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1. New additions to the C lus P ro server motivated by CAPRI

   https://doi.org/10.1002/prot.25219  

   Vajda, Sandor; Yueh, Christine; Beglov, Dmitri; Bohnuud, Tanggis; Mottarella, Scott E.; Xia, Bing; Hall, David R.; Kozakov, Dima (January 2017, Proteins: Structure, Function, and Bioinformatics)

   ABSTRACT The heavily used protein–protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X‐ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435–444. © 2016 Wiley Periodicals, Inc. 

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2. Manganese‐dependent transcription regulation by MntR and PerR in Thermus thermophilus HB8

   https://doi.org/10.1111/mmi.15278  

   Barrows, John_K; Stubbs, Kamya_A; Padilla‐Montoya, Irina_F; Leeper, Thomas_C; Van Dyke, Michael_W (May 2024, Molecular Microbiology)

   Abstract Bacteria contain conserved mechanisms to control the intracellular levels of metal ions. Metalloregulatory transcription factors bind metal cations and play a central role in regulating gene expression of metal transporters. Often, these transcription factors regulate transcription by binding to a specific DNA sequence in the promoter region of target genes. Understanding the preferred DNA‐binding sequence for transcriptional regulators can help uncover novel gene targets and provide insight into the biological role of the transcription factor in the host organism. Here, we identify consensus DNA‐binding sequences and subsequent transcription regulatory networks for two metalloregulators from the ferric uptake regulator (FUR) and diphtheria toxin repressor (DtxR) superfamilies inThermus thermophilusHB8. By homology search, we classify the DtxR homolog as a manganese‐specific, MntR (TtMntR), and the FUR homolog as a peroxide‐sensing, PerR (TtPerR). Both transcription factors repress separate ZIP transporter genes in vivo, andTtPerR acts as a bifunctional transcription regulator by activating the expression of ferric and hemin transport systems. We showTtPerR andTtMntR bind DNA in the presence of manganese in vitro and in vivo; however,TtPerR is unable to bind DNA in the presence of iron, likely due to iron‐mediated histidine oxidation. Unlike canonical PerR homologs,TtPerR does not appear to contribute to peroxide detoxification. Instead, theTtPerR regulon and DNA binding sequence are more reminiscent of Fur or Mur homologs. Collectively, these results highlight the similarities and differences between two metalloregulatory superfamilies and underscore the interplay of manganese and iron in transcription factor regulation. 

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3. Single Spot Rb‐Sr Isochron Dating of Biotite by LA‐MC‐ICP‐MS / MS

   https://doi.org/10.1111/ggr.12518  

   Cruz‐Uribe, Alicia M.; Craig, Grant; Garber, Joshua M.; Paul, Bence; Arkula, Cemil; Bouman, Claudia (July 2023, Geostandards and Geoanalytical Research)

   Laser ablation tandem mass spectrometry is a burgeoning field forin situRb‐Sr geochronology. Here, we determined simultaneous isotope ratios of⁸⁷Sr/⁸⁶Sr and⁸⁷Rb/⁸⁶Sr in metamorphic biotite from western Maine, using an ESL™ imageGEO™193 excimer laser ablation system coupled to a Thermo Scientific™ Neoma™ MC‐ICP‐MS/MS. Measurements were made on Faraday cups with Rb⁺at mass 87; Sr isotopes were reacted with SF₆gas and measured as SrF⁺at masses 103–107. Twenty‐two laser spots in biotite from a single sample yield a traditional Rb‐Sr isochron date of 289 ± 6 Ma. Time‐resolved signals reveal significant zoning in⁸⁷Sr/⁸⁶Sr and⁸⁷Rb/⁸⁶Sr within single spot analyses, which were used to construct single spot isochrons. Individual laser spots contain multiple isochronous subpopulations; some spots contain up to three distinct Rb‐Sr isochrons that are decoupled from variations in Rb/Sr. Thirty‐five isochron dates were determined using this sub‐spot approach, with⁸⁷Sr/⁸⁶Sr intercepts that systematically vary with Rb‐Sr date; two‐point isochrons were calculated for individual integrations (n= 780) based on these variable intercepts. Both methods yield age peaks at 303, 270 and 240 Ma. These data suggest that the Rb‐Sr system has the potential to record multiple heating, cooling or fluid‐alteration events spanning ~ 100 My within small domains in single biotite crystals. 

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4. Assessment of prediction methods for protein structures determined by NMR in CASP14 : Impact of AlphaFold2

   https://doi.org/10.1002/prot.26246  

   Huang, Yuanpeng Janet; Zhang, Ning; Bersch, Beate; Fidelis, Krzysztof; Inouye, Masayori; Ishida, Yojiro; Kryshtafovych, Andriy; Kobayashi, Naohiro; Kuroda, Yutaka; Liu, Gaohua; et al (December 2021, Proteins: Structure, Function, and Bioinformatics)
5. RASSF1 is identified by transcriptome coordination analysis as a target of ATF4

   https://doi.org/10.1002/2211-5463.13569  

   Zhang, Youwen; Huynh‐Dam, Kim‐Tuyen; Ding, Xiaokai; Sikirzhytski, Vitali; Lim, Chang‐uk; Broude, Eugenia; Kiaris, Hippokratis (March 2023, FEBS Open Bio)