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Magdalena Zofia Wiloch, Urszula Elżbieta Wawrzyniak, Iwona Ufnalska, Grzegorz Piotrowski, Arkadiusz Bonna, Wojciech Wróblewski
The influence of cation-π interactions on the electrochemical properties of copper(II) complexes with synthesized pentapeptide C-terminal fragment of Atrial Natriuretic Factor (ANF) hormone was studied in this work. Molecular modeling performed for Cu(II)-NSFRY-NH2 complex indicated that the cation-π interactions between Tyr and Cu(II), and also between Phe-Arg led to specific conformation defined as peptide box, in which the metal cation is isolated from the solvent by peptide ligand. Voltammetry experiments enabled to compare the redox properties and stability of copper(II) complexes with NSFRY-NH2 and its analogues (namely: NSFRA-NH2, NSFRF-NH2, NSAAY-NH2, NSAAA-NH2, AAAAA-NH2) as well as to evaluate the contribution of individual amino acid residues to these properties...
2016: PloS One
Mi Ni Huang, John R McPherson, Ioana Cutcutache, Bin Tean Teh, Patrick Tan, Steven G Rozen
Microsatellite instability (MSI) is a form of hypermutation that occurs in some tumors due to defects in cellular DNA mismatch repair. MSI is characterized by frequent somatic mutations (i.e., cancer-specific mutations) that change the length of simple repeats (e.g., AAAAA…., GATAGATAGATA...). Clinical MSI tests evaluate the lengths of a handful of simple repeat sites, while next-generation sequencing can assay many more sites and offers a much more complete view of their somatic mutation frequencies. Using somatic mutation data from the exomes of a 361-tumor training set, we developed classifiers to determine MSI status based on four machine-learning frameworks...
2015: Scientific Reports
Moshe C Silverstein, Kübra Bilici, Steven W Morgan, Yunjie Wang, Yanhang Zhang, Gregory S Boutis
Elastin, the principal component of the elastic fiber of the extracellular matrix, imparts to vertebrate tissues remarkable resilience and longevity. This work focuses on elucidating dynamical and structural modifications of porcine aortic elastin exposed to glucose by solid-state NMR spectroscopic and relaxation methodologies. Results from macroscopic stress-strain tests are also presented and indicate that glucose-treated elastin is mechanically stiffer than the same tissue without glucose treatment. These measurements show a large hysteresis in the stress-strain behavior of glucose-treated elastin-a well-known signature of viscoelasticity...
April 7, 2015: Biophysical Journal
Eriko Nagaoka, Ryota Hidese, Tadayuki Imanaka, Shinsuke Fujiwara
Thermococcus kodakarensis, which grows optimally at 85°C, expresses cold stress-inducible DEAD box RNA helicase (Tk-deaD) when shifted to 60°C. A DDA1 deletion (ΔTk-deaD) mutant exhibited decreased cell growth, and cells underwent lysis at 60°C in nutrient broth in the absence of elemental sulfur. In contrast, cells in medium containing elemental sulfur at 60°C did not undergo lysis, suggesting that Tk-deaD is necessary for cell growth in sulfur-free medium. To identify the element responsible for the cold response, a pTKR expression probe plasmid was constructed using thermostable catalase from Pyrobaculum calidifontis as a reporter...
August 2013: Journal of Bacteriology
Sylvère Durand, Maximiliano Rossa, Oscar Hernandez, Béla Paizs, Philippe Maître
The structure of peptide fragments was studied using "action" IR spectroscopy. We report on room temperature IR spectra of b4 fragments of protonated GGGGG, AAAAA, and YGGFL in the X-H (X = C, N, O) stretching region. Experiments were performed with a tandem mass spectrometer combined with a table top tunable laser, and the multiple photon absorption process was assisted using an auxiliary high-power CO2 laser. These experiments provided well-resolved spectra with relatively narrow peaks in the X-H (X = C, N, O) stretching region for the b4 fragments of protonated GGGGG, AAAAA, and YGGFL...
March 28, 2013: Journal of Physical Chemistry. A
Mohamed F Ali, Vishwanath B Chachadi, Armen Petrosyan, Pi-Wan Cheng
Core 2 N-acetylglucosaminyltransferase 1 (C2GnT1) is a key enzyme participating in the synthesis of core 2-associated sialyl Lewis x (C2-O-sLe(x)), a ligand involved in selectin-mediated leukocyte trafficking and cancer metastasis. To accomplish that, C2GnT1 needs to be localized to the Golgi and this step requires interaction of its cytoplasmic tail (CT) with a protein that has not been identified. Employing C2GnT1 CT as the bait to perform a yeast two-hybrid screen, we have identified Golgi phosphoprotein 3 (GOLPH3) as a principal candidate protein that interacts with C2GnT1 and demonstrated that C2GnT1 binds to GOLPH3 via the LLRRR(9) sequence in the CT...
November 16, 2012: Journal of Biological Chemistry
Alexis Taylor, Victoria E J Berryman, Russell J Boyd
A computational investigation of the electronic properties of an experimentally prepared ADADA helix indicates that the helix is held together with four strong hydrogen bonds as well as many other weak interactions. Determination of the electronic energy changes, as well as thermodynamic parameters, suggests that helix formation is a favorable process, driven by the formation of the hydrogen bonds. For instance, the unsubstituted helix has an electronic binding energy of -85.8 kJ/mol. Furthermore, the strength of binding can be tuned to some extent by the careful selection of substituents...
August 2, 2012: Journal of Physical Chemistry. A
Michael C Owen, Bela Viskolcz, Imre G Csizmadia
In order to elucidate the mechanisms of radical-initiated unfolding of a helix, the thermodynamic functions of hydrogen abstraction from the C(α), C(β), and amide nitrogen of Ala(3) in a homopeptapeptide (N-Ac-AAAAA-NH(2); A5) by HO(•), HO(2)(•), and O(2)(-•) were computed using the B3LYP density functional. The thermodynamic functions, standard enthalpy (ΔH(o)), Gibbs free energy (ΔG(o)), and entropy (ΔS(o)), of the reactants and products of these reactions were computed with A5 in the 3(10)-helical (A5(Hel)) and fully extended (A5(Ext)) conformations at the B3LYP/6-31G(d) and B3LYP/6-311+G(d,p) levels of theory, both in the gas phase and using the C-PCM implicit water model...
June 23, 2011: Journal of Physical Chemistry. B
Yue-Fen Cao, Xi-Wu Zhu, Yu Xiang, De-Qiang Li, Jia-Rong Yang, Qian-Zhuo Mao, Ji-Shuang Chen
Four novel double-stranded RNA segments were detected in a Verticillium dahliae Kleb. strain (V. dahliae isolate 0-21), a causal fungal agent of Verticillium wilt disease of cotton. Each dsRNA genome segment contains a single large open reading frame (ORF) that encodes a distinctive protein with modest levels of sequence similarities to the corresponding putative proteins in the genus Chrysovirus. These include an RNA-dependent RNA polymerase (RdRp), a coat protein, an undefined replication-related protein and an ovarian tumor domain peptidase...
July 2011: Virus Research
Bhavya Sharma, Sanford A Asher
We measured the UV resonance Raman excitation profiles and Raman depolarization ratios of the arginine (Arg) vibrations of the amino acid monomer as well as Arg in the 21-residue predominantly alanine peptide AAAAA(AAARA)(3)A (AP) between 194 and 218 nm. Excitation within the π → π* peptide bond electronic transitions result in UVRR spectra dominated by amide peptide bond vibrations. The Raman cross sections and excitation profiles indicate that the Arg side chain electronic transitions mix with the AP peptide bond electronic transitions...
May 12, 2011: Journal of Physical Chemistry. B
Rebecca A Hunt, Manoj Munde, Arvind Kumar, Mohamed A Ismail, Abdelbasset A Farahat, Reem K Arafa, Martial Say, Adalgisa Batista-Parra, Denise Tevis, David W Boykin, W David Wilson
Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and ATATA. The AAAAA and AAATT sequences have the largest intrinsic bend, whereas the TTTAA and ATATA sequences are relatively straight...
May 2011: Nucleic Acids Research
Benjamin J Bythell, Philippe Maître, Béla Paizs
a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory...
October 27, 2010: Journal of the American Chemical Society
Ming Hwa Wong, Lei Meng, Rajamuthiah Rajmohan, Shangjuan Yu, Thirumaran Thanabalu
Vrp1p (yeast WIP) forms a protein complex with Las17p (yeast WASP), however the physiological significance of the interaction has not been fully characterized. Vrp1p residues, (788)MPKPR(792) are essential for Vrp1p-Las17p interaction. While C-Vrp1p(364-817) complements all the defects of the vrp1Δ strain, C-Vrp1p(364-817)(5A) ((788)AAAAA(792)) does not complement any of the defects, due to its inability to localize to cortical patches. Targeting C-Vrp1p(364-817)(5A) to membranes using CAAX motif (C-Vrp1p(364-817)(5A)-CAAX) rescued the growth and endocytosis defect but not the actin patch polarization defect of vrp1Δ...
December 2010: Biochimica et Biophysica Acta
Kan Xiong, Sanford A Asher
We used CD and UV resonance Raman spectroscopy to study the impact of alcohols on the conformational equilibria and relative Gibbs free energy landscapes along the Ramachandran Psi-coordinate of a mainly poly-Ala peptide, AP with an AAAAA(AAARA)(3)A sequence. 2,2,2-Trifluoroethanol (TFE) most stabilizes the alpha-helix-like conformations, followed by ethanol, methanol, and pure water. The pi-bulge conformation is stabilized more than the alpha-helix, while the 3(10)-helix is destabilized due to the alcohol-increased hydrophobicity...
April 20, 2010: Biochemistry
Kan Xiong, Eliana K Asciutto, Jeffry D Madura, Sanford A Asher
We used CD, UV resonance Raman spectroscopy, and molecular dynamics simulation to examine the impact of salts on the conformational equilibria and the Ramachandran Psi angle (un)folding Gibbs free energy landscape coordinate of a mainly polyalanine alpha-helical peptide, AP of sequence AAAAA(AAARA)(3)A. NaClO(4) stabilizes alpha-helical-like conformations more than does NaCl, which stabilizes more than Na(2)SO(4) at identical ionic strengths. This alpha-helix stabilization ordering is the reverse of the Hofmeister series of anions in their ability to disorder water hydrogen bonding...
November 17, 2009: Biochemistry
Lori A Bastian
No abstract text is available yet for this article.
February 2009: Journal of General Internal Medicine
Bhavya Sharma, Sergei V Bykov, Sanford A Asher
UV resonance Raman (UVRR) excitation profiles and Raman depolarization ratios were measured for a 21-residue predominantly alanine peptide, AAAAA(AAARA) 3A (AP), excited between 194 and 218 nm. Excitation within the pi-->pi* electronic transitions of the amide group results in UVRR spectra dominated by amide vibrations. The Raman cross sections and excitation profiles provide information about the nature of the electronic transitions of the alpha-helix and polyproline II (PPII)-like peptide conformations...
September 18, 2008: Journal of Physical Chemistry. B
Gunhild M Mueller, Ossama B Kashlan, James B Bruns, Ahmad B Maarouf, Meir Aridor, Thomas R Kleyman, Rebecca P Hughey
Epithelial sodium channels (ENaCs) are assembled in the endoplasmic reticulum (ER) from alpha, beta, and gamma subunits, each with two transmembrane domains, a large extracellular loop, and cytoplasmic amino and carboxyl termini. ENaC maturation involves transit through the Golgi complex where Asn-linked glycans are processed to complex type and the channel is activated by furin-dependent cleavage of the alpha and gamma subunits. To identify signals in ENaC for ER retention/retrieval or ER exit/release, chimera were prepared with the interleukin alpha subunit (Tac) and each of the three cytoplasmic carboxyl termini of mouse ENaC (Tac-Ct) or with gamma-glutamyltranspeptidase and each of the three cytoplasmic amino termini (Nt-GGT)...
November 16, 2007: Journal of Biological Chemistry
Mark S Tichenor, John D Trzupek, David B Kastrinsky, Futoshi Shiga, Inkyu Hwang, Dale L Boger
Complementary to studies that provided the first yatakemycin total synthesis resulting in its structure revision and absolute stereochemistry assignment, a second-generation asymmetric total synthesis is disclosed herein. Since the individual yatakemycin subunits are identical to those of duocarmycin SA (alkylation subunit) or CC-1065 (central and right-hand subunits), the studies also provide an improvement in our earlier total synthesis of CC-1065 and, as detailed herein, have been extended to an asymmetric total synthesis of (+)-duocarmycin SA...
December 13, 2006: Journal of the American Chemical Society
James L Toth, John D Trzupek, Lloyd V Flores, Konstantinos Kiakos, John A Hartley, William T Pennington, Moses Lee
The design, synthesis and DNA binding properties of a novel achiral and amino-containing seco-cyclopropylindoline analog (seco-amino-CI-TMI, 1) of the duocarmycins are described. Thermal induced DNA cleavage studies on pUC18 DNA revealed compound 1 to preferentially bind in the minor groove and to covalently react with AT-rich sequences, particularly at the underlined adenine-N3 group of 5'-AAAAA(865)-3'. This sequence specificity is similar to adozelesin and CC-1065. Using a 4-day continuous exposure, compound 1 inhibited the growth of K562 human chronic myeloid leukemia cells in culture...
January 2005: Medicinal Chemistry
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