Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme.

Quillin, M.L.; Breyer, W.A.; Griswold, I.J.; Matthews, B.W.

doi:10.2210/pdb1c68/pdb

Macromolecule Content

Total Structure Weight: 19165.25
Atom Count: 1299
Residue Count: 164
Unique protein chains: 1

1C68

T4 LYSOZYME MUTANT C54T/C97A/L121A/L133A IN THE PRESENCE OF 8 ATM XENON

DOI: 10.2210/pdb1C68/pdb

Classification: HYDROLASE
Organism(s): Enterobacteria phage T4
Expression System: Escherichia coli
Mutation(s): 4

Deposited: 1999-12-21 Released: 2000-10-04
Deposition Author(s): Quillin, M.L., Matthews, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.5 Å

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme.

Quillin, M.L., Breyer, W.A., Griswold, I.J., Matthews, B.W.

(2000) J.Mol.Biol. 302: 955-977

PubMed: 10993735 Search on PubMed
DOI: 10.1006/jmbi.2000.4063
Primary Citation of Related Structures:
1C6T, 1C6Q, 1C6P, 1C6N, 1C6M, 1C6L, 1C6K, 1C6J, 1C6I, 1C6H, 1C6G, 1C6F, 1C6E, 1C6D, 1C6C, 1C6B, 1C6A, 1C69, 1C67, 1C66, 1C65, 1C64, 1C63, 1C62, 1C61, 1C60

PubMed Abstract:

To investigate the relative importance of size and polarizability in ligand binding within proteins, we have determined the crystal structures of pseudo wild-type and cavity-containing mutant phage T4 lysozymes in the presence of argon, krypton, and xenon. These proteins provide a representative sample of predominantly apolar cavities of varying size and shape. Even though the volumes of these cavities range up to the equivalent of five xenon atoms, the noble gases bind preferentially at highly localized sites that appear to be defined by constrictions in the walls of the cavities, coupled with the relatively large radii of the noble gases. The cavities within pseudo wild-type and L121A lysozymes each bind only a single atom of noble gas, while the cavities within mutants L133A and F153A have two independent binding sites, and the L99A cavity has three interacting sites. The binding of noble gases within two double mutants was studied to characterize the additivity of binding at such sites. In general, when a cavity in a protein is created by a "large-to-small" substitution, the surrounding residues relax somewhat to reduce the volume of the cavity. The binding of xenon and, to a lesser degree, krypton and argon, tend to expand the volume of the cavity and to return it closer to what it would have been had no relaxation occurred. In nearly all cases, the extent of binding of the noble gases follows the trend xenon>krypton>argon. Pressure titrations of the L99A mutant have confirmed that the crystallographic occupancies accurately reflect fractional saturation of the binding sites. The trend in noble gas affinity can be understood in terms of the effects of size and polarizability on the intermolecular potential. The plasticity of the protein matrix permits repulsion due to increased ligand size to be more than compensated for by attraction due to increased ligand polarizability. These results have implications for the mechanism of general anesthesia, the migration of small ligands within proteins, the detection of water molecules within apolar cavities and the determination of crystallographic phases.

Related Citations:

Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution
Weaver, L.H.,Matthews, B.W.
(1987) J.Mol.Biol. 193: 189
The Response of T4 Lysozyme to Large-to-Small Substitutions within the Core and its Relation to the Hydrophobic Effect
Xu, J.,Baase, W.A.,Baldwin, E.P.,Matthews, B.W.
(1998) Protein Sci. 7: 158

Organizational Affiliation:

Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR, 97403, USA.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (LYSOZYME)	A	164	Enterobacteria phage T4	Mutation(s): 4 Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB: P00720
Protein Feature View Full Protein Feature View for P00720

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
CL Query on CL Download SDF File Download CCD File	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
BME Query on BME Download SDF File Download CCD File	A	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Ligand Interaction
XE Query on XE Download SDF File Download CCD File	A	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Ligand Interaction