NMR structure and dynamics of the chimeric protein SH3-F2

Kutyshenko, V. P.; Gushchina, Liubov V.; Khristoforov, V. S.; Prokhorov, Dmitry; Timchenko, Maria; Kudrevatykh, Yu. A.; Fedyukina, Daria V.; Filimonov, Vladimir V.

doi:10.1134/s0026893310060129

Cited by 5 publications

(1 citation statement)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…When calculating models for a mean NMR structure, important structural restrictions can be imposed on permissible intervals of distances between partners in the O-NH and O-N inter peptide hydrogen bonds. For localizing such hydrogen bonds, data on H-D exchange rate for atoms of the NH peptide groups and on temperature dependence of their chemical shift coefficients are used as initial information [23,36]. The presence of inter peptide hydrogen bonds fixes positions of segments with the regular α and β back bone conformation, which, to a large degree, deter mines the general form of a protein molecule, or its tertiary structure.…”

Section: Energy Minimization Of Nmr Structuresmentioning

confidence: 99%

Crystallographic and NMR spectroscopic protein structures: Interresidue contacts

Abaturov

Nosova

2012

Mol Biol

View full text Add to dashboard Cite

Interresidue pair contacts were analyzed in detail for four pairs of protein structures solved using X ray analysis (X ray) and nuclear magnetic resonance (NMR). In the four NMR structures, at distances of ≤4.0 Å, the total number of pair contacts was 4-9% lower and, in general, the pair contacts were 0.02-0.16 Å shorter compared to the X ray structures. Each of the four structural pairs contained 83-94% common pair contacts (CPCs), which were formed by identical residues in both structures; the other 6-17% were longer intrinsic pair contacts (IPCs) formed by different residues in NMR and X ray structures, while the latter con tained more IPC. Every NMR structure contained three types of CPC that were shorter, longer, or equal to the identical contact pairs in the X ray structure of this protein. Methodologically different short CPCs pre vailed at a known distance dependence of the interresidue contact density in 60-61 pairs of NMR/X ray structures. Among the analyzed four structural pairs, contact shortening appeared upon the energy minimi zation of the crambin NMR structure and upon solving the ubiquitin, hen lysozyme, and monomeric hemo globin NMR structures using X PLOR software with decreased van der Waals atomic radii. The degree of contact shortening in the NMR structures diminished with an increase in the NMR data used to solve these structures. Among the 60 pairs of NMR/X ray structures, the major difference between α helical and β structural proteins in the dependences on interresidue distances of average contact density appeared due to strong α/β differences in the backbone local geometry.

show abstract

Section: Energy Minimization Of Nmr Structuresmentioning

confidence: 99%

Crystallographic and NMR spectroscopic protein structures: Interresidue contacts

Abaturov

Nosova

2012

Mol Biol

View full text Add to dashboard Cite

show abstract

High-Resolution Crystal Structure of Spectrin SH3 Domain Fused with a Proline-Rich Peptide

Gushchina

Габдулхаков

Nikonov

et al. 2011

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

A new chimeric protein, named WT-CIIA, was designed by connecting the proline-rich decapeptide PPPVPPYSAG to the C-terminus of the alpha-spectrin SH3 domain through a natural twelve-residue linker to obtain a single-chain model that would imitate intramolecular SH3-ligand interaction. The crystal structure of this fusion protein was determined at 1.7 Å resolution. The asymmetric unit of the crystal contained two SH3 globules contacting with one PPPVPPY fragment located between them. The domains are related by the two-fold non-crystallographic axis and the ligand lies in two opposite orientations with respect to the conservative binding sites of SH3 domains.

show abstract

Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-‘Bergerac’

Kutyshenko

Prokhorov

Molochkov

et al. 2013

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecylphosphocholine (DPC). This analysis revealed that retro-SHH does not contain rigid 3-D structure, but is characterized by the presence of residual secondary structure. Intriguingly, interaction with the DPC micelles affected the structures of SHH and retro-SHH very differently. In fact, micelles induce pronounced folding of retro-SHH, whereas micelle-bound SHH was noticeably disordered. Finally, we performed a disorder prediction with the PONDR-FIT algorithm and discovered that the reversal of the chain direction almost does not affect the propensity of a polypeptide for intrinsic disorder, since the disorder plot for retro-SHH was almost a mirror image of that for the normal SHH.

show abstract

NMR structure and dynamics of the chimeric protein SH3-F2

Cited by 5 publications

References 35 publications

Crystallographic and NMR spectroscopic protein structures: Interresidue contacts

Crystallographic and NMR spectroscopic protein structures: Interresidue contacts

High-Resolution Crystal Structure of Spectrin SH3 Domain Fused with a Proline-Rich Peptide

Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-‘Bergerac’

Contact Info

Product

Resources

About