Polyoxometalate binding to human serum albumin: a thermodynamic and spectroscopic approach

The molecular recognition of polyoxometalates by human serum albumin is studied using two different polyoxometalates (POMs) at pH 7.5. The results are compared with those obtained at pH 3.5 and 9.0. At pH 7.5, both POMs strongly interact with the protein with different binding behaviors. The Keggin shaped POM, [H(2)W(12)O(40)](6-) (H2W12), specifically binds the protein, forming a complex with a 1:1 stoichiometry with Ka = 2.9 x 10(6) M(-1). The binding constant decreased dramatically with the increase of the ionic strength, thus indicating a mostly electrostatic binding process. Isothermal titration calorimetry (ITC) experiments show that the binding is an enthalpically driven exothermic process. For the wheel shaped POM [NaP(5)W(30)O(110)](14-) (P5W30), there are up to five binding sites on the protein. Increasing the ionic strength changes the binding behavior significantly, leading to a simple exothermic process, with several binding sites. Competitive binding experiments indicate that the two POMs share one common binding site. In addition, they show the existence of another important binding site for P5W30. The two POMs exhibit different binding dependences on the pH. The combination of the experimental results with the knowledge of the surface map of the protein in its N-B conformation transition domain leads to the proposal for the probable binding site of POMs. The present work reveals a protein conformation change upon P5W30 binding, a new feature not explicitly documented in previous studies.     

Molecular modeling and spectroscopic studies on the binding of guaiacol to human immunoglobulin

The fluorogenic property of guaiacol was exploited for the first time to analyze the interaction with target protein as a probe by molecular modeling, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Molecular docking was performed to reveal the possible binding mode or mechanism and suggested that guaiacol can strongly bind to human immu- noglobulin (HIgG). It is considered that guaiacol binds to HIgG mainly by a hydrophobic interaction and there are two hydrogen bond interactions between the drug and the residues LEU 80 and ASP 65, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change △H0 and the entropy change △S0 were calculated to be 65.55 kJ·mol-1 and 132.95 J·mol-1·K-1 according to the Vant’ Hoff equation). Data obtained by the fluorescence spectroscopy indicated that binding of guaiacol with HIgG leads to dramatic enhancement in the fluorescence emission intensity along with significant occurrence of efficient Frster resonance energy transfer (FRET) from the residue of HIgG to the protein bound guaiacol. From the low value of fluorescence anisotropy (r = 0.06), it is argued that the probe molecule is located in the motionally unrestricted environment of the protein. The alterations of protein’s secondary structure in the presence of guaiacol in aqueous solution were quantitatively calculated by the evidences from FT-IR and CD spectroscopes.     

Tandem mass spectrometry of peptides with N-terminal glutamine studies on a prion protein peptide

Journal of The American Society for Mass Spectrometry - This paper reports the unusual collision-induced fragmentation of peptides having N-terminal glutamine. One of these glutamine-containing...     

Spectroscopic and electronic structure studies of copper(II) binding to His111 in the human prion protein fragment 106-115: evaluating the role of protons and methionine residues

The prion protein (PrP(C)) is implicated in the spongiform encephalopathies in mammals, and it is known to bind Cu(II) at the N-terminal region. The region around His111 has been proposed to be key for the conversion of normal PrP(C) to its infectious isoform PrP(Sc). The principal aim of this study is to understand the role of protons and methionine residues 109 and 112 in the coordination of Cu(II) to the peptide fragment 106-115 of human PrP, using different spectroscopic techniques (UV-vis absorption, circular dichroism, and electron paramagnetic resonance) in combination with detailed electronic structure calculations. Our study has identified a proton equilibrium with a pK(a) of 7.5 associated with the Cu(II)-PrP(106-115) complex, which is ascribed to the deprotonation of the Met109 amide group, and it converts the site from a 3NO to a 4N equatorial coordination mode. These findings have important implications as they imply that the coordination environment of this Cu binding site at physiological pH is a mixture of two species. This study also establishes that Met109 and Met112 do not participate as equatorial ligands for Cu, and that Met112 is not an essential ligand, while Met109 plays a more important role as a weak axial ligand, particularly for the 3NO coordination mode. A role for Met109 as a highly conserved residue that is important to regulate the protonation state and redox activity of this Cu binding site, which in turn would be important for the aggregation and amyloidogenic properties of the protein, is proposed.     

Investigation of synthetic hosts that model cation-pi sites found at protein binding domains

Small cyclophanes containing aromatic groups and dialkyl ammonium ions were created as model systems of the cation-pi complexes found at some protein binding domains. The hosts had different shapes in order to investigate the effect the arrangement of ammonium ions to aromatic surfaces has on their reactivity. pK(a) values of the hosts were substantially different in DMSO or (95/5) DMSO/D(2)O solutions, which showed that the ions existed in different environments of the hosts. Electrostatic charges, as determined by density functional calculations, revealed that the magnitude of a cationic charge depends on its position relative to an aromatic ring. Association constants of the hosts bound to the sodium salt of N-acetyl phenylalanine in d(6)-DMSO and in (95/5) d(6)-DMSO/D(2)O solutions were inversely proportional to the magnitude of the hosts' acidity constants. These results suggest that the magnitude of the positive charge for cationic groups of cation-pi complexes is reduced by being associated with electron-rich faces of aromatic rings. The aromatic rings, however, lessen the desolvation penalty that must be overcome for ligand binding, giving an overall more favorable association.     

Mercury binding by ferrocenoyl peptides with sulfur-containing side chains: Electrochemical, spectroscopic and structural studies

Ferrocenoyl peptides incorporating amino acids derived from either l-methionine, l-cysteine or dl-homocysteine have been synthesised and investigated as agents for heavy metal binding and detection. Heavy metal-peptide interactions have been characterised using cyclic voltammetry to follow changes in the potential of the Fe(II)/Fe(III) redox couple, revealing that these systems interact with mercury(II) ions more strongly than with other thiophilic heavy metals such as cadmium(II), silver(I) and lead(II). Proton NMR experiments have demonstrated 1:1 peptide:mercury binding and enabled quantitative characterisation of this binding interaction. Crystal structures for two of these ferrocenoyl peptide derivatives have been elucidated, revealing that these compounds adopt a P-1,3′ open solid state conformation in the absence of mercury; this arrangement precludes intramolecular hydrogen bonding between chains, while extensive intermolecular hydrogen bonding is evident. The particular affinity of these systems for mercury(II) opens the possibility of incorporating them in new, biologically inspired sensors for detecting this toxic pollutant.     

Copper-ion interaction with the 106-113 domain of the prion protein: a solution-equilibria study on model peptides

Prion diseases are characterized by a structural modification of the regular prion protein (PrP(C)) to its isoform, termed PrP(Sc)(scrapie). Such a modification involves the secondary and tertiary structure of the protein; the amino acidic sequence remains unchanged. PrP(Sc) is almost insoluble in non-denaturing solvents, resistant to proteases and it loses its redox activity. PrP(C) is able to bind copper and other metal ions: these complexes have been suggested to play an important role in the protein refolding leading to PrP(Sc). It is well-known that at least one relatively strong copper-binding site is located in the PrP(92--126) domain, where two His residues (96 and 111) are present. However, in the same domain, other amino acidic residues bear potentially donating atoms, i.e. Met, Asn and Lys residues. In order to shed light on the role of the side chains of such potentially tridentate amino acids on copper complexation, the polypeptide Ac-KTNMKHMA-NH(2), corresponding to the PrP(106--113) fragment, and some synthetic analogues have been investigated as ligands for the copper ion, by means of both thermodynamic and spectroscopic techniques. The pivotal role of imidazolic side chain of His in "anchoring" the metal ion has been confirmed. On the other hand, no clue was found on the participation of sulfur atom of Met or side amino-group of Lys residues to copper complex-formation.     

Synthesis and spectroscopic studies of model red fluorescent protein chromophores

[reaction: see text]. Here we describe the synthesis and spectroscopic characterization of two compounds designed to model the chromophore in DsRed, a red fluorescent protein. Comparison with model green fluorescent protein (GFP) chromophores indicates that the additional conjugation in the DsRed models can account, in part, for the red-shifted absorption and emission properties of DsRed compared to those of GFP. In contrast to the GFP models, the DsRed models are fluorescent with quantum yields of 0.002-0.01 in CHCl3.     

Homocysteine thiolactone and protein homocysteinylation: mechanistic studies with model peptides and proteins

In vitro incubations were performed to show that homocysteine thiolactone could generate covalent adducts with model peptides and proteins. MS and MS/MS data suggest that the thiolactone reacts with the side-chain amino group of lysine residues as well as with the N-terminal amino group or C-terminal carboxy group. For larger peptides and proteins, the contribution from the in-amino groups of lysine residues should be predominant. These data could help explain the detrimental effects of elevated levels of homocysteine and homocysteine thiolactone.     

人类朊蛋白的动力学稳定性研究（英文）

朊蛋白病是一种能在人类或者动物之间传播的致命的神经退行性疾病.尤其是人类朊蛋白疾病在近几年蔓延迅速,已经威胁到人类的健康.在本文中,我们使用分子动力学(MD)和流体分子动力学(FMD)模拟相结合的方法研究了人类朊蛋白(hPrPc)的动力学稳定性.我们通过FMD模拟产生了两个典型的hPrPc的变性结构,并进一步研究了在自然状态下这两个变性结构重折叠的过程,从关键残基、二级结构、残基-残基相互作用图等方面详细讨论了hPrPc的解折叠和重折叠路径.研究发现hPrPc的三个α-螺旋结构组成了一个疏水核心,在蛋白质的解折叠和重折叠过程中发挥了重要的作用.刚性的疏水核心就像是脚手架一般为hPrPc的重折叠提供便利.在重折叠过程中,π-螺旋和310螺旋出现几率较高,并且β-折叠的延长也更多地出现在完全解折叠的hPrPc体系中.     

A thermodynamic investigation on the binding of mercury ion with myelin basic protein at different temperatures

A thermodynamic study on the interaction of myelin basic protein with mercury ion was studied by using isothermal titration calonmetry,ITC,at 300.15,310.15 and 320.15 K in Tris buffer solution at pH 7.The enthalpies of MBP + Hg²⁺ interaction are reported and analysed in terms of the extended solvation model.It was found that MBP has two identical and non-cooperative binding sites for Hg²⁺ ions.The intrinsic dissociation equilibrium constants are 99.904,112.968 and 126.724μmol/L,and the molar enthalpy of binding are -11.634,-10.768 and -10.117kJ mol^-1 at 300.15,310.15 and 320.15 K,respectively.     

Copper(II) binding modes in the prion octapeptide PHGGGWGQ: a spectroscopic and voltammetric study

The N-terminal octapeptide repeat region of human prion protein (PrPc) is known to bind Cu(II). To investigate the binding modes of copper in PrPc, an octapeptide Ac-PHGGGWGQ-NH2 (1), which corresponds to an octa-repeat sequence, and a tetrapeptide Ac-HGGG-NH2 (2) have been synthesised. The copper(II) complexes formed with 1 and 2 have been studied by circular dichroism (CD) and electron spin resonance (ESR) spectroscopy. Both peptides form 1:1 complexes with Cu(II) at neutral and basic pH. CD, ESR and visible absorption spectra suggest a similar co-ordination sphere of the metal ion in both peptides, which at neutral pH consists of a square pyramidal geometry with three peptidic nitrogens and the imidazole nitrogen as donor atoms. Cyclic voltammetric measurements were used to confirm the geometrical features of these copper(II) complexes: the observation of negative redox potentials are in good agreement with the inferred geometry. All these results taken together suggest that peptide 1 provides a single metal binding site to which copper(II) binds strongly at neutral and basic pH and that the binding of the metal induces the formation of a stiffened structure in the HGGG peptide fragment.     

A model of cooperativity based on restricted binding: kinetic and thermodynamic analysis

Cooperative protein–ligand binding is an essential biochemical process. In this work, we introduce a model that can simulate the emergence of such phenomenon in the binding kinetics. It is based on the inability of the ligand molecules to fully utilize all the available binding sites due to some restriction, realized here in terms of a model parameter, called the restriction parameter. The theory is developed at the level of a single oligomeric protein molecule interacting with a ligand, maintained at a constant concentration, using a chemical master equation. The model provides stepwise binding constants related to the restriction parameter. The relative magnitudes of these constants, when compared to the Hill coefficients measuring cooperativity, give a physical insight in the development of the cooperative behavior and can also act as a reference frame. This can be useful for an alternative theoretical characterization of cooperativity in oligomeric proteins with large number of binding sites and arbitrary binding constants. We establish this point here by taking a tetrameric protein as a case study. A stochastic thermodynamic analysis is also performed, highlighting the energy–entropy contribution to the overall free energy change due to protein–ligand interaction for various cases of restricted binding.     

Interactions of vancomycin and ristocetin with peptides as a model for protein binding

The glycopeptide antibiotics vancomycin and ristocetin act by binding to peptides terminating in -D-Ala-D-Ala. Thermodynamic and kinetic parameters for the binding are evaluated and used in conjunction with previously determined stereochemical details to generate a complete picture of the binding interaction. A conformational change of the antibiotics is necessary to permit fast on-rates, and produces a hydrophobic pocket for the peptide carboxylate group. We discuss an unusual salt bridge and consider the origins of the high specificity of the antibiotics. The discussion is extended to macromolecule-substrate interactions. The importance of fast access to binding sites and complementarity of hydrogen bonding pairs is stressed.     

Theoretical studies on the structural,spectroscopic, thermodynamic,and electronic properties of zoledronic acid

The structure, spectroscopic, thermodynamic, and electronic properties of zoledronic acid (ZL, 1-hydroxy- 2-(1H-imidazol-1-yl)ethane-1,1-diyldiphosphonic acid), typical third-generation nitrogen-containing bisphosphonates (N-BPs), have been investigated systematically. Six conformations are taken into account, including three unprotonated and three protonated structures. They are optimized by four different density functional theory (DFT) methods combined with four different basis sets to evaluate their performance in predicting the structural and spectral features of ZL. Thermodynamic properties are calculated based on the harmonic vibrational analysis, including the standard heat capacity (C _p,m ⁰ ), entropy (S _m ⁰ ), and enthalpy (S _m ⁰ ). The ¹H and ¹³C NMR chemical shifts are calculated using the GIAO method and compared with the experimental data. Molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analyses are also performed to study the electronic characteristics of the title compound.     

Structural and dynamic characterization of copper(II) binding of the human prion protein outside the octarepeat region

Human prion protein (hPrP) fragments encompassing the 91-120 region, namely hPrP92-100 (SP1), hPrP106-113 (SP2), hPrP91-120 (LP1), and hPrP91-114 (LP2), were considered for delineation of the Cu(II)-binding site(s). NMR and EPR spectroscopy results obtained from LP1 or LP2 were compared with those obtained from SP1 and SP2. The coexistence of two binding sites, one centered at His96 and the other at His111, was evidenced and ratified by ESI mass spectrometry at low and high metal:peptide ratios. While room-temperature NMR spectroscopy data were consistent with the binding site centered on His111 being approximately fourfold stronger than that centered on His96, low-temperature EPR spectroscopy results yielded evidence for the opposite trend. This disagreement, which has also occurred in the literature, was clarified by temperature-dependent molecular dynamics runs that demonstrated Met112 approaching the metal at room temperature, a process that is expected to stabilize the His111-centered binding site through hydrophobic shielding of the metal coordination sphere.     

Binding of propene on small gold clusters and on Au(111): simple rules for binding sites and relative binding energies

We use density functional theory (DFT) to investigate the bonding of propene to small gas-phase gold clusters and to a Au(111) surface. The desorption energy trends and the geometry of the binding sites are consistent with the following set of rules. (1) The bond of propene to gold is formed by donation of electron density from the highest occupied molecular orbital (HOMO) of propene to one of the low-lying empty orbitals [denoted by LUMO1, LUMO2, em leader (LUMO-lowest unoccupied molecular orbital)] of the gold cluster. (2) Propene binds to a site on the Au cluster where one of the low-lying LUMOs protrudes in the vacuum. Different isomers (same cluster, but different binding sites for propene) correspond to sites where different low-lying LUMOs protrude in space. (3) The desorption energy of the lowest energy isomer correlates with the energy of the lowest empty orbital of the cluster; the lower the energy of that LUMO, the higher the desorption energy. (4) If the lowest-lying LUMO protrudes into space at two nonequivalent sites at the edge of a cluster, propene binds more strongly to the site with the lowest coordination. These rules are consistent with the calculated bond energies and geometries for [Au(n)(C(3)H(6))](q), for n=1-5 and n=8 and q=-1, 0, +1. Based on them we have made a number of predictions that have been confirmed by DFT calculations. The bond of propene to gold is strengthened as the net charge of the cluster varies from -1, to zero, to +1. Compared to a gas-phase cluster, a cluster on a support binds propene more strongly if the support takes electron density from the cluster (e.g., a Au cluster on a gold surface) and more weakly if the support donates electron density to the cluster (e.g., a Au cluster on an oxygen vacancy on an oxide surface).     

An "S"-shaped pentanuclear CuII cluster derived from the metal-assisted hydrolysis of pyCOpyCOpy: structural, magnetic and spectroscopic studies

Reaction of [Cu2(O2CMe)4(H2O)2] with 2,6-di-(2-pyridylcarbonyl)-pyridine (pyCOpyCOpy or dpcp) in MeCN-H2O 10:1, led to the pentanuclear copper(II) complex [Cu5(O2CMe)6{pyC(O)(OH)pyC(O)(OH)py}2] () which crystallizes in the triclinic P1 space group. The copper(II) atoms are arranged in an "S"-shaped configuration, and are bridged by the doubly deprotonated bis(gem-diol) form of the ligand, pyC(O)(OH)pyC(O)(OH)py2-. Magnetic susceptibility data indicate the interplay of both ferro- and antiferromagnetic intramolecular interactions stabilizing an S=3/2 ground state. Fitting of the data according to a next-nearest-neighbour model {H=-[J1(S1S2+S1'S2')+J2(S2S3+S3'S2')+J3(S1S3+S3'S1')+J4(S2S2')]} yields exchange coupling constants J1=+39.7 cm(-1), J2=-15.9 cm(-1), J3=-8.3 cm(-1) and J4=+4.3 cm(-1), leading to an S=3/2 ground state. X-Band EPR spectroscopy indicates a zero-field splitting of the ground state with |D3/2|=0.38 cm(-1).     

A thermodynamic study on the binding of magnesium with human growth hormone

The thermodynamic parameters underlying the binding of Mg²⁺ to the hydrophobic core of human growth hormone, hGH, are determined using isothermal titration calorimetry. The interaction between Mg²⁺ and hGH (35 μM) was studied at 27°C in NaCl solution. A new solvation model was used to reproduce the enthalpies of Mg²⁺-hGH interaction over the whole Mg²⁺ concentrations. The solvation parameters recovered from the new salvation model, were correlated to the structural changes of hGH due to the metal ion interaction.