| 1. |
- Pustovalova, Y., et al.
(author)
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NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR
- 2021
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In: Magnetic Resonance. - : Copernicus GmbH. - 2699-0016. ; 2:2, s. 843-861
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Journal article (peer-reviewed)abstract
- Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.
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| 2. |
- Zhang, R. Y., et al.
(author)
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Lysozyme's lectin-like characteristics facilitates its immune defense function
- 2017
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In: Quarterly Reviews of Biophysics. - : Cambridge University Press (CUP). - 0033-5835 .- 1469-8994. ; 50, s. 1-12
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Research review (peer-reviewed)abstract
- Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance. The crystal structure of the HL-tetrasaccharide complex revealed carbohydrate chain packing into the A, B, C, and D binding sites of HL, which primarily occurred through residue-specific, direct or water-mediated hydrogen bonds and hydrophobic contacts. Overall, these results support a crucial role of the Glu35/Asp53/Trp63/Asp102 residues in HL binding to the tetrasaccharide. These observations suggest an unknown glycan-guided mechanism that underlies recognition of the bacterial cell wall by lysozyme and may complement the HL immune defense function.
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| 3. |
- Zhang, R. Y., et al.
(author)
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Lysozyme's lectin-like characteristics facilitates its immune defense function
- 2017
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In: Quarterly Reviews of Biophysics. - : Cambridge University Press (CUP). - 1469-8994 .- 0033-5835. ; 50, s. 1-12
-
Journal article (peer-reviewed)abstract
- Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance. The crystal structure of the HL-tetrasaccharide complex revealed carbohydrate chain packing into the A, B, C, and D binding sites of HL, which primarily occurred through residue-specific, direct or water-mediated hydrogen bonds and hydrophobic contacts. Overall, these results support a crucial role of the Glu35/Asp53/Trp63/Asp102 residues in HL binding to the tetrasaccharide. These observations suggest an unknown glycan-guided mechanism that underlies recognition of the bacterial cell wall by lysozyme and may complement the HL immune defense function.
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| 4. |
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| 5. |
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| 6. |
- Billeter, J., et al.
(author)
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On decoupling rate processes in chemical reaction systems – Methods and applications
- 2018
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In: Computers and Chemical Engineering. - : Elsevier BV. - 0098-1354 .- 1873-4375. ; 114, s. 296-305
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Journal article (peer-reviewed)abstract
- Models of chemical reaction systems can be complex as they need to include information regarding the reactions and the mass and heat transfers. The commonly used state variables, namely, concentrations and temperatures, express the interplay between many phenomena. As a consequence, each state variable is affected by several rate processes. On the other hand, it is well known that it is possible to partition the state space into a reaction invariant subspace and its orthogonal complement using a linear transformation involving the reaction stoichiometry. This paper uses a more sophisticated linear transformation to partition the state space into various subspaces, each one linked to a single rate process such as a particular reaction, mass transfer or heat transfer. The implications of this partitioning are discussed with respect to several applications related to data reconciliation, state and rate estimation, modeling, identification, control and optimization of reaction systems.
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| 7. |
- Halbritter, Aud H., et al.
(author)
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Trait differentiation and adaptation of plants along elevation gradients
- 2018
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In: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 31:6, s. 784-800
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Research review (peer-reviewed)abstract
- Studies of genetic adaptation in plant populations along elevation gradients in mountains have a long history, but there has until now been neither a synthesis of how frequently plant populations exhibit adaptation to elevation nor an evaluation of how consistent underlying trait differences across species are. We reviewed studies of adaptation along elevation gradients (i) from a meta-analysis of phenotypic differentiation of three traits (height, biomass and phenology) from plants growing in 70 common garden experiments; (ii) by testing elevation adaptation using three fitness proxies (survival, reproductive output and biomass) from 14 reciprocal transplant experiments; (iii) by qualitatively assessing information at the molecular level, from 10 genomewide surveys and candidate gene approaches. We found that plants originating from high elevations were generally shorter and produced less biomass, but phenology did not vary consistently. We found significant evidence for elevation adaptation in terms of survival and biomass, but not for reproductive output. Variation in phenotypic and fitness responses to elevation across species was not related to life history traits or to environmental conditions. Molecular studies, which have focussed mainly on loci related to plant physiology and phenology, also provide evidence for adaptation along elevation gradients. Together, these studies indicate that genetically based trait differentiation and adaptation to elevation are widespread in plants. We conclude that a better understanding of the mechanisms underlying adaptation, not only to elevation but also to environmental change, will require more studies combining the ecological and molecular approaches.
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| 8. |
- Rodrigues, Diogo, et al.
(author)
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Fast Estimation of Plant Steady State for Imperfectly Known Dynamic Systems, with Application to Real-Time Optimization
- 2018
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In: Industrial & Engineering Chemistry Research. - : American Chemical Society (ACS). - 0888-5885 .- 1520-5045. ; 57:10, s. 3699-3716
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Journal article (peer-reviewed)abstract
- Experimental assessment or prediction of plant steady state is important for many applications in the area of modeling and operation of continuous processes. For example, the iterative implementation of static real-time optimization requires reaching steady state for each successive operating point, which may be quite time-consuming. This paper presents an approach to speed up the estimation of plant steady state for imperfectly known dynamic systems that are characterized by (i) the presence of fast and slow states, with no effect of the slow states on the fast states, and (ii) the fact that the unknown part of the dynamics depends only on the fast states. The proposed approach takes advantage of measurement-based rate estimation, which consists in estimating rate signals without the knowledge or identification of rate models. Since one can use feedback control to speed up the convergence to steady state of the fast part of the plant, this rate estimation allows estimating the steady state of the slow part during transient operation. It is shown how this approach can be used to speed up the static real-time optimization of continuous processes. A simulated example illustrates its application to a continuous stirred-tank reactor.
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| 9. |
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| 10. |
- Zhuravleva, Anastasia, 1979, et al.
(author)
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Gated electron transfers and electron pathways in azurin: a NMR dynamic study at multiple fields and temperatures.
- 2004
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In: Journal of molecular biology. - : Elsevier BV. - 0022-2836. ; 342:5, s. 1599-611
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Journal article (peer-reviewed)abstract
- Dynamic properties of electron transfer pathways in a small blue copper cupredoxin are explored using an extensive 15N NMR relaxation study of reduced Pseudomonas aeruginosa azurin at four magnetic fields (500-900 MHz) and at two temperatures chosen well below the melting point of the protein. Following a careful model-free analysis, several protein regions with different dynamic regimes are identified. Nanosecond time-scale mobility characterizes various residues of the hydrophobic surface patch believed to mark the natural entry point for electrons, notably the surface-exposed copper-ligand His117. These findings are consistent with a gated electron transfer process according to the "dynamic docking" model. Residues 47-49 along intramolecular pathways of electrons show rigidity that is remarkably conserved when increasing the temperature. Three different conformational exchange processes were observed in the millisecond range, one near the only disulfide bridge in the molecule and two near the copper ion. The latter two processes are consistent with previous data such as crystal structures at various pH values and NMR relaxation dispersion experiments; they may indicate an additional gated electron transfer mechanism at slower time-scales.
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