NMR paper Solution NMR analysis of the interaction between the actinoporin Sticholysin I and DHPC micelles. Correlation with backbone dynamics.

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[NMR paper] Solution NMR analysis of the interaction between the actinoporin Sticholysin I and DHPC micelles. Correlation with backbone dynamics.

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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:

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11-13-2013, 09:22 PM

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Solution NMR analysis of the interaction between the actinoporin Sticholysin I and DHPC micelles. Correlation with backbone dynamics.

Solution NMR analysis of the interaction between the actinoporin Sticholysin I and DHPC micelles. Correlation with backbone dynamics.

Related Articles Solution NMR analysis of the interaction between the actinoporin Sticholysin I and DHPC micelles. Correlation with backbone dynamics.

Proteins. 2013 Nov 12;

Authors: Castilla AL, Santos FP, Schreier S, Pires JR

Abstract
Sticholysin I (StI), an actinoporin expressed as a water-soluble protein by the sea anemone Stichodactyla helianthus, binds to natural and model membranes, forming oligomeric pores. It is proposed that the first event of a multistep pore formation mechanism consists of the monomeric protein attachment to the lipid bilayer. To date there is no high-resolution structure of the actinoporin pore or other membrane-bound form available. Here we evaluated StI:micelle complexes of variable lipid composition to look for a suitable model for NMR studies. Micelles of pure or mixed lysophospholipids and of dihexanoyl phosphatidylcholine (DHPC) were examined. The StI:DHPC micelle was found to be the best system, yielding a stable sample and good quality spectra. A comprehensive chemical shift perturbation analysis was performed to map the StI membrane recognition site in the presence of DHPC micelles. The region mapped (residues F(51) , R(52) , S(53) in loop 3; F(107) , D(108) , Y(109) , W(111) , Y(112) , W(115) in loop 7; Q12(9) , Y(132) , D(134) , M(135) , Y(136) , Y(137) , G(138) in helix-?2) is in agreement with previously reported data, but additional residues were found to interact, especially residues V(81) , A(82) , T(83) , G(84) in loop 5, and A(85) , A(87) in strand-?5. Backbone dynamics measurements of StI free in solution and bound to micelles highlighted the relevance of protein flexibility for membrane binding and suggested that a conformer selection process may take place during protein-membrane interaction. We conclude that the StI:DHPC micelles system is a suitable model for further characterization of an actinoporin membrane-bound form by solution NMR. © Proteins 2013;. © 2013 Wiley Periodicals, Inc.

PMID: 24218049 [PubMed - as supplied by publisher]

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