Autonomous Folding and Three-Dimensional Structure of the Carboxy-Terminal Domain of the Mouse Prion Protein, PrP(121–231)

1998 ◽  
pp. 203-216
Author(s):  
Rudi Glockshuber ◽  
Simone Hornemann ◽  
Roland Riek ◽  
Gerhard Wider ◽  
Martin Billeter ◽  
...  
Keyword(s):  
Prion Protein ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Carboxy Terminal

scholarly journals Proposed three-dimensional structure for the cellular prion protein.

1994 ◽  
Vol 91 (15) ◽  
pp. 7139-7143 ◽  
Author(s):  
Z. Huang ◽  
J. M. Gabriel ◽  
M. A. Baldwin ◽  
R. J. Fletterick ◽  
S. B. Prusiner ◽  
...  
Keyword(s):  
Prion Protein ◽  
Three Dimensional ◽  
Cellular Prion Protein ◽  
Dimensional Structure ◽  
Three Dimensional Structure

The dark and bright sides of an enzyme: a three dimensional structure of the N-terminal domain of Zophobas morio luciferase-like enzyme, inferences on the biological function and origin of oxygenase/luciferase activity

2016 ◽  
Vol 15 (5) ◽  
pp. 654-665 ◽  
Author(s):  
R. A. Prado ◽  
C. R. Santos ◽  
D. I. Kato ◽  
M. T. Murakami ◽  
V. R. Viviani
Keyword(s):  
Biological Function ◽  
Luciferase Activity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Catalytic Residue ◽  
Three Dimensional Structure ◽  
Catalytic Activities ◽  
Terminal Domain ◽  
Coa Ligase

The structure and catalytic activities of a Malpighian luciferase-like enzyme indicate a generalistic xenobiotic CoA-ligase and a catalytic residue for bioluminescence.

scholarly journals The structural and spectroscopic basis for modelling prion protein interactions

2001 ◽  
Vol 15 (3,4) ◽  
pp. 151-159
Author(s):  
Jim Warwicker ◽  
Chris Cole
Keyword(s):  
Conformational Change ◽  
Prion Protein ◽  
Protein Interactions ◽  
Prion Diseases ◽  
Protein Solubility ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Starting Point ◽  
Modelling Studies ◽  
Carboxy Terminal

Mammalian prion diseases are characterised by an α-helical to β-sheet conformational change within the prion protein, that was originally established with circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy. Since prion disease is transmissible, significant effort has been aimed at establishing the molecular details of conformational change and the specificity that underpins infectivity. The structure determined for the carboxy-terminal domain of the predominantly α-helical form by nuclear magnetic resonance (NMR) provides a starting point for considering questions at the molecular level. However, elucidation of atomic detail for the β-rich form is complicated by problems of protein solubility, and regions other than the carboxy-terminal domain of the α-rich form are likely to possess functionally significant, ordered domains in the presence of suitable ligands and solution conditions. Further spectroscopic analysis, particularly of polypeptide secondary structure, is playing a key role in constraining molecular modelling studies of prion protein folding and interactions. We present a review of this area of prion research.

scholarly journals Three-dimensional Structure of Acanthamoeba castellanii Myosin-IB (MIB) Determined by Cryoelectron Microscopy of Decorated Actin Filaments

1998 ◽  
Vol 141 (1) ◽  
pp. 155-162 ◽  
Author(s):  
James D. Jontes ◽  
E. Michael Ostap ◽  
Thomas D. Pollard ◽  
Ronald A. Milligan
Keyword(s):  
Actin Filaments ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Acanthamoeba Castellanii ◽  
Dimensional Structure ◽  
Cryoelectron Microscopy ◽  
Tail Domain ◽  
Three Dimensional Structure ◽  
Myosin I ◽  
Carboxy Terminal

The Acanthamoeba castellanii myosin-Is were the first unconventional myosins to be discovered, and the myosin-I class has since been found to be one of the more diverse and abundant classes of the myosin superfamily. We used two-dimensional (2D) crystallization on phospholipid monolayers and negative stain electron microscopy to calculate a projection map of a “classical” myosin-I, Acanthamoeba myosin-IB (MIB), at ∼18 Å resolution. Interpretation of the projection map suggests that the MIB molecules sit upright on the membrane. We also used cryoelectron microscopy and helical image analysis to determine the three-dimensional structure of actin filaments decorated with unphosphorylated (inactive) MIB. The catalytic domain is similar to that of other myosins, whereas the large carboxy-terminal tail domain differs greatly from brush border myosin-I (BBM-I), another member of the myosin-I class. These differences may be relevant to the distinct cellular functions of these two types of myosin-I. The catalytic domain of MIB also attaches to F-actin at a significantly different angle, ∼10°, than BBM-I. Finally, there is evidence that the tails of adjacent MIB molecules interact in both the 2D crystal and in the decorated actin filaments.

scholarly journals Three-dimensional structure of the amino-terminal domain of syntaxin 6, a SNAP-25 C homolog

2002 ◽  
Vol 99 (14) ◽  
pp. 9184-9189 ◽  
Author(s):  
K. M. S. Misura ◽  
J. B. Bock ◽  
L. C. Gonzalez ◽  
R. H. Scheller ◽  
W. I. Weis
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Amino Terminal ◽  
Terminal Domain ◽  
Amino Terminal Domain

scholarly journals Three-Dimensional Structure of N-Terminal Domain of DnaB Helicase and Helicase-Primase Interactions in Helicobacter pylori

PLoS ONE ◽  
2009 ◽  
Vol 4 (10) ◽  
pp. e7515 ◽  
Author(s):  
Tara Kashav ◽  
Ramgopal Nitharwal ◽  
S. Arif Abdulrehman ◽  
Azat Gabdoulkhakov ◽  
Wolfram Saenger ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Terminal Domain ◽  
Dnab Helicase

scholarly journals Comparing the fluctuations of the intrinsically disordered C-terminal domain of human SELK free in water and in lipid membrane

2015 ◽  
Author(s):  
Andrea Polo ◽  
Stefano Guariniello ◽  
Giovanni Colonna ◽  
Gennaro Ciliberto ◽  
Susan Costantini
Keyword(s):  
Endoplasmic Reticulum ◽  
Ab Initio ◽  
Lipid Bilayer ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Protein Interaction Data ◽  
Endoplasmic Reticulum Membrane ◽  
Three Dimensional Structure ◽  
Intrinsically Disordered ◽  
Terminal Domain

SELK is a single-pass trans-membrane protein that resides in the endoplasmic reticulum membrane (ER) with a C-terminal domain exposed to the cytoplasm that is known to interact with different components of the endoplasmic reticulum associated to the protein degradation (ERAD) pathway. This protein is resulted to be up-expressed in hepatocellular carcinoma and in other cancers, therefore there is a need to analyze its structure-function relationships. In this work we performed a detailed analysis of the C-terminal domain sequence of SELK, modeled its three-dimensional structure and analyzed its conformational changes by Molecular Dynamics simulations. Our analysis showed that the C-terminal domain of SELK is a weak polyelectrolyte and specifically, a polycation, which has the characteristic molecular signature of natively disordered segments. Since the search by BLAST has not evidenced possible templates with an acceptable sequence identity percentage with the C-terminal sequence of SELK, its three-dimensional structure was modeled by ab initio modeling. The best model is characterized by one short helix and the most part of residues with no regular secondary structure elements. This model was subjected to MD simulation at neutral pH in water to assess the stability of the modelled structural organization free in solution. To deepen the structural analysis of the C terminal domain, we have also studied the organization of the whole protein inserted into the membrane by a procedure of comparative modeling between fold recognition and folding ab initio. Then, the complete structure of SELK was subjected to MD simulations in the lipid bilayer and a water box. Analyzing the MD trajectories, we found that the C-terminal domain of SELK is still highly mobile during the simulation in water-lipid bilayer by showing a decrease of the structural compactness, a lesser number of H-bonds, as well as a higher value of the total void volume and of the total solvent accessible area compared to the simulation in only water system. However, in both the simulations this region is stabilized mainly by a marked number of H-bonds, and pi-cation and IAC interactions, which suggest a globule organization very different from the classic globular one. Furthermore, water-protein interaction data suggest, as for other IDPs, that the hydration water tends to cluster around the protein facilitating its organization to globule.

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