NMR paper Solution NMR structure investigation for releasing mechanism of neocarzinostatin chro

		BioNMR > Educational resources > Journal club
[NMR paper] Solution NMR structure investigation for releasing mechanism of neocarzinostatin chro

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

11-24-2010, 11:14 PM

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

Solution NMR structure investigation for releasing mechanism of neocarzinostatin chro

Solution NMR structure investigation for releasing mechanism of neocarzinostatin chromophore from the holoprotein.

Related Articles Solution NMR structure investigation for releasing mechanism of neocarzinostatin chromophore from the holoprotein.

J Biol Chem. 2005 Mar 25;280(12):11340-6

Authors: Takashima H, Yoshida T, Ishino T, Hasuda K, Ohkubo T, Kobayashi Y

Holo-neocarzinostatin (holo-NCS) is a complex protein carrying the anti-tumor active enediyne ring chromophore by a scaffold consisting of an immunoglobulin-like seven-stranded anti-parallel beta-barrel. Because of the labile chromophore reflecting its extremely strong DNA cleavage activity and complete stabilization in the complex, holo-NCS has attracted much attention in clinical use as well as for drug delivery systems. Despite many structural analyses for holo-NCS, the chromophore-releasing mechanism to trigger prompt attacks on the target DNA is still unclear. We determined the three-dimensional structure of the protein and the internal motion by multinuclear NMR to investigate the releasing mechanism. The internal motion studied by 13C NMR methine relaxation experiments showed that the complex has a rigid structure for its loops as well as the beta-barrel in aqueous solution. This agrees with the refined NMR solution structure, which has good convergence in the loop regions. We also showed that the chromophore displayed a similar internal motion as the protein moiety. The structural comparison between the refined solution structure and x-ray crystal structure indicated characteristic differences. Based on the findings, we proposed the chromophore-releasing mechanism by a three-state equilibrium, which sufficiently describes both the strong binding and the prompt releasing of the chromophore. We demonstrated that we could bridge the dynamic properties and the static structure features with simple kinetic assumptions to solve the biochemical function.

PMID: 15640161 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Solution NMR study of DNA recognition mechanism of IRF4 protein. Solution NMR study of DNA recognition mechanism of IRF4 protein. Related Articles Solution NMR study of DNA recognition mechanism of IRF4 protein. Nucleic Acids Symp Ser (Oxf). 2004;(48):105-6 Authors: Ishizaki I, Nomura M, Yamamoto K, Matsuyama T, Mishima M, Kojima C Transcription factor IRF-4 prefers the DNA sequence including CCGAAA. The consensus sequence of the IRF family proteins is NNGAAA, and all crystal structures indicate the NN region does not interact with IRF proteins directly. Here the sequence preference of IRF-4 was...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] NMR investigation of the catalytic mechanism of arylamine N-acetyltransferase from Sa NMR investigation of the catalytic mechanism of arylamine N-acetyltransferase from Salmonella typhimurium. Related Articles NMR investigation of the catalytic mechanism of arylamine N-acetyltransferase from Salmonella typhimurium. Biochim Biophys Acta. 2003 Mar 17;1620(1-3):8-14 Authors: Delgoda R, Lian LY, Sandy J, Sim E Arylamine N-acetyltransferases (NAT) are a family of enzymes found in both eucaryotes and procaryotes, which catalyse the N-acetylation of a range of arylamine and hydrazine drugs and carcinogenic arylamines, using acetyl...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] An NMR investigation of solution aggregation reactions preceding the misassembly of a An NMR investigation of solution aggregation reactions preceding the misassembly of acid-denatured cold shock protein A into fibrils. Related Articles An NMR investigation of solution aggregation reactions preceding the misassembly of acid-denatured cold shock protein A into fibrils. J Mol Biol. 1999 Sep 3;291(5):1191-206 Authors: Alexandrescu AT, Rathgeb-Szabo K At pH 2.0, acid-denatured CspA undergoes a slow self-assembly process, which results in the formation of insoluble fibrils. 1H-15N HSQC, 3D HSQC-NOESY, and 15N T2 NMR experiments have...	nmrlearner	Journal club	0	11-18-2010 08:31 PM
[NMR paper] Insights into the mechanism of heterodimerization from the 1H-NMR solution structure Insights into the mechanism of heterodimerization from the 1H-NMR solution structure of the c-Myc-Max heterodimeric leucine zipper. Related Articles Insights into the mechanism of heterodimerization from the 1H-NMR solution structure of the c-Myc-Max heterodimeric leucine zipper. J Mol Biol. 1998 Aug 7;281(1):165-81 Authors: Lavigne P, Crump MP, Gagné SM, Hodges RS, Kay CM, Sykes BD The oncoprotein c-Myc (a member of the helix-loop-helix-leucine zipper (b-HLH-LZ) family of transcription factors) must heterodimerize with the b-HLH-LZ Max...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
NMR structure of the first extracellular domain of corticotropin releasing factor rec NMR structure of the first extracellular domain of corticotropin releasing factor receptor 1 (ECD1-CRF-R1) complexed with a high affinity agonist. Related Articles NMR structure of the first extracellular domain of corticotropin releasing factor receptor 1 (ECD1-CRF-R1) complexed with a high affinity agonist. J Biol Chem. 2010 Sep 15; Authors: Grace CR, Perrin MH, Gulyas J, Rivier JE, Vale WW, Riek R The corticotropin releasing factor (CRF) peptide hormone family members coordinate endocrine, behavioral, autonomic and metabolic responses to...	nmrlearner	Journal club	0	09-17-2010 04:14 PM
[NMR paper] NMR investigation of the solution conformation of oxidized flavodoxin from Desulfovib NMR investigation of the solution conformation of oxidized flavodoxin from Desulfovibrio vulgaris. Determination of the tertiary structure and detection of protein-bound water molecules. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles NMR investigation of the solution conformation of oxidized flavodoxin from Desulfovibrio vulgaris. Determination of the tertiary structure and detection of protein-bound water molecules. Eur J Biochem. 1996 Jun...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular d Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to x-ray crystallographic and NMR data. Related Articles Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to x-ray crystallographic and NMR data. Protein Eng. 1995 Nov;8(11):1117-28 Authors: Li A, Daggett V The native solution structure and dynamics of chymotrypsin inhibitor 2 (CI2) have been studied using a long (5.3 ns) molecular dynamics (MD) simulation without any imposed...	nmrlearner	Journal club	0	08-22-2010 03:50 AM
[NMR paper] Three-dimensional solution structure of apo-neocarzinostatin from Streptomyces carzin Three-dimensional solution structure of apo-neocarzinostatin from Streptomyces carzinostaticus determined by NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Three-dimensional solution structure of apo-neocarzinostatin from Streptomyces carzinostaticus determined by NMR spectroscopy. Eur J Biochem. 1992 Feb 1;203(3):505-11 Authors: Adjadj E, Quiniou E, Mispelter J, Favaudon V, Lhoste JM The three-dimensional...	nmrlearner	Journal club	0	08-21-2010 11:41 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