Hydrogen bond coupling in the ketosteroid isomerase active site
Paul A Sigala1, Jose M M Caaveiro, Dagmar Ringe
1Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
Biochemistry
|May 28, 2009
Summary
Hydrogen bonds in enzymes are structurally coupled, meaning changes in one bond affect its neighbors. This study reveals how these coupled hydrogen bonds influence protein structure and function.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Hydrogen bond networks are crucial for biological macromolecules.
- Assessing hydrogen bond structural properties in complex systems is challenging.
- X-ray crystallography often fails to resolve hydrogen-bonded protons, limiting dynamic insights.
Purpose of the Study:
- To investigate the conformational coupling of hydrogen bonds in bacterial ketosteroid isomerase.
- To elucidate the structural properties of hydrogen bonds within an enzyme active site.
- To understand the role of coupled motions in enzyme function.
Main Methods:
- High-resolution X-ray crystallography (1.1-1.3 Å resolution).
- Proton Nuclear Magnetic Resonance ((1)H NMR).
- Site-directed mutagenesis and deuterium isotope effects.
Main Results:
- Demonstrated robust physical coupling between hydrogen bonds donated by Y16 and D103.
- Showed that a small change (0.01 Å) in one hydrogen bond length significantly alters the neighboring bond.
- Explained NMR-detected structural rearrangements due to mutations via observed coupling.
Conclusions:
- Elucidated fundamental structural properties of enzyme active site hydrogen bonds.
- Provided evidence for strong conformational coupling within enzyme hydrogen bond networks.
- Established a foundation for exploring coupled motions in biological systems.
Related Concept Videos
01:27¹H NMR: Long-Range Coupling
The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene π orbitals.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene π orbitals.
00:26Hydrogen Bonds
Hydrogen BondsHydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.Hydrogen Bonds Control the World!Because hydrogen has very weak electronegativity when it binds with a strongly electronegative atom, such as oxygen or nitrogen, electrons in the bond are...
01:04Hydrogen Bonds
A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...
01:22Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)
Vicinal or three-bond coupling is commonly observed between protons attached to adjacent carbons. Here, nuclear spin information is primarily transferred via electron spin interactions between adjacent C‑H bond orbitals. This generally favors the antiparallel arrangement of spins, so 3J values are usually positive.
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the involved orbitals. The...
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the involved orbitals. The...
01:20Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)
Two NMR-active nuclei bonded to a central atom can be involved in geminal or two-bond coupling. Geminal coupling is commonly seen between diastereotopic protons in chiral molecules and unsymmetrical alkenes, among others.
The central atom need not be NMR-active because its electrons are affected by the electron polarization of the spin-active atoms. However, spin information is transmitted less effectively than in one-bond coupling, and 2J values are usually weaker than 1J values. The energy of...
The central atom need not be NMR-active because its electrons are affected by the electron polarization of the spin-active atoms. However, spin information is transmitted less effectively than in one-bond coupling, and 2J values are usually weaker than 1J values. The energy of...
01:17Spin–Spin Coupling: One-Bond Coupling
Coupling interactions are strongest between NMR-active nuclei bonded to each other, where spin information can be transmitted directly through the pair of bonding electrons. While nuclei polarize their electrons to the opposite spins, the bonding electron pair has opposite spins. Configurations with antiparallel nuclear spins are expected to be lower in energy. When coupling makes antiparallel states more favorable, J is considered to have a positive value. The one-bond coupling constant, 1J,...