NMR paper Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

		BioNMR > Educational resources > Journal club
[NMR paper] Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

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

06-06-2023, 09:06 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,206

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

Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

Large-scale interdomain rearrangements are essential to protein function, governing the activity of large enzymes and molecular machineries. Yet, obtaining an atomic-resolution understanding of how the relative domain positioning is affected by external stimuli is a hard task in modern structural biology. Here, we show that combining structural modeling by AlphaFold2 with coarse-grained molecular dynamics simulations and NMR residual dipolar coupling data is sufficient to characterize the...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] A coarse-grained approach to NMR-data-assisted modeling of protein structures A coarse-grained approach to NMR-data-assisted modeling of protein structures The ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically selects consistent restraints. Hamiltonian replica exchange... More...	nmrlearner	Journal club	0	09-23-2022 06:24 AM
[NMR paper] Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR Variable domains of camelid antibodies (so-called nanobodies or V(H)H) are the smallest antibody fragments that retain complete functionality and therapeutic potential. Understanding of the nanobody-binding interface has become a pre-requisite for rational antibody design and engineering. The nanobody-binding interface consists of up to three hypervariable loops, known as the CDR loops. Here, we structurally and dynamically characterize the conformational diversity of an anti-GFP-binding... More...	nmrlearner	Journal club	0	05-29-2022 03:31 AM
[NMR paper] Probabilistic Modeling of RNA Ensembles Using NMR Chemical Shifts Probabilistic Modeling of RNA Ensembles Using NMR Chemical Shifts NMR-derived chemical shifts are structural fingerprints that are sensitive to the underlying conformational distributions of molecules. Thus, chemical shift data are now routinely used to infer the dynamical or conformational ensembles of peptides and proteins. However, for RNAs, techniques for inferring their conformational ensembles from chemical shift data have received less attention. Here, we used chemical shift data and the Bayesian/maximum entropy (BME) approach to model the secondary... More...	nmrlearner	Journal club	0	08-28-2021 07:56 AM
Closed model: NMR and X-rays open up enzyme clue Closed model: NMR and X-rays open up enzyme clue http://www.spectroscopynow.com/common/images/thumbnails/15baf3f399f.jpgA structural model of the closed state of the "energy budget" enzyme adenylate kinase emerges from a nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography study by European scientists. Read the rest at Spectroscopynow.com	nmrlearner	General	0	07-03-2017 02:31 AM
[NMR paper] Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Proc Natl Acad Sci U S A. 2015 Aug 24; Authors: Venditti V, Schwieters CD, Grishaev A, Clore GM Abstract Enzyme I (EI) is the first component in the bacterial phosphotransferase system, a signal transduction pathway in which phosphoryl transfer through a series...	nmrlearner	Journal club	0	08-26-2015 10:21 AM
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...	nmrlearner	Journal club	0	02-11-2012 10:31 AM
[NMR paper] Folding Trp-cage to NMR resolution native structure using a coarse-grained protein mo Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Related Articles Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys J. 2005 Jan;88(1):147-55 Authors: Ding F, Buldyrev SV, Dokholyan NV We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended conformation. We demonstrate the ability...	nmrlearner	Journal club	0	11-24-2010 10:03 PM
[NMR paper] Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia col Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR. Biochemistry. 1997 Mar 4;36(9):2517-30 Authors: Garrett DS, Seok YJ, Liao DI, Peterkofsky A, Gronenborn AM, Clore GM ...	nmrlearner	Journal club	0	08-22-2010 03:31 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