Local Backbone Flexibility as a Determinant of theApparent pKa Values of Buried IonizableGroups in Proteins

		BioNMR > Educational resources > Journal club
Local Backbone Flexibility as a Determinant of theApparent pKa Values of Buried IonizableGroups in Proteins

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

09-28-2017, 06:47 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Local Backbone Flexibility as a Determinant of theApparent pKa Values of Buried IonizableGroups in Proteins

Local Backbone Flexibility as a Determinant of theApparent pKa Values of Buried IonizableGroups in Proteins

Biochemistry
DOI: 10.1021/acs.biochem.7b00678

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins. NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins. Related Articles NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins. Structure. 2015 May 12; Authors: Zook J, Mo G, Sisco NJ, Craciunescu FM, Hansen DT, Baravati B, Cherry BR, Sykes K, Wachter R, Van Horn WD, Fromme P Abstract Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and...	nmrlearner	Journal club	0	05-26-2015 08:09 PM
NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins Publication date: Available online 21 May 2015 Source:Structure</br> Author(s): James Zook , Gina Mo , NicholasJ. Sisco , FeliciaM. Craciunescu , DebraT. Hansen , Bobby Baravati , BrianR. Cherry , Kathryn Sykes , Rebekka Wachter , WadeD. VanHorn , Petra Fromme</br> Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and many parts of northern Europe and Asia. The outer...	nmrlearner	Journal club	0	05-21-2015 04:28 PM
[NMR paper] Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation. Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation. Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation. Angew Chem Int Ed Engl. 2013 Mar 20; Authors: Stanek J, Saxena S, Geist L, Konrat R, Ko?mi?ski W Abstract Ab ultra-high-resolution NMR experiment for the measurement of intraresidue (1) H(i)-(15) N(i)-(13) C'(i) dipolar-chemical shift anisotropy relaxation interference is employed to extract information about local backbone...	nmrlearner	Journal club	0	03-23-2013 06:36 PM
Local protein backbone folds determined by calculated NMR chemical shifts. Local protein backbone folds determined by calculated NMR chemical shifts. Local protein backbone folds determined by calculated NMR chemical shifts. J Comput Chem. 2011 Sep 9; Authors: Czajlik A, Hudáky I, Perczel A Abstract NMR chemical shifts (CSs: ?N(NH) , ?C(?) , ?C(?) , ?C', ?H(NH) , and ?H(?) ) were computed for the amino acid backbone conformers (?(L) , ?(L) , ?(L) , ?(L) , ?(L) , ?(D) , ?(D) , ?(D) , and ?(D) ) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single ?-strands,...	nmrlearner	Journal club	0	09-10-2011 06:51 PM
[NMR paper] NMR studies of the backbone flexibility and structure of human growth hormone: a comp NMR studies of the backbone flexibility and structure of human growth hormone: a comparison of high and low pH conformations. Related Articles NMR studies of the backbone flexibility and structure of human growth hormone: a comparison of high and low pH conformations. J Mol Biol. 2002 May 3;318(3):679-95 Authors: Kasimova MR, Kristensen SM, Howe PW, Christensen T, Matthiesen F, Petersen J, Sørensen HH, Led JJ (15)N NMR relaxation parameters and amide (1)H/(2)H-exchange rates have been used to characterize the structural flexibility of human...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] Simulated and NMR-derived backbone dynamics of a protein with significant flexibility Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain. Related Articles Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain. J Am Chem Soc. 2001 Apr 4;123(13):3021-36 Authors: Pfeiffer S, Fushman D, Cowburn D A 7.6 ns molecular dynamics trajectory of the betaARK1 PH domain in explicit water with appropriate ions was calculated at 300 K. Spectral densities...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by m Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR. Related Articles Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR. Biochemistry. 2000 Oct 17;39(41):12614-22 Authors: Mulder FA, Hon B, Muhandiram DR, Dahlquist FW, Kay LE The Leu99-->Ala mutant of T4 lysozyme contains a large internal cavity in the core of its C-terminal domain that is capable of reversibly binding small hydrophobic compounds. Although the cavity is completely buried,...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] NMR characterization of side chain flexibility and backbone structure in the type I a NMR characterization of side chain flexibility and backbone structure in the type I antifreeze protein at near freezing temperatures. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR characterization of side chain flexibility and backbone structure in the type I antifreeze protein at near freezing temperatures. Biochemistry. 1996 Dec 24;35(51):16698-704 Authors: Gronwald W, Chao H, Reddy DV, Davies PL, Sykes BD, SÃ¶nnichsen FD The flexibility of the polar side chains in the...	nmrlearner	Journal club	0	08-22-2010 02:20 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