[ASAP] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations

		BioNMR > Educational resources > Journal club
[ASAP] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations

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

05-01-2018, 10:57 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

[ASAP] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations

[ASAP] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations

Biochemistry
DOI: 10.1021/acs.biochem.8b00195

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations. Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations. Related Articles Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations. Biochemistry. 2018 Apr 17;: Authors: Baird-Titus JM, Thapa M, Doerdelmann T, Combs KA, Rance M Abstract An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is...	nmrlearner	Journal club	0	04-18-2018 01:41 PM
[NMR paper] Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations. Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations. Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations. Biochemistry. 2018 Feb 07;: Authors: Solomentsev G, Diehl C, Akke M Abstract FKBP12 (FK506 binding protein 12 kDa) is an important drug target that attracts a great deal of interest as a model system for computational drug design and studies on the role of protein dynamics in ligand binding. NMR...	nmrlearner	Journal club	0	02-08-2018 04:32 PM
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins Publication date: 2 February 2018 Source:Biophysical Journal, Volume 114, Issue 3, Supplement 1</br> Author(s): Falk Hoffmann, Mengjun Xue, Frans Mulder, Lars Schäfer</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	02-07-2018 03:41 PM
[NMR paper] Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy. Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy. Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy. Chemistry. 2015 Jun 12; Authors: Ivanir-Dabora H, Nimerovsky E, Madhu PK, Goldbourt A Abstract Magic-angle spinning solid-state NMR spectroscopy has been applied to study the dynamics of CBM3b-Cbh9A from Clostridium thermocellum...	nmrlearner	Journal club	0	06-16-2015 07:24 PM
[NMR paper] Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations. Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations. Related Articles Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations. J Phys Chem B. 2014 Oct 28; Authors: Allnér O, Foloppe N, Nilsson L Abstract Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory...	nmrlearner	Journal club	0	10-29-2014 03:51 PM
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Biochim Biophys Acta. 2011 Aug;1808(8):2019-30 Authors: Romo TD, Bradney LA, Greathouse DV, Grossfield A Abstract One approach to the growing health problem of antibiotic resistant bacteria is the development of antimicrobial peptides (AMPs) as alternative treatments. The...	nmrlearner	Journal club	0	08-19-2011 02:56 PM
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy. Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy. Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy. J Am Chem Soc. 2010 Dec 27; Authors: Esadze A, Li DW, Wang T, Bru?schweiler R, Iwahara J Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics...	nmrlearner	Journal club	0	12-29-2010 04:04 PM
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy Alexandre Esadze, Da-Wei Li, Tianzhi Wang, Rafael Bru?schweiler and Junji Iwahara http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107847d/aop/images/medium/ja-2010-07847d_0007.gif Journal of the American Chemical Society DOI: 10.1021/ja107847d http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/iFwgRBt-zto	nmrlearner	Journal club	0	12-28-2010 05:27 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