The ONIOM molecular dynamics method for biochemical applications: Cytidine deaminase
نویسندگان
چکیده
منابع مشابه
The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase
We developed and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method t...
متن کاملCatalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study.
The catalytic mechanism of Bacillus subtilis guanine deaminase (bGD), a Zn metalloenzyme, has been investigated by a combination of quantum mechanical calculations using the multilayered ONIOM method and molecular dynamics simulations. In contrast to a previously proposed catalytic mechanism, which requires the bound guanine to assume a rare tautomeric state, the ONIOM calculations showed that ...
متن کاملMouse Kidney Cytidine Deaminase
A nucleoside aminohydrolase was prepared in 60-fold relative purity from the nonparticulate fraction of mouse kidney by denaturation at 60”, fractionation with (NH&S04, treatment with alumina gel Cr (pH 7.5), and dialysis in 0.02 M acetate buffer (pH 4.5). The’ optimal pH was 6.5. Cytidine, deoxycytidine, and I-/3-D-arabinofuranosylcytosine were deaminated, and the respective K, values were 7.5...
متن کاملActivation-induced cytidine deaminase (AID)
Activation-induced cytidine deaminase (AID) plays an essential role in the generation of a highly competent repertoire of antibodies by participating in class switch recombination (CSR) and somatic hypermutation (SHM). After B cell stimulation by antigens, AID initiates SHM and CSR by deamination of cytidine to uridine in the variable and constant regions of Ig genes. An adverse effect of AID’s...
متن کاملDeaminase-Independent Inhibition of Parvoviruses by the APOBEC3A Cytidine Deaminase
The APOBEC3 proteins form a multigene family of cytidine deaminases with inhibitory activity against viruses and retrotransposons. In contrast to APOBEC3G (A3G), APOBEC3A (A3A) has no effect on lentiviruses but dramatically inhibits replication of the parvovirus adeno-associated virus (AAV). To study the contribution of deaminase activity to the antiviral activity of A3A, we performed a compreh...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Chemical Physics Letters
سال: 2007
ISSN: 0009-2614
DOI: 10.1016/j.cplett.2007.01.085