Crystal and NMR structures of a Trp-cage [Biophysics and Computational Biology]

		BioNMR > Educational resources > Journal club
Crystal and NMR structures of a Trp-cage [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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

07-31-2012, 08:27 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

Crystal and NMR structures of a Trp-cage [Biophysics and Computational Biology]

Crystal and NMR structures of a Trp-cage [Biophysics and Computational Biology]

Scian, M., Lin, J. C., Le Trong, I., Makhatadze, G. I., Stenkamp, R. E., Andersen, N. H....
Date: 2012-07-31

To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data, including the structural basis for the increase in fold stability associated with motif cyclization and the manner in which a polar serine side chain is accommodated in the hydrophobic interior. A hexameric oligomer of the cyclic peptide is found in both crystal forms and indicates that under appropriate conditions, this minimized system may also serve as a model for protein–protein interactions. Read More

PNAS:
Number: 31
Volume: 109

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
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
Protein structure modeling using sparse NMR data [Biophysics and Computational Biology] Protein structure modeling using sparse NMR data Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D.... Date: 2012-06-19 While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...	nmrlearner	Journal club	0	06-20-2012 02:28 AM
Ultrahigh resolution protein structures using NMR chemical shift tensors [Biophysics and Computational Biology] Ultrahigh resolution protein structures using NMR chemical shift tensors Wylie, B. J., Sperling, L. J., Nieuwkoop, A. J., Franks, W. T., Oldfield, E., Rienstra, C. M.... Date: 2011-10-11 NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13C? and 15N (peptide backbone) groups in a protein, the ?1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13C? and...	nmrlearner	Journal club	0	10-12-2011 06:37 AM
Random phase detection in multidimensional NMR [Biophysics and Computational Biology] Random phase detection in multidimensional NMR Maciejewski, M. W., Fenwick, M., Schuyler, A. D., Stern, A. S., Gorbatyuk, V., Hoch, J. C.... Date: 2011-10-04 Despite advances in resolution accompanying the development of high-field superconducting magnets, biomolecular applications of NMR require multiple dimensions in order to resolve individual resonances, and the achievable resolution is typically limited by practical constraints on measuring time. In addition to the need for measuring long evolution times to obtain high resolution, the need to distinguish the sign of the frequency...	nmrlearner	Journal club	0	10-04-2011 08:47 PM
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR [Biophysics and Computational Biology] Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR Takayama, Y., Clore, G. M.... Date: 2011-05-31 The intra- and intermolecular translocation processes whereby the bi-domain transcription factor Oct1 searches for its specific DNA target site have been investigated by residual dipolar coupling (RDC) and paramagnetic relaxation enhancement (PRE) measurements. The RDC data show that the orientation of the POUS and POUHD domains of Oct1 relative to the long axis of the DNA is the same for specific 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
Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy [Biophysics and Computational Biology] Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy Masterson, L. R., Shi, L., Metcalfe, E., Gao, J., Taylor, S. S., Veglia, G.... Date: 2011-04-26 Protein kinase A (PKA) is a ubiquitous phosphoryl transferase that mediates hundreds of cell signaling events. During turnover, its catalytic subunit (PKA-C) interconverts between three major conformational states (open, intermediate, and closed) that are dynamically and allosterically activated by nucleotide binding. We show that the structural transitions between these...	nmrlearner	Journal club	0	04-27-2011 04:16 AM
Mapping allostery through the covariance analysis of NMR chemical shifts [Biophysics and Computational Biology] Mapping allostery through the covariance analysis of NMR chemical shifts Selvaratnam, R., Chowdhury, S., VanSchouwen, B., Melacini, G.... Date: 2011-04-12 Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical...	nmrlearner	Journal club	0	04-13-2011 01:15 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