NMR paper Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy.

		BioNMR > Educational resources > Journal club
[NMR paper] Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

06-15-2015, 02:45 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy.

Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy.

Related Articles Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy.

Biochim Biophys Acta. 2015 Jun 11;

Authors: Li Y, Li Q, Wong YL, Liew LS, Kang C

Abstract
Non-structural (NS) proteins of dengue virus (DENV) are important for viral replication. There are four membrane proteins that are coded by viral genome. NS2B was shown to be one of the membrane proteins and its main function was confirmed to regulate viral protease activity. Its membrane topology is still not known because only few studies have been conducted to understand its structure. Here we report the determination of membrane topology of NS2B from DENV serotype 4 using NMR spectroscopy. NS2B of DENV4 was expressed and purified in detergent micelles. The secondary structure of NS2B was first defined based on backbone chemical resonance assignment. Four helices were identified in NS2B. The membrane topology of NS2B was defined based on relaxation analysis and paramagnetic relaxation enhancement experiments. The last three helices were shown to be more stable than the first helices. The NS3 protease cofactor region between ?2 and ?3 is highly dynamic. Our results will be useful for further structural and functional analysis of NS2B.

PMID: 26072288 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Determinants of Dengue Virus NS4A Protein Oligomerization - Journal of Virology Determinants of Dengue Virus NS4A Protein Oligomerization - Journal of Virology <img alt="" height="1" width="1"> Determinants of Dengue Virus NS4A Protein Oligomerization Journal of Virology Nuclear magnetic resonance (NMR) analysis of NS4A amino acids 17 to 80 suggests that residues L31, L52, E53, G66, and G67 could participate in oligomerization. Ala substitution for 15 flavivirus conserved NS4A residues revealed that these amino acids ... Read here	nmrlearner	Online News	0	05-16-2015 01:45 PM
Mapping the Interactions between the NS4B and NS3 Proteins of Dengue Virus - Journal of Virology Mapping the Interactions between the NS4B and NS3 Proteins of Dengue Virus - Journal of Virology <img alt="" height="1" width="1"> Mapping the Interactions between the NS4B and NS3 Proteins of Dengue Virus Journal of Virology Using nuclear magnetic resonance (NMR), we found that the isolated cytoplasmic loop of NS4B is flexible, with a tendency to form a three-turn α-helix and two short β-strands. Upon binding to the NS3 helicase, 12 amino acids within the cytoplasmic loop ... Read here	nmrlearner	Online News	0	03-14-2015 06:49 AM
Mapping the Interactions between the NS4B and NS3 Proteins of Dengue Virus - Journal of Virology Mapping the Interactions between the NS4B and NS3 Proteins of Dengue Virus - Journal of Virology <img alt="" height="1" width="1"> Mapping the Interactions between the NS4B and NS3 Proteins of Dengue Virus Journal of Virology Using nuclear magnetic resonance (NMR), we found that the isolated cytoplasmic loop of NS4B is flexible, with a tendency to form a three-turn α-helix and two short β-strands. Upon binding to the NS3 helicase, 12 amino acids within the cytoplasmic loop ... Read here	nmrlearner	Online News	0	03-10-2015 07:22 PM
[NMR paper] Conformation and Topology of Diacylglycerol Kinase in E.coli Membranes Revealed by Solid-state NMR Spectroscopy. Conformation and Topology of Diacylglycerol Kinase in E.coli Membranes Revealed by Solid-state NMR Spectroscopy. Conformation and Topology of Diacylglycerol Kinase in E.coli Membranes Revealed by Solid-state NMR Spectroscopy. Angew Chem Int Ed Engl. 2014 Apr 2; Authors: Chen Y, Zhang Z, Tang X, Li J, Glaubitz C, Yang J Abstract Solid-state NMR is a powerful tool for studying membrane proteins in a native-like lipid environment. 3D magic angle spinning (MAS) NMR was employed to characterize the structure of E.coli diacylglycerol...	nmrlearner	Journal club	0	04-06-2014 02:01 AM
[NMR paper] Ca(2+) modulating ?-synuclein membrane transient interactions revealed by solution NMR spectroscopy. Ca(2+) modulating ?-synuclein membrane transient interactions revealed by solution NMR spectroscopy. Related Articles Ca(2+) modulating ?-synuclein membrane transient interactions revealed by solution NMR spectroscopy. Biochim Biophys Acta. 2013 Dec 4; Authors: Zhang Z, Dai C, Bai J, Xu G, Liu M, Li C Abstract ?-synuclein is involved in Parkinson's disease and its interaction with cell membrane is crucial to its pathological and physiological functions. Membrane properties, such as curvature, lipid composition have been shown to affect the...	nmrlearner	Journal club	0	12-10-2013 05:36 PM
[NMR paper] Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy. J Biomol NMR. 2013 Aug 21; Authors: Mote KR, Gopinath T, Veglia G Abstract The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy...	nmrlearner	Journal club	0	08-23-2013 01:07 AM
[NMR paper] NMR analysis of a novel enzymatically-active unlinked Dengue NS2B-NS3 protease complex. NMR analysis of a novel enzymatically-active unlinked Dengue NS2B-NS3 protease complex. Related Articles NMR analysis of a novel enzymatically-active unlinked Dengue NS2B-NS3 protease complex. J Biol Chem. 2013 Mar 19; Authors: Kim YM, Gayen S, Kang C, Joy J, Huang Q, Chen AS, Wee JL, Ang MJ, Lim HA, Hung AW, Li R, Noble CG, Lee LT, Yip A, Wang QY, Chia CS, Hill J, Shi PY, Keller TH Abstract The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a...	nmrlearner	Journal club	0	03-21-2013 02:58 PM
Probing membrane topology of the antimicrobial peptide distinctin by solid-state NMR Probing membrane topology of the antimicrobial peptide distinctin by solid-state NMR spectroscopy in zwitterionic and charged lipid bilayers. Related Articles Probing membrane topology of the antimicrobial peptide distinctin by solid-state NMR spectroscopy in zwitterionic and charged lipid bilayers. Biochim Biophys Acta. 2010 Aug 15; Authors: Verardi R, Traaseth NJ, Shi L, Porcelli F, Monfregola L, De Luca S, Amodeo P, Veglia G, Scaloni A Distinctin is a 47-residue antimicrobial peptide, which interacts with negatively charged membranes and is...	nmrlearner	Journal club	0	08-21-2010 01:02 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off