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Biological Molecules (biological + molecule)
Selected AbstractsElectrical Conductance in Biological MoleculesADVANCED FUNCTIONAL MATERIALS, Issue 12 2010M. Waleed Shinwari Abstract Nucleic acids and proteins are not only biologically important polymers. They have recently been recognized as novel functional materials surpassing conventional materials in many aspects. Although Herculean efforts have been undertaken to unravel fine functioning mechanisms of the biopolymers in question, there is still much more to be done. Here the topic of biomolecular charge transport is presented with a particular focus on charge transfer/transport in DNA and protein molecules. The experimentally revealed details, as well as the presently available theories, of charge transfer/transport along these biopolymers are critically reviewed and analyzed. A summary of the active research in this field is also given, along with a number of practical recommendations. [source] Cyclic Adenosine Monophosphate Regulation of Ion Transport in Porcine Vocal Fold Mucosae,THE LARYNGOSCOPE, Issue 8 2008Mahalakshmi Sivasankar PhD Abstract Objectives/Hypothesis: Cyclic adenosine monophosphate (cAMP) is an important biological molecule that regulates ion transport and inflammatory responses in epithelial tissue. The present study examined whether the adenylyl cyclase activator, forskolin, would increase cAMP concentration in porcine vocal fold mucosa and whether the effects of increased cAMP would be manifested as a functional increase in transepithelial ion transport. Additionally, changes in cAMP concentrations following exposure to an inflammatory mediator, tumor necrosis factor-, (TNF,) were investigated. Study Design: In vitro experimental design with matched treatment and control groups. Methods: Porcine vocal fold mucosae (N = 30) and tracheal mucosae (N = 20) were exposed to forskolin, TNF,, or vehicle (dimethyl sulfoxide) treatment. cAMP concentrations were determined with enzyme-linked immunosorbent assay. Ion transport was measured using electrophysiological techniques. Results: Thirty minute exposure to forskolin significantly increased cAMP concentration and ion transport in porcine vocal fold and tracheal mucosae. However, 30-minute and 2-hour exposure to TNF, did not significantly alter cAMP concentration. Conclusions: We demonstrate that forskolin-sensitive adenylyl cyclase is present in vocal fold mucosa, and further, that the product, cAMP increases vocal fold ion transport. The results presented here contribute to our understanding of the intracellular mechanisms underlying vocal fold ion transport. As ion transport is important for maintaining superficial vocal fold hydration, data demonstrating forskolin-stimulated ion transport in vocal fold mucosa suggest opportunities for developing pharmacological treatments that increase surface hydration. [source] Purification, crystallization and preliminary crystallographic analysis of a thermostable endonuclease IV from Thermotoga maritimaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Ronny C. Hughes The DNA-repair enzyme endonuclease IV from the thermophilic bacterium Thermotoga maritima MSB8 (reference sequence NC_000853) has been expressed in Escherichia coli and crystallized for X-ray analysis. T. maritima endonuclease IV is a 287-amino-acid protein with 32% sequence identity to E. coli endonuclease IV. The protein was purified to homogeneity and was crystallized using the sitting-drop vapor-diffusion method. The protein crystallized in space group P61, with one biological molecule in the asymmetric unit, corresponding to a Matthews coefficient of 2.39,Å3,Da,1 and 47% solvent content. The unit-cell parameters of the crystals were a = b = 123.2, c = 35.6,Å. Microseeding and further optimization yielded crystals with an X-ray diffraction limit of 2.36,Å. A single 70° data set was collected and processed, resulting in an overall Rmerge and a completeness of 9.5% and 99.3%, respectively. [source] Purification, crystallization and preliminary crystallographic study of haemoglobin from camel (Camelus dromedarius): a high oxygen-affinity lowland speciesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009M. Balasubramanian Haemoglobin is a prototypical allosteric protein that is mainly involved in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs in an intrinsically coordinated manner to maintain the viability of cells. Haemoglobin from Camelus dromedarius provides an interesting case study of adaptation to life in deserts at extremely high temperatures. An ambition to unravel the integrated structural and functional aspects of the casual survival of this animal at high temperatures led us to specifically work on this problem. The present work reports the preliminary crystallographic study of camel haemoglobin. Camel blood was collected and the haemoglobin was purified by anion-exchange chromatography and crystallized using the hanging-drop vapour-diffusion method under buffered high salt concentration using PEG 3350 as a precipitant. Intensity data were collected using a MAR 345 dtb image-plate detector system. Camel haemoglobin crystallized in the monoclinic space group P21, with one whole biological molecule (,2,2) in the asymmetric unit and unit-cell parameters a = 52.759, b = 116.782, c = 52.807,Å, , = 120.07°. [source] Purification, crystallization and preliminary X-ray analysis of haemoglobin from ostrich (Struthio camelus)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009S. S. Sundaresan Haemoglobin is a tetrameric protein that carries oxygen from the lungs to tissues and carbon dioxide from tissues back to the lungs. The oxygen-binding properties of haemoglobin are regulated through the binding of allosteric effectors. The respiratory system of avian species is unique and complex in nature when compared with that of mammals. In avian species, inositol pentaphosphate (inositol-P5) is present in the erythrocytes of the adult and is thought to be the major factor responsible for the relatively high oxygen affinity of the whole blood. The ostrich (Struthio camelus) is a large flightless bird which contains inositol tetrakisphosphate (inositol-P4) in its erythrocytes and its whole blood oxygen affinity is higher. Efforts have been made to explore the structure,function relationship of ostrich haemoglobin. Ostrich haemoglobin was purified using ion-exchange chromatography. Haemoglobin crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant in 50,mM phosphate buffer pH 7.2. Data were collected using a MAR345 image-plate detector system. The crystals of ostrich haemoglobin diffracted to 2.2,Å resolution. They belonged to the orthorhombic space group P212121 with one whole biological molecule in the asymmetric unit; the unit-cell parameters were a = 80.93, b = 81.68, c = 102.05,Å. [source] Adenosyl Radical: Reagent and Catalyst in Enzyme ReactionsCHEMBIOCHEM, Issue 5 2010E. Neil G. Marsh Prof. Abstract Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B12, AdoCbl) or by single-electron reduction of S -adenosylmethionine (AdoMet) complexed to an iron,sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans. [source] Nanowire-Based Electrochemical BiosensorsELECTROANALYSIS, Issue 6 2006Abstract We review recent advances in biosensors based on one-dimensional (1-D) nanostructure field-effect transistors (FET). Specifically, we address the fabrication, functionalization, assembly/alignment and sensing applications of FET based on carbon nanotubes, silicon nanowires and conducting polymer nanowires. The advantages and disadvantages of various fabrication, functionalization, and assembling procedures of these nanosensors are reviewed and discussed. We evaluate how they have been used for detection of various biological molecules and how such devices have enabled the achievement of high sensitivity and selectivity with low detection limits. Finally, we conclude by highlighting some of the challenges researchers face in the 1-D nanostructures research arena and also predict the direction toward which future research in this area might be directed. [source] Biological significance of metals partitioned to subcellular fractions within earthworms (Aporrectodea caliginosa),ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 3 2006Martina G. Vijver Abstract Metal ions in excess of metabolic requirements are potentially toxic and must be removed from the vicinity of important biological molecules to protect organisms from adverse effects. Correspondingly, metals are sequestrated in various forms, defining the accumulation pattern and the magnitude of steady-state levels reached. To investigate the subcellular fractions over which Ca, Mg, Fe, Cu, Zn, Cd, Pb, Ni, and As are distributed, earthworms (Aporrectodea caliginosa) collected from the field were analyzed by isolating metal-rich granules and tissue fragments from intracellular microsomal and cytosolic fractions (i.e., heat-stable proteins and heat-denatured proteins). The fractions showed metal-specific binding capacity. Cadmium was mainly retrieved from the protein fractions. Copper was equally distributed over the protein fraction and the fraction comprising tissue fragments, cell membranes, and intact cells. Zinc, Ca, Mg, and As were mainly found in this fraction as well. Lead, Fe, and Ni were mainly isolated from the granular fraction. To study accumulation kinetics in the different fractions, three experiments were conducted in which earthworms were exposed to metal-spiked soil and a soil contaminated by anthropogenic inputs and, indigenous earthworms were exposed to field soils. Although kinetics showed variation, linear uptake and steady-state types of accumulation patterns could be understood according to subcellular compartmentalization. For risk assessment purposes, subcellular distribution of metals might allow for a more precise estimate of effects than total body burden. Identification of subcellular partitioning appears useful in determining the biological significance of steady-state levels reached in animals. [source] Neptunium uptake by serum transferrinFEBS JOURNAL, Issue 7 2005Isabelle Llorens Although of major impact in terms of biological and environmental hazards, interactions of actinide cations with biological molecules are only partially understood. Human serum transferrin (Tf) is one of the major iron carriers in charge of iron regulation in the cell cycle and consequently contamination by actinide cations is a critical issue of nuclear toxicology. Combined X-ray absorption spectroscopy (XAS) and near infrared absorption spectrometry were used to characterize a new complex between Tf and Np (IV) with the synergistic nitrilotriacetic acid (NTA) anion. Description of the neptunium polyhedron within the iron coordination site is given. [source] In-Film Bioprocessing and Immunoanalysis with Electroaddressable Stimuli-Responsive PolysaccharidesADVANCED FUNCTIONAL MATERIALS, Issue 10 2010Xiaohua Yang Abstract Advances in thin-film fabrication are integral to enhancing the power of microelectronics while fabrication methods that allow the integration of biological molecules are enabling advances in bioelectronics. A thin-film-fabrication method that further extends the integration of biology with microelectronics by allowing living biological systems to be assembled, cultured, and analyzed on-chip with the aid of localized electrical signals is described. Specifically, the blending of two stimuli-responsive film-forming polysaccharides for electroaddressing is reported. The first, alginate, can electrodeposit by undergoing a localized sol,gel transition in response to electrode-imposed anodic signals. The second, agarose, can be co-deposited with alginate and forms a gel upon a temperature reduction. Electrodeposition of this dual polysaccharide network is observed to be a simple, rapid, and spatially selective means for assembly. The bioprocessing capabilities are examined by co-depositing a yeast clone engineered to display a variable lymphocyte receptor protein on the cell surface. Results demonstrate the in-film expansion and induction of this cell population. Analysis of the cells' surface proteins is achieved by the electrophoretic delivery of immunoreagents into the film. These results demonstrate a simple and benign means to electroaddress hydrogel films for in-film bioprocessing and immunoanalysis. [source] The implications of solar UV radiation exposure for fish and fisheriesFISH AND FISHERIES, Issue 3 2001Horacio E Zagarese Abstract Ultraviolet radiation (UVR) possesses three important properties that combine to make it a potent environmental force. These include the potential to induce damage: UVR carries more energy per photon than any other wavelength reaching the Earth's surface. Such highly energetic photons are known to damage many biological molecules, such as DNA and proteins. In addition, they can initiate a series of redox reactions to form reactive oxygen species (ROS), which cause oxidative stress to cells and tissues. The second property is ubiquity: owing to their dependence on light, primary producers and most visual predators, such as fish, are also necessarily exposed to damaging levels of UVR. Thirdly, the combined effect of UVR and additional environmental factors may result in synergistic effects, such as the photoactivation of organic pollutants and photosensitisation. In natural environments, the concentration of dissolved organic matter (DOM) and habitat depth are the two main factors controlling the degree of UVR exposure experienced by fish. Additional factors include vegetation coverage, particulate materials in suspension, pH and hydrological characteristics, and site location (latitude, elevation). The range of potential effects on fish includes direct DNA damage resulting in embryo and larval mortality, and adult and juvenile sunburn, as well as indirect oxidative stress, phototoxicity and photosensitisation. [source] Macroporous Silicon Microcavities for Macromolecule Detection,ADVANCED FUNCTIONAL MATERIALS, Issue 11 2005H. Ouyang Abstract Macroporous silicon microcavities for detection of large biological molecules have been fabricated from highly doped n-type silicon. Well-defined controllable pore sizes up to 120,nm have been obtained by systematically optimizing the etching parameters. The dependence of the sensor sensitivity on pore size is discussed. Excellent infiltration inside these macroporous silicon microcavities is demonstrated using 60,nm diameter latex spheres and rabbit IgG (150,kDa; 1Da,=,1,g,mol,1). The sensing performance of the device is tested using a biotin/streptavidin couple, and protein concentration down to 1,2,,M (equivalent to 0.3,ng,mm,2) could be detected. Simulations show that the sensitivity of the technique is currently approximately 1,2,% of a protein monolayer. [source] Advanced Optical Microscopy Course at the Canale GrandeIMAGING & MICROSCOPY (ELECTRONIC), Issue 1 2007Alberto Diaspro Biophysics is a molecular science rapidly moving to the nanoscale. It seeks to explain biological function in terms of the molecular structures and properties of specific molecules. The size of these molecules varies dramatically, from small fatty acids and sugars (,1 nm = 10,9 m), to macromolecules like proteins (5,10 nm), starches (bigger than 1,000 nm), and the enormously elongated DNA molecules. Much effort in biophysics is directed to determining the structure of specific biological molecules and of the larger structures into which they assemble. Some of this effort involves inventing new methods and building new instruments for monitoring these structures. [source] Mineral-Coated Polymer Microspheres for Controlled Protein Binding and ReleaseADVANCED MATERIALS, Issue 19 2009Leenaporn Jongpaiboonkit Polymer microspheres with a bone-like mineral coatings are generated via a biomimetic process, and this biodegradable coating is used as a carrier for delivery of biological molecules. Acidic and basic proteins are controllably bound and released from these microspheres, suggesting that this approach can be used for binding and delivery of a broad range of biologically active molecules. [source] Detection and analysis of alternative splicing in the silkworm by aligning expressed sequence tags with the genomic sequenceINSECT MOLECULAR BIOLOGY, Issue 2 2005X.-F. Zha Abstract We identified 277 alternative splice forms in silkworm genes based on aligning expressed sequence tags with genomic sequences, using a transcipt assembly program. A large fraction (74%) of these alternative splices are located in protein-coding regions and alter protein products, whereas only 26% are in untranslated regions. From the alternative splices located in protein-coding regions, some (43%) affect protein domains that bind various biological molecules. The vast majority of the detected alternative forms in this study appear to be novel, and potentially affect biologically meaningful control of function in silkworm genes. Our results indicate that alternative splicing in silkworm largely produces protein diversity and functional diversity, and is a widely used mechanism for regulating gene expression. [source] Silica-Incorporated Polyelectrolyte-Complex Fibers as Tissue-Engineering Scaffolds,ADVANCED MATERIALS, Issue 5 2006Fibers of polyelectrolyte complexes incorporated in silica are synthesized by combining the polymerization of hydrolyzed tetraethylorthosilicate with the process of interfacial polyelectrolyte complexation. The resulting fibers are hydro-entangled to successfully produce porous scaffolds that act as a platform for the immobilization of biological molecules for tissue engineering (see Figure). [source] Correlating the positional reactivity of a masked electrophilic center to the topology of the electron densityINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Harry L. Price Abstract Masking of electrophilic centers in biological molecules via structural modifications serves to control chemical reactivity and in some cases may affect the regioselectivity of a reaction. In the work presented the regioselective reactivity of the electrophilic cyclopropylpyrrololindole (CPI) center in the DNA alkylator CC-1065, a highly toxic antibiotic that has served as a structural template for the development of a series of novel anticancer drugs containing the CPI reactive center has been examined. The CPI reactive center is an interesting example of chemical masking as it relates to acid-dependent electrophilicity, and regioselective addition of a nucleophile to an electrophilic center. In an effort to better understand the reactivity of the CPI center, calculations using the B3LYP density functional theory (DFT) method, the 6-31G(d) basis set, and the atoms in molecules (AIM) theory were performed on unprotonated and protonated forms of the CPI reactive center. The results of these calculations demonstrate that activation of the CPI group via protonation induces significant changes in the electron density (,), the Laplacian of the density (,2,), and the bond ellipticity (,), and that these changes are linked to the observed reactivity of the CPI reaction center. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Functional and molecular MR imaging of angiogenesis: Seeing the target, seeing it workJOURNAL OF CELLULAR BIOCHEMISTRY, Issue S39 2002Michal NeemanArticle first published online: 16 JAN 200 Abstract Intensive research over the last years led to the discovery of multiple molecular pathways and intricate regulatory network controlling the growth and regression of blood vessels in general and angiogenesis in particular. The difficulties in elucidation of the regulation of angiogenesis, stems from the inherent complexity due to participation of many cell types, under a dominant impact of physiological and environmental effects of flow, perfusion, and oxygenation. Major advances were achieved with the use of sophisticated transgenic mice models engineered so as to provide spatially and temporally controlled expression of specific factors alone or in combination. In vivo analysis of these models frequently requires the use of non-invasive imaging modalities for measurement of functional parameters of the vasculature along with dynamic molecular information. Optical methods are extensively applied for the study of angiogenesis [Brown et al., 2001] but provide very limited tissue penetration. MRI offers the advantage of being non-invasive with uniform and relatively high spatial resolution for deep tissues. Multiple MRI approaches for monitoring angiogenesis were developed over the last years, each looking at a particular step in the process. The aim of this paper is to analyze the clinical, pharmaceutical, and biological needs for imaging of angiogenesis, and to critically evaluate the strengths and weaknesses of functional and molecular imaging for monitoring angiogenesis. The inherent problem of validation of different measures of angiogenesis, and the advantages and limitations associated with application of MRI based methods, as surrogates for other measurements of angiogenesis will be discussed. The terms molecular imaging and functional imaging are frequently loosely defined with a significant overlap between the two. For the sake of this paper we will apply a narrower definition of both terms, where molecular imaging will apply to methods directed towards detection of specific biological molecules that participate directly in (regulation of) a physiological process; while functional imaging will be used to describe those methods that aim to detect the physiological response to a defined (molecular) stimulus. J. Cell. Biochem. Suppl. 39: 11,17, 2002. © 2002 Wiley-Liss, Inc. [source] A generalized higher order kernel energy approximation methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Stewart N. Weiss Abstract We present a general mathematical model that can be used to improve almost all fragment-based methods for ab initio calculation of total molecular energy. Fragment-based methods of computing total molecular energy mathematically decompose a molecule into smaller fragments, quantum-mechanically compute the energies of single and multiple fragments, and then combine the computed fragment energies in some particular way to compute the total molecular energy. Because the kernel energy method (KEM) is a fragment-based method that has been used with much success on many biological molecules, our model is presented in the context of the KEM in particular. In this generalized model, the total energy is not based on sums of all possible double-, triple-, and quadruple-kernel interactions, but on the interactions of precisely those combinations of kernels that are connected in the mathematical graph that represents the fragmented molecule. This makes it possible to estimate total molecular energy with high accuracy and no superfluous computation and greatly extends the utility of the KEM and other fragment-based methods. We demonstrate the practicality and effectiveness of our model by presenting how it has been used on the yeast initiator tRNA molecule, ytRN (1YFG in the Protein Data Bank), with kernel computations using the Hartree-Fock equations with a limited basis of Gaussian STO-3G type. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Analyzing single-molecule manipulation experimentsJOURNAL OF MOLECULAR RECOGNITION, Issue 5 2009Christopher P. Calderon Abstract Single-molecule manipulation studies can provide quantitative information about the physical properties of complex biological molecules without ensemble artifacts obscuring the measurements. We demonstrate computational techniques which aim at more fully utilizing the wealth of information contained in noisy experimental time series. The "noise" comes from multiple sources e.g., inherent thermal motion, instrument measurement error, etc. The primary focus of this paper is a methodology that uses time domain based methods to extract the effective molecular friction from single-molecule pulling data. We studied molecules composed of eight tandem repeat titin I27 domains, but the modeling approaches have applicability to other single-molecule mechanical studies. The merits and challenges associated with applying such a computational approach to existing single-molecule manipulation data are also discussed. Copyright © 2009 John Wiley & Sons, Ltd. [source] What is the biological relevance of the specific bond properties revealed by single-molecule studies?,JOURNAL OF MOLECULAR RECOGNITION, Issue 6 2007Philippe Robert Abstract During the last decade, many authors took advantage of new methodologies based on atomic force microscopy (AFM), biomembrane force probes (BFPs), laminar flow chambers or optical traps to study at the single-molecule level the formation and dissociation of bonds between receptors and ligands attached to surfaces. Experiments provided a wealth of data revealing the complexity of bond response to mechanical forces and the dependence of bond rupture on bond history. These results supported the existence of multiple binding states and/or reaction pathways. Also, single bond studies allowed us to monitor attachments mediated by a few bonds. The aim of this review is to discuss the impact of this new information on our understanding of biological molecules and phenomena. The following points are discussed: (i) which parameters do we need to know in order to predict the behaviour of an encounter between receptors and ligands, (ii) which information is actually yielded by single-molecule studies and (iii) is it possible to relate this information to molecular structure? Copyright © 2007 John Wiley & Sons, Ltd. [source] New environmentally responsive fluorescent N -isopropylacrylamide copolymer and its application to DNA sensingJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 19 2006Chang-Chung Yang Abstract We report two novel multifunctional copolymers consisting of a temperature-responsive poly(N -isopropylacrylamide) (PNIPAA) segment and a fluorescent fluorene-containing acrylic polymer segment with pH responsiveness and/or DNA-sensing ability. The functional acrylic monomer with a fluorene dimer side group substituted with amino units was synthesized first. Then, it was copolymerized with N -isopropylacrylamide to result in a new water-soluble, fluorescent PNIPAA copolymer (P1). The fluorescent properties of P1 under neutral and acidic conditions did not change with the temperature. However, significant variation was observed under basic conditions. The protonation of the amino moiety at a low pH improved the solubility and prevented aggregation for fluorescence quenching, but not under the basic conditions. Although aggregation of the fluorene units was significant at room temperature under basic conditions, the aggregation was resolved at a temperature above the lower critical solution temperature. These findings indicated the pH- and temperature-responsive characteristics of P1. Moreover, after the amino groups were quaternized, the obtained polymer could be used as a biosensor because the fluorescence intensity was quenched with the addition of DNA. This study demonstrates that multifunctional materials with pH- and temperature-sensing characteristics and biological molecules could be realized by the incorporation of a functional fluorene-containing moiety with PNIPAA. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5495,5504, 2006 [source] Raman optical activity of an achiral element in a chiral environmentJOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2009Andrew M. Smith Abstract Raman optical activity (ROA) is a relatively new technique used to determine the structure of chiral molecules and is proving useful in the study of biological molecules such as proteins and DNA/RNA. Here, for the first time, we demonstrate the applicability of ROA as a technique to study achiral groups in chiral environments, detecting the induced chirality of N -(fluorenyl-9-methoxycarbonyl) (Fmoc) in a chiral self-assembled structure of Fmoc-dipeptides. This technique is therefore of interest to those studying self-assembled systems that adopt a chiral structure. Copyright © 2009 John Wiley & Sons, Ltd. [source] Experimental and statistical analysis methods for peptide detection using surface-enhanced Raman spectroscopyJOURNAL OF RAMAN SPECTROSCOPY, Issue 3 2008Breeana L. Mitchell Abstract Surface-enhanced Raman spectroscopy (SERS) has the potential to make a significant impact in biology research due to its ability to provide information orthogonal to that obtained by traditional techniques such as mass spectrometry (MS). While SERS has been well studied for its use in chemical applications, detailed investigations with biological molecules are less common. In addition, a clear understanding of how methodology and molecular characteristics impact the intensity, the number of peaks, and the signal-to-noise of SERS spectra is largely missing. By varying the concentration and order of addition of the SERS-enhancer salt (LiCl) with colloidal silver, we were able to evaluate the impact of these variables on peptide spectra using a quantitative measure of spectra quality based on the number of peaks and peak intensity. The LiCl concentration and order of addition that produced the best SERS spectra were applied to a panel of synthetic peptides with a range of charges and isoelectric points (pIs) where the pI was directly correlated with higher spectral quality. Those peptides with moderate to high pIs and spectra quality scores were differentiated from each other using the improved method and a hierarchical clustering algorithm. In addition, the same method and algorithm was applied to a set of highly similar phosphorylated peptides, and it was possible to successfully classify the majority of peptides on the basis of species-specific peak differences. Copyright © 2008 John Wiley & Sons, Ltd. [source] Radiation damage to crystalline biological molecules: current viewJOURNAL OF SYNCHROTRON RADIATION, Issue 6 2002Elspeth Garman First page of article [source] Modifications and oxidation of lipids and proteins in human serum detected by thermochemiluminescenceLUMINESCENCE: THE JOURNAL OF BIOLOGICAL AND CHEMICAL LUMINESCENCE, Issue 2 2003Sergei Shnizer Abstract Detection of electronically excited species (EES) in body fluids may constitute an important diagnostic tool in various pathologies. Examples of such products are triplet excited carbonyls (TEC), which can be a source for photon emission in the 400,550,nm range. The aim of the present study was to determine the actual contribution of lipid and protein components (protein carbonyls) to photon emission generated by thermochemiluminescence (TCL) during the heating of biological fluids. In this study, a new TCL Photometer device, designed by Lumitest Ltd, Israel, was used. Samples were heated to a constant temperature of 80,±,0.5°C for 280,s and photon emission was measured at several time points. In order to compare the results of TCL measurements to conventional methods of detecting lipid and protein oxidation, each examined sample was also heated in a waterbath at 80°C for 10,280,s. Lipid and protein oxidation were subsequently measured using conventional methods. The TCL of four polyunsaturated fatty acids (PUFA) with three to six double bonds was measured. The elevation of the PUFA TCL amplitude correlated with the increase in the number of double bonds of PUFA. A correlation between the increase in TCL intensity and protein carbonyl generation in bovine serum albumin (BSA) was also observed. In the venous blood serum, our study showed that an increase of TCL intensity during heating reflected the cleavage of TEC of lipid origin. Our study suggests that biological molecules such as proteins, lipids and other molecules, which may become unstable during heating, are capable of generating EES. We demonstrated that a TCL curve can be used as a kinetic model for measuring oxidative processes, which reflects modifications of different molecules involved in the oxidative stress phenomena. Copyright © 2003 John Wiley & Sons, Ltd. [source] Ultraviolet photofragmentation of biomolecular ionsMASS SPECTROMETRY REVIEWS, Issue 3 2009James P. Reilly Abstract Mass spectrometric identification of all types of molecules relies on the observation and interpretation of ion fragmentation patterns. Peptides, proteins, carbohydrates, and nucleic acids that are often found as components of complex biological samples represent particularly important challenges. The most common strategies for fragmenting biomolecular ions include low- and high-energy collisional activation, post-source decay, and electron capture or transfer dissociation. Each of these methods has its own idiosyncrasies and advantages but encounters problems with some types of samples. Novel fragmentation methods that can offer improvements are always desirable. One approach that has been under study for years but is not yet incorporated into a commercial instrument is ultraviolet photofragmentation. This review discusses experimental results on various biological molecules that have been generated by several research groups using different light wavelengths and mass analyzers. Work involving short-wavelength vacuum ultraviolet light is particularly emphasized. The characteristics of photofragmentation are examined and its advantages summarized. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:425,447, 2009 [source] Femtosecond electron diffraction: Direct probe of ultrafast structural dynamics in metal filmsMICROSCOPY RESEARCH AND TECHNIQUE, Issue 3 2009Shouhua Nie Abstract Femtosecond electron diffraction is a rapidly advancing technique that holds a great promise for studying ultrafast structural dynamics in phase transitions, chemical reactions, and function of biological molecules at the atomic time and length scales. In this paper, we summarize our development of a tabletop femtosecond electron diffractometer. Using a delicate instrument design and careful experimental configurations, we demonstrate the unprecedented capability of detecting submilli-ångström lattice spacing change on a subpicosecond timescale with this new technique. We have conducted an in-depth investigation of ultrafast coherent phonon dynamics induced by an impulsive optical excitation in thin-film metals. By probing both coherent acoustic and random thermal lattice motions simultaneously in real time, we have provided the first and unambiguous experimental evidence that the pressure of hot electrons contributes significantly to the generation of coherent acoustic phonons under nonequilibrium conditions when electrons and phonons are not thermalized. Based on these observations, we also propose an innovative approach to measure the electronic Grüneisen parameter in magnetic materials at and above room temperature, which provides a way to gain new insights into electronic thermal expansion in ferromagnetic transition metals. Microsc. Res. Tech. 2009. © 2009 Wiley-Liss, Inc. [source] Photodynamic Action of Benzo[a]pyrene in K562 CellsPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 6 2007Daza De Moraes Vaz Batista Filgueira Benzo[a]pyrene (BaP) is ubiquitously distributed in the environment, being considered the most phototoxic element among polycyclic aromatic hydrocarbon (PAHs). In presence of oxygen, PAHs can act as a photosensitizer by means of promoting photo-oxidation of biological molecules (photodynamic action, PDA). Thus, the present study analyzed the photodynamic action of BaP under UVA irradiation (BaP + UVA) and its oxidative effects on K562 cells. The evaluation of BaP kinetics showed that the highest intracellular concentration occurred after 18 h of incubation. Cell viability, reactive oxygen species (ROS) generation, lipid peroxidation, DNA damage (breaks and DNA,protein cross-link [DNAPC]) were assessed after exposure to BaP, UVA and BaP plus UVA irradiation (BaP + UVA). Cell viability was decreased just after exposure to BaP + UVA. Lipid peroxidation and DNA breaks increased after BaP + UVA exposure, while the DNAPC increased after BaP, UVA and BaP + UVA exposure, suggesting that BaP + UVA effects were a consequence of both type II (producing mainly singlet oxygen) and type I (producing others ROS) mechanisms of PDA. [source] Reflection anisotropy spectroscopy of biological molecules with the 4GLS sourcePHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 8 2008P. Weightman Abstract The main characteristics of the UK Fourth Generation Light Source (4GLS) are described. It is explained how the output of 4GLS could be used in studies of biological systems using Reflection Anisotropy Spectroscopy (RAS). (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] | ||||||||||||||||||||||||||||||||||