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Structure-function relationship of KaiC around dawn. 黎明前后 KaiC 的结构-功能关系。
Biophysics and physicobiology Pub Date : 2023-12-16 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0001
Yoshihiko Furuike, Eiki Yamashita, Shuji Akiyama
{"title":"Structure-function relationship of KaiC around dawn.","authors":"Yoshihiko Furuike, Eiki Yamashita, Shuji Akiyama","doi":"10.2142/biophysico.bppb-v21.0001","DOIUrl":"10.2142/biophysico.bppb-v21.0001","url":null,"abstract":"<p><p>KaiC is a multifunctional enzyme functioning as the core of the circadian clock system in cyanobacteria: its N-terminal domain has adenosine triphosphatase (ATPase) activity, and its C-terminal domain has autokinase and autophosphatase activities targeting own S431 and T432. The coordination of these multiple biochemical activities is the molecular basis for robust circadian rhythmicity. Therefore, much effort has been devoted to elucidating the cooperative relationship between the two domains. However, structural and functional relationships between the two domains remain unclear especially with respect to the dawn phase, at which KaiC relieves its nocturnal history through autodephosphorylation. In this study, we attempted to design a double mutation of S431 and T432 that can capture KaiC as a fully dephosphorylated form with minimal impacts on its structure and function, and investigated the cooperative relationship between the two domains in the night to morning phases from many perspectives. The results revealed that both domains cooperate at the dawn phase through salt bridges formed between the domains, thereby non-locally co-activating two events, ATPase de-inhibition and S431 dephosphorylation. Our further analysis using existing crystal structures of KaiC suggests that the states of both domains are not always in one-to-one correspondence at every phase of the circadian cycle, and their coupling is affected by the interactions with KaiA or adjacent subunits within a KaiC hexamer.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210001"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159238","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: 0
Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics. 小分子粘合剂和非粘合剂与 FMN 核糖开关的结合自由能图谱:全原子分子动力学
Biophysics and physicobiology Pub Date : 2023-12-13 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0047
Junichi Higo, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Yoshifumi Fukunishi
{"title":"Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.","authors":"Junichi Higo, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Yoshifumi Fukunishi","doi":"10.2142/biophysico.bppb-v20.0047","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0047","url":null,"abstract":"<p><p>A small and flexible molecule, ribocil A (non-binder) or B (binder), binds to the deep pocket of the aptamer domain of the FMN riboswitch, which is an RNA molecule. This binding was studied by mD-VcMD, which is a generalized-ensemble simulation method. Ribocil A and B are structurally similar because they are optical isomers to each other. In the initial conformation of simulation, the ligands and the aptamer were completely dissociated in explicit solvent. The aptamer-ribocil B binding was stronger than the aptamer-ribocil A binding, which agrees with experiments. The computed free-energy landscape for the aptamer-ribocil B binding was funnel-like, whereas that for the aptamer-ribocil A binding was rugged. When passing through the gate (named \"front gate\") of the binding pocket, each ligand interacted with bases of the riboswitch by non-native π-π stackings, and the stackings restrained the ligand's orientation to be advantageous to reach the binding site smoothly. When the ligands reached the binding site in the pocket, the non-native stackings were replaced by the native stackings. The ligand's orientation restriction is discussed referring to a selection mechanism reported in an earlier work on a drug-GPCR interaction. The present simulation showed another pathway leading the ligands to the binding site. The gate (\"rear gate\") for this pathway was located completely opposite to the front gate on the aptamer's surface. However, the approach from the rear gate required overcoming a free-energy barrier regarding ligand's rotation before reaching the binding site.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"20 4","pages":"e200047"},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10853809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725620","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: 0
Residue-based correlation between equilibrium and rate constants is an experimental formulation of the consistency principle for smooth structural changes of proteins. 基于残基的平衡常量与速率常数之间的相关性是蛋白质结构平滑变化的一致性原则的实验表述。
Biophysics and physicobiology Pub Date : 2023-12-13 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0046
Daisuke Kohda, Seiichiro Hayashi, Daisuke Fujinami
{"title":"Residue-based correlation between equilibrium and rate constants is an experimental formulation of the consistency principle for smooth structural changes of proteins.","authors":"Daisuke Kohda, Seiichiro Hayashi, Daisuke Fujinami","doi":"10.2142/biophysico.bppb-v20.0046","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0046","url":null,"abstract":"<p><p>The consistency principle represents a physicochemical condition requisite for ideal protein folding. It assumes that any pair of amino acid residues in partially folded structures has an attractive short-range interaction <i>only if</i> the two residues are in contact within the native structure. The residue-specific equilibrium constant, <i>K</i>, and the residue-specific rate constant, <i>k</i> (forward and backward), can be determined by NMR and hydrogen-deuterium exchange studies. Linear free energy relationships (LFER) in the rate-equilibrium free energy relationship (REFER) plots (i.e., log <i>k</i> vs. log <i>K</i>) are widely seen in protein-related phenomena, but our REFER plot differs from them in that the data points are derived from one polypeptide chain under a single condition. Here, we examined the theoretical basis of the residue-based LFER. First, we derived a basic equation, ρ<i><sub>ij</sub></i>=½(φ<i><sub>i</sub></i>+φ<i><sub>j</sub></i>), from the consistency principle, where ρ<i><sub>ij</sub></i> is the slope of the line segment that connects residues <i>i</i> and <i>j</i> in the REFER plot, and φ<i><sub>i</sub></i> and φ<i><sub>j</sub></i> are the local fractions of the native state in the transient state ensemble (TSE). Next, we showed that the general solution is the alignment of the (log <i>K</i>, log <i>k</i>) data points on a parabolic curve in the REFER plot. Importantly, unlike LFER, the quadratic free energy relationship (QFER) is compatible with the heterogeneous formation of local structures in the TSE. Residue-based LFER/QFER provides a unique insight into the TSE: A foldable polypeptide chain consists of several folding units, which are <i>consistently</i> coupled to undergo smooth structural changes.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"20 4","pages":"e200046"},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10850467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725622","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: 0
Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation. 多酚对淀粉样蛋白-β(16-22)聚集的抑制作用--利用复制置换与溶质调温分子动力学模拟。
Biophysics and physicobiology Pub Date : 2023-12-09 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0045
Daiki Fukuhara, Satoru G Itoh, Hisashi Okumura
{"title":"Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.","authors":"Daiki Fukuhara, Satoru G Itoh, Hisashi Okumura","doi":"10.2142/biophysico.bppb-v20.0045","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0045","url":null,"abstract":"<p><p>Aggregates of amyloid-β (Aβ) peptides are thought to cause Alzheimer's disease. Polyphenolic compounds are known to inhibit Aβ aggregation. We applied replica permutation with solute tempering (RPST) to the system of Aβ fragments, Aβ(16-22), and polyphenols to elucidate the mechanism of inhibition of Aβ aggregation. The RPST molecular dynamics simulations were performed for two polyphenols, myricetin (MYC) and rosmarinic acid (ROA). Two Aβ fragments were distant, and the number of residues forming the intermolecular β-sheet was reduced in the presence of MYC and ROA compared with that in the absence of polyphenols. MYC was found to interact with glutamic acid and phenylalanine of Aβ fragments. These interactions induce helix structure formation of Aβ fragments, making it difficult to form β-sheet. ROA interacted with glutamic acid and lysine, which reduced the hydrophilic interaction between Aβ fragments. These results indicate that these polyphenols inhibit the aggregation of Aβ fragments with different mechanisms.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"20 4","pages":"e200045"},"PeriodicalIF":0.0,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10850463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725621","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: 0
Welcome to the borderless rhodopsin world. 欢迎来到无边界的红光素世界。
Biophysics and physicobiology Pub Date : 2023-12-01 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0044
Takahiro Yamashita, Satoshi P Tsunoda
{"title":"Welcome to the borderless rhodopsin world.","authors":"Takahiro Yamashita, Satoshi P Tsunoda","doi":"10.2142/biophysico.bppb-v20.0044","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0044","url":null,"abstract":"","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"20 4","pages":"e200044"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10850464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725623","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: 0
Announcement of BPPB paper awards 2023. 宣布 2023 年 BPPB 论文奖。
Biophysics and physicobiology Pub Date : 2023-10-24 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0040
Haruki Nakamura
{"title":"Announcement of BPPB paper awards 2023.","authors":"Haruki Nakamura","doi":"10.2142/biophysico.bppb-v20.0040","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0040","url":null,"abstract":"","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"20 4","pages":"e200040"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10850468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725619","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: 0
Chapter 8: Brownian Motion.
IF 1.6
Biophysics and physicobiology Pub Date : 2023-09-15 eCollection Date: 2021-01-01 DOI: 10.2142/biophysico.bppb-v18.s010
{"title":"Chapter 8: Brownian Motion.","authors":"","doi":"10.2142/biophysico.bppb-v18.s010","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.s010","url":null,"abstract":"","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"18 ","pages":"S066-S075"},"PeriodicalIF":1.6,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627316","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: 0
Chapter 7: Local Temperature.
IF 1.6
Biophysics and physicobiology Pub Date : 2023-09-15 eCollection Date: 2021-01-01 DOI: 10.2142/biophysico.bppb-v18.s009
{"title":"Chapter 7: Local Temperature.","authors":"","doi":"10.2142/biophysico.bppb-v18.s009","DOIUrl":"10.2142/biophysico.bppb-v18.s009","url":null,"abstract":"","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"18 ","pages":"S056-S065"},"PeriodicalIF":1.6,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627315","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: 0
Part II. Application of Statistical Mechanics in Biological Phenomena.
IF 1.6
Biophysics and physicobiology Pub Date : 2023-09-15 eCollection Date: 2021-01-01 DOI: 10.2142/biophysico.bppb-v18.s008
{"title":"Part II. Application of Statistical Mechanics in Biological Phenomena.","authors":"","doi":"10.2142/biophysico.bppb-v18.s008","DOIUrl":"10.2142/biophysico.bppb-v18.s008","url":null,"abstract":"","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"18 ","pages":"S044-S055"},"PeriodicalIF":1.6,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11901661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618028","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: 0
Ring formation by Vibrio fusion protein composed of FliF and FliG, MS-ring and C-ring component of bacterial flagellar motor in membrane. 由 FliF 和 FliG 组成的弧菌融合蛋白、MS 环和细菌鞭毛运动的 C 环在膜中形成环。
Biophysics and physicobiology Pub Date : 2023-06-09 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0028
Kanji Takahashi, Tatsuro Nishikino, Hiroki Kajino, Seiji Kojima, Takayuki Uchihashi, Michio Homma
{"title":"Ring formation by <i>Vibrio</i> fusion protein composed of FliF and FliG, MS-ring and C-ring component of bacterial flagellar motor in membrane.","authors":"Kanji Takahashi, Tatsuro Nishikino, Hiroki Kajino, Seiji Kojima, Takayuki Uchihashi, Michio Homma","doi":"10.2142/biophysico.bppb-v20.0028","DOIUrl":"10.2142/biophysico.bppb-v20.0028","url":null,"abstract":"<p><p>The marine bacterium <i>Vibrio alginolyticus</i> has a single flagellum as a locomotory organ at the cell pole, which is rotated by the Na<sup>+</sup>-motive force to swim in a liquid. The base of the flagella has a motor composed of a stator and rotor, which serves as a power engine to generate torque through the rotor-stator interaction coupled to Na<sup>+</sup> influx through the stator channel. The MS-ring, which is embedded in the membrane at the base of the flagella as part of the rotor, is the initial structure required for flagellum assembly. It comprises 34 molecules of the two-transmembrane protein FliF. FliG, FliM, and FliN form a C-ring just below the MS-ring. FliG is an important rotor protein that interacts with the stator PomA and directly contributes to force generation. We previously found that FliG promotes MS-ring formation in <i>E. coli</i>. In the present study, we constructed a <i>fliF-fliG</i> fusion gene, which encodes an approximately 100 kDa protein, and the successful production of this protein effectively formed the MS-ring in <i>E. coli</i> cells. We observed fuzzy structures around the ring using either electron microscopy or high-speed atomic force microscopy (HS-AFM), suggesting that FliM and FliN are necessary for the formation of a stable ring structure. The HS-AFM movies revealed flexible movements at the FliG region.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"20 2","pages":"e200028"},"PeriodicalIF":0.0,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140145021","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: 0
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