Guillermo G. Montich

Protein stability induced by ligand binding correlates with changes in protein flexibility

The interaction between ligands and proteins usually induces changes in protein thermal stability with modifications in the midpoint denaturation temperature, enthalpy of unfolding, and heat capacity. These modifications are due to the coupling of unfolding with binding equilibrium. Furthermore, they can be attained by changes in protein structure and conformational flexibility induced by ligand interaction. To study these effects we have used bovine serum albumin (BSA) interacting with three different anilinonaphthalene sulfonate derivatives (ANS). These ligands have different effects on protein stability, conformation, and dynamics. Protein stability was studied by differential scanning calorimetry and fluorescence spectroscopy, whereas conformational changes were detected by circular dichroism and infrared spectroscopy including kinetics of hydrogen/deuterium exchange. The order of calorimetric midpoint of denaturation was: 1,8‐ANS‐BSA > 2,6‐ANS‐BSA > free BSA >> (nondetected) bis‐ANS‐BSA. Both 1,8‐ANS and 2,6‐ANS did not substantially modify the secondary structure of BSA, whereas bis‐ANS induced a distorted α‐helix conformation with an increase of disordered structure. Protein flexibility followed the order: 1,8‐ANS‐BSA < 2,6‐ANS‐BSA < free BSA << bis‐ANS‐BSA, indicating a clear correlation between stability and conformational flexibility. The structure induced by an excess of bis‐ANS to BSA is compatible with a molten globule‐like state. Within the context of the binding landscape model, we have distinguished five conformers (identified by subscript): BSA1,8‐ANS, BSA2,6‐ANS, BSAfree, BSAbis‐ANS, and BSAunfolded among the large number of possible states of the conformational dynamic ensemble. The relative population of each distinguishable conformer depends on the type and concentration of ligand and the temperature of the system.

Surface topography of sulfatide and gangliosides in unilamellar vesicles of dipalmitoylphosphatidylcholine

The property of the dyes, acridine orange and methylene blue, to exhibit metachromatic changes upon binding to negatively charged groups that are within a defined spatial separation was employed to study the lateral and transverse topography of sulfatide and gangliosides GM1 and GD1a mixed with dipalmitoylphosphatidylcholine (DPPC) in unilamellar vesicles. The spectral changes of the dyes in the presence of liposomes containing anionic glycosphingolipids (GSLs) (hypochromism and frequency shift) are typical of polyanionic lattices while minor changes are found for neutral lipids. The metachromatic changes are abolished by the presence of Ca2+ in the external medium. The proportion of anionic GSLs accessible to the dyes on the external surface of the liposomes is greater as the GSLs are more complex (sulfatide less than GM1 less than GD1a) and as its proportion in the mixture decreases. The number of molecules of anionic GSLs that are laterally distributed on the external surface in a position favorable for the formation of dye dimers (at intermolecular distances not exceeding 1 nm) is greater for sulfatide than for ganglioside. This is correlated to the greater intermolecular distances and delocalization in ganglioside-, compared to sulfatide-containing interfaces. The experimental values indicate that the mixture with DPPC of any of the anionic GSLs studied behaves as if it was more enriched in the GSLs compared to the proportions of the whole mixture.

Interactions of chicken liver basic fatty acid-binding protein with lipid membranes.

The interactions of chicken liver basic fatty acid-binding protein (Lb-FABP) with large unilamellar vesicles (LUVs) of palmitoyloleoyl phosphatidylcholine (POPC) and palmitoyloleoyl phosphatidylglycerol (POPG) were studied by binding assays, Fourier transform infrared (FT-IR) spectroscopy, monolayers at air-water interface, and low-angle X-ray diffraction. Lb-FABP binds to POPG LUVs at low ionic strength but not at 0.1 M NaCl. The infrared (IR) spectra of the POPG membrane-bound protein showed a decrease of the band corresponding to beta-structures as compared to the protein in solution. In addition, a cooperative decrease of the beta-edge band above 70 degrees C in solution was also evident, while the transition was less cooperative and took place at lower temperature for the POPG membrane-bound protein. Low- and wide-angle X-ray diffraction experiments with lipid multilayers indicate that binding of the protein produces a rearrangement of the membrane structure, increasing the interlamellar spacing and decreasing the compactness of the lipids.

Interaction of 1-anilinonaphthalene 8-sulfonic acid with interfaces containing cerebrosides, sulfatides and gangliosides

The fluorescence lifetime, quantum yield and emission spectra of 1-anilinonaphthalene 8-sulfonic acid (ANS) associated with interfaces of pure dipalmitoylphosphatidylcholine or its mixtures with phosphatidylserine, galactosylceramide, sulfatide or gangliosides GM1 and GD1a were studied at low and high ionic strength. Modification of the molecular organization of the lipid interfaces in the presence of the probe was also studied with mixed lipid monolayers. ANS has little affect on the intermolecular packing of the lipids but influences their surface potential, consistent with a location of ANS in the polar head group region of the interface. ANS senses a more polar microenvironment when associated with interfaces containing anionic glycosphingolipids at low ionic strength but, except for interfaces containing phosphatidylserine, it detects approximately the same polarity for neutral or anionic interfaces in 0.25 M NaCl.

On the Ewald Artifacts in Computer Simulations. The Test-Case of the Octaalanine Peptide With Charged Termini

Abstract The treatment of electrostatic interactions in molecular simulations is of fundamental importance. Ewald and related methods are being increasingly used to the detriment of cutoff schemes, which are known to produce several artifacts. A potential drawback of the Ewald method is the spatial periodicity that is imposed to the system, which could produce artifacts when applied in the simulation of liquids. In this work we analyze the octaalanine peptide with charged termini in explicit solvent, for which severe effects due to the use of Ewald sums were predicted using continuum electrostatics. Molecular Dynamics simulations for a total of 158 nanoseconds were performed in cells of different sizes. From the comparison of the results of different system sizes, no significant periodicity-induced artifacts were observed. It is argued that in current biomolecular simulations, the incomplete sampling is likely to affect the results to a larger extent than the artifacts induced by the use of Ewald sums.

Binding and interactions of L-BABP to lipid membranes studied by molecular dynamic simulations.

Chicken liver bile acid-binding protein (L-BABP) is a member of the fatty acid-binding proteins super family. The common fold is a beta-barrel of ten strands capped with a short helix-loop-helix motif called portal region, which is involved in the uptake and release of non-polar ligands. Using multiple-run molecular dynamics simulations we studied the interactions of L-BABP with lipid membranes of anionic and zwitterionic phospholipids. The simulations were in agreement with our experimental observations regarding the electrostatic nature of the binding and the conformational changes of the protein in the membrane. We observed that L-BABP migrated from the initial position in the aqueous bulk phase to the interface of anionic lipid membranes and established contacts with the head groups of phospholipids through the side of the barrel that is opposite to the portal region. The conformational changes in the protein occurred simultaneously with the binding to the membrane. Remarkably, these conformational changes were observed in the portal region which is opposite to the zone where the protein binds directly to the lipids. The protein was oriented with its macrodipole aligned in the configuration of lowest energy within the electric field of the anionic membrane, which indicates the importance of the electrostatic interactions to determine the preferred orientation of the protein. We also identified this electric field as the driving force for the conformational change. For all the members of the fatty acid-binding protein family, the interactions with lipid membranes is a relevant process closely related to the uptake, release and transfer of the ligand. The observations presented here suggest that the ligand transfer might not necessarily occur through the domain that directly interacts with the lipid membrane. The interactions with the membrane electric field that determine orientation and conformational changes described here can also be relevant for other peripheral proteins.

Identification of a Site in Sar1 Involved in the Interaction with the Cytoplasmic Tail of Glycolipid Glycosyltransferases

Glycolipid glycosyltransferases (GGT) are transported from the endoplasmic reticulum (ER) to the Golgi, their site of residence, via COPII vesicles. An interaction of a (R/K)X(R/K) motif at their cytoplasmic tail (CT) with Sar1 is critical for the selective concentration in the transport vesicles. In this work using computational docking, we identify three putative binding pockets in Sar1 (sites A, B, and C) involved in the interaction with the (R/K)X(R/K) motif. Sar1 mutants with alanine replacement of amino acids in site A were tested in vitro and in cells. In vitro, mutant versions showed a reduced ability to bind immobilized peptides with the CT sequence of GalT2. In cells, Sar1 mutants (Sar1D198A) specifically affect the exiting of GGT from the ER, resulting in an ER/Golgi concentration ratio favoring the ER. Neither the typical Golgi localization of GM130 nor the exiting and transport of the G protein of the vesicular stomatitis virus were affected. The protein kinase inhibitor H89 produced accumulation of Sec23, Sar1, and GalT2 at the ER exit sites; Sar1D189A also accumulated at these sites, but in this case GalT2 remained disperse along ER membranes. The results indicate that amino acids in site A of Sar1 are involved in the interaction with the CT of GGT for concentration at ER exiting sites.

Calreticulin-dimerization induced by post-translational arginylation is critical for stress granules scaffolding.

Protein arginylation mediated by arginyl-tRNA protein transferase is a post-translational modification that occurs widely in biology, it has been shown to regulate protein and properties and functions. Post-translational arginylation is critical for embryogenesis, cardiovascular development and angiogenesis but the molecular effects of proteins arginylated in vivo are largely unknown. In the present study, we demonstrate that arginylation reduces CRT (calreticulin) thermostability and induces a greater degree of dimerization and oligomerization. R-CRT (arginylated calreticulin) forms disulfide-bridged dimers that are increased in low Ca(2+) conditions at physiological temperatures, a similar condition to the cellular environment that it required for arginylation of CRT. Moreover, R-CRT self-oligomerizes through non-covalent interactions that are enhanced at temperatures above 40 °C, condition that mimics the heat shock treatment where R-CRT is the only isoespecies of CRT that associates in cells to SGs (stress granules). We show that in cells lacking CRT the scaffolding of larger SGs is impaired; the transfection with CRT (hence R-CRT expression) restores SGs assembly whereas the transfection with CRT mutated in Cys146 does not. Thus, R-CRT disulfide-bridged dimers (through Cys146) are essential for the scaffolding of larger SGs under heat shock, although these dimers are not required for R-CRT association to SGs. The alteration in SGs assembly is critical for the normal cellular recover of cells after heat induced stress. We conclude that R-CRT is emerging as a novel protein that has an impact on the regulation of SGs scaffolding and cell survival.

Fatty acid-indole fluorescent derivatives as probes to measure the polarity of interfaces containing gangliosides

Abstract The fluorescence emission properties of three indole derivative probes N-2-(3-indolyl)ethyl-tetradecanoyl carboxamide (N-myrTAM), 2-tetradecanoyl carboxamidyl-3-(3-indolyl)propanoic acid (N-myrTRP) and 11-N(2-[3-in-dolyl]ethylamino)-9-en-methyloxy carbonyldecenate (11-TAMundec) were studied in solvents of different polarities in pure lysophosphatidylcholine micelles (lysoPC) and in total brain gangliosides (TBG) micelles using steady-state and phase-modulation fluorometry. By comparing the fluorescence emission spectra in solvent mixtures with the spectra in lipid micelles it is concluded that the probes detect a more polar environment in TBG compared to lysoPC micelles. Quenching experiments with acrylamide indicate that the indole group of N-myrTRP and N-myrTAM are more exposed to the aqueous medium than the indole group of 11-TAMundec both in lysoPC and TBG micelles. Quenching of the indole fluorescence with brominated fatty acid at the position 9–10 of the acyl chain is in the following order: 11-TAMundec N-MyrTAM > N-MyrTRP in lysoPC micelles whereas in TBG micelles only 11-TAMundec fluorescence is quenched. Based on the results of accessibility of the probes to the aqueous quencher and the dielectric constant calculated for their environment, we estimated the surface to core polarity gradient of the micelles. The polarity gradient is higher in TBG micelles compared to lysoPC micelles.

A novel lipid binding protein is a factor required for MgATP stimulation of the squid nerve Na+/Ca2+ exchanger.

Here we identify a cytosolic factor essential for MgATP up-regulation of the squid nerve Na(+)/Ca(2+) exchanger. Mass spectroscopy and Western blot analysis established that this factor is a member of the lipocalin super family of lipid binding proteins of 132 amino acids in length. We named it Regulatory protein of the squid nerve sodium calcium exchanger (ReP1-NCXSQ). ReP-1-NCXSQ was cloned, over expressed and purified. Far-UV circular dichroism and infrared spectra suggest a majority of beta-strand in the secondary structure. Moreover, the predicted tertiary structure indicates ten beta-sheets and two short alpha-helices characteristic of most lipid binding proteins. Functional experiments showed that in order to be active ReP1-NCXSQ must become phosphorylated in the presence of MgATP by a kinase that is Staurosporin insensitive. Even more, the phosphorylated ReP1-NCXSQ is able to stimulate the exchanger in the absence of ATP. In addition to the identification of a new member of the lipid binding protein family, this work shows, for the first time, the requirement of a lipid binding protein for metabolic regulation of an ion transporting system.