Dissociation of Multisubunit Protein–Ligand Complexes in the Gas Phase. Evidence for Ligand Migration

The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB₅) with the pentasaccharide (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp (GM1)) and corresponding glycosphingolipid (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S₄) with biotin (B) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB₅ + 5GM1)ⁿ⁺ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB₅ + 5GM1)^n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S₄ + 4B)^n+/– ions, as well as for deprotonated (S₄ + 4Btl)^n– ions, was loss of the ligand. However, subunit loss from the (S₄ + 4B)ⁿ⁺ ions was observed as a minor pathway. The (S₄ + 4Btl)ⁿ⁺ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB₅ + 5GM1)¹⁵⁺ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein–ligand complexes in the gas phase depend, not only on the native topology of the complex, but also on structural changes that occur upon collisional activation.

Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S（CH2）7CH3, S（CH2）7OH and S（CH2）7COOH, which self-assembled on Au（111） surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affin- ity is in the order as COOH-SAMs〉OH-SAMs〉CH3-SAMs, while 100% COOH-SAMs〉5% COOH-SAMS in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.     

Ligand Migration in the Gaseous Insulin-CB7 Complex—A Cautionary Tale About the Use of ECD-MS for Ligand Binding Site Determination

Knowledge of the structure of protein?Cligand complexes can aid in understanding their roles within complex biological processes. Here we use electrospray ionization (ESI) coupled to a Fourier transform ion cyclotron resonance mass spectrometer to investigate the noncovalent binding of the macrocycle cucurbit[7]uril (CB7) to bovine insulin. Recent condensed-phase experiments (Chinai et al., J. Am. Chem. Soc. 133:8810?C8813, 2011) indicate that CB7 binds selectively to the N-terminal phenylalanine of the insulin B-chain. Competition experiments employing ESI mass spectrometry to assess complex formation between CB7 and wild type insulin B-chain vs. a mutant B-chain, confirm that the N-terminal phenylalanine plays in important role in solution-phase binding. However, analysis of fragment ions produced by electron capture dissociation (ECD) of CB7 complexed to intact insulin and to the insulin B-chain suggests a different picture. The apparent gas-phase binding site, as identified by the ECD, lies further along the insulin B-chain. Together, these studies thus indicate that the CB7 ligand migrates in the ESI mass spectrometry analysis. Migration is likely aided by the presence of additional interactions between CB7 and the insulin B-chain, which are not observed in the crystal structure. While this conformational difference may result simply from the removal of solvent and addition of excess protons by the ESI, we propose that the migration may be enhanced by charge reduction during the ECD process itself because ion-dipole interactions are key to CB7 binding. The results of this study caution against using ECD-MS as a stand-alone structural probe for the determination of solution-phase binding sites.     

Guest Binding with Sulfated Cyclodextrins: Does the Size of Cavity Matter?

Sulfated cyclodextrins have recently emerged as potential candidates for producing host–induced guest aggregation with properties better than p-sulfonatocalixarenes that have previously shown numerous applications involving the phenomena of host-induced guest aggregation. In the class of sulfated cyclodextrins (SCD), sulfated β-cyclodextrin (β-SCD) remains the most extensively investigated host molecule. Although it is assumed that the host-induced guest aggregation is predominantly an outcome of interaction of the guest molecule with the charges on the exterior of SCD cavity, it has not been deciphered whether the variation in the cavity size will make a difference in the efficiency of host-induced guest-aggregation process. In this investigation, we present a systematic study of host–induced guest aggregation of a cationic molecular rotor dye, Thioflavin T (ThT) with three different sulfated cyclodextrin molecules, α-SCD, β-SCD and γ-SCD, which differ in their cavity size, using steady-state emission, ground-state absorption and time-resolved emission measurements. The obtained photophysical properties of ThT, upon interaction with different SCD molecules, indicate that the binding strength of ThT with different SCD molecules correlate with the cavity size of the host molecule, giving rise to the strongest complexation of ThT with the largest host molecule (γ-SCD). The binding affinity of ThT towards different host molecules has been supported by molecular docking calculations. The results obtained are further supported with the temperature and ionic strength dependent studies performed on the host-guest complex. Our results indicate that for host–induced guest aggregation, involving oppositely charged molecules, the size of the cavity also plays a crucial role beside the charge density on the exterior of host cavity.     

How Does Glycation Affect Binding Parameters of the Albumin-Gliclazide System in the Presence of Drugs Commonly Used in Diabetes? In Vitro Spectroscopic Study

In this research, the selected drugs commonly used in diabetes and its comorbidities (gliclazide, cilazapril, atorvastatin, and acetylsalicylic acid) were studied for their interactions with bovine serum albumin—native and glycated. Two different spectroscopic methods, fluorescence quenching and circular dichroism, were utilized to elucidate the binding interactions of the investigational drugs. The glycation process was induced in BSA by glucose and was confirmed by the presence of advanced glycosylation end products (AGEs). The interaction between albumin and gliclazide, with the presence of another drug, was confirmed by calculation of association constants (0.11–1.07 × 10⁴ M⁻¹). The nature of changes in the secondary structure of a protein depends on the drug used and the degree of glycation. Therefore, these interactions may have an influence on pharmacokinetic parameters.     

How Does the Axial Ligand of Cytochrome P450 Biomimetics Influence the Regioselectivity of Aliphatic versus Aromatic Hydroxylation?

How deep is your orbital? Density functional theory studies on the axial ligand effect of aliphatic versus aromatic hydroxylation of ethylbenzene by iron–oxo complexes with a variable axial ligand show that strong (anionic) ligands pull the metal inside the plane of the haeme and destabilise cationic intermediates through orbital interactions (see picture).

     

Selection of Peptide Ligands Specific for Baculovirus DNA‐Binding Protein from the Flitrx™ Random Peptide Display Library

Abstract

Autographa californica nucleopolyhedrovirus (AcNPV) is a baculovirus that is widely employed as a vector for the expression of foreign genes and pest control. Although baculoviruses, including AcNPV, efficiently replicate in the nuclei of arthropod cells, the dynamics and mechanism of DNA replication within the infected cell are still poorly understood. It has been found that the DNA‐binding protein (DBP) is an early gene product and appears to be crucial for viral DNA replication.

Presented here is the selection of peptide ligands that specifically bind to DBP for AcNPV from the FliTrx? random peptide display library; this entails the amplification, cloning of the DNA‐binding protein (DBP) gene from AcNPV and the construction of the expression plasmid for DBP, and the expression and purification of the recombinant His.Tag AcNPV DBP that was used as a target molecule for the selection of the peptide ligands specific for AcNPV DBP. The affinity and efficiency of such peptide ligands were then measured by ELISA procedures.

The beneficial aspect of this research is the monospecificity quality of the peptide ligands specific for AcNPV DBP. They could be used for the study of the dynamics of the viral genome and its replication within the infected cell, for the development of a quantitative method for the determination of the presence of baculovirus in various samples, for the development of a peptide ligandbased assay for the determination of baculovirus titers; or they could be immobilized on a chromatographic support for an improved affinity purification of AcNPV DBP.     

What Can We Learn from Molecular Recognition in Protein–Ligand Complexes for the Design of New Drugs?

The understanding of noncovalent interactions in protein–ligand complexes is essential in modern biochemistry and should contribute toward the discovery of new drugs. In the present review, we summarize recent work aimed at a better understanding of the physical nature of molecular recognition in protein–ligand complexes and also at the development and application of new computational tools that exploit our current knowledge on structural and energetic aspects of protein–ligand interactions in the design of novel ligands. These approaches are based on the exponentially growing amount of information about the geometry of protein structures and the properties of small organic molecules exposed to a structured molecular environment. The various contributions that determine the binding affinity of ligands toward a particular receptor are discussed. Their putative binding site conformations are analyzed, and some predictions are attempted. The similarity of ligands is examined with respect to their recognition properties. This information is used to understand and propose binding modes. In addition, an overview of the existing methods for the design and selection of novel protein ligands is given.     

Native Biomolecules in the Gas Phase? The Case of Green Fluorescent Protein

Green fluorescent protein (GFP) was ionized by native electrospray ionization and trapped for many seconds in high vacuum, allowing fluorescence emission to be measured as a probe of its biological function, to answer the question whether GFP exists in the native form in the gas phase or not. Although a narrow charge‐state distribution, a collision cross‐section very close to that expected for correctly folded GFP, and a large stability against dissociation all support a near‐native gas‐phase structure, no fluorescence emission was observed. The loss of the native form is attributed to the absence of residual water in the gas phase, which normally stabilizes the para‐hydroxybenzylidene imidazolone chromophore of GFP.     

Does the DNA Binding Mode of a Molecule Affect its Ability to Interact With Singlet Oxygen?

Singlet oxygen is known to be a potent mutagenic agent and several biologically relevant molecules have been proposed to act as scavengers for this noxious species. However, numerous studies have been conducted in homogenous solution and the reactivity of singlet oxygen scavengers known to bind DNA has never been investigated in double-stranded DNA. In the following paper, we present the results obtained regarding the interaction between 4',6-diamidino-2-phenylindole (DAPI) and singlet oxygen. We show the molecule to be a potent scavenger of singlet oxygen in aqueous solution with an absolute rate constant (chemical and physical quenching of singlet oxygen) of (1.7 ± 0.3) × 10⁷  m ⁻¹ s⁻¹. In addition, we demonstrate that the binding mode of a singlet oxygen scavenger to DNA can strongly influence its reactivity toward singlet oxygen. In the case of DAPI, while the molecule exhibits a chemical reaction with singlet oxygen when the molecule is free in aqueous solution or intercalated in GC sequences of DNA, DAPI becomes chemically unreactive toward singlet oxygen when bound in the minor groove of DNA AT sequences.     

How to explain the difficulties in the coffinite synthesis from the study of uranothorite?

The preparation of Th(1-x)U(x)SiO(4) uranothorite solid solutions was successfully undertaken under hydrothermal conditions (T = 250 °C). From XRD and EDS characterization, the formation of a complete solid solution between x = 0 (thorite) and x = 0.8 was evidenced. Nevertheless, additional (Th,U)O(2) dioxide and amorphous silica were systematically observed for the highest uranium mole loadings. The influence of kinetics parameters was then studied to avoid the formation of such side products. The variation of the synthesis duration allowed us to point out the initial formation of oxide phases then their evolution to a silicate phase through a dissolution/precipitation process close to that already described as coffinitization. Also, the uranium mole loading initially considered was found to significantly influence the kinetics of reaction, as this latter strongly slows down for x > 0.3. Under these conditions, the difficulties frequently reported in the literature for the synthesis of pure USiO(4) coffinite were assigned to a kinetic hindering associated with the coffinitization reaction.     

1H-NMR Investigation of the Binding of 2-Methylnaphthalene to α-Cyclodextrin in D2O Solutions

As -cyclodextrin (-CD) was added to D₂Osolutions of 2-methylnaphthalene, its proton signals shifted to lower fieldsat low concentrations of -CD. At 2.0 × 10^-2 moldm^-3 of -CD, however, a reverse, higher-field shift wasobserved for the H-8 signal, indicating the formation of 1 : 1 and 2 : 1-CD–2-methylnaphthalene inclusion complexes. Intrinsic chemicalshift differences of all the protons in 2-methylnaphthalene have beenevaluated for both the 1 : 1 and the 2 : 1-CD–2-methylnaphthalene inclusion complexes. These intrinsicchemical shift differences suggest that the first -CD molecule has noselectivity in accommodating one end of uncomplexed 2-methylnaphthalene;-CD binds to a methyl group, as well as a naphthalene ring-end havingno methyl group, to form the 1 : 1 inclusion complex, resulting in theformation of two kinds of 1 : 1 complexes.     

Binding of alkaloids into the S1 specificity pocket of α-chymotrypsin: evidence from induced circular dichroism spectra

Non-covalent binding of planar aromatic molecules into the S1 specificity pocket of the serine protease α-chymotrypsin (αCHT) can be detected by measuring induced circular dichroism (CD) spectroscopic signals. Utilizing this phenomenon, αCHT association of proflavine (PRF), the well known serine protease inhibitor has been investigated together with plant-derived compounds including isoquinoline, pyridocarbazole and indoloquinoline alkaloids, of which αCHT binding has never been reported. Non-degenerate exciton coupling between π-π* transitions of the ligand molecules and two tryptophan residues (Trp172 and Trp215) near to the binding site is proposed to be responsible for the induced CD activity. The association constants calculated from CD titration data indicated strong αCHT association of sanguninarine, ellipticine, desmethyl-isocryptolepine and isoneocryptolepine (K(a) ≈ 10(5) M(-1)) while berberine, coptisine and chelerythrine bind to the enzyme with lower, PRF-like affinity (K(a) ≈ 10(4) M(-1)). PRF-trypsin and ellipticine-trypsin binding interactions have also been demonstrated. The binding of the alkaloids into the S1 pocket of αCHT has been confirmed by CD competition experiments. Molecular docking calculations showed the inclusion of PRF as well as the alkaloid molecules in the S1 cavity where they are stabilized by hydrophobic and H-bonding interactions. These novel nonpeptidic scaffolds can be used for developing selective inhibitors of serine proteases having chymotrypsin-like folds. Furthermore, the results provide a novel, CD spectroscopic based approach for probing the ligand binding of αCHT and related proteases.     

Generation of transient neutrals in the gas phase from anionic precursors. Does energised CNCCO rearrange to NCCCO?

The stability and reactivity of the neutral species CNCCO generated by one electron oxidation of the anion [CNCCO](-) have been investigated by a combination of theoretical calculations (carried out at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31G(d) level of theory) and tandem mass spectrometric experiments. Some of the neutrals formed in this way are stable for the microsecond duration of the experiment, but others are energised. The neutrals which are energised may either (i) dissociate [CNCCO --> CNC + CO (+92 kJ mol(-1))], and/or (ii), undergo the isonitrile to nitrile rearrangement to yield NCCCO energised neutrals (barrier 133 kJ mol(-1), reaction exothermic by 105 kJ mol(-1)). Some of these rearranged neutrals NCCCO have excess energies as high as 238 kJ mol(-1) and will dissociate [NCCCO --> NCC + CO (+203 kJ mol(-1))].     

Does core size matter in the kinetics of ligand exchanges of monolayer-protected Au clusters?

This paper compares the kinetics of exchanges of phenylethanethiolate ligands (PhC2S-) of the monolayer-protected clusters (MPCs) Au(38)(SC2Ph)(24) and Au(140)(SC2Ph)(53) with p-substituted arylthiols (p-X-PhSH), where X = NO(2), Br, CH(3), OCH(3), and OH. First-order rate constants at 293 K for exchange of the first ca. 25% of the ligands on the molecule-like Au(38)(SC2Ph)(24) MPC, measured using (1)H NMR, vary linearly with the in-coming arythiol concentration; ligand exchange is an overall second-order reaction. Remarkably, the second-order rate constants for ligand exchange on Au(38)(SC2Ph)(24) are very close to those of corresponding exchange reactions on the larger nanoparticle Au(140)(SC2Ph)(53) MPCs. These are the first results that quantitatively show that the chemical reactivity of different sized nanocrystals is almost independent of size; presumably, this is because the locus of the initial ligand exchanges is a common kind of site, thought to be the nanocrystal vertexes. The rates of later stages of exchange (beyond ca. 25%) differ for Au(38) and Au(140) cores, the latter being much slower presumably due to its larger terrace-like surface atom content. The reverse exchange reaction was studied for Au(38)(p-X-arylthiolate)(24) MPCs (X = NO(2), Br, and CH(3)), where the in-coming ligand is now phenylethanethiol. Remarkably, the rate constants of both forward and reverse exchanges display identical substituent effects, which implies a concurrent bonding of both in-coming and leaving ligands to the Au core in the rate-determining step, as in an associative mechanism. X = NO(2) gives the fastest rates, and the ratio of forward and reverse rate constants gives an equilibrium constant of K(EQ,PE) = 4.0 that is independent of X.     

How Does a Coordinated Radical Ligand Affect the Spin Crossover Properties in an Octahedral Iron(II) Complex?

The influence of a coordinated π‐radical on the spin crossover properties of an octahedral iron(II) complex was investigated by preparing and isolating the iron(II) complex containing the tetradentate N,N′‐dimethyl‐2,11‐diaza[3.3](2,6)pyridinophane and the radical anion of N,N′‐diphenyl‐acenaphtene‐1,2‐diimine as ligands. This spin crossover complex was obtained by a reduction of the corresponding low‐spin iron(II) complex with the neutral diimine ligand, demonstrating that the reduction of the strong π‐acceptor ligand is accompanied by a decrease in the ligand field strength. Characterization of the iron(II) radical complex by structural, magnetochemical, and spectroscopic methods revealed that spin crossover equilibrium occurs above 240 K between an S=1/2 ground state and an S=3/2 excited spin state. The possible origins of the fast spin interconversion observed for this complex are discussed.     

Protein Flexibility and Multiple Docking in Ligand Docking and Virtual Screening to the BRAF (Type Ⅰ1/2) Inhibitors

BRAF has been recognized as a promising target for cancer therapy. A number of crystal structures have been published. Molecular docking is one of the most effective techniques in the field of computer-aided drug design(CADD). Appropriate protein conformation and docking method are essential for the successful virtual screening experiments. One approach considering protein flexibility and multiple docking methods was proposed in this study. Six DFG-in/αC-helix-out crystal structures of BRAF, three docking programs(Glide, GOLD and Ligand Fit) and 12 scoring functions were applied for the best combination by judging from the results of pose prediction and retrospective virtual screening(VS). The most accurate results(mean RMSD of about 0.6 ?) of pose prediction were obtained with two complex structures(PDB: 3 C4 C and 3 SKC) using Glide SP. From the retrospective VS, the most active compounds were identified by using the complex structure of 3 SKC, indicated by a ROC/AUC score of 0.998 and an EF of 20.6 at 5% of the database screen with Glide-SP. On the whole, PDB 3 SKC could achieve a higher rate of correct reproduction, a better enrichment and more diverse compounds. A comparison of 3 SKC and the other X-ray crystal structures led to a rationale for the docking results. PDB 3 SKC could achieve a broad range of sulfonamide substitutions through an expanded hydrophobic pocket formed by a further shift of the αC-helix. Our study emphasized the necessity and significance of protein flexibility and scoring functions in both ligand docking and virtual screening.     

Electrostatic Perturbations from the Protein Affect C−H Bond Strengths of the Substrate and Enable Negative Catalysis in the TmpA Biosynthesis Enzyme

The nonheme iron dioxygenase 2-(trimethylammonio)-ethylphosphonate dioxygenase (TmpA) is an enzyme involved in the regio- and chemoselective hydroxylation at the C¹-position of the substrate as part of the biosynthesis of glycine betaine in bacteria and carnitine in humans. To understand how the enzyme avoids breaking the weak C²−H bond in favor of C¹-hydroxylation, we set up a cluster model of 242 atoms representing the first and second coordination sphere of the metal center and substrate binding pocket, and investigated possible reaction mechanisms of substrate activation by an iron(IV)-oxo species by density functional theory methods. In agreement with experimental product distributions, the calculations predict a favorable C¹-hydroxylation pathway. The calculations show that the selectivity is guided through electrostatic perturbations inside the protein from charged residues, external electric fields and electric dipole moments. In particular, charged residues influence and perturb the homolytic bond strength of the C¹−H and C²−H bonds of the substrate, and strongly strengthens the C²−H bond in the substrate-bound orientation.