The Chemistry of Carbodiimides.

Khorana, H. G.

doi:10.1021/cr60165a001

Cited by 472 publications

(189 citation statements)

References 51 publications

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“…Carbodiimide chemistry was used to condense solvent exposed primary amine lysine residues on CPMV-T184C with carboxylated IO [26]. To a solution of IO in PBS buffer (pH ¼ 7.5), 50 mM EDC (1-ethyl3-(3-dimethylaminopropyl)carbodiimide hydrochloride) was added to form a highly reactive O-acylisourea intermediate for 15 min, followed by 15 min ester formation with 5 mM sulfo-NHS (N-hydroxysulfosuccinimide) to extend the half life of the carboxylate to hours [27].…”

Section: Methodsmentioning

confidence: 99%

Synthesis and Characterization of Iron Oxide Derivatized Mutant Cowpea Mosaic Virus Hybrid Nanoparticles

et al. 2008

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A novel nanoparticle hybrid is attained by the covalent attachment of iron oxide (γ‐Fe2O3) nanoclusters onto the surface of a mutagenized cow pea mosaic virus (CPMV‐T184C). Using a stepwise substrate‐based integration, monodisperse CPMV‐IO hybrids are anchored on a gold substrate. The physical and magnetic properties of individual CPMV‐IO hybrids are qualitatively investigated by atomic/magnetic force microscopy (AFM/ MFM). During MFM characterization a ‘boundary‐effect’ is observed at the CPMV/IO interface.

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Section: Methodsmentioning

confidence: 99%

Synthesis and Characterization of Iron Oxide Derivatized Mutant Cowpea Mosaic Virus Hybrid Nanoparticles

et al. 2008

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“…Assuming a high pK a value for VDAC as well, VDAC is partially protonated in solution at the pH used here (6.8). Furthermore, the reaction with DCCD requires the presence of carboxylate (41), indirectly proving the existence of a (partial) charge in solution. DCCD inhibits the channel activity of VDAC1 in a voltagedependent manner, requiring incubation at high negative or positive potentials.…”

Section: μS-ms Dynamics Are Significantly Increased For the N-terminamentioning

confidence: 99%

Functional dynamics in the voltage-dependent anion channel

Villinger

Briones

Giller

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

105

129

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The voltage-dependent anion channel (VDAC), located in the outer mitochondrial membrane, acts as a gatekeeper for the entry and exit of mitochondrial metabolites. Here we reveal functional dynamics of isoform one of VDAC (VDAC1) by a combination of solution NMR spectroscopy, Gaussian network model analysis, and molecular dynamics simulation. Micro-to millisecond dynamics are significantly increased for the N-terminal six β-strands of VDAC1 in micellar solution, in agreement with increased B-factors observed in the same region in the bicellar crystal structure of VDAC1. Molecular dynamics simulations reveal that a charge on the membrane-facing glutamic acid 73 (E73) accounts for the elevation of N-terminal protein dynamics as well as a thinning of the nearby membrane. Mutation or chemical modification of E73 strongly reduces the micro-to millisecond dynamics in solution. Because E73 is necessary for hexokinase-I-induced VDAC channel closure and inhibition of apoptosis, our results imply that microto millisecond dynamics in the N-terminal part of the barrel are essential for VDAC interaction and gating.membrane protein | molecular dynamics | NMR spectroscopy | protein-lipid interactions | structure D ynamics of proteins provide the essential link between structure and function. Membrane protein dynamics are gaining more attention due to an increasing number of high-resolution structures. A versatile experimental method for the study of membrane protein dynamics is NMR spectroscopy, providing atomic resolution information from nanoseconds to seconds (for an overview see ref. 1). In addition, when a three-dimensional structure is available, insight into fast dynamics of proteins, which occur on the nanosecond time scale, might be gained from molecular dynamics (MD) simulation and elastic network models (2, 3).NMR studies have revealed large conformational changes essential for the physiological function of α-helical membrane proteins, such as the interaction of phospholamban with effectors modulating heart muscle contractility (4, 5) and antimicrobial peptides adopting different conformations in membranes or solution (6, 7). Less well characterized are motions of outer membrane β-barrels. A pioneering solution NMR study revealed μs-ms interconversion of the catalytic loop of PagP between an excited and a nonexcited state, enabling both ligand binding and enzymatic catalysis (8). Nonenzymatic β-barrel channels exhibit more general dynamic features, such as loop flexibility and slow conformational exchange towards the extracellular barrel edges, altogether indicating relevance for substrate conductance and gating (9-11).The voltage-dependent anion channel (VDAC) is one of the few β-barrel membrane proteins, the structure of which has been determined to date (12-14). Serving as the major pass-through for metabolites between mitochondria and the cytosol (15), the highly abundant channel is regarded as a key regulator of cellular energy metabolism (16). Metabolite flow is regulated by a voltage-dependent conformational c...

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“…Chemical Modification of cSBL 14) The pH of the reaction mixture consisting of cSBL (0.25 mg/ml) and a nucleophile (0.6 M) was adjusted to 5.0 by the addition of 1 M NaOH, then 40 mM EDC (final concentration) was added to the reaction mixture with stirring. The reaction was performed at room temperature for 30-120 min.…”

Section: )mentioning

confidence: 99%

Effect of Modification of the Carboxyl Groups of the Sialic Acid Binding Lectin from Bullfrog (Rana catesbeiana) Oocyte on Anti-tumor Activity.

Iwama

Ogawa

Sasaki

et al. 2001

Biological & Pharmaceutical Bulletin

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The sialic acid binding lectin from Rana catesbeiana oocyte (cSBL) is known to have anti-tumor activity.2) cSBL is a multifunctional protein which has pyrimidine base specific ribonuclease activity. 3,4) In respect to RNase, cSBL belongs to the RNase A family, and is a very heat stable enzyme. It remained 100% active after heating at 100°C. 3,5) Four RNases belonging to the RNase A family have been isolated from Rana family frogs to date. Their primary structures are shown in Fig. 1. They have anti-tumor activity, except for that from bullfrog liver. 11)They are a simple protein and constituted from 104 to 111 amino acid residues. The anti-tumor activity of one of them, onconase, obtained from Rana pipiens, has been studied in detail, and is on its way to application as an anti-tumor drug, now in phase III clinical trials. 12,13) On the other hand, the anti-tumor activity of cSBL has been reported by Nitta et al.2) Although the mechanism of the anti-tumor activity of cSBL is not fully elucidated to date, the first step of the action was different from that of onconase. That is, the interaction of cSBL with sialoglycoprotein on the surface of tumor cells is thought to be essential for cSBL action. The interaction enhances the internalization of cSBL into the tumor cells. However, in contrast to cSBL, for onconase, the contribution of sialic acid to the action has not been identified to date.Nitta et al. showed that the chemical modification of cSBL with a water-soluble carbodiimide (EDC) in the presence of glycine methylester increased the anti-tumor activity. The The sialic acid binding lectin from bullfrog Rana catesbeiana oocyte (cSBL) is known to have anti-tumor activity. In order to investigate the relationship between the net charge of cSBL and its anti-tumor effect, cSBL was modified with a water-soluble carbodiimide (EDC) in the presence of three kinds of nucleophiles, taurine, glycine methylester and ethylenediamine. cSBL having four carboxyl groups was partially modified (ca. 2 residues). The anti-tumor activity of modified cSBLs was in the order of ethylenediamine-modified cSBLϾglycine methylestermodified cSBLϾtaurine modified cSBLмnative cSBL. The results suggested that anti-tumor activity seems to increase with the increase in positive net charge, possibly enhancing the interaction of cSBL with sialoglycoprotein on the surface of tumor cells. The ribonuclease activity of ethylenediamine-modified cSBL decreased with the progress of the reaction, but the number of internalized molecules in the tumor cell increased. Thus, for antitumor activity, a higher incorporation of cSBL with reasonable RNase activity seems to be more important than total RNase activity.

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The Chemistry of Carbodiimides.

Cited by 472 publications

References 51 publications

Synthesis and Characterization of Iron Oxide Derivatized Mutant Cowpea Mosaic Virus Hybrid Nanoparticles

Synthesis and Characterization of Iron Oxide Derivatized Mutant Cowpea Mosaic Virus Hybrid Nanoparticles

Functional dynamics in the voltage-dependent anion channel

Effect of Modification of the Carboxyl Groups of the Sialic Acid Binding Lectin from Bullfrog (Rana catesbeiana) Oocyte on Anti-tumor Activity.

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