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Gabor Pohl, Amparo Asensio, J J Dannenberg
We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand...
February 4, 2014: Biochemistry
Hoang-Tang, G H Liang
The genomic relationship between cultivated sorghum [Sorghum bicolar (L.) Moench, race bicolor, De Wet, 2n=20] and Johnsongrass [S. halepense (L.) Pers., 2n=40] has been a subject of extensive studies. Nevertheless, there is no general consensus concerning the ploidy level and the number of genomes present in the two species. This research tested the validity of four major genomic models that have been proposed previously for the two species by studying chromosome behaviors in the parental species, 30-chromosome hybrids [sorghum, (2n=20) x Johnsongrass, (2n=40)], 40-chromosome hybrids [sorghum, (2n=40) x Johnsongrass, (2n=40)] and 60-chromosome amphiploids...
August 1988: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
O I Obolensky, Wells W Wu, Rong-Fong Shen, Yi-Kuo Yu
RATIONALE: The hypothesis that dissociation energies can serve as a predictor of observability of b- and y-peaks is tested for seven hexapeptides. If the hypothesis holds true for large classes of peptides, one would be able to improve the scoring accuracy of peptide identification tools by excluding theoretical peaks that cannot be observed in practical product ion spectra due to various physical, chemical or thermodynamic considerations. METHODS: Product ion m/z spectra of hexapeptides AAAAAA, AAAFAA, AAAVAA, AAFAAA, AAVAAA, AAFFAA and AAVVAA have been acquired on a Finnigan LTQ XL mass spectrometer in the collision-induced dissociation (CID) activation mode on a grid of activation times 0...
January 15, 2013: Rapid Communications in Mass Spectrometry: RCM
Joshua A Plumley, J J Dannenberg
We present ONIOM calculations using B3LYP/d95(d,p) as the high and AM1 as the low level on parallel β-sheets containing from two to ten strands of Ac-VQIVYK-NHMe and Ac-VQIINK-NHMe, as well as both parallel and antiparallel Ac-AAAAAA-NHMe. We find that the first two sequences form more stable sheets due to the additional H-bonding between the Q's in the side chains of both and the N's in the side chain of Ac-VQIINK-NHMe. However, the H-bonds in the amyloid chains are significantly weakened by attractive strain, which prevents all the interstrand H-bonds from achieving their optimal geometries simultaneously and requires high distortion energies for the individual strands in the sheets...
September 8, 2011: Journal of Physical Chemistry. B
Keita Kamijo, Yuji Takeda
The relationship between physical activity levels and executive control functioning was examined in 40 young adults (mean age = 21.4 yrs; 19 females) who were grouped on the basis of their regular physical activity level. Participants performed a task switching paradigm with two conditions. The pure task condition required repeated performance on a single task (e.g., AAAAAA...); the mixed-task condition required participants to change rapidly between different tasks (e.g., AABBAA...). The mixed-task condition created greater executive control requirements due to working memory demands for the maintenance of multiple task sets in memory (compared to the pure task; i...
March 2010: International Journal of Psychophysiology
Jing Li, Edvards Liepinsh, Andreas Almlén, Johan Thyberg, Tore Curstedt, Hans Jörnvall, Jan Johansson
Mature lung surfactant protein C (SP-C) corresponds to residues 24-58 of the 21 kDa proSP-C. A late processing intermediate, SP-Ci, corresponding to residues 12-58 of proSP-C, lacks the surface activity of SP-C, and the SP-Ci alpha-helical structure does not unfold in contrast to the metastable nature of the SP-C helix. The NMR structure of an analogue of SP-Ci, SP-Ci(1-31), with two palmitoylCys replaced by Phe and four Val replaced by Leu, in dodecylphosphocholine micelles and in ethanol shows that its alpha-helix vs...
March 2006: FEBS Journal
Aurelia Jacquette, Geneviève Le Roux, Chantal Lacombe, Michel Goossens, Serge Pissard
More than 200 mutations that are associated with beta-thalassemia (thal) have been found. In most cases, studies to detect a mutation in a patient is made easier because of the existence of geographical sets of mutations that allow the use of a dedicated mutation detection kit. We describe here a patient who originated from Tunisia, in whom we found two as yet unreported mutations, showing that even in a well-studied population a full gene study might be needed to characterize mutation(s).
August 2004: Hemoglobin
Howard G Harvey, Ben Slater, Martin P Attfield
We report here on the solvothermal synthesis and crystal structure of the hybrid organic-inorganic framework material Al(2)[O(3)PC(3)H(6)PO(3)](H(2)O)(2)F(2).H(2)O (orthorhombic, Pmmn, a = 12.0591(2) A, b = 19.1647(5) A, c = 4.91142(7) A, Z = 4), the second member of the Al(2)[O(3)PC(n)H(2n)PO(3)](H(2)O)(2)F(2).H(2)O series. The structure consists of corrugated chains of corner-sharing AlO(4)F(2) octahedra in which alternating AlO(4)F(2) octahedra contain two fluorine atoms in a trans or a cis configuration...
July 5, 2004: Chemistry: a European Journal
Shu-Chen Wei, Yi-Ning Su, Jyy-Jih Tsai-Wu, C-H Herbert Wu, Yen-Len Huang, Jin-Chuan Sheu, Cheng-Yi Wang, Jau-Min Wong
Colorectal cancer has become the third leading cause of death from cancer in Taiwan. Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease characterized by the presence of multiple adenomatous polyps in the colon and rectum. The gene responsible for FAP (APC) was cloned in 1991. Extensive analyses of the mutation spectra in FAP kindreds have been performed in different countries, but the results have been highly variable (30-80%). In this study, we used denaturing high-performance liquid chromatography (DHPLC) followed by automatic sequencing in an effort to establish the mutation spectrum of APC from DNA of peripheral blood cells...
March 2004: Journal of Biomedical Science
M Elena Garrido, Montserrat Bosch, Ricardo Medina, Anna Bigas, Montserrat Llagostera, Ana M Pérez De Rozas, Ignacio Badiola, Jordi Barbé
Treatment of bacterial cultures with chelating agents such as 2,2'-dipyridyl (DPD) induces expression of iron-regulated genes. It is known that in the gamma-Proteobacteria, the Fur protein is the major regulator of genes encoding haem- or haemoglobin-binding proteins. Electrophoretic analysis of outer-membrane proteins of the gamma-proteobacterium Pasteurella multocida has revealed the induction of two proteins of 60 and 40 kDa in DPD-treated cultures in both wild-type and fur-defective strains. These two proteins have the same N-terminal amino acid sequence, which identifies this protein as the product of the PM0592 ORF...
August 2003: Microbiology
J W Flora, D C Muddiman
Complete peptide nucleic acids (PNAs) sequence information is obtained from the unimolecular decomposition of singly-charged PNA oligomers in the negative-ion mode using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) and sustained off-resonance irradiation collision induced dissociation. The 4-mers, n-CATT-c, n-AGCT-c, n-AACT-c, and n-acetylated-AACT-c and two 6-mers, n-AAAAAA-c and n-CCCCCC-c, were investigated to explore the unimolecular decomposition of mixed-nucleobase and homopolymer PNAs representing purine and pyrimidine oligomers, respectively...
July 2001: Journal of the American Society for Mass Spectrometry
D C St Louis, D Gotte, E Sanders-Buell, D W Ritchey, M O Salminen, J K Carr, F E McCutchan
Recombinant forms of human immunodeficiency virus type 1 (HIV-1) have been shown to be of major importance in the global AIDS pandemic. Viral RNA dimer formation mediated by the dimerization initiation sequence (DIS) is believed to be essential for viral genomic RNA packaging and therefore for RNA recombination. Here, we demonstrate that HIV-1 recombination and replication are not restricted by variant DIS loop sequences. Three DIS loop forms found among HIV-1 isolates, DIS (CG), DIS (TA), and DIS (TG), when introduced into deletion mutants of HIV-1 recombined efficiently, and the progeny virions replicated with comparable kinetics...
May 1998: Journal of Virology
P André, A Kim, K Khrapko, W G Thilly
The study of rare genetic changes in human tissues requires specialized techniques. Point mutations at fractions at or below 10(-6) must be observed to discover even the most prominent features of the point mutational spectrum. PCR permits the increase in number of mutant copies but does so at the expense of creating many additional mutations or "PCR noise". Thus, each DNA sequence studied must be characterized with regard to the DNA polymerase and conditions used to avoid interpreting a PCR-generated mutation as one arising in human tissue...
August 1997: Genome Research
K P Vatsis, W W Weber
The human N-acetylation polymorphism is a genetic trait phenotypically reflected by differences in N-acetyltransferase (NAT) activity with therapeutic agents (rapid and slow acetylation), but a genetic invariability in N-acetylation of some arylamine drugs is also known. There are two highly similar human NAT genes: NAT1 is thought to encode a genetically invariant protein, whereas NAT2 has conclusively been shown to represent a polymorphic locus. This study demonstrates the presence of discrete NAT1 structural variants among Caucasians...
February 15, 1993: Archives of Biochemistry and Biophysics
D L Boger, D S Johnson, W Yun, C M Tarby
A detailed evaluation of the DNA alkylation selectivity of (+)-CC-1065, ent-(-)-CC-1065 and a series of aborted and extended analogs possessing the CPI alkylation subunit is detailed and the refinement of a model that accommodates the offset AT-rich adenine N3 alkylation selectivity of the enantiomeric agents is presented. The natural enantiomers bind in the minor groove in the 3'-->5' direction starting from the adenine N3 alkylation site across a 2 base (N-BOC-CPI; i.e. 5'-AA), 3.5 base (CPI-CDPI1/CPI-PDE-I1; i...
February 1994: Bioorganic & Medicinal Chemistry
Z Guo, F Sherman
It was previously shown that three distinct but interdependent elements are required for 3' end formation of mRNA in the yeast Saccharomyces cerevisiae: (i) the efficiency element TATATA and related sequences, which function by enhancing the efficiency of positioning elements; (ii) positioning elements, such as TTAAGAAC and AAGAA, which position the poly(A) site; and (iii) the actual site of polyadenylation. In this study, we have shown that several A-rich sequences, including the vertebrate poly(A) signal AATAAA, are also positioning elements...
November 1995: Molecular and Cellular Biology
K M Saing, H Orii, Y Tanaka, K Yanagisawa, A Miura, H Ikeda
We constructed a recombinant plasmid containing the 2.1 kb HindIII fragment of plasmid pDG1, isolated from the cellular slime mold (Dictyostelium sp. strain GA11), and using pAG60 as cloning vector. We found that deletions of the recombinant plasmid took place frequently in Escherichia coli wild-type cells. However, the deletion was not observed when the plasmid was introduced into a strain that was an isogenic temperature-sensitive mutant of the gyrA gene. These results suggest that E. coli DNA gyrase is involved in the mechanisms of the deletion formation...
September 1988: Molecular & General Genetics: MGG
F Seela, T Grein
7-Deaza-2'-deoxyadenosine (1, c7Ad) and 3-deaza-2'-deoxyadenosine (2, c3Ad) have been incorporated into d(AAAAAA) tracts replacing dA at various positions within oligonucleotides. For this purpose suitably protected phosphonates have been prepared and oligonucleotides were synthesized on solid-phase. The oligomers were hybridized with their cognate strands. The duplexes were phosphorylated at OH-5' by polynucleotide kinase and self-ligated to multimers employing T4 DNA ligase. Oligomerized DNA-fragments were analyzed by polyacrylamide gel electrophoresis and the bending was determined from anomalies of electrophoretic mobility...
July 11, 1992: Nucleic Acids Research
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