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Zhi-jie Tan - One of the best experts on this subject based on the ideXlab platform.

  • Predicting 3D structure and stability of RNA pseudoknots in monovalent and Divalent Ion solutIons.
    PLoS computational biology, 2018
    Co-Authors: Ya-zhou Shi, Lei Jin, Chen-jie Feng, Ya-lan Tan, Zhi-jie Tan
    Abstract:

    RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensIonal (3D) structures and stability play essential roles in a variety of biological functIons. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functIons. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictIons and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/Divalent Ion solutIons. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictIons for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/Divalent Ion concentratIons. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in Ion solutIons. Our analyses for extensive pseudokonts and the wide range of monovalent/Divalent Ion concentratIons verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solutIon Ion conditIons.

  • The comparisons between predictIons (lines) and experiments (symbols) for MMTV and T2 pseudoknots in Divalent Ion solutIons.
    2018
    Co-Authors: Ya-zhou Shi, Lei Jin, Chen-jie Feng, Ya-lan Tan, Zhi-jie Tan
    Abstract:

    (a) MMTV pseudoknot at 50mM [K+] with 0.5mM [Mg2+] and 3.0mM [Mg2+], respectively. Symbols: the heat capacity Cp for MMTV pseudoknot at 50mM [K+] with 0.5mM [Mg2+]. (c) T2 pseudoknot at 100mM [K+] with 0.1mM [Mg2+] and 1.0mM [Mg2+], respectively. Symbols: dA/dT, the first derivative of absorbance with respect to temperature. (b, d) The melting temperatures Tm1 and Tm2 of two transitIons (F→I and I→U) as functIons of [Mg2+] for MMTV pseudoknot in the presence of 50mM [K+] (b) and T2 pseudoknot in the presence of 100mM [K+] (d). Symbols: experimental Tm1 (blue square) and Tm2 (red triangle) [75,77]. Lines: corresponding predictIons.

  • Divalent Ion mediated dna dna interactIons a comparative study of triplex and duplex
    Biophysical Journal, 2017
    Co-Authors: Zhongliang Zhang, Jianping Sang, Zhi-jie Tan
    Abstract:

    Abstract Ion-mediated interactIon between DNAs is essential for DNA condensatIon, and it is generally believed that monovalent and nonspecifically binding Divalent catIons cannot induce the aggregatIon of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal Ions such as Mg 2+ can induce the aggregatIon of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulatIons to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg 2+ solutIons. Our calculatIons show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg 2+ ], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg 2+ ]. Our analyses show that Mg 2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg 2+ is much stronger for tsDNA. Such stronger external binding of Mg 2+ for tsDNA favors more apparent Ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging Ions, as a special part of external binding Ions, are tightly and positively coupled to Ion-mediated attractIon between DNAs.

  • predicting 3d structure flexibility and stability of rna hairpins in monovalent and Divalent Ion solutIons
    Biophysical Journal, 2015
    Co-Authors: Ya-zhou Shi, Lei Jin, Fenghua Wang, Xiaolong Zhu, Zhi-jie Tan
    Abstract:

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensIonal (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in Divalent/monovalent Ion solutIons. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental Ion conditIons with an overall improved accuracy compared to the experimental data; the model also makes reliable predictIons for the flexibility of RNA hairpins with bulge loops of different lengths at several Divalent/monovalent Ion conditIons. In additIon, the model successfully predicts the stability of RNA hairpins with various loops/stems in Divalent/monovalent Ion solutIons.

Joseph M Lane - One of the best experts on this subject based on the ideXlab platform.

Michael T. Henzl - One of the best experts on this subject based on the ideXlab platform.

  • CharacterizatIon of parvalbumin and polcalcin Divalent Ion binding by isothermal titratIon calorimetry.
    Methods in enzymology, 2009
    Co-Authors: Michael T. Henzl
    Abstract:

    Abstract The elucidatIon of structure-affinity relatIonships in EF-hand proteins requires a reliable assay of Divalent Ion affinity. In principle, isothermal titratIon calorimetry (ITC) should be capable of furnishing estimates for Ca 2+ - and Mg 2+ -binding constants in these systems. And because the method yields the binding enthalpy directly, ITC can provide a more detailed view of binding energetics than methods that rely on 45 Ca 2+ or fluorescent indicators. For several reasons, however, it is generally not possible to extract reliable binding parameters from single ITC experiments. Ca 2+ affinity is often too high, and Mg 2+ affinity is invariably too low. Moreover, least-squares minimizatIon of multisite systems may not afford a unique fit because of strong parameter correlatIons. This chapter outlines a strategy for analyzing two-site systems that overcomes these obstacles. The method—which involves simultaneous, or global, least-squares analysis of direct and competitive ITC data—yields binding parameters for both Ca 2+ and Mg 2+ . ApplicatIon of the method is demonstrated for two systems. The S55D/E59D variant of rat α-parvalbumin, noteworthy for its elevated metal Ion affinity, binds Divalent Ions noncooperatively and is amenable to analysis using an independent two-site model. On the other hand, Phl p 7, a pollen-specific EF-hand protein from timothy grass, binds Ca 2+ with positive cooperativity. Divalent Ion-binding data for the protein must be analyzed using a two-site Adair model.

  • Leucine 85 Is an Important Determinant of Divalent Ion Affinity in Rat β-Parvalbumin (Oncomodulin)
    Biochemistry, 2008
    Co-Authors: Michael T. Henzl, Meredith E. Davis, Anmin Tan
    Abstract:

    Despite 69% sequence identity with chicken parvalbumin 3 (CPV3), rat beta-parvalbumin (beta-PV) exhibits a substantially lower Ca(2+) affinity (DeltaDeltaG degrees ' = 2.0 kcal/mol). This difference largely reflects the disparate behavior of the respective CD sites. Replacement of the rat beta-PV codon with the CPV3 codon at positIons 49, 50, and 57-60 produces virtual sequence identity with the CPV3 CD site. However, the resulting protein exhibits a modest (0.5 kcal/mol) improvement in Ca(2+) affinity, implying that sequence differences beyond the binding site modulate Divalent Ion binding behavior. The solutIon structure of Ca(2+)-free rat beta-PV suggested that Leu-85, phenylalanine in CPV3, might be an important determinant. Therefore, the impact of the L85F mutatIon on Divalent Ion affinity was examined in rat beta-PV, in the variant harboring all six of the aforementIoned CD site mutatIons, and in the intermediate CD site variants. We find that the identity of residue 85, located within the E helix, strongly influences Divalent Ion affinity in the mammalian beta-PV isoform and that its impact is mediated by interactIons with residues in the CD site. In the wild-type protein, L85F primarily affects the EF site. By contrast, in the presence of the six CD site mutatIons, L85F also improves the CD site performance, yielding a protein with Ca(2+) affinity rivaling that of CPV3 and markedly enhanced Mg(2+) affinity as well. The impact of L85F on CD site Ca(2+) affinity is particularly sensitive to the identities of residues 59 and 60. Interestingly, however, significant improvement in CD site Mg(2+) affinity also requires mutatIon of additIonal CD site residues.

  • Influence of monovalent catIon identity on parvalbumin Divalent Ion-binding properties.
    Biochemistry, 2004
    Co-Authors: Michael T. Henzl, John D. Larson, Sayeh Agah
    Abstract:

    Rat α- and β-parvalbumins have distinct monovalent catIon-binding properties [Henzl et al. (2000) Biochemistry 39, 5859−5867]. β binds two Na+ or one K+, and α binds one Na+ and no K+. Ca2+ abolishes these binding events, suggesting that the monovalent Ions occupy the EF-hand motifs. This study compares α and β Divalent Ion affinities in Na+ and K+ solutIons. Solvent catIon identity seriously affects α. In Hepes-buffered NaCl, at 5 °C, the macroscopic Ca2+-binding constants are 2.6 × 108 and 6.4 × 107 M-1 and the Mg2+ constants, 1.8 × 104 and 4.3 × 103 M-1. In Hepes-buffered KCl, the Ca2+ values increase to 2.9 × 109 and 6.6 × 108 M-1 and the Mg2+ values to 2.2 × 105 and 3.7 × 104 M-1. Monte Carlo simulatIon of α binding dataemploying site-specific constants and explicitly considering Na+ bindingyields a KNa of 630 M-1 and indicates that Divalent Ion-binding is positively cooperative. NMR data suggest that the lone Na+ Ion occupies the CD loop. Solvent catIon identity has a smaller impact on β. In Na+, th...

Barbara L Golden - One of the best experts on this subject based on the ideXlab platform.

  • two active site Divalent Ions in the crystal structure of the hammerhead ribozyme bound to a transitIon state analogue
    Biochemistry, 2016
    Co-Authors: Aamir Mir, Barbara L Golden
    Abstract:

    The crystal structure of the hammerhead ribozyme bound to the pentavalent transitIon state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositIoning a Divalent metal Ion such that it could, ultimately, interact directly with the scissile phosphate. This Ion could also positIon a water molecule to serve as a general acid in the cleavage reactIon. A second Divalent Ion is observed coordinated to O6 of G12. This metal Ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

Y. Vathanapanich - One of the best experts on this subject based on the ideXlab platform.

  • A Study of Multi-Component Ion Exchange by Ammonium Ion during Low Salinity Waterflooding in Sandstone FormatIon
    80th EAGE Conference and Exhibition 2018, 2018
    Co-Authors: F. Srisuriyachai, Y. Vathanapanich
    Abstract:

    Ammonium Ion which is a positively charged polyatomic catIon has been widely used as clay control agent. As this Ion has similar characteristics to potassium Ion including Ionic diameter and hydratIon number, ammonium Ion should be able to displace Divalent Ion bridging between oil and rock surface during Multi-component Ion Exchange (MIE) mechanism as same as potassium Ion. This study is performed to evaluate the effectiveness of ammonium Ion compared to potassium Ion and sodium Ion. The result shows that both ammonium Ion and potassium Ion which are similar in hydrated properties can displace Divalent Ion better than sodium Ion as well as deIonized water. From coreflood experiment, there is a relatIonship between number of Divalent Ions in effluent and oil recovery factor. The higher the amount of Divalent Ions in effluent, the more oil is recovered. It is also observed that portIon of calcium Ion expelled from rock surface is increased when monovalent is present in injected water. From this study, it can be concluded that hydrated properties of monovalent Ion in injected water affects the MIE mechanism. Small amount of ammonium Ion can be added into injected water to improve the effectiveness of the mechanism.

  • Effects of Potassium Ion on Low Salinity Waterflooding in Sandstone FormatIon
    IOR 2017 - 19th European Symposium on Improved Oil Recovery, 2017
    Co-Authors: F. Srisuriyachai, S. Meekangwal, C. Charoentanaworakun, Y. Vathanapanich
    Abstract:

    Multi-Component Ion Exchange (MIE) is a mechanism that has been proven to take place during low salinity waterflooding. In sandstone surface, oil containing organic acid may be attached onto rock surface through an aid of Divalent Ion binding. SubstitutIon of monovalent Ion onto the linking Divalent Ion site results in liberatIon of oil. Minimum quantity of Divalent Ion such as Calcium Ion and Magnesium Ion together with presence of monovalent Ion in injected brine would be therefore favorable conditIons for the MIE mechanism. In this study, spontaneous imbibitIon test is performed to observe ability in replacement of monovalent Ion by excluding effect from injectIon rate. FormatIon brine is prepared to have total salinity of 100,000 ppm, using an average Ion proportIon from sandstone oilfields around the globe. Effects of Potassium Ion which is much smaller in quantity in brine and seawater compared to Sodium Ion, is investigated. From the experiment, Potassium Chloride solutIon at 35,000 ppm can imbibe into rock sample with total increment of water saturatIon of 0.42, whereas Sodium Chloride solutIon at the same salinity can only increase water saturatIon of about 0.27. Potassium Ion is usually accompanied by 1-4 molecules of water, whereas Sodium Ion is surrounded by 5-11 molecules. This causes hydrated Potassium to be smaller in size and more active in replacing Divalent Ion compared to hydrated Sodium. Lowering concentratIon of Potassium Chloride to 5,000 ppm shows an adverse effect on imbibitIon ability. As number of active monovalent Ion is reduced, replacement of Divalent Ion occurs slowly. As a result, only 0.24 of water saturatIon is increased from initial water saturatIon. Comparing to seawater at the same total salinity which contains Potassium Ion only 369 ppm, seawater imbibes at higher degree compared to solely Potassium Chloride which is about 0.47 of water saturatIon. This can be explained that, adequate total salinity could favor Potassium Ion to approach the surface. Moreover, presence of Calcium Ion would help induce liberatIon of oil through formatIon of Calcium Carboxylate complex. Last, seawater without Potassium Ion is prepared to confirm effect of Potassium Ion and it is observed that 0.40 of water saturatIon is increased during the test. In summary, Potassium Ion is more potential in replacing Divalent Ion compared to Sodium Ion. A presence of only small quantity of Potassium Ion is adequate for spontaneous imbibitIon as this can be offset by presence of other potential Ions.