1P040 Study of the photoresponsive mechanism of LOV-HTH protein using μs scale molecular dynamics simulations(01B. Protein:Structure & Function,Poster)
1P040 μsスケールの分子動力学シミュレーションによる光受容タンパク質LOV-HTHの光応答機構の研究(01B. 蛋白質:構造機能相関,ポスター,日本生物物理学会年会第51回(2013年度))

Tetsuo Kokubu, Tadaomi Furuta, Minoru Sakurai
2013 Seibutsu Butsuri  
ATP Binding Cassette transporters are membrane proteins moving substrates energized by ATP hydrolysis. A eukaryotic ABC transporter consists of two domains: nucleotide-binding domains hydrolyzing ATP and transmembrane domains facilitating substrate-transport. These domains contact via two helices called coupling helices, CH1 and CH2, from the transmembrane domain. To understand the roles of CH1 and CH2 in the ATP-driven transport mechanism, we performed functional study by sitedirected
more » ... is based on the crystal structure of a new eukaryote ABC exporter, we recently determined at high resolution. This study revealed some residues on CH1 and CH2 play important functions such as maintaining the structure of the helices or mediating interaction of the two domains. 1P038 分子動力学シミュレーションで探る CFTR における変異の 影響 CFTR is a member of ABC transporters, and is a unique chloride channel. The channel opening is triggered by the ATP-driven NBD dimerization. There are several mutations in the CFTR gene, which lead to the genetic disease cystic fibrosis (CF). In spite of intense investigation, the effects of mutations have not been understood in detail. In this study, we focus on the conformational changes of CFTR wild type and mutants. We conducted the comparison between dynamics of wild type and those of several mutants by molecular dynamics simulations, where simulations were started from inward-facing homology models. We will discuss the structure-function relationships in CFTR, and also the role of ATP on NBD dimerization. 1P039 分子動力学シミュレーションで探るセルラーゼ TrCel7A の 基質取り込みのメカニズム Mechanism of substrate uptake in cellulase TrCel7A as studied by molecular dynamics simulations Takashi Kanazawa, Minoru Sakurai, Tadaomi Furuta (Center for Biol. Res. Info., Tokyo Tech) Cellobiohydrolases is an enzyme that hydrolyzes glycosidic linkages in cellulose, and its catalytic domain has a tunnel with aromatic residues, which is important for substrate uptake. Here, we conducted molecular dynamics (MD) simulations and free energy calculations to clarify the roles of tryptophan residues in Trichoderma reesei cellobiohydrolase Cel7A. The MD results show that the cellulose chain entered into the tunnel from subsite -6 to -3 in W40A mutant (in which the entrance Trp40 is mutated to alanine), whereas no apparent entering was observed in wild type. Moreover, from the free energy calculation, we found that the tryptophan residues lining up along the tunnel have a significant effect on substrate binding in TrCel7A. 1P040 μs スケールの分子動力学シミュレーションによる光受容タ ンパク質 LOV-HTH の光応答機構の研究 Study of the photoresponsive mechanism of LOV-HTH protein using μs scale molecular dynamics simulations Tetsuo Kokubu, Tadaomi Furuta, Minoru Sakurai (Center for Biol. Res. & Inform., Tokyo Tech) LOV (light-oxygen-voltage) domains are blue light-activated signaling modules integral to a wide range of photosensory proteins. To reveal their photoresponsive mechanism, we performed μs scale MD simulations for a light-regulated DNA-binding protein construct LOV-HTH (helix-turnhelix) in both the dark (before light absorption) and light states (after light absorption). The present simulations indicated that formation of the cysteinyl-FMN (LOV chromophore) adduct causes significant dynamics changes in the HTH domain and does the H-bond network among residues in the vicinity of FMN in the light state. Based on these results, we propose the light signal path ways through Q136-S137-R215 and via Jα-helix. ATP-binding into the nucleotide-binding domains (NBDs) of ABC transporter induces NBD dimerization, which triggers the transportation of substrates across membranes. However the energetics of these processes has not been well understood. Here, we evaluated the free energy difference (ΔG bind ) of NBD dimerization in MalK and CFTR cases by the MM/3D-RISM method. In the case of MalK, the ΔG bind of ATP-bound NBDs is -6.34 kcal/mol, which is in good agreement with the experimental value. We also found that the processes are driven by a large entropy gain of water, and that the subsequent Pi releases destabilize the NBD dimer with a significant decrease of entropy gain of water. Similarly an entropydriven NBD dimerization was also observed in the case of CFTR. 1P042 ADP/ATP 透過担体の大規模構造変化に関する理論的研究 A theoretical study on the large conformational change of ADP/ ATP carrier Koichi Tamura, Shigehiko Hayashi (Grad. Sch. Sci., Univ. Kyoto) ADP/ATP carrier(AAC) is a membrane protein embedded in the inner membrane of mitochondria. Its fundamental function is to exchange an ADP or ATP in one side of membrane to an ADP(ATP) in the other side. The exchange is thought to be accompanied with protein's large conformational change and the strctural analysis of AAC will explain the mechanism of the 1:1 exchange. The only available structure (PDBid: 1okc) is opened toward the inter membrane space and the other structure is still not available. LRPF method, which enables us to predict protein's conformational transition pathway, was applied to the problem and revealed a channel-like intermediate structure.
doi:10.2142/biophys.53.s112_4 fatcat:ge4lxjrojzcnri2yvmusiwc5hq