NMR paper Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment

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[NMR paper] Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment

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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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08-22-2010, 03:33 AM

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Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment

Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment of an antibody in solution investigated by heteronuclear three-dimensional NMR spectroscopy.

Related Articles Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment of an antibody in solution investigated by heteronuclear three-dimensional NMR spectroscopy.

Biochemistry. 1994 Mar 22;33(11):3296-303

Authors: Freund C, Ross A, Plückthun A, Holak TA

Fv fragments, heterodimers of the variable light (VL) and variable heavy chain (VH) domains, are the smallest functional antibody units with molecular masses of approximately 26 kDa. The structural and dynamic properties of the Fv fragment and the corresponding single-chain Fv fragment (scFv: VH-linker-VL, 252 amino acids) of the phosphorylcholine-binding antibody McPC603 in the presence of hapten have been studied in solution by heteronuclear multidimensional NMR spectroscopy. Both 15N TOCSY-HMQC and triple-resonance experiments (HNCA and HN(CA)H, with 15N-13C-labeled protein) gave poor spectra, due to short T2 relaxation times for most of the backbone 1H, 15N, and 13C alpha atoms. The assignment procedure therefore relied upon the combination of amino acid and domain (VL) specifically labeled spectra and the 3D NOESY-HMQC spectrum of the uniformly 15N labeled Fv and scFv fragments. Approximately 80% of the 15N and 1H backbone and 60% of the 1H side-chain resonances have been assigned. Short- and long-range NOEs were used to determine the extent of beta-sheet structure and were compared to the X-ray crystallographic data. The 1H-15N NOE data indicate that the scFv backbone has a well-defined structure of limited conformational flexibility. However, the linker of the scFv fragment exhibits substantial fast internal motion (on the picosecond to nanosecond time scale) compared with the overall rotational correlation time of the whole molecule. Several residues in the CDRs, in turns, or at the C-terminal end of the protein have smaller NOEs, reflecting some degree of rapid motion in the protein backbone.

PMID: 8136365 [PubMed - indexed for MEDLINE]

Source: PubMed

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