Die Affinitäten von Wirten – ausgehend von kleinen synthetischen Cavitanten bis hin zu großen Pro... more Die Affinitäten von Wirten – ausgehend von kleinen synthetischen Cavitanten bis hin zu großen Proteinen – für organische Moleküle sind gut dokumentiert. Die mittleren Assoziationskonstanten für die Bindung organischer Moleküle durch Cyclodextrine, synthetische Wirte und Albumine in Wasser sowie von katalytischen Antikörpern oder Enzymen für Substrate betragen im Allgemeinen 103.5±2.5 M−1. Die Bindungsaffinitäten steigen bei der Komplexierung von Übergangszuständen und biologischen Antigenen durch Antikörper oder von Enzymen durch Inhibitoren auf 108±2 M−1 und auf 1016±4 M−1 für Enzym-Übergangszustands-Komplexe. Die Gründe für die unterschiedlichen Stabilitäten dieser Wirt-Gast-Systeme sollen hier untersucht werden, und wir beschreiben Ansätze zur computergestützten Analyse der Wirt-Gast-Komplexbildung in Lösung. Bei vielen Komplexklassen besteht eine ungefähre Korrelation der Bindungsaffinität mit der Größe der Oberfläche, die bei der Komplexierung vergraben wird. Enzyme folgen dieser Korrelation nicht, sondern binden Übergangszustände sehr viel stärker als es anhand der Oberfläche zu erwarten wäre.
American Journal of Physiology-regulatory Integrative and Comparative Physiology, 2006
We review gases that can affect oxidative stress and that themselves may be radicals. We discuss ... more We review gases that can affect oxidative stress and that themselves may be radicals. We discuss O(2) toxicity, invoking superoxide, hydrogen peroxide, and the hydroxyl radical. We also discuss superoxide dismutase (SOD) and both ground-state, triplet oxygen ((3)O(2)), and the more energetic, reactive singlet oxygen ((1)O(2)). Nitric oxide ((*)NO) is a free radical with cell signaling functions. Besides its role as a vasorelaxant, (*)NO and related species have other functions. Other endogenously produced gases include carbon monoxide (CO), carbon dioxide (CO(2)), and hydrogen sulfide (H(2)S). Like (*)NO, these species impact free radical biochemistry. The coordinated regulation of these species suggests that they all are used in cell signaling. Nitric oxide, nitrogen dioxide, and the carbonate radical (CO(3)(*-)) react selectively at moderate rates with nonradicals, but react fast with a second radical. These reactions establish "cross talk" between reactive oxygen (ROS) and reactive nitrogen species (RNS). Some of these species can react to produce nitrated proteins and nitrolipids. It has been suggested that ozone is formed in vivo. However, the biomarkers that were used to probe for ozone reactions may be formed by non-ozone-dependent reactions. We discuss this fascinating problem in the section on ozone. Very low levels of ROS or RNS may be mitogenic, but very high levels cause an oxidative stress that can result in growth arrest (transient or permanent), apoptosis, or necrosis. Between these extremes, many of the gasses discussed in this review will induce transient adaptive responses in gene expression that enable cells and tissues to survive. Such adaptive mechanisms are thought to be of evolutionary importance.
The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge ... more The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.
The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds a... more The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond forming reactions should be broadly useful in synthetic chemistry.
The electronic ground states of [n]cyclacenes, as well as short-zigzag nanotubes, computed at unr... more The electronic ground states of [n]cyclacenes, as well as short-zigzag nanotubes, computed at unrestricted broken spin-symmetry density functional theory (UBS-DFT), were found to be open-shell singlets, rather than triplets. Computations for [6]cyclacene at complete active space self-consistent field (CASSCF) and multireference perturbation theory (MRMP2) levels support this conclusion. Along with strain, the radical character of the open-shell singlet with antiferromagnetically coupled electron spins may contribute to the difficulties in synthesizing [n]cyclacenes.
... K. N. Houk,*le Michael N. Paddon-Row,lb DC Spellmeyer,'" Nelson G. ... more ... K. N. Houk,*le Michael N. Paddon-Row,lb DC Spellmeyer,'" Nelson G. Rondan,'" and Shigeru NagaseIc Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Yokohama National ... 102. I~ (10) Schlegel, H. B.; Sosa, C., submitted for publication. ...
Die Affinitäten von Wirten – ausgehend von kleinen synthetischen Cavitanten bis hin zu großen Pro... more Die Affinitäten von Wirten – ausgehend von kleinen synthetischen Cavitanten bis hin zu großen Proteinen – für organische Moleküle sind gut dokumentiert. Die mittleren Assoziationskonstanten für die Bindung organischer Moleküle durch Cyclodextrine, synthetische Wirte und Albumine in Wasser sowie von katalytischen Antikörpern oder Enzymen für Substrate betragen im Allgemeinen 103.5±2.5 M−1. Die Bindungsaffinitäten steigen bei der Komplexierung von Übergangszuständen und biologischen Antigenen durch Antikörper oder von Enzymen durch Inhibitoren auf 108±2 M−1 und auf 1016±4 M−1 für Enzym-Übergangszustands-Komplexe. Die Gründe für die unterschiedlichen Stabilitäten dieser Wirt-Gast-Systeme sollen hier untersucht werden, und wir beschreiben Ansätze zur computergestützten Analyse der Wirt-Gast-Komplexbildung in Lösung. Bei vielen Komplexklassen besteht eine ungefähre Korrelation der Bindungsaffinität mit der Größe der Oberfläche, die bei der Komplexierung vergraben wird. Enzyme folgen dieser Korrelation nicht, sondern binden Übergangszustände sehr viel stärker als es anhand der Oberfläche zu erwarten wäre.
American Journal of Physiology-regulatory Integrative and Comparative Physiology, 2006
We review gases that can affect oxidative stress and that themselves may be radicals. We discuss ... more We review gases that can affect oxidative stress and that themselves may be radicals. We discuss O(2) toxicity, invoking superoxide, hydrogen peroxide, and the hydroxyl radical. We also discuss superoxide dismutase (SOD) and both ground-state, triplet oxygen ((3)O(2)), and the more energetic, reactive singlet oxygen ((1)O(2)). Nitric oxide ((*)NO) is a free radical with cell signaling functions. Besides its role as a vasorelaxant, (*)NO and related species have other functions. Other endogenously produced gases include carbon monoxide (CO), carbon dioxide (CO(2)), and hydrogen sulfide (H(2)S). Like (*)NO, these species impact free radical biochemistry. The coordinated regulation of these species suggests that they all are used in cell signaling. Nitric oxide, nitrogen dioxide, and the carbonate radical (CO(3)(*-)) react selectively at moderate rates with nonradicals, but react fast with a second radical. These reactions establish "cross talk" between reactive oxygen (ROS) and reactive nitrogen species (RNS). Some of these species can react to produce nitrated proteins and nitrolipids. It has been suggested that ozone is formed in vivo. However, the biomarkers that were used to probe for ozone reactions may be formed by non-ozone-dependent reactions. We discuss this fascinating problem in the section on ozone. Very low levels of ROS or RNS may be mitogenic, but very high levels cause an oxidative stress that can result in growth arrest (transient or permanent), apoptosis, or necrosis. Between these extremes, many of the gasses discussed in this review will induce transient adaptive responses in gene expression that enable cells and tissues to survive. Such adaptive mechanisms are thought to be of evolutionary importance.
The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge ... more The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.
The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds a... more The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond forming reactions should be broadly useful in synthetic chemistry.
The electronic ground states of [n]cyclacenes, as well as short-zigzag nanotubes, computed at unr... more The electronic ground states of [n]cyclacenes, as well as short-zigzag nanotubes, computed at unrestricted broken spin-symmetry density functional theory (UBS-DFT), were found to be open-shell singlets, rather than triplets. Computations for [6]cyclacene at complete active space self-consistent field (CASSCF) and multireference perturbation theory (MRMP2) levels support this conclusion. Along with strain, the radical character of the open-shell singlet with antiferromagnetically coupled electron spins may contribute to the difficulties in synthesizing [n]cyclacenes.
... K. N. Houk,*le Michael N. Paddon-Row,lb DC Spellmeyer,'" Nelson G. ... more ... K. N. Houk,*le Michael N. Paddon-Row,lb DC Spellmeyer,'" Nelson G. Rondan,'" and Shigeru NagaseIc Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Yokohama National ... 102. I~ (10) Schlegel, H. B.; Sosa, C., submitted for publication. ...
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