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Recent Publications

The following list was auto-generated 6 days ago.

• 1. Gromova AV
  2. Ciszewski JM
  3. Miller BL
  (2012 Feb 18). Ternary resin-bound dynamic combinatorial chemistry. Chem Commun (Camb). 48, 2131-3.
• 1. Peng HI
  2. Strohsahl CM
  3. Miller BL
  (2012 Feb 02). Microfluidic nanoplasmonic-enabled device for multiplex DNA detection. Lab Chip. In press.
• 1. Horn JN
  2. Sengillo JD
  3. Lin D
  4. Romo TD
  5. Grossfield A
  (2012 Feb 01). Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics. Biochim Biophys Acta. 1818, 212-8.
• 1. Bauer WJ
  2. Heath J
  3. Jenkins JL
  4. Kielkopf CL
  (2012 Jan 27). Three RNA Recognition Motifs Participate in RNA Recognition and Structural Organization by the Pro-Apoptotic Factor TIA-1. J Mol Biol. 415, 727-40.
• 1. Seetin MG
  2. Mathews DH
  (2012 Jan 27). TurboKnot: Rapid Prediction of Conserved RNA Secondary Structures Including Pseudoknots. Bioinformatics. In press.
• 1. Takeyama M
  2. Wakabayashi H
  3. Fay PJ
  (2012 Jan 24). Factor VIII Light Chain Contains a Binding Site for Factor X That Contributes to the Catalytic Efficiency of Factor Xase. Biochemistry. 51, 820-8.
• 1. Olausson BE
  2. Grossfield A
  3. Pitman MC
  4. Brown MF
  5. Feller SE
  6. Vogel A
  (2012 Jan 23). Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes. J Am Chem Soc. In press.
• 1. Nguyen LA
  2. Daddacha W
  3. Rigby S
  4. Bambara RA
  5. Kim B
  (2012 Jan 13). Altered strand transfer activity of a multiple-drug-resistant human immunodeficiency virus type 1 reverse transcriptase mutant with a dipeptide fingers domain insertion. J Mol Biol. 415, 248-62.
• 1. Gibbs PE
  2. Miralem T
  3. Lerner-Marmarosh N
  4. Tudor C
  5. Maines MD
  (2012 Jan 06). Formation of ternary complex of human biliverdin reductase-protein kinase Cδ-ERK2 protein is essential for ERK2-mediated activation of Elk1 protein, nuclear factor-κB, and inducible nitric-oxidase synthase (iNOS). J Biol Chem. 287, 1066-79.
• 1. Wangler NJ
  2. Santos KL
  3. Schadock I
  4. Hagen FK
  5. Escher E
  6. Bader M
  7. Speth RC
  8. Karamyan VT
  (2012 Jan 02). Identification of membrane-bound variant of metalloendopeptidase neurolysin (EC 3.4.24.16) as the non-angiotensin type 1 (non-AT1), non-AT2 angiotensin binding site. J Biol Chem. 287, 114-22.
• 1. Hagen FK
  (2012 Jan 01). Proteoglycan: site mapping and site-directed mutagenesis. Methods Mol Biol. 836, 23-34.
• 1. Liu N
  2. Hayes JJ
  (2012 Jan 01). Preparation of nucleosomes containing a specific H2A-H2A cross-link forming a DNA-constraining loop structure. Methods Mol Biol. 833, 351-71.
• 1. Lippa GM
  2. Liberman JA
  3. Jenkins JL
  4. Krucinska J
  5. Salim M
  6. Wedekind JE
  (2012 Jan 01). Crystallographic analysis of small ribozymes and riboswitches. Methods Mol Biol. 848, 159-84.
• 1. McArdle J
  2. Moorman NJ
  3. Munger J
  (2012 Jan 01). HCMV Targets the Metabolic Stress Response through Activation of AMPK Whose Activity Is Important for Viral Replication. PLoS Pathog. 8, e1002502.
• 1. Wang R
  2. Dillon CP
  3. Shi LZ
  4. Milasta S
  5. Carter R
  6. Finkelstein D
  7. McCormick LL
  8. Fitzgerald P
  9. Chi H
  10. Munger J
  11. Green DR
  (2011 Dec 23). The transcription factor Myc controls metabolic reprogramming upon T lymphocyte activation. Immunity. 35, 871-82.
• 1. Wakabayashi H
  2. Griffiths AE
  3. Fay PJ
  (2011 Dec 20). Enhancing Factor VIII and VIIIa Stability by Combining Mutations at the A2 Domain Interface and A1 - C2 Domain Interface. J Thromb Haemost. In press.
• 1. Grant TD
  2. Snell EH
  3. Luft JR
  4. Quartley E
  5. Corretore S
  6. Wolfley JR
  7. Elizabeth Snell M
  8. Hadd A
  9. Perona JJ
  10. Phizicky EM
  11. Grayhack EJ
  (2011 Dec 17). Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase. Nucleic Acids Res. In press.
• 1. Xu Z
  2. Almudevar A
  3. Mathews DH
  (2011 Dec 01). Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Res. In press.
• 1. Ahmad A
  2. Kravets A
  3. Rustchenko E
  (2011 Nov 30). Transcriptional Regulatory Circuitries in the Human Pathogen Candida albicans Involving Sense-antisense Interactions. Genetics. In press.
• 1. Yang Z
  2. Hayes JJ
  (2011 Nov 22). The divalent cations Ca2+ and Mg2+ play specific roles in stabilizing histone-DNA interactions within nucleosomes that are partially redundant with the core histone tail domains. Biochemistry. 50, 9973-81.
• 1. Rudenko MI
  2. Holmes MR
  3. Ermolenko DN
  4. Lunt EJ
  5. Gerhardt S
  6. Noller HF
  7. Deamer DW
  8. Hawkins A
  9. Schmidt H
  (2011 Nov 15). Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip. Biosens Bioelectron. 29, 34-9.
• 1. Wilusz JE
  2. Whipple JM
  3. Phizicky EM
  4. Sharp PA
  (2011 Nov 11). tRNAs marked with CCACCA are targeted for degradation. Science. 334, 817-21.
• 1. Van Nostrand KP
  2. Kennedy SD
  3. Turner DH
  4. Mathews DH
  (2011 Nov 08). Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change. J Chem Theory Comput. 7, 3779-3792.
• 1. Marimuthu S
  2. Chivukula RS
  3. Alfonso LF
  4. Moridani M
  5. Hagen FK
  6. Bhat GJ
  (2011 Nov 01). Aspirin acetylates multiple cellular proteins in HCT-116 colon cancer cells: Identification of novel targets. Int J Oncol. 39, 1273-83.
• 1. DeAngelis JP
  2. Varfaj F
  3. Wakabayashi H
  4. Fay PJ
  (2011 Nov 01). The role of P4-P3' residues flanking Arg336 in facilitating activated protein C-catalyzed cleavage and inactivation of factor VIIIa. Thromb Res. 128, 470-6.
• 1. Meyer S
  2. Becker NB
  3. Syed SH
  4. Goutte-Gattat D
  5. Shukla MS
  6. Hayes JJ
  7. Angelov D
  8. Bednar J
  9. Dimitrov S
  10. Everaers R
  (2011 Nov 01). From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: nanoscale modeling of the nucleosomal stem. Nucleic Acids Res. 39, 9139-54.
• 1. Fang H
  2. Clark DJ
  3. Hayes JJ
  (2011 Oct 22). DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain. Nucleic Acids Res. In press.
• 1. Smith HC
  2. Bennett RP
  3. Kizilyer A
  4. McDougall WM
  5. Prohaska KM
  (2011 Oct 06). Functions and regulation of the APOBEC family of proteins. Semin Cell Dev Biol. In press.
• 1. Kang DC
  2. Venkataraman PA
  3. Dumont ME
  4. Maloney PC
  (2011 Oct 04). Oligomeric state of the oxalate transporter, OxlT. Biochemistry. 50, 8445-53.
• 1. Liu N
  2. Peterson CL
  3. Hayes JJ
  (2011 Oct 01). SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol Cell Biol. 31, 4165-75.
• 1. Wang J
  2. Zhang G
  3. Bambara RA
  4. Li D
  5. Liang H
  6. Wu H
  7. Smith HM
  8. Lowe NR
  9. Demeter LM
  10. Dykes C
  (2011 Oct 01). Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection. J Virol. 85, 10861-73.
• 1. Wu G
  2. Yu AT
  3. Kantartzis A
  4. Yu YT
  (2011 Sep 29). Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation. Wiley Interdiscip Rev RNA. 2, 571-81.
• 1. Liberman JA
  2. Wedekind JE
  (2011 Sep 28). Riboswitch structure in the ligand-free state. Wiley Interdiscip Rev RNA. In press.
• 1. Muchiri JM
  2. Rigby ST
  3. Nguyen LA
  4. Kim B
  5. Bambara RA
  (2011 Sep 23). HIV-1 reverse transcriptase dissociates during strand transfer. J Mol Biol. 412, 354-64.
• 1. Senior AE
  (2011 Sep 13). Reaction chemistry ABC-style. Proc Natl Acad Sci U S A. 108, 15015-6.
• 1. McDougall WM
  2. Smith HC
  (2011 Sep 09). Direct evidence that RNA inhibits APOBEC3G ssDNA cytidine deaminase activity. Biochem Biophys Res Commun. 412, 612-7.
• 1. McDougall WM
  2. Okany C
  3. Smith HC
  (2011 Sep 02). Deaminase activity on single-stranded DNA (ssDNA) occurs in vitro when APOBEC3G cytidine deaminase forms homotetramers and higher-order complexes. J Biol Chem. 286, 30655-61.
• 1. Gregoire S
  2. Xiao J
  3. Silva BB
  4. Gonzalez I
  5. Agidi PS
  6. Klein MI
  7. Ambatipudi KS
  8. Rosalen PL
  9. Bauserman R
  10. Waugh RE
  11. Koo H
  (2011 Sep 01). Role of glucosyltransferase B in interactions of Candida albicans with Streptococcus mutans and with an experimental pellicle on hydroxyapatite surfaces. Appl Environ Microbiol. 77, 6357-67.
• 1. Lerman YV
  2. Kennedy SD
  3. Shankar N
  4. Parisien M
  5. Major F
  6. Turner DH
  (2011 Sep 01). NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions. RNA. 17, 1664-77.
• 1. Yu AT
  2. Ge J
  3. Yu YT
  (2011 Sep 01). Pseudouridines in spliceosomal snRNAs. Protein Cell. 2, 712-25.
• 1. Shen W
  2. Gorelick RJ
  3. Bambara RA
  (2011 Aug 26). HIV-1 nucleocapsid protein increases strand transfer recombination by promoting dimeric G-quartet formation. J Biol Chem. 286, 29838-47.
• 1. Balakrishnan L
  2. Bambara RA
  (2011 Aug 15). The changing view of Dna2. Cell Cycle. 10, 2620-1.
• 1. Romo TD
  2. Bradney LA
  3. Greathouse DV
  4. Grossfield A
  (2011 Aug 01). Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Biochim Biophys Acta. 1808, 2019-30.
• 1. Griffiths AE
  2. Wang W
  3. Hagen FK
  4. Fay PJ
  (2011 Aug 01). Use of affinity-directed liquid chromatography-mass spectrometry to map the epitopes of a factor VIII inhibitor antibody fraction. J Thromb Haemost. 9, 1534-40.
• 1. Hwang J
  2. Maquat LE
  (2011 Aug 01). Nonsense-mediated mRNA decay (NMD) in animal embryogenesis: to die or not to die, that is the question. Curr Opin Genet Dev. 21, 422-30.
• 1. Gewandter JS
  2. Bambara RA
  3. O'Reilly MA
  (2011 Aug 01). The RNA surveillance protein SMG1 activates p53 in response to DNA double-strand breaks but not exogenously oxidized mRNA. Cell Cycle. 10, 2561-7.
• 1. Yildirim I
  2. Stern HA
  3. Tubbs JD
  4. Kennedy SD
  5. Turner DH
  (2011 Jul 28). Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions. J Phys Chem B. 115, 9261-70.
• 1. Wakabayashi H
  2. Griffiths AE
  3. Fay PJ
  (2011 Jul 22). Increasing hydrophobicity or disulfide bridging at the factor VIII A1 and C2 domain interface enhances procofactor stability. J Biol Chem. 286, 25748-55.
• 1. Miller BL
  (2011 Jul 19). DCC in the Development of Nucleic Acid Targeted and Nucleic Acid Inspired Structures. Top Curr Chem. In press.
• 1. Jenkins JL
  2. Krucinska J
  3. McCarty RM
  4. Bandarian V
  5. Wedekind JE
  (2011 Jul 15). Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. J Biol Chem. 286, 24626-37.