Functionally important residues in the peptidyl-prolyl isomerase Pin1 revealed by unigenic evolution.

Pin1 is a phosphorylation-dependent member of the parvulin family of peptidyl-prolyl isomerases exhibiting functional conservation between yeast and man. To perform an unbiased analysis of the regions of Pin1 essential for its functions, we generated libraries of randomly mutated forms of the human Pin1 cDNA and identified functional Pin1 alleles by their ability to complement the Pin1 homolog Ess1 in Saccharomyces cerevisiae. We isolated an extensive collection of functional mutant Pin1 clones harboring a total of 356 amino acid substitutions. Surprisingly, many residues previously thought to be critical in Pin1 were found to be altered in this collection of functional mutants. In fact, only 17 residues were completely conserved in these mutants and in Pin1 sequences from other eukaryotic organisms, with only two of these conserved residues located within the WW domain of Pin1. Examination of invariant residues provided new insights regarding a phosphate-binding loop that distinguishes a phosphorylation-dependent peptidyl-prolyl isomerase such as Pin1 from other parvulins. In addition, these studies led to an investigation of residues involved in catalysis including C113 that was previously implicated as the catalytic nucleophile. We demonstrate that substitution of C113 with D does not compromise Pin1 function in vivo nor does this substitution abolish catalytic activity in purified recombinant Pin1. These findings are consistent with the prospect that the function of residue 113 may not be that of a nucleophile, thus raising questions about the model of nucleophilic catalysis. Accordingly, an alternative catalytic mechanism for Pin1 is postulated.

Glycosaminoglycan binding properties of the myxoma virus CC-chemokine inhibitor, M-T1.

Poxviruses encode a number of secreted virulence factors that function to mitigate or modulate the host immune response. M-T1 is a secreted 43-kDa glycoprotein produced by the myxoma virus, a poxvirus pathogen of rabbits, that binds CC-chemokines with high affinity, blocks binding to their cognate G-protein coupled receptors, and thereby inhibits chemokine-induced leukocyte chemotaxis. The present study indicates that M-T1, but not the related vaccinia virus 35-kDa CC-chemokine-binding protein, can localize to cell surfaces through an interaction with glycosaminoglycan molecules. In addition to biochemically characterizing the nature of this interaction, we demonstrate that M-T1 can also simultaneously interact with CC-chemokines while bound to heparin, suggesting that the binding sites on M-T1 for chemokines and heparin are distinct. Furthermore, using recombinant baculovirus-expressed M-T1 truncation and internal deletion mutants, we localize the heparin-binding region of M-T1 to the C terminus of the protein, a region that contains a high abundance of basic residues and includes two clusters of basic amino acid residues that resemble Cardin and Weintraub heparin-binding consensus sequences. The ability of M-T1 to simultaneously interact with chemokines and glycosaminoglycans may enable M-T1 to tether to endothelial surfaces or extracellular matrix and capture host chemokines that are expressed close to sites of virus infection.

The b subunit of Escherichia coli ATP synthase.

The b subunit of ATP synthase is a major component of the second stalk connecting the F1 and F0 sectors of the enzyme and is essential for normal assembly and function. The 156-residue b subunit of the Escherichia coli ATP synthase has been investigated extensively through mutagenesis, deletion analysis, and biophysical characterization. The two copies of b exist as a highly extended, helical dimer extending from the membrane to near the top of F1, where they interact with the delta subunit. The sequence has been divided into four domains: the N-terminal membrane-spanning domain, the tether domain, the dimerization domain, and the C-terminal delta-binding domain. The dimerization domain, contained within residues 60-122, has many properties of a coiled-coil, while the delta-binding domain is more globular. Sites of crosslinking between b and the a, alpha, beta, and delta subunits of ATP synthase have been identified, and the functional significance of these interactions is under investigation. The b dimer may serve as an elastic element during rotational catalysis in the enzyme, but also directly influences the catalytic sites, suggesting a more active role in coupling.

Crystallization and preliminary analysis of chondroitinase AC from Flavobacterium heparinum.

Chondroitinase AC (E.C. 4.2.2.5) overexpressed in its host, Flavobacterium heparinum, was crystallized by vapor diffusion using polyethylene glycol methyl ether as precipitant. It crystallizes in the space group P43212 or its enantiomorph with a = b = 87.1 and c = 193.1 A and one molecule in the asymmetric unit. Crystals diffract to a maximum of 2.5 A resolution on a rotating-anode source. Screening for heavy-atom derivatives identified a lead compound that binds to a single site on the protein. Further screening is in progress.

Escherichia coli SecA shape and dimensions.

SecA shape and conformational flexibility in solution were studied by small angle X-ray scattering. Dimeric SecA is a very elongated molecule, 15 nm long and 8 nm wide. SecA is therefore four times as long as the membrane is wide. The two globular protomers are distinctly separated and share limited surface of intermolecular contacts. ATP, ADP or adenylyl-imidodiphosphate (AMP-PNP) binding does not alter the SecA radius of gyration. A SecA mutant that catalyzes multiple rounds of ATP hydrolysis does not undergo conformational changes detectable by small angle X-ray scattering (SAXS). We conclude that SecA conformational alterations observed biochemically during nucleotide interaction are only small-scale and localized. The ramifications of these findings on SecA/SecYEG interaction are discussed.

Crystal structure of Kex1deltap, a prohormone-processing carboxypeptidase from Saccharomyces cerevisiae,.

Kex1p is a prohormone-processing serine carboxypeptidase found in Saccharomyces cerevisiae. In contrast to yeast serine carboxypeptidase (CPD-Y) and wheat serine carboxypeptidase II (CPDW-II), Kex1p displays a very narrow specificity for lysyl or arginyl residues at the C-terminus of the substrate. The structure of Kex1Deltap, an enzyme that lacks the acidic domain and membrane-spanning portion of Kex1p, has been solved by a combination of molecular replacement and multiple isomorphous replacement and refined to a resolution of 2.4 A. The S1' site of Kex1Deltap is sterically restricted compared to those from CPD-Y or CPDW-II; it also contains two acidic groups that are well positioned to interact with the basic group of a lysine or arginine side chain. The high specificity of Kex1p can therefore be explained by a combination of steric and electronic factors. The structure of the S1 site of Kex1Deltap is also well suited for binding of a lysine or arginine side chain, and the enzyme may therefore exhibit a preference for these residues at P1.

Conformational changes of three periplasmic receptors for bacterial chemotaxis and transport: the maltose-, glucose/galactose- and ribose-binding proteins.

Small-angle X-ray scattering experiments were carried out for the maltose-, glucose/galactose- and ribose-binding proteins of Gram negative bacteria. All were shown to be monomers that decrease in radius of gyration on ligand binding. The results obtained for the maltose-binding protein agree well with crystal structures of the closed, ligand-bound, and open, ligand-free protein, suggesting that these are indeed the primary forms in solution. The closed form is stabilized by protein-sugar interactions, while the open conformation is stabilized by close contacts between the two domains. Since it is the proper special relationship of the domains in the closed form that is most important for interaction with chemotaxis and transport partners, the stabilization of the open form would help keep ligand-free molecules from interfering in function. The scattering results also provide evidence that a large conformational change takes place in association with ligand binding to the glucose/galactose- and ribose-binding proteins, and that the two changes are similar. Modeling suggests that the open forms resemble those found in the related leucine and leucine/isoleucine/valine-binding proteins, but are different from those observed for the maltose-binding protein and the related purine repressor.

Crystal structures and solution conformations of a dominant-negative mutant of Escherichia coli maltose-binding protein.

A mutant of the periplasmic maltose-binding protein (MBP) with altered transport properties was studied. A change of residue 230 from tryptophan to arginine results in dominant-negative MBP: expression of this protein against a wild-type background causes inhibition of maltose transport. As part of an investigation of the mechanism of such inhibition, we have solved crystal structures of both unliganded and liganded mutant protein. In the closed, liganded conformation, the side-chain of R230 projects into a region of the surface of MBP that has been identified as important for transport while in the open form, the same side-chain takes on a different, and less ordered, conformation. The crystallographic work is supplemented with a small-angle X-ray scattering study that provides evidence that the solution conformation of unliganded mutant is similar to that of wild-type MBP. It is concluded that dominant-negative inhibition of maltose transport must result from the formation of a non-productive complex between liganded-bound mutant MBP and wild-type MalFGK2. A general kinetic framework for transport by either wild-type MalFGK2 or MBP-independent MalFGK2 is used to understand the effects of dominant-negative MBP molecules on both of these systems.

Crystallization of a soluble form of the Kex1p serine carboxypeptidase from Saccharomyces cerevisiae.

A soluble form of the killer factor and prohormone-processing carboxypeptidase, "Kex1 delta p," from Saccharomyces cerevisiae, has been crystallized in 17-22% poly(enthylene glycol) methyl ether (average M(r) = 5,000), 100 mM ammonium acetate, 5% glycerol, pH 6.5, at 20 degrees C. A native data set (2.8 A resolution) and four derivative data sets (3.0-3.2 A resolution) were collected at the Photon Factory (lambda = 1.0 A). The crystals belong to space group P2(1)2(1)2(1) with a =56.6 A, b = 84.0 A, c = 111.8 A. Freezing a Kex1 delta p crystal has facilitated the collection of a 2.4-A data set using a rotating anode source (lambda = 1.5418 A). Molecular replacement models have been built based on the structures of wheat serine carboxypeptidase (CPDW-II; Liao DI et al., 1992, Biochemistry 31:9796-9812) and yeast carboxypeptidase Y.

Simple models for the analysis of binding protein-dependent transport systems.

Mathematical modeling was used to evaluate experimental data for bacterial binding protein-dependent transport systems. Two simple models were considered in which ligand-free periplasmic binding protein interacts with the membrane-bound components of transport. In one, this interaction was viewed as a competition with the ligand-bound binding protein, whereas in the other, it was considered to be a consequence of the complexes formed during the transport process itself. Two sets of kinetic parameters were derived for each model that fit the available experimental results for the maltose system. By contrast, a model that omitted the interaction of ligand-free binding protein did not fit the experimental data. Some applications of the successful models for the interpretation of existing mutant data are illustrated, as well as the possibilities of using mutant data to test the original models and sets of kinetic parameters. Practical suggestions are given for further experimental design.

Site specificity of glycation of horse liver alcohol dehydrogenase in vitro.

The site specificity of in vitro glycation of horse liver alcohol dehydrogenase (ADH) was examined and the results interpreted in terms of structural features of the enzyme molecule. In a phosphate buffer solution, glycation occurred at Lys231 (the main site of glycation in vivo), at Lys228 (which is not glycated in vivo), and at several unidentified positions. Buffer anions or NAD+ did not affect glycation of Lys231; this supported our hypothesis that the base catalyst which removes a proton from carbon 2 of a Lys231-attached aldimine is part of the ADH molecule [Shilton, B.H. & Walton, D.J. (1991) J. Biol. Chem. 266, 5587-5592]. Use of a molecular modelling programme indicated that this catalyst was likely to be the imidazole group of His348, exerting its effect through the hydroxyl of Thr347. Glycation of Lys228 occurred only in the presence of phosphate; in this case molecular modelling showed that the base catalyst could be a phosphate ion, bound to ADH at a positive region of the coenzyme binding site. NAD+ inhibited glycation of Lys228 by binding to the enzyme and restricting access to glucose.

Sites of glycation of human and horse liver alcohol dehydrogenase in vivo.

Sites of in vivo glycation of human and horse liver alcohol dehydrogenase were identified by cleavage of the borotritide-treated enzyme with trypsin, followed by gas-phase sequencing of the resulting tritium-labeled glycated peptides. A blank sequencing result, i.e. failure to detect an amino acid phenylthiohydantoin after completion of an Edman degradation cycle, was ascribed to an N-(1-deoxyhexitolyl)lysyl residue, which represented a glycation site on the original enzyme subunit. In human liver alcohol dehydrogenase the sites affected were the epsilon-amino groups of lysines 10, 39, 231, 248, and 325, which were glycated to the relative extents of 10, 5, 75, 5, and 5%, respectively. The site specificity of in vivo glycation of the horse enzyme is similar; 70-75% of it had occurred at lysine 231. A computer image of the crystal structure of horse liver alcohol dehydrogenase was examined. As a result, it was proposed that the high rate of glycation at lysine 231 is due to acid-base catalysis of the Amadori rearrangement by the imidazole group of histidine 348. This hypothesis was supported by showing that imidazole groups were close to sites of glycation in several other proteins.

Site specificity of protein glycation.

The rate of nonenzymatic glycation of a protein amino group is dependent upon a number of factors, such as the accessibility to glucose molecules in solution, and local acid-base catalysis of the rearrangement of the Schiff base that is formed initially. This is illustrated by a study of the site specificity of liver alcohol dehydrogenase, in which an attempt has been made to interpret the data in terms of the three-dimensional structure of the enzyme molecule.

Fructose mediated crosslinking of proteins.

10-20% of the hexose bound to human ocular lens proteins was found to be attached to epsilon-amino groups of lysyl residues via carbon 2. It was concluded that the proteins had undergone nonenzymatic reactions with endogenous fructose. This process may be important in some mammalian tissues, owing to the high crosslinking potential of fructose.

Evidence for glycation of horse liver alcohol dehydrogenase in vivo.

A procedure involving HPLC of N-phenylthiocarbamyl derivatives of N-(1-deoxyhexitolyl) amino acids was used to show that borohydride-treated alcohol dehydrogenase, from horse liver, contained 0.16 mol of N epsilon-(1-deoxyhexitolyl) lysine per mol of enzyme. The identity of this compound was confirmed by mass spectrometry. It was concluded that glycation of alcohol dehydrogenase had occurred in vivo, resulting in the formation of N epsilon-(1-deoxyfructosyl) lysyl residues. The presence of the latter accounted for the retention of 14% of the enzyme by an agaroseboronate gel. These findings are interesting in view of the observation [Tsai, C. S., and White, J. H. (1983) Biochem. J. 209, 309-314] that the enzyme was activated when it was glycated in vitro.

Role of fructose in glycation and cross-linking of proteins.

Incubation of carbohydrate-free human serum albumin (HSA) with fructose in an aqueous buffer at pH 7.4 resulted in glycation of epsilon-amino groups of lysyl residues. A recently developed procedure, involving analysis of hexitol amino acids by high-performance liquid chromatography of phenylthiocarbamyl derivatives, was used to show that 85% of the bound hexose was attached to protein via carbon 2 (C-2). The remainder was attached to protein via carbon 1 (C-1). When incubations were conducted with glucose under identical conditions, all the hexose was attached via C-1. Examination of human ocular lens proteins showed that the majority of the covalently bound hexose was connected to epsilon-amino groups of lysyl residues via C-1; this was attributed mainly to nonenzymatic glucosylation in vivo, which has already been documented. A significant proportion (10-20%) of the bound hexose was connected via C-2. In view of the HSA-hexose incubation results (above), this indicated that the lens proteins had reacted with endogenous fructose; i.e., they had undergone nonenzymatic fructosylation in vivo. The model protein bovine pancreatic ribonuclease A reacted with fructose and glucose at similar rates under physiological conditions. However, covalent, non-disulfide cross-linking, which could be inhibited by D-penicillamine, was induced 10 times more rapidly by fructose than by glucose. It is postulated that some of the protein cross-linking that occurs in vivo is fructose-induced. The possible significance of these processes in diabetic subjects is discussed.