In vitro Fab display: a cell-free system for IgG discovery.

Selection technologies such as ribosome display enable the rapid discovery of novel antibody fragments entirely in vitro. It has been assumed that the open nature of the cell-free reactions used in these technologies limits selections to single-chain protein fragments. We present a simple approach for the selection of multi-chain proteins, such as antibody Fab fragments, using ribosome display. Specifically, we show that a two-chain trastuzumab (Herceptin) Fab domain can be displayed in a format which tethers either the heavy or light chain to the ribosome while retaining functional antigen binding. Then, we constructed synthetic Fab HC and LC libraries and performed test selections against carcinoembryonic antigen (CEA) and vascular endothelial growth factor (VEGF). The Fab selection output was reformatted into full-length immunoglobulin Gs (IgGs) and directly expressed at high levels in an optimized cell-free system for immediate screening, purification and characterization. Several novel IgGs were identified using this cell-free platform that bind to purified CEA, CEA positive cells and VEGF.

SAR and in vivo evaluation of 4-aryl-2-aminoalkylpyrimidines as potent and selective Janus kinase 2 (JAK2) inhibitors.

We report the discovery of a series of 4-aryl-2-aminoalkylpyrimidine derivatives as potent and selective JAK2 inhibitors. High throughput screening of our in-house compound library led to the identification of hit 1, from which optimization resulted in the discovery of highly potent and selective JAK2 inhibitors. Advanced lead 10d demonstrated a significant dose-dependent pharmacodynamic and antitumor effect in a mouse xenograft model. Based upon the desirable profile of 10d (XL019) it was advanced into clinical trials.

Ionic-strength dependence of the conformational change in the unphosphorylated sodium pump.

The conformational change in the unphosphorylated sodium pump was studied as a function of ionic strength to learn whether the rate of the reaction is affected. The results corroborate our proposal [Smirnova, I. N., Lin, S.-H., and Faller, L. D. (1995) Biochemistry 34, 8657-8667] that competitive binding of the transported ions to two (or more) equivalent sites regulates a concerted change in protein conformation. An approximately 10-fold increase in ionic strength decreased the intrinsic affinity of the Na+ conformation of the enzyme for both Na+ and K+ roughly 3-fold, decreased the rate of the change from Na+ to K+ conformation by more than half, and increased the rate of the reverse reaction by about an order of magnitude. The logarithm of the first-order rate constant for the change from Na+ to K+ conformation depended inversely upon the square root of the ionic strength with the extrapolated value at zero ionic strength expressed as a second-order rate constant (1.1 x 10(9) M(-1) sec(-1)) approaching the limit for a diffusion-controlled reaction. The first-order rate constant for the change from K+ to Na+ conformation depended directly upon ionic strength and extrapolated to a zero-ionic-strength value (0.002 s(-1)) far below the diffusion limit. The results are compatible with shielding of oppositely charged domains that move through the solvent when the pump cycles between conformations. Electrostatic interactions between domains evidently contribute to the driving force for the change from Na+ to K+ conformation and to the stability of the K+ conformation.

Interplay between site-specific mutations and cyclic nucleotides in modulating DNA recognition by Escherichia coli cyclic AMP receptor protein.

Mutagenesis of various amino acids in Escherichia coli cyclic AMP receptor protein (CRP) has been shown to modulate protein compressibility and dynamics [Gekko et al. (2004) Biochemistry 43, 3844-3852]. Cooperativity of cAMP binding to CRP and the apparent DNA binding affinity are perturbed [Lin and Lee (2002) Biochemistry 41, 11857-11867]. The aim of this study is to explore the effects of mutation on the surface chemistry of CRP and to define the consequences of these changes in affecting specific DNA sequence recognition by CRP. Furthermore, the role of the interplay between mutation and specific identity of the bound cyclic nucleotide in this DNA recognition was explored. In the current study, effects of eight site-specific mutations (K52N, D53H, S62F, T127L, G141Q, L148R, H159L, and K52N/H159L) on DNA recognition of four sequences (Class I (site PI of lac), Class II (site PI of gal), and synthetic sequences that are hybrids of Classes I and II sites) modulated by three different cyclic nucleotides (cAMP, cCMP, and cGMP) were investigated. All mutations altered the surface chemistry of CRP as evidenced by the change in elution properties of these proteins from different matrixes. While T127L, S62F, K52N, and H159L exhibited unexpected behavior under combinations of specific experimental conditions, such as the identity of bound cyclic nucleotide and DNA sequence, in general, results showed that the affinities of CRP for DNA were sequence-dependent, increasing in the order of lacgal26 < gal26 < lac26 < gallac26 for all the mutants in the presence of 200 microM cAMP. The apparent association constants significantly increased in the order of no cyclic nucleotide approximately cGMP < cCMP < cAMP for all the examined DNA sequences. Linear correlation between the DeltaG for CRP-DNA complex formation and the cooperativity energy for cAMP binding was observed with gallac26, gal26, and lacgal26; however, the slope of this linear correlation is DNA sequence dependent. Structural information was presented to rationalize the interplay between CRP sequence and cyclic nucleotides in defining the recognition of DNA sequences.

Determinants of DNA bending in the DNA-cyclic AMP receptor protein complexes in Escherichia coli.

The activated Escherichia coli cAMP receptor protein, CRP, is capable of regulating the expression of more than 20 genes by binding to specific DNA sites. DNA bending is an important structural feature that has been observed in the regulatory mechanism of gene expression by CRP. On the basis of the results of the fluorescence energy transfer study of the gal P1 promoter, gal bends asymmetrically upon binding to CRP, although DNA bends symmetrically in the CRP-lac complex. The flanking sequence proximal to the TGTGA motif is involved in a sharper bend than the other side with an overall bending angle of approximately 90-125 degrees, without wrapping around the CRP molecule. To understand the factors that control the symmetry in DNA bending, a series of DNA sequences was tested to dissect the contribution of half-sites and flanking sequences, using the natural gal P1 and lac P1 sequences as initial targets. The extent of DNA bending induced by CRP was monitored by the difference in fluorescence anisotropy between free DNA and the DNA-CRP complex. The extent of bending was sequence-dependent, and most importantly, the symmetry of bending was a function of the symmetry of the DNA sequence. For example, in the lac promoter the two binding half-sites (TGTGA and TCACT) were almost symmetric as an inverted repeat. The recognition F-helices of the two CRP subunits would bind to these half-sites with a 2-fold symmetry. The flanking sequences (ATAAA and CATTA) were almost identical mirror images. Thus, they are expected to bend in a similar manner. Finally, the sequence symmetry properties of a series of natural CRP promoters were analyzed. A strong tendency for symmetry sequence was encoded in class I promoter sites but not in class II promoter sites. Results from this analysis support the conclusion that the geometry of the CRP-DNA complex plays a major role in determining the molecular mechanism in gene transcription.

Linkage of multiequilibria in DNA recognition by the D53H Escherichia coli cAMP receptor protein.

The transcription factor cyclic AMP receptor protein, CRP, regulates the operons that encode proteins involved in translocation and metabolism of carbohydrates in Escherichia coli. The structure of the CRP-cAMP complex reveals the presence of two sets of cAMP binding sites. Solution biophysical studies show that there are two high-affinity and two low-affinity binding sites, to which the binding of cAMP is characterized by varying degrees of cooperativity. A stoichiometry of four implies that potentially CRP can exist in five conformers with different numbers of bound cAMP. These conformers may exhibit differential affinities for specific DNA sequences. In this study, the affinity between DNA and each conformer of D53H CRP was defined through a dissection of the thermodynamic linkage scheme that included all the conformers. Loading of the high- and low-affinity sites with cAMP leads to high and low affinity for DNA, respectively. The specific magnitude of the binding constants of these conformers is DNA sequence dependent. The various association constants defined by the present study provide a solution to address an enigma of the CRP system, namely, the 3 orders of magnitude difference between the cAMP binding constants determined by in vitro studies and the cAMP concentration regime to which the bacteria respond. Under physiological conditions, the apo-CRP-DNA complex is the dominant species. As a consequence of the 1000-fold stronger affinity of cAMP to the apo-CRP-DNA complex than that to CRP, the relevant reaction is the binding of cAMP to this DNA-protein complex. The binding constant is of the order of 10(7) M(-)(1), the same concentration regime as that of cellular concentration of cAMP. In addition, under physiological conditions the species that binds to the lac and gal operons is predicted to be CRP-(cAMP)(1). A comparison of parameters between the wild type and the mutant CRP shows that the mutation apparently shifts the various thermodynamically linked equilibria without a change in the basic mechanism that governs CRP activities. Thus, the conclusions derived from a study of the mutant are relevant to wild-type CRP. A dissection of the individual binding constants in this multiequilibria reaction scheme leads to a definition of the mechanism of action of this transcription factor.

Communications between the high-affinity cyclic nucleotide binding sites in E. coli cyclic AMP receptor protein: effect of single site mutations.

The binding of adenosine 3',5'-cyclic monophosphate (cAMP) and its nonfunctional analogue, guanosine 3',5'-cyclic monophosphate (cGMP), to the adenosine 3',5'-cyclic monophosphate receptor protein (CRP) from Escherichia coli was investigated by means of fluorescence and isothermal titration calorimetry (ITC) at pH 7.8 and 25 degrees C. A biphasic fluorescence titration curve was observed, confirming the previous observation reported by this laboratory (Heyduk and Lee (1989) Biochemistry 28, 6914-6924). However, the triphasic titration curve obtained from the ITC study suggests that the cAMP binding to CRP is more complicated than the previous conclusion that CRP binds sequentially two molecules of cAMP with negative cooperativity. The binding data can best be represented by a model for two identical interactive high-affinity sites and one low-affinity binding site. Unlike cAMP, the binding of cGMP to CRP exhibits no cooperativity between the high-affinity sites. The effects of mutations on the bindings of cAMP and cGMP to CRP were also investigated. The eight CRP mutants studied were K52N, D53H, S62F, T127L, G141Q, L148R, H159L, and K52N/H159L. These sites are located neither in the ligand binding site nor at the subunit interface. The binding was monitored by fluorescence. Although these mutations are at a variety of locations in CRP, the basic mechanism of CRP binding to cyclic nucleotides has not been affected. Two cyclic nucleotide molecules bind to the high-affinity sites of CRP. The cooperativity of cAMP binding is affected by mutation. It ranges from negative to positive cooperativity. The binding of cGMP shows none. With the exception of the T127L mutant, the free energy change for DNA-CRP complex formation increases linearly with increasing free energy change associated with the cooperativity of cAMP binding. This linear relationship implies that the protein molecule modulates the signal in the binding of cAMP, even though the mutation is not directly involved in cAMP or DNA binding. In addition, the significant differences in the amplitude of fluorescent signal indicate that the mutations also affect the surface characteristics of CRP. These results imply that these mutations are not perturbing specific pathways of signal transmission. Instead, these results are more consistent with the concept that CRP exists as an ensemble of native states, the distribution of which can be altered by these mutations.

Temporal and spatial expression of biologically active human factor VIII in the milk of transgenic mice driven by mammary-specific bovine alpha-lactalbumin regulation sequences.

Hemophilia A is one of the major inherited bleeding disorders caused by a deficiency or abnormality in coagulation factor VIII (FVIII). Hemophiliacs have been treated with whole plasma or purified FVIII concentrates. The risk of transmitting blood-borne viruses and the cost of highly purified FVIII are the major factors that restrict prophylaxis in hemophilia therapy. One of the challenges created by the biotechnology revolution is the development of methods for the economical production of highly purified proteins in large scales. Recent developments indicate that manipulating milk composition using transgenesis has focused mainly on the mammary gland as a bioreactor to produce pharmaceuticals. In the present study, a hybrid gene containing bovine alpha-lactalbumin and human FVIII cDNA was constructed for microinjection into the pronuclei of newly fertilized mouse eggs. The alphaLA-hFVIII hybrid gene was confirmed to be successfully integrated and stably germ-line transmitted in 12 (seven females/five males) lines. Western-blot analysis of milk samples obtained from eight of the transgenic founders and F1 offspring indicated that the recombinant hFVIII was secreted into the milk of the transgenic mice. The concentrations of rFVIII ranged from 7.0 to 50.2 microg/ml, over 35-200-fold higher than that in normal human plasma. Up to 13.4 U/ml of rFVIII was detected in an assay in which rFVIII restored normal clotting activity to FVIII-deficient human plasma.

Ability of E. coli cyclic AMP receptor protein to differentiate cyclic nucelotides: effects of single site mutations.

Escherichia coli cyclic AMP receptor protein (CRP) is a global transcriptional regulator which controls the expression of many different genes. Although different cyclic nucleotides can bind to CRP with almost equal affinity, only in the presence of cAMP could wild-type CRP bind to specific DNA sequences. Molecular genetic studies have identified a class of mutants, CRP*, which either do not require exogenous cAMP for activation or can be activated by cGMP. Thus, these mutants might aid in identifying the structural elements that are involved in the modulation of CRP to correctly differentiate the messages embedded in cyclic nucleotides. In this in vitro study, five CRP* mutants, namely, D53H, S62F, G141Q, G141K, and L148R, were tested for their abilities to bind the lac promoter sequence and the effects of cyclic nucleotides in modulating DNA sequence recognition. For comparison, non-CRP* mutants K52N, T127L, H159L, and K52N/H159L were studied. cCMP and cGMP can replace cAMP as an allosteric effector in all of these CRP mutants except S62F and non-CRP* mutants. The D53H, G141Q, G141K, and L148R mutants exhibit significantly higher affinity for the lac promoter sequence than wild-type CRP while S62F and the non-CRP* mutants exhibit reduced affinity. To probe the pathway of communication, the energetics of subunit assembly in these mutants were monitored by sedimentation equilibrium, and the conformational states of these mutants were probed by proteolysis and accessibility of Cys178 to chemical modifications. Results from these studies imply that signals due to mutations are mostly transmitted through the subunit interface. Thus, residues in CRP outside of the cyclic nucleotide binding site modulate the ability of CRP to differentiate these three cyclic nucleotides through long-range communication. Furthermore, this study shows that CRP* mutations do not impart any unique properties to CRP except that the DNA binding constants are shifted to a regime of higher affinity.