binding orientation
Recently Published Documents


TOTAL DOCUMENTS

65
(FIVE YEARS 11)

H-INDEX

22
(FIVE YEARS 1)

2021 ◽  
Vol 478 (18) ◽  
pp. 3423-3428
Author(s):  
Helen S. Toogood ◽  
Nigel S. Scrutton

Nitroreductases catalyse the NAD(P)H-dependent nitro reduction in nitrofuran antibiotics, which activates them into cytotoxic molecules leading to cell death. The design of new effective nitrofuran antibiotics relies on knowledge of the kinetic mechanism and nitrofuran binding mode of microbial nitroreductases NfsA and NfsB. This has been hampered by multiple co-crystallisation studies revealing ligand binding in non-electron transfer competent states. In a recent study by Day et al. (2021) the authors investigated the likely reaction mechanism and mode of nitrofurantoin binding to NfsA using potentiometry, global kinetics analysis, crystallography and molecular dynamics simulations. Their findings suggest nitrofurantoin reduction proceeds via a direct hydride transfer from reduced FMN, while the crystallographic binding orientation is an inhibitory complex. Molecular dynamics simulations suggest ligand binding orientations is dependent on the oxidation state of the FMN. This study highlights the importance of utilising computational studies alongside traditional crystallographic approaches, when multiple stable ligand binding orientations can occur.


Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 224
Author(s):  
Miaomiao Gao ◽  
Kaili Nie ◽  
Meng Qin ◽  
Haijun Xu ◽  
Fang Wang ◽  
...  

Hydroxysteroid dehydrogenases (HSDHs) are from two superfamilies of short-chain dehydrogenase (SDR) and aldo–keto reductase (AKR). The HSDHs were summarized and classified according to their structural and functional differences. A typical pair of enzymes, 7α–hydroxysteroid dehydrogenase (7α–HSDH) and 7β–hydroxysteroid dehydrogenase (7β–HSDH), have been reported before. Molecular docking of 7-keto–lithocholic acid(7–KLA) to the binary of 7β–HSDH and nicotinamide adenine dinucleotide phosphate (NADP+) was realized via YASARA, and a possible binding model of 7β-HSDH and 7-KLA was obtained. The α side of 7–KLA towards NADP+ in 7β–HSDH, while the β side of 7–KLA towards nicotinamide adenine dinucleotide (NAD+) in 7α-HSDH, made the orientations of C7–OH different in products. The interaction between Ser193 and pyrophosphate of NAD(P)+ [Ser193–OG···3.11Å···O1N–PN] caused the upturning of PN–phosphate group, which formed a barrier with the side chain of His95 to make 7–KLA only able to bind to 7β–HSDH with α side towards nicotinamide of NADP+. A possible interaction of Tyr253 and C24 of 7–KLA may contribute to the formation of substrate binding orientation in 7β–HSDH. The results of sequence alignment showed the conservation of His95, Ser193, and Tyr253 in 7β–HSDHs, exhibiting a significant difference to 7α–HSDHs. The molecular docking of other two enzymes, 17β–HSDH from the SDR superfamily and 3(17)α–HSDH from the AKR superfamily, has furtherly verified that the stereospecificity of HSDHs was related to the substrate binding orientation.


2020 ◽  
Vol 11 (22) ◽  
pp. 9552-9556
Author(s):  
Orion M. Pearce ◽  
Jeremiah S. Duncan ◽  
Bimala Lama ◽  
Gordana Dukovic ◽  
Niels H. Damrauer

2020 ◽  
Vol 142 (23) ◽  
pp. 10544-10549
Author(s):  
Katsuhiko Abe ◽  
Yuki Hirose ◽  
Haruhiko Eki ◽  
Kazuki Takeda ◽  
Toshikazu Bando ◽  
...  

2020 ◽  
Author(s):  
Mark A. Hix ◽  
G. Andres Cisneros

There are several available crystal structures for APOBEC3H, however, none with bound substrate. Our manuscript presents a theoretical investigation of the binding orientation of the ssDNA substrate for the DNA deaminase APOBEC3H. Here, we have used classical MD simulations to explore the possible<br>binding orientation of a dsDNA substrate, as well as the possible factors leading to the observed substrate sequence selectivity.


Author(s):  
Mark A. Hix ◽  
G. Andres Cisneros

There are several available crystal structures for APOBEC3H, however, none with bound substrate. Our manuscript presents a theoretical investigation of the binding orientation of the ssDNA substrate for the DNA deaminase APOBEC3H. Here, we have used classical MD simulations to explore the possible<br>binding orientation of a dsDNA substrate, as well as the possible factors leading to the observed substrate sequence selectivity.


2020 ◽  
Author(s):  
Mark A. Hix ◽  
G. Andres Cisneros

There are several available crystal structures for APOBEC3H, however, none with bound substrate. Our manuscript presents a theoretical investigation of the binding orientation of the ssDNA substrate for the DNA deaminase APOBEC3H. Here, we have used classical MD simulations to explore the possible<br>binding orientation of a dsDNA substrate, as well as the possible factors leading to the observed substrate sequence selectivity.


2019 ◽  
Author(s):  
Eric Lazear ◽  
Michel M. Sun ◽  
Xiaoli Wang ◽  
Theresa L. Geurs ◽  
Christopher A. Nelson ◽  
...  

AbstractNKG2D is a key component of cytotoxic antitumor and antiviral responses. Multiple viruses evade NKG2D recognition by blocking NKG2D ligand expression on infected cells. In contrast, cowpox virus targets NKG2D directly by encoding a secreted antagonist, Orthopoxvirus MHC Class I-like Protein (OMCP). We have previously reported that OMCP also binds to the orphan receptor FcRL5 on innate B cells. Here, we demonstrate that mammalian-derived, glycosylated OMCP binds NKG2D but not FcRL5. Cowpox viruses either lacking OMCP, or expressing an NKG2D-binding deficient mutant, are significantly attenuated in wild type and FcRL5-deficient mice but not NKG2D-deficient mice, demonstrating that OMCP is critical in subverting NKG2D-mediated immunity in vivo. Next we determined the structure of OMCP bound to human NKG2D. Despite a structure similar to that of host NKG2D ligands, OMCP uses a drastically different orientation for NKG2D binding. The re-orientation of OMCP is associated with dramatically higher affinity for human NKG2D and the targeted interface is highly conserved in mammalian NKG2Ds, increasing the zoonotic potential of cowpox virus. We also show that cell surface presented OMCP can trigger NKG2D effector functions equivalently to host NKG2D ligands, demonstrating that NKG2D-mediated signaling requires clustering but is insensitive to binding orientation. Thus, in contrast to TCR/MHC interactions, the docking topology of NKG2D with its ligands does not appear to regulate its activation.Author SummaryVirally infected or tumor-transformed cells display NKG2D ligands (NKG2DLs) on their cell surface, which activates NKG2D-bearing lymphocytes to kill the transformed cell. Pathogens are known to counter this by blocking NKG2DL expression and/or surface display. In contrast, some tumor cells cleave endogenous NKG2DLs creating soluble NKG2D antagonists. Unlike other viral pathogens, cowpox virus uses a strategy analogous to cancer cells by targeting NKG2D directly with a soluble, high affinity NKG2D-antagonist named OMCP. We determined that OMCP’s virulence in vivo is attributed to blocking NKG2D-mediated NK cell responses with no apparent effect due to binding to other receptors or cell types. We have also determined the crystal structure of cowpox OMCP bound to human NKG2D, revealing that despite conservation of the ligand scaffolding with host NKG2DLs, the viral protein is engaged with a radically altered orientation compared to all host NKG2DLs. Our structure provides key insight into how OMCP binds with an ∼5,000-fold increased affinity compared to human NKG2DLs and show that the OMCP binding site is exceptionally conserved among primates and rodents, suggesting that the ability of OMCP to recognize this conserved interface contributes to the broad zoonotic potential of cowpox virus. Finally, we show that cell membrane-anchored OMCP can trigger equivalent NKG2D-mediated killing as host NKG2DLs, demonstrating that NKG2D signaling is insensitive to ligand binding orientation.


Sign in / Sign up

Export Citation Format

Share Document