Kinetic studies of protein farnesyltransferase mutants establish active substrate conformation

The zinc metalloenzyme protein farnesyltransferase (FTase) catalyzes the transfer of a 15-carbon farnesyl moiety from farnesyl diphosphate (FPP) to a cysteine residue near the C-terminus of a protein substrate. Several crystal structures of inactive FTase.FPP.peptide complexes indicate that K164alpha interacts with the alpha-phosphate and that H248beta and Y300beta form hydrogen bonds with the beta-phosphate of FPP [Strickland, C. L., et al. (1998) Biochemistry 37, 16601-16611]. Mutations K164Aalpha, H248Abeta, and Y300Fbeta were prepared and analyzed by single turnover kinetics and ligand binding studies. These mutations do not significantly affect the enzyme affinity for FPP but do decrease the farnesylation rate constant by 30-, 10-, and 500-fold, respectively. These mutations have little effect on the pH and magnesium dependence of the farnesylation rate constant, demonstrating that the side chains of K164alpha, Y300beta, and H248beta do not function either as general acid-base catalysts or as magnesium ligands. Mutation of H248beta and Y300beta, but not K164alpha, decreases the farnesylation rate constant using farnesyl monophosphate (FMP). These data suggest that, contrary to the conclusions derived from analysis of the static crystal structures, the transition state for farnesylation is stabilized by interactions between the alpha-phosphate of the isoprenoid substrate and the side chains of Y300beta and H248beta. These results suggest an active substrate conformation for FTase wherein the C1 carbon of the FPP substrate moves toward the zinc-bound thiolate of the protein substrate to react, resulting in a rearrangement of the diphosphate group relative to its ground state position in the binding pocket.     

Kinetic model of alcohol dehydrogenase function taking into account changes in protein conformation

A model of dimeric enzyme functioning is proposed concerning cooperativity of active-sites due to conformation changes. The rates of such changes are estimated from fitting the experimental data on steady-state kinetics of cyclohexanol oxidation.     

Rapid subpicogram protein detection on a microchip without denaturing

Protein size separation based on sodium dodecyl sulfate-gel electrophoresis (SDS-GE) requires denaturing, but we propose that denaturing is unnecessary for analysis by microchip electrophoresis (micro-CE). By omitting the protein denaturing process, we achieved not only shortened total analysis time, but also dramatically improved sensitivity without compromising size determination. The detection limit was improved to 0.1 ng/microL under conditions without denaturing and 600 pg (9.0 femtomol) of bovine serum albumin was detectable, which equals levels detectable by Silver stain, although a routine method by microchips in the Coomassie Blue detection level.     

Phosphoinositide-dependent protein kinase 1, a sensor of protein conformation

Phosphoinositide-dependent protein kinase 1 (PDK1) is a protein kinase that phosphorylates and activates several other protein kinases from the AGC group (which includes PKA, PKG and PKC), to which PDK1 also belongs. Recent data suggests that PDK1 specificity is achieved by regulation of its interaction with substrates and supports a rather simple model explaining how PDK1 interacts with different substrates. The data further suggests that PDK1 interacts with its substrates when they are in a particular conformation (inactive). PDK1 has the ability to recognize, interact with and phosphorylate specific substrate conformations and thus sets PDK1 at the centre of a protein conformation sensor mechanism. The PDK1-substrate interaction model describes, at a molecular level, the mechanism used by PDK1 to sense the conformation of its substrates.     

Stabilization of a strained protein loop conformation through protein engineering.

Staphylococcal nuclease is found in two folded conformations that differ in the isomerization of the Lys 116-Pro 117 peptide bond, resulting in two different conformations of the residue 112-117 loop. The cis form is favored over the trans with an occupancy of 90%. Previous mutagenesis studies have shown that when Lys 116 is replaced by glycine, a trans conformation is stabilized relative to the cis conformation by the release of steric strain in the trans form. However, when Lys 116 is replaced with alanine, the resulting variant protein is identical to the wild-type protein in its structure and in the dominance of the cis configuration. The results of these studies suggested that any nuclease variant with a non-glycine residue at position 116 should also favor the cis form because of steric requirements of the beta-carbon at this position. In this report, we present a structural analysis of four nuclease variants with substitutions at position 116. Two variants, K116E and K116M, follow the "beta-carbon" hypothesis by favoring the cis form. Furthermore, the crystal structure of K116E is nearly identical to that of the wild-type protein. Two additional variants, K116D and K116N, provide exceptions to this simple "beta-carbon" rule in that the trans conformation is stabilized relative to the cis configuration by these substitutions. Crystallographic data indicate that this stabilization is effected through the addition of tertiary interactions between the side chain of position 116 with the surrounding protein and water structure. The detailed trans conformation of the K116D variant appears to be similar to the trans conformation observed in the K116G variant, suggesting that these two mutations stabilize the same conformation but through different mechanisms.     

Measuring protein interactions by microchip self-interaction chromatography

The self-interaction of proteins is of paramount importance in aggregation and crystallization phenomena. Solution conditions leading to a change in the state of aggregation of a protein, whether amorphous or crystalline, have mainly been discovered by the use of trial and error screening of large numbers of solutions. Self-interaction chromatography has the potential to provide a quantitative method for determination of protein self-interactions amenable to high-throughput screening. This paper describes the construction and characterization of a microchip separation system for low-pressure self-interaction chromatography using lysozyme as a model protein. The retention time was analyzed as a function of mobile-phase composition, amount of protein injected, flow rate, and stationary-phase modification. The capacity factors (k') as a function of crystallizing agent concentration are compared with previously published values for the osmotic second virial coefficient (B(22)) obtained by static light scattering, showing the ability of the chip to accurately determine protein-protein interactions. A 500-fold reduction in protein consumption and the possibility of using conventional instrumentation and automation are some of the advantages over currently used methodologies for evaluating protein-protein interactions.     

Probing protein conformation with a minimal photochemical reagent

3H-diazirine (3H-DZN), a photoreactive gas similar in size to water, was used to probe the topography of the surface and inner space of proteins. On photolysis 3H-DZN generates 3H-methylene carbene, which reacts unselectively with its molecular cage, inserting even into C-H bonds. Labeling of bovine alpha-lactalbumin (alpha-LA, MW: 14,200) with 1 mM (3)H-DZN yielded 0.0041 mol CH2/mol of protein, in agreement with the expectation for an unspecific surface-labeling phenomenon. The cooperative urea-induced unfolding of alpha-LA, as monitored by the extent of 3H-methylene labeling, agrees with that measured by circular dichroism spectroscopy in the far and near ultraviolet regions. At 8 M urea, the unfolded state U was labeled 25-30% more than the native state N primarily because of the increase in the accessible surface area (ASA) of the protein occurring upon unfolding. However, this result lies below the approximately 100% increment expected from theoretical estimates of ASA of state U. Among other factors, most likely the existence of a residual structure in U, that involves helices H2 and H4 of the alpha subdomain, might account for this fact, as shown by a comparative analysis of peptide labeling patterns of N and U samples. In this paper, we demonstrate the usefulness of the 3H-methylene labeling method to monitor conformational transitions and map solvent accessibility along the polypeptide sequence, thus opening the possibility of outlining structural features of nonnative states (i.e., denatured states, molten globule). We anticipate that this technique also would help to identify ligand binding and oligomerization sites in proteins.     

Prediction of protein conformation using a doublet code method

It is suggested that regions of irregular structure, beta-structure, and alpha-helix are composed of 2, 3, and 5 amino acid residue long elements (structurons), respectively, and that the structurons are encoded solely by residue pairs (doublet codons) (i, i + 1), (i, i + 2), (i, i + 4), respectively. Tables of codons are obtained by statistical analysis of the data on the distribution of these pairs in available secondary structures of 62 proteins. These tables are used to obtain distributions of t-, beta- and alpha-codons for an amino acid sequence of protein. When codons of different structures superpose, that is, include the same sequence regions, selection is performed, the selection being performed so to obtain as much as possible number of the non-superposed codons of different structures. The distributions of structurons obtained after this selection are used for localization of structurons in the sequence and prediction of secondary structure on the basis of this localization. The prediction method is illustrated. An accuracy of the method has been tested on the basis an casual selection of fifteen proteins and found equal 64% for secondary structure on the whole and 79%, 53%, 61% for alpha-helix, beta-structure and coil respectively. This result is similar or better than that communicated for contemporary methods.     

Short fragments of a protein globule with predominant conformation

It has been found that 1500 tetrapeptides out of 160000 possible combinations occurring in proteins exhibit preference for particular conformational states. Most conformationally stable tetrapeptides obtained in the analysis of a sampling containing 706 proteins are in the alpha-helical form. The features of the amino acid composition of conformationally stable oligopeptides have been studied.     

Kinetic measurements of binding of galectin 3 to a laminin substratum

Galectin 3, a -galactoside binding protein, contains a C-terminal carbohydrate recognition domain (CRD) and an N-terminal segment including multiple repeats of a proline/tyrosine/glycine-rich motif. Previous work has shown that galectin 3 but not the isolated CRD binds to laminin, a multivalent ligand, with positive cooperativity indicating the formation of multiple interactions although the lectin in solution is monomeric. Using surface plasmon resonance, we find that hamster galectin 3 at sub-µmolar concentrations or its isolated CRD at all concentrations binds to a laminin substratum with similar association (k_ass; 10 – 30 000 M^–1 S^–1) and dissociation (k_diss; 0.2 – 0.3 S ₁ ^–1 ) rates and weak affinity (Ka; 1 - 3 X 10⁵ M^–1). At higher concentrations of galectin 3 the off rate decreases ten fold leading to increased affinity. Ligation of an N-terminal epitope of galectin 3 with a monoclonal Fab fragment increases association and dissociation rates ten fold. A recombinant protein obtained by deletion of the first 93 N-terminal residues binds to laminin with positive cooperativity and a slowly dissociating fraction (K_diss; 0.002 S^–1) accummulates on the substratum. The data suggest that homophilic interactions between CRD as well as N terminal domains are implicated in galectin 3 aggregation on the substratum leading to positive binding cooperativity.     

Kinetic measurements of molecular interactions by spectrofluorometry

The kinetics of antibody–antigen interactions are reviewed in terms of general trends observed in both polyclonal and monoclonal antibody populations. Anti-fluorescein antibodies are featured in the review as model proteins to explore fluorescence-based kinetic measurements. Since the fluorescence of the fluorescein ligand is significantly quenched upon interaction with both polyclonal and monoclonal anti-fluorescein antibodies, the quenching parameter can be advantageously employed in measuring the rates of association (k₁) and dissociation (k₂). The near diffusion-limited k₁ rates and the prolonged k₂ rates are discussed in terms of antibody affinity and mechanisms involved in ligand binding. Specific prolongation effects of reagents, such as anti-metatype antibodies, on the dissociation rate are discussed in terms of antibody dynamics and conformational substates.     

Activity measurement of protein kinase and protein phosphatase by microchip phosphate-affinity electrophoresis

We previously proposed microchip-based phosphate-affinity electrophoresis (μPAE) and demonstrated its application to activity measurement of a tyrosine kinase, c-Src. In this study, we extended the μPAE application to a serine/threonine kinase, protein kinase A (PKA), and to a tyrosine phosphatase, leukocyte antigen-related protein tyrosine phosphatase (LAR PTPase). For standard peptide samples, we obtained linear calibration plots, and the limits of detection were 1.2% (PKA) and 1.5% (LAR PTPase) product peptides in the total peptides. The μPAE was also proven to be effective for unpurified enzyme reaction products.     

Selective protein removal and desalting using microchip CE

This paper describes the on-line sample pretreatment and analysis of proteins and peptides with a poly(methylmethacrylate) (PMMA) microfluidic device (IonChip). This chip consists of two hyphenated electrophoresis channels with integrated conductivity detectors. The first channel can be used for sample preconcentration and sample clean-up, while in the second channel the selected compounds are separated. Isotachophoresis (ITP) combined with zone electrophoresis (CZE) was used to preconcentrate a myoglobin sample by a factor of about 65 before injection into the second dimension and to desalt a mixture of six proteins with 100 mM NaCl. However, ITP-CZE could not be used for the removal of two proteins from a protein/peptide sample since the protein zone in the ITP step was too small to remove certain compounds. Therefore, we used CZE-CZE for the removal of proteins from a protein/peptide mixture, thereby injecting only the peptides into the second CZE separation channel.     

Kinetic measurements of T----R structural transitions in insulin.

The T6----T3R3 and T3R3----R6-structural transitions of cobalt insulin hexamers as induced by SCN ions or m-cresol were studied in stopped-flow experiments using the absorption in the visible for monitoring their time course. The T6----T3R3 transition induced by either SCN or limited concentrations of m-cresol is mono-exponential with a rate constant of 0.1 s-1 and 0.4 s-1, respectively. A mono-exponential time course is also encountered for the m-cresol-induced T3R3----R6 transition when starting from the T3R3 state preestablished by either SCN or m-cresol. The corresponding rate constants are 1.3 s-1 and 0.49 s-1, respectively. If m-cresol is used beyond the concentration range where transformation is limited to one trimer, two exponentials are required for fitting the time course. The second exponential corresponds to the T3R3----R6 step with a concentration-independent rate constant of 0.4 s-1. The rate constant for the faster T6----T3R3 transition, however, increases with increasing excess of m-cresol.