Journal of Molecular Biology

ISSN: 0022-2836

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Datasets associated with articles published in Journal of Molecular Biology

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  • DNA sequences (primers, gene inserts, and vectors)
    Data Types:
    • Tabular Data
    • Dataset
  • Single turnover kinetic data for the cA4 degradation by the enzyme Tthb144
    Data Types:
    • Tabular Data
    • Dataset
  • DNA sequences
    Data Types:
    • Dataset
    • File Set
  • DNA sequences
    Data Types:
    • Dataset
    • File Set
  • The data comprises the raw data files of the manuscript titled "Dissection of protonations sites for antibacterial recognition and transport in QacA, a multi-drug efflux transporter", authored by Majumder et al.
    Data Types:
    • Image
    • Sequencing Data
    • Tabular Data
    • Dataset
  • Table S1A. All hydrogen deuterium exchange (HDX) peptide data for experiments examining the global exchange of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. In the Raw Data column, the two time points (0.3s and full) are labelled, and the relative level of HDX is coloured according to the amount of deuterium incorporated, on a blue to red continuum. The data listed for the 0.3s time point are the average of three independent experiments, with SD shown next to all HDX values. In the Normalized to Full Deuteration column, the 0.3s data has been normalised to the full deuteration measurements with the exception of those data (surrounded by black lines) where the full deuteration measurement was lower than 20% deuterium incorporation. The third column denotes the corresponding peptide centroid. Table S1B. All HDX peptide data for experiments examining the complex dynamics of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The two columns represent each state examined (+/- PI4KIIIA) and contain the data for five time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values. Table S1C. All HDX peptide data for experiments examining the dynamics of inhibitor specificity of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The three columns represent each state examined (+/- inhibitor) and contain the data for four time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values.
    Data Types:
    • Tabular Data
    • Dataset
  • BFDCA is a comprehensive tool of using Bayes factor for Differential Co-expression (DC) analysis. This package contains three main functions: (1) clustering condition-specific genes into functional DC subunits; (2) quantitatively characterizing the regulatory impact of genes based on their differential connectivity within DC structures; (3) providing a DC-based prediction model to predict case/control phenotypes by taking DC significant gene pairs as markers.
    Data Types:
    • Software/Code
    • Dataset
    • Document
    • File Set
  • One of the great ambitions of structural biology is to describe structure-function relationships quantitatively. Statistical thermodynamics is a powerful, general tool for computing the behavior of biological macromolecules at equilibrium, because it establishes a direct link between structure and function. Complex behavior emerges as equilibria of multiple reactions are coupled. Analytical treatment of linked equilibria scales poorly with increasing numbers of reactions and states as the algebraic constructs rapidly become unwieldy. We therefore developed a generalizable, but straightforward computational method to handle arbitrarily complex systems. To demonstrate this approach, we collected a multi-dimensional fluorescence landscape of an engineered fluorescent glucose biosensor and showed that its features could be modeled with ten intricately linked ligand-binding and conformational-exchange reactions. This protein represents a minimalist model of sufficient complexity to encompass fundamental biomolecular structure-function relationships: two- and multi-state conformational ensembles, conformational hierarchies, osmolytes, coupling between different binding sites and coupling between ligand binding and conformational change. The successful fit of this complex, multifaceted system demonstrates generality of the method.
    Data Types:
    • Dataset
  • Diffraction images of SeMet labeled crystals of a fragment of human plectin that includes the first and second spectrin repeats (SR1-SR2) of the plakin domain. The two Cys in the wild type sequence were replaced by Ala. This Se-Met MAD dataset was used for the de novo phasing of the pdb entry 2ODV (http://www.rcsb.org/pdb/explore/explore.do?structureId=2ODV).   Data was collected at the BM14 beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using a Mar CCD detector. Data from the same crystal were collected at two wavelengths : Remote wavelength (0.9185 Å): 180 images (1 degree oscillation per image). Peak wavelength ( 0.9785 Å): 360 images (1 degree oscillation per image).
    Data Types:
    • Software/Code
    • Dataset
    • Text
    • File Set
  • Diffraction images of a native crystals of a fragment of human plectin that includes the first and second spectrin repeats (SR1-SR2) of the plakin domain. The two Cys in the wild type sequence were replaced by Ala. Images correspond to the dataset used to refine the pdb entry 2ODV (http://www.rcsb.org/pdb/explore/explore.do?structureId=2ODV).   Data was collected at the BM14 beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using radiation of 0.9785 Å wavelength and a Mar CCD detector. The dataset consists of 360 images (1 degree oscillation per image). Data extend to ~1.85 Å resolution.
    Data Types:
    • Software/Code
    • Dataset
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