Literature DB >> 19761238

Phage-induced alignment of membrane proteins enables the measurement and structural analysis of residual dipolar couplings with dipolar waves and lambda-maps.

Sang Ho Park1, Woo Sung Son, Rishi Mukhopadhyay, Homayoun Valafar, Stanley J Opella.   

Abstract

At pH > 6 added filamentous bacteriophage fd is compatible with many of the detergents used to solubilize membrane proteins for solution NMR studies of membrane proteins and, therefore, serves as an alignment media. In combination with strained polyacrylamide gel alignment, Dipolar Waves can be used to directly assess the secondary structure and a lambda-map extracts the order tensors for de novo structure calculation of membrane proteins without distance restraints.

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Year:  2009        PMID： 19761238      PMCID： PMC2771775          DOI： 10.1021/ja905640d

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


  23 in total

1.  Correlation of the structural and functional domains in the membrane protein Vpu from HIV-1.

Authors:  F M Marassi; C Ma; H Gratkowski; S K Straus; K Strebel; M Oblatt-Montal; M Montal; S J Opella
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-07       Impact factor: 11.205

2.  Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes.

Authors:  H J Sass; G Musco; S J Stahl; P T Wingfield; S Grzesiek
Journal:  J Biomol NMR       Date:  2000-12       Impact factor: 2.835

Review 3.  Dipolar couplings in macromolecular structure determination.

Authors:  A Bax; G Kontaxis; N Tjandra
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

4.  A simple apparatus for generating stretched polyacrylamide gels, yielding uniform alignment of proteins and detergent micelles.

Authors:  J J Chou; S Gaemers; B Howder; J M Louis; A Bax
Journal:  J Biomol NMR       Date:  2001-12       Impact factor: 2.835

5.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

6.  Structure and dynamics of a membrane protein in micelles from three solution NMR experiments.

Authors:  Sangwon Lee; Michael F Mesleh; Stanley J Opella
Journal:  J Biomol NMR       Date:  2003-08       Impact factor: 2.835

7.  Dipolar waves map the structure and topology of helices in membrane proteins.

Authors:  Michael F Mesleh; Sangwon Lee; Gianluigi Veglia; David S Thiriot; Francesca M Marassi; Stanley J Opella
Journal:  J Am Chem Soc       Date:  2003-07-23       Impact factor: 15.419

8.  Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule.

Authors:  Junji Iwahara; Charles D Schwieters; G Marius Clore
Journal:  J Am Chem Soc       Date:  2004-05-12       Impact factor: 15.419

9.  Calmodulin tagging provides a general method of using lanthanide induced magnetic field orientation to observe residual dipolar couplings in proteins in solution.

Authors:  J Feeny; B Birdsall; A F Bradbury; R R Biekofsky; P M Bayley
Journal:  J Biomol NMR       Date:  2001-09       Impact factor: 2.835

10.  Efficient and accurate estimation of relative order tensors from lambda-maps.

Authors:  Rishi Mukhopadhyay; Xijiang Miao; Paul Shealy; Homayoun Valafar
Journal:  J Magn Reson       Date:  2009-03-05       Impact factor: 2.229
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  13 in total

1.  Structure and dynamics of the membrane-bound form of Pf1 coat protein: implications of structural rearrangement for virus assembly.

Authors:  Sang Ho Park; Francesca M Marassi; David Black; Stanley J Opella
Journal:  Biophys J       Date:  2010-09-08       Impact factor: 4.033

Review 2.  Comparative NMR studies demonstrate profound differences between two viroporins: p7 of HCV and Vpu of HIV-1.

Authors:  Gabriel A Cook; Hua Zhang; Sang Ho Park; Yan Wang; Stanley J Opella
Journal:  Biochim Biophys Acta       Date:  2010-08-18

3.  Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings.

Authors:  Mikhail Simin; Stephanie Irausquin; Casey A Cole; Homayoun Valafar
Journal:  J Biomol NMR       Date:  2014-11-18       Impact factor: 2.835

4.  Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings.

Authors:  Stefan Bibow; Marta G Carneiro; T Michael Sabo; Claudia Schwiegk; Stefan Becker; Roland Riek; Donghan Lee
Journal:  Protein Sci       Date:  2014-05-06       Impact factor: 6.725

5.  Backbone resonance assignment and order tensor estimation using residual dipolar couplings.

Authors:  Paul Shealy; Yizhou Liu; Mikhail Simin; Homayoun Valafar
Journal:  J Biomol NMR       Date:  2011-06-12       Impact factor: 2.835

6.  Triton X-100 as the "short-chain lipid" improves the magnetic alignment and stability of membrane proteins in phosphatidylcholine bilayers for oriented-sample solid-state NMR spectroscopy.

Authors:  Sang Ho Park; Stanley J Opella
Journal:  J Am Chem Soc       Date:  2010-09-15       Impact factor: 15.419

7.  Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR.

Authors:  S K Straus; W R P Scott; C D Schwieters; D A Marvin
Journal:  Eur Biophys J       Date:  2010-11-17       Impact factor: 1.733

8.  Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein.

Authors:  Paul Shealy; Mikhail Simin; Sang Ho Park; Stanley J Opella; Homayoun Valafar
Journal:  J Magn Reson       Date:  2010-07-30       Impact factor: 2.229

9.  Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings.

Authors:  Rishi Mukhopadhyay; Stephanie Irausquin; Christopher Schmidt; Homayoun Valafar
Journal:  J Bioinform Comput Biol       Date:  2014-01-07       Impact factor: 1.122

10.  DNA nanotubes for NMR structure determination of membrane proteins.

Authors:  Gaëtan Bellot; Mark A McClintock; James J Chou; William M Shih
Journal:  Nat Protoc       Date:  2013-03-21       Impact factor: 13.491
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