Probing the 3-D Structure,Dynamics, and Stability of Bacterial Collagenase Collagen Binding Domain (apo- versus holo-) by Limited Proteolysis MALDI-TOF MS

Pairing limited proteolysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to probe clostridial collagenase collagen binding domain (CBD) reveals the solution dynamics and stability of the protein, as these factors are crucial to CBD effectiveness as a drug-delivery vehicle. MS analysis of proteolytic digests indicates initial cleavage sites, thereby specifying the less stable and highly accessible regions of CBD. Modulation of protein structure and stability upon metal binding is shown through MS analysis of calcium-bound and cobalt-bound CBD proteolytic digests. Previously determined X-ray crystal structures illustrate that calcium binding induces secondary structure transformation in the highly mobile N-terminal arm and increases protein stability. MS-based detection of exposed residues confirms protein flexibility, accentuates N-terminal dynamics, and demonstrates increased global protein stability exported by calcium binding. Additionally, apo- and calcium-bound CBD proteolysis sites correlate well with crystallographic B-factors, accessibility, and enzyme specificity. MS-observed cleavage sites with no clear correlations are explained either by crystal contacts of the X-ray crystal structures or by observed differences between Molecules A and B in the X-ray crystal structures. The study newly reveals the absence of the βA strand and thus the very dynamic N-terminal linker, as corroborated by the solution X-ray scattering results. Cobalt binding has a regional effect on the solution phase stability of CBD, as limited proteolysis data implies the capture of an intermediate-CBD solution structure when cobalt is bound.     

PHYCOBILIPROTEINS: COMPARISON OF SOLUTION AND SINGLE CRYSTAL FLUORESCENCE FOR C-PHYCOCYANIN AND B-PHYCOERYTHRIN*

Abstract— Trimeric and hexameric solution forms of C-phycocyanin (CPC) from the cyanophyte Agme-nellum quadruplicatum have been isolated and their spectral properties compared to those obtained from single crystals. Although the absorbance peak of a suspension of small C-phycocyanin crystals is red-shifted only 7 nm relative to the solution forms, the single crystal fluorescence is red-shifted 60 nm relative to the solution forms. The crystal fluorescence spectrum exhibits a single peak at LD_max= 708 nm when excited at 514.5 or 530.9 nm and two peaks (LD_max= 661 and 708 nm) when excitation occurs at 568.2 nm. Fluorescence depolarization measurements indicate that extensive energy transfer could occur for both solution and crystal forms with the latter being dependent upon the relative orientation of the crystal with respect to the excitation dipole. Similar results were obtained with B-phycoerythrin (BPE) from the red alga Porphyridium cruentum where the single crystal fluorescence is red-shifted =50nm relative to the solution spectra with two peaks (LD_max= 583 and 617 nm) observed whose relative intensities are dependent on the excitation wavelength (LD_max– 514.5 and 530.9 nm). Single crystal fluorescent lifetimes exhibited considerable shortening relative to that observed for the solution forms. The implications of these results are discussed with respect to the possible relationships of the crystalline structures to the assembly forms present within phycobilisomes.     

Structure determination of protein-ligand complexes by transferred paramagnetic shifts

Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent (1)H and (13)C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the epsilon exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit theta, and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.     

Cross metathesis approach to retinoids and other β-apocarotenoids

Cross metathesis (CM) reactions between polyenes, such as β-carotene, canthaxanthin or retinyl acetate, and various alkenes or dienes in the presence of second generation Hoveyda-Grubbs (H II) or Grubbs (G II) catalysts were investigated. Depending on the cross partner different apocarotenoids were obtained. Cross metathesis reactions of retinyl acetate proved to be fully regioselective. Carotenoid CM reactions afforded mixtures of two products due to competing cleavage of the C11-C12 and C15-C15′ double bonds. However, regioselectivity can be controlled by choice of appropriate reaction conditions. The reactions of polyenes with dienes worked better in respect of yields and diastereoselectivities than those with monounsaturated cross partners.     

Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite

The formation of biogenic materials requires the interaction of organic molecules with the mineral phase. In forming enamel, the amelogenin proteins contribute to the mineralization of hydroxyapatite (HAp). Leucine-rich amelogenin protein (LRAP) is a naturally occurring splice variant of amelogenin that comprises amelogenin's predicted HAp binding domains. We determined the partial structure of phosphorylated and non-phosphorylated LRAP variants bound to HAp using combined solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. New ssNMR measurements in the N-terminus indicate a largely extended structure for both variants, though some measurements are consistent with a partially helical N-terminal segment. The N-terminus of the phosphorylated variant is found to be consistently closer to the HAp surface than the non-phosphorylated variant. Structure prediction was biased using 21 ssNMR measurements in the N- and C-terminus at five HAp crystal faces. The predicted fold of LRAP is similar at all HAp faces studied, regardless of phosphorylation. Largely consistent with experimental observations, LRAP's predicted structure is relatively extended with a helix-turn-helix motif in the N-terminal domain and some helix in the C-terminal domain, and the N-terminal domain of the phosphorylated variant binds HAp more closely than the N-terminal domain of the non-phosphorylated variant. Predictions for both variants show some potential binding specificity for the {010} HAp crystal face, providing further support that amelogenins block crystal growth on the a and b faces to allow elongated crystals in the c-axis.     

Photochemically generated carotenoid radicals on Nafion film and silica gel: an EPR and ENDOR study

Carotenoid cation radicals have been observed at 120 K, by EPR and proton ENDOR measurements, to be formed upon 77 K photolysis of thin films of Nafion or silica gel coated with the carotenoids, β-carotene and canthaxanthin. The powder ENDOR spectra consist of resolvable lines due to couplings larger than 2.8 MHz but smaller than 17 MHz assigned to the methyl protons of the carotenoid cation radical and to an -proton of the planar polyene chain.     

Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor

The AppA protein with the BLUF (blue light using flavin adenine dinucleotide) domain is a blue light photoreceptor that cycle between dark-adapted and light-induced functional states. We characterized possible reaction intermediates in the photocycle of AppA BLUF. Molecular dynamics (MD), quantum chemical and quantum mechanical-molecular mechanical (QM/MM) calculations were carried out to describe several stable structures of a molecular system modeling the protein. The coordinates of heavy atoms from the crystal structure (PDB code 2IYG) of the protein in the dark state served as starting point for 10 ns MD simulations. Representative MD frames were used in QM(B3LYP/cc-pVDZ)/MM(AMBER) calculations to locate minimum energy configurations of the model system. Vertical electronic excitation energies were estimated for the molecular clusters comprising the quantum subsystems of the QM/MM optimized structures using the SOS-CIS(D) quantum chemistry method. Computational results support the occurrence of photoreaction intermediates that are characterized by spectral absorption bands between those of the dark and light states. They agree with crystal structures of reaction intermediates (PDB code 2IYI) observed in the AppA BLUF domain. Transformations of the Gln63 side chain stimulated by photo-excitation and performed with the assistance of the chromophore and the Met106 side chain are responsible for these intermediates.     

RNA aptamers as pathway-specific MAP kinase inhibitors

BACKGROUND: In eukaryotic cells, many intracellular signaling pathways have closely related mitogen activated protein kinase (MAPK) paralogs as central components. Although MAPKs are therefore obvious targets to control the cellular responses resulting from the activation of these signaling pathways, the development of inhibitors which target specific cell signaling pathways involving MAPKs has proven difficult. RESULTS: We used an RNA combinatorial approach to isolate RNAs that inhibit the in vitro phosphorylation activity of extracellular regulated kinase 2 (ERK2). These inhibitors block phosphorylation by ERK1 and ERK2, but do not inhibit Jun N-terminal kinase or p38 MAPKs. Kinetic analysis indicates these inhibitors function at high picomolar concentrations through the steric exclusion of substrate and ATP binding. In one case, we identified a compact RNA structural domain responsible for inhibition. CONCLUSIONS: RNA reagents can selectively recognize and inhibit MAPKs involved in a single signal transduction pathway. The methodology described here is readily generalizable, and can be used to develop inhibitors of MAPKs involved in other signal transduction pathways. Such reagents may be valuable tools to analyze and distinguish homologous effectors which regulate distinct signaling responses.     

Mesogen-jacketed Liquid Crystal Polymers With Mesogens of Aromatic Amide Structure

The synthesis and property of a new series of "mesogen-jacketed liquid crystal polymers" are reported. These polymers have aromatic amide structures as the mesogenic groups and are represented by poly-2,5-bis(4-methoxy- benzamido)styrene. The preliminary study on properties shows that the polymers have very high glass transition temperatures as well as very low critical concentrations for the formation of the lyotropic liquid crystal phase. The results indicate a high degree of chain rigidity. However, the liquid crystalline order of molecular organization in bulk samples disappears upon heating to the glass transition temperature as revealed by polarizing microscopy and by X-ray diffractometer. Therefore, the liquid crystalline order of these polymers forms only through solution but not through heating. This behavior is different from that of the previously studied poly-2,5-bis[(4-methoxybenzoyl)oxy]styrene and its homologs. The latter polymers are liquid crystals both lyotropically and thermotropically. © 1997 John Wiley & Sons, Ltd.     

Properties of GST-CALM expressed in E. coli

Clathrin-coated vesicles (CCVs) are involved in protein and lipid trafficking between intracellular compartments in eukaryotic cells. CCVs are composed of clathrin and assembly proteins. The clathrin assembly protein lymphoid myeloid leukemia (CALM) gene, encodes a homologoue of the neuronal clathrin assembly protein AP180. In this study, we characterized the properties of the CALM expressed in E. coli. The molecular weight of bacterially expressed GST-CALM fusion protein was approximately 105 kD on SDS-PAGE. The CALM protein could promote clathrin triskelia into clathrin cages and could bind the preformed clathrin cage. However, 33 kD N-terminal domain of CALM could not bind pre-assembled clathrin cages, but assemble clathrin triskelia into clathrin cages. The CALM protein was bound to SH3 domain through N-terminal domain1, in vitro. The CALM protein is proteolyzed by caspase 3, caspase 8 and calpain through C-terminal domain.     

Control of the Optical Properties of a Star Copolymer with a Hyperbranched Conjugated Polymer Core and Poly(ethylene glycol) Arms by Self‐Assembly

A self‐assembly approach to tuning the optical properties of a star copolymer is reported herein. The star copolymer HCP‐star‐PEG with a hyperbranched conjugated polymer (HCP) core and many linear poly(ethylene glycol) (PEG) arms has been prepared successfully. The HCP core was synthesized by Wittig coupling of N‐(n‐hexyl)‐3,6‐diformylcarbazole and 1,3,5‐bis[(triphenylphosphonio)methyl]benzene tribromide. Subsequently, the linear PEG arms were grafted onto the HCP core by acylhydrazone connection. It was found that the optical properties of HCP‐star‐PEG in chloroform solution changed on addition of acid. Both ¹H NMR and UV/Vis spectroscopic investigations confirmed that the variation of the optical properties was related to the complexation of the acid and the imine bond in the acylhydrazone group. HCP‐star‐PEG self‐assembled into core–shell micelles in the mixed solvent of chloroform and acetonitrile, which affected the protonation of the imine bond. Therefore the optical properties of HCP‐star‐PEG can be readily controlled by self‐assembly.     

乙型肝炎病毒表面抗原三维结构的同源模建及功能预测

结合生物信息学方法及分子模拟手段, 通过同源模建方法构建了乙型肝炎病毒表面抗原(HBsAg)Pres12的三维空间结构, 并结合生物实验在分子水平上探讨了乙型肝炎病毒表面抗原Pres12作为抗乙型肝炎病毒重要靶标的机理. 研究结果表明, HBsAg三维空间结构是由构型性的Pres1和线性的Pres2组成, 此结构由疏水氨基酸形成3个α-螺旋结构及Loop结构域, 并且N端由Pres1中残基构成了一个开裂, 形成了HBsAg可能的活性部位. 静电势分析结果证实, N端可能的活性部位具有较大的静电势分布, 因而具有与受体细胞蛋白相互作用的能力, 这为HBV病毒抑制剂药物分子的设计提供了有益帮助.     

Time, space, and spectrally resolved studies on J-aggregate interactions in zeolite L nanochannels

Temporally and spectrally resolved confocal microscopy has been used to explore the behavior of pyronine intercalated zeolite L crystals at different loadings. The low pyronine loading of 0.6% exhibits photophysical behavior similar to that of the free molecule in solution, indicating molecules are isolated from each other in the crystal channels. The higher loading of 20% results in a dye gradient along the channel axis, and the presence of an additional red-shifted spectroscopic transition, with shorter lifetimes. The new band is assigned to an inline arrangement of the molecules undergoing a J-aggregate-type coupling, a process so far not observed in subnanometer channels.     

Fluorescence spectroscopic properties and crystal structure of a series of donor-acceptor diphenylpolyenes

A series of p-nitro-p'-alkoxy(OR)-substituted (E,E,E)-1,6-diphenyl-1,3,5-hexatrienes (1a, R = Me; 1b, R = Et; 1c, R = n-Pr; 1d, R = n-Bu) were prepared. The absorption and fluorescence spectra in solution were almost independent of the alkoxy chain length. The absorption maximum showed only a small dependence on the solvent polarity, whereas the fluorescence maximum red-shifted largely as the polarity increased. The solid-state absorption and fluorescence spectra were red-shifted relative to those in low polar solvents and were clearly dependent on the alkoxy chain length. The fluorescence maxima for the crystals of 1b and 1d were observed at 635-650 nm, which were red-shifted by 40-50 nm relative to those for 1a and 1c. The Stokes shifts were all relatively small (3000-3500 cm-1). For all four compounds, the fluorescence decay curves in the solid state were able to be analyzed by single-exponential fitting to give the lifetimes of 1.1-1.3 ns. This indicates that the emission of 1a-d is not originated from an excimer or molecular aggregates, but from only one emitting monomeric species. The fluorescence quantum yields of 1a-d were considerably high compared with the values for organic solids, which is consistent with their monomeric origin of emission. Single-crystal X-ray structure analyses of 1a, 1c, and 1d showed that the crystal packing was dependent on the alkoxy chain length. The crystals of 1a and 1c had herringbone structure, whereas that of 1d had pi-stacked structure. Strong pi-pi interaction in the crystal of 1d would be the cause of the spectral red shifts relative to those for 1a and 1c. No observation of excimer fluorescence from crystal 1d can be attributed to the limited overlap between the pi-planes of the molecules due to its "slipped-parallel" structure.     

Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans

Acetylated glucuronoxylan is one of the most common types of hemicellulose in nature. The structure is formed by a β-(1→4)-linked D-xylopyranosyl (Xylp) backbone that can be substituted with an acetyl group at O-2 and O-3 positions, and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Acetyl xylan esterases (AcXE) that target mono- or doubly acetylated Xylp are well characterized; however, the previously studied AcXE from Flavobacterium johnsoniae (FjoAcXE) was the first to remove the acetyl group from 2-O-MeGlcpA-3-O-acetyl-substituted Xylp units, yet structural characteristics of these enzymes remain unspecified. Here, six homologs of FjoAcXE were produced and three crystal structures of the enzymes were solved. Two of them are complex structures, one with bound MeGlcpA and another with acetate. All homologs were confirmed to release acetate from 2-O-MeGlcpA-3-O-acetyl-substituted xylan, and the crystal structures point to key structural elements that might serve as defining features of this unclassified carbohydrate esterase family. Enzymes comprised two domains: N-terminal CBM domain and a C-terminal SGNH domain. In FjoAcXE and all studied homologs, the sequence motif around the catalytic serine is Gly-Asn-Ser-Ile (GNSI), which differs from other SGNH hydrolases. Binding by the MeGlcpA-Xylp ligand is directed by positively charged and highly conserved residues at the interface of the CBM and SGNH domains of the enzyme.     

Time-resolved limited proteolysis of mitogen-activated protein kinase-activated protein kinase-2 determined by LC/MS only

Mass spectrometry has gained prominence in limited proteolysis studies largely due to its unparalleled precision in determining protein molecular mass. However, proteolytic fragments usually cannot be identified through direct mass measurement, since multiple subsequences of a protein can frequently be matched to observed masses of proteolytic fragments. Therefore, additional information from N-terminal sequencing is often needed. Here we demonstrate that mass spectrometry analysis of the time course of limited proteolysis reactions provides new information that is self-sufficient to identify all proteolytic fragments. The method uses a non-specific protease like subtilisin and exploits information contained in the time-resolved dataset such as: increased likelihood of identifying larger fragments generated during initial proteolysis solely by their masses, additivity of the masses of two mutually exclusive sequence regions that generate the full-length molecule (or an already assigned subfragment), and analyses of the proteolytic subfragment patterns that are facilitated by having established the initial cleavage sites. We show that the identities of the observed proteolytic fragments can be determined by LC/MS alone because enough constraints exist in the time-resolved dataset. For a medium-sized protein, it takes about 8 h to complete the study, a significant improvement over the traditional SDS-PAGE and N-terminal sequencing method, which usually takes several days. We illustrate this method with application to the catalytic domain of mitogen-activated protein kinase-activated protein kinase-2, and compare the results with N-terminal sequencing data and the known X-ray crystal structure.     

Fluorinated diphenylpolyenes: crystal structures and emission properties

(E,E,E)-1,6-Diaryl(Ar)-1,3,5-hexatrienes (2, Ar = 4-fluorophenyl; 3, Ar = 2,4-difluorophenyl; 4, Ar = 2,4,6-trifluorophenyl; 5, Ar = perfluorophenyl) and (E,E,E)-1-perfluorophenyl-6-phenyl-1,3,5-hexatriene (6) were prepared. The absorption and fluorescence spectra in methylcyclohexane solution showed only a small dependence on the fluorine ring substituent, and were similar to those of the unsubstituted parent compound (1, Ar = phenyl). The solid-state absorption and fluorescence spectra shifted to red relative to those in solution and strongly depended on the substituent. The emission from crystals 1-5 originated mainly from monomeric species with the maximum wavelength (lambda f(max)) of 440-465 nm, which overlapped the emission from molecular aggregates (1-4) or excimeric species (5) in the red region. Crystal 6 exhibited red-shifted (lambda f(max) = 530 nm) and structureless emission due to excimers. The cocrystal of 1 and 5 (1/5) showed red-shifted (lambda f(max) = 558 nm) and distinctly structured emission, not from exciplexes but from the excited states of molecular aggregates in which molecules 1 and 5 strongly interact already in the ground state. These assignments were confirmed by the results of fluorescence lifetime and quantum yield measurements in the solid state. Single-crystal X-ray structure analyses showed that the molecules were basically planar in each crystal, whereas the crystal packing was strongly substituent-dependent. Weak pi-pi interactions in the herringbone (1 and 2) and in the pi-stacked but largely offset structures (3 and 4) account for their predominantly monomeric origin of emission. The observation of excimer fluorescence from 5 was rather unexpected, since the molecules in this crystal were arranged in an offset stacking fashion due to perfluorophenyl-perfluorophenyl (C6F5...C6F5) interaction. The structures of 6 and 1/5 considerably resembled each other, in which molecules were pi-stacked with more face-to-face geometries than those in 5, as a result of strongly attractive perfluorophenyl-phenyl (C6F5...C6H5) interaction. Nevertheless, the fluorescence origin was clearly different for 6 and 1/5. This can be ascribed to the difference in the strength of orbital-orbital interaction between molecular pi-planes in the ground and excited states in crystals.     

Molecular and collective modes in ferroelectric liquid crystals studied by dielectric spectroscopy

The complex dielectric permittivity has been measured for a ferroelectric liquid crystal in the range 102-109Hz. Six different relaxations have been obtained and characterized: soft mode (SmA* and SmC* phases), Goldstone mode (SmC* phase), rotation around molecular long axis, rotation around molecular short axis, ferroelectric domain mode (SmC* phase) and an internal motion associated with a polar group. Strengths and frequencies of these modes have been obtained for the different phases for different bias fields. Using these results together with spontaneous polarization and molecular tilt measurements we have also obtained the rotational viscosities associated with the soft mode and the Goldstone mode. We explain the results in the light of the so-called Landau extended model, concluding that the biquadratic coupling between polarization and tilt is quite important with regard to the bilinear coupling. This fact has been used to explain the noticeable increase of the activation energy of the frequency of the mode related to the rotation around the molecular long axis at the SmA*-SmC* phase transition.