Structural Dynamics-Us最新文献_第4页

High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability. 色氨酸- trna合成酶组合突变体的高通量热变性揭示了构象稳定性的高阶能量耦合决定因素。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-07-01 DOI: 10.1063/4.0000182

Violetta Weinreb, Gabriel Weinreb, Charles W Carter

{"title":"High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability.","authors":"Violetta Weinreb, Gabriel Weinreb, Charles W Carter","doi":"10.1063/4.0000182","DOIUrl":"https://doi.org/10.1063/4.0000182","url":null,"abstract":"Landscape descriptions provide a framework for identifying functionally significant dynamic linkages in proteins but cannot supply details. Rate measurements of combinatorial mutations can implicate dynamic linkages in catalysis. A major difficulty is filtering dynamic linkages from the vastly more numerous static interactions that stabilize domain folding. The Geobacillus stearothermophilus (TrpRS) D1 switch is such a dynamic packing motif; it links domain movement to catalysis and specificity. We describe Thermofluor and far UV circular dichroism melting curves for all 16 D1 switch variants to determine their higher-order impact on unliganded TrpRS stability. A prominent transition at intermediate temperatures in TrpRS thermal denaturation is molten globule formation. Combinatorial analysis of thermal melting transcends the protein landscape in four significant respects: (i) bioinformatic methods identify dynamic linkages from coordinates of multiple conformational states. (ii) Relative mutant melting temperatures, δTM, are proportional to free energy changes. (iii) Structural analysis of thermal melting implicates unexpected coupling between the D1 switch packing and regions of high local frustration. Those segments develop molten globular characteristics at the point of greatest complementarity to the chemical transition state and are the first TrpRS structures to melt. (iv) Residue F37 stabilizes both native and molten globular states; its higher-order interactions modify the relative intrinsic impacts of mutations to other D1 switch residues from those estimated for single point mutants. The D1 switch is a central component of an escapement mechanism essential to free energy transduction. These conclusions begin to relate the escapement mechanism to differential TrpRS conformational stabilities.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10449480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10109298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Quasi-elastic neutron scattering reveals the relationship between the dynamical behavior of phospholipid headgroups and hydration water. 准弹性中子散射揭示了磷脂头基的动力学行为与水合水之间的关系。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-07-01 DOI: 10.1063/4.0000184

Md Khalidur Rahman, Takeshi Yamada, Norifumi L Yamada, Mafumi Hishida, Yuji Higuchi, Hideki Seto

{"title":"Quasi-elastic neutron scattering reveals the relationship between the dynamical behavior of phospholipid headgroups and hydration water.","authors":"Md Khalidur Rahman, Takeshi Yamada, Norifumi L Yamada, Mafumi Hishida, Yuji Higuchi, Hideki Seto","doi":"10.1063/4.0000184","DOIUrl":"https://doi.org/10.1063/4.0000184","url":null,"abstract":"The dynamics of hydration water (HW) in 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE) was investigated by means of quasi-elastic neutron scattering (QENS) and compared with those observed in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). The headgroup dynamics of DMPE was investigated using a mixture of tail-deuterated DMPE and D2O, and the QENS profiles were interpreted as consisting of three modes. The fast mode comprised the rotation of hydrogen atoms in -NH3+ and -CH2- groups in the headgroup of DMPE, the medium-speed mode comprised fluctuations in the entire DMPE molecule, and the slow mode comprised fluctuations in the membrane. These interpretations were confirmed using molecular dynamics (MD) simulations. The HW dynamics analysis was performed on a tail-deuterated DMPE and H2O mixture. The QENS profiles were analyzed in terms of three modes: (1) a slow mode, identified as loosely bound HW in the DMPC membrane; (2) a medium-speed mode similar to free HW in the DMPC membrane; and (3) a fast mode, identified as rotational motion. The relaxation time for the fast mode was approximately six times shorter than that of rotational water in DMPC, consistent with the results of terahertz time-domain spectroscopy. The activation energy of medium-speed HW in DMPE differed from that of free HW in DMPC, suggesting the presence of different hydration states or hydrogen-bonded networks around the phosphocholine and phosphoethanolamine headgroups.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10449016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10483337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

A theoretical study of the time-resolved x-ray absorption spectrum of the photoionized BT-1T cation. 光离子化 BT-1T 阳离子的时间分辨 X 射线吸收光谱理论研究。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-05-26 eCollection Date: 2023-05-01 DOI: 10.1063/4.0000183

Anna Kristina Schnack-Petersen, Mátyás Pápai, Sonia Coriani, Klaus Braagaard Møller

{"title":"A theoretical study of the time-resolved x-ray absorption spectrum of the photoionized BT-1T cation.","authors":"Anna Kristina Schnack-Petersen, Mátyás Pápai, Sonia Coriani, Klaus Braagaard Møller","doi":"10.1063/4.0000183","DOIUrl":"10.1063/4.0000183","url":null,"abstract":"The time-resolved x-ray absorption spectrum of the BT-1T cation (BT-1T+) is theoretically simulated in order to investigate the charge transfer reaction of the system. We employ both trajectory surface hopping and quantum dynamics to simulate the structural evolution over time and the changes in the state populations. To compute the static x-ray absorption spectra (XAS) of the ground and excited states, we apply both the time-dependent density functional theory and the coupled cluster singles and doubles method. The results obtained are in good agreement between the methods. It is, furthermore, found that the small structural changes that occur during the reaction have little effect on the static XAS. Hence, the tr-XAS can be computed based on the state populations determined from a nuclear dynamics simulation and one set of static XAS calculations, utilizing the ground state optimized geometry. This approach can save considerable computational resources, as the static spectra need not to be calculated for all geometries. As BT-1T is a relatively rigid molecule, the outlined approach should only be considered when investigating non-radiative decay processes in the vicinity of the Franck-Condon point.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10224778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9830635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

And now some updates for SDY readers from the Editor…. 现在编辑为SDY读者提供一些更新....

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-05-01 DOI: 10.1063/4.0000198

George N Phillips

引用次数: 0

Low-pass spectral analysis of time-resolved serial femtosecond crystallography data. 时间分辨连续飞秒晶体学数据的低通光谱分析。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-05-01 DOI: 10.1063/4.0000178

Cecilia M Casadei, Ahmad Hosseinizadeh, Spencer Bliven, Tobias Weinert, Jörg Standfuss, Russell Fung, Gebhard F X Schertler, Robin Santra

{"title":"Low-pass spectral analysis of time-resolved serial femtosecond crystallography data.","authors":"Cecilia M Casadei, Ahmad Hosseinizadeh, Spencer Bliven, Tobias Weinert, Jörg Standfuss, Russell Fung, Gebhard F X Schertler, Robin Santra","doi":"10.1063/4.0000178","DOIUrl":"https://doi.org/10.1063/4.0000178","url":null,"abstract":"Low-pass spectral analysis (LPSA) is a recently developed dynamics retrieval algorithm showing excellent retrieval properties when applied to model data affected by extreme incompleteness and stochastic weighting. In this work, we apply LPSA to an experimental time-resolved serial femtosecond crystallography (TR-SFX) dataset from the membrane protein bacteriorhodopsin (bR) and analyze its parametric sensitivity. While most dynamical modes are contaminated by nonphysical high-frequency features, we identify two dominant modes, which are little affected by spurious frequencies. The dynamics retrieved using these modes shows an isomerization signal compatible with previous findings. We employ synthetic data with increasing timing uncertainty, increasing incompleteness level, pixel-dependent incompleteness, and photon counting errors to investigate the root cause of the high-frequency contamination of our TR-SFX modes. By testing a range of methods, we show that timing errors comparable to the dynamical periods to be retrieved produce a smearing of dynamical features, hampering dynamics retrieval, but with no introduction of spurious components in the solution, when convergence criteria are met. Using model data, we are able to attribute the high-frequency contamination of low-order dynamical modes to the high levels of noise present in the data. Finally, we propose a method to handle missing observations that produces a substantial dynamics retrieval improvement from synthetic data with a significant static component. Reprocessing of the bR TR-SFX data using the improved method yields dynamical movies with strong isomerization signals compatible with previous findings.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10233406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9582631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural biology and public health response to biomedical threats. 结构生物学和公共卫生应对生物医学威胁。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-05-01 DOI: 10.1063/4.0000186

Joanna Lenkiewicz, Vanessa Bijak, Shrisha Poonuganti, Michal Szczygiel, Michal Gucwa, Krzysztof Murzyn, Wladek Minor

引用次数: 1

Imaging temperature and thickness of thin planar liquid water jets in vacuum. 真空中薄平面液态水射流的成像温度和厚度。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-05-01 DOI: 10.1063/4.0000188

Tillmann Buttersack, Henrik Haak, Hendrik Bluhm, Uwe Hergenhahn, Gerard Meijer, Bernd Winter

引用次数: 1

Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data. 投影提取垂直分量(PEPC)方法从时间分辨数据中提取动力学。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-05-01 DOI: 10.1063/4.0000189

H Ki, J Gu, Y Cha, K W Lee, H Ihee

{"title":"Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data.","authors":"H Ki, J Gu, Y Cha, K W Lee, H Ihee","doi":"10.1063/4.0000189","DOIUrl":"https://doi.org/10.1063/4.0000189","url":null,"abstract":"Time-resolved x-ray liquidography (TRXL) is a potent method for investigating the structural dynamics of chemical and biological reactions in the liquid phase. It has enabled the extraction of detailed structural aspects of various dynamic processes, the molecular structures of intermediates, and kinetics of reactions across a wide range of systems, from small molecules to proteins and nanoparticles. Proper data analysis is key to extracting the information of the kinetics and structural dynamics of the studied system encrypted in the TRXL data. In typical TRXL data, the signals from solute scattering, solvent scattering, and solute-solvent cross scattering are mixed in the q-space, and the solute kinetics and solvent hydrodynamics are mixed in the time domain, thus complicating the data analysis. Various methods developed so far generally require prior knowledge of the molecular structures of candidate species involved in the reaction. Because such information is often unavailable, a typical data analysis often involves tedious trial and error. To remedy this situation, we have developed a method named projection to extract the perpendicular component (PEPC), capable of removing the contribution of solvent kinetics from TRXL data. The resulting data then contain only the solute kinetics, and, thus, the solute kinetics can be easily determined. Once the solute kinetics is determined, the subsequent data analysis to extract the structural information can be performed with drastically improved convenience. The application of the PEPC method is demonstrated with TRXL data from the photochemistry of two molecular systems: [Au(CN)2-]3 in water and CHI3 in cyclohexane.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10306411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9736031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases. DNA聚合酶活性位点动力学和瞬态金属离子结合的结晶观察。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-05-01 DOI: 10.1063/4.0000187

Caleb Chang, Grace Zhou, Yang Gao

引用次数: 0

Pump-probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates. 在MHz重复率下光诱导磁化动力学的泵-探针x射线显微镜。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2023-03-01 DOI: 10.1063/4.0000167

Kathinka Gerlinger, Bastian Pfau, Martin Hennecke, Lisa-Marie Kern, Ingo Will, Tino Noll, Markus Weigand, Joachim Gräfe, Nick Träger, Michael Schneider, Christian M Günther, Dieter Engel, Gisela Schütz, Stefan Eisebitt

{"title":"Pump-probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates.","authors":"Kathinka Gerlinger, Bastian Pfau, Martin Hennecke, Lisa-Marie Kern, Ingo Will, Tino Noll, Markus Weigand, Joachim Gräfe, Nick Träger, Michael Schneider, Christian M Günther, Dieter Engel, Gisela Schütz, Stefan Eisebitt","doi":"10.1063/4.0000167","DOIUrl":"https://doi.org/10.1063/4.0000167","url":null,"abstract":"We present time-resolved scanning x-ray microscopy measurements with picosecond photo-excitation via a tailored infrared pump laser at a scanning transmission x-ray microscope. Specifically, we image the laser-induced demagnetization and remagnetization of thin ferrimagnetic GdFe films proceeding on a few nanoseconds timescale. Controlling the heat load on the sample via additional reflector and heatsink layers allows us to conduct destruction-free measurements at a repetition rate of 50 MHz. Near-field enhancement of the photo-excitation and controlled annealing effects lead to laterally heterogeneous magnetization dynamics which we trace with 30 nm spatial resolution. Our work opens new opportunities to study photo-induced dynamics on the nanometer scale, with access to picosecond to nanosecond time scales, which is of technological relevance, especially in the field of magnetism.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10038236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9546626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1