Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.

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Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.

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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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05-04-2011, 04:14 PM

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Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.

Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.

Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.

J Phys Chem B. 2011 May 2;

Authors: Hwang S, Shao Q, Williams H, Hilty C, Gao YQ

A combined simulation and experimental study was performed to investigate how methanol affects the structure of a model peptide BBA5. BBA5 forms a stable ?-hairpin-?-helix structure in aqueous solutions. Molecular dynamics simulations were performed in water and methanol/water solutions using all-atom explicit models. NMR experiments were used to test the calculated results. The combined theoretical and experimental studies suggest that methanol strengthens the interactions between the polar backbone of the peptide and thus enhances the secondary structure formation; at the same time methanol weakens the hydrophobic interactions and results in an expansion of the hydrophobic core and an increase in gyration.

PMID: 21534580 [PubMed - as supplied by publisher]

Source: PubMed

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