PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 30188715-2 2018 Here we show that water dynamics and interactions can be controlled by the protonation state of ligand using continuous constant pH molecular dynamics simulations of two closely related model systems, beta-secretase 1 and 2 (BACE1 and BACE2), in complex with a small-molecule inhibitor. Water 18-23 beta-secretase 2 Homo sapiens 235-240 31140794-4 2019 When the concentration is in the mM range, the binding occurs with cis-VOL2(H2O), L = ma, koj, dhp, and mim, or with VO(acac)2: in the first case, the equatorial coordination of His68, Glu16, Glu18, or Asp21 residues yields species with formula n[VOL2]-Ub where n = 2-3, while with VO(acac)2 only noncovalent surface interactions are revealed. Water 76-79 beta-secretase 2 Homo sapiens 202-207 10587314-7 1999 cyclo(-D-Asp1-Asp2-Gly3-Ahd4-Ahd5-Gly6-) (C3) clearly exhibits two different conformations with a shifted beta,beta-turn motif in CDCI3 and SDS/H2O solutions. Water 144-147 beta-secretase 2 Homo sapiens 9-13 25246550-7 2014 We suggest that Asp21 and His84 provide a network of interactions that stabilize the positions of the gamma-phosphate and the nucleophilic water, respectively, and thus play an indirect catalytic role in the GTPase mechanism on the ribosome. Water 139-144 beta-secretase 2 Homo sapiens 16-21