High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation an

		BioNMR > Educational resources > Journal club
High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation an

Webservers

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-17-2010, 01:53 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation an

High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation and Implications for Protofilament Assembly and Structure .

Related Articles High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation and Implications for Protofilament Assembly and Structure .

Biochemistry. 2010 Aug 13;

Authors: Bayro MJ, Maly T, Birkett NR, Macphee CE, Dobson CM, Griffin RG

The SH3 domain of the PI3 kinase (PI3-SH3 or PI3K-SH3) readily aggregates into fibrils in vitro and has served as an important model system in the investigation of the molecular properties and mechanism of formation of amyloid fibrils. We describe the molecular conformation of PI3-SH3 in amyloid fibril form as revealed by magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy. The MAS NMR spectra of these fibrils display excellent resolution, with narrow (13)C and (15)N line widths, representing a high degree of structural order and the absence of extensive molecular motion for the majority of the polypeptide chain. We have identified the spin systems of 82 of the 86 residues in the protein and obtained sequential resonance assignments for 75 of them. Chemical shift analysis indicates that the protein subunits making up the fibril adopt a compact conformation consisting of four well-defined beta-sheet regions and four random-coil elements with varying degrees of local dynamics or disorder. The backbone conformation of PI3-SH3 in fibril form differs significantly from that of the native state of the protein, both in secondary structure and in the location of dynamic or disordered segments. The site-specific MAS NMR analysis of PI3-SH3 fibrils we report here is compared with previously published mechanistic and structural data, resulting in a detailed interpretation of the factors that mediate fibril formation by PI3-SH3 and allowing us to propose a possible model of the core structure of the fibrils. Our results confirm the structural similarities between PI3-SH3 fibrils and amyloid assemblies directly related to degenerative and infectious diseases.

PMID: 20707313 [PubMed - as supplied by publisher]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using Î´ subunit (20 kDa) of Bacillus subtilis RNA polymerase...	nmrlearner	Journal club	0	02-21-2012 03:40 AM
Solid-state NMR analysis of interaction sites of curcumin and 42-residue amyloid ?-protein fibrils. Solid-state NMR analysis of interaction sites of curcumin and 42-residue amyloid ?-protein fibrils. Solid-state NMR analysis of interaction sites of curcumin and 42-residue amyloid ?-protein fibrils. Bioorg Med Chem. 2011 Aug 27; Authors: Masuda Y, Fukuchi M, Yatagawa T, Tada M, Takeda K, Irie K, Akagi KI, Monobe Y, Imazawa T, Takegoshi K Abstract Aggregation of 42-residue amyloid ?-protein (A?42) plays a pivotal role in the etiology of Alzheimer's disease (AD). Curcumin, the yellow pigment in the rhizome of turmeric, attracts...	nmrlearner	Journal club	0	09-20-2011 03:10 PM
Sensitive 13Câ??13C correlation spectra of amyloid fibrils at very high spinning frequencies and magnetic fields Sensitive 13Câ??13C correlation spectra of amyloid fibrils at very high spinning frequencies and magnetic fields Abstract Sensitive 2D solid-state 13Câ??13C correlation spectra of amyloid Î² fibrils have been recorded at very fast spinning frequencies and very high magnetic fields. It is demonstrated that PARIS-xy recoupling using moderate rf amplitudes can provide structural information by promoting efficient magnetization transfer even under such challenging experimental conditions. Furthermore, it has been shown both experimentally and by numerical simulations that the method is not...	nmrlearner	Journal club	0	04-01-2011 09:23 AM
Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy. Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy. Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy. J Am Chem Soc. 2010 Oct 6;132(39):13765-75 Authors: Van Melckebeke H, Wasmer C, Lange A, Ab E, Loquet A, Böckmann A, Meier BH We present a strategy to solve the high-resolution structure of amyloid fibrils by solid-state NMR and use it to determine the atomic-resolution structure of the prion domain of the fungal prion HET-s...	nmrlearner	Journal club	0	01-21-2011 12:00 PM
Characterization of amyloid fibrils of human beta-2-microglobulin by high-resolution magic-angle spinning NMR. Characterization of amyloid fibrils of human beta-2-microglobulin by high-resolution magic-angle spinning NMR. Characterization of amyloid fibrils of human beta-2-microglobulin by high-resolution magic-angle spinning NMR. Chembiochem. 2010 Sep 3;11(13):1829-32 Authors: Skora L, Becker S, Zweckstetter M	nmrlearner	Journal club	0	01-05-2011 09:51 PM
[NMR paper] High-resolution molecular structure of a peptide in an amyloid fibril determined by m High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Related Articles High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):711-6 Authors: Jaroniec CP, MacPhee CE, Bajaj VS, McMahon MT, Dobson CM, Griffin RG Amyloid fibrils are self-assembled filamentous structures associated with protein deposition conditions including Alzheimer's disease and the transmissible...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
Atomic-Resolution Three-Dimensional Structure of HET-s(218-289) Amyloid Fibrils by So Atomic-Resolution Three-Dimensional Structure of HET-s(218-289) Amyloid Fibrils by Solid-State NMR Spectroscopy He?le?ne Van Melckebeke, Christian Wasmer, Adam Lange, Eiso AB, Antoine Loquet, Anja Bo?ckmann and Beat H. Meier http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja104213j/aop/images/medium/ja-2010-04213j_0001.gif Journal of the American Chemical Society DOI: 10.1021/ja104213j http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/qGRhA6CtOVc	nmrlearner	Journal club	0	09-10-2010 12:48 AM
High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation an High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation and Implications for Protofilament Assembly and Structure http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi100864t/aop/images/medium/bi-2010-00864t_0004.gifBiochemistry, Volume 0, Issue 0, Articles ASAP (As Soon As Publishable). More...	nmrlearner	Journal club	0	08-18-2010 12:19 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off