2L6Q

New high resolution NMR structure of gpW (W protein of bacteriophage lambda) at neutral pH

2L6Q の概要

• エントリーDOI: 10.2210/pdb2l6q/pdb
• 関連するPDBエントリー: 2L6R
• NMR情報: BMRB: 17321
• 分子名称: Head-to-tail joining protein W (GpW) from bacteriophage origin (1 entity in total)
• 機能のキーワード: gpw, fast protein folding, downhill protein folding, folding simulation, viral protein
• 由来する生物種: Enterobacteria phage lambda
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 6989.05

構造登録者

Sborgi, L.,Verma, A.,Munoz, V.,de Alba, E. (登録日: 2010-11-24, 公開日: 2011-11-16, 最終更新日: 2024-05-01)

主引用文献

Sborgi, L.,Verma, A.,Munoz, V.,de Alba, E.
Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage Lambda
Plos One, 6:e26409-e26409, 2011

PubMed Abstract: GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.

PubMed: 22087227
DOI: 10.1371/journal.pone.0026409

実験手法

SOLUTION NMR