Biophysics (Nagoya-shi, Japan)最新文献_第7页

Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift. 细菌视紫质吸收最大值的全量子化学计算:对导致视紫质移位的氨基酸残基的综合分析。

Biophysics (Nagoya-shi, Japan) Pub Date : 2012-07-27 eCollection Date: 2012-01-01 DOI: 10.2142/biophysics.8.115

Tomohiko Hayashi, Azuma Matsuura, Hiroyuki Sato, Minoru Sakurai

{"title":"Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift.","authors":"Tomohiko Hayashi, Azuma Matsuura, Hiroyuki Sato, Minoru Sakurai","doi":"10.2142/biophysics.8.115","DOIUrl":"https://doi.org/10.2142/biophysics.8.115","url":null,"abstract":"Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"8 ","pages":"115-25"},"PeriodicalIF":0.0,"publicationDate":"2012-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.8.115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34624810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Comparative study of the different mechanisms for zinc ion stress sensing in two cyanobacterial strains, Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803. 聚藻球菌(Synechococcus sp. PCC 7942)和聚藻球菌(synechocytis sp. PCC 6803)对锌离子胁迫感知机制的比较研究

Biophysics (Nagoya-shi, Japan) Pub Date : 2012-07-06 eCollection Date: 2012-01-01 DOI: 10.2142/biophysics.8.103

Eugene Hayato Morita, Satsuki Kawamoto, Shunnosuke Abe, Yoshitaka Nishiyama, Takahisa Ikegami, Hidenori Hayashi

{"title":"Comparative study of the different mechanisms for zinc ion stress sensing in two cyanobacterial strains, Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803.","authors":"Eugene Hayato Morita, Satsuki Kawamoto, Shunnosuke Abe, Yoshitaka Nishiyama, Takahisa Ikegami, Hidenori Hayashi","doi":"10.2142/biophysics.8.103","DOIUrl":"https://doi.org/10.2142/biophysics.8.103","url":null,"abstract":"In response to an increased level of Zn(2+), Synechococcus sp. PCC 7942 expresses SmtA, a metallothionein-like metal-chelating protein, while Synechocystis sp. PCC 6803 expresses ZiaA, a transporter of Zn(2+). The gene expression of these proteins is regulated by repressor protein, SmtB and ZiaR, respectively. In spite of contributing to different response systems, both repressor proteins belong to the ArsR family and are highly homologous to each other. To understand the different systems responsible for dealing with excess Zn(2+), we examined the cis-elements in the promoter regions of smtA and ziaA, as well as the binding affinities of recombinant SmtB and ZiaR proteins. The operator/promoter region of smtA included two palindromic sequences and that of ziaA included one. Electrophoretic mobility shift assay revealed that SmtB formed four different complexes with the operator/promoter region of smtA, whereas it formed only two different complexes with the corresponding region of ziaA. For ZiaR, the corresponding results were quite the same as those for SmtB. Furthermore, the complex formation between SmtB and operator/promoter regions is inhibited in the presence of Zn(2+) at higher concentrations than 16 μM. On the other hand, the corresponding Zn(2+) concentration is 128 μM. These results demonstrate that the degrees of protein-DNA complex formation between repressor proteins and the operator/promoter regions of regulated genes depend on the structures of the operator/promoter regions, and the effects of Zn(2+) on the dissociation of these complexes are mainly associated with the structures of the repressors. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"8 ","pages":"103-9"},"PeriodicalIF":0.0,"publicationDate":"2012-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.8.103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34624808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Extraction and purification of a luminiferous substance from the luminous mushroom Mycena chlorophos. 从发光蘑菇绿足菌中提取和纯化一种发光物质。

Biophysics (Nagoya-shi, Japan) Pub Date : 2012-07-06 eCollection Date: 2012-01-01 DOI: 10.2142/biophysics.8.111

Shuhei Hayashi, Ryuichi Fukushima, Naohisa Wada

引用次数: 11

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. GIRAF:一种在原子分辨率下快速搜索和灵活定位蛋白质配体结合界面的方法。

Biophysics (Nagoya-shi, Japan) Pub Date : 2012-05-31 eCollection Date: 2012-01-01 DOI: 10.2142/biophysics.8.79

Akira R Kinjo, Haruki Nakamura

{"title":"GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.","authors":"Akira R Kinjo, Haruki Nakamura","doi":"10.2142/biophysics.8.79","DOIUrl":"https://doi.org/10.2142/biophysics.8.79","url":null,"abstract":"Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"8 ","pages":"79-94"},"PeriodicalIF":0.0,"publicationDate":"2012-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.8.79","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34733428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

mDia1 and formins: screw cap of the actin filament. mDia1和formins:肌动蛋白丝的螺旋帽。

Biophysics (Nagoya-shi, Japan) Pub Date : 2012-05-31 eCollection Date: 2012-01-01 DOI: 10.2142/biophysics.8.95

Hiroaki Mizuno, Naoki Watanabe

{"title":"mDia1 and formins: screw cap of the actin filament.","authors":"Hiroaki Mizuno, Naoki Watanabe","doi":"10.2142/biophysics.8.95","DOIUrl":"https://doi.org/10.2142/biophysics.8.95","url":null,"abstract":"Formin homology proteins (formins) are actin nucleation factors which remain bound to the growing barbed end and processively elongate actin filament (F-actin). Recently, we have demonstrated that a mammalian formin mDia1 rotates along the long-pitch helix of F-actin during processive elongation (helical rotation) by single-molecule fluorescence polarization. We have also shown processive depolymerization of mDia1-bound F-actin during which helical rotation was visualized. In the cell where F-actins are highly cross-linked, formins should rotate during filament elongation. Therefore, when formins are tightly anchored to cellular structures, formins may not elongate F-actin. Adversely, helical rotation of formins might affect the twist of F-actin. Formins could thus control actin elongation and regulate stability of cellular actin filaments through helical rotation. On the other hand, ADP-actin elongation at the mDia1-bound barbed end turned out to become decelerated by profilin, in marked contrast to its remarkably positive effect on mDia1-mediated ATP-actin elongation. This deceleration is caused by enhancement of the off-rate of ADP-actin. While mDia1 and profilin enhance the ADP-actin off-rate, they do not apparently increase the ADP-actin on-rate at the barbed end. These results imply that G-actin-bound ATP and its hydrolysis may be part of the acceleration mechanism of formin-mediated actin elongation. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"8 ","pages":"95-102"},"PeriodicalIF":0.0,"publicationDate":"2012-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.8.95","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34624807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

Chemomechanical coupling of F1-ATPase under hydrolysis conditions. f1 - atp酶在水解条件下的化学-力学偶联。

Biophysics (Nagoya-shi, Japan) Pub Date : 2012-04-13 eCollection Date: 2012-01-01 DOI: 10.2142/biophysics.8.73

Rikiya Watanabe, Hiroyuki Noji

引用次数: 2