NMR paper Solution structure of a de novo helical protein by 2D-NMR spectroscopy.

		BioNMR > Educational resources > Journal club
[NMR paper] Solution structure of a de novo helical protein by 2D-NMR spectroscopy.

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

08-22-2010, 03:33 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,700

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 of a de novo helical protein by 2D-NMR spectroscopy.

Solution structure of a de novo helical protein by 2D-NMR spectroscopy.

Related Articles Solution structure of a de novo helical protein by 2D-NMR spectroscopy.

J Mol Biol. 1994 Feb 25;236(3):862-8

Authors: Kuroda Y, Nakai T, Ohkubo T

The de novo design of proteins represents a critical test for our knowledge of protein structure. However, no structure of a successfully designed protein has yet been reported. This paper reports the design and the tertiary structure of a de novo 35-residue helix-loop-helix protein (ALIN), with helices arranged in an anti-parallel manner. For the helical region, we designed sequences that have high helicities even as isolated peptides. A flexible loop containing glycine residues was used to connect the two helices and the interhelical hydrophobic interaction was stabilized by the introduction of an SS-bridge. This arrangement of two consecutive helices bridged by a disulfide bond is not observed in any natural proteins. The protein is highly soluble and monomeric in aqueous solution. The structure of ALIN, determined by 1H-NMR and distance geometry calculation, agrees well with the design. In addition, the exchange rates of amide protons indicate the presence of stable hydrogen bonds in the helical region. ALIN is the first de novo designed protein with a stable tertiary fold confirmed by NMR.

PMID: 8114099 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Structure and dynamics of the lipid modifications of a transmembrane ?-helical peptide determined by (2)H solid-state NMR spectroscopy. Structure and dynamics of the lipid modifications of a transmembrane ?-helical peptide determined by (2)H solid-state NMR spectroscopy. Structure and dynamics of the lipid modifications of a transmembrane ?-helical peptide determined by (2)H solid-state NMR spectroscopy. Biochim Biophys Acta. 2010 Dec 28; Authors: Penk A, Müller M, Scheidt HA, Langosch D, Huster D The fusion of biological membranes is mediated by integral membrane proteins with ?-helical transmembrane segments. Additionally, those proteins are often modified by the covalent...	nmrlearner	Journal club	0	01-05-2011 09:51 PM
[NMR paper] NMR solution structure of a highly stable de novo heterodimeric coiled-coil. NMR solution structure of a highly stable de novo heterodimeric coiled-coil. Related Articles NMR solution structure of a highly stable de novo heterodimeric coiled-coil. Biopolymers. 2004 Dec 5;75(5):367-75 Authors: Lindhout DA, Litowski JR, Mercier P, Hodges RS, Sykes BD The NMR solution structure of a highly stable coiled-coil IAAL-E3/K3 has been solved. The E3/K3 coiled-coil is a 42-residue de novo designed coiled-coil comprising three heptad repeats per subunit, stabilized by hydrophobic contacts within the core and electrostatic...	nmrlearner	Journal club	0	11-24-2010 10:03 PM
[NMR paper] Validation of helical tilt angles in the solution NMR structure of the Z domain of St Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data. Related Articles Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data. Protein Sci. 2004 Feb;13(2):549-54 Authors: Zheng D, Aramini JM, Montelione GT Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] De novo protein structure determination using sparse NMR data. De novo protein structure determination using sparse NMR data. Related Articles De novo protein structure determination using sparse NMR data. J Biomol NMR. 2000 Dec;18(4):311-8 Authors: Bowers PM, Strauss CE, Baker D We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] Synthesis and NMR solution structure of an alpha-helical hairpin stapled with two dis Synthesis and NMR solution structure of an alpha-helical hairpin stapled with two disulfide bridges. Related Articles Synthesis and NMR solution structure of an alpha-helical hairpin stapled with two disulfide bridges. Protein Sci. 2000 May;9(5):942-55 Authors: Barthe P, Rochette S, Vita C, Roumestand C Helical coiled-coils and bundles are some of the most common structural motifs found in proteins. Design and synthesis of alpha-helical motifs may provide interesting scaffolds that can be useful as host structures to display functional sites,...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] De novo determination of protein structure by NMR using orientational and long-range De novo determination of protein structure by NMR using orientational and long-range order restraints. Related Articles De novo determination of protein structure by NMR using orientational and long-range order restraints. J Mol Biol. 2000 May 19;298(5):927-36 Authors: Hus JC, Marion D, Blackledge M Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] Solution structure of a de novo helical protein by 2D-NMR spectroscopy. Solution structure of a de novo helical protein by 2D-NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution structure of a de novo helical protein by 2D-NMR spectroscopy. J Mol Biol. 1994 Feb 25;236(3):862-8 Authors: Kuroda Y, Nakai T, Ohkubo T The de novo design of proteins represents a critical test for our knowledge of protein structure. However, no structure of a successfully designed protein has yet been reported. This paper reports the design...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] Protein structure determination in solution by NMR spectroscopy. Protein structure determination in solution by NMR spectroscopy. Related Articles Protein structure determination in solution by NMR spectroscopy. J Biol Chem. 1990 Dec 25;265(36):22059-62 Authors: WÃ¼thrich K The introduction of nuclear magnetic resonance (NMR) spectroscopy as a second method for protein structure determination at atomic resolution, in addition to x-ray diffraction in single crystals, has already led to a significant increase in the number of known protein structures. The NMR method provides data that are in many ways...	nmrlearner	Journal club	0	08-21-2010 11:04 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