Protein-ligand dynamics

Tilton, Robert D.; Singh, U. Chandra; Kuntz, Irwin D.; Kollman, Peter A.

doi:10.1016/0022-2836(88)90389-0

Cited by 68 publications

(26 citation statements)

References 30 publications

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“…Ligand entry must involve large-amplitude movements of the atoms gating the cavity. Molecular dynamics simulations of the entry of Xe into internal cavities of metmyoglobin (17) have illustrated protein breathing motions in such hydrophobic ligand binding, which involve transient atomic displacements of several A but no overall change in the cavity structures. Similarly, the refined electron-density maps of the insulin crystals with and without dichloroethane ( Over the pH range 6-11 at ionic strength 0.1-3 M dichloroethane occupancy remained complete, and the atomic positions of the cavity-forming atoms did not measurably change, as indicated by the refined electron-density maps.…”

Section: Resultsmentioning

confidence: 99%

Stereospecific dihaloalkane binding in a pH-sensitive cavity in cubic insulin crystals.

Gursky

Fontano

Bhyravbhatla

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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Crystallographic analysis at 2-A resolution of the selective binding of dihalogenated methane, ethane, and ethylene compounds in the cavity on the cubic insulin dimer axis provides a model for anesthetic-protein interactions. At pH 6-11, 1,2-dichloroethane binds isomorphically in the righthanded cis-conformation, displacing four water molecules from the invariant cavity. Lowering the pH to 5.7 in 1 M Na2SO4 without dihaloalkanes induces a cooperative structural transition in which the dyad cavities between B13 glutamate pairs are constricted, and SO2-ions are bound by rearranged triads of Bi NH' groups. In the presence of dichloroethane at pH 5-5.5, the equilibrium is shifted to a mixture of the ligand-bound and ligand-excluding cavity structures, with halfoccupancy of the sulfate sites, exemplifying how a volatile anesthetic can act as an allosteric effector. Measurements at pH 9 of the occupancies of structurally similar dihaloalkanes demonstrate a high degree of binding selectivity. Induced polarization of the ligand and bound water by the charge distribution in the binding cavity apparently provides the selective electrostatic interactions that discriminate between dihaloalkanes of comparable size and polarity.Insulin (51 amino acids, 5.8 kDa) crystallizes from zinc-free alkaline solutions as a symmetric dimer arranged in orthogonal cross-connected rows in the cubic space group I213 (a = 78.9 A) (1, 2). The crystal lattice, which contains 65% solvent volume, is stable from pH 7-10 in 0.1 M monovalent cation salt solutions (3) and from pH 5-11 in 1 M Na2SO4. The pH-dependent local conformational changes and coupled binding of monovalent cations, which have been crystallographically characterized in pH range 7-11 (4), demonstrate the usefulness of this system for studying the effects of altered electrostatic interactions on the protein and solvent structure. Following our observation (4) that cubic insulin crystals in alkaline 0.1-1 M salt solutions bind 1,2-dichloroethane (ClH2C-CH2CI) with unit occupancy at a site on the dimer axis ( Fig. 1), we have characterized this binding at pH 5-11 and compared the binding of similar dihaloalkanes at pH 9. § Such binding exemplifies the type of hydrophobic ligand-protein interactions that may underlie the action of inhalational general anesthetics (6, 7). MATERIALS AND METHODSCrystal Preparation and X-Ray Data Collection. Cubic Zn-free crystals of bovine insulin, grown from phosphate buffer at pH 9 (1, 4), were equilibrated by dialysis against sodium salt solutions that varied in pH from 5 to 11 and subsequently equilibrated with liquid dihaloalkanes. Dihaloalkane binding was discovered by exposing the crystals to 1,2-dichloroethane as solvent for Formvar, which was applied in the capillary to cast an encasing film that prevents crystal slippage (8). Binding at the dyad site, as detected by x-ray diffraction, was complete after 30-sec direct exposure to liquid dichloroethane or after overnight soaking in a saturated aqueous solution. The x-ray data were collect...

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Section: Resultsmentioning

confidence: 99%

Stereospecific dihaloalkane binding in a pH-sensitive cavity in cubic insulin crystals.

Gursky

Fontano

Bhyravbhatla

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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“…However, results from later NMR studies indicated that small organic gas molecules reside for Ͼ1 ns in internal protein cavities, pointing to the importance of the internal cavities to allow for specific gas transport through proteins (35). The appearance of such cavities and dynamics are intimately linked and central for ligand binding, where the fluctuations in the atomic positions are crucial for permitting ligands to diffuse (8)(9)(10)36). Consequently, a rigid region of a protein structure would require a specific channel to allow gas transport into a specific site.…”

Section: Discussionmentioning

confidence: 99%

A single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter

Salomonsson

Lee

Gennis

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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Proteins undergo structural fluctuations between nearly isoenergetic substates. Such fluctuations are often intimately linked with the functional properties of proteins. However, in some cases, such as in transmembrane ion transporters, the control of the ion transport requires that the protein is designed to restrict the motions in specific regions. In this study, we have investigated the dynamics of a membrane-bound respiratory oxidase, which acts both as an enzyme catalyzing reduction of O 2 to H2O and as a transmembrane proton pump. The segment of the protein where proton translocation is controlled (''gating'' region) overlaps with a channel through which O 2 is delivered to the catalytic site. We show that the replacement of an amino acid residue with a small side chain (Gly) by one with a larger side chain (Val), in a narrow part of this channel, completely blocks the O 2 access to the catalytic site and results in formation of a compartment around the site that is impermeable to small gas molecules. Thus, the protein motions cannot counter the blockage introduced by the mutation. These results indicate that the protein motions are restricted in the proton-gating region and that rapid O 2 delivery to the catalytic site requires a gas channel, which is confined within a rigid protein body.membrane protein ͉ cytochrome c oxidase ͉ proton transfer ͉ dynamics ͉ respiratory oxidases

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“…1). Molecular dynamics simulations have provided additional support for indirect pathways involving Xe sites (14,15). More recently, Huang and Boxer (16) suggested the existence of multiple entry and exit routes based on changes in the kinetics of geminate and overall O 2 and CO rebinding to random point mutants of myoglobin expressed in crude Escherichia coli lysates.…”

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confidence: 99%

“…The locations of these residues are shown in Fig. 1, and the wild-type and mutant amino acids are listed in Tables I-V. Replacements were made at virtually all positions in or near the heme pocket and at locations near the Xe binding sites and along the escape routes proposed by Tilton et al (13,14), Elber and Karplus (15), and Huang and Boxer (16). Additional residues were chosen on the basis of ligand movements observed in molecular dynamics simulations by Gibson and co-workers over the past 6 years (17,(23)(24)(25)(26).…”

mentioning

confidence: 99%