Conformations of stevastelin C3 analogs: computational deconvolution of NMR data reve

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Conformations of stevastelin C3 analogs: computational deconvolution of NMR data reve

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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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11-06-2010, 11:02 AM

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Conformations of stevastelin C3 analogs: computational deconvolution of NMR data reve

Conformations of stevastelin C3 analogs: computational deconvolution of NMR data reveals conformational heterogeneity and novel motifs.

Related Articles Conformations of stevastelin C3 analogs: computational deconvolution of NMR data reveals conformational heterogeneity and novel motifs.

Biopolymers. 2010 Nov;93(11):968-76

Authors: Jogalekar AS

The stevastelins are depsipeptide natural products that show valuable immunomodulatory and phosphatase inhibitory activity. A previous report described the synthesis, conformational analysis, and biological activity of modified diastereomeric C3 analogs (1) of these molecules and deduced a single dominant conformational scaffold for each of the six benzylated stevastelin diastereomers in solution. In this study, we report a combined computational and experimental approach (NAMFIS) of these analogs based on geometric variables from the NMR data and extensive conformational searching that suggests a more subtle and complex distribution of conformations in solution. Although the results indicate some conformations to be similar to those previously proposed, they include novel motifs not observed earlier such as gamma turns. In addition, the NAMFIS analysis confirms dramatic changes in conformations accompanying a chirality change at the C3 center and also establishes the conformational homogeneity of the D-serine diastereomers. The NAMFIS analysis thus suggests the use of D-serine as a possible constraining element in peptide design and derives a set of experimental solution conformers that could shed light on the bioactive conformation of the stevastelins. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 968-976, 2010.

PMID: 20564058 [PubMed - indexed for MEDLINE]

Source: PubMed

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