Studies of protein hydration in aqueous solution by high-resolution nuclear magnetic resonance spectroscopy

Individual hydration water molecules in aqueous protein solutions have been observed using experimental schemes for homonuclear two-dimensional and heteronuclear three-dimensional NMR experiments in H₂O solution, which do not require suppression of the solvent line by presaturation. In these experiments, the location of the hydration waters is determined from their nuclear Overhauser effects (NOE s) with individual hydrogen atoms of distinct amino acid residues. In the basic pancreatic trypsin inhibitor (BPTI ), four internal water molecules that had been reported in three different crystal forms were also found to be in the same locations in the solution structure, with lifetimes with respect to exchange of the water protons in excess of 0.3 ns. Additional NOE s with polypeptide protons located on the protein surface may involve either hydration water molecules or hydroxyl protons of amino acid side chains. Their total number is small compared to the number of NOE s expected from the hydration water molecules identified in the crystal structures of BPTI .     

A rat brain protein expression map including cytosolic and enriched mitochondrial and microsomal fractions

Proteomics is a powerful tool to screen brain protein expression but the methodology is hampered by low abundance of proteins or compartmentalization or overload of high-abundance proteins. It was therefore the aim of the study to determine the expression of brain proteins by using enriched cellular subfractions and pre-electrophoretic chromatographical separation of brain homogenates. We used two-dimensional electrophoresis with subsequent matrix-assisted laser desorption/ionization (MALDI) detection and characterization of brain proteins. Subfractionation into cytosolic, mitochondrial and microsomal compartments was performed by ultracentrifugation. Pre-electrophoretic fractionation of the cytosolic fractions was carried out by ion exchange column chromatography. We detected and identified a large series of 437 proteins in rat brain and have shown proteins specific for the individual subcellular compartments. These proteins included housekeeping, signaling, cytoskeletal, intermediary metabolism, antioxidant proteins on the one and neuron and synaptosomal specific proteins on the other hand. Using fractionations of brain homogenates we were able to improve the power of the method on forming the basis for brain protein expressional studies and providing a reference map as a powerful tool for the neuroscientist.     

Crystal structure and spectroscopic characterization of K8(VO)2O(SO4)6

Red and yellow dichroistic crystals of a vanadium(V) compound, potassium (mu-oxo, di-mu-sulfato)bis(oxodisulfatovanadate), K(8)(VO)(2)O(SO(4))(6), have been obtained from the ternary catalytic model melt system K(2)S(2)O(7)[bond]K(2)SO(4)[bond]V(2)O(5). By slow cooling of the melt from 420 to 355 degrees C, crystal growth occurred, using solid V(2)O(5) crystals present in the melt as nucleation promoter. The compound crystallizes in the monoclinic space group P2(l) with a = 13.60(9) A, b = 13.93(9) A, c = 14.05(9) A, beta = 90.286(10) degrees, and Z = 2. It contains two VO(6) octahedra linked together by a mu-oxo and two mu-sulfato bridges. Furthermore, each octahedron has two monodentate sulfate ligands, making the dimeric entity coordinatively saturated. IR spectroscopy shows bands arising from V[bond]O[bond]V and V[double bond]O stretches as well as splitting of sulfate bands due to the different degrees of freedom present for different conformations of sulfate ligands. The coordination of vanadium in K(8)(VO)(2)O(SO(4))(6) is discussed in relation to the reaction mechanism of SO(2) oxidation catalysis.     

Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid state

A new indirect detection scheme for obtaining (15)N/(1)H shift correlation spectra in crystalline proteins is described. Excellent water suppression is achieved without the need for pulsed field gradients, and using only a 2-step phase cycle. Careful attention to overall NMR instrument stability was found critical for obtaining the best resolution and sensitivity. Magnetic dilution by deuteration of the protein in combination with high-speed magic angle spinning produces (1)H resonances averaging only 0.22 ppm in width, and in some cases lines as narrow as 0.17 ppm are obtained. In application to two different polymorphs of ubiquitin, structure dependent differences in both (15)N and (1)H amide chemical shifts are observed. In one case, distinct shifts for different molecules in the asymmetric unit are seen, and all differ substantially from solution NMR shifts. A gain of 7 in sensitivity makes the method competitive with solution NMR as long as nanocrystalline samples are available.     

Induced fit process in the selective distal binding of imidazoles in zinc(II) porphyrin receptors

The respective affinities of various imidazole derivatives, imidazole (ImH), 2-methylimidazole (2-MeImH), 2-phenylimidazole (2-PhImH), N-methylimidazole (N-MeIm), 2-methylbenzimidazole (2-MeBzImH), and 4,5-dimethylbenzimidazole (4,5-Me(2)BzImH), for two phenanthroline (Phen) strapped zinc(II) porphyrin receptors porphen-Zn 1-Zn and 2-Zn have been studied. The formation of a supplementary H-bond considerably enhances the affinity of the zinc(II)-porphen receptor for imidazoles unsubstituted on the pyrrolic nitrogen (ImH) versus N-substituted imidazoles such as N-MeIm. The ImHs subset porphen-Zn complexes are formed with association constants up to 4 orders of magnitude superior to those measured either for N-MeIm as substrate or TPP-Zn as receptor. Distal or proximal binding of the substrates was determined by (1)H NMR measurements and titration. In two cases, the very high stability of the inclusion complex enabled the use of 2D NMR techniques. Excellent correlation between solution and solid-state structures has been obtained. A total of six X-ray structures are detailed in this article showing that the evolution of the shape of the zinc(II) receptor is mostly dependent on the steric constraints induced by the substitution on the imidazole. Hindered guests also progressively induce considerable mobility restrictions and severe distortions on the receptor, especially in the case of 2-MeBzImH and 2-PhImH.     

A Singular System with Precise Dosing and Spatiotemporal Control of CRISPR‐Cas9

Several genome engineering applications of CRISPR‐Cas9, an RNA‐guided DNA endonuclease, require precision control of Cas9 activity over dosage, timing, and targeted site in an organism. While some control of Cas9 activity over dose and time have been achieved using small molecules, and spatial control using light, no singular system with control over all the three attributes exists. Furthermore, the reported small‐molecule systems lack wide dynamic range, have background activity in the absence of the small‐molecule controller, and are not biologically inert, while the optogenetic systems require prolonged exposure to high‐intensity light. We previously reported a small‐molecule‐controlled Cas9 system with some dosage and temporal control. By photocaging this Cas9 activator to render it biologically inert and photoactivatable, and employing next‐generation protein engineering approaches, we have built a system with a wide dynamic range, low background, and fast photoactivation using a low‐intensity light while rendering the small‐molecule activator biologically inert. We anticipate these precision controls will propel the development of practical applications of Cas9.     

Benign synthesis of carboxamide ligands,H2Me2bqb and H2Me2bpb. Preparation,characterization and electrochemistry of Ni(II) complexes: The crystal structure of [Ni(Me2bqb)]

A novel and highly efficient approach for the synthesis of H₂Me₂bqb and H₂Me₂bpb using ionic liquid as an environmentally benign reaction medium has been developed, eliminating the need for the pyridine as a toxic solvent. The Ni(II) complex of the dianionic ligand Me₂bqb²⁻, [Me₂bqb²⁻ = 1,2-bis(quinoline-2-carboxamide)-4,5-dimethyl-benzene dianion], has been synthesized and characterized by elemental analyses and spectroscopic methods, and the crystal and molecular structure of [Ni(Me₂bqb)] (1), has been determined by X-ray crystallography. The complex exhibits distorted square-planar NiN₄ coordination geometry with two short and two long Ni–N bonds (Ni–N ∼1.85 and ∼1.96 Å, respectively). The electrochemical behavior of [Ni(Me₂bqb)] (1), has been studied by cyclic voltammetry and compared with the analogous complex, [Ni(Me₂bpb)] (2).     

Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: retention prediction

An ion-pair reversed-phase HPLC method was evaluated for the separation of synthetic oligonucleotides. Mass transfer in the stationary phase was found to be a major factor contributing to peak broadening on porous C18 stationary phases. A small sorbent particle size (2.5 microm), elevated temperature and a relatively slow flow-rate were utilized to enhance mass transfer. A short 50 mm column allows for an efficient separation up to 30mer oligonucleotides. The separation strategy consists of a shallow linear gradient of organic modifier, optimal initial gradient strength, and the use of an ion-pairing buffer. The triethylammonium acetate ion-pairing mobile phases have been traditionally used for oligonucleotide separations with good result. However, the oligonucleotide retention is affected by its nucleotide composition. We developed a mathematical model for the prediction of oligonucleotide retention from sequence and length. We used the model successfully to select the optimal initial gradient strength for fast HPLC purification of synthetic oligonucleotides. We also utilized ion-pairing mobile phases comprised of triethylamine (TEA) buffered by hexafluoroisopropanol (HFIP). The TEA-HFIP aqueous buffers are useful for a highly efficient and less sequence-dependent separation of heterooligonucleotides.