scholarly journals Cover Picture: Defining a Substrate-Binding Model of a Polysialyltransferase (ChemBioChem 15/2013)

ChemBioChem ◽  
2013 ◽  
Vol 14 (15) ◽  
pp. 1909-1909
Author(s):  
Friedrich Freiberger ◽  
Raphael Böhm ◽  
David Schwarzer ◽  
Rita Gerardy-Schahn ◽  
Thomas Haselhorst ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Binding Model

scholarly journals Structural Flexibility of Peripheral Loops and Extended C-Term Domain of Short Length Substrate Binding Protein from Rhodothermus marinus

2019 ◽  
Author(s):  
Ji-Eun Bae ◽  
In Jung Kim ◽  
Yongbin Xu ◽  
Ki Hyun Nam
Keyword(s):  
Substrate Binding ◽  
Peripheral Region ◽  
Short Length ◽  
Structural Flexibility ◽  
Rhodothermus Marinus ◽  
Binding Model ◽  
Recognition Mechanism ◽  
Comparative Structure ◽  
High Level ◽  
Electron Density Map

Substrate binding proteins (SBP) bind to specific ligands in the periplasmic region and bind to membrane proteins to participate in transport or signal transduction. Typical SBPs consist of two α/β domains and recognize the substrate by hinge motion between two domains. Conversely, short length Rhodothermus marinus SBP (named as RmSBP) exists around the methyl-accepting chemotaxis protein. We previously determined the crystal structure of RmSBP consisting of a single α/β domain, but the substrate recognition mechanism is still unclear. To better understand the short length RmSBP, we performed comparative structure analysis, computational substrate docking, and X-ray crystallographic study. RmSBP shares a high level of similarity in α/β domain with other SBP proteins, but it has a distinct topology in the C-term region. The substrate binding model suggested that conformational change in the peripheral region of RmSBP was required to recognize the substrate. We determined the crystal structures of RmSBP at pH 5.5, 6.0, and 7.5. RmSBP showed structural flexibility of the β1-α2 loop, β5-β6 loop, and extended C-term domain based on the electron density map and temperature B-factor analysis. These results provide information that will further the understanding of the function of the short length SBP.

Trinuclear Zn(II) and Cu(II) Homo and Heterotrimetallic Complexes Involvingd-Glucopyranosyl and Biscarboxylate Bridging Ligands. A Substrate Binding Model of Xylose Isomerases

2001 ◽  
Vol 40 (16) ◽  
pp. 3943-3953 ◽  
Author(s):  
Tomoaki Tanase ◽  
Hiromi Inukai ◽  
Tomoko Onaka ◽  
Merii Kato ◽  
Shigenobu Yano ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Binding Model ◽  
Bridging Ligands

Defining a Substrate-Binding Model of a Polysialyltransferase

ChemBioChem ◽  
2013 ◽  
Vol 14 (15) ◽  
pp. 1949-1953 ◽  
Author(s):  
Friedrich Freiberger ◽  
Raphael Böhm ◽  
David Schwarzer ◽  
Rita Gerardy-Schahn ◽  
Thomas Haselhorst ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Binding Model

scholarly journals Substrate-binding Model of the Chlorophyll Biosynthetic Magnesium Chelatase BchH Subunit

2008 ◽  
Vol 283 (17) ◽  
pp. 11652-11660 ◽  
Author(s):  
Nickolche Sirijovski ◽  
Joakim Lundqvist ◽  
Matilda Rosenbäck ◽  
Hans Elmlund ◽  
Salam Al-Karadaghi ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Binding Model ◽  
Magnesium Chelatase

scholarly journals Impact of peripheral mutations on the access channels of human cytochrome P450 1A2

2019 ◽  
Author(s):  
Beili Ying ◽  
Yang Zhong ◽  
Jingfang Wang
Keyword(s):  
Cytochrome P450 ◽  
Lipid Membranes ◽  
Substrate Binding ◽  
Membrane Binding ◽  
Water Channel ◽  
Significant Inhibition ◽  
Free Energy Calculations ◽  
Binding Model ◽  
Channel Opening ◽  
Human Cyp1a2

AbstractAs an important member of cytochrome P450 (CYP) enzymes, human CYP1A2 is associated with the metabolism of caffeine and melatonin and the activation of precarcinogens. Besides, this CYP protein also involves in metabolizing 5-10% of clinical medicines. Some peripheral mutations in CYP1A2 (P42R, I386F, R431W, and R456H) significantly decrease the enzyme activities, resulting in a vital reduction in substrate metabolisms. To explore the effects of these peripheral mutations, we constructed a membrane-binding model for the full-length human CYP1A2 and studied their dynamic behaviors on lipid membranes. Free energy calculations indicate that the peripheral mutations donot influence substrate binding. P42R is located in the N-terminal anchor, and its positive charged sidechain is adverse to membrane binding. I386F enhances the van der Waals contacts of the water channel bottleneck and R456H breaks the hydrogen bonding interactions that function to position the BC loop, both of which result in a significant inhibition on the water channel. R431W causes a sidechain conformational rearrangement for aromatic residues around the substrate channel, making it in a closed state in most cases. Our computational simulations demonstrate that pi-pi stacking interactions are essential for substrate binding and channel opening. We hope that these findings may be of general relevance to the mutation-induced activity changes for CYP proteins, providing useful information for understanding the CYP-mediated drug metabolism.

Fibronexus-Like Adhesion Sites are Present at the Invasive Zones of Human Epidermoid Carcinomas

1982 ◽  
Vol 40 ◽  
pp. 106-109
Author(s):  
Irwin I. Singer
Keyword(s):  
Cell Cycle ◽  
Serum Concentration ◽  
Substrate Binding ◽  
High Serum ◽  
Adhesion Sites ◽  
Substrate Adhesion ◽  
Focal Contacts ◽  
Adhesion Complex ◽  
Low Serum

Our previous results indicate that two types of fibronectin-cytoskeletal associations may be formed at the fibroblast surface: dorsal matrixbinding fibronexuses generated in high serum (5% FBS) cultures, and ventral substrate-adhering units formed in low serum (0.3% FBS) cultures. The substrate-adhering fibronexus consists of at least vinculin (VN) and actin in its cytoplasmic leg, and fibronectin (FN) as one of its major extracellular components. This substrate-adhesion complex is localized in focal contacts, the sites of closest substratum approach visualized with interference reflection microscopy, which appear to be the major points of cell-tosubstrate adhesion. In fibroblasts, the latter substrate-binding complex is characteristic of cultures that are arrested at the G1 phase of the cell cycle due to the low serum concentration in their medium. These arrested fibroblasts are very well spread, flattened, and immobile.

Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase

2001 ◽  
Vol 268 (6) ◽  
pp. 1640-1645
Author(s):  
Annelise Matharu ◽  
Hideyuki Hayashi ◽  
Hiroyuki Kagamiyama ◽  
Bruno Maras ◽  
Robert A. John
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Aspartate Aminotransferase ◽  
Substrate Binding ◽  
Arginine Residues
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