Structure and Ligand Binding Properties of Myoglobins Reconstituted with Monodepropionated Heme:  Functional Role of Each Heme Propionate Side Chain†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (33) ◽  
pp. 9406-9416 ◽  
Author(s):  
Katsuyoshi Harada ◽  
Masatomo Makino ◽  
Hiroshi Sugimoto ◽  
Shun Hirota ◽  
Takashi Matsuo ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Functional Role ◽  
Side Chain ◽  
Binding Properties

scholarly journals Structural and Functional Role of the Extracellular S5-P Linker in the HERG Potassium Channel

2002 ◽  
Vol 120 (5) ◽  
pp. 723-737 ◽  
Author(s):  
Jie Liu ◽  
Mei Zhang ◽  
Min Jiang ◽  
Gea-Ny Tseng
Keyword(s):  
Functional Role ◽  
Function Analysis ◽  
Voltage Sensor ◽  
Herg Channel ◽  
Side Chain ◽  
Voltage Sensitivity ◽  
Fast Kinetics ◽  
Channel Function ◽  
Outer Vestibule

C-type inactivation in the HERG channel is unique among voltage-gated K channels in having extremely fast kinetics and strong voltage sensitivity. This suggests that HERG may have a unique outer mouth structure (where conformational changes underlie C-type inactivation), and/or a unique communication between the outer mouth and the voltage sensor. We use cysteine-scanning mutagenesis and thiol-modifying reagents to probe the structural and functional role of the S5-P (residues 571–613) and P-S6 (residues 631–638) linkers of HERG that line the outer vestibule of the channel. Disulfide formation involving introduced cysteine side chains or modification of side chain properties at “high-impact” positions produces a common mutant phenotype: disruption of C-type inactivation, reduction of K+ selectivity, and hyperpolarizing shift in the voltage-dependence of activation. In particular, we identify 15 consecutive positions in the middle of the S5-P linker (583–597) where side chain modification has marked impact on channel function. Analysis of the degrees of mutation-induced perturbation in channel function along 583–597 reveals an α-helical periodicity. Furthermore, the effects of MTS modification suggest that the NH2-terminal of this segment (position 584) may be very close to the pore entrance. We propose a structural model for the outer vestibule of the HERG channel, in which the 583–597 segment forms an α-helix. With the NH2 terminus of this helix sitting at the edge of the pore entrance, the length of the helix (∼20 Å) allows its other end to reach and interact with the voltage-sensing domain. Therefore, the “583–597 helix” in the S5-P linker of the HERG channel serves as a bridge of communication between the outer mouth and the voltage sensor, that may make important contribution to the unique C-type inactivation phenotype.

scholarly journals Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties

2012 ◽  
Vol 446 (1) ◽  
pp. 149-157 ◽  
Author(s):  
Marianne Schimpl ◽  
Christina L. Rush ◽  
Marie Betou ◽  
Ian M. Eggleston ◽  
Anneliese D. Recklies ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Active Site ◽  
Elevated Serum ◽  
Serum Levels ◽  
Chitinase Activity ◽  
Active Site Residues ◽  
Binding Properties ◽  
Binding Partners ◽  
Tryptophan Residues

The chitinase-like proteins YKL-39 (chitinase 3-like-2) and YKL-40 (chitinase 3-like-1) are highly expressed in a number of human cells independent of their origin (mesenchymal, epithelial or haemapoietic). Elevated serum levels of YKL-40 have been associated with a negative outcome in a number of diseases ranging from cancer to inflammation and asthma. YKL-39 expression has been associated with osteoarthritis. However, despite the reported association with disease, the physiological or pathological role of these proteins is still very poorly understood. Although YKL-39 is homologous to the two family 18 chitinases in the human genome, it has been reported to lack any chitinase activity. In the present study, we show that human YKL-39 possesses a chitinase-like fold, but lacks key active-site residues required for catalysis. A glycan screen identified oligomers of N-acetylglucosamine as preferred binding partners. YKL-39 binds chitooligosaccharides and a newly synthesized derivative of the bisdionin chitinase-inhibitor class with micromolar affinity, through a number of conserved tryptophan residues. Strikingly, the chitinase activity of YKL-39 was recovered by reverting two non-conservative substitutions in the active site to those found in the active enzymes, suggesting that YKL-39 is a pseudo-chitinase with retention of chitinase-like ligand-binding properties.

Evaluation of the Functional Role of the Heme-6-propionate Side Chain in Cytochrome P450cam

2008 ◽  
Vol 130 (2) ◽  
pp. 432-433 ◽  
Author(s):  
Katsuyoshi Harada ◽  
Keisuke Sakurai ◽  
Kenichiro Ikemura ◽  
Takashi Ogura ◽  
Shun Hirota ◽  
...  
Keyword(s):  
Functional Role ◽  
Side Chain ◽  
Cytochrome P450cam

scholarly journals Distinct effects of Q925 mutation on intracellular and extracellular Na+ and K+ binding to the Na+, K+-ATPase

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hang N. Nielsen ◽  
Kerri Spontarelli ◽  
Rikke Holm ◽  
Jens Peter Andersen ◽  
Anja P. Einholm ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Binding Sites ◽  
Functional Role ◽  
Transmembrane Helix ◽  
Binding Properties ◽  
Ion Translocation ◽  
Extracellular Side ◽  
Insight Into

Abstract Three Na+ sites are defined in the Na+-bound crystal structure of Na+, K+-ATPase. Sites I and II overlap with two K+ sites in the K+-bound structure, whereas site III is unique and Na+ specific. A glutamine in transmembrane helix M8 (Q925) appears from the crystal structures to coordinate Na+ at site III, but does not contribute to K+ coordination at sites I and II. Here we address the functional role of Q925 in the various conformational states of Na+, K+-ATPase by examining the mutants Q925A/G/E/N/L/I/Y. We characterized these mutants both enzymatically and electrophysiologically, thereby revealing their Na+ and K+ binding properties. Remarkably, Q925 substitutions had minor effects on Na+ binding from the intracellular side of the membrane – in fact, mutations Q925A and Q925G increased the apparent Na+ affinity – but caused dramatic reductions of the binding of K+ as well as Na+ from the extracellular side of the membrane. These results provide insight into the changes taking place in the Na+-binding sites, when they are transformed from intracellular- to extracellular-facing orientation in relation to the ion translocation process, and demonstrate the interaction between sites III and I and a possible gating function of Q925 in the release of Na+ at the extracellular side.

scholarly journals Characterization of the functional role of the N-glycans in the AMPA receptor ligand-binding domain

2003 ◽  
Vol 84 (5) ◽  
pp. 1184-1192 ◽  
Author(s):  
Arja Pasternack ◽  
Sarah K. Coleman ◽  
James Féthière ◽  
Dean R. Madden ◽  
Jean-Pierre LeCaer ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Ampa Receptor ◽  
Functional Role ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Receptor Ligand

Amino acid mutagenesis within ligand-binding loops in αv confers loss-of-function or gain-of-function phenotype on integrin αvβ3

2004 ◽  
Vol 92 (11) ◽  
pp. 1092-1098 ◽  
Author(s):  
Shigenori Honda ◽  
Hirokazu Kashiwagi ◽  
Teruo Kiyoi ◽  
Hisashi Kato ◽  
Satoru Kosugi ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Functional Role ◽  
Integrin Αvβ3 ◽  
Adhesion Assay ◽  
Loss Of Function ◽  
Perfect Agreement ◽  
Fibrinogen Binding ◽  
Contact Residues ◽  
Amino Acid Mutagenesis

SummaryThe crystal structure of αvβ3 in complex with a cyclic RGDcontaining ligand has recently been demonstrated. However, the functional significance of each residue within ligand binding loops has not been fully elucidated. Here, by employing alaninescanning mutagenesis, we have examined the functional role of ligand contact residues in αv. Tyr178 –> Ala substitution (Tyr178Ala) and Asp218Ala abolished a monovalent ligand, WOW-1 Fab binding as well as soluble fibrinogen binding, which is in perfect agreement with the crystallography. However, Asp150Ala showed no or only a modest inhibition of ligand binding. In contrast, Tyr substitution at Ala215 (Ala215Tyr) increased WOW-1 Fab binding, suggesting that the substitution increased the integrin affinity. The adhesion assay to immobilized fibrinogen showed essentially the same data as obtained using soluble ligands. Our present data indicate that Tyr178 and Asp218, but not Asp150 in αv is critically involved in ligand-binding and that Ala215 could regulate the affinity of αvβ3.

Sign in / Sign up

Export Citation Format

Share Document