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NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Unread 03-17-2005, 04:27 PM
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The following information about research projects in Dr. Elisar Barbar lab was found on her website.
************************************************** ****************



Research Interests:
  • The Dynein Motor Protein Complex
  • Protein Structure and Dynamics
  • Protein Folding
  • Protein-Protein Interactions
The major research focus of my lab is the structural biology and assembly of cytoplasmic dynein, a principal motor for minus end directed transport along microtubules. Cytoplasmic dynein is a large protein complex composed of two globular heads joined by flexible stalk domains to a common base. The head and stalk domains comprise the heavy chain motor subunits (~530 kDa) which contain the microtubule binding sites and the hydrolytic ATP-binding sites required for force production. The base of the motor complex contains two 74 kDa intermediate chains, four light intermediate chains (52-61 kDa), and several light chains (10-25 kDa). By comparison to the multiplicity of kinesin heavy chain genes, the diversity of cytoplasmic dynein heavy chains is quite limited. This has fostered the hypothesis that the multiple functions of dynein are mediated through variations in the composition, modification, and interactions of the intermediate, light intermediate and light chains. The heterogeneity of these accessory subunits within the base of the motor complex could enable coupling of the dynein motor to a wide variety of intracellular cargoes.



To understand this system, we use a 'ground up' approach, whereby the structure and dynamics of the individual proteins are examined first, then the interactions between subunits and cargo are characterized. We employ a variety of techniques primarily heteronuclear NMR and mass spectrometry to determine the three-dimensional structure of individual subunits and their complexes. Electrospray mass spectrometry and MALDI can give valuable information about structure and protein interactions using hydrogen isotope exchange techniques, limited proteolysis and chemical cross-linking.



We hope that our work on dynein will lead to new methods for controlling certain diseases. The cancer drug Taxol, for example, is effective in preventing spindle formation in rapidly dividing cells; a complementary therapy would prevent transport of chromosomes by dynein along the spindle. Perhaps just as important, however, will be advances in our fundamental understanding of protein-protein interactions, molecular recognition, and the assembly of biologically important protein complexes.
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