Literature DB >> 19852475

Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins.

Alfonso De Simone1, Andrea Cavalli, Shang-Te Danny Hsu, Wim Vranken, Michele Vendruscolo.   

Abstract

We present a method for calculating accurate random coil chemical shift values of proteins. These values are obtained by analyzing the relationship between the amino acid sequences in flexible loop regions of native states and the corresponding experimentally measured chemical shifts. We estimate the errors in the random coil chemical shift scales to be 0.31 ppm for (13)C(alpha), 0.37 ppm for (13)C(beta), 0.31 ppm for (13)CO, 0.68 ppm for (15)N, 0.09 ppm for (1)H, and 0.04 ppm for (1)H(alpha).

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Year:  2009        PMID： 19852475     DOI： 10.1021/ja904937a

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   15.419


  31 in total

1.  Energy landscape of the prion protein helix 1 probed by metadynamics and NMR.

Authors:  Carlo Camilloni; Daniel Schaal; Kristian Schweimer; Stephan Schwarzinger; Alfonso De Simone
Journal:  Biophys J       Date:  2012-01-03       Impact factor: 4.033

2.  Intrinsic disorder modulates protein self-assembly and aggregation.

Authors:  Alfonso De Simone; Craig Kitchen; Ann H Kwan; Margaret Sunde; Christopher M Dobson; Daan Frenkel
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-16       Impact factor: 11.205

3.  A soluble α-synuclein construct forms a dynamic tetramer.

Authors:  Wei Wang; Iva Perovic; Johnathan Chittuluru; Alice Kaganovich; Linh T T Nguyen; Jingling Liao; Jared R Auclair; Derrick Johnson; Anuradha Landeru; Alana K Simorellis; Shulin Ju; Mark R Cookson; Francisco J Asturias; Jeffrey N Agar; Brian N Webb; Chulhee Kang; Dagmar Ringe; Gregory A Petsko; Thomas C Pochapsky; Quyen Q Hoang
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-17       Impact factor: 11.205

4.  Conformational analysis of the full-length M2 protein of the influenza A virus using solid-state NMR.

Authors:  Shu Yu Liao; Keith J Fritzsching; Mei Hong
Journal:  Protein Sci       Date:  2013-10-07       Impact factor: 6.725

5.  Effect of zinc binding on β-amyloid structure and dynamics: implications for Aβ aggregation.

Authors:  Nasrollah Rezaei-Ghaleh; Karin Giller; Stefan Becker; Markus Zweckstetter
Journal:  Biophys J       Date:  2011-09-07       Impact factor: 4.033

6.  Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH.

Authors:  Magnus Kjaergaard; Søren Brander; Flemming M Poulsen
Journal:  J Biomol NMR       Date:  2011-01-15       Impact factor: 2.835

7.  Structure-based prediction of methyl chemical shifts in proteins.

Authors:  Aleksandr B Sahakyan; Wim F Vranken; Andrea Cavalli; Michele Vendruscolo
Journal:  J Biomol NMR       Date:  2011-07-12       Impact factor: 2.835

8.  Reply to: "Only kinetics can prove conformational selection".

Authors:  Alfonso De Simone
Journal:  Biophys J       Date:  2014-10-21       Impact factor: 4.033

9.  Cyclic N-terminal loop of amylin forms non amyloid fibers.

Authors:  Stephanie M Cope; Sandip Shinde; Robert B Best; Giovanna Ghirlanda; Sara M Vaiana
Journal:  Biophys J       Date:  2013-10-01       Impact factor: 4.033

10.  Validation of archived chemical shifts through atomic coordinates.

Authors:  Wolfgang Rieping; Wim F Vranken
Journal:  Proteins       Date:  2010-08-15
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