Literature DB >> 20486142

Characterization of reversible associations by sedimentation velocity with UltraScan.

Borries Demeler1, Emre Brookes, Renjing Wang, Virgil Schirf, Chongwoo A Kim.   

Abstract

We compare here the utility of sedimentation velocity (SV) to sedimentation equilibrium (SE) analysis for the characterization of reversible systems. Genetic algorithm optimization in UltraScan is used to optimize the model and to obtain solution properties of all components present in the system. We apply our method to synthetic and experimental data, and suggest limits for the accessible kinetic range. We conclude that equilibrium constants obtained from SV and SE analysis are equivalent, but that SV experiments provide better confidence for the K(d), can better account for the presence of contaminants and provide additional information including rate constants and shape parameters.

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Year:  2010        PMID: 20486142     DOI: 10.1002/mabi.200900481

Source DB:  PubMed          Journal:  Macromol Biosci        ISSN: 1616-5187            Impact factor:   4.979


  23 in total

1.  Structure-function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control.

Authors:  Jennifer M Crowther; Penelope J Cross; Michael R Oliver; Mary M Leeman; Austin J Bartl; Anthony W Weatherhead; Rachel A North; Katherine A Donovan; Michael D W Griffin; Hironori Suzuki; André O Hudson; Müge Kasanmascheff; Renwick C J Dobson
Journal:  J Biol Chem       Date:  2019-04-08       Impact factor: 5.157

2.  Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair.

Authors:  Nicholas L Adkins; Sarah G Swygert; Parminder Kaur; Hengyao Niu; Sergei A Grigoryev; Patrick Sung; Hong Wang; Craig L Peterson
Journal:  J Biol Chem       Date:  2017-02-15       Impact factor: 5.157

3.  A parametrically constrained optimization method for fitting sedimentation velocity experiments.

Authors:  Gary Gorbet; Taylor Devlin; Blanca I Hernandez Uribe; Aysha K Demeler; Zachary L Lindsey; Suma Ganji; Sabrah Breton; Laura Weise-Cross; Eileen M Lafer; Emre H Brookes; Borries Demeler
Journal:  Biophys J       Date:  2014-04-15       Impact factor: 4.033

4.  The E2 domains of APP and APLP1 share a conserved mode of dimerization.

Authors:  Sangwon Lee; Yi Xue; Jian Hu; Yongcheng Wang; Xuying Liu; Borries Demeler; Ya Ha
Journal:  Biochemistry       Date:  2011-05-26       Impact factor: 3.162

5.  The self-association and thermal denaturation of caprine and bovine β-lactoglobulin.

Authors:  Jennifer M Crowther; Jane R Allison; Grant A Smolenski; Alison J Hodgkinson; Geoffrey B Jameson; Renwick C J Dobson
Journal:  Eur Biophys J       Date:  2018-04-16       Impact factor: 1.733

6.  Methods for the design and analysis of sedimentation velocity and sedimentation equilibrium experiments with proteins.

Authors:  Borries Demeler
Journal:  Curr Protoc Protein Sci       Date:  2010-04

7.  Structural Characterization of the Extracellular Domain of CASPR2 and Insights into Its Association with the Novel Ligand Contactin1.

Authors:  Eva N Rubio-Marrero; Gabriele Vincelli; Cy M Jeffries; Tanvir R Shaikh; Irene S Pakos; Fanomezana M Ranaivoson; Sventja von Daake; Borries Demeler; Antonella De Jaco; Guy Perkins; Mark H Ellisman; Jill Trewhella; Davide Comoletti
Journal:  J Biol Chem       Date:  2015-12-31       Impact factor: 5.157

8.  Analysis of PKR-RNA interactions by sedimentation velocity.

Authors:  C Jason Wong; Katherine Launer-Felty; James L Cole
Journal:  Methods Enzymol       Date:  2011       Impact factor: 1.600

9.  The balanced regulation of Hsc70 by DNJ-13 and UNC-23 is required for muscle functionality.

Authors:  Katharina Papsdorf; Julia Sacherl; Klaus Richter
Journal:  J Biol Chem       Date:  2014-07-22       Impact factor: 5.157

10.  Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.

Authors:  Fanomezana M Ranaivoson; Qun Liu; Francesca Martini; Francesco Bergami; Sventja von Daake; Sheng Li; David Lee; Borries Demeler; Wayne A Hendrickson; Davide Comoletti
Journal:  Structure       Date:  2015-07-30       Impact factor: 5.006

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