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- Ucisik, Melek
N.; Bevilacqua, Philip C.; Hammes-Schiffer, Sharon
- Biochemistry 2016 v.55 no.27 pp. 3834-3846
- active sites; catalytic activity; cations; crystal structure; hydrogen bonding; magnesium; melting; metal ions; molecular dynamics; nucleotides; sodium
- ... The recently discovered twister ribozyme is thought to utilize general acid–base catalysis in its self-cleavage mechanism, but the roles of nucleobases and metal ions in the mechanism are unclear. Herein, molecular dynamics simulations of the env22 twister ribozyme are performed to elucidate the structural and equilibrium dynamical properties, as well as to examine the role of Mg²⁺ ions and possib ...
- PubMed Central:
- Krishna Deepak, R. N.
V.; Sankararamakrishnan, Ramasubbu
- Biochemistry 2016 v.55 no.27 pp. 3774-3783
- catalytic activity; data collection; histidine; hydrogen bonding; nitrogen; proteins
- ... The amino acid histidine can play a significant role in the structure and function of proteins. Its various functions include enzyme catalysis, metal binding activity, and involvement in cation−π, π–π, salt-bridge, and other types of noncovalent interactions. Although histidine’s imidazole nitrogens (Nδ and Nε) are known to participate in hydrogen bond (HB) interactions as an acceptor or a donor, ...