Thermodynamic analysis of a hydrophobic binding site: probing the PDZ domain with nonproteinogenic peptide ligands

[structure: see text] Isothermal titration calorimetry (ITC) is used to study the thermodynamic consequences of systematically modifying the hydrophobic character of a single residue in a series of protein-binding ligands. By substituting standard and nonproteinogenic aliphatic amino acids for the C-terminal valine of the hexapeptide KKETEV, binding to the third PDZ domain (PDZ3) of the PSD-95 protein is characterized by distinct changes in the Gibbs free energy (DeltaG), enthalpy (DeltaH), and entropy (TDeltaS) parameters. One notable observation is that peptide binding affinity can be improved with a nonstandard residue.     

Assessment of solvent residues accessibility using three Sulfo-NHS-biotin reagents in parallel: application to footprint changes of a methyltransferase upon binding its substrate

NHS-biotin modification as a specific lysine probe coupled to mass spectrometry detection is increasingly used over the past years for assessing amino acid accessibility of proteins or complexes as an alternative when well-established methods are challenged. We present a strategy based on usage in parallel of three commercially available reagents (Sulfo-NHS-biotin, Sulfo-NHS-LC-biotin, and Sulfo-NHS-LC-LC-biotin) to efficiently assess the solvent accessibility of amino acids using MALDI-TOF mass spectrometry. The same qualitative pattern of reactivity was observed for these three reagents on the THUMPalpha protein at four reagent/polypeptide molar ratios (2 : 1, 6 : 1, 13 : 1, and 26 : 1). Peptide assignment of the detected ions gains in accuracy because of the triple redundancy due to specific increments of monoisotopic mass. These reagents are a good alternative to isotope labeling when using only a single MALDI-TOF mass spectrometer. We observed that hydroxyl groups of serine and tyrosine residues were also modified by these Sulfo-NHS-biotin reagents. The low amount of protein required and the method's simplicity make this procedure accessible and affordable in order to obtain topological information on proteins difficult to purify. This method was used to identify two lysine residues of the TrmG10 methyltransferase from Pyrococcus abyssi that were differentially reactive, modified in the protein but not in the tRNA-protein complex.     

Folding of a salivary intrinsically disordered protein upon binding to tannins

We used ion mobility spectrometry to explore conformational adaptability of intrinsically disordered proteins bound to their targets in complex mixtures. We investigated the interactions between a human salivary proline-rich protein IB5 and a model of wine and tea tannin: epigallocatechin gallate (EgCG). Collisional cross sections of naked IB5 and IB5 complexed with N = 1-15 tannins were recorded. The data demonstrate that IB5 undergoes an unfolded to folded structural transition upon binding with EgCG.     

M35 oxidation induces Abeta40-like structural and dynamical changes in Abeta42

Oxidizing a single M35 residue of Abeta leads to delayed aggregation and reduced toxicity. To understand the molecular mechanism of this effect, we examined the structural and dynamical consequences of M35 oxidation. We found the mobility of the C-terminal residues of Abeta42 is greatly enhanced upon M35 oxidation. In contrast, methyl groups in the central hydrophobic cluster become less flexible. Taken together, we conclude that Abeta42ox undergoes Abeta40-like structural and dynamical changes, which contribute to its reduced aggregation and toxicity.     

Solid-state NMR reveals structural and dynamical properties of a membrane-anchored electron-carrier protein, cytochrome b5

Cytochrome b5 (cyt b5) is a membrane-anchored electron-carrier protein containing a heme in its soluble domain. It enhances the enzymatic turnover of selected members of the cytochrome P450 superfamily of catabolic enzymes, localized in the endoplasmic reticulum of liver cells. Remarkably, its alpha-helical membrane-anchoring domain is indispensable for the cyt b5/cyt P450 interaction. Here, we present the first solid-state NMR studies on holo-cyt b5 in a membrane environment, namely, macroscopically oriented DMPC:DHPC bicelles. We have presented approaches to selectively investigate different domains of the protein using spectral editing NMR techniques that utilize the unique motional properties of each domain. Two-dimensional 1H-15N HIMSELF spectra showed PISA-wheel patterns reporting on the structure and dynamics of the membrane anchor of the protein.     

Energetics of binding and protein unfolding upon amphiphilic drug complexation with a globular protein in different aqueous media

The interactions and complexation process of the structurally related amphiphilic phenothiazines promazine and triflupromazine hydrochlorides with horse myoglobin in aqueous buffered solutions of pH 2.5, 5.5 and 9.0 have been examined by zeta-potential, isothermal titration calorimetry (ITC), UV-vis spectroscopy and dynamic light-scattering techniques with the aim of analyzing the effect of hydrophobic and electrostatic forces, the alteration of protein conformation and the effect of substituents in the drug molecular structure on the binding mechanism and structure of the resulting complexes. The energetics and stoichiometry of the binding process was derived from ITC. The enthalpies of binding obtained are small and exothermic, and the Gibbs energies of binding are dominated by large increases in entropy consistent with hydrophobic interactions. Binding isotherms were obtained from microcalorimetric data by using a theoretical model based on the Langmuir isotherm. zeta-Potential data showed a reversal in the sign of the protein charge at pH 9.0 as a consequence of drug binding. Gibbs energies of drug binding per mole of drug were also derived from zeta-potential data. On the other hand, binding of the phenothiazines causes a conformational transition on protein structure which was followed as a function of drug concentration by using UV-vis spectroscopy. These data were analyzed to obtain the Gibbs energy of the transition in water (DeltaG(w)(degrees)) and in a hydrophobic environment (DeltaG(hc)(degrees)). Finally, the population distribution of the different species in solution and their size was analyzed through dynamic light scattering. The existence of an aggregation process of drug/protein complexes, mainly at pH 2.5, was observed. We think this is a consequence of the already expanded structure of the protein at this pH and the subsequent binding of drug molecules to the protein.     

Change of line tension in phase-separated vesicles upon protein binding

We measured the effect of a model membrane-binding protein on line tension and morphology of phase-separated lipid-bilayer vesicles. We studied giant unilamellar vesicles composed of a cholesterol/dioleoylphosphatidylcholine/palmitoylsphingomyelin mixture and a controlled mole fraction of a Ni-chelating lipid. These vesicles exhibited two coexisting fluid-phase domains at room temperature. Owing to the line tension, σ, between the two phases, the boundary between them was pulled like a purse string so that the smaller domain formed a bud. While observing the vesicles in a microscope, histidine-tagged green fluorescent protein was added, which bound to the Ni-chelating lipid. As protein bound, the vesicle shape changed and the length of the phase boundary increased. The change in morphology was attributed to a reduction of σ between the two phases because of preferential accumulation of histidine-tagged green fluorescent protein-Ni-chelating lipid clusters at the domain boundary. Greater reductions of σ were found in samples with higher concentrations of Ni-chelating lipid; this trend provided an estimate of the binding energy at the boundary, approximately k(B)T. The results show how domain boundaries can lead to an accumulation of membrane-binding proteins at their boundaries and, in turn, how proteins can alter line tension and vesicle morphology.     

Influence of static and dynamical structural changes on ultrafast processes mediated by conical intersections

The technological needs imposed by the exponential miniaturization trend of conventional electronic devices has drawn attention towards the development of smaller and faster devices like ultrafast molecular switches. In recent years molecular switches emerge again in the focus of active and innovative research with state-of-the-art optical tools recording their dynamics in real time. Still many questions about the underlying microscopic mechanism are left open, including potential factors that effect the switching process in either way, improve or worsen it. Due to the complexity of such molecules it is difficult to obtain a global answer from experiment alone. On the other side molecular switches are generally too large for a complete quantum chemical and quantum dynamical calculation. In our group we therefore developed an ab initio based modular model to handle the laser induced quantum dynamics in molecular switches like fulgides. It enables us to study the effect of internal molecular coupling and of the molecular response to external fields. We can investigate the related wave packet dynamics, the switching efficiency and the controllability. Our results focus on the laser induced ring opening in fulgides, which equals one direction of the switching process. Presented are the influence of a conical intersection seam and of time-dependent potentials, mimicking the mean interaction with the environment. Furthermore the relation of controllability and the wave packet's momentum is studied and the influence of potential barriers on the switching dynamics is shown.     

Magneto-optic spectroscopy of a protein tetramer binding two exciton-coupled chlorophylls

In vitro chlorophyll (Chl) aggregates have often served as models for in vivo forms of long-wavelength Chl. However, the interaction of protein-bound Chl molecules is typically different than that occurring in solvent-based self-aggregates. We have chosen a water-soluble Chl-binding protein (WSCP) from cauliflower in order to help characterize the spectroscopic properties of Chl in a single well-defined native environment and also to study the pigment-pigment (exciton) interactions present in assemblies of this protein. WSCP forms tetrameric units upon binding two Chl molecules. We present the absorption, circular dichroism (CD), magnetic circular dichroism (MCD), and emission spectra at 1.7 K of recombinant WSCP tetramers containing either Chl a or Chl d. The spectroscopic characteristics provide evidence for significant exciton interaction between equivalent Chl molecules. Our simple exciton analysis allows an estimate of the molecular geometry of the dimer, which is predicted to have an "open sandwich"-type structure. We find that the ratio of the magnetic circular dichroism to absorption, deltaA/A, is substantially increased (approximately 60%) for Chl a in this system compared to its value in solution. This increase is in marked contrast to substantial reductions (>50%) of deltaA/A seen in solvent-based Chl aggregates and in photosynthetic reaction centers. Current theoretical models are unable to account for such large variations in the MCD to absorption ratio for Chl. We propose that spectroscopic studies of WSCP mutants will enable a fundamental understanding of Chl-Chl and Chl-protein interactions.     

Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis

Optimization of fragment hits toward high-affinity lead compounds is a crucial aspect of fragment-based drug discovery (FBDD). In the current study, we have successfully optimized a fragment by growing into a ligand-inducible subpocket of the binding site of acetylcholine-binding protein (AChBP). This protein is a soluble homologue of the ligand binding domain (LBD) of Cys-loop receptors. The fragment optimization was monitored with X-ray structures of ligand complexes and systematic thermodynamic analyses using surface plasmon resonance (SPR) biosensor analysis and isothermal titration calorimetry (ITC). Using site-directed mutagenesis and AChBP from different species, we find that specific changes in thermodynamic binding profiles, are indicative of interactions with the ligand-inducible subpocket of AChBP. This study illustrates that thermodynamic analysis provides valuable information on ligand binding modes and is complementary to affinity data when guiding rational structure- and fragment-based discovery approaches.     

Ligand exchange upon oxidation of a dinuclear Mn complex--detection of structural changes by FT-IR spectroscopy and ESI-MS

The structural rearrangements triggered by oxidation of the dinuclear Mn complex [Mn(2)(bpmp)(mu-OAc)2]+(bpmp = 2,6-bis[bis(2-pyridylmethyl)amino]methyl-4-methylphenol anion) in the presence of water have been studied by combinations of electrochemistry with IR spectroscopy and with electrospray ionization mass spectrometry (ESI-MS). The exchange of acetate bridges for water (D2O) derived ligands in different oxidation states could be monitored by mid-IR spectroscopy in CD(3)CN-D(2)O mixtures following the v(as(C-O)) bands of bound acetate at 1594.4 cm(-1)(II,II), 1592.0 cm(-1)(II,III) and 1586.5 cm(-1)(III,III). Substantial loss of bound acetate occurs at much lower water content (< 0.5% v/v) in the III,III state than in the II,II and II,III states (> or = 10%). The ligand-exchange reactions do not initially reduce the overall charge of the complex but facilitate further oxidation by proton-coupled electron transfer as the water-derived ligands are increasingly deprotonated in higher oxidation states. In the IR spectra deprotonation could be followed by the formation of acetic acid (DOAc, approximately 1725 cm(-1), v(C-O)) from the released acetate (1573.6 cm(-1), v(as(C-O))). By the on-line combination of an electrochemical flow cell with ESI-MS several product complexes could be identified. A di-mu-oxo bridged III,IV dimer [Mn(2)(bpmp)(mu-O)(2)](2+)(m/z 335.8) can be generated at potentials below the III,III/II,III couple of the di-mu-acetato complex (0.61 V vs. ferrocene). The ligand-exchange reactions allow for three metal-centered oxidation steps to occur from II,II to III,IV in a potential range of only 0.5 V, explaining the formation of a spin-coupled III,IV dimer by photo-oxidation with [Ru[bpy)(3)](3+) in previous EPR studies.     

Structure and photoreaction of photoactive yellow protein, a structural prototype of the PAS domain superfamily

Photoactive yellow protein (PYP) is a water-soluble photosensor protein found in purple photosynthetic bacteria. Unlike bacterial rhodopsins, photosensor proteins composed of seven transmembrane helices and a retinal chromophore in halophilic archaebacteria, PYP is a highly soluble globular protein. The alpha/beta fold structure of PYP is a structural prototype of the PAS domain superfamily, many members of which function as sensors for various kinds of stimuli. To absorb a photon in the visible region, PYP has a p-coumaric acid chromophore binding to the cysteine residue via a thioester bond. It exists in a deprotonated trans form in the dark. The primary photochemical event is photo-isomerization of the chromophore from trans to cis form. The twisted cis chromophore in early intermediates is relaxed and finally protonated. Consequently, the chromophore becomes electrostatically neutral and rearrangement of the hydrogen-bonding network triggers overall structural change of the protein moiety, in which local conformational change around the chromophore is propagated to the N-terminal region. Thus, it is an ideal model for protein conformational changes that result in functional change, responding to stimuli and expressing physiological activity. In this paper, recent progress in investigation of the photoresponse of PYP is reviewed.     

Structural and luminescent properties of a series of Cd(II) pyridyl benzimidazole complexes that exhibit extended three-dimensional hydrogen bonded networks

Five new coordination complexes, [CdI₂(3-PyBim)](H₂O)₃ (1), [Cd(SO₄)(3-PyBim)(H₂O)₄] (2), [CdCl₂(4-PyBim)₂(H₂O)₂] (3), [CdBr₂(4-PyBim)₂(H₂O)₂] (4) and [CdI₂(4-PyBim)₂(H₂O)₂] (5) [3-PyBim=2-Pyridin-3-yl-1H-benzoimidazole, 4-PyBim=2-Pyridin-4-yl-1H-benzoimidazole], were obtained under hydrothermal conditions and characterized by single crystal X-ray diffraction, IR, elemental analysis, and powder X-ray diffraction. All of the complexes have mononuclear structures. Among the crystal structures of these complexes, there exist a variety of intermolecular hydrogen bonding interactions and π?π interactions, which further extend to a 3-D supramolecular architecture. The solid state photoluminescent properties of 1–5 vary with the electronegativity of the coordination anion. Additionally, the thermogravimetric analyses of these complexes are discussed.     

Conformational changes of high-molecular-weight DNA upon binding to noble metal nanoparticles in solution

Changes in the secondary and tertiary structure of DNA upon binding to silver, gold, and palladium nanoparticles (NPs) in solution were studied using UV spectroscopy, viscometry, dynamic light scattering, flow birefringence, and atomic force microscopy. A method for preparation of NP bioconjugates with DNA was developed. The enhancement of optical anisotropy of the macromolecule upon its contacts with metal NPs was detected. The effect of the formed structures on the persistence length of DNA and on the volume effects in the system was analyzed. A mechanism of NP formation upon the reduction of DNA-bound metal ions was proposed.

     

蛋白质分子与配体结合过程构象变化的研究

蛋白质分子与配体的作用模式主要有直接的环区结合及铰链式结合两种方式。针对这两种不同的作用方式,我们提出采用不同的策略进行结合过程的构象研究。对于直接的环区结合模式,通过建立环区主链构象库,来实现蛋白质环区与配体的准柔性对接,并以链霉抗生物素蛋白体系为例对构象库建立的可行性进行了验证计算。对铰链结合方式,采用分步对接的方法进行计算,并具体应用于HIV蛋白酶与其小分子配体的结合过程。计算结果表明,这两种处理方法分别能较好地模拟不同类型的蛋白质与配体结合的的构象变化。     

Binding properties and structural changes of human growth hormone upon interaction with cobalt ion

Binding properties and structural changes of human growth hormone (hGH) due to the interaction by cobalt ion (Co²⁺) were done at 27°C in NaCl solution, 50 mM, using different techniques of UV-Vis spectroscopy, circular dichroism (CD), isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) techniques. There is a set of three identical and non-interacting binding sites for cobalt ions. The intrinsic association equilibrium constant and the molar enthalpy of binding obtained by ITC are 0.80 mM⁻¹ and −16.70 kJ mol⁻¹, respectively. The intrinsic association equilibrium constant obtained by a standard isothermal titration UV-Vis spectrophotometry method is also 0.79 mM⁻¹, which is in good agreement with the value obtained from ITC. The Gibbs free energy and entropy changes due to the binding of cobalt ion on hGH are −16.67 kJ mol⁻¹ and −0.1 J K⁻¹ mol⁻¹, respectively. Energetic domains analysis by DSC shows that phase transition of hGH in the presence of cobalt occurs at one main transition. Deconvolution of the main transition provides two sub-transitions with different values of the melting point and enthalpy of unfolding (33°C and 164 kJ mol⁻¹ for the first and 49°C and 177 kJ mol⁻¹ for the second, respectively). Interaction of cobalt ions with hGH prevents aggregation by an affect on the hydrophobicity of the protein macromolecule and provide useful information about its structure due to becoming reversible of protein thermal denaturation.     

A comparative study on the structural changes in leucoemeraldine and emeraldine base upon doping by perchlorate

The changes in the structure of leucoemeraldine (LM) and emeraldine (EM) base upon doping by perchlorate anions are studied by X-ray photoelectron spectroscopy (XPS) and infrared (IR) absorption spectroscopy. In the case of LM, interactions of the amine nitrogens with the perchlorate anions result in a nitrogenonium ion structure analogous to that arising from the protonation of imine nitrogens in EM by HCl except the chloride anion in the latter has been replaced by the perchlorate anion. A small amount of partially ionic and covalent chlorine is also incorporated in the LM–perchlorate complexes. The maximum electrical conductivity that is achieved in these complexes is about 4 S/cm. In contrast, the maximum conductivity of the EM–perchlorate complexes is three orders of magnitude lower. The interactions of perchlorate anions with EM base result in the preferential disappearance of the imine units over the amine units.