Phillip J. Elms

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Recently, the role of force in cellular processes has become more evident, and now with advances in force spectroscopy, the response of proteins to force can be directly studied. Such studies have found that native proteins are brittle, and thus not very deformable. Here, we examine the mechanical properties of a class of intermediates referred to as the(More)
The replication-dependent histone mRNAs, the only eukaryotic mRNAs that do not have poly(A) tails, are present only in S-phase cells. Coordinate posttranscriptional regulation of histone mRNAs is mediated by the stem-loop at the 3' end of histone mRNAs. The protein that binds the 3' end of histone mRNA, stem-loop binding protein (SLBP), is required for(More)
Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are(More)
John D. Chodera,1, ∗ Phillip Elms,1, 2, 3 Frank Noé,4 Bettina Keller,4 Christian M. Kaiser,1, 5 Aaron Ewall-Wice,6 Susan Marqusee,1, 7, 3 Carlos Bustamante,1, 7, 3, 5, 8, 9 and Nina Singhal Hinrichs10 California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA Biophysics Graduate Group, University of California,(More)
Many biological processes generate force, and proteins have evolved to resist and respond to tension along different force axes. Single-molecule force spectroscopy allows for molecular insight into the behavior of proteins under force and the mechanism of protein folding in general. Here, we have used src SH3 to investigate the effect of different pulling(More)
Monobromobimane (MBB) is a lipophilic reagent that selectively modifies free cysteine residues in proteins. Because of its lipophilic character, MBB is capable of labeling cysteine residues in membrane proteins under native conditions. Reaction of MBB with the sulfhydryl groups of free cysteines leads to formation of highly fluorescent derivatives. Here we(More)
Single-molecule force spectroscopy has provided important insights into the properties and mechanisms of biological molecules and systems. A common experiment is to measure the force dependence of conformational changes at equilibrium. Here, we demonstrate that the commonly used technique of force feedback has severe limitations when used to evaluate rapid(More)
Protein chip technology permits analysis of the expression and modification status of numerous targeted proteins within a single experiment, mainly through the use of antibody-based microarrays. Despite recent improvements in these protein chips, their applications are still limited for a variety of reasons, which include technical challenges in fabrication(More)
California Institute of Quantitative Biosciences (QB3), 4 University of California, Berkeley, California 94720, USA 5 Biophysics Graduate Group, University of California, Berkeley, California 94720, USA 6 Jason L. Choy Laboratory of Single Molecule Biophysics, 7 University of California, Berkeley, CA 94720, USA 8 IBM Almaden Research Center, San Jose, CA(More)
Our ability to engineer organisms with new biosynthetic pathways and genetic circuits is limited by the availability of protein characterization data and the cost of synthetic DNA. With new tools for reading and writing DNA, there are opportunities for scalable assays that more efficiently and cost effectively mine for biochemical protein characteristics.(More)