Mechanisms of ligand binding and activation of G protein-coupled receptors are particularly important, due to their ubiquitous expression and potential as drug targets. Molecular interactions between ligands and these receptors are best defined for small molecule ligands that bind within the transmembrane helices. Extracellular domains seem to be more important for peptide ligands, based largely on effects of receptor mutagenesis, where interference with binding or activity can reflect allosteric as well as direct effects. We now take the more direct approach of photoaffinity labeling the active site of the cholecystokinin (CCK) receptor, using a photolabile analogue of CCK having a blocked amino terminus. Guanine nucleotide-binding protein (G protein) 1 -coupled receptors are the largest group of plasma membrane receptors, representing a superfamily with a remarkable diversity of activating ligands. Our best understanding of the molecular basis for ligand binding to members of this superfamily is the binding of the chromophore to rhodopsin and the binding of biogenic amines to adrenergic receptors. These insights come from complementary studies of receptor mutagenesis, photoaffinity labeling, and reciprocal chemical modification of ligand and receptor (1-6). All available data focus the relevant interactions to sites at the core of the coalescence of transmembrane helices, in the outer third of the bilayer. Even with this extensive information, the constrained nature of the ligands, and the relatively confined space for ligand docking, the debate continues regarding the specific siting of the agonist ligands in some of these receptor systems (7,8).Understanding the interactions between peptide ligands and their G protein-coupled receptors represents an even greater challenge. By first principles, these ligands are quite flexible and can achieve many conformations. Whereas some peptides appear to have some preferred conformation in solution (9), there is little information regarding how such structures relate to the receptor-bound states of these ligands. Most of our insights into binding domains for peptide ligands have come from receptor mutagenesis studies, which have focused attention on receptor domains predicted to be outside the membrane (7,8). Given the extended size of the pharmacophoric domains and the solubilities of the peptide ligands, these regions of interaction seem plausible. We know, however, that receptor mutagenesis can modify receptor function nonspecifically, interfering with biosynthetic processing or trafficking or having an allosteric effect, rather than necessarily directly interfering with a site of ligand-receptor interaction. For a very limited number of peptide receptors in this family, direct sites of contact have been recently described using photoaffinity labeling approaches (10 -13).Cholecystokinin (CCK) is a peptide hormone and neurotransmitter that has a wide spectrum of physiologic actions (14). These relate largely to control of nutrient assimilation, through regulation of...

Sodium channels initiate the electrical cascade responsible for cardiac rhythm, and certain life-threatening arrhythmias arise from Na(+) channel dysfunction. We propose a novel mechanism for modulation of Na(+) channel function whereby calcium ions bind directly to the human cardiac Na(+) channel (hH1) via an EF-hand motif in the C-terminal domain. A functional role for Ca(2+) binding was identified electrophysiologically, by measuring Ca(2+)-induced modulation of hH1. A small hH1 fragment containing the EF-hand motif was shown to form a structured domain and to bind Ca(2+) with affinity characteristic of calcium sensor proteins. Mutations in this domain reduce Ca(2+) affinity in vitro and the inactivation gating effects of Ca(2+) in electrophysiology experiments. These studies reveal the molecular basis for certain forms of long QT syndrome and other arrhythmia-producing syndromes, and suggest a potential pharmacological target for antiarrhythmic drug design.

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We draw on an old technique for improving the accuracy of mesh-based field calculations to extend the popular Smooth Particle Mesh Ewald (SPME) algorithm as the Staggered Mesh Ewald (StME) algorithm. StME improves the accuracy of computed forces by up to 1.2 orders of magnitude and also reduces the drift in system momentum inherent in the SPME method by averaging the results of two separate reciprocal space calculations. StME can use charge mesh spacings roughly 1.5× larger than SPME to obtain comparable levels of accuracy; the one mesh in an SPME calculation can therefore be replaced with two separate meshes, each less than one third of the original size. Coarsening the charge mesh can be balanced with reductions in the direct space cutoff to optimize performance: the efficiency of StME rivals or exceeds that of SPME calculations with similarly optimized parameters. StME may also offer advantages for parallel molecular dynamics simulations because it permits the use of coarser meshes without requiring higher orders of charge interpolation and also because the two reciprocal space calculations can be run independently if that is most suitable for the machine architecture. We are planning other improvements to the standard SPME algorithm, and anticipate that StME will work synergistically will all of them to dramatically improve the efficiency and parallel scaling of molecular simulations.

Atomic resolution crystallographic studies of streptavidin and its biotin complex have been carried out at 1.03 and 0.95 Å, respectively. The wild‐type protein crystallized with a tetramer in the asymmetric unit, while the crystals of the biotin complex contained two subunits in the asymmetric unit. Comparison of the six subunits shows the various ways in which the protein accommodates ligand binding and different crystal‐packing environments. Conformational variation is found in each of the polypeptide loops connecting the eight strands in the β‐sandwich subunit, but the largest differences are found in the flexible binding loop (residues 45–52). In three of the unliganded subunits the loop is in an `open' conformation, while in the two subunits binding biotin, as well as in one of the unliganded subunits, this loop `closes' over the biotin–binding site. The `closed' loop contributes to the protein's high affinity for biotin. Analysis of the anisotropic displacement parameters included in the crystallographic models is consistent with the variation found in the loop structures and the view that the dynamic nature of the protein structure contributes to the ability of the protein to bind biotin so tightly.

Distinct spatial approximations between residues within the secretin pharmacophore and its receptor can provide important constraints for modeling this agonist-receptor complex. We previously used a series of probes incorporating photolabile residues into positions 6, 12, 13, 14, 18, 22, and 26 of the 27-residue peptide and demonstrated that each covalently labeled a site within the receptor amino terminus. Although supporting a critical role of this domain for ligand binding, it does not explain the molecular mechanism of receptor activation. Here, we developed probes having photolabile residues at the amino terminus of secretin to explore possible approximations with a different receptor domain. The first probe incorporated a photolabile pbenzoyl-L-phenylalanine into the position of His 1 of rat secretin ([Bpa 1 ,Tyr 10 ]secretin-27). Because His 1 is critical for function, we also positioned a photolabile Bpa as an amino-terminal extension, in positions ؊1 (rat [Bpa ؊1 ,Tyr 10 ]secretin-27) and ؊2 (rat [Bpa ؊2 ,Gly ؊1 ,-Tyr 10 ]secretin-27). Each analog was shown to be a full agonist, stimulating cAMP accumulation in receptorbearing Chinese hamster ovary-SecR cells in a concentration-dependent manner, with the position ؊2 probe being most potent. They bound specifically and saturably, although the position 1 analog had lowest affinity, and all were able to label the receptor efficiently. Sequential specific cleavage, purification, and sequencing demonstrated that the sites of covalent attachment for each probe were high within the sixth transmembrane segment. This suggests that secretin binding may exert tension between the receptor amino terminus and the transmembrane domain to elicit a conformational change effecting receptor activation.The secretin receptor is prototypic of the Class B family of guanine nucleotide-binding protein (G protein)-coupled receptors which includes many important drug targets. Understanding of the molecular basis of ligand binding of receptors is important for the rational design of receptor-active drugs. However, the molecular basis of ligand binding of Class B receptors is less well understood than that of members of the Class A family, such as rhodopsin and the adrenergic receptor. This likely reflects the facts that natural ligands for Class B G protein-coupled receptors are relatively large peptides with diffuse phamacophoric domains and that these receptors have long and complex amino-terminal domains that are important for binding. Both of these interacting domains are flexible, with active conformations that have not been clearly defined.One of the distinct characteristics of the Class B receptor family is the long amino terminus that exceeds 120 residues in length. It contains 6 conserved Cys residues that have been demonstrated to form intradomain disulfide bonds (1-5) and to be critical for ligand binding. These disulfide bonds could provide key constraints for building a model of the secretin receptor, but definitive mapping of these bonds in an active receptor has not...

Insight into the molecular basis of cholecystokinin (CCK) binding to its receptor has come from receptor mutagenesis and photoaffinity labeling studies, with both contributing to the current hypothesis that the acidic Tyr-sulfate-27 residue within the peptide is situated adjacent to basic Arg 197 in the second loop of the receptor. Here, we refine our understanding of this region of interaction by examining a structure-activity series of these positions within both ligand and receptor and by performing three-dimensional molecular modeling of key pairs of modified ligand and receptor constructs. The important roles of Arg 197 and Tyr-sulfate-27 were supported by the marked negative impact on binding and biological response with their natural partner molecule when the receptor residue was replaced by acidic Asp or Glu and when the peptide residue was replaced by basic Arg, Lys, p-amino-Phe, p-guanidino-Phe, or p-methylamino-Phe. Complementary ligand-receptor chargeexchange experiments were unable to regain the lost function.This was supported by the molecular modeling, which demonstrated that the charge-reversed double mutants could not form a good interaction without extensive rearrangement of receptor conformation. The models further predicted that R197D and R197E mutations would lead to conformational changes in the extracellular domain, and this was experimentally supported by data showing that these mutations decreased peptide agonist and antagonist binding and increased nonpeptidyl antagonist binding. These receptor constructs also had increased susceptibility to trypsin degradation relative to the wild-type receptor. In contrast, the relatively conservative R197K mutation had modest negative impact on peptide agonist binding, again consistent with the modeling demonstration of loss of a series of stabilizing inter-and intramolecular bonds. The strong correlation between predicted and experimental results support the reported refinement in the three-dimensional structure of the CCK-occupied receptor.

RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.