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Article ; Online: X-ray free electron lasers motivate bioanalytical characterization of protein nanocrystals: serial femtosecond crystallography.

Bogan, Michael J

2013 Volume 85, Issue 7, Page(s) 3464–3471

Abstract: Atomic resolution structures of large biomacromolecular complexes can now be recorded at room temperature from crystals with submicrometer dimensions using intense femtosecond pulses delivered by the world's largest and most powerful X-ray machine, a ... ...

Abstract	Atomic resolution structures of large biomacromolecular complexes can now be recorded at room temperature from crystals with submicrometer dimensions using intense femtosecond pulses delivered by the world's largest and most powerful X-ray machine, a laser called the Linac Coherent Light Source. Abundant opportunities exist for the bioanalytical sciences to help extend this revolutionary advance in structural biology to the ultimate goal of recording molecular-movies of noncrystalline biomacromolecules. This Feature will introduce the concept of serial femtosecond crystallography to the nonexpert, briefly review progress to date, and highlight some potential contributions from the analytical sciences.
MeSH term(s)	Animals ; Crystallography, X-Ray/instrumentation ; Crystallography, X-Ray/methods ; Equipment Design ; Humans ; Lasers ; Nanoparticles/chemistry ; Proteins/chemistry
Chemical Substances	Proteins
Language	English
Publishing date	2013-04-02
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac303716r
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Article: Preliminary investigation of electrodynamic charged droplet processing to couple capillary liquid chromatography with matrix-assisted laser desorption/ionization mass spectrometry.

Bogan, Michael J / Agnes, George R

Rapid communications in mass spectrometry : RCM

2004 Volume 18, Issue 22, Page(s) 2673–2681

Abstract: Charged droplet processing methodology, that utilizes electrodynamic levitation technology to control the trajectories of picoliter volume charged droplets and deliver them to a target plate at atmospheric pressure, has been developed. Termed wall-less ... ...

Abstract	Charged droplet processing methodology, that utilizes electrodynamic levitation technology to control the trajectories of picoliter volume charged droplets and deliver them to a target plate at atmospheric pressure, has been developed. Termed wall-less sample preparation (WaSP), this methodology offers several features that could prove beneficial to the preparation of sample spots from separation column effluents for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis. These features include solute pre-concentration factors of 10(1) to 10(3) due to volatile solvent evaporation prior to droplet deposition onto the target plate, high spatial accuracy of the deposition position of each processed droplet (+/-5 microm), and the ability to prepare sample spots as small as 20 microm in diameter from a single droplet. Here a new mode of operation of this methodology is described and used as an offline post-column pre-concentrating interface between capillary liquid chromatography (capLC) and a target plate for offline MALDI-MS. Using a fraction from the capLC separation of peptides produced by the proteolytic digestion of the protein cytidine 5'-triphosphate:phosphocholine cytidylyltransferase, MALDI sample spots were prepared using the dried-droplet method, direct piezoelectric droplet dispensing, and the processing of piezo-dispensed droplets by WaSP. The sample spot morphology was investigated using light microscopy, and peptide ion abundances produced by MALDI were measured using time-of-flight (TOF) MS. The advantages of developing an online capLC/WaSP interface with MALDI-MS in the future are discussed along with some of the challenges that may be encountered in such an endeavor.
MeSH term(s)	Choline-Phosphate Cytidylyltransferase/chemistry ; Chromatography, Micellar Electrokinetic Capillary/instrumentation ; Chromatography, Micellar Electrokinetic Capillary/methods ; Cytidine Triphosphate/chemistry ; Microchemistry/instrumentation ; Microchemistry/methods ; Peptides/analysis ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Chemical Substances	Peptides ; Cytidine Triphosphate (65-47-4) ; Choline-Phosphate Cytidylyltransferase (EC 2.7.7.15)
Language	English
Publishing date	2004
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	58731-x
ISSN	1097-0231 ; 0951-4198
ISSN (online)	1097-0231
ISSN	0951-4198
DOI	10.1002/rcm.1670
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Article: Wall-less sample preparation of microm-sized sample spots for femtomole detection limits of proteins from liquid based UV-MALDI matrices.

Bogan, Michael J / Agnes, George R

Journal of the American Society for Mass Spectrometry

2004 Volume 15, Issue 4, Page(s) 486–495

Abstract: Previously, we introduced wall-less sample preparation (WaSP), technology that involves the use of an electrodynamic balance (EDB) to prepare microm-sized sample spots for analysis by matrix-assisted laser desorption/ionization time-of-flight mass ... ...

Abstract	Previously, we introduced wall-less sample preparation (WaSP), technology that involves the use of an electrodynamic balance (EDB) to prepare microm-sized sample spots for analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In that work we demonstrated the detection of femtomole quantities of a low molecular weight peptide and a hydrophobic ester (both <600 Da). Here we use WaSP to test the hypothesis that the use of small sample spot sizes and an instrument equipped with delayed extraction would increase the analytical utility of liquid sample spots for peptide and protein (>2500 Da) analysis by UV-MALDI-TOF-MS (Sze et al.; J. Am. Soc. Mass Spectrom. 1998, 9, 166-174). To aid the optimization of preparing microm-sized sample spots by WaSP, optical microscopy and mass spectrometry were used to investigate nonvolatile solute concentration effects on droplet fission and sample spot size, modifications of the EDB electric field to control droplet ejection, and the use of multiple droplet deposition to increase sample loading. Also described is a rapid deposition mode of operation for WaSP that allows single droplets generated at 1 Hz to be levitated briefly ( approximately 500 ms) before being ejected autonomously and deposited as a concentrated sample spot with a spatial accuracy of +/-5 microm. To test the sensitivity of the method, one hundred glycerol droplets (270 pL each, 27 nL total) each containing 32 amol lysozyme were deposited on top of each other one-at-a-time to create a single sample spot. Using a mass spectrometer equipped with delayed extraction to analyze this sample spot, we verified the hypothesis of Sze et al. by achieving detection limits three orders of magnitude below that previously observed for the detection of a protein by UV-MALDI-TOF-MS with a chemical-doped liquid matrix sample preparation.
MeSH term(s)	Adrenocorticotropic Hormone/analysis ; Electrodes ; Equipment Design ; Microchemistry ; Muramidase/analysis ; Proteins/analysis ; Sensitivity and Specificity ; Specimen Handling ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Surface Tension ; Ultraviolet Rays
Chemical Substances	Proteins ; Adrenocorticotropic Hormone (9002-60-2) ; Muramidase (EC 3.2.1.17)
Language	English
Publishing date	2004-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1073671-2
ISSN	1044-0305
ISSN	1044-0305
DOI	10.1016/j.jasms.2003.11.012
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Article: Time-of-flight mass spectrometric analysis of ions produced from adjacent sample spots irradiated simultaneously by a single 337 nm laser.

Bogan, Michael J / Agnes, George R

Rapid communications in mass spectrometry : RCM

2003 Volume 17, Issue 22, Page(s) 2557–2562

MeSH term(s)	Angiotensin II/analysis ; Image Processing, Computer-Assisted ; Lasers ; Mass Spectrometry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Chemical Substances	Angiotensin II (11128-99-7)
Language	English
Publishing date	2003
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	58731-x
ISSN	1097-0231 ; 0951-4198
ISSN (online)	1097-0231
ISSN	0951-4198
DOI	10.1002/rcm.1215
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Article: MALDI-TOF-MS analysis of droplets prepared in an electrodynamic balance: "wall-less" sample preparation.

Bogan, Michael J / Agnes, George R

Analytical chemistry

2002 Volume 74, Issue 3, Page(s) 489–496

Abstract: Methodology enabling mass spectral analysis of the composition of droplet(s) prepared in an electrodynamic balance (EDB) by matrix-assisted laser desorption/ionization (MALDI) is described. The dc field surrounding the electrodynamic balance was ... ...

Abstract	Methodology enabling mass spectral analysis of the composition of droplet(s) prepared in an electrodynamic balance (EDB) by matrix-assisted laser desorption/ionization (MALDI) is described. The dc field surrounding the electrodynamic balance was manipulated to eject single droplets at a time from the EDB thereby causing their deposition onto a MALDI sample plate precoated with matrix. When the laser was directed onto the droplet(s) and held stationary, marked gains in the signal-to-noise and signal-to-background ratios were realized with each subsequent mass spectrum due to the suppression of matrix cluster ion formation. Optical microscopy of the plate, after 1024 laser shots were fired at eight droplets that had been deposited one on top of the other, revealed a residual island of droplet matter (area approximately 3.1 x 10(-9) m2) inside the region where the crystalline matrix had been ablated away within the laser spot (area approximately 1.6 x 10(-8) m2). Removing the predried crystalline matrix layer and, instead, adding matrix into the starting solution was found to be a more effective means of suppressing matrix cluster ion formation. The chemical composition of the droplet(s) prepared in the EDB is discussed with regard to sample preconcentration, the images of the laser spot after MALDI, matrix cluster ion suppression, and the possibility for improved quantitation and detection limits by MALDI-TOF-MS.
MeSH term(s)	Animals ; Chenodeoxycholic Acid/analysis ; Enkephalin, Leucine/analysis ; Equipment Design ; Humans ; Sensitivity and Specificity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Static Electricity
Chemical Substances	Chenodeoxycholic Acid (0GEI24LG0J) ; Enkephalin, Leucine (58822-25-6)
Language	English
Publishing date	2002-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac015638n
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Article: Poly(ethylene glycol) doubly and singly cationized by different alkali metal ions: relative cation affinities and cation-dependent resolution in a quadrupole ion trap mass spectrometer.

Bogan, Michael J / Agnes, George R

Journal of the American Society for Mass Spectrometry

2002 Volume 13, Issue 2, Page(s) 177–186

Abstract: Structural information of gas phase complexes of poly(ethylene glycol) (PEG) cationized by one or two different alkali metal ions is inferred from MS and MS/MS experiments performed with an electrospray quadrupole ion trap mass spectrometer. The ... ...

Abstract	Structural information of gas phase complexes of poly(ethylene glycol) (PEG) cationized by one or two different alkali metal ions is inferred from MS and MS/MS experiments performed with an electrospray quadrupole ion trap mass spectrometer. The rationale for selecting PEG was that its sites for cation binding are non-selective with respect to the repeating monomeric unit of the polymer, but there is selectivity with respect to the formation of an inner coordination sphere specific to each metal ion. The dissociation of [M1+ M2+ (EO23)], where EO23 = linear polymer of ethylene oxide, 23 units in length, resulted in loss of one of the alkali metal ions, with preference for loss of the larger cation, with no fragmentation of the PEG backbone for Na, K, Rb, and Cs. Li was not examined in this portion of the study. The selectivity for loss of the larger alkali metal ion was [Na+ K+ (EO23)] to [Na+ (EO23)] + K+ at 100%; [K+ Rb+ (EO23)] to [K+ (EO23)] + Rb+ at 93%; and [Rb+ Cs+ (EO23)] to [Rb+ (Eo23)] + Cs+ at 99%. The resolution of [M+ (EOx)] for x = 20-30 was dependent on the alkali metal ion, with the highest resolution observed for Cs+ and the lowest for Na+. These results are discussed with respect to the packing of the oxygen atoms on PEG (M.W.(avg) = 1000) around an alkali metal ion of different radius, and how this packing leads to an ensemble of unique structures, and therefore mobilities for [M+ (EOx)].
Language	English
Publishing date	2002-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1044-0305
ISSN	1044-0305
DOI	10.1016/S1044-0305(01)00350-6
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Article: Promotion of alpha-cyano-4-hydroxycinnamic acid and peptide cocrystallization within levitated droplets with net charge.

Bogan, Michael J / Bakhoum, Samuel F W / Agnes, George R

Journal of the American Society for Mass Spectrometry

2005 Volume 16, Issue 2, Page(s) 254–262

Abstract: Many reactions occur as a result of charge imbalance within or between reactive species in reaction vessels that have zero net charge. Here, chemical processes taking place within reaction vessels having net excess charge were studied. For mass ... ...

Abstract	Many reactions occur as a result of charge imbalance within or between reactive species in reaction vessels that have zero net charge. Here, chemical processes taking place within reaction vessels having net excess charge were studied. For mass spectroscopists, a familiar example of vessels that defy electroneutrality are the charged droplets produced by an electrospray ion source. Evidence is presented that control of the magnitude of the net charge contained in a reaction vessel, in this case a levitated droplet, can be used to promote nucleation and crystal growth of a mixture of an organic acid, alpha-cyano-4-hydroxycinnamic acid (CHCA), with one or more peptides. This phenomenon was first observed during our ongoing development of wall-less sample preparation (WaSP), electrodynamic charged droplet processing methodology capable of creating micrometer-sized sample spots for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) from subnanoliter volumes of sample material. Peptide ion signal-to-noise (S/N) ratios obtained by MALDI-TOF-MS from sample spots created from droplets that had high relative magnitude of net charge were consistently greater than those detected from sample spots created from droplets that had lower net charge. To study this unexpected phenomenon further, WaSP methodology was developed to process different mass-to-charge (m/z) droplets levitated in an electrodynamic balance (EDB), facilitating their deposition onto different positions of a target to create arrays of droplet residues ordered from highest to lowest m/z. This capability allowed simultaneous levitation with subsequent separation of a population of droplets created from a single starting solution, but the droplets had varied magnitudes of net charge. After the droplets were ejected from the EDB and collected on a glass slide or MALDI plate, the solids contained in the deposited droplets were characterized using microscopy and MALDI-TOF-MS. Factors impacting the chemical processing in droplets having net excess charge levitated in an EDB are discussed with particular emphasis on their possible roles in the promotion of crystal nucleation and growth.
MeSH term(s)	Coumaric Acids/chemistry ; Crystallization ; Microchemistry ; Peptides/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Static Electricity
Chemical Substances	Coumaric Acids ; Peptides ; alpha-cyano-4-hydroxycinnamate (28166-41-8)
Language	English
Publishing date	2005-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1073671-2
ISSN	1044-0305
ISSN	1044-0305
DOI	10.1016/j.jasms.2004.11.006
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Zs.MO 241: Show issues

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Article: Archiving and absolute quantitation of solutes separated by single charged droplet coulomb explosion.

Bakhoum, Samuel F W / Bogan, Michael J / Agnes, George R

Analytical chemistry

2005 Volume 77, Issue 11, Page(s) 3461–3465

Abstract: The electrospray (ES) ion source relies on the transfer of low-volatility solutes to the gas phase as an outcome of coulomb explosion events of charged droplets generated by electrical atomization. Introduced here are two methods for archiving compounds ... ...

Abstract	The electrospray (ES) ion source relies on the transfer of low-volatility solutes to the gas phase as an outcome of coulomb explosion events of charged droplets generated by electrical atomization. Introduced here are two methods for archiving compounds separated by coulomb explosion of single droplets having net charge that had been levitated in an electrodynamic balance. We categorized compounds separated by the explosion as either material ejected, including progeny droplets, or the material retained in the main residue. The potential for this methodology is illustrated by (i) qualitative characterization of solute states, aqueous versus precipitated in the separated material, and (ii) absolute quantitation of solutes separated by such an event. For a droplet containing 5 x 10(7) 20-nm-diameter fluospheres, its first encountered coulomb explosion event resulted in the ejection of 1.70% of them. The capability to acquire such detailed information regarding the individual steps in the process of transferring low-volatility solutes to the gas phase in an ES ion source is essential to develop strategies for absolute quantitation in applications of ES mass spectrometry.
Language	English
Publishing date	2005-06-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac048113e
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Article ; Online: How Cubic Can Ice Be?

Amaya, Andrew J / Pathak, Harshad / Modak, Viraj P / Laksmono, Hartawan / Loh, N Duane / Sellberg, Jonas A / Sierra, Raymond G / McQueen, Trevor A / Hayes, Matt J / Williams, Garth J / Messerschmidt, Marc / Boutet, Sébastien / Bogan, Michael J / Nilsson, Anders / Stan, Claudiu A / Wyslouzil, Barbara E

The journal of physical chemistry letters

2017 Volume 8, Issue 14, Page(s) 3216–3222

Abstract: Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r ≈ 10 nm) at ∼225 K. The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice ... ...

Abstract	Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r ≈ 10 nm) at ∼225 K. The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 μs of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, χ, in the range of 0.78 ± 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. The high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a ∼1 μs time scale in single nanodroplets.
Language	English
Publishing date	2017-07-20
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.7b01142
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Article: Interdomain and membrane interactions of CTP:phosphocholine cytidylyltransferase revealed via limited proteolysis and mass spectrometry.

Bogan, Michael J / Agnes, George R / Pio, Frederic / Cornell, Rosemary B

The Journal of biological chemistry

2005 Volume 280, Issue 20, Page(s) 19613–19624

Abstract: CTP:phosphocholine cytidylyltransferase (CCT) is a multi-domain enzyme that regulates phosphatidylcholine synthesis. It converts to an active form upon binding cell membranes, and interdomain dissociations have been hypothesized to accompany this process. ...

Abstract	CTP:phosphocholine cytidylyltransferase (CCT) is a multi-domain enzyme that regulates phosphatidylcholine synthesis. It converts to an active form upon binding cell membranes, and interdomain dissociations have been hypothesized to accompany this process. To identify these interdomain and membrane interactions, the tertiary structures of three forms of CCTalpha were probed by monitoring accessibility to proteases. Time-limited digestion with chymotrypsin or arginine C of soluble CCTalpha (CCT(sol)), phospholipid vesicle-bound CCT (CCT(mem)), and a soluble constitutively active CCT truncated at amino acid 236 generated complex mixtures of peptides that were resolved and identified by gel electrophoresis/immunoblotting and by matrix-assisted laser desorption/ionization-mass spectrometry, with or without coupling to capillary liquid chromatography. Identification of cleavage sites enabled assembly of peptide bond accessibility maps for each CCT form. Our results reveal a approximately 80-residue core within the catalytic domain (domain C) as the most inaccessible region in all three forms and the C-terminal phosphorylation domain as the most accessible. Membrane binding has little effect on the protease accessibility of these domains. To map the protease sites onto the catalytic domain, its three-dimensional structure was modeled from the atomic coordinates of glycerol-phosphate cytidylyltransferase (Protein Data Bank code 1COZ). The protease inaccessibility of most sites in domain C could be explained by burial or location within secondary structural elements. The accessibility of the N-terminal domain (domain N) was enhanced upon membrane binding. Residues Phe(234)-Leu(303) were inaccessible in CCT(mem), suggesting burial in the membrane. Surprisingly, residues Leu(274)-Leu(303) of this domain were also inaccessible in CCT(sol). We propose that this region is buried by interdomain contacts with domain N in CCT(sol). Membrane binding and burial of domain M in the lipid bilayer may disrupt this interaction, leading to increased exposure of sites in domain N.
MeSH term(s)	Amino Acid Sequence ; Animals ; Catalytic Domain ; Choline-Phosphate Cytidylyltransferase/chemistry ; Choline-Phosphate Cytidylyltransferase/genetics ; Chymotrypsin ; Electrophoresis, Polyacrylamide Gel ; In Vitro Techniques ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/chemistry ; Peptide Fragments/genetics ; Peptide Fragments/isolation & purification ; Peptide Mapping ; Phosphorylation ; Protein Structure, Tertiary ; Rats ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	Peptide Fragments ; Recombinant Proteins ; Choline-Phosphate Cytidylyltransferase (EC 2.7.7.15) ; Chymotrypsin (EC 3.4.21.1)
Language	English
Publishing date	2005-02-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M414028200
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