Journal Articles

  • Spotlights on Recent JACS Publications
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja511195g
    Categories: Journal Articles
  • Interconversion between Three Overstretched DNA Structures
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja5090805
    Categories: Journal Articles
  • A New Organocatalytic Concept for Asymmetric α-Alkylation of Aldehydes
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja510475n
    Categories: Journal Articles
  • A Crystal Structure of an Oligoproline PPII-Helix, at Last
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja507405j
    Categories: Journal Articles
  • A Diruthenium μ-Carbido Complex That Shows Singlet-Carbene-like Reactivity
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja509364d
    Categories: Journal Articles
  • Long-Range Correlated Dynamics in Intrinsically Disordered Proteins
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja506820r
    Categories: Journal Articles
  • Atomic Layer Deposition of l-Alanine Polypeptide
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja5043403
    Categories: Journal Articles
  • Multiple Quantum Coherences from Hyperfine Transitions in a Vanadium(IV) Complex
    [Nov 2014]

    Journal of the American Chemical SocietyDOI: 10.1021/ja507846k
    Categories: Journal Articles
  • An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: Application to neuroserpin reveals regions that differentially regulate inhibitory activity
    [Nov 2014]

    Abstract

    The analysis of sequence conservation is commonly used to predict functionally important sites in proteins. We have developed an approach that first identi-fies highly conserved sites in a set of orthologous sequences using a weighted substitution-matrix-based conservation score and then filters these conserved sites based on the pattern of conservation present in a wider alignment of se-quences from the same family and structural information to identify surface exposed sites. This allows us to detect specific functional sites in the target protein and exclude regions that are likely to be generally important for the structure or function of the wider protein family. We applied our method to two members of the serpin family of serine protease inhibitors. We first confirmed that our method successfully detected the known heparin binding site in antithrombin while excluding residues known to be general important in the serpin family. We next applied our sequence analysis approach to neuroserpin and used our results to guide site-directed polyalanine mutagenesis experiments. The majority of the mutant neuroserpin proteins were found to fold correctly and could still form inhibitory complexes with tissue plasminogen activator (tPA). Kinetic analysis of tPA inhibition, however, revealed altered inhibitory kinetics in several of the mutant proteins, with some mutants showing decreased association with tPA and others showing more rapid dissociation of the covalent complex. Altogether, these results confirm that our sequence analysis approach is a useful tool that can be used to guide mutagenesis experiments for the detection of specific functional sites in proteins. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • A shortcut for multiple testing on the directed acyclic graph of gene ontology
    [Oct 2014]

    Background: Gene set testing has become an important analysis technique in high throughput microarray and next generation sequencing studies for uncovering patterns of differential expression of various biological processes. Often, the large number of gene sets that are tested simultaneously require some sort of multiplicity correction to account for the multiplicity effect. This work provides a substantial computational improvement to an existing familywise error rate controlling multiplicity approach (the Focus Level method) for gene set testing in high throughput microarray and next generation sequencing studies using Gene Ontology graphs, which we call the Short Focus Level. Results: The Short Focus Level procedure, which performs a shortcut of the full Focus Level procedure, is achieved by extending the reach of graphical weighted Bonferroni testing to closed testing situations where restricted hypotheses are present, such as in the Gene Ontology graphs. The Short Focus Level multiplicity adjustment can perform the full top-down approach of the original Focus Level procedure, overcoming a significant disadvantage of the otherwise powerful Focus Level multiplicity adjustment. The computational and power differences of the Short Focus Level procedure as compared to the original Focus Level procedure are demonstrated both through simulation and using real data. Conclusions: The Short Focus Level procedure shows a significant increase in computation speed over the original Focus Level procedure (as much as ~15,000 times faster). The Short Focus Level should be used in place of the Focus Level procedure whenever the logical assumptions of the Gene Ontology graph structure are appropriate for the study objectives and when either no a priori focus level of interest can be specified or the focus level is selected at a higher level of the graph, where the Focus Level procedure is computationally intractable.
    Categories: Journal Articles
  • Examination of polypeptide substrate specificity for E. coli ClpB
    [Oct 2014]

    Abstract

    E. coli ClpB is a molecular chaperone that belongs to the Clp/Hsp100 family of AAA+ proteins. ClpB is able to form a hexameric ring structure to catalyze protein disaggregation with the assistance of the DnaK chaperone system. Our knowledge of the mechanism of how ClpB recognizes its substrates is still limited. In this work, we have quantitatively investigated ClpB binding to a number of unstructured polypeptides using steady-state anisotropy titrations. To precisely determine the binding affinity for the interaction between ClpB hexamers and polypeptide substrates the titration data were subjected to global non-linear least squares analysis incorporating the dynamic equilibrium of ClpB assembly. Our results show that ClpB hexamers bind tightly to unstructured polypeptides with binding affinities in the range of ˜3 – 16 nM. ClpB exhibits a modest preference of binding to Peptide B1 with a binding affinity of (1.7 ± 0.2) nM. Interestingly, we found that ClpB binds to an unstructured polypeptide substrate of 40 and 50 amino acids containing the SsrA sequence at the C-terminus with an affinity of (12 ± 3) nM and (4 ± 2) nM, respectively. Whereas, ClpB binds the 11-amino acid SsrA sequence with an affinity of (140 ± 20) nM, which is significantly weaker than other polypeptide substrates that we tested here. We hypothesize that ClpB, like ClpA, requires substrates with a minimum length for optimal binding. Finally, we present evidence showing that multiple ClpB hexamers are involved in binding to polypeptides ≥ 152 amino acids. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
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