Zinc-binding structure of a catalytic amyloid from solid-state NMR [Biophysics and Computational Biology]

		BioNMR > Educational resources > Journal club
Zinc-binding structure of a catalytic amyloid from solid-state NMR [Biophysics and Computational Biology]

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

06-13-2017, 09:46 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,184

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

Zinc-binding structure of a catalytic amyloid from solid-state NMR [Biophysics and Computational Biology]

Zinc-binding structure of a catalytic amyloid from solid-state NMR [Biophysics and Computational Biology]

Myungwoon Lee, Tuo Wang, Olga V. Makhlynets, Yibing Wu, Nicholas F. Polizzi, Haifan Wu, Pallavi M. Gosavi, Jan Stohr, Ivan V. Korendovych, William F. DeGrado, Mei Hong...
Date: 2017-06-13

Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of their small molecular size and their ability to self-purify and catalyze chemical reactions. They also provide attractive backbones... Read More

PNAS:
Number: 24
Volume: 114

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Zinc-binding structure of a catalytic amyloid from solid-state NMR. Zinc-binding structure of a catalytic amyloid from solid-state NMR. Related Articles Zinc-binding structure of a catalytic amyloid from solid-state NMR. Proc Natl Acad Sci U S A. 2017 May 31;: Authors: Lee M, Wang T, Makhlynets OV, Wu Y, Polizzi NF, Wu H, Gosavi PM, Stöhr J, Korendovych IV, DeGrado WF, Hong M Abstract Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of...	nmrlearner	Journal club	0	06-02-2017 08:33 PM
Fluorine-19 NMR and computational quantification of isoflurane binding to the voltage-gated sodium channel NaChBac [Biophysics and Computational Biology] Fluorine-19 NMR and computational quantification of isoflurane binding to the voltage-gated sodium channel NaChBac Monica N. Kinde, Vasyl Bondarenko, Daniele Granata, Weiming Bu, Kimberly C. Grasty, Patrick J. Loll, Vincenzo Carnevale, Michael L. Klein, Roderic G. Eckenhoff, Pei Tang, Yan Xu... Date: 2016-11-29 Voltage-gated sodium channels (NaV) play an important role in general anesthesia. Electrophysiology measurements suggest that volatile anesthetics such as isoflurane inhibit NaV by stabilizing the inactivated state or altering the inactivation kinetics. Recent computational...	nmrlearner	Journal club	0	11-29-2016 09:02 PM
ssNMR structure of helical filaments [Biophysics and Computational Biology] ssNMR structure of helical filaments He, L., Bardiaux, B., Ahmed, M., Spehr, J., Konig, R., Lunsdorf, H., Rand, U., Luhrs, T., Ritter, C.... Date: 2016-01-19 The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled... Read More PNAS: Number: 3	nmrlearner	Journal club	0	01-20-2016 09:01 AM
Structure of CAP-Gly on microtubules by MAS NMR [Biophysics and Computational Biology] Structure of CAP-Gly on microtubules by MAS NMR Yan, S., Guo, C., Hou, G., Zhang, H., Lu, X., Williams, J. C., Polenova, T.... Date: 2015-11-24 Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant... Read More PNAS: Number: 47	nmrlearner	Journal club	0	11-24-2015 09:32 PM
Class II preQ1 riboswitch NMR structure [Biophysics and Computational Biology] Class II preQ1 riboswitch NMR structure Kang, M., Eichhorn, C. D., Feigon, J.... Date: 2014-02-11 Prequeuosine (preQ1) riboswitches are RNA regulatory elements located in the 5? UTR of genes involved in the biosynthesis and transport of preQ1, a precursor of the modified base queuosine universally found in four tRNAs. The preQ1 class II (preQ1-II) riboswitch regulates preQ1 biosynthesis at the translational level. We present the... Read More PNAS: Number: 6	nmrlearner	Journal club	0	02-11-2014 09:58 PM
Cu-SOD structure and dynamics by solid-state NMR [Biophysics and Computational Biology] Cu-SOD structure and dynamics by solid-state NMR Knight, M. J., Pell, A. J., Bertini, I., Felli, I. C., Gonnelli, L., Pierattelli, R., Herrmann, T., Emsley, L., Pintacuda, G.... Date: 2012-07-10 We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with 1H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of 15N and 13C nuclear relaxation rates. The system on which we demonstrate these methods is the...	nmrlearner	Journal club	0	07-10-2012 06:01 PM
Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method [Biophysics and Computational Biology] Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method Verardi, R., Shi, L., Traaseth, N. J., Walsh, N., Veglia, G.... Date: 2011-05-31 Phospholamban (PLN) is a type II membrane protein that inhibits the sarcoplasmic reticulum Ca2+-ATPase (SERCA), thereby regulating calcium homeostasis in cardiac muscle. In membranes, PLN forms pentamers that have been proposed to function either as a storage for active monomers or as ion channels. Here, we report the T-state structure of pentameric PLN solved by a hybrid solution and...	nmrlearner	Journal club	0	05-31-2011 11:41 PM
Solid-state 2H NMR relaxation illuminates functional dynamics of retinal cofactor in membrane activation of rhodopsin [Biophysics and Computational Biology] Solid-state 2H NMR relaxation illuminates functional dynamics of retinal cofactor in membrane activation of rhodopsin Struts, A. V., Salgado, G. F. J., Brown, M. F.... Date: 2011-05-17 Rhodopsin is a canonical member of the family of G protein-coupled receptors, which transmit signals across cellular membranes and are linked to many drug interventions in humans. Here we show that solid-state 2H NMR relaxation allows investigation of light-induced changes in local ps–ns time scale motions of retinal bound to rhodopsin. Site-specific 2H labels were introduced into methyl groups of the...	nmrlearner	Journal club	0	05-17-2011 08:40 PM

« 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