Intact Transition Epitope Mapping-Force Interferences by Variable Extensions (ITEM-FIVE)

Investigations on binding strength differences of non-covalent protein complex components were performed by mass spectrometry. T4 fibritin foldon (T4Ff) is a well-studied miniprotein, which together with its biotinylated version served as model system to represent a compactly folded protein to which an Intrinsically Disordered Region (IDR) was attached. The apparent enthalpies of the gas phase dissociation reactions of the homo-trimeric foldon F-F-F and of the homo-trimeric triply biotinylated foldon bF-bF-bF have been determined to be rather similar (3.32 kJ/mol and 3.85 kJ/mol) but quite distinct from those of the singly and doubly biotinylated hetero-trimers F-F-bF and F-bF-bF (1.86 kJ/mol and 1.08 kJ/mol). Molecular dynamics simulations suggest that the ground states of the (biotinylated) T4Ff trimers are highly symmetric and well comparable to each other, indicating that the energy levels of all four (biotinylated) T4Ff trimer ground states are nearly indistinguishable. The experimentally determined differences and/or similarities in enthalpies of the complex dissociation reactions are explained by entropic spring effects, which are noticeable in the T4Ff hetero-trimers but not in the T4Ff homo-trimers. A lowering of the transition state energy levels of the T4Ff hetero-trimers seems likely because the biotin moieties, mimicking intrinsically disordered regions (IDRs), induced asymmetries in the transition states of the biotinylated T4Ff hetero-trimers. This transition state energy level lowering effect is absent in the T4Ff homo-trimer, as well as in the triply biotinylated T4Ff homo-trimer. In the latter, the IDR-associated entropic spring effects on complex stability cancel each other out. ITEM-FIVE enabled semi-quantitative determination of energy differences of complex dissociation reactions, whose differences were modulated by IDRs attached to compactly folded proteins.

Incorporation of Epoxy Carbon onto CeO2-Supported Pt to Tackle the CO Self-Poisoning Issue

The catalytic oxidation of carbon monoxide (CO) under ambient conditions plays a crucial role in the abatement of indoor CO, which poses risks to human health. Despite the notable activity exhibited by Pt-based catalysts in CO oxidation, their efficacy is usually diminished by the CO self-poisoning issue. In this work, three different Pt/CeO2-based catalysts, which have distinct coordinative environments of Pt but an identical Pt/CeO2 substrate structure, were synthesized by activating the catalyst with CO using different temperatures and durations. Compared with clean and graphite-covered Pt on CeO2, the one modified by epoxy carbon showed higher activity and stability. The combination of characterizations and density functional theory modeling demonstrated that the clean Pt on CeO2 rapidly deactivated due to the CO self-poisoning albeit high initial activity, and conversely, low initial activity was observed for the more stable graphite-covered catalyst due to the obstruction of the Pt site. In contrast, epoxy carbon species on Pt shifted the d-band of Pt to lower energy, weakening the Pt-CO binding strength. Such a modification mitigated the self-poisoning effect while maintaining ample active sites and enabling the complete oxidative removal of CO under ambient conditions. This work may provide a general approach to tackling the self-poisoning issue.

Intrinsic protein disorder uncouples affinity from binding specificity

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins often function by molecular recognition, in which they undergo induced folding. Based on prior generalizations, the idea prevails in the IDP field that due to the entropic penalty of induced folding, the major functional advantage associated with this binding mode is "uncoupling" specificity from binding strength. Nevertheless, both weaker binding and high specificity of IDPs/IDRs rest on limited experimental observations, making these assumptions more speculations than evidence-supported facts. The issue is also complicated by the rather vague concept of specificity that lacks an exact measure, such as the K_d for binding strength. We addressed these issues by creating and analyzing a comprehensive dataset of well-characterized ID/globular protein complexes, for which both the atomic structure of the complex and free energy (ΔG, K_d ) of interaction is known. Through this analysis, we provide evidence that the affinity distributions of IDP/globular and globular/globular complexes show different trends, whereas specificity does not connote to weaker binding strength of IDPs/IDRs. Furthermore, protein disorder extends the spectrum in the direction of very weak interactions, which may have important regulatory consequences and suggest that, in a biological sense, strict correlation of specificity and binding strength are uncoupled by structural disorder.

Epitope Fine Mapping by Mass Spectrometry: Investigations of Immune Complexes Consisting of Monoclonal Anti-HpTGEKP Antibody and Zinc Finger Protein Linker Phospho-Hexapeptides

Accurate formation of antibody-antigen complexes has been relied on in both, multitudes of scientific projects and ample therapeutic and diagnostic applications. Mass spectrometrically determined dissociation behavior of immune complexes with the anti-HpTGEKP antibody revealed that the ten most frequently occurring phospho-hexapeptide linker sequences from C2H2 zinc finger proteins could be divided into two classes: orthodox binders, where strong noncovalent interactions developed as anticipated, and unorthodox binders with deviating structures and weaker binding. Phosphorylation of threonine was compulsory for antibody binding in an orthodox manner. Gas phase dissociation energy determinations of seven C2H2 zinc finger protein linker phospho-hexapeptides with orthodox binding properties revealed a bipolar binding motif of the antibody paratope. Epitope peptides, which in addition to the negatively charged phospho-threonine residue were C-terminally flanked by positively charged residues provided stronger binding, i. e. dissociation was endothermic, than peptides with acidic amino acid residues at these positions, for which dissociation was exothermic.

Binding and Degradation Reaction of Hydroxide Ions with Several Quaternary Ammonium Head Groups of Anion Exchange Membranes Investigated by the DFT Method

Commercialization of anion exchange membrane fuel cells (AEMFCs) has been limited due to the chemical degradation of various quaternary ammonium (QA) head groups, which affects the transportation of hydroxide (OH−) ions in AEMs. Understanding how various QA head groups bind and interact with hydroxide ions at the molecular level is of fundamental importance to developing high-performance AEMs. In this work, the binding and degradation reaction of hydroxide ions with several QA head groups—(a) pyridinium, (b) 1,4-diazabicyclo [2.2.2] octane (DABCO), (c) benzyltrimethylammonium (BTMA), (d) n-methyl piperidinium, (e) guanidium, and (f) trimethylhexylammonium (TMHA)—are investigated using the density functional theory (DFT) method. Results of binding energies (“∆” EBinding) show the following order of the binding strength of hydroxide ions with the six QA head groups: (a) > (c) > (f) > (d) > (e) > (b), suggesting that the group (b) has a high transportation rate of hydroxide ions via QA head groups of the AEM. This trend is in good agreement with the trend of ion exchange capacity from experimental data. Further analysis of the absolute values of the LUMO energies for the six QA head groups suggests the following order for chemical stability: (a) < (b)~(c) < (d) < (e) < (f). Considering the comprehensive studies of the nucleophilic substitution (SN2) degradation reactions for QA head groups (c) and (f), the chemical stability of QA (f) is found to be higher than that of QA (c), because the activation energy (“∆” EA) of QA (c) is lower than that of QA (f), while the reaction energies (“∆” ER) for QA (c) and QA (f) are similar at the different hydration levels (HLs). These results are also in line with the trends of LUMO energies and available chemical stability data found through experiments.

Interactions between PAMAM-NH2 and 6-Mercaptopurine: Qualitative and Quantitative NMR studies

Despite being used as an anti-leukemic drug, the poor solubility of 6-mercaptopurine (6-MP) limits its use in topical and parenteral applications. Dendrimers are commonly used as drug carriers to improve their solubility in aqueous solution. In this work, the interactions between 6-MP and the amine-terminated poly(amidoamine) dendrimers (PAMAM-NH₂ ) were investigated by various NMR technology. The chemical shift titrations disclosed that the 6-MP interacted with the surface of PAMAM-NH₂ mainly through electrostatics. The determination of diffusion coefficient and relaxation measurements further confirmed the presence of interactions in 6-MP/PAMAM-NH₂ complexes. In addition, the encapsulation of 6-MP within the cavity of PAMAM-NH₂ was revealed through nuclear Overhauser effect spectroscopy and Saturation Transfer Double Difference analysis. Finally, the binding strength (H-8 is 100% and H-2 is 70%) of 6-MP to PAMAM-NH₂ was quantitatively expressed using epitope maps. This study provides a systematic methodology for qualitative and quantitative studies of the interactions between dendrimers and drug molecules in general.

Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions

We investigated the influence of a solvent’s composition on the stability of desorbed and multiply charged RNAse S ions by analyzing the non-covalent complex’s gas-phase dissociation processes. RNAse S was dissolved in electrospray ionization-compatible buffers with either increasing organic co-solvent content or different pHs. The direct transition of all the ions and the evaporation of the solvent from all the in-solution components of RNAse S under the respective in-solution conditions by electrospray ionization was followed by a collision-induced dissociation of the surviving non-covalent RNAse S complex ions. Both types of changes of solvent conditions yielded in mass spectrometrically observable differences of the in-solution complexation equilibria. Through quantitative analysis of the dissociation products, i.e., from normalized ion abundances of RNAse S, S-protein, and S-peptide, the apparent kinetic and apparent thermodynamic gas-phase complex properties were deduced. From the experimental data, it is concluded that the stability of RNAse S in the gas phase is independent of its in-solution equilibrium but is sensitive to the complexes’ gas-phase charge states. Bio-computational in-silico studies showed that after desolvation and ionization by electrospray, the remaining binding forces kept the S-peptide and S-protein together in the gas phase predominantly by polar interactions, which indirectly stabilized the in-bulk solution predominating non-polar intermolecular interactions. As polar interactions are sensitive to in-solution protonation, bio-computational results provide an explanation of quantitative experimental data with single amino acid residue resolution.

Trace mineral source impacts rumen trace mineral metabolism and fiber digestion in steers fed a medium-quality grass hay diet

Twelve Angus steers (BW 452.8 ± 6.1 kg) fitted with ruminal cannulae were used to determine the impact of trace mineral (TM) source on digestibility, ruminal volatile fatty acid (VFA) composition, ruminal soluble concentrations of Cu, Zn, and Mn, and relative binding strength of trace minerals located in the rumen insoluble digesta fraction. Steers were fed a medium-quality grass hay diet (DM basis: 10.8% CP, 63.1% neutral detergent fiber [NDF], 6.9 mg Cu/kg, 65.5 mg Mn/kg, and 39.4 mg Zn/kg) supplemented with protein for 21 d. Treatments consisted of either sulfate (STM) or hydroxy (HTM) sources (n = 6 steers/treatment) to provide 20, 40, and 60 mg supplemental Cu, Mn, and Zn/kg DM, respectively. Following a 21-d adaptation period, total fecal output was collected for 5 d. Dry matter (P < 0.07) and CP (P < 0.06) digestibility tended to be reduced, and NDF (P < 0.04) and acid detergent fiber (ADF) (P < 0.05) digestibility were reduced in STM- vs. HTM-supplemented steers. On day 6, ruminal fluid was collected at 0, 2, and 4 h post-feeding and analyzed for VFA. There were no treatment x time interactions for VFA. Steers receiving HTM had less (P < 0.02) molar proportions of butyric acid and greater (P < 0.05) total VFA concentrations than STM-supplemented steers. Steers were then fed the same diet without supplemental Cu, Zn, or Mn for 14 d. On day 15 steers received a pulse dose of 20 mg Cu, 40 mg Mn, and 60 mg Zn/kg DM from either STM or HTM (n = 6 steers/treatment). Ruminal samples were obtained at 2-h intervals starting at -4 and ending at 24 h relative to dosing. There was a treatment x time interaction (P < 0.03) for ruminal soluble Cu, Mn, and Zn concentrations. Ruminal soluble mineral concentrations were greater (P < 0.05) for Cu at 4, 6, 8, 10, 12, and 14 h; for Mn at 4 and 6 h; and for Zn at 4, 6, and 8 h post-dosing in STM compared with HTM-supplemented steers. Copper concentrations were greater (P < 0.05) at 12 and 24 h and Zn concentrations in ruminal solid digesta were greater at 24 h in HTM-supplemented steers. Upon dialysis against Tris-EDTA, the percent Zn released from digesta was greater (P < 0.05) at 12 h (P < 0.03) and 24 h (P < 0.05), and the percent Cu released was greater (P < 0.02) at 24 h post-dosing in HTM steers when compared with STM-supplemented steers. Results indicate that Cu and Zn from HTM have low solubility in the rumen and appear to be less tightly bound to ruminal solid digesta than Cu and Zn from STM. The lower ruminal soluble concentrations of Cu and Zn in steers given HTM were associated with greater fiber digestibility.

Single-Molecule Analysis Demonstrates Stress-Enhanced Binding between Staphylococcus aureus Surface Protein IsdB and Host Cell Integrins

Binding of Staphylococcus aureus surface proteins to endothelial cell integrins plays essential roles in host cell adhesion and invasion, eventually leading to life-threatening diseases. The staphylococcal protein IsdB binds to β3-containing integrins through a mechanism that has never been thoroughly investigated. Here, we identify and characterize at the nanoscale a previously undescribed stress-dependent adhesion between IsdB and integrin α_Vβ₃. The strength of single IsdB-α_Vβ₃ interactions is moderate (∼100 pN) under low stress, but it increases dramatically under high stress (∼1000-2000 pN) to exceed the forces traditionally reported for the binding between integrins and Arg-Gly-Asp (RGD) sequences. We suggest a mechanism where high mechanical stress induces conformational changes in the integrin from a low-affinity, weak binding state to a high-affinity, strong binding state. This single-molecule study highlights that direct adhesin-integrin interactions represent potential targets to fight staphylococcal infections.

Measurement of binding strength between prey proteins interacting with Toxoplasma gondii SAG1 and SAG2 using isothermal titration calorimetry (ITC)

Following the outcome from a previously performed yeast two-hybrid experiment, the binding strength between T. gondii SAG1 and SAG2 and their respective prey proteins were further confirmed in this study. The sag1, sag2 and their prey genes were amplified and cloned into a pGEMT vector. To express the recombinant proteins, the fragments were then subcloned into a pRSETA vector and transformed into E. coli BL21 (DE3) cells. The recombinant proteins were expressed optimally at 37°C and 1mM of IPTG. The 6X His-tag fusion proteins were purified, dialyzed and concentrated. To confirm the expressed proteins, the recombinant proteins were analysed by SDS-PAGE and Western blot. As expected, the size of SAG1, SAG2, HLY and HZF protein were 32, 23, 28 and 37 kDa, respectively. The purified proteins were loaded onto a MicroCal Auto-iTC200 calorimeter from MicroCal™ to quantify binding strength. ITC results indicated there was a typical binding curve for interactions between SAG1 and HLY protein. However, there was an atypical binding curve obtained for interactions between SAG2 and HZF protein. By observing the data obtained from the ITC assay, both of the human proteins (HLY and HZF) were demonstrated to bind to their respective SAG1 and SAG2 proteins.

GingisKHAN™ protease cleavage allows a high-throughput antibody to Fab conversion enabling direct functional assessment during lead identification of human monoclonal and bispecific IgG1 antibodies

The determination of the binding strength of immunoglobulins (IgGs) to targets can be influenced by avidity when the targets are soluble di- or multimeric proteins, or associated to cell surfaces, including surfaces introduced from heterogeneous assays. However, for the understanding of the contribution of a second drug-to-target binding site in molecular design, or for ranking of monovalent binders during lead identification, affinity-based assessment of the binding strength is required. Typically, monovalent binders like antigen-binding fragments (Fabs) are generated by proteolytic cleavage with papain, which often results in a combination of under- and over-digestion, and requires specific optimization and chromatographic purification of the desired Fabs. Alternatively, the Fabs are produced by recombinant approaches. Here, we report a lean approach for the functional assessment of human IgG1s during lead identification based on an in-solution digestion with the GingisKHAN™ protease, generating a homogenous pool of intact Fabs and Fcs and enabling direct assaying of the Fab in the digestion mixture. The digest with GingisKHAN™ is highly specific and quantitative, does not require much optimization, and the protease does not interfere with methods typically applied for lead identification, such as surface plasmon resonance or cell-based assays. GingisKHAN™ is highly suited to differentiate between affinity and avidity driven binding of human IgG1 monoclonal and bispecific antibodies during lead identification.

Design of [2]rotaxane through image threshold segmentation of electrostatic potential image

An electrostatic potential (ESP)-based image segmentation method has been used to estimate the ability of proton donation and acceptance involved in ring-rod recognition. The relative binding strength of [2]rotaxane has also been further estimated from the difference of the characteristic image-segmentation derived ESP between proton donor and proton acceptor. The size and electrostatic compatibility criteria are introduced to guide the design of interlocked [2]rotaxane. A library of 75 thermodynamically stable [2]rotaxane candidates has been generated, including 16 experimentally known systems. The theoretical results for 16 experimentally known [2]rotaxanes are in good agreement with both the experimental association constants and density functional theory-calculated binding energies. Our ESP-based image segmentation model is also applicable to the tristable [2]rotaxane molecular shuttle as well as [1]rotaxane with self-inclusion function, indicating this simple method is generic in the field of constructing other supramolecular architectures formed with donor/acceptor molecular recognition. © 2016 Wiley Periodicals, Inc.

Self-assembled β-lactoglobulin-oleic acid and β-lactoglobulin-linoleic acid complexes with antitumor activities

β-Lactoglobulin (β-LG) can bind to fatty acids such as oleic acid (OA) and linoleic acid (LA). Another whey protein, α-lactalbumin (α-LA), can also bind to OA to give the complex α-LA-OA, which has antitumor properties. Based on reports that the activity of α-LA-OA is highly dependent on OA, as well as the acquisition of similar complexes using other proteins, such as lysozyme and lactoferrin, we speculated whether β-LG could also kill tumor cells after binding to other fatty acids. Therefore, we prepared complexes of β-LG with OA (β-LG-OA) and LA (β-LG-LA) in the current study and evaluated them in terms of antitumor activity and thermostability using the methylene blue method and differential scanning calorimetry, respectively. The structural features of these complexes were also evaluated using fluorescence spectroscopy and circular dichroism. The binding dynamics of OA and LA to β-LG were studied using isothermal titration calorimetry. Cell viability results revealed that β-LG-LA and β-LG-OA exhibited similar antitumor activities. Interestingly, the binding of β-LG to LA led to an increase in its thermostability, whereas its binding to OA had very little effect. The environments of the tryptophan residues in the β-LG-OA and β-LG-LA complexes were very different, with the residues being blue- and red-shifted, respectively. Furthermore, the hydrophobic regions in β-LG were buried after binding of OA, which was slightly changed in β-LG-LA. Circular dichroism results showed that β-LG-OA enhanced the tertiary structure, which was partially lost in β-LG-LA. There were more binding sites for OA than for LA on β-LG, although the binding constants of the 2 fatty acids were similar, with both acids interacting with the protein though van der Waals and hydrogen bonding interactions. This study could help provide a deeper understanding of the structural basis for formation of antitumor protein-fatty acid complexes.

Cadherin interaction probed by atomic force microscopy

Single molecule atomic force microscopy was used to characterize structure, binding strength (unbinding force), and binding kinetics of a classical cadherin, vascular endothelial (VE)-cadherin, secreted by transfected Chinese hamster ovary cells as cis-dimerized full-length external domain fused to Fc-portion of human IgG. In physiological buffer, the external domain of VE-cadherin dimers is a approximately 20-nm-long rod-shaped molecule that collapses and dissociates into monomers (V-shaped structures) in the absence of Ca(2+). Trans-interaction of dimers is a low-affinity reaction (K(D) = 10(-3)-10(-5) M, k(off) = 1.8 s(-1), k(on) = 10(3)-10(5) M(-1) x s(-1)) with relatively low unbinding force (35-55 pN at retrace velocities of 200-4,000 nm x s(-1)). Higher order unbinding forces, that increase with interaction time, indicate association of cadherins into complexes with cumulative binding strength. These observations favor a model by which the inherently weak unit binding strength and affinity of cadherin trans-interaction requires clustering and cytoskeletal immobilization for amplification. Binding is regulated by low-affinity Ca(2+) binding sites (K(D) = 1.15 mM) with high cooperativity (Hill coefficient of 5.04). Local changes of free extracellular Ca(2+) in the narrow intercellular space may be of physiological importance to facilitate rapid remodeling of intercellular adhesion and communication.

Controlled unzipping of a bacterial surface layer with atomic force microscopy

We have combined high-resolution atomic force microscopy (AFM) imaging and force spectroscopy to gain insight into the interaction forces between the individual protomers of the hexagonally packed intermediate (HPI) layer of Deinococcus radiodurans. After imaging the HPI layer, the AFM stylus was attached to individual protomers by enforced stylus-sample contact to allow force spectroscopy experiments. Imaging of the HPI layer after recording force-extension curves allowed adhesion forces to be correlated with structural alterations. By using this approach, individual protomers of the HPI layer were found to be removed at pulling forces of approximately 300 pN. Furthermore, it was possible to sequentially unzip entire bacterial pores formed by six HPI protomers. The combination of high-resolution AFM imaging of individual proteins with the determination of their intramolecular forces is a method of studying the mechanical stability of supramolecular structures at the level of single molecules.