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[F.sub.1][F.sub.o]-ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain [F.sub.1] of the [F.sub.1][F.sub.o] complex, [F.sub.1]-ATPase, has the ability to hydrolyze ATP. A fundamental problem in the development of a detailed mechanism for this enzyme is that it has not been possible to determine experimentally the relation between the ligand binding affinities measured in solution and the different conformations of the catalytic [beta] subunits ([[beta].sub.TP], [[beta].sub.DP],[[beta].sub.E]) observed in the crystal structures of the mitochondrial enzyme, M[F.sub.1]. Using free energy difference simulations for the hydrolysis reaction ATP+[H.sub.2]O [right arrow] ADP+[P.sub.i] in the [[beta].sub.TP] and [[beta].sub.DP] sites and unisite hydrolysis data, we are able to identify [[beta].sub.TP] as the 'tight' ([K.sub.D] = [10.sup.-12] M, M[F.sub.1]) binding site for ATP and [[beta].sub.DP] as the 'loose' site. An energy decomposition analysis demonstrates how certain residues, some of which have been shown to be important in catalysis, modulate the free energy of the hydrolysis reaction in the [[beta].sub.TP] and [[beta].sub.DP] sites, even though their structures are very similar. Combined with the recently published simulations of the rotation cycle of [F.sub.1]-ATPase, the present results make possible a consistent description of the binding change mechanism of [F.sub.1]-ATPase at an atomic level of detail.

Research proposes a mechanism for the active site peptide loop conformational change, in pyridoxine 5(sup)' -phosphate synthase, by the substrates so as to provide access to the active site, whose residues in turn rearrange for catalysis and pyridoxine 5'-phosphate formation.

Results indicate that amino acid residues R71, D75, and H98 mediate the stabilization of the semiquinone state in the high-affinity binding site in cytochrome bo(sub)3 of Escherichia coli.

The fluorescence analysis reveals an activation-dependent conformational change in the G protein alpha leading to increased hydrophobic environment of the N-terminal region. The conformational changes occur upon G protein betagamma binding and activated to either the GDP-AlF(sub)4(sup)- or the GTP-gammaS bound conformation.

Results reveal that there exists a functional metal ion selectivity in the Synechococcus PCC7942 SmtB family of metal sensor proteins. Cysteine substitution or derivatization in the alpha3N metal binding site does not affect allosteric negative regulation by divalent zinc, while zinc-ligand substitution in the alpha5 metal binding site renders SmtB refractory to SmtB-DNA complexes.

The homodimer of the cysteine substituted mutant SmtB metalloregulatory protein of the Synechococcus PCC7942 binds divalent zinc or cobalt in one of the two metal binding sites, alpha3N and alpha5. Data suggest that the differential binding behavior of the metal binding sites accounts for the functional diversity of this family of proteins.

Results show that the binding of 6-hydroxymethyl-7,8-dihydropterin by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase is medited by a step or steps after the chemical transformation and serve as rate-limiting steps of the reactions catalyzed by the enzyme and magnesium.

The activation of the recombinant factor XIII by calcium and thrombin results only in subtle structural changes that are localized to different areas of the enzyme, suggesting that the calcium and thrombin individually contribute towards enzyme activation for substrate binding and active site exposure.

The X-ray crystal analysis of human c8gamma reveals a typical lipocalin fold forming a calyx and exhibiting a binding site for a small molecule, whose identity is unknown. C8gamma is a subunit of human C8 which in turn a component of the cytolytic membrane attack complex of complement.

Research demonstrates that within the N-terminus domain of the oxytocin rceptor, Arg34 is involved in the high-affinity agonist binding to the receptor as shown by a 2000-fold decrease in oxytocin affinity by removal or substitution of Arg34. Further, the arginyl residue is agonist-specific and is not essential for peptide or antagonist binding.

Research discusses the substrate-binding step in the peptide hydrolysis reaction by Aeromonas proteolytica aminopeptidase. Data indicate that the second step in the enzyme catalysis is carbonyl binding to zinc(sub)1, which activates the amide bond carbon atom for nucleophilic attack. The tetrahedral transition state is stabilized by two metal centers.

To understand how snake neurotoxins interact with nicotinic acetylcholine receptors, we have elaborated an experimentally based model of the [alpha]-cobratoxin-[alpha]7 receptor complex. This model was achieved by using (i) a three-dimensional model of the [alpha]7 extracellular domain derived from the crystallographic structure of the homologous acetylcholine-binding protein, (ii) the previously solved x-ray structure of the toxin, and (iii) nine pairs of residues identified by cycle-mutant experiments to make contacts between the [alpha]-cobratoxin and [alpha]7 receptor. Because the receptor loop F occludes entrance of the toxin binding pocket, we submitted this loop to a dynamics simulation and selected a conformation that allowed the toxin to reach its binding site. The three-dimensional structure of the toxin-receptor complex model was validated a posteriori by an additional double-mutant experiment. The model shows that the toxin interacts perpendicularly to the receptor axis, in an equatorial position of the extracellular domain. The tip of the toxin central loop plugs into the receptor between two subunits, just below the functional receptor loop C, the C-terminal tail of the toxin making adjacent additional interactions at the receptor surface. The receptor establishes major contacts with the toxin by its loop C, which is assisted by principal (loops A and B) and complementary (loops D, F, and 1) functional regions. This model explains the antagonistic properties of the toxin toward the neuronal receptor and opens the way to the design of new antagonists.

The crystal structure of the inactive human VHR protein phosphatase mutant in complex with the bisphosphorylated MAP kinase peptide reveals that the two phospho residues are situated in distinct pockets and the phosphotyrosine binds to the exposed active site cleft formed by the residues.

The kinetics of the binding of huprine X inhibitor to the Torpedo californica acetylcholinesterase reveal that it binds to the anionic site and obstructs access to the esteratic site as shown by molecular dynamics simulation of the huprine X inhibitor/enzyme complex crystal structure.

The pigment-protein interactions in the photosystem II antenna protein, Lhcb4, reveal that removal of a any bound cofactor from any sites of the chlorophyll a binding sites, a2, a4, and a5 leads to a loss of bands of the particular chlorophyll molecule and a structural impact on the protein folding.

The contribution of the internal A16 side chain leucine to insulin's structure, stability, and activity is elucidated. Nonpolar amino acid substitution indicate that while leucine is important for stability, the A16 side chain does not connect with the receptor.

The globular domain of the maltose/maltooligosaccharide-binding receptor protein domian binds to polar ligands through nonpolar interactions in preference to polar interactions, even if the conditions favor the latter. Data indicate that the receptor exhibits polar and nonpolar binding domains and possesses 'closed' and 'open' configuration.

Results show that the tubulin-like loop is part of the active site of the prokaryotic cell division protein FitZ, a tubulin homologue, and is involved in GTP hydrolysis mediated by FitZ. Data indicate that FitZ is formed by two of its own monomers.

The poly(A)binding protein homolog, nonstructural protein 3 (NSP3), binds to viral mRNA 3' consensus sequence. Crystal structure analysis shows that NSP3 exhibits two similar N- and to dissimilar C-terminal segments, which intervene to form a tunnel that envelopes the mRNA 3' end.

Research demonstrates process of biomineralization of a hydrated protein using salivary statherin adsorbed to hydroxyapatite surface. Nuclear paramagnetic resonance analysis indicate that the highly anioninc N-terminus of the protein is strongly adsorbed and immobilized on the hydroxyapatite surface with middle and C-terminal regions exhibiting weak interaction.

A mutation of uracil to cytosine at position 2609 of 23S ribosomal RNA renders Escherichia coli cells resistant to two ketolides while maintaining susceptibility to other macrolides. Mutational and binding data suggest that the macrolide binding site is located in the nascent peptide exit tunnel.

Results reveal that alanine substitution in Escherichia coli glycerol kinase at amino acid residue positions 476-481, functions as a cooperative unit in relation to IIA(sup)Glc inhibition and zinc(II)-ion promoted association. Data indicate that P472 residue may participate in the folding and stability of glycerol kinase.

Research shows that the pi-helix exhibits stable interactions with the hydrogen bonds between residues i, and i+5 in a short polypeptide. Data suggest that in the presence of zinc and cetyltrimethylammonium bromide micelles, the peptide assumes a pi-helical conformation.

Results show that mutations in the myosin binding sites cause structural changes within actin that are involved in the strong binding of myosin. However, they do not affect structural dynamics of the strongly bound actomyosin complex.

Results demonstrate that conserved amino acid residues of the N, G1, G2, and F boxes contribute to the ATP binding site as well as autokinase active sites of the chemotaxis component, signal-transducing protein kinase, CheA. Data on the structure-functional aspects and effects specific mutations on CheA autophosphorylation reaction are discussed.

Results point out that the basic-region leucine zipper peptides, containing yeast transcriptional activator GCN4 at the C-terminal to its leucine zipper, bind specifically to DNA. This suggests that there is no thermodynamic basis for the N-terminal locus for the zipper peptides in the natural basic-region leucine zipper proteins.

Results suggest that the genetic asymmetry of cosN site results from terminase interactions with cosB site of bacteriophage lambda DNA and that functional asymmetry of cosN is dependent on the presence of cosB. Data indicate that terminase-cosN interactions in the nicking complex are dependent on the terminase anchoring to cosB.

The molecular structure of the cystin knot protein family member Ptu1 reveals a 2-stranded antiparallel beta-sheet forming the secondary structure. Results demonstrate that the acidic Asp-16 residue of the loop 2 is involved in the binding of the toxin to N-type calcium-channels, although with low affinity.

A single water molecule is tightly hydrogen bonded to the NH of methionine-26 in the cobra P-type cardiotoxin water-binding loop, which mediates toxin binding to the membranes. Data indicate that proline residues in the consensus sequence of the protein are involved in the formation of the water binding loop.

Results indicate that the conformational change in the structure of beta-ketoacyl-[acyl carrier protein] reductase of Escherichia coli leads to an allosteric regulation with the enzyme's homotetramer. Data show that upon cofactor binding, the tetrameric enzyme organizes the active-site triad in a manner that changes the affinity of the substrate-binding sites.

Research describes the first atomic structure of the 350-kilodalton native chicken fibrinogen complexed with two synthetic peptides. Structural details include the central domain polypeptide chain arrangement and a putative thrombin-binding site.

Results demonstrate that ferric P450 isomerase interacts with bis-allylic hydroperoxides by reducing them and resulting in higher ratios of heterolytic:homolytic O-O bond cleavage. The reactions also lend themselves for comparing regio- and stereochemistry of peroxyquinol isomerization coupled with monooxygenation of the relevant quinols.

Results demonstrate that the N-terminal domain of ActA binds one actin monomer and the Arp2/3 complex mimicking the C-terminal domain of WASp family proteins. Data show that filament debranching is 3-4-fold faster with ActA activated Arp2/3 that by the C-terminal domain of N-Wasp.

The two cation binding sites of subtilisin BPN', site A and site B in the tertiary structure of the enzyme contribute their binding energy to the stability of native enzyme. Research shows that the stabilizing effects of cation binding at site B by using a mutant enzyme lacking site A.

Crystal structure analyses reveal that N-terminal FERM domain of moesin is made of three subdomains consisting of a unique 47-residue helix. Data indicate that removal of the C-terminal C-ERMAD domain does not cause major rearrangement of the FERM domain but small changes are observed in the activated radixin structure.

The metal-mediated L-leucinephosphonic acid peptide hydrolysis, catalyzed by the Aminopeptidase of Aeromonas proteolytica, is discussed in conjunction with the X-ray crystallographic and spectroscopic analyses. Results show that the peptide interacts with the two metal centers in the active site of the enzyme as an eta-1,2-micron-phosphonate.

Research reveals that the truncated hemoglobin of Synechocystis sp. PCC slr 2097 possesses a proximal histidine70 and another histidine46 as the sixth ligand to the iron ion. Data suggest that the sixth ligand position is critical for the protein's chemical and functional properties.

Crystal structure analysis of the xylanase C-terminal module of the family 9 carbohydrate-binding module shows that it exhibits a beta-sandwich fold and three metal binding sites. Data indicate that the sugar-binding site containing two tryptophan residues binds exclusively to the reducing ends of oligosaccharides.

Results demonstrate that gamma-boronic acid analogue of L-glutamic acid, 3-amino-3carboxypropaneboronic acid (gamma-boroGlu) inhibits gamma-glutamyl transpeptidase by combining with the active site hydroxyl of the enzyme. Data indicate that gamma-boroGlu is also a competitive inhibitor of the enzyme-catalyzed hydrolysis of gamma-glutamyl-7-amido-4-methylcoumarin.

Three-dimensional structure of E-cadherin cytoplasmic domains complexed with beta-catenin reveals that beta-catenin binds its various partners on to the same surface. In the phosphorylated state, E-cadherin interacts with a hydrophobic patch of beta-catenin.

Results show that the ADP-ribosylation factor (ARF) interacts with heat-labile toxin A1 (LTA1) through switch regions I and II leading to LTA1 binding to the ARF via C-terminal domian and LTA1 residues. Data further indicate that LTA2 and ARF are similar in amino acid sequence homology.

Results demonstrate that the fatty sulfate substrates such as linoleyl sulfate, cis-11,14-eicosadienoyl sulfate, and arachidonyl sulfate are good substrates, but not inhibitors, for soybean lipoxygenase whereas in case of the human lipoxygenase, they are substrates at low concentrations and inhibitors at high concentrations.

Results demonstrate that the double-stranded RNA binding motifs of the RNA-dependent protein kinase binds RNA, placing its loop between beta1 and beta2 of the single-stranded RNA loop. Data further indicate that defects in the RNA stem do not influence the binding pattern.

Research examines the mechanism of cleavage of beta,gamma-bond of GTP at the active site of RAS protein using infrared difference spectroscopy technique. Results reveal the bonding changes occurring in magnesium.GDP and magnesium.GTP as they move from solution into the RAS active site.

Results reveal that the DNA-binding domain of the rat DNA polymerase is homogeneous with a even spread of the protein-DNA contacts and no significant base specificity. Data indicate that the domain exhibits an affinity toward the double-stranded DNA conformation.

Results from one- and two-dimensional electron spin-echo envelope modulation spectra demonstrate strong interactions of the unpaired electron Q(sub)H(sup)._ in association with a nitrogen nucleus. Data suggest that ubisemiquinone radical nucleus belongs to a protein backbone nitrogen.

Research demonstrates that metal-ion site engineering techniques stabilize dimers in green fluorescent protein thereby facilitating enhanced fluorescence resonance energy transfer signaling between spectral variants of the protein.

Research describes construction and purification of gaf gene cluster encoded GafD lectin from Escherichia coli for structure-function analysis of the fimbrial adhesisn protein. Results show that GafD is a soluble non-fusion form of the lectin and its protease-resistant subdomain exhibits receptor-binding specificity.

Results demonstrate that the ligand rebinding kinetics from encapsulated hemoglobin can be measured using sol-gel encapsulated samples and an appropriate encapsulation protocol. Data indicate that maintaining or locking the initial structure of the encapsulated protein is dependent on the encapsulation protocol.