The 2 A crystal structure of subtilisin E with PMSF inhibitor

Using enzyme prepared by the DNA recombination technique, subtilisinE from Bacillus subtilis was crystallizedin space group P2₁2₁2₁with two molecules in an asymmetric unit. The crystal structureof PMSF-inhibited subtilisin E was solved by molecular replacementfollowed by refinement with the X-PLOR program. This resultedin the 2.0 Å structure of subtilisin E with an R-factorof 0.191 for 8–2 Å data and r.m.s. deviations fromideal values of 0.021 Å and 2.294° for bond lengthsand bond angles respectively. The PMSF group covalently boundto Ser221 appeared very clearly in the electron density map.Except for the active site disturbed by PMSF binding, the structuralfeatures of subtilisin E are almost the same as in other subtilisins.The calcium-binding sites are different in detail in the twoindependent molecules of subtilisin E. Based on the structure,the remarkably enhanced heat stability of mutant N118S of subtilisinE is discussed. It is very likely that there is an additionalwater molecule in the mutant structure, which is hydrogen bondedto side chains of Serll8 and its neighbouring residues Lys27and Asp 120.     

1.85 A structure of anti-fluorescein 4-4-20 Fab

The crystal complex of fluorescein bound to the high-affinityanti-fluorescein 4-4-20 Fab {K_a = 10¹⁰ M^–1 at 2°C)has been determined at 1.85 Å. Isomorphous crystals oftwo isoelectric forms (p1 = 7.5 and 7.9) of the antifluorescein4-4-20 Fab, an IgG2A [Gibson et al (1988)Proteins: Struct. FunctGenet., 3, 155–160], have been grown. Both complexes crystallizewith one molecule in the asymmetric unit in space group P1,with a = 42.75 Å, b =43.87 Å, c = 58.17 Å, = 95.15° , ß = 86.85° and = 98.01°.The final structure has an R value of 0.188 at 1.85 Åresolution. Interactions between bound fluorescein, the complementarity-determiningregions (CDRs) of the Fab and the active-site mutants of the4-4-20 single-chain Fv will be discussed. Differences were foundbetween the structure reported here and the previously reported2.7 Å 4-4-20 Fab structure [Herron et al. (1989) Proteins:Struct. Fund., 5, 271–280]. Our structure determinationwas based on 26 328 unique reflections — four times theamount of data used in the previous report. Differences in thetwo structures could be explained by differences in interpretingthe electron density maps at the various resolutions. The r.m.s.deviations between the variable and constant domains of thetwo structures were 0.77 and 1.54 Å, respectively. Fourregions of the light chain and four regions of the heavy chainhad r.m.s. backbone deviations of >4 Å. The most significantof these was the conformation of the light chain CDR 1.     

Crystallization and structure solution at 4 A resolution of the recombinant synthase domain of N(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli complexed to a substrate analogue

The recombinant synthase domain of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilateisomerase:indole-3-glycerol-phosphate synthase from Escherichiacoli has been crystallized, and the structure has been solvedat 4 Å resolution. Two closely related crystal forms grownfrom ammonium sulphate diffract to 2 Å resolution. Oneform (space group R32, a = 163 Å, = 29.5°) containsthe unliganded synthase domain; the second crystal form (spacegroup P6₃22, a = 144 Å, c = 158 Å) is co-crystallizedwith the substrate analogue N-(5'-phosphoribit-1-yl)anthranilate.The structure of the synthase–inhibitor complex has beensolved by the molecular replacement method. This achievementrepresents the first successful use of a (ß)_g-barrelmonomer as a trial model. The recombinant synthase domain associatesas a trimer in the crystal, the molecules being related by apseudo-crystallographic triad. The interface contacts betweenthe three domains are mediated by those residues that are alsoinvolved in the domain interface of the bifunctional enzyme.This system provides a model for an interface which is usedin both intermolecular and intramolecular domain contacts.     

The 3.0 A crystal structure of xylose isomerase from Streptomyces olivochromogenes

The crystal structure of xylose isomerase [E.C. 5.3.1.5 [EC] ] fromStreptomyces olivochromogenes has been determined to 3.0 Åresolution. The crystals belong to space group P22₁2₁ with unitcell parameters a = 98.7, b = 93.9, c = 87.7. The asymmetricunit contains half of a tetrameric molecule of 222 symmetry.The two-fold axis relating the two molecules in the asymmetricunit is close to where a crystallographic two-fold would beif the space group were 1222. This causes the diffraction patternto have strong 1222 pseudo-symmetry, so all data were collectedin this pseudo-space group. Since the sequence of this enzymehas not been reported, a polyalanine backbone has been fittedto the electron density. Xylose isomerase has two domains: theN-terminal domain is an eight-stranded /ß barrel of299 residues. The C-terminal domain is a large loop of 50 residueswhich is involved in inter-molecular contacts. Comparison ofxylose isomerase with the archetypical /ß barrel protein,triose phosphate isomerase, reveals that the proteins overlapbest when the third (ß) strand of xylose isomeraseis superimposed on the first (ß) strand of triosephosphate isomerase. This same overlap has also been found betweenthe muconate lactonising enzyme and triose phosphate isomerase[Goldman et al. (1987) J. Mol. Biol., in press].     

Comparison of backbone structures of glucose isomerase from Streptomyces and Arthrobacter

The C backbones of the glucose isomerase molecules of Streptomycesrubiginosus and Arthrobacter have been determined by X-ray crystallographyand compared. Each molecule is a tetramer of eight-stranded/ß barrels, and the mode of association of the tetramersis identical in each case. The Arthrobacter electron densityshows four additional amino acids at the carboxyl terminus.There is also an insertion of six amino acids at position 277,and two individual insertions at about positions 348 and 357(numbering according to the Streptomyces structure). There isa close structural homology throughout the whole molecule, whichis most accurate up to position 325. The r.m.s. displacementfor 315 homologous C positions up to this position is 0.92 Å.     

The structure of a designed peptidomimetic inhibitor complex of {alpha}-thrombin

Thrombin displays remarkable specificity, effecting the removalof fibrinopeptides A and B of fibrinogen through the selectivecleavage of two Arg–Gly bonds between the 181 Arg/Lys–Xaabonds in fibrinogen. Significant advances have been made inrecent years towards understanding the origin of the specificityof cleavage of the Argl6–Gly17 bond of the A-chain ofhuman fibrinogen. We have previously proposed a model for thebound structure of fibrinopeptide A_7–16 (FPA), based uponNMR data, computer-assisted molecular modeling and the synthesisand study of peptidomimetic substrates and inhibitors of thrombin.We now report the structure of the ternary complex of an FPAmimetic (FPAM), hirugen and thrombin at 2.5 Å resolution(R-factor = 0.138) and specificity data for the inhibition ofthrombin and related trypsin-like proteinases by FPAM. The crystallographicstructures of FPA and its chloromethyl ketone derivative boundto thrombin were determined. Although there are differencesbetween these structures in the above modeled FPA structureand that of the crystal structure of FPAM bound to thrombin,the , angles in the critical region of P1–P2–P3in all of the structures are similar to those of bovine pancreatictrypsin inhibitor (BPTI) in the BPTI–trypsin complex andD–Phe–Pro–Arg (PPACK) in the PPACK–thrombinstructure. A comparison between these and an NMR-derived structureis carried out and discussed.     

Site-directed mutagenesis of pseudoazurin from Alcatigenes faecalis S-6; Pro80Ala mutant exhibits marked increase in reduction potential

Pseudoazurin (a blue copper protein or cupredoxin) of a denitrifyingbacterium Alcaligenes faecalis S-6 is a direct electron carrierfor a Cu-containing nitrite reductase (NIR) of the same organism.Site-directed mutagenesis of the pseudoazurin was carried outusing an Escherichia coli expression system. Replacement ofTyr74 by Phe to remove an internal hydrogen bond in the ß-barrelcaused a slight decrease in heat stability as well as a requirementfor a higher concentration of Cu²⁺ for production in the E.colihost. Exchange of Ala for Pro80 adjacent to His81, one of thefour ligands binding a type I Cu atom, caused a marked increasein reduction potential by 139 mV without change in the opticalabsorption spectrum. The ability of the pseudoazurin to transferelectrons to NIR was markedly diminished but the apparent K_mof NIR for pseudoazurin was not affected by the mutation. X-raydiffraction data collected on the oxidized and reduced formsof the Pro80Ala mutant show that a water molecule occupies thepocket created by the absent side chain. This observation suggeststhat the increase in reduction potential may be caused due tothe increased solvent accessibility to the Cu atom. The electrondensity difference maps on these structures (at 2.0 Å)show that this water moves during the change in oxidation state,and that there are small, but localized, conformational changes>6.5 Å from the copper site, as well as movement ofboth the Cu²⁺ and the cysteinate sulfur.     

Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase

Platelet-activating factor acetylhydrolases (PAF-AHs) are uniquePLA2s which hydrolyze the sn-2 ester linkage in PAF-like phospholipidswith a marked preference for very short acyl chains, typicallyacetyl. The recent solution of the crystal structure of the₁ catalytic subunit of isoform Ib of bovine brain intracellularPAF-AH at 1.7 Å resolution paved the way for a detailedexamination of the molecular basis of substrate specificityin this enzyme. The crystal structure suggests that the sidechains of Thr103, Leu48 and Leu194 are involved in substraterecognition. Three single site mutants (L48A, T103S and L194A)were overexpressed and their structures were solved to 2.3 Åresolution or better by X-ray diffraction methods. Enzyme kineticsshowed that, compared with wild-type protein, all three mutantshave higher relative activity against phospholipids with sn-2acyl chains longer than an acetyl. However, for each of themutants we observed an unexpected and substantial reductionin the V_max of the reaction. These results are consistent withthe model in which residues Leu48, Thr103 and Leu194 indeedcontribute to substrate specificity and in addition suggestthat the integrity of the specificity pocket is critical forthe expression of full catalytic function, thus conferring veryhigh substrate selectivity on the enzyme.     

The subunit structure of human macrophage migration inhibitory factor: evidence for a trimer

The subunit structure of human macrophage migration inhibitoryfactor (MIF) has been studied by preliminary X-ray analysisof wild-type and selenomethionine-MIF and dynamic light scattering.Crystal form I of MIF belongs to space group P2₁2₁2₁ and isgrown from 2 M ammonium sulfate at pH 8.5. A native data sethas been collected to 2.4 Å resolution. Self-rotationstudies and V_m values indicate that three molecules per asymmetricunit are present A data set to 2.8 Å resolution has beencollected for crystal form II, which belongs to space groupP3¹21 or P3²21 and grows from 2 M ammonium sulfate, 2% polyethyleneglycol (average molecular mass 400), 0.1 M HEPES, pH 7.5. Three,four, five or six monomers in the asymmetric unit are consistentwith V_m values for this crystal form. Analysis of crystal formII containing selenomethionine-MIF indicates nine selenium sitesare present per asymmetric unit. Dynamic light scattering ofMIF suggests that the major form of the protein in solutionis a trimer. The results of these studies are in contrast toprevious reports indicating that MIF is a monomer or dimer.The subunit arrangement of MIF is similar to that of tumor necrosisfactor and suggests that signal transduction might require trimerizationof receptor subunits.     

The structure-function relationship of the lipases from Pseudomonas aeruginosa and Bacillus subtilis

Within the BRIDGE T-project on lipases we investigate the structure-functionrelationships of the lipases from Bacillus subtilis and Pseudomonasaeruginosa. Construction of an overproducing Bacillus. strainallowed the purification of > 100 mg lipase from 30 l culturesupernatant. After testing a large variety of crystallizationconditions, the Bacillus lipase gave crystals of reasonablequality in PEG-4000 (38-45%), Na₂SO₄ and octyl-ß-glucosideat 22°C, pH 9.0. A 2.5 Å; dataset has been obtainedwhich is complete from 15 to 2.5 A resolution. P.aeruginosawild-type strain PAC1R was fermented using conditions of maximumlipase production. More than 90% of the lipase was cell boundand could be solubilized by treatment of the cells with TritonX-100. This permitted the purification of 50 mg lipase. So far,no crystals of sufficient quality were obtained. Comparisonof the model we built for the Pseudomonas lipase, on the basisof sequences and structures of various hydrolases which werefound to possess a common folding pattern (/ß hydrolasefold), with the X-ray structure of the P.glumae lipase revealedthat it is possible to correctly build the structure of thecore of a protein even in the absence of obvious sequence homologywith a protein of known 3-D structure.     

Peroxynitrite modification of glutathione reductase: modeling studies and kinetic evidence suggest the modification of tyrosines at the glutathione disulfide binding site

The catalytic properties of glutathione reductase for its substrate,glutathione disulfide, were altered following a 60 s exposureto a 100-fold molar excess of peroxynitrite; the K_M value wasincreased by {small tilde}2.5-fold and the V_max value was decreasedby {small tilde}1.7-fold. The kinetic alterations are thoughtto result from nitrotyrosine formation as the intrinsic Tyrfluorescence is diminished. The UV-visible spectrum of glutathionereductase exhibited absorbance at {small tilde}423 nm, characteristicof nitrotyrosine. In addition, the presence of nitrotyrosinehas been detected by Western immunoblots with an anti-nitrotyrosineantibody. The peroxynitrite-induced inactivation is not observedin the presence of excess glutathione disulfide. However, excessNADPH offered no protection against peroxynitriteinduced inactivation.These observations suggest that the modification of {small tilde}1.8Tyr per subunit, at or near the glutathione disulfide bindingdomain, probably results in the observed catalytic alterations.To test this hypothesis, the two tyrosines closest to the glutathionedisulfide binding domain (Tyr114 and Tyr106), as indicated bythe X-ray crystallographic data [Karplus and Schulz (1989) J.Biol. Chem, 210,163–180], were each converted to nitrotyrosinesby molecular modeling and the structure energy was minimized.These theoretical calculations indicate that the bond lengthsbetween Tyr114-O and the Gly-N and Cys II-N of glutathione disulfidebound to glutathione reductase (Karplus and Schulz, 1989) increasedby 3.0 and 4.3 Å, respectively, upon nitration. In thecase of Tyr106, the O–Cys II-N distance also increasesby {small tilde}1.6 Å. The loss of these hydrogen bondingcontacts is likely to result in the observed catalytic alterationsupon reaction with peroxy-nitrite.     

Evolutionary divergence and conservation of trypsin

The trypsin sequences currently available in the data bankshave been collected and aligned using first the amino acid sequencehomology and, subsequently, the superposed crystal structuresof trypsins from the cow, the bacterium Streptomyces griseusand the fungus Fusarium oxysporum. The phylogenetic tree constructedaccording to this multiple alignment is consistent with a continuousevolutionary divergence of trypsin from a common ancestor ofboth prokaryotes and eukaryotes. Comparison of crystal structuresreveals a strict conservation of secondary structure. Similarly,in the alignment of all the sequences, insertions and deletionsoccur only in regions corresponding to loops between the secondarystructure elements in the known crystal structures. The conservedresidues cluster around the active site. Almost all conservedresidues can be associated with one of the basic functionalfeatures of the protein: zymogen activation, catalysis and substratespecificity. In contrast, the residues of the hydrophobic coreof the protein and the calcium ion binding sites are generallynot conserved. The conserved features of trypsin and the natureof the conservation are discussed In detail     

3-D structure of the D153G mutant of Escherichia coli alkaline phosphatase: an enzyme with weaker magnesium binding and increased catalytic activity

The substitution of aspartate at position 153 in Escherichiacoli alkaline phosphatase by glycine results in a mutant enzymewith 5-fold higher catalytic activity (k_cat but no change inKm at pH 8.0 in 50 mM Tris-HCl. The increased k_cat is achievedby a faster release of the phosphate product as a result ofthe lower phosphate affinity. The mutation also affects Mg²⁺binding, resulting in an enzyme with lower metal affinity. The3-D X-ray structure of the D153G mutant has been refined at2.5 Å to a crystallographic Rfactor of 16.2%. An analysisof this structure has revealed that the decreased phosphateaffinity is caused by an apparent increase in flexibility ofthe guanidinium side chain of Argl66 involved in phosphate binding.The mutation of Aspl53 to Gly also affects the position of thewater ligands of Mg²⁺, and the loop Glnl52–Thrl55 is shiftedby 0.3 Å away from the active site. The weaker Mg²⁺ bindingof the mutant compared with the wild type is caused by an alteredcoordination sphere in the proximity of the Mg²⁺ ion, and alsoby the loss of an electrostatic interaction (Mg²⁺.COO^-Aspl53)in the mutant Its ligands W454 and W455 and hydroxyl of Thrl55,involved in the octahedral coordination of the Mg²⁺ ion, arefurther apart in the mutant compared with the wild-type     

Interactions of (Ala*Ala*Lys*Pro)n and (Lys*Lys*Ser*Pro)n with DNA. Proposed coiled-coil structure of AlgR3 and AlgP from Pseudomonas aeruginosa

The proteins, AlgR3 and AlgP, are involved in the regulationof alginate synthesis in Pseudomonas. They contain multiplerepeats of Ala^*Ala^*Lys^*Pro as do several other proteins thatresemble histones. The interactions of synthesis oligopeptidescomposed of repeated Ala^*Ala^*Lys^*Pro or Lys^*Lys^*Ser^*Pro unitswith DNA were studied by fluorescence of the Fmoc (9-fluorenylmethyloxycarbonyl)group attached to the N-termini of the peptides. DNA quenchingof the Fmoc fluorescence of the peptides was used to estimatethe apparent association constants for the interaction of Fmoc(AAKP)_nOH(n = 2, 4, 8, 18, 32) and of Fmoc(KKSP)_nOH (n = 2, 4, 8, 16,20, 32) with DNA. The Fmoc(AAKP)_nOH peptides bind to DNA onlyat low ionic strength; the Fmoc(KKSP)_n OH peptides interactwith DNA at both low (0.05 M KCl) and high (0.2 M KCl) saltAt low ionic strength an increase in the number of the repeatunits causes an increase in the apparent association constantup to {small tilde}2 x 10⁶ M^–1 for both types of peptidesat N 24. The insertion of an AAKTA unit into the middle ofthe Fmoc(AAKP)₈OH peptide increases its affinity to DNA. Wepropose a model of (AAKP)_n and of its interaction with DNA.The repeat unit consists of a single turn of -helix followedby a bend necessitated by Pro. The resultant coiled-coil formsa right-handed superhelix with 10 AAKPs per repeat distanceof {small tilde}33 Å. With only slight modification ofthe canonical parameters of this model the AAKP super helixfits into the major groove of B-form DNA with one AAKP tetramerper base pair repeat of 3.4 Å. The -amine nitrogen ofLys can form a polar hydrogen bond with a phosphate oxygen atomof the DNA backbone. A better fit is obtained when the modelis modified to accommodate [(AAKP)₅AAKTA]_n as actually observedin AlgR3. We suggest that this coiled-coil represents a generalmotif for other protein–DNA interactions.     

The X-ray structure of (MeBm2t)1-cyclosporin complexed with cyclophilin A provides an explanation for its anomalously high immunosuppressive activity

For most of the cyclosporin A (CsA) analogs, there is generallya good correlation between cyclophilin binding and immunosuppression.However, this relationship does not seem to hold for 4-[(E)-2-butenyl]-4,4,N-trimethyl-L-threonine¹(MeBm₂t)¹-CsA.Its affinity for cyclophilin was reported to be {small tilde}1percent; that of CsA and its immunosuppressive activity invitro was shown to be {small tilde} 30% that of CsA. We reporthere the crystal structure of a complex between recombinanthuman cyclophilin A (CypA) and (MeBm₂t)¹-CsA which has beendetermined by X-ray crystallography at 2.2 Å resolutionand refined to an Rfactor of 16.3%. (MeBm₂t)¹-CsA shows a similarbound conformation and network of interactions to CypA as CsA.The measured lower affinity for CypA cannot therefore be explainedby a different mode of binding. We propose that the poor affinityto CypA could be accounted for by the existence of an equilibriumin aqueous solution between a ‘cyclophilin bound conformation’and a ‘nonbinding conformation’ of (MeBm₂t)¹-CsA.The relatively high immunosuppressive activity is suggestedto result from slight conformational differences observed inthe effector domain     

Dissimilarity in the oxidative folding of onconase and ribonuclease A, two structural homologues

The oxidative folding of frog onconase (ONC), a member of theribonuclease A family, was examined and shows markedly differentbehavior compared to its structural homologue bovine pancreaticribonuclease A (RNase A) under similar conditions. Applicationof a reduction pulse (using a small amount of reduced dithiothreitol)during the oxidative regeneration of ONC indicated the survivalof the native protein along with three other (structured) species,I₁, I₂ and I₃, with the rest of the unstructured species beingconverted to fully reduced protein. Mass spectrometry indicatesthat I₁ has two disulfide bonds, whereas I₂ and I₃ have threedisulfide bonds each. A disulfide mapping method, based on cyanylation,was used to identify I₂ and I₃ as des-[30–75] and des-[19–68],respectively. On enzymatic digestion using trypsin, I₁ was identifiedas des-[19–68, 30–75]. Differences in the intermediatesthat are generated during the oxidative folding of the two structuralhomologues, RNase A and ONC, demonstrate that regenerative pathwaysare not necessarily influenced by tertiary structure. This indicatesthat the lack of a disulfide bond in ONC, analogous to the (65–72)disulfide bond in RNase A which plays an important role in itsoxidative regeneration, does not adversely affect the oxidativefolding of ONC.     

Determination of the pKa values of titratable groups of an antigen-antibody complex, HyHEL-5-hen egg lysozyme

The titration behavior of the ionizable residues of the HyHEL-5–henegg lysozyme complex and its individual components has beenstudied using continuum electrostatic calculations. Severalresidues of HyHEL-5 had pK_a values shifted away from model valuesfor isolated residues by more than three pH units. Shifts awayfrom the model values were smaller for the residues of hen egglysozyme. A moderate variation in the pK_a values of the titratablegroups was observed upon increase of the ionic strength from0 to 100 mM, amounting to 1–2 pH units in most cases.Under physiological conditions, the net charge of HyHEL-5 wasopposite that for hen egg lysozyme. Several residues, includingthose involved in the Arg–Glu salt bridges that have beenproposed to be important in antibody-antigen binding, had pK_avalues that were changed significantly upon binding. The maintitration event upon antibody-antigen binding appears to beloss of a proton from residue GluH50 of the Fv molecule. Thelimitations of our calculation methods and the role they mightplay in the design of antibodies for use in assays, sensorsand separations are discussed     

High-level expression, purification, kinetic characterization and crystallization of protein farnesyltransferase -subunit C-terminal mutants

Protein farnesyltransferase (FPT) is a 97 000 Da heterodimericenzyme that catalyzes post-translational farnesylation of manycellular regulatory proteins including p21 Ras. To facilitatethe construction of site-directed mutants, a novel translationallycoupled, two-cistron Escherichia coli expression system forrat FPT has been developed. This expression system enabled yieldsof >5 mg of purified protein per liter of E.coli cultureto be obtained. The E.coli-derived FPT demonstrated an activitycomparable to that of protein isolated from other sources. Thereported expression system was used to construct three ß-subunitC-terminal truncation mutants, 5, 10 and 14, which were designedto eliminate a lattice interaction between the ß-subunitC-terminus of one molecule and the active site of a symmetry-relatedmolecule. Steady-state kinetic analyses of these mutants showedthat deletion up to 14 residues at the C-terminus did not reducethe value of k_cat; however, K_m values for both peptide and FPPincreased 2–3-fold. A new crystalline form of FPT was obtainedfor the 10 C-terminal mutant grown in the presence of the substrateanalogs acetyl-Cys-Val-Ile-Met-COOH peptide and -hydroxyfarnesylphosphonicacid. The crystals diffract to beyond 2.0 Å resolution.The refined structure clearly shows that both substrate analogsadopt extended conformations within the FPT active site cavity.     

Ligand-induced conformational changes in wild-type and mutant yeast pyruvate kinase

A mutant form of pyruvate kinase in which serine 384 has beenmutated to proline has been engineered in the yeast Saccharomycescerevisiae. Residue 384 is located in a helix in a subunit interfaceof the tetrameric enzyme, and the mutation was anticipated toalter the conformation of the helix and hence destabilize theinterface. Previous results indicate that the mutant favoursthe T quarternary conformation over the R conformation, andthis is confirmed by the results presented here. Addition ofphosphoenol-pyruvate (PEP), ADP and fructose-1,6-bisphosphate(Fru 1,6-P₂) singly to the wild-type and mutant enzymes resultsin a significant quenching of tryptophan fluorescence (12–44%),and for Fru-1,6-P₂, a red shift of 15 nm in the emission maximum.Fluorescence titration experiments showed that PEP, ADP andFru-1,6-P₂ induce conformations which have similar ligand-bindingproperties in the wild-type and mutant enzymes. However, theFru-1,6-P₂ induced conformation is demonstrably different fromthose induced by either ADP or PEP. The enzymes differ in theirsusceptibility to trypsin digestion and N-ethylmaleimide inhibition.The thermal stability of the enzyme is unaltered by the mutantion.Far-UV CD spectra show that both enzymes adopt a similar overallsencondary structure in solution. Taken together, the resultssuggest that the Ser384-Pro mutaion causes the enzyme to adopta diffenrent tertiary and/or quaternary structure from the wild-typeenzyme and affects the type and extent of the conformationalchanges induced in the enzyme upon ligand binding. A simplifiedminimal reaction mechanism is proposed in which the R and Tstates differ in both affinity and K_cat. Thus, in terms of themodels of cooperativity and allsoteric interaction, pyruvatekinase is both a K and a V system.     

Testing the procedure of simulated annealing by refining homologous immunoglobulin light-chain dimers

The refinement of antigen-binding fragment structures by themethod of simulated annealing was tested. Using the programX-PLOR, we refined the structure of one immunoglobulin light-chaindimer against 2.8 Å diffraction data collected for a homologouslight-chain dimer. The refinement proceeded smoothly; -carbonsof the conserved segments of the domain moved to the positionsin the reference structure solved independently. An averagemovement of –1.5 Å for atoms in the variable domains(half of the molecule) was observed. Though the final R-factorsand energy terms of the reference and test structures were verysimilar, some of the chain segments of the hypervariable loops(HVR3s₃) and the ends of some side chains did not converge tothe positions in the reference structure. Therefore, althoughglobally the refinement worked very well, positions of the loopsand the side chains that are critical for immunoglobulin functionhave to be carefully examined by difference Fourier techniques.