angle, or order parameters. Nevertheless, there are local perturbations of the host system that are confined to a 10 angstroms neighboring shell around the spin label molecule. To study the interactions that determine the position of the labeled molecules in the bilayer, we performed simulations at different lateral pressures, which allowed us to extract important conclusions.

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The effects of the insertion of a spin-labeled molecule (10-doxyl-stearic acid) on the structure and dynamics of model lipid bilayers in gel-like as well as in liquid-ordered-like phases are studied using molecular dynamic simulations. The perturbing effects of the labeled molecule on the structure of the bilayers are analyzed. We have also studied the relationship between the structural and dynamic properties of the bilayer phase and those of the labeled molecule. We found that the insertion of the labeled molecule in the bilayer at the concentration considered here (1:70) produces local and global perturbations in the gel-like phase. There is an increase of the area associated with the lipid molecules that produces a larger tilting angle of this condensed phase. In this gel-like phase, we also found that the z component of the order parameter of the labeled molecule associated with the electron paramagnetic resonance (EPR) spectra has the same temperature dependence as the axial correlation times of the lipid molecules. The mechanism by which the doxyl reorientation senses the dynamics of the layers is determined by the correlation between the gauche defect transitions of the labeled alkyl chain and its environment. For the liquid-ordered-like phase, we found that cholesterol molecules play the role of wedges that open free spaces in the lipid structure below the ring position and order the alkyl chains at the depths of the rings, leading to small inclination angles. The doxyl ring of the labeled molecule is located just below the cholesterol ring moiety, having fewer gauche defects than in the case of the gel-like phase. The change in depth of the doxyl ring causes a reorientation of this group that leads to an increase of the order parameter as the temperature rises.

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The magnetic properties of the Cu(II)-peptide compounds (L-tyrosyl-L-leucinato)Cu(II) and (L-tryptophyl-glycinato)Cu(II), to be identified as Cu(II)Tyr-Leu and Cu(II)Trp-Gly, respectively, have been investigated by specific heat (0.08 < T < 28 K), dc magnetization (2 < T < 80 K, with B(0) = mu(o)H < or = 9 T), and ac magnetic susceptibility (with B(0) = 0 for 0.03 < T < 3 K and B(0) up to 9 T for 2 < T < 80 K) measurements. Above approximately 1 K, the specific heat and magnetization of both compounds display a ferromagnetic (FM) spin chain behavior sustained by syn-anti carboxylate bridges connecting equatorially Cu(II) ions at about 5 A. To model this behavior, we calculated the eigenvalues of Heisenberg chains with up to 20 spins 1/2 and used the method of Bonner and Fisher. A global fit of the model to the specific heat and magnetization data gives 2J(0)/k(B) = 3.60(5) K and 2.59(5) K for the intrachain exchange interactions in Cu(II)Tyr-Leu and Cu(II)Trp-Gly, respectively (H(ex)(i,j) = -2J(0) S(i).S(j)). These values of 2J(0) are discussed in terms of structural properties of the carboxylate bridges in the two compounds. Using the parameters obtained from the global fit, we calculated isothermal susceptibilities in agreement with the ac susceptibilities measured with small applied dc magnetic fields. However, the ac susceptibility measured with applied dc fields larger than 1 T lie between the values calculated for the isothermal and adiabatic susceptibilities. At 0.16 K for Cu(II)Tyr-Leu and 0.53 K for Cu(II)Trp-Gly, the observed specific heat and magnetic susceptibility display peaks associated to three-dimensional magnetic phase transitions. The interchain exchange couplings 2J(1) producing the 3D magnetic order are ferromagnetic and have magnitudes 2J(1)/k(B) approximately 0.015 and 0.073 K for Cu(II)Tyr-Leu and Cu(II)Trp-Gly, respectively.

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