An in silico approach to elucidate structure based functional evolution of oxacillinase

Bacterial Oxacillinases (OXAs), genetically being extremely diverse and highly versatile in hydrolyzing antibiotics of different classes, holds utmost significant clinical importance. Hence, to analyze functional evolution of this enzyme, plausible changes in drug profile, affinity and binding stability of different subclasses of OXA with their preferred drugs, viz. penicillin, ceftazidime, imipenem/meropenem were investigated. Maximum-Likelihood dendrogram was constructed and based on tree topology, the least and most divergent variants of each clade were selected. Pocket characterization, enzyme structural stability and mutational effect were analyzed in silico. Modes of interaction of selected OXA variants with respective antibiotics were analyzed by Autodock4.0 and LIGPLOT. Comparative mobility profiling and subsequent ΔG° and Km calculations of representative OXA variants revealed that after RSBL evolution, perhaps, two competitive strategies evolved among the OXA variants. Either loops flanking helix5 gets stabilized or it becomes more flexible. Therefore, while OXA variants (e.g. OXA-2, OXA-32, OXA-23, OXA-133, OXA-24, OXA-25, OXA-51 and OXA-75) with highly stabilized loops flanking helix5 exhibited improved binding stability and affinity towards carbapenems, especially meropenem, OXA variants (e.g. OXA-10, OXA-251, OXA-48 and OXA-247) possessing highly flexibile loops flanking helix5 revealed their catalytic proficiency towards ceftazidime. Moreover, LIGPLOT and PROMALS3D jointly identified ten consensuses/conserved residues, viz. P68, A69, F72, K73, W105, V120, W164, L169, K216 and G218 to be critical for drug hydrolysis. Hence, novel inhibitors could be designed to target these sites.     

The chemical bonding and spectral assignments of rhodium(III)‐catalyzed closo‐dodecaborate complexes: Ab initio study

The chemical bonding and spectral assignments of rhodium(III)‐catalyzed closo‐dodecaborate (RhCD) complex are systematically studied using the density functional theory calculations. It is found that the calculated main bond lengths of framework are in good agreement with experimental X‐ray observation, and the pronounced hybridization of B‐2p and Rh‐4d states is responsible for the structural stability, reflected by the large dissociation energy and HOMO–LUMO energy gap. The AdNDP chemical bonding analysis indicates that the RhCD complex can be stabilized by two H‐bridged 3c‐2e σ‐bonds (B‐H‐Rh triangles). Additionally, the theoretical calculations reproduce well the main experimental IR spectrum, and the characteristic peaks are properly assigned. These results will be helpful for further insight into the unique electronic structure of the species, and provide valuable references for potential applications in novel materials.     

On the Temperature–Pressure Free‐Energy Landscape of Proteins

We studied the thermodynamic stability of a small monomeric protein, staphylococcal nuclease (Snase), as a function of both temperature and pressure, and expressed it as a 3D free‐energy surface on the p,T‐plane using a second‐order Taylor expansion of the Gibbs free‐energy change ΔG upon unfolding. We took advantage of a series of different techniques (small‐angle Xray scattering, Fourier‐transform infrared spectroscopy, differential thermal analysis, pressure perturbation calorimetry and densitometry) in the evaluation of the conformation of the protein and in evaluating the changes in the thermodynamic parameters upon unfolding, such as the heat capacity, enthalpy, entropy, volume, isothermal compressibility and expansivity. The calculated results of the free‐energy landscape of the protein are in good agreement with experimental data of the p,T‐stability diagram of the protein over a temperature range from 200 to 400 K and at pressures from ambient pressure to 4000 bar. The results demonstrate that combined temperature–pressure‐dependent studies can help delineate the free‐energy landscape of proteins and hence help elucidate which features and thermodynamic parameters are essential in determining the stability of the native conformational state of proteins. The approach presented may also be used for studying other systems with so‐called re‐entrant or Tamman loop‐shaped phase diagrams.     

In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations

The accumulation of polyethylene terephthalate (PET) seriously harms the environment because of its high resistance to degradation. The recent discovery of the bacteria-secreted biodegradation enzyme, PETase, sheds light on PET recycling; however, the degradation efficiency is far from practical use. Here, in silico alanine scanning mutagenesis (ASM) and site-saturation mutagenesis (SSM) were employed to construct the protein sequence space from binding energy of the PETase–PET interaction to identify the number and position of mutation sites and their appropriate side-chain properties that could improve the PETase–PET interaction. The binding mechanisms of the potential PETase variant were investigated through atomistic molecular dynamics simulations. The results show that up to two mutation sites of PETase are preferable for use in protein engineering to enhance the PETase activity, and the proper side chain property depends on the mutation sites. The predicted variants agree well with prior experimental studies. Particularly, the PETase variants with S238C or Q119F could be a potential candidate for improving PETase. Our combination of in silico ASM and SSM could serve as an alternative protocol for protein engineering because of its simplicity and reliability. In addition, our findings could lead to PETase improvement, offering an important contribution towards a sustainable future.     

Thermal Stability of Immobilised α-chymotrypsinogen

The unfolding of α-chymotrypsinogen covalently immobilized on silica beads has been studied by differential scanning calorimetry (DSC). The enzyme undergoes an unfolding transition which, unlike the free protein, cannot be approximated by a single two-state process. After immobilization, the unfolding is characterized by the presence of two partially overlapping transitions, both of them show two-state behavior. The two processes correspond to the separate unfolding of the two domains of the α-chymotrypsinogen molecule. The loss of cooperativity behavior is a consequence of the covalent immobilization. The two domains showed different thermal stability as functions of pH. One of them unfolded with a transition temperature T _m2 higher than T _m of the free enzyme, implying stabilization effect of immobilization. However, below pH 4.5, its native structure is lost. The other transition shows a remarkable pH-independent thermal stability from pH 2.5 to 7.0. This revised version was published online in July 2006 with corrections to the Cover Date.     

Sugar–Protein Connectivity Impacts on the Immunogenicity of Site‐Selective Salmonella O‐Antigen Glycoconjugate Vaccines

A series of glycoconjugates with defined connectivity were synthesized to investigate the impact of coupling Salmonella typhimurium O‐antigen to different amino acids of CRM₁₉₇ protein carrier. In particular, two novel methods for site‐selective glycan conjugation were developed to obtain conjugates with single attachment site on the protein, based on chemical modification of a disulfide bond and pH‐controlled transglutaminase‐catalyzed modification of lysine, respectively. Importantly, conjugation at the C186‐201 bond resulted in significantly higher anti O‐antigen bactericidal antibody titers than coupling to K37/39, and in comparable titers to conjugates bearing a larger number of saccharides. This study demonstrates that the conjugation site plays a role in determining the immunogenicity in mice and one single attachment point may be sufficient to induce high levels of bactericidal antibodies.     

Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites

To mimic a hypothetical pathway for protein evolution, we previously tailored a monomeric protein (cyt cb₅₆₂) for metal-mediated self-assembly, followed by re-design of the resulting oligomers for enhanced stability and metal-based functions. We show that a single hydrophobic mutation on the cyt cb₅₆₂ surface drastically alters the outcome of metal-directed oligomerization to yield a new trimeric architecture, (TriCyt1)_3. This nascent trimer was redesigned into second and third-generation variants (TriCyt2)₃ and (TriCyt3)₃ with increased structural stability and preorganization for metal coordination. The three TriCyt variants combined furnish a unique platform to 1) provide tunable coupling between protein quaternary structure and metal coordination, 2) enable the construction of metal/pH-switchable protein oligomerization motifs, and 3) generate a robust metal coordination site that can coordinate all mid-to-late first-row transition-metal ions with high affinity.     

Tuning the Protein‐Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics

Rational design of light‐capturing properties requires understanding the molecular and electronic structure of chromophores in their native chemical or biological environment. We employ here large‐scale quantum chemical calculations to study the light‐capturing properties of retinal in recently designed human cellular retinol binding protein II (hCRBPII) variants (Wang et al. Science, 2012 , 338, 1340–1343). Our calculations show that these proteins absorb across a large part of the visible spectrum by combined polarization and electrostatic effects. These effects stabilize the ground or excited state energy levels of the retinal by perturbing the Schiff‐base or β‐ionone moieties of the chromophore, which in turn modulates the amount of charge transfer within the molecule. Based on the predicted tuning principles, we design putative in silico mutations that further shift the absorption properties of retinal in hCRBPII towards the ultraviolet and infrared regions of the spectrum.     

Achieving High‐Temperature Stability of Metastable α‐MoC1‐x by Suppressing Phase Transformation with Mounted Atoms for Lithium Storage Performance

Despite a significant advancement in preparing metastable materials, one common problem is the strict and precious reaction conditions due to their metastable structures. Herein, we achieved the preparation of high‐temperature stabilized metastable α‐MoC_1?x by mounting zinc atoms into its lattice structure. Such a structural construction could suppress the phase transformation from α‐MoC_1?x to β‐Mo₂C through restricting the displacement of Mo atoms upon increased temperature. The resultant metastable α‐MoC_1?x can be stabilized up to 1000 °C and this stability temperature is the highest for the metastable α‐MoC_1?x so far. Synchrotron X‐ray absorption spectroscopy (XAS) and X‐ray photoelectron spectroscopy (XPS) confirm the structure of Zn‐mounted α‐MoC_1?x. Density functional theory (DFT) calculations reveal that the introduction of the Zn atoms in the lattice structure of α‐MoC_1?x could significantly decrease the energy difference (ΔE) between α‐MoC_1?x and β‐Mo₂C, thus effectively suppressing the phase transformation from α‐MoC_1?x to β‐Mo₂C and accordingly maintaining the high‐temperature stability of α‐MoC_1?x. This novel strategy can be used as a universal method to be extended to synthesize metastable α‐MoC_1?x from different precursors or other mounted elements. Moreover, the optimal product exhibits excellent lithium storage performances in terms of the cycling stability and rate performance.     

Photobodies: Light‐Activatable Single‐Domain Antibody Fragments

Photocaged antibody fragments, termed photobodies, have been developed that are impaired in their antigen‐binding capacity and can be activated by irradiation with UV light (365 nm). This rational design concept builds on the selective photocaging of a single tyrosine in a nanobody (a single‐domain antibody fragment). Tyrosine is a frequently occurring residue in central positions of the paratope region. o‐Nitrobenzyl‐protected tyrosine variants were incorporated into four nanobodies, including examples directed against EGFR and HER2, and photodeprotection restores the native sequence. An anti‐GFP photobody exhibited an at least 10 000‐fold impaired binding affinity before photodeprotection compared with the parent nanobody. A bispecific nanobody–photobody fusion protein was generated to trigger protein heterodimerization by light. Photoactivatable antibodies are expected to become versatile protein reagents and to enable novel approaches in diagnostic and therapeutic applications.     

Synthesis and Characterization of a Metal‐Organic Coordination Polymer

A novel energetic microporous metal‐organic coordination polymer {[Ni(tnbpdc)(bpy)(H₂O)₂] · 1.5(DMF)}_n ( 1 ) (tnbpdc = 2, 2′,6, 6′‐tetranitro‐4, 4′‐biphenyl dicarboxylate, bpy = 4, 4′‐bipyridine) was prepared solvothermally and characterized by elemental, IR spectroscopic, and single‐crystal X‐ray diffraction analyses. The X‐ray crystal structure of 1 revealed a rectangular‐shaped grid constructed with tnbpdc linkers and bpy linkers, with the free tunnel size estimated as 11 × 15 Ų. The thermal stability of the compound was evaluated by differential scanning calorimetry and thermogravimetric analysis. Such complexes may find application as novel heat‐resistant energetic materials.     

A sensitive liquid chromatography–mass spectrometry bioanalytical assay for a novel anticancer candidate – ZMC1

ZMC1 {azetidinecarbothioic acid, [1‐(2‐pyridinyl) ethylidene] hydrazide} is a lead compound being developed as one of the first mutant p53 targeted anti‐cancer drugs. Establishing a precise quantitative method is an integral component of this development. The aim of this study was to develop a sensitive LC/MS/MS assay suitable for assessing purity, stability and preclinical pharmacokinetic studies of ZMC1. Acetonitrile protein precipitation extraction was chosen for plasma sample preparation with satisfactory recovery (84.2–92.8%) for ZMC1. Chromatographic separation was achieved on an Xterra C₁₈ column (50 × 4.6 mm, 3.5 µm) using a gradient elution with mobile phase of 0.1% formic acid in water and acetonitrile. ZMC1 and internal standard 2‐amino‐6‐bromobenzothiazole were identified using selected‐ion monitoring mode at m/z 235.2/178.2 and m/z 231.0/150.0 at retention times of 5.2 and 6.3 min, respectively. The method was validated with a linearity range of 3.9–500.0 ng/mL in human plasma and showed acceptable reproducibility with intra‐ and interday precisions <5.9 and 10.5%, and accuracy within ±5.4% of nominal values. This analytical method together with basic stability data in plasma and plasma binding experiments provides a reliable protocol for the study of ZMC1 pharmacokinetics. This will greatly facilitate the pre‐clinical development of this novel anti‐cancer drug. Copyright © 2015 John Wiley & Sons, Ltd.     

Computationally Driven Discovery of a Family of Layered LiNiB Polymorphs

Two novel lithium nickel boride polymorphs, RT‐LiNiB and HT‐LiNiB, with layered crystal structures are reported. This family of compounds was theoretically predicted by using the adaptive genetic algorithm (AGA) and subsequently synthesized by a hydride route with LiH as the lithium source. Unique among the known ternary transition‐metal borides, the LiNiB structures feature Li layers alternating with nearly planar [NiB] layers composed of Ni hexagonal rings with a B–B pair at the center. A comprehensive study using a combination of single crystal/synchrotron powder X‐ray diffraction, solid‐state ⁷Li and ¹¹B NMR spectroscopy, scanning transmission electron microscopy, quantum‐chemical calculations, and magnetism has shed light on the intrinsic features of these polymorphic compounds. The unique layered structures of LiNiB compounds make them ultimate precursors for exfoliation studies, thus paving a way toward two‐dimensional transition‐metal borides, MBenes.     

Synthesis of a One‐dimensional Coordination Polymer Based on Copper(II) Nitrate and 1,2‐Bis(5‐monomethylhydrazinyl‐1H‐tetrazolyl)ethane

A one‐dimensional coordination polymer based on copper(II) nitrate and 1,2‐bis(5‐monomethylhydrazinyl‐1H‐tetrazolyl)ethane as ligand was prepared. The thermal and physical stability was determined by differential scanning calorimetry and BAM methods. The polymer was investigated by vibrational spectroscopy and single X‐ray diffraction. Moreover, the ligand itself and the 1,2‐bis(1H‐tetrazolyl)ethane were characterized as energetic material by bomb calorimetric measurements along with calculations using the EXPLO5 software. Both compounds have moderate energetic properties along with a high thermal and physical stability. These findings render these compounds into promising environment friendly gas generating agents.     

A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP‐Binding RNA Aptamer

RNA tertiary structure motifs are stabilized by a wide variety of hydrogen‐bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pK _a values are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP‐binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pK _a value for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pK _a for A nucleotides in single‐stranded RNA. This is the largest pK _a shift for an A residue in structured nucleic acids reported so far, and similar in size to the largest pK _a shifts observed for amino acid side chains in proteins. Both RNA pre‐folding and ligand binding contribute to the pK _a shift.     

Computational analysis of the cathepsin B inhibitors activities through LR‐MMPBSA binding affinity calculation based on docked complex

Cathepsin B, a ubiquitous lysosomal cysteine protease, is involved in many biological processes related to several human diseases. Inhibitors targeting the enzyme have been investigated as possible diseases treatments. A set of 37 compounds were recently found active in a high throughput screening assay to inhibit the catalytic activity of Cathepsin B, with chemical structures and biological test results available to the public in the PubChem BioAssay Database (AID 820). In this study, we compare these experimental activities to the results of theoretical predictions from binding affinity calculation with a LR‐MM‐PNSA approach based on docked complexes. Strong correlations (r² = 0.919 and q² = 0.887 for the best) are observed between the theoretical predictions and experimental biological activity. The models are cross‐validated by four independent predictive experiments with randomly split compounds into training and test sets. Our results also show that the results based on protein dimer show better correlations with experimental activity when compared to results based on monomer in the in silico calculations. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Engineering the Donor Selectivity of D‐Fructose‐6‐Phosphate Aldolase for Biocatalytic Asymmetric Cross‐Aldol Additions of Glycolaldehyde

D ‐Fructose‐6‐phosphate aldolase (FSA) is a unique catalyst for asymmetric cross‐aldol additions of glycolaldehyde. A combination of a structure‐guided approach of saturation mutagenesis, site‐directed mutagenesis, and computational modeling was applied to construct a set of FSA variants that improved the catalytic efficiency towards glycolaldehyde dimerization up to 1800‐fold. A combination of mutations in positions L107, A129, and A165 provided a toolbox of FSA variants that expand the synthetic possibilities towards the preparation of aldose‐like carbohydrate compounds. The new FSA variants were applied as highly efficient catalysts for cross‐aldol additions of glycolaldehyde to N‐carbobenzyloxyaminoaldehydes to furnish between 80–98 % aldol adduct under optimized reaction conditions. Donor competition experiments showed high selectivity for glycolaldehyde relative to dihydroxyacetone or hydroxyacetone. These results demonstrate the exceptional malleability of the active site in FSA, which can be remodeled to accept a wide spectrum of donor and acceptor substrates with high efficiency and selectivity.     

The Effect of Precipitation pH on Protein Recovery Yield and Emulsifying Properties in the Extraction of Protein from Cold-Pressed Rapeseed Press Cake

Rapeseed is the second most cultivated oilseed after soybean and is mainly used to produce vegetable oil. The by-product rapeseed press cake is rich in high-quality proteins, thus having the possibility of becoming a new plant protein food source. This study aimed to investigate how the precipitation pH affects the protein yield, protein content, and emulsifying properties when industrially cold-pressed rapeseed press cake is used as the starting material. Proteins were extracted under alkaline conditions (pH 10.5) with an extraction coefficient of 52 ± 2% followed by precipitation at various pH (3.0–6.5). The most preferred condition in terms of process efficiency was pH 4.0, which is reflected in the zeta potential results, where the proteins’ net charge was 0 at pH 4.2. pH 4.0 also exhibited the highest protein recovery yield (33 ± 0%) and the highest protein concentration (64 ± 1%, dry basis). Proteins precipitated at pH 6.0–6.5 stabilized emulsions with the smallest initial droplet size, although emulsions stabilized by rapeseed protein precipitated at pH 5.0–6.0 showed the highest emulsion stability at 37 °C for 21 days, with a limited layer of free oil. Overall, emulsion stabilized by protein precipitated at pH 5.0 was the most stable formulation, with no layer of free oil after 21 days of incubation.     

A new oxidation state of aniline pentamer observed in water‐soluble electroactive oligoaniline‐chitosan polymer

A novel water‐soluble electroactive polymer, aniline pentamer crosslinked chitosan (Pentamer‐c‐Chi), was prepared by condensation polymerization of the terminal carboxyl groups in aniline pentamer with the amino side groups in chitosan in aqueous solution. The carboxyl groups were activated by N‐hydroxysuccinimide (NHS) and N,N′‐dicyclohexylcarbodiimide (DCC). The electrochemical behavior of anilinepentamer in this kind of crosslinked polymer was studied in acidic aqueous solution by means of cyclic voltammetry (CV), UV–vis, and electron spin resonance (ESR) spectroscopy. There were three reversible redox peaks in the CV of Pentamer‐c‐Chi. A new emeraldine oxidization state in the form of radical cations was proposed, which was associated with the new absorption band at 370 nm in the UV–vis spectra. The ESR of the aqueous solution of Pentamer‐c‐Chi showed a single Lorentzian shaped signal, which suggested the existence of radical cations. The new redox state was pH dependent and appeared only at pH < 3. The stability of radical cations could be attributed to the hydrogen bonds between radical cations, water, and chitosan. Morphological structure of the Pentamer‐c‐Chi can be adjusted by varying the content of aniline pentamer. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1124–1135, 2008     

Stable neutral double hydrophilic block copolymer capillary coating for capillary electrophoretic separations

Quaternized diblock copolymer, poly(N‐methyl‐2‐vinylpyridinium iodide‐block‐ethylene oxide), was successfully used as a neutral, dynamic coating to suppress the electroosmotic flow. The block copolymer consisted of two polymers that were linked covalently together. The cationic block (poly(N‐methyl‐2‐vinylpyridinium iodide)) was bound efficiently to the negatively charged capillary wall via electrostatic interactions, and the hydrophilic block (ethylene oxide) stabilized the system and created a neutral capillary surface with ultralow electroosmotic flow (+2.0 ± 4.5 × 10^?10 m²/Vs). The main advantages of the coating were simple and fast preparation, easy regeneration and automation, and stable electroosmotic flow. To emphasize the potential of this type of coating its stability was measured at a wide pH range demonstrating a high stability in the pH range of 4.0–10.5 and lifetime up to 8 days. The successful studies carried out with beta‐blockers, basic proteins, and lipoproteins proved the suitability of the coating for the separation of different sized analytes. Furthermore, the neutral coating developed is useful in a wide range of protein analysis and biological interaction studies under physiological condition.