6 research outputs found
A Music Composition Through the Use of Animal Sounds
The knowledge on animals has been studied over many years by researching and understanding animal behavior and creativity with music. Bioacoustics shows a great deal when it comes to collecting sounds through many principles for sound data collection. With saved recording of animals, music, speeches, and so much more, it has impacted the way music is created through technology. Music production has been advancing in many creative ways. The foundation of sound manipulation is musique concrète. The project uses these concepts of audio recording and digital sounds to produce a composition that includes animal sounds
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Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase.
The rate-limiting chemical reaction catalyzed by soybean lipoxygenase (SLO) involves quantum mechanical tunneling of a hydrogen atom from substrate to its active site ferric-hydroxide cofactor. SLO has emerged as a prototypical system for linking the thermal activation of a protein scaffold to the efficiency of active site chemistry. Significantly, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) experiments on wild type and mutant forms of SLO have uncovered trends in the enthalpic barriers for HDX within a solvent-exposed loop (positions 317-334) that correlate well with trends in the corresponding enthalpic barriers for kcat. A model for this behavior posits that collisions between water and loop 317-334 initiate thermal activation at the protein surface that is then propagated 15-34 Ă… inward toward the reactive carbon of substrate in proximity to the iron catalyst. In this study, we have prepared protein samples containing cysteine residues either at the tip of the loop 317-334 (Q322C) or on a control loop, 586-603 (S596C). Chemical modification of cysteines with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (Badan, BD) provides site-specific probes for the measurement of fluorescence relaxation lifetimes and Stokes shift decays as a function of temperature. Computational studies indicate that surface water structure is likely to be largely preserved in each sample. While both loops exhibit temperature-independent fluorescence relaxation lifetimes as do the Stokes shifts for S596C-BD, the activation enthalpy for the nanosecond solvent reorganization at Q322C-BD (Ea(ksolv) = 2.8(0.9) kcal/mol)) approximates the enthalpy of activation for catalytic C-H activation (Ea(kcat) = 2.3(0.4) kcal/mol). This study establishes and validates the methodology for measuring rates of rapid local motions at the protein/solvent interface of SLO. These new findings, when combined with previously published correlations between protein motions and the rate-limiting hydride transfer in a thermophilic alcohol dehydrogenase, provide experimental evidence for thermally induced protein quakes as the origin of enthalpic barriers in catalysis
Solvent and Temperature Probes of the Long-Range Electron-Transfer Step in Tyramine β‑Monooxygenase: Demonstration of a Long-Range Proton-Coupled Electron-Transfer Mechanism
Tyramine
β-monooxygenase (TβM) belongs to a family
of physiologically important dinuclear copper monooxygenases that
function with a solvent-exposed active site. To accomplish each enzymatic
turnover, an electron transfer (ET) must occur between two solvent-separated
copper centers. In wild-type TβM, this event is too fast to
be rate limiting. However, we have recently shown [Osborne, R. L.;
et al. <i>Biochemistry</i> <b>2013</b>, <i>52</i>, 1179] that the Tyr216Ala variant of TβM leads to rate-limiting
ET. In this study, we present a pH–rate profile study of Tyr216Ala,
together with deuterium oxide solvent kinetic isotope effects (KIEs).
A solvent KIE of 2 on <i>k</i><sub>cat</sub> is found in
a region where <i>k</i><sub>cat</sub> is pH/pD independent.
As a control, the variant Tyr216Trp, for which ET is not rate determining,
displays a solvent KIE of unity. We conclude, therefore, that the
observed solvent KIE arises from the rate-limiting ET step in the
Tyr216Ala variant, and show
how small solvent KIEs (ca. 2) can be fully accommodated from equilibrium effects within the Marcus equation. To gain insight into the role of the enzyme in the long-range
ET step, a temperature dependence study was also pursued. The small
enthalpic barrier of ET (<i>E</i><sub>a</sub> = 3.6 kcal/mol)
implicates a significant entropic barrier, which is attributed to
the requirement for extensive rearrangement of the inter-copper environment
during PCET catalyzed by the Tyr216Ala variant. The data lead to the
proposal of a distinct inter-domain pathway for PCET in the dinuclear
copper monooxygenases
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Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase.
The rate-limiting chemical reaction catalyzed by soybean lipoxygenase (SLO) involves quantum mechanical tunneling of a hydrogen atom from substrate to its active site ferric-hydroxide cofactor. SLO has emerged as a prototypical system for linking the thermal activation of a protein scaffold to the efficiency of active site chemistry. Significantly, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) experiments on wild type and mutant forms of SLO have uncovered trends in the enthalpic barriers for HDX within a solvent-exposed loop (positions 317-334) that correlate well with trends in the corresponding enthalpic barriers for kcat. A model for this behavior posits that collisions between water and loop 317-334 initiate thermal activation at the protein surface that is then propagated 15-34 Ă… inward toward the reactive carbon of substrate in proximity to the iron catalyst. In this study, we have prepared protein samples containing cysteine residues either at the tip of the loop 317-334 (Q322C) or on a control loop, 586-603 (S596C). Chemical modification of cysteines with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (Badan, BD) provides site-specific probes for the measurement of fluorescence relaxation lifetimes and Stokes shift decays as a function of temperature. Computational studies indicate that surface water structure is likely to be largely preserved in each sample. While both loops exhibit temperature-independent fluorescence relaxation lifetimes as do the Stokes shifts for S596C-BD, the activation enthalpy for the nanosecond solvent reorganization at Q322C-BD (Ea(ksolv) = 2.8(0.9) kcal/mol)) approximates the enthalpy of activation for catalytic C-H activation (Ea(kcat) = 2.3(0.4) kcal/mol). This study establishes and validates the methodology for measuring rates of rapid local motions at the protein/solvent interface of SLO. These new findings, when combined with previously published correlations between protein motions and the rate-limiting hydride transfer in a thermophilic alcohol dehydrogenase, provide experimental evidence for thermally induced "protein quakes" as the origin of enthalpic barriers in catalysis
Modulating OxyB-Catalyzed Cross-Coupling Reactions in Vancomycin Biosynthesis by Incorporation of Diverse d‑Tyr Analogues
We
report a general method for synthesizing diverse d-Tyr
analogues, one of the constituents of the antibiotic vancomycin, using
a Negishi cross-coupling protocol. Several analogues were incorporated
into the vancomycin substrate–peptide and reacted with the
biosynthetic enzymes OxyB and OxyA, which install the characteristic
aromatic cross-links. We find that even small structural perturbations
are not accepted by OxyA. The same modifications, however, enhance
the catalytic capabilities of OxyB leading to the formation of a new
macrocycle within the vancomycin framework