Improvement of binding of Puumala virus neutralization site resembling peptide with a second-generation phage library

We have previously selected a peptide insert FPCDRLSGYWERGIPSPCVRrecognizing the Puumala virus (PUUV) G2-glycoprotein-specificneutralizing monoclonal antibody (MAb) 1C9 with K_d of 2.85x10^–8from a random peptide library X₂CX₁₄CX₂ expressed on the pIIIprotein of the filamentous phage fd-tet. We have now createda second-generation phage-displayed peptide library in whicheach amino acid of the peptide was mutated randomly to anotherwith a certain probability. Peptides were selected for higheraffinity for MAb 1C9 and for a common binding motif for MAb4G2 having an overlapping epitope with MAb 1C9 in G2 glycoprotein.The resulting peptides were synthesized as spots on cellulosemembrane. Amino acid changes which improved the reactivity ofthe peptides to MAb 1C9 were combined in the peptide ATCDKLFGYYERGIPLPCALwith K_d of 1.49x10^–9 in biosensor measurements. Our resultsshow that the binding properties of peptides, the affinity andthe specificity can be improved and the binding specificitydetermining amino acids and structural factors can be analyzedby combining binding assays with synthetic peptides on membranewith the use of second-generation phage display libraries. Received October 18, 2002; revised April 16, 2003; accepted May 26, 2003.     

VL position 34 is a key determinant for the engineering of stable antibodies with fast dissociation rates

Predictive engineering of antibodies exhibiting fast kineticproperties could provide reagents for biotechnological applicationssuch as continuous monitoring of compounds or affinity chromatography.Based on covariance analysis of murine germline antibody variabledomains, we selected position L34 (Kabat numbering) for mutationalstudies. This position is located at the VL/VH interface, atthe base of the paratope but with limited antigen contacts,thus making it an attractive position for mild alterations ofantigen binding properties. We introduced a serine at positionL34 in two different antibodies: Fab (fragment antigen binding)57P (Asn34Ser) and scFv (single chain fragment variable) 1F4(Gln34Ser), that recognize peptides derived from the coat proteinof tobacco mosaic virus and the oncoprotein E6, respectively.Both mutated antibodies exhibited similar properties: (i) expressionlevels of active fragments in Escherichia coli were markedlyimproved; (ii) thermostability was enhanced; and (iii) dissociationrate parameters (k_off) were increased by 2- and at least 57-foldfor scFv1F4 and Fab57P, respectively, while their associationrate parameters (k_on) remained unchanged. The L34 Ala and Thrmutants of both antibody fragments did not possess these properties.This first demontration of similar effects observed in two antibodieswith different specificities may open the way to the predictivedesign of molecules with enhanced stability and fast dissociationrates. Received October 3, 2002; revised March 7, 2003; accepted April 4, 2003.     

Inhibition of the CD28-CD80 co-stimulation signal by a CD28-binding affibody ligand developed by combinatorial protein engineering

CD28 is one of the key molecules for co-stimulatory signallingin T cells. Here, novel ligands (affibodies) showing selectivebinding to human CD28 (hCD28) have been selected by phage displaytechnology from a protein library constructed through combinatorialmutagenesis of a 58-residue three-helix bundle domain derivedfrom staphylococcal protein A. Analysis of selected affibodiesshowed a marked sequence homology and biosensor analyses showedthat all investigated affibodies bound to hCD28 with micromolaraffinities (K_D). No cross-reactivity towards the related proteinhuman CTLA-4 could be observed. This lack of cross-reactivityto hCTLA-4 suggests that the recognition site on hCD28 for theaffibodies resides outside the conserved MYPPPYY motif. Theapparent binding affinity for hCD28 could be improved throughfusion to an Fc fragment fusion partner, resulting in a divalentpresentation of the affibody ligand. For the majority of selectedanti-CD28 affibodies, in co-culture experiments involving JurkatT-cells and CHO cell lines transfected to express human CD80(hCD80) or LFA-3 (hLFA-3) on the cell surface, respectively,pre-incubation of Jurkat cells with affibodies resulted in inhibitionof IL-2 production when they were co-cultured with CHO (hCD80⁺)cells, but not with CHO (hLFA-3⁺) cells. For one affibody variantdenoted Z_CD28:5 a clear concentration-dependent inhibition wasseen, indicating that this affibody binds hCD28 and specificallyinterferes in the interaction between hCD28 and hCD80. Received March 11, 2003; revised June 30, 2003; accepted July 30, 2003.     

Differential effects of zinc on functionally distinct human growth hormone mutations

Human growth hormone (hGH) binds and activates lactogenic receptorsby a sequential receptor dimerization mechanism. The affinityfor the first lactogenic receptor is increased due to one zincmolecule linking hGH residues H18 and E174, located in helices1 and 4, respectively, with two adjacent residues in the lactogenicreceptor (D187 and H188). Two functionally unique groups ofmutant hGHs have been identified. Addition of 25 µM zincto lactogenic bioassays differentially affects mutant activitiesbased on which group they belong to. One mutation (G120R) islocated within the binding surface of hGH that interacts withthe second lactogenic receptor. In the presence of endogenouszinc, G120R reduces the maximal activity of hGH without alteringeither the agonist or antagonist phases of the bell-shaped dose–responsecurve. Addition of zinc to this assay further reduces the activityof this protein. In contrast, mutations within a hydrophobicmotif in hGH that functionally couples the two lactogenic receptorbinding sites decrease the sensitivity (right-shift) of theagonist phase of the dose–response curve without similarlyaffecting the antagonist phase. The addition of zinc to theselactogenic assays increases the sensitivity (left-shifts) ofthe dose–response curves, largely negating the effectof these mutations. The effects of zinc differentiate betweenmutations within these two distinct functional motifs by limitingthe pool of potential conformations that are available for bindingwithin either of the receptor binding sites of this ligand. Received April 10, 2003; revised June 7, 2003; accepted June 8, 2003.     

Purinergic Signaling: Impact of GPCR Structures on Rational Drug Design

The purinergic signaling system includes membrane-bound receptors for extracellular purines and pyrimidines, and enzymes/transporters that regulate receptor activation by endogenous agonists. Receptors include: adenosine (A₁, A_2A, A_2B, and A₃) and P2Y (P2Y₁, P2Y₂, P2Y₄, P2Y₆, P2Y₁₁, P2Y₁₂, P2Y₁₃, and P2Y₁₄) receptors (all GPCRs), as well as P2X receptors (ion channels). Receptor activation, especially accompanying physiological stress or damage, creates a temporal sequence of signaling to counteract this stress and either mobilize (P2Rs) or suppress (ARs) immune responses. Thus, modulation of this large signaling family has broad potential for treating chronic diseases. Experimentally determined structures represent each of the three receptor families. We focus on selective purinergic agonists (A₁, A₃), antagonists (A₃, P2Y₁₄), and allosteric modulators (P2Y₁, A₃). Examples of applying structure-based design, including the rational modification of known ligands, are presented for antithrombotic P2Y₁R antagonists and anti-inflammatory P2Y₁₄R antagonists and A₃AR agonists. A₃AR agonists are a potential, nonaddictive treatment for chronic neuropathic pain.     

A grafting approach to obtain site-specific metal-binding properties of EF-hand proteins

The EF-hand calcium-binding loop III from calmodulin was insertedwith glycine linkers into the scaffold protein CD2.D1 at threelocations to study site-specific calcium binding propertiesof EF-hand motifs. After insertion, the host protein retainsits native structure and forms a 1:1 metal–protein complexfor calcium and its analog, lanthanum. Tyrosine-sensitized Tb³⁺energy transfer exhibits metal binding and La³⁺ and Ca²⁺ competefor the metal binding site. The grafted EF-loop III in differentenvironments has similar La³⁺ binding affinities, suggestingthat it is largely solvated and functions independently fromthe host protein. Received May 25, 2002; revised January 23, 2003; accepted April 25, 2003.     

Bivalent Argininamide‐Type Neuropeptide Y Y1 Antagonists Do Not Support the Hypothesis of Receptor Dimerisation

Bivalent ligands are potential tools to investigate the dimerisation of G‐protein‐coupled receptors. Based on the (R)‐argininamide BIBP 3226, a potent and selective neuropeptide Y Y₁ receptor (Y₁R) antagonist, we prepared a series of bivalent Y₁R ligands with a wide range of linker lengths (8–36 atoms). Exploiting the high eudismic ratio (>1000) of the parent compound, we synthesised sets of R,R‐, R,S‐ and S,S‐configured bivalent ligands to gain insight into the “bridging” of two Y₁Rs by simultaneous interaction with both binding sites of a putative receptor dimer. Except for the S,S isomers, the bivalent ligands are high‐affinity Y₁R antagonists, as determined by Ca²⁺ assays on HEL cells and radioligand competition assays on human Y₁R‐expressing SK‐N‐MC and MCF‐7 cells. Whereas the R,R enantiomers are most potent, no marked differences were observed relative to the corresponding meso forms. The difference between R,R and R,S diastereomers was most pronounced (about sixfold) in the case of the Y₁R antagonist containing a spacer of 20 atoms in length. Among the R,R enantiomers, linker length and structural diversity had little effect on Y₁R affinity. Although the bivalent ligands preferentially bind to the Y₁R, the selectivity toward human Y₂, Y₄, and Y₅ receptors was markedly lower than that of the monovalent argininamides. The results of this study neither support the presence of Y₁R dimers nor the simultaneous occupation of both binding pockets by the twin compounds. However, as the interaction with Y₁R dimers cannot be unequivocally ruled out, the preparation of a bivalent radioligand is suggested to determine the ligand–receptor stoichiometry. Aiming at such radiolabelled pharmacological tools, prototype twin compounds were synthesised, containing an N‐propionylated amino‐functionalised branched linker (K_i≥18 nM ), a tritiated form of which can be easily prepared.     

The structural roles of conserved Pro196, Pro197 and His199 in the mechanism of thymidylate synthase

We generated replacement sets for three highly conserved residues,Pro196, Pro197 and His199, that flank the catalytic nucleophile,Cys198. Pro196 and Pro197 have restricted mobility that couldbe important for the structural transitions known to be essentialfor activity. To test this hypothesis we obtained and characterized13 amino acid substitutions for Pro196, 14 for Pro197 and 14for His199. All of the Pro196 and Pro197 variants, except P197R,and four of the His199 variants complemented TS-deficient Escherichiacoli cells, indicating they had at least 1% of wild-type activity.For all His199 mutations, k_cat/K_m for substrate and cofactordecreased more than 40-fold, suggesting that the conserved hydrogenbond network co-ordinated by His199 is important for catalysis.Pro196 can be substituted with small hydrophilic residues withlittle loss in k_cat, but 15- to 23-fold increases in K_m^dUMP.Small hydrophobic substitutions for Pro197 were most active,and the most conservative mutant, P197A, had only a 5-fold lowerk_cat/K_m^dUMP than wild-type TS. Several Pro196 and Pro197 variantswere temperature sensitive. The small effects of Pro196 or Pro197mutations on enzyme kinetics suggest that the conformationalrestrictions encoded by the Pro–Pro sequence are largelymaintained when either member of the pair is mutated. Received February 24, 2003; revised June 19, 2003; accepted June 20, 2003.     

Structure-oriented rational design of chymotrypsin inhibitor models

Three peptides modelling a highly potent, 35-residue chymotrypsininhibitor (Schistocerca gregaria chymotrypsin inhibitor) weredesigned and synthesized by convergent peptide synthesis. Foreach model peptide, the inhibitory constant (K_i) on chymotrypsinand the solution structure were determined. In addition, moleculardynamics calculations were performed for all of them. Two modelscontaining approximately half of the parent inhibitor (17 of35 residues) were designed and subsequently found to have nosubstantial inhibitory activity (K_i values in the mM range).The third model composed of 24 amino acid residues proved tobe an effective (K_i 10^–7) inhibitor of bovine chymotrypsin.Both the solution structure properties determined by NMR spectroscopyand the dynamic behaviour of the latter model system are comparableto the native inhibitor. In contrast, the structure and dynamicsof the first two related model peptides show characteristicdifferences. We suggest that the conformation and flexibilityof the modelled protease inhibitor are crucial for its biologicalefficiency. Moreover, the structural and dynamic features ofthe binding loop (28–33) and those of the rest of themolecule appear to be interdependent. Most importantly, thesestructural characteristics can be rationally modified, at leastpartially, by peptide design. Received March 7, 2003; revised August 25, 2003; accepted August 26, 2003.     

An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins

A computer program system was developed to predict carbohydrate-bindingsites on three-dimensional (3D) protein structures. The programssearch for binding sites by referring to the empirical rulesderived from the known 3D structures of carbohydrate–proteincomplexes. A total of 80 non-redundant carbohydrate–proteincomplex structures were selected from the Protein Data Bankfor the empirical rule construction. The performance of theprediction system was tested on 50 known complex structuresto determine whether the system could detect the known bindingsites. The known monosaccharide-binding sites were detectedamong the best three predictions in 59% of the cases, whichcovered 69% of the polysaccharide-binding sites in the targetproteins, when the performance was evaluated by the overlapbetween residue patches of predicted and known binding sites. Received April 24, 2003; revised June 2, 2003; accepted June 10, 2003.     

六氨氯化镁热解过程及其非等温动力学

利用热重（TG）分析技术对六氨氯化镁的热分解过程及动力学进行了研究,考察了六氨氯化镁在4、7、10、13、16 K·min^-1线性升温速率和空气气氛下热分解机理,六氨氯化镁热解过程分为3个阶段。提出了一种整体优化的多升温速率迭代的等转化率求取活化能方法,采用该方法,得到六氨氯化镁热解3个阶段的活化能分别为51.38、64.70、73.55 kJ·mol^-1。采用整体优化的多升温速率等温法确立了六氨氯化镁热解3个阶段的热解机理函数与指前因子：第1步反应的热解机理属于固体相边界反应机理（n=1/4）,指前因子为3.281×10⁵ s^-1;第2步反应的热解机理属成核与生长机理（n=1.8）,指前因子为5.624×10⁶ s^-1;第3步反应属化学反应机理（1.5级反应）,指前因子为5.862×10⁵ s^-1。     

Mapping the Binding Sites of UDP and Prostaglandin E2 Glyceryl Ester in the Nucleotide Receptor P2Y6

Cyclooxygenase-2 catalyzes the biosynthesis of prostaglandins from arachidonic acid and the biosynthesis of prostaglandin glycerol esters (PG-Gs) from 2-arachidonoylglycerol. PG-Gs are mediators of several biological actions such as macrophage activation, hyperalgesia, synaptic plasticity, and intraocular pressure. Recently, the human UDP receptor P2Y₆ was identified as a target for the prostaglandin E2 glycerol ester (PGE₂-G). Here, we show that UDP and PGE₂-G are evolutionary conserved endogenous agonists at vertebrate P2Y₆ orthologs. Using sequence comparison of P2Y₆ orthologs, homology modeling, and ligand docking studies, we proposed several receptor positions participating in agonist binding. Site-directed mutagenesis and functional analysis of these P2Y₆ mutants revealed that both UDP and PGE₂-G share in parts one ligand-binding site. Thus, the convergent signaling of these two chemically very different agonists has already been manifested in the evolutionary design of the ligand-binding pocket.     

Isolation from phage display libraries of lysine-deficient human epidermal growth factor variants for directional conjugation as targeting ligands

Ligand-targeted anticancer therapeutics represent an opportunityfor the selective and efficient delivery of drugs to tumours.The chemical coupling of ligands to drugs or drug carrier systemsis, however, often hampered by the presence of multiple reactivegroups within the ligand, for example, -NH₂ groups in lysineside chains. In this paper, we describe the isolation by phagedisplay of human epidermal growth factor (EGF) variants withoutlysine and a reduced number of arginine residues. The selectionon A431 carcinoma cells also revealed that R41 is indispensablefor EGF binding activity as all EGF variants contained an arginineresidue at this position. One EGF variant (EGFm1) with K28Q,R45S, K48S and R53S mutations was expressed in bacteria andshowed an identical binding activity as wild-type EGF. EGFm1could be labelled with fluorescein isothiocyanate demonstratingthe accessibility of the N-terminal amino group for couplingreagents. Furthermore, coupling of EGFm1 to PEGylated liposomesresulted in target cell-specific binding and internalizationof the liposomes. These human EGF variants should be advantageousfor the generation of anticancer therapeutics targeting theEGF receptor, which is overexpressed by a wide variety of differenttumours. Received July 8, 2003; revised October 23, 2003; accepted October 30, 2003     

Simple consensus procedures are effective and sufficient in secondary structure prediction

We have analyzed the performance of majority voting on minimalcombination sets of three state-of-the-art secondary structureprediction methods in order to obtain a consensus prediction.Using three large benchmark sets from the EVA server, our resultsshow a significant improvement in the average Q₃ predictionaccuracy of up to 1.5 percentage points by consensus formation.The application of an additional trivial filtering procedurefor predicted secondary structure elements that are too short,does not significantly affect the prediction accuracy. Our analysisalso provides valuable insight into the similarity of the resultsof the prediction methods that we combine as well as the higherconfidence in consistently predicted secondary structure. Received March 7, 2003; revised May 24, 2003; accepted June 6, 2003.     

Catalytic mechanism of fungal glucoamylase as defined by mutagenesis of Asp176, Glu179 and Glu180 in the enzyme from Aspergillus awamori

Asp176, Glu179 and Glu180 of Aspergillus awamori glucoamylaseappeared by differential labeling to be in the active site.To test their functions, they were replaced by mutagenesis withAsn, Gln and Gln respectively, and kinetic parameters and pHdependencies of all enzyme forms were determined. Glu179 –Gln glucoamylase was not active on maltose or isomaltose, whilethe k_cat for maltoheptaose hydrolysis decreased almost 2000-foldand the K_M was essentially unchanged from wild-type glucoamylase.The Glu180 – Gln mutation drastically increased the K_Mand moderately decreased the k_cat with maltose and maltoheptaose,but affected isomaltose hydrolysis less. Differences in substrateactivation energies between Glu180 – Gln and wild-typeglucoamylases indicate that Glu180 binds D-glucosyl residuesin subsite 2. The Asp176 – Asn substitution gave moderateincreases and decreases in K_M and k_cat respectively, and thereforesimilar increases in activation energies for the three substrates.This and the differences in subsite binding energies betweenAsp176 – Asn and wild-type glucoamylases suggest thatAsp176 is near subsite 1, where it stabilizes the transitionstate and interacts with Trp120 at subsite 4. Glu179 and Asp176are thus proposed as the general catalytic acid and base ofpK_a 5.9 and 2.7 respectively. The charged Glu180 contributesto the high pK_a value of Glul79. Received May 25, 1989; accepted October 19, 1989.     

Role of tryptophan 121 in the soluble CuA domain of cytochrome c oxidase: structure and electron transfer studies

To investigate the contribution of tryptophan-121 (Trp121) residueto the structure and function of soluble Cu_A domain of cytochromec oxidase, three mutant proteins, Trp121Tyr, Trp121Leu and Trp121-deletedmutant of the soluble domain of Paracoccus versutus cytochromec oxidase, were constructed and expressed in Escherichia coliBL21 (DE3). Optical spectral studies showed that both the coordinationstructure of the Cu_A center and the secondary structure of theprotein were changed significantly in the Leu substitution anddeletion mutants of Trp121. Their electron transfer activitywith cytochrome c was inhibited severely, as shown in stopped-flowkinetic studies. However, the Cu_A center can be reconstructedin the Trp121Tyr mutant although its stability decreases comparedwith the wild-type protein. This mutant keeps the same secondarystructure as the wild-type protein, but can only transfer electronswith cytochrome c at a rate of one-seventh-fold. Based on theinformation on the structure, we also investigated and analyzedthe possible factors that affect electron transfer. It appearsthat the aromatic ring, the size of the side chain and the hydrogenbonding ability of the Trp121 are crucial to the structure andfunction of the soluble Cu_A domain. Received September 11, 2002; revised February 26, 2003; accepted May 27, 2003.     

Stabilization of a chitinase from Serratia marcescens by Gly->Ala and Xxx->Pro mutations

This paper describes attempts to increase the kinetic stabilityof chitinase B from Serratia marcescens (ChiB) by the introductionof semi-automatically designed rigidifying mutations of theGlyAla and XxxPro type. Of 15 single mutants, several displayedsignificant increases in thermal stability, whereas most mutantsshowed minor effects. All mutations with non-marginal effectson stability clustered in a limited, surface-exposed regionof the enzyme, indicating that this region is involved in apartial unfolding process that triggers irreversible thermalinactivation (aggregation). A double mutant containing two stabilizingmutations in this region (G188A, A234P) displayed a 10-foldincrease in half-life at 57°C and a 4.2°C increase inapparent T_m. These results show that entropic stabilizationworks well for ChiB and they pinpoint a region whose unfoldingmay be crucial for the kinetic stability of this enzyme. Received June 18, 2003; revised September 3, 2003; accepted September 12, 2003.     

Effect of mutations involving charged residues on the stability of staphylococcal nuclease: a continuum electrostatics study

A continuum electrostatics model is used to calculate the relativestabilities of 117 mutants of staphylococcal nuclease (SNase)involving the mutation of a charged residue to an unchargedresidue. The calculations are based on the crystallographicstructure of the wild-type protein and attempt to take implicitlyinto account the effect of the mutations in the denatured stateby assuming a linear relationship between the free energy changescaused by the mutation in the native and denatured states. Agood correlation (linear correlation coefficient of 0.8) isfound with published experimental relative stabilities of thesemutants. The results suggest that in the case of SNase (i) chargedresidues contribute to the stability of the native state mainlythrough electrostatic interactions, and (ii) native-like electrostaticinteractions may persist in the denatured state. The continuumelectrostatics method is only moderately sensitive to modelparameters and leads to quasi-predictive results for the relativemutant stabilities (error of 2–3 kJ mol^–1 or ofthe order of k_BT), except for mutants in which a charged residueis mutated to glycine. Received March 24, 2003; revised August 11, 2003; accepted September 12, 2003.     

Shuttling of Peptide-Drug Conjugates by G Protein-Coupled Receptors Is Significantly Improved by Pulsed Application

G protein-coupled receptors (GPCRs) can be used to shuttle peptide-drug conjugates into cells. But, for efficient therapy, a high concentration of cargo needs to be delivered. To explore this, we studied the pharmacologically interesting neuropeptide Y₁ receptor (Y₁R) in one recombinant and three oncogenic cell systems that endogenously express the receptor. We demonstrate that recycled receptors behave identically to newly synthesized receptors with respect to ligand binding and internalization pathways. Depending on the cell system, biosynthesis, recycling efficiency, and peptide uptake differ partially, but shuttling was efficient in all systems. However, by comparing continuous application of the ligand for four hours to four cycles of internalization and recycling in between, a significantly higher amount of peptide uptake was achieved in the pulsed application (150–250 % to 300–400 %). Accordingly, in this well-suited drug shuttle system pulsed application is superior under all investigated conditions and should be considered for innovative, targeted drug delivery in general.