Literature DB >> 28373928

Nanodiscs and Solution NMR: preparation, application and challenges.

Robbins Puthenveetil1, Khiem Nguyen2, Olga Vinogradova2.   

Abstract

Nanodiscs provide an excellent system for the structure-function investigation of membrane proteins. Its direct advantage lies in presenting a water soluble form of an otherwise hydrophobic molecule, making it amenable to a plethora of solution techniques. Nuclear Magnetic Resonance is one such high resolution approach that looks at the structure and dynamics of a protein with atomic level precision. Recently, there has been a breakthrough in making nanodiscs more susceptible for structure determination by solution NMR, yet it still remains to become the preferred choice for a membrane mimetic. In this practical review, we provide a general discourse on nanodisc and its application to solution NMR. We also offer potential solutions to remediate the technical challenges associated with nanodisc preparation and the choice of proper experimental set-ups. Along with discussing several structural applications, we demonstrate an alternative use of nanodiscs for functional studies, where we investigated the phosphorylation of a cell surface receptor, Integrin. This is the first successful manifestation of observing activated receptor phosphorylation in nanodiscs through NMR. We additionally present an on-column method for nanodisc preparation with multiple strategies and discuss the potential use of alternative nanoscale phospholipid bilayer systems like SMA lipid discs and Saposin-A lipoprotein discs.

Entities:  

Keywords:  Integrin; Nanodisc; SMALP; Saposin-A; Styrene Maleic Acid; beta barrel; membrane proteins; nanoscale phospholipid bilayers; solution NMR; transmembrane

Year:  2016        PMID: 28373928      PMCID: PMC5375033          DOI: 10.1515/ntrev-2016-0076

Source DB:  PubMed          Journal:  Nanotechnol Rev        ISSN: 2191-9089            Impact factor:   7.848


  61 in total

1.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Authors:  A Krogh; B Larsson; G von Heijne; E L Sonnhammer
Journal:  J Mol Biol       Date:  2001-01-19       Impact factor: 5.469

2.  Phenotology of disease-linked proteins.

Authors:  Jeffrey K Myers; Lauren A Beihoffer; Charles R Sanders
Journal:  Hum Mutat       Date:  2005-01       Impact factor: 4.878

3.  CHARMM-GUI: a web-based graphical user interface for CHARMM.

Authors:  Sunhwan Jo; Taehoon Kim; Vidyashankara G Iyer; Wonpil Im
Journal:  J Comput Chem       Date:  2008-08       Impact factor: 3.376

4.  Randomization improves sparse sampling in multidimensional NMR.

Authors:  Jeffrey C Hoch; Mark W Maciejewski; Blagoje Filipovic
Journal:  J Magn Reson       Date:  2008-05-21       Impact factor: 2.229

5.  NMR studies of protein structure and dynamics - a look backwards and forwards.

Authors:  Lewis E Kay
Journal:  J Magn Reson       Date:  2011-08-31       Impact factor: 2.229

6.  Reconstitution of the Cytb5-CytP450 Complex in Nanodiscs for Structural Studies using NMR Spectroscopy.

Authors:  Meng Zhang; Rui Huang; Rose Ackermann; Sang-Choul Im; Lucy Waskell; Anna Schwendeman; Ayyalusamy Ramamoorthy
Journal:  Angew Chem Int Ed Engl       Date:  2016-02-29       Impact factor: 15.336

7.  NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating.

Authors:  Zakhar O Shenkarev; Alexander S Paramonov; Ekaterina N Lyukmanova; Lyudmila N Shingarova; Sergei A Yakimov; Maxim A Dubinnyi; Vladimir V Chupin; Mikhail P Kirpichnikov; Marcel J J Blommers; Alexander S Arseniev
Journal:  J Am Chem Soc       Date:  2010-04-28       Impact factor: 15.419

8.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

9.  G Protein-Coupled Receptor Kinase 2 (GRK2) and 5 (GRK5) Exhibit Selective Phosphorylation of the Neurotensin Receptor in Vitro.

Authors:  Sayaka Inagaki; Rodolfo Ghirlando; Sergey A Vishnivetskiy; Kristoff T Homan; Jim F White; John J G Tesmer; Vsevolod V Gurevich; Reinhard Grisshammer
Journal:  Biochemistry       Date:  2015-07-08       Impact factor: 3.162

10.  A detergent-free strategy for the reconstitution of active enzyme complexes from native biological membranes into nanoscale discs.

Authors:  Ashley R Long; Catherine C O'Brien; Ketan Malhotra; Christine T Schwall; Arlene D Albert; Anthony Watts; Nathan N Alder
Journal:  BMC Biotechnol       Date:  2013-05-11       Impact factor: 2.563

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  17 in total

1.  The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region.

Authors:  Khiem Nguyen; Jin Li; Robbins Puthenveetil; Xiaochen Lin; Michael M Poe; Chia-Hung Christine Hsiao; Olga Vinogradova; Andrew J Wiemer
Journal:  FASEB J       Date:  2017-07-13       Impact factor: 5.191

Review 2.  Spectroscopic studies of the cytochrome P450 reaction mechanisms.

Authors:  Piotr J Mak; Ilia G Denisov
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2017-06-28       Impact factor: 3.036

Review 3.  The role of small-angle scattering in structure-based screening applications.

Authors:  Po-Chia Chen; Janosch Hennig
Journal:  Biophys Rev       Date:  2018-10-10

Review 4.  Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments.

Authors:  Robbins Puthenveetil; Olga Vinogradova
Journal:  J Biol Chem       Date:  2019-09-24       Impact factor: 5.157

5.  Isotopic Labeling of Eukaryotic Membrane Proteins for NMR Studies of Interactions and Dynamics.

Authors:  Igor Dikiy; Lindsay D Clark; Kevin H Gardner; Daniel M Rosenbaum
Journal:  Methods Enzymol       Date:  2018-12-18       Impact factor: 1.600

6.  Macrodiscs Comprising SMALPs for Oriented Sample Solid-State NMR Spectroscopy of Membrane Proteins.

Authors:  Jasmina Radoicic; Sang Ho Park; Stanley J Opella
Journal:  Biophys J       Date:  2018-06-15       Impact factor: 4.033

Review 7.  Recent advances in nanodisc technology for membrane protein studies (2012-2017).

Authors:  John E Rouck; John E Krapf; Jahnabi Roy; Hannah C Huff; Aditi Das
Journal:  FEBS Lett       Date:  2017-07-06       Impact factor: 4.124

8.  K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function.

Authors:  Shufen Cao; Stacey Chung; SoonJeung Kim; Zhenlu Li; Danny Manor; Matthias Buck
Journal:  J Biol Chem       Date:  2019-02-21       Impact factor: 5.157

9.  Metal-Chelated Polymer Nanodiscs for NMR Studies.

Authors:  Nathaniel Z Hardin; Vojč Kocman; Giacomo M Di Mauro; Thirupathi Ravula; Ayyalusamy Ramamoorthy
Journal:  Angew Chem Int Ed Engl       Date:  2019-10-17       Impact factor: 15.336

Review 10.  Nanodiscs: A toolkit for membrane protein science.

Authors:  Stephen G Sligar; Ilia G Denisov
Journal:  Protein Sci       Date:  2020-11-16       Impact factor: 6.993

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