6 research outputs found
Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein
Hydrogen bonds are fundamental to
biological systems and are regularly
found in networks implicated in folding, molecular recognition, catalysis,
and allostery. Given their ubiquity, we asked the fundamental questions
of whether, and to what extent, hydrogen bonds within networks are
structurally coupled. To address these questions, we turned to three
protein systems, two variants of ketosteroid isomerase and one of
photoactive yellow protein. We perturbed their hydrogen bond networks
via a combination of site-directed mutagenesis and unnatural amino
acid substitution, and we used <sup>1</sup>H NMR and high-resolution
X-ray crystallography to determine the effects of these perturbations
on the lengths of the two oxyanion hole hydrogen bonds that are donated
to negatively charged transition state analogs. Perturbations that
lengthened or shortened one of the oxyanion hole hydrogen bonds had
the opposite effect on the other. The oxyanion hole hydrogen bonds
were also affected by distal hydrogen bonds in the network, with smaller
perturbations for more remote hydrogen bonds. Across 19 measurements
in three systems, the length change in one oxyanion hole hydrogen
bond was propagated to the other, by a factor of −0.30 ±
0.03. This common effect suggests that hydrogen bond coupling is minimally
influenced by the remaining protein scaffold. The observed coupling
is reproduced by molecular mechanics and quantum mechanics/molecular
mechanics (QM/MM) calculations for changes to a proximal oxyanion
hole hydrogen bond. However, effects from distal hydrogen bonds are
reproduced only by QM/MM, suggesting the importance of polarization
in hydrogen bond coupling. These results deepen our understanding
of hydrogen bonds and their networks, providing strong evidence for
long-range coupling and for the extent of this coupling. We provide
a broadly predictive quantitative relationship that can be applied
to and can be further tested in new systems
Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein
Hydrogen bonds are fundamental to
biological systems and are regularly
found in networks implicated in folding, molecular recognition, catalysis,
and allostery. Given their ubiquity, we asked the fundamental questions
of whether, and to what extent, hydrogen bonds within networks are
structurally coupled. To address these questions, we turned to three
protein systems, two variants of ketosteroid isomerase and one of
photoactive yellow protein. We perturbed their hydrogen bond networks
via a combination of site-directed mutagenesis and unnatural amino
acid substitution, and we used <sup>1</sup>H NMR and high-resolution
X-ray crystallography to determine the effects of these perturbations
on the lengths of the two oxyanion hole hydrogen bonds that are donated
to negatively charged transition state analogs. Perturbations that
lengthened or shortened one of the oxyanion hole hydrogen bonds had
the opposite effect on the other. The oxyanion hole hydrogen bonds
were also affected by distal hydrogen bonds in the network, with smaller
perturbations for more remote hydrogen bonds. Across 19 measurements
in three systems, the length change in one oxyanion hole hydrogen
bond was propagated to the other, by a factor of −0.30 ±
0.03. This common effect suggests that hydrogen bond coupling is minimally
influenced by the remaining protein scaffold. The observed coupling
is reproduced by molecular mechanics and quantum mechanics/molecular
mechanics (QM/MM) calculations for changes to a proximal oxyanion
hole hydrogen bond. However, effects from distal hydrogen bonds are
reproduced only by QM/MM, suggesting the importance of polarization
in hydrogen bond coupling. These results deepen our understanding
of hydrogen bonds and their networks, providing strong evidence for
long-range coupling and for the extent of this coupling. We provide
a broadly predictive quantitative relationship that can be applied
to and can be further tested in new systems
Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein
Hydrogen bonds are fundamental to
biological systems and are regularly
found in networks implicated in folding, molecular recognition, catalysis,
and allostery. Given their ubiquity, we asked the fundamental questions
of whether, and to what extent, hydrogen bonds within networks are
structurally coupled. To address these questions, we turned to three
protein systems, two variants of ketosteroid isomerase and one of
photoactive yellow protein. We perturbed their hydrogen bond networks
via a combination of site-directed mutagenesis and unnatural amino
acid substitution, and we used <sup>1</sup>H NMR and high-resolution
X-ray crystallography to determine the effects of these perturbations
on the lengths of the two oxyanion hole hydrogen bonds that are donated
to negatively charged transition state analogs. Perturbations that
lengthened or shortened one of the oxyanion hole hydrogen bonds had
the opposite effect on the other. The oxyanion hole hydrogen bonds
were also affected by distal hydrogen bonds in the network, with smaller
perturbations for more remote hydrogen bonds. Across 19 measurements
in three systems, the length change in one oxyanion hole hydrogen
bond was propagated to the other, by a factor of −0.30 ±
0.03. This common effect suggests that hydrogen bond coupling is minimally
influenced by the remaining protein scaffold. The observed coupling
is reproduced by molecular mechanics and quantum mechanics/molecular
mechanics (QM/MM) calculations for changes to a proximal oxyanion
hole hydrogen bond. However, effects from distal hydrogen bonds are
reproduced only by QM/MM, suggesting the importance of polarization
in hydrogen bond coupling. These results deepen our understanding
of hydrogen bonds and their networks, providing strong evidence for
long-range coupling and for the extent of this coupling. We provide
a broadly predictive quantitative relationship that can be applied
to and can be further tested in new systems
Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein
Hydrogen bonds are fundamental to
biological systems and are regularly
found in networks implicated in folding, molecular recognition, catalysis,
and allostery. Given their ubiquity, we asked the fundamental questions
of whether, and to what extent, hydrogen bonds within networks are
structurally coupled. To address these questions, we turned to three
protein systems, two variants of ketosteroid isomerase and one of
photoactive yellow protein. We perturbed their hydrogen bond networks
via a combination of site-directed mutagenesis and unnatural amino
acid substitution, and we used <sup>1</sup>H NMR and high-resolution
X-ray crystallography to determine the effects of these perturbations
on the lengths of the two oxyanion hole hydrogen bonds that are donated
to negatively charged transition state analogs. Perturbations that
lengthened or shortened one of the oxyanion hole hydrogen bonds had
the opposite effect on the other. The oxyanion hole hydrogen bonds
were also affected by distal hydrogen bonds in the network, with smaller
perturbations for more remote hydrogen bonds. Across 19 measurements
in three systems, the length change in one oxyanion hole hydrogen
bond was propagated to the other, by a factor of −0.30 ±
0.03. This common effect suggests that hydrogen bond coupling is minimally
influenced by the remaining protein scaffold. The observed coupling
is reproduced by molecular mechanics and quantum mechanics/molecular
mechanics (QM/MM) calculations for changes to a proximal oxyanion
hole hydrogen bond. However, effects from distal hydrogen bonds are
reproduced only by QM/MM, suggesting the importance of polarization
in hydrogen bond coupling. These results deepen our understanding
of hydrogen bonds and their networks, providing strong evidence for
long-range coupling and for the extent of this coupling. We provide
a broadly predictive quantitative relationship that can be applied
to and can be further tested in new systems
Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein
Hydrogen bonds are fundamental to
biological systems and are regularly
found in networks implicated in folding, molecular recognition, catalysis,
and allostery. Given their ubiquity, we asked the fundamental questions
of whether, and to what extent, hydrogen bonds within networks are
structurally coupled. To address these questions, we turned to three
protein systems, two variants of ketosteroid isomerase and one of
photoactive yellow protein. We perturbed their hydrogen bond networks
via a combination of site-directed mutagenesis and unnatural amino
acid substitution, and we used <sup>1</sup>H NMR and high-resolution
X-ray crystallography to determine the effects of these perturbations
on the lengths of the two oxyanion hole hydrogen bonds that are donated
to negatively charged transition state analogs. Perturbations that
lengthened or shortened one of the oxyanion hole hydrogen bonds had
the opposite effect on the other. The oxyanion hole hydrogen bonds
were also affected by distal hydrogen bonds in the network, with smaller
perturbations for more remote hydrogen bonds. Across 19 measurements
in three systems, the length change in one oxyanion hole hydrogen
bond was propagated to the other, by a factor of −0.30 ±
0.03. This common effect suggests that hydrogen bond coupling is minimally
influenced by the remaining protein scaffold. The observed coupling
is reproduced by molecular mechanics and quantum mechanics/molecular
mechanics (QM/MM) calculations for changes to a proximal oxyanion
hole hydrogen bond. However, effects from distal hydrogen bonds are
reproduced only by QM/MM, suggesting the importance of polarization
in hydrogen bond coupling. These results deepen our understanding
of hydrogen bonds and their networks, providing strong evidence for
long-range coupling and for the extent of this coupling. We provide
a broadly predictive quantitative relationship that can be applied
to and can be further tested in new systems
Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein
Hydrogen bonds are fundamental to
biological systems and are regularly
found in networks implicated in folding, molecular recognition, catalysis,
and allostery. Given their ubiquity, we asked the fundamental questions
of whether, and to what extent, hydrogen bonds within networks are
structurally coupled. To address these questions, we turned to three
protein systems, two variants of ketosteroid isomerase and one of
photoactive yellow protein. We perturbed their hydrogen bond networks
via a combination of site-directed mutagenesis and unnatural amino
acid substitution, and we used <sup>1</sup>H NMR and high-resolution
X-ray crystallography to determine the effects of these perturbations
on the lengths of the two oxyanion hole hydrogen bonds that are donated
to negatively charged transition state analogs. Perturbations that
lengthened or shortened one of the oxyanion hole hydrogen bonds had
the opposite effect on the other. The oxyanion hole hydrogen bonds
were also affected by distal hydrogen bonds in the network, with smaller
perturbations for more remote hydrogen bonds. Across 19 measurements
in three systems, the length change in one oxyanion hole hydrogen
bond was propagated to the other, by a factor of −0.30 ±
0.03. This common effect suggests that hydrogen bond coupling is minimally
influenced by the remaining protein scaffold. The observed coupling
is reproduced by molecular mechanics and quantum mechanics/molecular
mechanics (QM/MM) calculations for changes to a proximal oxyanion
hole hydrogen bond. However, effects from distal hydrogen bonds are
reproduced only by QM/MM, suggesting the importance of polarization
in hydrogen bond coupling. These results deepen our understanding
of hydrogen bonds and their networks, providing strong evidence for
long-range coupling and for the extent of this coupling. We provide
a broadly predictive quantitative relationship that can be applied
to and can be further tested in new systems