Reproducibility in the unfolding process of protein induced by an external electric field

The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas-phase proteins, such as single particle imaging using free-electron lasers and gas-phase small angle X-ray scattering, has the potential to open up a new era in time-resolved studies of gas-phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short-pulsed X-ray sources such as free-electron lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.

Controlled unfolding of proteins can reveal structural properties and give insights of the proteins'' dynamics. We show the feasibility of unfolding proteins in the gas phase using electric fields, with a well-defined path at high field strengths.     

A vibrational sum frequency spectroscopy study of the liquid-gas interface of acetic acid-water mixtures: 1. Surface speciation

Aqueous acetic acid solutions have been studied by vibrational sum frequency spectroscopy (VSFS) in order to acquire molecular information about the liquid-gas interface. The concentration range 0-100% acetic acid has been studied in the CH/OH and the C-O/C=O regions, and in order to clarify peak assignments, experiments with deuterated acetic acid and water have also been performed. Throughout the whole concentration range, the acetic acid is proven to be protonated. It is explicitly shown that the structure of a water surface becomes disrupted even at small additions of acetic acid. Furthermore, the spectral evolution upon increasing the concentration of acetic acid is explained in terms of the different complexes of acetic acid molecules, such as the hydrated monomer, linear dimer, and cyclic dimer. In the C=O region, the hydrated monomer is concluded to give rise to the sum frequency (SF) signal, and in the CH region, the cyclic dimer contributes to the signal as well. The combination of results from the CH/OH and the C-O/C=O regions allows a thorough characterization of the behavior of the acetic acid molecules at the interface to be obtained.     

Influence of backbone conformations of human carbonic anhydrase II on carbon dioxide hydration: hydration pathways and binding of bicarbonate

In this study, the hydration of carbon dioxide and the formation of bicarbonate in human carbonic anhydrase II have been examined. From semiempirical QM/MM molecular dynamics studies, dominant conformations of the protein backbone, possibly contributing to the catalytic activity, have been isolated and further examined by means of density functional QM/MM methods. In agreement with experimental observations, a binding site for cyanate, which acts as an inhibitor, has been located, whereas for carbon dioxide, depending on the conformation of the protein environment, either a different binding site or no binding site has been found. In the latter case, carbon dioxide diffuses barrierless to the zinc-bound oxygen, and then a weakly bound bicarbonate complex is formed. The formed complex is characterized by a long C-O bond to the zinc-bound hydroxide. The nature of the calculated stationary points was verified by determination of vibrational frequencies. Finally, the dissociation of the formed bicarbonate from zinc has been considered. Therefore, a water molecule was included in the QM zone of the QM/MM hybrid potential, and minimization yielded a pentacoordinated intermediate. From a potential energy scan, an activation energy of 6.2 kcal/mol for dissociation of bicarbonate from Zn has been found.     

Design,Synthesis, and Biological Evaluation of Quercetagetin Analogues as JNK1 Inhibitors

The recent discovery of c‐Jun NH₂‐terminal kinase JNK1 suppression by natural quercetagetin ( 1 ) is a promising lead for the development of novel anticancer agents. Using both X‐ray structure and docking analyses we predicted that 5′‐hydroxy‐ ( 2 ) and 5′‐hydroxymethyl‐quercetagetin ( 3 ) would inhibit JNK1 more actively than the parent compound 1 . Notably, our drug design was based on the active enzyme–ligand complex as opposed to the enzyme’s relatively open apo structure. In this paper we test our theoretical predictions, aided by docking‐model experiments, and report the first synthesis and biological evaluation of quercetagetin analogues 2 and 3 . As calculated, both compounds strongly suppress JNK1 activity. The IC₅₀ values were determined to be 3.4 μM and 12.2 μM , respectively, which shows that 2 surpasses the potency of the parent compound 1 (IC₅₀=4.6 μM ). Compound 2 was also shown to suppress matrix metalloproteinase‐1 expression with high specificity after UV irradiation.     

A Domino Approach to the Enantioselective Total Syntheses of Blennolide C and Gonytolide C

The first enantioselective total syntheses of the tetrahydroxanthenone (?)‐blennolide C (ent‐ 4 ) and related γ‐lactonyl chromanone (?)‐gonytolide C (ent‐ 3 ) are reported. Key to the syntheses is an enantioselective domino‐Wacker/carbonylation/methoxylation reaction to set up the stereocentre at C‐4a. Various chiral BOXAX ligands were investigated, including novel (S,S)‐iBu‐BOXAX, and allowed access to chromane 8 in an excellent enantioselectivity of 99 %. The second stereocentre at C‐4 was established employing a diastereoselective Sharpless dihydroxylation. An extensive survey of (DHQ)‐ and (DHQD)‐based ligands enabled the preparation of both the anti‐isomer 14 a and the syn‐isomer 14 b in very good to reasonable selectivities of 13.7:1 and 1:3.7, respectively. While 14 a was further converted to ent‐ 3 and ent‐ 4 , 14 b was elaborated to syn‐acid 25 and 2′‐epi‐gonytolide C 28 .     

A Hexameric Peptide Barrel as Building Block of Amyloid‐β Protofibrils

Oligomeric and protofibrillar aggregates formed by the amyloid‐β peptide (Aβ) are believed to be involved in the pathology of Alzheimer’s disease. Central to Alzheimer pathology is also the fact that the longer Aβ₄₂ peptide is more prone to aggregation than the more prevalent Aβ₄₀. Detailed structural studies of Aβ oligomers and protofibrils have been impeded by aggregate heterogeneity and instability. We previously engineered a variant of Aβ that forms stable protofibrils and here we use solid‐state NMR spectroscopy and molecular modeling to derive a structural model of these. NMR data are consistent with packing of residues 16 to 42 of Aβ protomers into hexameric barrel‐like oligomers within the protofibril. The core of the oligomers consists of all residues of the central and C‐terminal hydrophobic regions of Aβ, and hairpin loops extend from the core. The model accounts for why Aβ₄₂ forms oligomers and protofibrils more easily than Aβ₄₀.     

Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules

Biomolecular simulations with atomistic detail are often required to describe interactions with chemical accuracy for applications such as the calculation of free energies of binding or chemical reactions in enzymes. Force fields are typically used for this task but these rely on extensive parameterisation which in cases can lead to limited accuracy and transferability, for example for ligands with unusual functional groups. These limitations can be overcome with first principles calculations with methods such as density functional theory (DFT) but at a much higher computational cost. The use of electrostatic embedding can significantly reduce this cost by representing a portion of the simulated system in terms of highly localised charge distributions. These classical charge distributions are electrostatically coupled with the quantum system and represent the effect of the environment in which the quantum system is embedded. In this paper we describe and evaluate such an embedding scheme in which the polarisation of the electronic density by the embedding charges occurs self-consistently during the calculation of the density. We have implemented this scheme in a linear-scaling DFT program as our aim is to treat with DFT entire biomolecules (such as proteins) and large portions of the solvent. We test this approach in the calculation of interaction energies of ligands with biomolecules and solvent and investigate under what conditions these can be obtained with the same level of accuracy as when the entire system is described by DFT, for a variety of neutral and charged species.     

Determining under- and oversampling of individual particle distributions in microfluidic electrophoresis with orthogonal laser-induced fluorescence detection

This report investigates the effects of sample size on the separation and analysis of individual biological particles using microfluidic devices equipped with an orthogonal LIF detector. A detection limit of 17 +/- 1 molecules of fluorophore is obtained using this orthogonal LIF detector under a constant flow of fluorescein, which is a significant improvement over epifluorescence, the most common LIF detection scheme used with microfluidic devices. Mitochondria from rat liver tissue and cultured 143B osteosarcoma cells are used as model biological particles. Quantile-quantile (q-q) plots were used to investigate changes in the distributions. When the number of detected mitochondrial events became too large (>72 for rat liver and >98 for 143B mitochondria), oversampling occurs. Statistical overlap theory is used to suggest that the cause of oversampling is that separation power of the microfluidic device presented is not enough to adequately separate large numbers of individual mitochondrial events. Fortunately, q-q plots make it possible to identify and exclude these distributions from data analysis. Additionally, when the number of detected events became too small (<55 for rat liver and <81 for 143B mitochondria) there were not enough events to obtain a statistically relevant mobility distribution, but these distributions can be combined to obtain a statistically relevant electrophoretic mobility distribution.     

Double hydrogen tunneling revisited: the breakdown of experimental tunneling criteria

Formic acid dimer was chosen as a model system to investigate synchronous double proton transfer by means of variational transition state theory (VTST) for various isotopically modified hydrogen species. The electronic barrier for the double proton transfer was evaluated to be 7.9 kcal/mol, thus being significantly lower than it was determined in previous studies. The tunneling probabilities were evaluated at temperatures from 100 up to 400 K and typical Arrhenius behavior with enhancement by tunneling is observed. When comparing the transmission factors kappa in dependence of the mass of the tunneling hydrogen, it was found that there are two maxima, one at very low masses (e.g., 0.114 amu, corresponding to the muonium entity) and one maximum at around 2 amu (corresponding to deuterium). With the knowledge of the VTST-hydrogen transfer rates and the corresponding tunneling corrections, various tunneling criteria were tested (e.g., Swain-Schaad exponents) and were shown to fail in this reaction in predicting the extent of tunneling. This finding adds another aspect in the ongoing "Tunneling-Enhancement by Enzymes" discussion, as the used tunneling criteria based on experimental reaction rates may fail to predict tunneling behavior correctly.     

Thermodynamics of folding, stabilization, and binding in an engineered protein--protein complex

We analyzed the thermodynamics of a complex protein-protein binding interaction using the (engineered) Z(SPA)(-)(1) affibody and it's Z domain binding partner as a model. Free Z(SPA)(-)(1) exists in an equilibrium between a molten-globule-like (MG) state and a completely unfolded state, wheras a well-ordered structure is observed in the Z:Z(SPA)(-)(1) complex. The thermodynamics of the MG state unfolding equilibrium can be separated from the thermodynamics of binding and stabilization by combined analysis of isothermal titration calorimetry data and a separate van't Hoff analysis of thermal unfolding. We find that (i) the unfolding equilibrium of free Z(SPA)(-)(1) has only a small influence on effective binding affinity, that (ii) the Z:Z(SPA)(-)(1) interface is inconspicuous and structure-based energetics calculations suggest that it should be capable of supporting strong binding, but that (iii) the conformational stabilization of the MG state to a well-ordered structure in the Z:Z(SPA)(-)(1) complex is associated with a large change in conformational entropy that opposes binding.