Protein Chemistry (protein + chemistry)

Distribution by Scientific Domains


Selected Abstracts


Nutrition-Driven Assembly of Colloidal Nanoparticles: Growing Fungi Assemble Gold Nanoparticles as Microwires,

ADVANCED MATERIALS, Issue 1 2007
A. Sugunan
The use of a living fungus to ,actively' assemble presynthesized gold nanoparticles over its hyphae, resulting in conducting microstructures (see figure), is reported. This physiologically (nutrition) driven process of colloidal self-organization avoids the need for sophisticated DNA/protein chemistry for facilitating interfacing with biological surfaces. The obtained gold-laden microstructures can be modified into flat ribbonlike or tubular morphologies by simple post-formation processing. [source]


From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics.

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2009
Part II 198
Abstract This is the continuation of a personal retrospective on the developments that since 1965 have given shape to Mass Spectrometry (MS) and taken it from a position of simply playing a role in Protein Chemistry to becoming an indispensable tool in Proteomics, all within a 40-year span. Part I covered the period from 1965 to 1984. This second part reviews the Mass Spectrometry timeline of events from 1985 to 2000, stopping at various time points where MS made significant contributions to protein chemistry or where the development of new instrumentation for MS represented a major advance for peptide and protein work. Major highlights in the field and their significance for peptide and protein characterization such as the advent and practical consequences of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are covered, including work done with triple quads, the development of time-of-flight (TOF) instruments and new ion traps and going on to the more recent work on the full characterization of the Proteome with ion traps, TOF instruments and new ionization and tagging techniques for protein sequencing. Copyright 2009 John Wiley & Sons, Ltd. [source]


Regioselective Carbon,Carbon Bond Formation in Proteins with Palladium Catalysis; New Protein Chemistry by Organometallic Chemistry

CHEMBIOCHEM, Issue 1 2006
Koichiro Kodama
Abstract Palladium-catalyzed reactions have contributed to the advancement of many areas of organic chemistry, in particular, the synthesis of organic compounds such as natural products and polymeric materials. In this study, we have used a Mizoroki,Heck reaction for site-specific carbon,carbon bond formation in the Ras protein. This was performed by the following two steps: 1) the His6 -fused Ras protein containing 4-iodo- L -phenylalanine at position 32 (iF32-Ras-His) was prepared by genetic engineering and 2) the aryl iodide group on the iF32-Ras-His was coupled with vinylated biotin in the presence of a palladium catalyst. The biotinylation was confirmed by Western blotting and liquid chromatography,mass spectrometry (LC-MS). The regioselectivity of the Mizoroki,Heck reaction was furthermore confirmed by LC-MS/MS analysis. However, in addition to the biotinylated product (bF32-Ras-His), a dehalogenated product (F32-Ras-His) was detected by LC-MS/MS. This dehalogenation resulted from the undesired termination of the Mizoroki,Heck reaction due to steric and electrostatic hindrance around residue 32. The biotinylated Ras showed binding activity for the Ras-binding domain as its downstream target, Raf-1, with no sign of decomposition. This study is the first report of an application of organometallic chemistry in protein chemistry. [source]


Identification of Modified Proteins by Mass Spectrometry

IUBMB LIFE, Issue 2 2002
Albert Sickmann
Abstract Because it is obvious that high-throughput genomics do not lead to a molecular description or even a prediction of protein function, modern techniques for protein analysis become increasingly more important. Sequence analysis of proteins and peptides is not limited to the elucidation of the primary structure of a protein. The analysis of posttranslational modifications is an important task of protein chemistry in proteome research. Increased sensitivity in mass spectrometry as a result of more efficient ionization techniques and better detection systems has allowed the stepwise reduction of protein quantity for analysis. Protein spots of 2D-PAGE separated samples are now sufficient for an unequivocal identification of a protein by mass spectrometry. In addition to protein identification, a closer look at posttranslational modifications is now also possible. It is assumed that modifications such as phosphorylation or glycosylation exist on every second protein and that they are important for the protein function. [source]


From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics.

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2009
Part II 198
Abstract This is the continuation of a personal retrospective on the developments that since 1965 have given shape to Mass Spectrometry (MS) and taken it from a position of simply playing a role in Protein Chemistry to becoming an indispensable tool in Proteomics, all within a 40-year span. Part I covered the period from 1965 to 1984. This second part reviews the Mass Spectrometry timeline of events from 1985 to 2000, stopping at various time points where MS made significant contributions to protein chemistry or where the development of new instrumentation for MS represented a major advance for peptide and protein work. Major highlights in the field and their significance for peptide and protein characterization such as the advent and practical consequences of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are covered, including work done with triple quads, the development of time-of-flight (TOF) instruments and new ion traps and going on to the more recent work on the full characterization of the Proteome with ion traps, TOF instruments and new ionization and tagging techniques for protein sequencing. Copyright 2009 John Wiley & Sons, Ltd. [source]


Detection and characterization of variant and modified structures of proteins in blood and tissues by mass spectrometry

MASS SPECTROMETRY REVIEWS, Issue 5 2006
Akira Shimizu
Abstract Some variant proteins cause diseases, and some diseases result in increases of proteins with abnormally modified structures. The detection, characterization, and estimation of the relative amounts of protein variants and abnormally modified proteins are important for clinical diagnosis and for elucidation of the mechanisms of the pathogenesis of diseases. Analysis of the covalent structures of proteins using matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography-electrospray ionization MS (LC-ESI-MS), which had been developed by the early 1990s, have largely replaced analyses by conventional protein chemistry. Here, we review the detection and characterization of hemoglobin variants, HbA1c measurement, detection of carbohydrate-deficient transferrin, and identification of variants of transthyretin (TTR) and Cu/Zn-superoxide dismutase (SOD-1) using soft ionization MS. We also propose the diagnostic application of the signals of modified forms of TTR, that is, S-sulfonated TTR and S-homocysteinyl TTR. The relative peak height ratio of the abnormal/normal components gives valuable information about the instability of variants and enables the detection of unstable Hb subunits or thalassemia heterozygotes. We found unique modified structures of TTR that suggested changes in amyloid fibrils. 2006 Wiley Periodicals, Inc. [source]


Molecular targets of botulinum toxin at the mammalian neuromuscular junction

MOVEMENT DISORDERS, Issue S8 2004
Dorothy D. Whelchel MS
Abstract The molecular targets of botulinum neurotoxins (BoNTs) are SNARE (soluble N -ethylmaleimide-sensitive factor- attachment protein- receptor) proteins necessary for neurotransmitter release. BoNT are powerful therapeutic agents in the treatment of numerous neurological disorders. The goals of this study were to (1) assess toxin diffusion by measuring substrate cleavage in adjacent and distant muscles, and (2) characterize the clinical course using SNARE protein chemistry. A small volume of BoNT/A was injected unilaterally into the mouse gastrocnemius muscle. Motor impairment was limited to the toxin-treated limb. No systemic illness or deaths occurred. At five time points, a subset of mice were killed, and muscles from both hindlimbs, and the diaphragm, were collected. Protein samples were examined for changes in SNAP-25 (synaptosomal-associated protein of Mr = 25 kDa) using immunochemistry. SNAP-25 cleavage product was noted in the toxin-treated limb as early as 1 day postinjection and continued through day 28. Onset and peak levels of substrate cleavage corresponded to the onset and peak clinical response. Cleavage was observed in adjacent and distant muscles, demonstrating that substrate cleavage is a sensitive indicator of toxin diffusion. Significant increases in full-length SNAP-25 and vesicle-associated membrane protein II were evident early in the impaired limb and continued through day 28. The increased SNARE protein most likely originates from nerve terminal sprouts. 2004 Movement Disorder Society [source]


Amino acids and glycine ethyl ester as new crystallization reagents for lysozyme

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010
Len Ito
Several amino acids and their derivatives are prominent additives in the field of protein chemistry. This study reports the use of charged amino acids and glycine ethyl ester as precipitants in protein crystallization, using hen egg-white lysozyme (HEWL) as a model. A discussion of the crystallization of HEWL using these reagents as precipitating agents is given. [source]


Expression, purification, and analysis of unknown translation factors from Escherichia coli: A synthesis approach

BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 1 2010
Justin D. Walter
Abstract New approaches are currently being developed to expose biochemistry and molecular biology undergraduates to a more interactive learning environment. Here, we propose a unique project-based laboratory module, which incorporates exposure to biophysical chemistry approaches to address problems in protein chemistry. Each of the experiments described herein contributes to the stepwise process of isolating, identifying, and analyzing a protein involved in a central biological process, prokaryotic translation. Students are provided with expression plasmids that harbor an unknown translation factor, and it is their charge to complete a series of experiments that will allow them to develop hypotheses for discovering the identity of their unknown (from a list of potential candidates). Subsequent to the identification of their unknown translation factor, a series of protein unfolding exercises are performed employing circular dichroism and fluorescence spectroscopies, allowing students to directly calculate thermodynamic parameters centered around determining the equilibrium constant for unfolding as a function of denaturant (temperature or chemical). The conclusion of this multi-part laboratory exercise consists of both oral and written presentations, emphasizing synthesis of the roles of each translation factor during the stepwise process of translation. [source]


Salt fractionation of plasma proteins: A procedure to teach principles of protein chemistry

BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 4 2003
A. C. C. Spadaro
Abstract A two-step laboratory exercise in biochemistry is proposed, comprising salt fractionation of plasma proteins and protein quantification. This exercise targets mainly undergraduate students, namely in the second year of Pharmacy, who are up to this point more used to deal with physical and chemical properties of micromolecules than macromolecules. The exercise requires simple equipment usually available in basic laboratories. Students work in small teams or alone depending on the laboratory conditions. Questions are proposed to check and reinforce the essential concepts involved as a preparation for detailed comprehension of protein chemistry. After salt fractionation, protein samples can be stored before quantification, allowing a two-period schedule for the laboratory work. Exercises as proposed here are very useful to guide students to a detailed analysis of fundamental aspects determining structure and physicochemical properties of proteins. [source]


Scalaradial, a Dialdehyde-Containing Marine Metabolite That Causes an Unexpected Noncovalent PLA2 Inactivation

CHEMBIOCHEM, Issue 13 2007
Maria Chiara Monti Dr.
Abstract Several marine terpenoids that contain at least one reactive aldehyde group, such as manoalide and its congeners, possess interesting anti-inflammatory activities that are mediated by the covalent inactivation of secretory phospholipase A2 (sPLA2). Scalaradial, a 1,4-dialdehyde marine terpenoid that was isolated from the sponge Cacospongia mollior, is endowed with a relevant anti-inflammatory profile, both in vitro and in vivo, through selective sPLA2 inhibition. Due to its peculiar dialdehyde structural feature, it has been proposed that scalaradial exerts its enzymatic inactivation by means of an irreversible covalent modification of its target. In the context of our on-going research on anti-PLA2 natural products and their interaction at a molecular level, we studied scalaradial in an attempt to shed more light on the molecular mechanism of its PLA2 inhibition. A detailed analysis of the reaction profile between scalaradial and bee venom PLA2, a model sPLA2 that shares a high structural homology with the human synovial enzyme, was performed by a combination of spectroscopic techniques, chemical reactions (selective modifications, biomimetic reactions), and classical protein chemistry (such as proteolytic digestion, HPLC and mass spectrometry), along with molecular modeling studies. Unexpectedly, our data clearly indicated the noncovalent forces to be the leading event in the PLA2 inactivation process; thus, the covalent modification of the enzyme emerges as only a minor side event in the ligand,enzyme interaction. The overall picture might be useful in the design of SLD analogues as new potential anti-inflammatory compounds that target sPLA2 enzymes. [source]


Regioselective Carbon,Carbon Bond Formation in Proteins with Palladium Catalysis; New Protein Chemistry by Organometallic Chemistry

CHEMBIOCHEM, Issue 1 2006
Koichiro Kodama
Abstract Palladium-catalyzed reactions have contributed to the advancement of many areas of organic chemistry, in particular, the synthesis of organic compounds such as natural products and polymeric materials. In this study, we have used a Mizoroki,Heck reaction for site-specific carbon,carbon bond formation in the Ras protein. This was performed by the following two steps: 1) the His6 -fused Ras protein containing 4-iodo- L -phenylalanine at position 32 (iF32-Ras-His) was prepared by genetic engineering and 2) the aryl iodide group on the iF32-Ras-His was coupled with vinylated biotin in the presence of a palladium catalyst. The biotinylation was confirmed by Western blotting and liquid chromatography,mass spectrometry (LC-MS). The regioselectivity of the Mizoroki,Heck reaction was furthermore confirmed by LC-MS/MS analysis. However, in addition to the biotinylated product (bF32-Ras-His), a dehalogenated product (F32-Ras-His) was detected by LC-MS/MS. This dehalogenation resulted from the undesired termination of the Mizoroki,Heck reaction due to steric and electrostatic hindrance around residue 32. The biotinylated Ras showed binding activity for the Ras-binding domain as its downstream target, Raf-1, with no sign of decomposition. This study is the first report of an application of organometallic chemistry in protein chemistry. [source]


Synthesis and Reactivity of 6,7-dihydrogeranylazides: Reagents for Primary Azide Incorporation into Peptides and Subsequent Staudinger Ligation

CHEMICAL BIOLOGY & DRUG DESIGN, Issue 2 2006
Juhua Xu
Protein farnesyltransferase (PFTase) catalyzes the attachment of a geranylazide moiety to a peptide substrate, N -dansyl-GCVIA. Because geranylazide is actually a mixture of isomeric, interconverting primary and secondary azides, incorporation of this isoprenoid into peptides can potentially result in a corresponding mixture of prenylated peptides. Here, we first examined the reactivity of geranyl azide in a model Staudinger reaction and determined that a mixture of products is formed. We then describe the synthesis of 6,7-dihydrogeranylazide diphosphate and demonstrate that this compound allows exclusive incorporation of a primary azide into a peptide. The resulting azide-containing peptide was derivatized with a triphenylphosphine-based reagent to generate an O -alkyl imidate-linked product. Finally, we show, using a series of model reactions, that the Staudinger ligation frequently produces small amounts of O -alkyl imidate products in addition to the major amide-linked products. Thus, the alkoxyimidates we have observed as the exclusive products in the reactions of peptides containing prenylated azides also appear to be a common type of product formed using other azide-containing reactants, although at greatly reduced levels. This method for chemical modification of the C-terminus of a protein should be useful for a variety of applications in protein chemistry. [source]