Analysis of neighboring aromatic groups in four biphenyl peptides or peptide analogs and 34 proteins reveals a specific aromatic-aromatic interaction. Aromatic pairs (less than 7 A between phenyl ring centroids) were analyzed for the frequency of pair type, their interaction geometry (separation and dihedral angle), their nonbonded interaction energy, the secondary structural locations of interacting residues, their environment, and their conservation in related molecules. The results indicate that on average about 60 percent of aromatic side chains in proteins are involved in aromatic pairs, 80 percent of which form networks of three or more interacting aromatic side chains. Phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 A, and dihedral angles approaching 90 degrees are most common. Nonbonded potential energy calculations indicate that a typical aromatic-aromatic interaction has energy of between -1 and -2 kilocalories per mole. The free energy contribution of the interaction depends on the environment of the aromatic pair. Buried or partially buried pairs constitute 80 percent of the surveyed sample and contribute a free energy of between -0.6 and -1.3 kilocalories per mole to the stability of the protein's structure at physiologic temperature. Of the proteins surveyed, 80 percent of these energetically favorable interactions stabilize tertiary structure, and 20 percent stabilize quaternary structure. Conservation of the interaction in related molecules is particularly striking.

binary enzyme-substrate (2; throughout the text, the bold numbers refer to species in Fig. The Catalytic Pathway of 1) and enzyme-product (4) complexes have Cytochrome P450cam a t been so characterized (4). Some features of the dioxygen-bound or activated oxygen intermediates, in particular the geometry of the Atomic Resolution six-coordinate low-spin heme, have been deduced from the structure of the ferrous llme ~chlichting,'* Joel Berendzen,' Kelvin Chu,'? Ann M. S t~c k ,~ (FelI+) carbonmonoxy complex (3) of Shelley A. M a v e~,~ David E. enso on,^ Robert M. S~e e t ,~ P450cam (5).However, the binding of carbon Dagmar Ringe,6 Gregory A. ~e t s k o ,~ monoxide to heme is likely to be different in Stephen G. Sligar'~~ a number of important ways from the binding Members o f t h e cytochrome P450 superfamily catalyze t h e addition o f m o -of oxygen ( 6 ) , and regardless, carbon monlecular oxygen t o nonactivated hydrocarbons a t physiological temperature-a oxide is an inhibitor, not a substrate, of reaction t h a t requires high temperature t o proceed i n t h e absence o f a catalyst. P450cam. Hence, the primary evidence for Structures were obtained for three intermediates i n the hydroxylation reaction the structures of the ferrous enzyme-substrate o f camphor b y P450cam w i t h trapping techniques and cryocrystallography. The complex (5), the dioxy intermediate (6), and structure o f t h e ferrous dioxygen adduct o f P450cam was determined w i t h 0.91

The crystal structure of the H‐ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp has been determined at 1.35 A resolution. 211 water molecules have been built into the electron density. The structure has been refined to a final R‐factor of 19.8% for all data between 6 A and 1.35 A. The binding sites of the nucleotide and the magnesium ion are revealed in high detail. For the stretch of amino acid residues 61‐65, the temperature factors of backbone atoms are four times the average value of 16.1 A2 due to the multiple conformations. In one of these conformations, the side chain of Gln61 makes contact with a water molecule, which is perfectly placed to be the nucleophile attacking the gamma‐phosphate of GTP. Based on this observation, we propose a mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in‐line attack of water. Nucleophilic displacement is facilitated by hydrogen bonds from residues Thr35, Gly60 and Lys16. A mechanism for rate enhancement by GAP is also proposed.

Loss-of-function DJ-1 mutations can cause early-onset Parkinson's disease. The function of DJ-1 is unknown, but an acidic isoform accumulates after oxidative stress, leading to the suggestion that DJ-1 is protective under these conditions. We addressed whether this represents a posttranslational modification at cysteine residues by systematically mutating cysteine residues in human DJ-1. WT or C53A DJ-1 was readily oxidized in cultured cells, generating a pI 5.8 isoform, but an artificial C106A mutant was not. We observed a cysteine-sulfinic acid at C106 in crystalline DJ-1 but no modification of C53 or C46. Oxidation of DJ-1 was promoted by the crystallization procedure. In addition, oxidation-induced mitochondrial relocalization of DJ-1 and protection against cell death were abrogated in C106A but not C53A or C46A. We suggest that DJ-1 protects against neuronal death, and that this is signaled by acidification of the key cysteine residue, C106.