Solution NMR structure of <i>Escherichia coli</i> ytfP expands the structural coverage of the UPF0131 protein domain family

Aramini, James M.; Huang, Yuanpeng Janet; Swapna, G.V.T.; Cort, John; Rajan, P.K.; Xiao, Rong; Shastry, R.; Acton, Thomas; Liu, Jinfeng; Rost, Burkhard; Kennedy, Michael A.; Montelione, Gaetano T.

doi:10.1002/prot.21450

Cited by 8 publications

(8 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our present multinuclear NMR data (obtained in collaboration with Perczel's laboratory at Eötvös University) show that TPPP/p25 possesses a highly flexible core situated between the unfolded N‐ and C‐terminal segments (unpublished results). These structural features of TPPP/p25 are complementary to the NMR data of Aramini et al .,15 who defined the structure of TPPP3/p20 (an N‐terminal‐free paralog of TPPP/p25) and provided conclusive evidence that the well‐defined core structure with five α‐helices is coupled with a >70 amino acid length unfolded C‐terminal tail15 (Fig. 1).…”

Section: Structural Characteristicssupporting

confidence: 72%

“…The predictors used were PONDR®,27 DisoPred2,28 and IUPred 29. Amino acids in rectangles and squares label α helices and β sheets, respectively, determined by NMR spectroscopy in TPPP3/p2015 or predicted by us using PSIPRED66 in TPPP/p25. Amino acid residues that are identical in the two proteins are in bold and those that are similar in italics.…”

Section: Structural Characteristicsmentioning

confidence: 99%

See 1 more Smart Citation

An unstructured protein with destructive potential: TPPP/p25 in neurodegeneration

Ovádi

Orosz

2009

BioEssays

View full text Add to dashboard Cite

TPPP/p25 is a recently discovered, unstructured protein involved in brain function. It is found predominantly in oligodendrocytes in normal brain but is enriched in neuronal and glial inclusions of Parkinson's disease and other synucleinopathies. Its physiological function seems to be the dynamic stabilization of microtubular ultrastructures, as well as the projections of mature oligodendrocytes and ciliary structures. We reappraise the earlier belief that TPPP/p25 is a brain-specific protein. We have identified and cloned two shorter (N-terminal-free) homologs of TPPP/p25 that behave differently from each other and from TPPP/p25. Two unique cell models have been established and used to study the effect of the unstructured protein on the energy metabolism and the formation of pathological aggregates. Our data suggest that the intracellular level of TPPP/p25 influences the cell differentiation, proliferation and the formation of protein aggregates, and consequently, the etiology of central nervous system diseases.

show abstract

Section: Structural Characteristicssupporting

confidence: 72%

Section: Structural Characteristicsmentioning

confidence: 99%

An unstructured protein with destructive potential: TPPP/p25 in neurodegeneration

Ovádi

Orosz

2009

BioEssays

View full text Add to dashboard Cite

show abstract

“…A structural similarity search, performed with the coordinates of the hypothetical protein using the DALI server,17 showed no structural similarity, indicating that 13879369 is a new fold. The recently solved structure of the hypothetical protein Ytfp from E. coli (PDB: 1xhs)18 shows significant similarity, with a root mean square deviation (RMSD) of 3.1 Å over 109 aligned residues with 22% sequence identity. Comparison with the shorter Ytfp structure (115 residues) reveals good overall agreement of both structures, but with three significant differences at the local structural level [Fig.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 Å resolution reveals a new fold

Klock

Schwarzenbacher

et al. 2005

Proteins

View full text Add to dashboard Cite

“…All NMR data were collected at 20 °C on Varian INOVA 500 and 600 MHz and Bruker AVANCE 600 and 800 NMR spectrometers. Complete 1 H, 13 C, and 15 N resonance assignments for full length B. subtilis YnzC and YnzC(1-46), were determined using GFT NMR data collection methods32,33 and conventional triple resonance NMR methods, respectively,34 and deposited in the BioMagResDB (BMRB accession numbers 7225 and 15476). 1 H- 15 N heteronuclear NOEs were measured with gradient sensitivity-enhanced 2D heteronuclear NOE approaches 35,36.…”

Section: Methodsmentioning

confidence: 99%

Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

et al. 2009

Self Cite

View full text Add to dashboard Cite

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three-dimensional structure determination of the ordered regions of proteins by NMR methods. In this paper, we demonstrate the application of 1 H/ 2 H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N-and Cterminal tails were evaluated using 1 H-15 N HSQC and 1 H-15 N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMSbased truncated construct for a 77-residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination.

show abstract

Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family

Cited by 8 publications

References 36 publications

An unstructured protein with destructive potential: TPPP/p25 in neurodegeneration

An unstructured protein with destructive potential: TPPP/p25 in neurodegeneration

Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 Å resolution reveals a new fold

Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

Contact Info

Product

Resources

About