El Yacoubi, Basma, Lyons, Benjamin, Cruz, Yulien, Reddy, Robert, Nordin, Brian, Agnelli, Fabio, ...
Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in...
Envelope: interactive software for modeling and fitting complex isotope distributions (2008)
Sykes, Michael T, Williamson, James R
Abstract Background An important aspect of proteomic mass spectrometry involves quantifying and interpreting the isotope distributions arising from mixtures of macromolecules with different isotope...
Edgcomb, Stephen P., Aschrafi, Angelique, Kompfner, Elizabeth, Williamson, James R., Gerace, Larry, Hennig, Mirko
The translation of the unspliced and partially spliced viral mRNAs that encode the late, structural proteins of HIV-1 depends on the viral-protein Rev. Oligomeric binding of Rev to the Rev response...
Naidoo, Nishen, Harrop , Stephen J, Sobti, Meghna, Haynes, Paul A, Szymczyna, Blair R, Williamson, James R, ...
Sm and Sm-like (Lsm) proteins are core components of the ribonucleoprotein complexes essential to key nucleic acid processing events within the eukaryotic cell. They assemble as polyprotein ring...
Bmc Bioinformatics, Michael T Sykes, James R Williamson, Open Access, Michael T Sykes, James R Williamson
Software Envelope: interactive software for modeling and fitting complex isotope distributions
The RNA Ontology Consortium: An open invitation to the RNA community (2006)
LEONTIS, NEOCLES B., ALTMAN, RUSS B., BERMAN, HELEN M., BRENNER, STEVEN E., BROWN, JAMES W., ENGELKE, DAVID R., ...
The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and...
The RNA Ontology Consortium: An open invitation to the RNA community (2006)
LEONTIS, NEOCLES B., ALTMAN, RUSS B., BERMAN, HELEN M., BRENNER, STEVEN E., BROWN, JAMES W., ENGELKE, DAVID R., ...
The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and...
The RNA Ontology Consortium: An open invitation to the RNA community (2006)
LEONTIS, NEOCLES B., ALTMAN, RUSS B., BERMAN, HELEN M., BRENNER, STEVEN E., BROWN, JAMES W., ENGELKE, DAVID R., ...
The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and...
Klostermeier, Dagmar, Sears, Pamela, Wong, Chi-Huey, Millar, David P., Williamson, James R.
In one of the first steps of prokaryotic ribosome assembly, the ribosomal protein S15 binds to a three‐way junction in the central domain of the 16S rRNA. Binding causes a conformational change...
RYDER, SEAN P., WILLIAMSON, JAMES R.
Inadequate formation and maintenance of myelin is the basis for several neurodegenerative disorders, including leukodystrophy and multiple sclerosis. In mice, oligodendrocyte differentiation and...
RYDER, SEAN P., WILLIAMSON, JAMES R.
Inadequate formation and maintenance of myelin is the basis for several neurodegenerative disorders, including leukodystrophy and multiple sclerosis. In mice, oligodendrocyte differentiation and...
Structural mimicry in the phage {phi}21 N peptide-boxB RNA complex (2003)
CILLEY, CHRISTOPHER D., WILLIAMSON, JAMES R.
We determined the solution structure of a 22-amino-acid peptide from the amino-terminal domain of the bacteriophage &phis;21 N protein in complex with its cognate 24-mer boxB RNA hairpin using...
After the ribosome structures: How are the subunits assembled? (2003)
The recent structures of the ribosome and the ribosomal subunits only heighten the intrigue of trying to understand how the ribosome is assembled. Biochemical and mechanistic studies have mapped out...
GONSALVEZ, GRAYDON B., LEHMANN, KATRINA A., HO, DEREK K., STANITSA, ELENI S., WILLIAMSON, JAMES R., LONG, ROY M.
In Saccharomyces cerevisiae, ASH1 mRNA is localized to the tip of daughter cells during anaphase of the cell cycle. ASH1 mRNA localization is dependent on four cis-acting localization elements as...
Grossberg, Stephen, Williamson, James R.
A neural model suggests how horizontal and interlaminar connections in visual cortical areas V1 and V2 develop within a laminar cortical architecture and give rise to adult visual percepts. The model...
Hennig, Mirko, Williamson, James R.
Hydrogen bond networks stabilize RNA secondary and tertiary structure and are thus essentially important for protein recognition. During structure refinements using either NMR or X-ray techniques,...
A simple method for preparing pools of synthetic oligonucleotides with random point deletions (1995)
Batey, Robert T., Inada, Maki, Kujawinski, Elizabeth, Puglisi, Joseph D., Williamson, James R.
A general method for large scale preparation of uniformly isotopically labeled ribonucleotides and RNAs is described. Bacteria are grown on isotopic growth medium, and their nucleic acids are...
Williamson, James R., Boxer, Steven G.
A thymidine phospharamidite labelled at C6 with 13C has been synthesized, and incorporated into a synthetic oligonuckotide, d(CGCGT*T*GT*T*CGCG), which adopts a hairpin conformation. NMR relaxation...
The Yankee-Pennamite Wars, 1769-1784 :--a military history /--by James R. Williamson. (1972)
Thesis (M.A.)--Butler University, 1972.
Ligand-induced conformational changes observed in single RNA molecules
Ha, Taekjip, Zhuang, Xiaowei, Kim, Harold D., Orr, Jeffrey W., Williamson, James R., Chu, Steven
We present the first demonstration that fluorescence resonance energy transfer can be used to track the motion of a single molecule undergoing conformational changes. As a model system, the...
An optimal Mg2+ concentration for kinetic folding of the Tetrahymena ribozyme
Rook, Martha S., Treiber, Daniel K., Williamson, James R.
Divalent metal ions, such as Mg2+, are generally required for tertiary structure formation in RNA. Although the role of Mg2+ binding in RNA-folding equilibria has been studied extensively, little is...
Hennig, Mirko, Williamson, James R.
Hydrogen bond networks stabilize RNA secondary and tertiary structure and are thus essentially important for protein recognition. During structure refinements using either NMR or X-ray techniques,...
Kim, Harold D., Nienhaus, G. Ulrich, Ha, Taekjip, Orr, Jeffrey W., Williamson, James R., Chu, Steven
Fluorescence correlation spectroscopy (FCS) of fluorescence resonant energy transfer (FRET) on immobilized individual fluorophores was used to study the Mg2+-facilitated conformational change of an...
Klostermeier, Dagmar, Sears, Pamela, Wong, Chi-Huey, Millar, David P., Williamson, James R.
In one of the first steps of prokaryotic ribosome assembly, the ribosomal protein S15 binds to a three-way junction in the central domain of the 16S rRNA. Binding causes a conformational change that...
Torres, Francisco E., Kuhn, Peter, De Bruyker, Dirk, Bell, Alan G., Wolkin, Michal V., Peeters, Eric, ...
We report the fabrication of enthalpy arrays and their use to detect molecular interactions, including protein–ligand binding, enzymatic turnover, and mitochondrial respiration. Enthalpy arrays...
RNA–protein interactions promote asymmetric sorting of the ASH1 mRNA ribonucleoprotein complex
GONSALVEZ, GRAYDON B., LEHMANN, KATRINA A., HO, DEREK K., STANITSA, ELENI S., WILLIAMSON, JAMES R., LONG, ROY M.
In Saccharomyces cerevisiae, ASH1 mRNA is localized to the tip of daughter cells during anaphase of the cell cycle. ASH1 mRNA localization is dependent on four cis-acting localization elements as...
After the ribosome structures: How are the subunits assembled?
The recent structures of the ribosome and the ribosomal subunits only heighten the intrigue of trying to understand how the ribosome is assembled. Biochemical and mechanistic studies have mapped out...
Structural mimicry in the phage φ21 N peptide–boxB RNA complex
CILLEY, CHRISTOPHER D., WILLIAMSON, JAMES R.
We determined the solution structure of a 22-amino-acid peptide from the amino-terminal domain of the bacteriophage φ21 N protein in complex with its cognate 24-mer boxB RNA hairpin using...
Specificity of the STAR/GSG domain protein Qk1: Implications for the regulation of myelination
RYDER, SEAN P., WILLIAMSON, JAMES R.
Inadequate formation and maintenance of myelin is the basis for several neurodegenerative disorders, including leukodystrophy and multiple sclerosis. In mice, oligodendrocyte differentiation and...
An assembly landscape for the 30S ribosomal subunit
Talkington, Megan W. T., Siuzdak, Gary, Williamson, James R.
Self-assembling macromolecular machines drive fundamental cellular processes, including transcription, mRNA processing, translation, DNA replication, and cellular transport. The ribosome, which...
The RNA Ontology Consortium: An open invitation to the RNA community
LEONTIS, NEOCLES B., ALTMAN, RUSS B., BERMAN, HELEN M., BRENNER, STEVEN E., BROWN, JAMES W., ENGELKE, DAVID R., ...
The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and...
Ligand-induced conformational changes observed in single RNA molecules
Ha, Taekjip, Zhuang, Xiaowei, Kim, Harold D., Orr, Jeffrey W., Williamson, James R., Chu, Steven
We present the first demonstration that fluorescence resonance energy transfer can be used to track the motion of a single molecule undergoing conformational changes. As a model system, the...
An optimal Mg2+ concentration for kinetic folding of the Tetrahymena ribozyme
Rook, Martha S., Treiber, Daniel K., Williamson, James R.
Divalent metal ions, such as Mg2+, are generally required for tertiary structure formation in RNA. Although the role of Mg2+ binding in RNA-folding equilibria has been studied extensively, little is...
Hennig, Mirko, Williamson, James R.
Hydrogen bond networks stabilize RNA secondary and tertiary structure and are thus essentially important for protein recognition. During structure refinements using either NMR or X-ray techniques,...
Kim, Harold D., Nienhaus, G. Ulrich, Ha, Taekjip, Orr, Jeffrey W., Williamson, James R., Chu, Steven
Fluorescence correlation spectroscopy (FCS) of fluorescence resonant energy transfer (FRET) on immobilized individual fluorophores was used to study the Mg2+-facilitated conformational change of an...
Klostermeier, Dagmar, Sears, Pamela, Wong, Chi-Huey, Millar, David P., Williamson, James R.
In one of the first steps of prokaryotic ribosome assembly, the ribosomal protein S15 binds to a three-way junction in the central domain of the 16S rRNA. Binding causes a conformational change that...
Torres, Francisco E., Kuhn, Peter, De Bruyker, Dirk, Bell, Alan G., Wolkin, Michal V., Peeters, Eric, ...
We report the fabrication of enthalpy arrays and their use to detect molecular interactions, including protein–ligand binding, enzymatic turnover, and mitochondrial respiration. Enthalpy arrays...
RNA–protein interactions promote asymmetric sorting of the ASH1 mRNA ribonucleoprotein complex
GONSALVEZ, GRAYDON B., LEHMANN, KATRINA A., HO, DEREK K., STANITSA, ELENI S., WILLIAMSON, JAMES R., LONG, ROY M.
In Saccharomyces cerevisiae, ASH1 mRNA is localized to the tip of daughter cells during anaphase of the cell cycle. ASH1 mRNA localization is dependent on four cis-acting localization elements as...
After the ribosome structures: How are the subunits assembled?
The recent structures of the ribosome and the ribosomal subunits only heighten the intrigue of trying to understand how the ribosome is assembled. Biochemical and mechanistic studies have mapped out...
Structural mimicry in the phage φ21 N peptide–boxB RNA complex
CILLEY, CHRISTOPHER D., WILLIAMSON, JAMES R.
We determined the solution structure of a 22-amino-acid peptide from the amino-terminal domain of the bacteriophage φ21 N protein in complex with its cognate 24-mer boxB RNA hairpin using...
Specificity of the STAR/GSG domain protein Qk1: Implications for the regulation of myelination
RYDER, SEAN P., WILLIAMSON, JAMES R.
Inadequate formation and maintenance of myelin is the basis for several neurodegenerative disorders, including leukodystrophy and multiple sclerosis. In mice, oligodendrocyte differentiation and...
The RNA Ontology Consortium: An open invitation to the RNA community
LEONTIS, NEOCLES B., ALTMAN, RUSS B., BERMAN, HELEN M., BRENNER, STEVEN E., BROWN, JAMES W., ENGELKE, DAVID R., ...
The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and...
Karnaukhov, Alexey V., Karnaukhova, Elena V., Williamson, James R.
A flexible Numerical Matrices Method (NMM) for nonlinear system identification has been developed based on a description of the dynamics of the system in terms of kinetic complexes. A set of related...
Edgcomb, Stephen P., Aschrafi, Angelique, Kompfner, Elizabeth, Williamson, James R., Gerace, Larry, Hennig, Mirko
The translation of the unspliced and partially spliced viral mRNAs that encode the late, structural proteins of HIV-1 depends on the viral-protein Rev. Oligomeric binding of Rev to the Rev response...
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
El Yacoubi, Basma, Lyons, Benjamin, Cruz, Yulien, Reddy, Robert, Nordin, Brian, Agnelli, Fabio, ...
Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in...
Sharpe Elles, Lisa M., Sykes, Michael T., Williamson, James R., Uhlenbeck, Olke C.
Escherichia coli DbpA is an ATP-dependent RNA helicase with specificity for hairpin 92 of 23S ribosomal RNA, an important part of the peptidyl transferase center. The R331A active site mutant of DbpA...