Kinetic analysis of acetylation-dependent Pb1 bromodomain-histone interactions

Stopped-flow fluorescence anisotropy was used to determine the kinetic parameters that define acetylation-dependent bromodomain-histone interactions. Bromodomains are acetyllysine binding motifs found in many chromatin associated proteins. Individual bromodomains were derived from the polybromo-1 protein, which is a subunit of the PBAF chromatin-remodeling complex that has six tandem bromodomains in the amino-terminal region. The average k(on) and k(off) values for the formation of high-affinity complexes are 275 M(-1) s(-1) and 0.41 x 10(-3) s(-1), respectively. The average k(on) and k(off) values for the formation of low-affinity complexes are 119 M(-1) s(-1) and 1.42 x 10(-3) s(-1), respectively. Analysis of the on- and off-rates yields acetylation site-dependent equilibrium dissociation constants averaging 1.4 and 12.9 microM for high- and low-affinity complexes, respectively. This work represents the first examination of kinetic mechanisms of acetylation-dependent bromodomain-histone interactions.     

Purification and immunological properties of proton-ATPase complexes from yeast and rat liver mitochondria

Proton-ATPase complexes from yeast and rat liver mitochondria were isolated by a simple method previously employed for the purification of the proton-ATPase complex from chloroplasts. After reconstitution into liposomes, the purified complexes were active in the ATP-Pi exchange reaction, the rate of which was 120 and at least 200 nmol/mg of protein/min for the rat liver and yeast mitochondria ATPases, respectively. Upon sodium dodecyl sulfate polyacrylamide gel electrophoresis, each complex exhibited 11 to 12 different polypeptides. The isolated ATPase complexes from rat liver and yeast mitochondria, from Swiss chard chloroplasts, and Escherichia coli membranes were reacted with antibodies prepared against the various subunits of ATPase complexes. From all the combinations of antigen-antibody examined, only the antibodies against beta subunit cross-reacted with the corresponding subunit of all the ATPase complexes tested. These results indicate that certain amino acid sequences in the beta subunit have been preserved in all of the proton-ATPase complexes.     

Gz, a guanine nucleotide-binding protein with unique biochemical properties

Cloning of a complementary DNA (cDNA) for Gz alpha, a newly appreciated member of the family of guanine nucleotide-binding regulatory proteins (G proteins), has allowed preparation of specific antisera to identify the protein in tissues and to assay it during purification from bovine brain. Additionally, expression of the cDNA in Escherichia coli has resulted in the production and purification of the recombinant protein. Purification of Gz from bovine brain is tedious, and only small quantities of protein have been obtained. The protein copurifies with the beta gamma subunit complex common to other G proteins; another 26-kDa GTP-binding protein is also present in these preparations. The purified protein could not serve as a substrate for NAD-dependent ADP-ribosylation catalyzed by either pertussis toxin or cholera toxin. Purification of recombinant Gz alpha (rGz alpha) from E. coli is simple, and quantities of homogeneous protein sufficient for biochemical analysis are obtained. Purified rGz alpha has several properties that distinguish it from other G protein alpha subunit polypeptides. These include a very slow rate of guanine nucleotide exchange (k = 0.02 min-1), which is reduced greater than 20-fold in the presence of mM concentrations of Mg2+. In addition, the rate of the intrinsic GTPase activity of Gz alpha is extremely slow. The hydrolysis rate (kcat) for rGz alpha at 30 degrees C is 0.05 min-1, or 200-fold slower than that determined for other G protein alpha subunits. rGz alpha can interact with bovine brain beta gamma but does not serve as a substrate for ADP-ribosylation catalyzed by either pertussis toxin or cholera toxin. These studies suggest that Gz may play a role in signal transduction pathways that are mechanistically distinct from those controlled by the other members of the G protein family.     

Rational design of faster associating and tighter binding protein complexes

A protein design strategy was developed to specifically enhance the rate of association (k(on)) between a pair of proteins without affecting the rate of dissociation (k(off)). The method is based on increasing the electrostatic attraction between the proteins by incorporating charged residues in the vicinity of the binding interface. The contribution of mutations towards the rate of association was calculated using a newly developed computer algorithm, which predicted accurately the rate of association of mutant protein complexes relative to the wild type. Using this design strategy, the rate of association and the affinity between TEM1 beta-lactamase and its protein inhibitor BLIP was enhanced 250-fold, while the dissociation rate constant was unchanged. The results emphasize that long range electrostatic forces specifically alter k(on), but do not effect k(off). The design strategy presented here is applicable for increasing rates of association and affinities of protein complexes in general.     

Relaxation kinetics of ribonuclease T1 binding with guanosine and 3'-GMP.

Temperature-jump relaxation kinetic studies were undertaken at 25 degrees C with ribonuclease T1 (RNase T1) alone and in the presence of guanosine (Guo) and 3'-guanylic acid (3'-GMP). No relaxations were observed in the absence of ligands and only one process was observed in their presence which reflected a simple on-off reaction in both cases. Apparent association rate constants, k(on), and dissociation rate constants, k(off), were evaluated at several pH values and their ratios, k(on)/k(off), were contrasted with independently determined values of the equilibrium association constant, Ka(eq). The value of k(on)/k(off) for Guo was significantly greater than Ka(eq), whereas Ka(eq) was significantly greater than k(on)/k(off) for 3'-GMP. The simplest interpretation of the result for Guo is that free RNase T1 undergoes a relatively slow undetected isomerization and Guo can bind only with one isomer. 3'-GMP can be considered to bind with the same preference, but in this case the initial enzyme complex undergoes a relatively slow undetected isomerization. These results are consistent with a recent NMR study which suggested that RNase T1 binding with Guo and 3'-GMP are coupled to slow exchange processes in a ligand dependent manner (Shimada, I. and Inagaki, F. (1990) Biochemistry 29, 757-764). It is tentatively concluded that binding of Guo and 3'-GMP at the active site of RNase T1 is limited to a sub-population of conformers involving the base-recognition site and that the phosphomonoester group of the nucleotide can engage in additional conformationally linked interactions at the adjacent catalytic site.     

The pST44 polycistronic expression system for producing protein complexes in Escherichia coli

Protein complexes are responsible for key biological processes, but methods to produce recombinant protein complexes for biochemical and biophysical studies are limited. We have developed a second generation Escherichia coli polycistronic expression system which improves on the modularity of our original pST39 polycistronic system. This pST44 expression system simplifies the construction of polycis-tronic plasmids, particularly of variant plasmids expressing deletion or point mutations in any subunit. To facilitate purification of the expressed complex, we have prepared a suite of 72 plasmids which allows individual subunits to be tagged at the N- or C-terminus with six permanent or cleavable peptide affinity tags. We demonstrate these new features in a detailed deletion analysis of a three protein yeast Piccolo NuA4 histone acetyltransferase complex, and in the affinity purification of a human Piccolo NuA4 complex. We also utilize the modular design to show that the order of expression of the three subunits along the polycistronic plasmid does not affect the reconstitution of the yeast Piccolo complex in E. coli.     

Biotin-Tag Affinity Purification of a Centromeric Nucleosome Assembly Complex

Centromeres are chromosomal sites of microtubule binding that ensure correct mitotic segregation of chromosomes to daughter cells. This process is mediated by a special centromere-specific histone H3 variant (CenH3), which packages centromeric chromatin and epigenetically maintains the centromere at a distinct chromosomal location. However, CenH3 is present at low abundance relative to canonical histones, presenting a challenge for the isolation and characterization of the chaperone machinery that assembles CenH3 into nucleosomes at centromeres. To address this challenge, we used controlled overexpression of Drosophila CenH3 (CID) and an efficient biochemical purification strategy offered by in vivo biotinylation of CID to successfully purify and characterize the soluble CID nucleosome assembly complex. It consists of a singlechaperone protein, RbAp48, complexed with CID and histone H4. RbAp48 is also found in protein complexes that assemble canonical histone H3 and replacement histone H3.3. Here, we highlight the benefits of our improved biotin-mediated purification method, and address the question of how the simple CID/H4-RbAp48 chaperone complex can mediate nucleosome assembly specifically at centromeres.     

Separation methods in the analysis of protein membrane complexes

The separation of membrane protein complexes can be divided into two categories. One category, which is operated on a relatively large scale, aims to purify the membrane protein complex from membrane fractions while retaining its native form, mainly to characterize its nature. The other category aims to analyze the constituents of the membrane protein complex, usually on a small scale. Both of these face the difficulty of isolating the membrane protein complex without interference originating from the hydrophobic nature of membrane proteins or from the close association with membrane lipids. To overcome this difficulty, many methods have been employed. Crystallized membrane protein complexes are the most successful example of the former category. In these purification methods, special efforts are made in the steps prior to the column chromatography to enrich the target membrane protein complexes. Although there are specific aspects for each complex, the most popular method for isolating these membrane protein complexes is anion-exchange column chromatography, especially using weak anion-exchange columns. Another remarkable trend is metal affinity column chromatography, which purifies the membrane protein complex as an intact complex in one step. Such protein complexes contain subunit proteins which are genetically engineered so as to include multiple-histidine tags at carboxyl- or amino-termini. The key to these successes for multi-subunit complex isolation is the idea of keeping the expression at its physiological level, rather than overexpression. On the other hand, affinity purification using the Fv fragment, in which a Strep tag is genetically introduced, is ideal because this method does not introduce any change to the target protein. These purification methods supported by affinity interaction can be applied to minor membrane protein complexes in the membrane system. Isoelectric focusing (IEF) and blue native (BN) electrophoresis have also been employed to prepare membrane protein complexes. Generally, a combination of two or more chromatographic and/or electrophoretic methods is conducted to separate membrane protein complexes. IEF or BN electrophoresis followed by 2nd dimension electrophoresis serve as useful tools for analytical demand. However, some problems still exist in the 2D electrophoresis using IEF. To resolve such problems, many attempts have been made, e.g. introduction of new chaotropes, surfactants, reductants or supporting matrices. This review will focus in particular on two topics: the preparative methods that achieved purification of membrane protein complexes in the native (intact) form, and the analytical methods oriented to resolve the membrane proteins. The characteristics of these purification and analytical methods will be discussed along with plausible future developments taking into account the nature of membrane protein complexes.     

Mass spectrometry-based proteomic analysis of the epitope-tag affinity purified protein complexes in eukaryotes

In recent years, MS has been widely used to study protein complex in eukaryotes. The identification of interacting proteins of a particular target protein may help defining protein-protein interaction and proteins of unknown functions. To isolate protein complexes, high-speed ultracentrifugation, sucrose density-gradient centrifugation, and coimmunoprecipitation have been widely used. However, the probability of getting nonspecific binding is comparatively high. Alternatively, by use of one- or two-step (tandem affinity purification) epitope-tag affinity purification, protein complexes can be isolated by affinity or immunoaffinity columns. These epitope-tags include protein A, hexahistidine (His), c-Myc, hemaglutinin (HA), calmodulin-binding protein, FLAG, maltose-binding protein, Strep, etc. The isolated protein complex can then be subjected to protease (i.e., trypsin) digestion followed by an MS analysis for protein identification. An example, the epitope-tag purification of the Arabidopsis cytosolic ribosomes, is addressed in this article to show the success of the application. Several representative protein complexes in eukaryotes been isolated and characterized by use of this approach are listed. In this review, the comparison among different tag systems, validation of interacting relationship, and choices of MS analysis method are addressed. The successful rate, advantages, limitations, and challenges of the epitope-tag purification are also discussed.     

Insight into covalent flavinylation and catalysis from redox, spectral, and kinetic analyses of the R474K mutant of the flavoprotein subunit of p-cresol methylhydroxylase

Each flavoprotein subunit (PchF) of p-cresol methylhydroxylase (PCMH) has flavin adenine dinucleotide (FAD) covalently tethered to Tyr384. The PCMH structure suggests that Arg474 in PchF is required for self-catalytic covalent flavinylation and for substrate oxidation. The replacement of Arg474 with Lys was carried out to probe the subtleties of the role of Arg474 in these processes. In nearly all of the aspects examined, the mutant protein showed compromised properties relative to the wild-type protein, including the tenacity of noncovalent FAD binding to the apo-protein, the rate of covalent flavinylation, the affinity of the covalent flavoprotein for PchC (the cytochrome subunit), the k(cat) for substrate oxidation, and the affinity for substrate analogues in the formation of FAD-charge-transfer complexes (CT complexes). Nevertheless, because the mutant retains these attributes, the comparison allows for an examination of the role of this residue in the various properties of the enzyme. A correlation is proposed to exist between nu(m), the frequency for the absorbance maximum of the CT complex with a substrate analogue, and k(cat), the steady-state rate constant for oxidation of p-cresol by various forms of PCMH and PchF; both nu(m) and k(cat) can be expressed as functions of the ionization potential of the donor (I(D)) and the electron affinity of the acceptor (E(A)). This correlation is a better predictor of the rate constant for substrate oxidation than is the magnitude of the redox potential, E(m,7), of the bound FAD, which was determined for the various mutant enzyme species and compared with those of the wild type.     

The function of Mg-ATP in interactions between the regulatory and catalytic subunits of type I cAMP-dependent protein kinase from rabbit skeletal muscle

The regulatory subunit of Type I cAMP-dependent protein kinase from rabbit skeletal muscle can bind [3H]cAMP to form the R-[3H]cAMP complex, and the slow phase of the enhanced exchange of free cAMP with [3H]cAMP from the R-[3H]cAMP complexes was studied under various conditions using the equilibrium isotope exchange technique. Results indicate that Mg-ATP and the catalytic subunit are absolutely required for the enhanced exchange reaction to occur, but phosphorylation of the regulatory subunit by Mg-ATP does not play a determining role in the slow rate of the dissociation/association of the Type I protein-kinase in the presence of cAMP and the catalytic subunit. We interpret the role of Mg-ATP as being one in which it may provide the structural attributes required for formation of a stabilized transient state of the cAMP-regulatory subunit-catalytic subunit ternary complex, an obligatory intermediate involved in the dissociation/association of Type I cAMP-dependent protein kinase.     

Evidence for dynamics in proteins as a mechanism for ligand dissociation

Signal transduction, regulatory processes and pharmaceutical responses are highly dependent upon ligand residence times. Gaining insight into how physical factors influence residence times (1/k(off)) should enhance our ability to manipulate biological interactions. We report experiments that yield structural insight into k(off) involving a series of eight 2,4-diaminopyrimidine inhibitors of dihydrofolate reductase whose binding affinities vary by six orders of magnitude. NMR relaxation-dispersion experiments revealed a common set of residues near the binding site that undergo a concerted millisecond-timescale switching event to a previously unidentified conformation. The rate of switching from ground to excited conformations correlates exponentially with the binding affinity K(i) and k(off), suggesting that protein dynamics serves as a mechanical initiator of ligand dissociation within this series and potentially for other macromolecule-ligand systems. Although the forward rate of conformational exchange, k(conf,forward), is faster than k(off), the use of the ligand series allowed for connections to be drawn between kinetic events on different timescales.     

Subunit flow in F-actin under steady-state conditions. Application of a novel method to determination of the rate of subunit exchange of F-actin at the terminals

We developed a novel method to determine the subunit exchange rates of F-actin at its terminals under quasi-steady-state conditions by using a powerful fluorescent probe, N-(1-pyrenyl)iodoacetamide. The applicability of the method was checked with regard to both theoretical and experimental aspects. We determined the rates of subunit exchange of F-actin and F-actin-tropomyosin complex under various ionic conditions. We found that: (i) KCl accelerated both on and off rates at each end, and lowered the critical concentration of the P-end while the critical concentration of the B-end was not affected; (ii) binding of tropomyosin drastically reduced the subunit flow in F-actin by suppressing the off rate principally of the P-end. It is therefore believed that tropomyosin exerts an anisotropic constraint on F-actin and regulates its dynamic polarity.     

Purification of heterotrimeric G protein alpha subunits by GST-Ric-8 association: primary characterization of purified G alpha(olf)

Ric-8A and Ric-8B are nonreceptor G protein guanine nucleotide exchange factors that collectively bind the four subfamilies of G protein α subunits. Co-expression of Gα subunits with Ric-8A or Ric-8B in HEK293 cells or insect cells greatly promoted Gα protein expression. We exploited these characteristics of Ric-8 proteins to develop a simplified method for recombinant G protein α subunit purification that was applicable to all Gα subunit classes. The method allowed production of the olfactory adenylyl cyclase stimulatory protein Gα(olf) for the first time and unprecedented yield of Gα(q) and Gα(13). Gα subunits were co-expressed with GST-tagged Ric-8A or Ric-8B in insect cells. GST-Ric-8·Gα complexes were isolated from whole cell detergent lysates with glutathione-Sepharose. Gα subunits were dissociated from GST-Ric-8 with GDP-AlF(4)(-) (GTP mimicry) and found to be >80% pure, bind guanosine 5'-[γ-thio]triphosphate (GTPγS), and stimulate appropriate G protein effector enzymes. A primary characterization of Gα(olf) showed that it binds GTPγS at a rate marginally slower than Gα(s short) and directly activates adenylyl cyclase isoforms 3, 5, and 6 with less efficacy than Gα(s short).     

Coupling tandem affinity purification and quantitative tyrosine iodination to determine subunit stoichiometry of protein complexes

Rapid protein purification methodologies, such as strategies involving the tandem affinity purification module, have resulted in the identification of a tremendous number of multisubunit protein complexes. Furthermore, in this modern genomic age, mass spectrometry methods are often coupled with affinity purification to identify the genes that encode each protein subunit. However, simple methodologies to determine the stoichiometry of individual subunits within a multisubunit complex have not received much attention. In this article we describe a procedure to rapidly and efficiently determine the stoichiometry of subunits within multisubunit complexes using a combination of tandem affinity purification and quantitative 125I labeling of subunit tyrosines.     

Chaperone-subunit-usher interactions required for donor strand exchange during bacterial pilus assembly

The assembly of type 1 pili on the surface of uropathogenic Escherichia coli proceeds via the chaperone-usher pathway. Chaperone-subunit complexes interact with one another via a process termed donor strand complementation whereby the G1beta strand of the chaperone completes the immunoglobulin (Ig) fold of the pilus subunit. Chaperone-subunit complexes are targeted to the usher, which forms a channel across the outer membrane through which pilus subunits are translocated and assembled into pili via a mechanism known as donor strand exchange. This is a mechanism whereby chaperone uncapping from a subunit is coupled with the simultaneous assembly of the subunit into the pilus fiber. Thus, in the pilus fiber, the N-terminal extension of every subunit completes the Ig fold of its neighboring subunit by occupying the same site previously occupied by the chaperone. Here, we investigated details of the donor strand exchange assembly mechanism. We discovered that the information necessary for targeting the FimC-FimH complex to the usher resides mainly in the FimH protein. This interaction is an initiating event in pilus biogenesis. We discovered that the ability of an incoming subunit (in a chaperone-subunit complex) to participate in donor strand exchange with the growing pilus depended on a previously unrecognized function of the chaperone. Furthermore, the donor strand exchange assembly mechanism between subunits was found to be necessary for subunit translocation across the outer membrane usher.     

The tandem affinity purification (TAP) method: a general procedure of protein complex purification

Identification of components present in biological complexes requires their purification to near homogeneity. Methods of purification vary from protein to protein, making it impossible to design a general purification strategy valid for all cases. We have developed the tandem affinity purification (TAP) method as a tool that allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the TAP tag, either N- or C-terminally, to the target protein of interest. Starting from a relatively small number of cells, active macromolecular complexes can be isolated and used for multiple applications. Variations of the method to specifically purify complexes containing two given components or to subtract undesired complexes can easily be implemented. The TAP method was initially developed in yeast but can be successfully adapted to various organisms. Its simplicity, high yield, and wide applicability make the TAP method a very useful procedure for protein purification and proteome exploration.     

Characterization of noncovalent complexes of recombinant human monoclonal antibody and antigen using cation exchange, size exclusion chromatography, and BIAcore.

The binding of fully human monoclonal antibodies (MAbs) D2E7 and 2SD4 to their antigen, human tumor necrosis factor-alpha (TNFalpha), was investigated by BIAcore, cation exchange (CIEX), and size exclusion liquid chromatography (SEC) using ultraviolet and laser light scattering detectors. D2E7 has a higher affinity for TNFalpha than 2SD4 and the two antibodies (Abs) differ by 12 amino acids in the antigen (Ag) binding regions. A BIAcore biosensor instrument was used to determine the association, k(on) and dissociation, k(off), rate constants for the binding of TNFalpha to D2E7 and 2SD4. The HPLC methods were used to resolve and to study D2E7, 2SD4, and TNFalpha molecules and the noncovalent complexes of D2E7 and 2SD4 with TNFalpha. The CIEX method demonstrated that all D2E7 charged-variants bound TNFalpha equally well. There was no preferential binding for any one of D2E7 charged-variants to TNFalpha. D2E7 and 2SD4 Abs were resolved by the CIEX method. When a mixture of D2E7 and 2SD4 was mixed with excess TNFalpha, D2E7. TNFalpha complexes were formed before any 2SD4. TNFalpha complexes. Thus, the CIEX method was able to rank the affinities of the MAbs. D2E7 and TNFalpha formed complexes of 600-5000 kDa. The molecular weights of various D2E7. TNFalpha complexes were determined by a SEC method with light scattering (LS) and refractive index (RI) detectors. Upon overnight incubation, a 598-kDa complex emerged as the most stable and the only D2E7. TNFalpha complex. The molar ratio of D2E7 to TNFalpha in this complex was approximately 1:1. Based on molecular weights and the molar ratio, an immune complex, consisting of alternating three D2E7 and three TNFalpha molecules, is proposed as the most stable complex.     

Characterisation of reaction centers and their phospholipids from Rhodospirillum rubrum.

1. Reaction centers from Rhodospirillum rubrum have been extracted with the zwitterionic detergent lauryl dimethyl amine oxide. Subsequent purification has been achieved by gel filtration and ion-exchange chromatography. The pure reaction centers are composed of three protein subunits (L, M, H), bacteriocholorophyll and bacteriopheophytin in the ratio 2 : 1 and phospholipids. 2. The phospholipid composition has been found to be similar to that of whole chromatophore membrane, except that diphosphatidyl glycerol is present in higher amount in the isolated complex. When the detergent treatment of the chromatophore membrane is done in the presence of NaCl, a lower phospholipid content in isolated reaction centers has been found together with a lower stability in the association among the protein subunits. In this complex, the largest subunit H is easily split off and a LM complex is obtained. It is concluded that the phospholipids play an important role in the stability of reaction center complexes.     

Conservation of critical functional domains in murine plasminogen activator inhibitor-1

Plasminogen activator inhibitor-1 is the main physiological regulator of tissue-type plasminogen activator in normal plasma. In addition to its critical function in fibrinolysis, plasminogen activator inhibitor-1 has been implicated in roles in other physiological and pathophysiological processes. To investigate structure-function aspects of mouse plasminogen activator inhibitor-1, the recombinant protein was expressed in Escherichia coli and purified. Five variant recombinant murine proteins (R76E, Q123K, R346A, R101A, and Q123K/R101A) were also generated using site-directed mutagenesis. The variant (R346A) was found to be defective in its inhibitory activity against tissue plasminogen activator relative to its wild-type counterpart. Enzyme-linked immunosorbent assay and surface plasmon resonance experiments demonstrated reduced vitronectin-binding affinity of the (Q123K) variant (K(D) = 1800 nm) relative to the wild-type protein (K(D) = 5.4 nm). Kinetic analyses indicated that the (Q123K) variant had a slower association (k(on) = 2.92 x 10(4) m(-1) s(-1)) to, and a faster dissociation from, vitronectin (k(off) = 5.3 x 10(-2) s(-1)), (wild-type k(on) = 1.03 x 10(6) m(-1) s(-1) and k(off) = 5.27 x 10(-3) s(-1)). The Q123K/R101A variant demonstrated an even lower vitronectin-binding ability. Low density lipoprotein receptor-related protein binding was decreased for the (R76E) variant. It was also demonstrated that the plasminogen activator inhibitor-1/vitronectin complex decreased the interaction of plasminogen activator inhibitor-1 with low density lipoprotein receptor-related protein. These results indicate that the complex interactions traditionally associated with different plasminogen activator inhibitor-1 functions apply to the murine system, thus showing a commonality of subtle functions among different species and evolutionary conservation of this protein. Further, this study provides additional evidence that the human hemostasis system can be studied effectively in the mouse, which is a great asset for investigations with gene-altered mice.