James Lincoff
University of California, Berkeley
20 Papers
62 Citations
James Lincoff is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Chemistry & Membrane. The author has an hindex of 6, co-authored 12 publications. Previous affiliations of James Lincoff include University of California, San Francisco.
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Papers
Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States.
James Lincoff,James Lincoff,Mojtaba Haghighatlari,Mickael Krzeminski,João M.C. Teixeira,Gregory-Neal W. Gomes,Claudiu C. Gradinaru,Julie D. Forman-Kay,Teresa Head-Gordon +8 more
- 09 Jun 2020
TL;DR: A comprehensive Bayesian framework is introduced, the Extended Experimental Inferential Structure Determination (X-EISD) method, which calculates the maximum log-likelihood of a disordered protein ensemble, and finds that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types.
Allosteric cooperation in a de novo-designed two-domain protein
Fabio Pirro,Nathan W. Schmidt,James Lincoff,Zachary X Widel,Nicholas F. Polizzi,Lijun Liu,Michael J. Therien,Michael Grabe,Marco Chino,Angela Lombardi,William F. DeGrado +10 more
TL;DR: Methods to design multidomain proteins entirely from scratch are developed and the premier de novo design of an allosterically regulated phenol oxidase that responds to the binding of a synthetic porphyrin is achieved.
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The combined force field-sampling problem in simulations of disordered amyloid-β peptides.
TL;DR: This work investigates the combined force field-sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm.
Brominated Lipid Probes Expose Structural Asymmetries in Constricted Membranes
TL;DR: Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane remodeling system, this paper observed leaflet-level and protein-localized lipid structural patterns within highly constricted and thinned membrane nanotubes.
Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-β.
TL;DR: Molecular simulation provides a complementary approach to resolving the potential structural perturbations introduced by reporter tags that can aid in the interpretation of paramagnetic relaxation enhancement, double electron-electron resonance, and fluorescence resonance energy transfer experiments applied to IDPs.
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