Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets [0.03%]
相似度测定差异对采用位点矢量表示的配体结合袋比较的影响分析
Tsukasa Nakamura,Kentaro Tomii
Tsukasa Nakamura
Comprehensive analysis and comparison of protein ligand-binding pockets are important to predict the ligands which bind to parts of putative ligand binding pockets. Because of the recent increase of protein structure information, such analy...
Effects of substrate conformational strain on binding kinetics of catalytic antibodies [0.03%]
底物共价结合对催化抗体亲和力的影响
Masayuki Oda,Takeshi Tsumuraya,Ikuo Fujii
Masayuki Oda
We analyzed the correlation between the conformational strain and the binding kinetics in antigen-antibody interactions. The catalytic antibodies 6D9, 9C10, and 7C8 catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivat...
Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state [0.03%]
ATP结合诱导的GroEL闭合状态构象变化引发向开放状态转变
Yuka Suzuki,Kei Yura
Yuka Suzuki
We investigated the effect of ATP binding to GroEL and elucidated a role of ATP in the conformational change of GroEL. GroEL is a tetradecamer chaperonin that helps protein folding by undergoing a conformational change from a closed state t...
Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes [0.03%]
动态谱系分析表征酶中的动力学诱导别构位点
Junko Taguchi,Akio Kitao
Junko Taguchi
We examine the dynamic features of non-trivial allosteric binding sites to elucidate potential drug binding sites. These allosteric sites were previously found to be allosteric after determination of the protein-drug co-crystal structure. A...
Specificity of broad protein interaction surfaces for proteins with multiple binding partners [0.03%]
具有多个结合伴侣的蛋白质与广义蛋白互作表面的特异性
Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue et al.
Nobuyuki Uchikoga et al.
Analysis of protein-protein interaction networks has revealed the presence of proteins with multiple interaction ligand proteins, such as hub proteins. For such proteins, multiple ligands would be predicted as interacting partners when pred...
Determination of locked interfaces in biomolecular complexes using Haptimol_RD [0.03%]
基于Haptimol_RD的生物大分子复合物刚性核心的确定方法
Georgios Iakovou,Stephen Laycock,Steven Hayward
Georgios Iakovou
Interactive haptics-assisted docking provides a virtual environment for the study of molecular complex formation. It enables the user to interact with the virtual molecules, experience the interaction forces via their sense of touch, and ga...
Kentaro Ishii,Masanori Noda,Susumu Uchiyama
Kentaro Ishii
The interactions of small molecules with proteins (protein-ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to...
Wataru Tanaka,Mitsuo Shoji,Fumiaki Tomoike et al.
Wataru Tanaka et al.
A uridine-cytidine kinase (UCK) catalyzes the phosphorylation of uridine (Urd) and cytidine (Cyd) and plays a significant role in the pyrimidine-nucleotide salvage pathway. Unlike ordinary ones, UCK from Thermus thermophilus HB8 (ttCK) lose...
Cation-limited kinetic model for microbial extracellular electron transport via an outer membrane cytochrome C complex [0.03%]
通过外膜细胞色素C复合物进行微生物胞外电子传递的阳离子限制动力学模型
Akihiro Okamoto,Yoshihide Tokunou,Junki Saito
Akihiro Okamoto
Outer-membrane c-type cytochrome (OM c-Cyt) complexes in several genera of iron-reducing bacteria, such as Shewanella and Geobacter, are capable of transporting electrons from the cell interior to extracellular solids as a terminal step of ...