Piotr Bonarek

Two modes of fatty acid binding to bovine β‐lactoglobulin—crystallographic and spectroscopic studies

Lactoglobulin is a natural protein present in bovine milk and common component of human diet, known for binding with high affinity wide range of hydrophobic compounds, among them fatty acids 12–20 carbon atoms long. Shorter fatty acids were reported as not binding to β‐lactoglobulin. We used X‐ray crystallography and fluorescence spectroscopy to show that lactoglobulin binds also 8‐ and 10‐carbon caprylic and capric acids, however with lower affinity. The determined apparent association constant for lactoglobulin complex with caprylic acid is 10.8 ± 1.7 × 103 M−1, while for capric acid is 6.0 ± 0.5 × 103 M−1. In crystal structures determined with resolution 1.9 Å the caprylic acid is bound in upper part of central calyx near polar residues located at CD loop, while the capric acid is buried deeper in the calyx bottom and does not interact with polar residues at CD loop. In both structures, water molecule hydrogen‐bonded to carboxyl group of fatty acid is observed. Different location of ligands in the binding site indicates that competition between polar and hydrophobic interactions is an important factor determining position of the ligand in β‐barrel. Copyright

Structural and thermodynamic studies of binding saturated fatty acids to bovine β-lactoglobulin ☆

Lactoglobulin is a globular milk protein for which physiological function has not been clarified. Due to its binding properties lactoglobulin might serve as a carrier for bioactive molecules. Binding of 12-, 14-, 16- and 18-carbon saturated fatty acids to bovine β-lactoglobulin has been characterised by isothermal titration calorimetry and X-ray crystallography as a part of systematic studies of lactoglobulin complexes with ligands of biological importance. The thermodynamic parameters have been determined for lauric, myristic and palmitic acid complexes revealing systematic decrease of enthalpic and increase of entropic component of ΔG with elongation of aliphatic chain. In all crystal structures determined with resolution 1.9-2.1Å, single fatty acid molecule was found in the β-barrel in extended conformation with individual pattern of interactions. Location of a fatty acid in the binding site depends on the length of aliphatic chain and influences polar interactions between protein and ligand. Systematic changes of entropic component indicate important role of water in binding process.

cAMP Receptor Protein from Escherichia coli as a Model of Signal Transduction in Proteins – A Review

In Escherichia coli, cyclic AMP receptor protein (CRP) is known to regulate the transcription of about 100 genes. The signal to activate CRP is the binding of cyclic AMP. It has been suggested that binding of cAMP to CRP leads to a long-distance signal transduction from the N-terminal cAMP-binding domain to the C-terminal domain of the protein, which is responsible for interaction with specific sequences of DNA. The signal transduction plays a crucial role in the activation of the protein. The most sophisticated spectroscopic techniques, other techniques frequently used in structural biochemistry, and site-directed mutagenesis have been used to investigate the details of cAMP-mediated allosteric control over CRP conformation and activity as a transcription factor. The aim of this review is to summarize recent works and developments pertaining to cAMP-dependent CRP signal transduction in E. coli.

Binding of 18-carbon unsaturated fatty acids to bovine β-lactoglobulin—Structural and thermodynamic studies

Binding of 18-carbon unsaturated oleic and linoleic acid to lactoglobulin, the milk protein, has been studied for the first time by isothermal titration calorimetry (ITC) and X-ray crystallography. Crystal structures determined to resolution 2.10 Å have revealed presence of single fatty acid molecule bound in β-barrel, the primary binding site, with carboxyl group hydrogen bonded to Glu62. The aliphatic chain of both ligands is in almost linear conformation and their interactions with the protein are similar to observed in structure of lactoglobulin with stearic acid. The ITC experiments showed that binding of unsaturated fatty acids to LGB is spontaneous and exothermic. The stoichiometry of binding is lower than 1.0, association constant is 9.7 × 10(5)M(-1) and 9.0 × 10(5)M(-1) for oleic and linoleic acid, respectively. Solvent relief seems to be the major contributor to entropic changes upon fatty acid binding to lactoglobulin.

Conformational variability of goat β-lactoglobulin: crystallographic and thermodynamic studies.

Goat β-lactoglobulin (GLG), lipocalin protein sharing high sequence similarity to bovine β-lactoglobulin (BLG), has been structurally and thermodynamically characterized. Two crystal forms of GLG have been obtained, trigonal (P3121) and orthorhombic (P21212), with unique molecular packing, not observed previously for BLG. In the trigonal structure, GLG molecules have EF-loop in closed conformation while in the orthorhombic structure, for the first time, symmetric and asymmetric dimers of β-lactoglobulin are observed simultaneously. It indicates that the opening or closing EF-loop does not occur in both subunits at the same time but might be sequential and cooperative. Comparison of GLG and BLG structures revealed presence of various conformers of EF and GH. ITC studies showed that at pH 7.5 GLG binds sodium dodecyl sulfate with Gibbs energy similar to BLG, however, with different contribution from enthalpic and entropic component. At pH 7.5 GLG forms dimers with dimerization constant Ka = 34.28 × 10(3) M(-1), significantly higher than observed for BLG. Similar mechanism of conformational changes and ligand binding indicates that GLG and BLG may play analogous biological role.

The differences in binding 12-carbon aliphatic ligands by bovine beta-lactoglobulin isoform A and B studied by isothermal titration calorimetry and X-ray crystallography

Isoforms A (LGB‐A) and B (LGB‐B) of bovine lactoglobulin, the milk protein, differ in positions 64 (D↔G) and 118 (V↔A). Interactions of LGB‐A and LGB‐B with sodium dodecyl sulfate (SDS), dodecyltrimethylammonium chloride (DTAC) and lauric acid (LA), 12‐carbon ligands possessing differently charged polar groups, were investigated using isothermal titration calorimetry and X‐ray crystallography, to study the proton linkage phenomenon and to distinguish between effects related to different isoforms and different ligand properties. The determined values of ΔS and ΔH revealed that for all ligands, binding is entropically driven. The contribution from enthalpy change is lower and shows strong dependence on type of buffer that indicates proton release from the protein varying with protein isoform and ligand type and involvement of LA and Asp64 (in isoform A) in this process. The ligand affinities for both isoforms were arranged in the same order, DTAC < LA < SDS, and were systematically lower for variant B. The entropy change of the complexation process was always higher for isoform A, but these values were compensated by changes in enthalpy, resulting in almost identical ΔG for complexes of both isoforms. The determined crystal structures showed that substitution in positions 64 and 118 did not influence the overall structure of LGB complexes. The chemical character of the ligand polar group did not affect the position of its aliphatic chain in protein β‐barrel, indicating a major role of hydrophobic interactions in ligand binding that prevailed even with the repulsion between positively charged DTAC and lysine residues located at binding site entrance. Copyright

Fenofibrate attenuates contact-stimulated cell motility and gap junctional coupling in DU-145 human prostate cancer cell populations

In the present study, we investigated the effects of fenofibrate on the invasive potential of DU-145 human prostate cancer cells in the context of gap junctional intercellular coupling and the formation of reactive oxygen species. Time-lapse analyses of cell motility, accompanied by tests of cell viability, membrane microviscosity, reactive oxygen species accumulation and the function of gap junctional protein connexin 43 were performed in monolayer cultures of DU-145 cells following fenofibrate administration. Fenofibrate inhibited the motility of DU-145 cells and attenuated gap junctional intercellular coupling in a manner independent of its effects on cell viability, PPARα activation and cell membrane micro-viscosity. Instead, N-acetyl-L-cysteine, a scavenger of reactive oxygen species, restored cell motility and gap junctional coupling in fenofibrate-treated DU-145 cell populations. These data indicate that two parameters crucial for cancer cell metastatic potential, i.e. cell motility and gap junctional coupling, are inhibited by fenofibrate. Thus, fenofibrate affects prostate cancer cell invasion via an orchestrated action on versatile cancer cell properties determining this process. A novel mechanism of anti-invasive activity of fenofibrate, which depends on its interference with cell motility and the function of gap junctions regulated by reactive oxygen species, is suggested.

An investigation of the affinities, specificity and kinetics involved in the interaction between the Yin Yang 1 transcription factor and DNA

Human transcription factor Yin Yang 1 (YY1) is a four zinc‐finger protein that regulates a large number of genes with various biological functions in processes such as development, carcinogenesis and B‐cell maturation. The natural binding sites of YY1 are relatively unconserved and have a short core sequence (CCAT). We were interested in determining how YY1 recognizes its binding sites and achieves the necessary sequence selectivity in the cell. Using fluorescence anisotropy, we determined the equilibrium dissociation constants for selected naturally occurring YY1 binding sites that have various levels of similarity to the consensus sequence. We found that recombinant YY1 interacts with its specific binding sites with relatively low affinities from the high nanomolar to the low micromolar range. Using a fluorescence anisotropy competition assay, we determined the affinity of YY1 for non‐specific DNA to be between 30 and 40 μm, which results in low specificity ratios of between 3 and 220. Additionally, surface plasmon resonance measurements showed rapid association and dissociation rates, suggesting that the binding strength is regulated through changes in both ka and kd. In conclusion, we propose that, in the cell, YY1 may achieve higher specificity by associating with co‐regulators or as a part of multi‐subunit complexes.

A thermosensitive carrageenan-based polymer: Synthesis, characterization and interactions with a cationic surfactant

Novel polyelectrolytes were obtained by grafting N-isopropylacrylamide (NIPAM) on the ι-carrageenan (CAR) chain. Two polymers with different grafting degrees were synthesized. The polymers were found to show the lower critical solution temperature (LCST) close to that of PNIPAM. The LCST values were dependent on the concentration of salt and cationic surfactant. The interactions of CAR-graft-PNIPAM with a model cationic surfactant-dodecyltrimethyl ammonium chloride (DTAC) in water and 0.15M NaCl were studied. It was found that both ι-carrageenan and CAR-graft-PNIPAM polymers interact with DTAC. The presence of CAR-graft-PNIPAM in the solution of DTAC induces formation of surfactant aggregates at the critical aggregation concentration much lower than the cmc of the surfactant. Cac increased with ionic strength. The values of cac for CAR-graft-PNIPAM - DTAC system and standard free enthalpy changes attributed to the complexation process were determined. The results obtained for CAR-graft-PNIPAM were compared with these for the non-modified ι-carrageenan. The surfactant interactions with non-modified and grafted polymers were found to be different in nature.

Kinetic Studies of cAMP-induced Allosteric Changes in Mutants T127I, S128A, and T127I/S128A of the cAMP Receptor Protein from Escherichia coli

The cAMP receptor protein (CRP) regulates the expression of several genes in Escherichia coli. The protein is a homodimer, and each monomer is folded into two distinct structural domains. After allosteric transitions resulting from the binding of cAMP, CRP specifically binds to DNA and activates transcription. We have used stopped-flow fluorometry measurements of CRP mutants bearing amino acid substitutions T127I, S128A, and T127I/S128A to study the kinetics of conformational changes in the protein induced by cAMP binding. Amino acid substitutions at positions 127 and 128 were chosen because these residues play a crucial role in interdomain and intersubunit communication during allosteric transition. Using N-iodoacetylaminoethyl-5-naphthylamine-1-sulfonic acid-labeled Cys178, localized in the protein helix-turn helix motif, we observed conformational changes in the helix-turn helix, localized in the C-terminal domain, upon binding of cAMP to high affinity sites (CRP·cAMP2) in the N-terminal domain of CRP. The rate constants for the forward and backward conformational changes depend on the amino acid substitution: kc = 3.62 s–1 and k–c = 3.13s–1 for CRP T127I and kc = 0.42 s–1 and k–c = 0.78 s–1 for CRP S128A. These values can be compared with kc = 9.7 s–1 and k–c = 0.31 s–1 for wild-type CRP. The observed conformational changes can be described by the sequential model of allostery, with the amino acid substitutions influencing the allosteric changes. In the case of the double mutant, the observed rate constant of cAMP binding supports the suggestion that this unligated mutant possesses the structure that is close to the allosteric conformation necessary for promoter binding. The results of intrinsic fluorescence measurements suggest that the formation of the CRP·cAMP4 complex results from displacement of equilibrium between the two forms of the CRP·cAMP2 complex in the mutants studied, similar to wild-type CRP. The observed conformational changes occur according to a concerted model of allostery, and isomerization equilibrium between the two CRP states depends on the amino acid substitution. The data presented in this study indicate that Ser128 and Thr127 in CRP play an important role in the kinetics of intramolecular transitions triggered by cAMP.