Structure--function relationship of the human erythrocyte plasma membrane Ca(2+)-ATPase revealed by V8 protease treatment

The application of 'kisser' probes for resolving the distribution and microenvironment of membrane proteins in situ

Membrane proteins play a lead role in the formation and function of synapses, but, despite revolutions in immunology and molecular genetics, limitations persist in our ability to investigate membrane proteins in the context of an intact synapse. Here, we introduce a simple but novel approach to resolving the distribution of endogenous membrane proteins in either live or fixed tissues. The technique involves transgenic expression of a protein with an extracellular tag, a generic transmembrane domain, and an intracellular terminus that mimics the intracellular anchoring motifs of the endogenous protein of interest. We provide three examples where these kisser probes can be used to answer questions regarding the synaptic distribution of endogenous proteins and their microenvironment that would be difficult to resolve by other contemporary means: (i) the live distribution of untagged proteins at the neuromuscular junction (Cacophony and Shaker), (ii) the relative distribution of an untagged protein (PMCA) in pre- versus post-synaptic membranes separated by only 20 nm across the cleft of a fixed synapse, and (iii) the live targeting of functional probes (chemical and protein fluorescent pH reporters) to membrane protein-defined subcellular domains.

Polymerase evolution: efforts toward expansion of the genetic code

Genetic information is encoded by, but potentially not limited to, a four-letter alphabet. A variety of predominantly hydrophobic nucleobase analogues that form self-pairs in DNA have been examined as third base pair candidates. For example, the PICS self-pair is both stable in duplex DNA and synthesized by some wild-type polymerases with reasonable efficiency. These efforts to expand the genetic code are expected to be facilitated by optimizing both the unnatural nucleobase analogues and the polymerases that replicate them. Here, we report the use of an activity-based selection system to evolve a DNA polymerase that more efficiently replicates DNA containing the PICS self-pair. The selection system is based on the co-display on phage of DNA polymerase libraries and a DNA substrate containing the self-pair. Only polymerases that accept the unnatural substrate incorporate a biotin-dUTP to the attached primer and may then be isolated on a streptavidin solid support. A mutant of Sf polymerase, P2, was evolved which both inserts dPICSTP opposite dPICS in the template and extends the unnatural primer terminus by incorporation of the next correct natural dNTP, where the parental enzyme catalyzes neither step at detectable rates. P2 was found to be a triple mutant of Sf, with the mutations F598I, I614F, and Q489H. The evolved properties of P2, as well as the observed mutations, are consistent with an increased affinity for the DNA primer-template containing the self-pair.

Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair

Understanding fidelity-the faithful replication or repair of DNA by polymerases-requires tracking of the structural and energetic changes involved, including the elusive transient intermediates, for nucleotide incorporation at the template/primer DNA junction. We report, using path sampling simulations and a reaction network model, strikingly different transition states in DNA polymerase beta's conformational closing for correct dCTP versus incorrect dATP incoming nucleotide opposite a template G. The cascade of transition states leads to differing active-site assembly processes toward the "two-metal-ion catalysis" geometry. We demonstrate that these context-specific pathways imply different selection processes: while active-site assembly occurs more rapidly with the correct nucleotide and leads to primer extension, the enzyme remains open longer, has a more transient closed state, and forms product more slowly when an incorrect nucleotide is present. Our results also suggest that the rate-limiting step in pol beta's conformational closing is not identical to that for overall nucleotide insertion and that the rate-limiting step in the overall nucleotide incorporation process for matched as well as mismatched systems occurs after the closing conformational change.

Conformational Transition Pathway of Polymerase β/DNA upon Binding Correct Incoming Substrate

The closing conformational transition of wild-type polymerase beta bound to DNA template/primer before the chemical step (nucleotidyl transfer reaction) is simulated using the stochastic difference equation (in length version, "SDEL") algorithm that approximates long-time dynamics. The order of the events and the intermediate states during pol beta's closing pathway are identified and compared to a separate study of pol beta using transition path sampling (TPS) (Radhakrishnan, R.; Schlick, T. Proc. Natl. Acad. Sci. USA 2004, 101, 5970-5975). Results highlight the cooperative and subtle conformational changes in the pol beta active site upon binding the correct substrate that may help explain DNA replication and repair fidelity. These changes involve key residues that differentiate the open from the closed conformation (Asp192, Arg258, Phe272), as well as residues contacting the DNA template/primer strand near the active site (Tyr271, Arg283, Thr292, Tyr296) and residues contacting the beta and gamma phosphates of the incoming nucleotide (Ser180, Arg183, Gly189). This study compliments experimental observations by providing detailed atomistic views of the intermediates along the polymerase closing pathway and by suggesting additional key residues that regulate events prior to or during the chemical reaction. We also show general agreement between two sampling methods (the stochastic difference equation and transition path sampling) and identify methodological challenges involved in the former method relevant to large-scale biomolecular applications. Specifically, SDEL is very quick relative to TPS for obtaining an approximate path of medium resolution and providing qualitative information on the sequence of events; however, associated free energies are likely very costly to obtain because this will require both successful further refinement of the path segments close to the bottlenecks and large computational time.

Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly

To dissect the effects of the nucleotide-binding and catalytic metal ions on DNA polymerase mechanisms for DNA repair and synthesis, aside from the chemical reaction, we investigate their roles in the conformational transitions between closed and open states and assembly/disassembly of the active site of polymerase beta/DNA complexes before and after the chemical reaction of nucleotide incorporation. Using dynamics simulations, we find that closing before chemical reaction requires both divalent metal ions in the active site while opening after the chemical reaction is triggered by release of the catalytic metal ion. The critical closing is stabilized by the interaction of the incoming nucleotide with conserved catalytic residues (Asp190, Asp192, Asp256) and the two functional magnesium ions; without the catalytic ion, other protein residues (Arg180, Arg183, Gly189) coordinate the incomer's triphosphate group through the nucleotide-binding ion. Because we also note microionic heterogeneity near the active site, Mg(2+) and Na(+) ions can diffuse into the active site relatively rapidly, we suggest that the binding of the catalytic ion itself is not a rate-limiting conformational or overall step. However, geometric adjustments associated with functional ions and proper positioning in the active site, including subtle but systematic motions of protein side chains (e.g., Arg258), define slow or rate-limiting conformational steps that may guide fidelity mechanisms. These sequential rearrangements are likely sensitively affected when an incorrect nucleotide approaches the active site. Our suggestion that subtle and slow adjustments of the nucleotide-binding and catalytic magnesium ions help guide polymerase selection for the correct nucleotide extends descriptions of polymerase pathways and underscores the importance of the delicate conformational events both before and after the chemical reaction to polymerase efficiency and fidelity mechanisms.

Intramolecular interactions of the regulatory region with the catalytic core in the plasma membrane calcium pump

The access of three proteases to their sites of cleavage was used as a measure of regulatory interactions in the plasma membrane Ca2+ pump isoform 4b (PMCA4b). When the proteases could not cut at their sites in the C-terminal regulatory region, the interaction was judged to be tight. This was the case in the absence of Ca2+, when chymotrypsin and caspase cut PMCA only very slowly. Ca2+ accelerated the fragmentation, but the digestion remained incomplete. In the presence of Ca2+ plus calmodulin, the digestion became nearly complete in all cases, indicating a more flexible conformation of the carboxyl terminus in the fully activated state. The acceleration of proteolysis by Ca2+ or Ca2+ plus calmodulin occurred equally at the caspase site upstream of the calmodulin-binding domain and the chymotrypsin and calpain sites downstream of that domain. Replacing Trp1093 (a key residue within the calmodulin-binding domain) with alanine had a much more specific effect, because it exposed only proteolytic sites within the calmodulin-binding domain that had previously been shielded in the native protein. At these sites, both calpain and chymotrypsin cut the Trp1093 --> Ala mutant in the absence of calmodulin. These data indicate that, in the auto-inhibited conformation, the calmodulin-binding/auto-inhibitory sequence and the regions both upstream and downstream are in close contact with the catalytic core. Trp1093 plays an essential role not only in stabilizing the Ca2+-calmodulin/calmodulin-binding domain complex but also in the formation or stability of the inhibitory conformation of that domain when it interacts with the catalytic core of PMCA4b.

A novel calcium-dependent bacterial phosphatidylinositol-specific phospholipase C displaying unprecedented magnitudes of thio effect, inverse thio effect, and stereoselectivity

Understanding the potential range of enzymatic thio effects (kO/kS) is of great value when using sulfur-substituted phosphate analogues to study phosphoryl transfer reactions in enzymes and ribozymes. Herein we report that a newly discovered Ca2+-dependent Streptomyces antibioticus phosphatidylinositol-specific phospholipase C and its mutants display unprecedented magnitudes of thio effect, inverse thio effect, and RP/SP stereoselectivity. We demonstrate that for a single enzyme the bridging thio effect can vary from 0.002 to 20 and the nonbridging thio effect can vary from 1 to 108. These values fall outside the range of those reported for nonenzymatic reactions, emphasizing the need for cautious interpretation when using thio effects to elucidate details of enzyme catalysis.

Varied Molecular Interactions at the Active Sites of Several DNA Polymerases: Nonpolar Nucleoside Isosteres as Probes

We describe a survey of protein-DNA interactions with seven different DNA polymerases and reverse transcriptases, carried out with nonpolar nucleoside isosteres F (a thymidine analog) and Z and Q (deoxyadenosine analogues). Previous results have shown that Z and F can be efficiently replicated opposite each other by the exonuclease-free Klenow fragment of DNA polymerase I from Escherichia coli (KF(-)), although both of them lack Watson-Crick H-bonding ability. We find that exonuclease-inactive T7 DNA polymerase (T7(-)), Thermus aquaticus DNA polymerase (Taq), and HIV-reverse transcriptase (HIV-RT) synthesize the nonnatural base pairs A-F, F-A, F-Z, and Z-F with high efficiency, similarly to KF(-). Steady-state kinetics were also measured for T7(-) and the efficiency of insertion is very similar to that of KF(-); interestingly, the replication selectivity with this pair is higher for T7(-) than KF(-), possibly due to a tighter active site. A second group comprised of calf thymus DNA polymerase α (Pol α) and avian myeloblastosis virus reverse transcriptase (AMV-RT) was able to replicate the A-F and F-A base pairs to some extent but not the F-Z and the Z-F base pairs. Most of the insertion was recovered when Z was replaced by the nucleoside Q (9-methyl-1-H-imidazo[(4,5)-b]pyridine), which is analogous to Z but possesses a minor groove acceptor nitrogen. This strongly supports the existence of an energetically important hydrogen-bonded interaction between the polymerase and the minor groove at the incipient base pair for these enzymes. A third group, formed by human DNA polymerase β (Pol β) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT), failed to replicate the F-Z and Z-F base pairs. No insertion recovery was observed when Z was replaced by Q, possibly indicating that hydrogen bonds are needed at both the template and the triphosphate sites. The results point out the importance of DNA minor groove interactions at the incipient base pair for the activity of some polymerases, and demonstrate the variation in these interactions from enzyme to enzyme.

Okadaic acid as a probe for regulation in vitro of Mg(2+), Ca(2+)-ATPase activity in rat cortical and cerebellar synaptosomal membranes

The in vitro effect of okadaic acid on basal phorbol 12-myristate 13-acetate (PMA)-, and cyclic adenosine monophosphate (cAMP)-stimulated Mg(2+)-dependent Ca(2+)-adenosine triphosphatase (ATPase) activity in synaptosomal membranes isolated from rat brain cortex and cerebellum was investigated. The basal activity was enhanced by okadaic acid in both examined regions. This inhibitor differed in the regulation of Mg2+, Ca(2+)-ATPase activity in PMA- and cAMP-incubated membranes. Stimulation by calmodulin (CaM) of basal Mg2+, Ca(2+)-ATPase activity declined in cortex and cerebellum after treatment with okadaic acid. The presence of PMA or cAMP decreases the stimulatory effect of CaM. These results suggest that Mg2+, Ca(2+)-ATPase activity in the rat-brain synaptosomal membrane may be regulated in vitro by dephosphorylation processes.

Use of the polymerase chain reaction for the detection of alternatively spliced mRNAs of plasma membrane calcium pump

Polymerase chain reaction [PCR, reverse transcriptase-PCR (RT-PCR)] has been used to amplify the mRNA subspecies of the plasma membrane calcium pump isoform 1 (PMCA1) in total RNA extracted from hamster tissues. Two primers were synthesized that encompass the site at which a 154-bp exon is included totally (PMCA1a), partially (PMCA1c and d), or completely excluded (PMCA1b) in the carboxy-terminal regulatory region. PCR amplification revealed two bands (PMCA1b and 1c) that are more abundant in various tissues, while Southern hybridization of the samples after PCR amplification has detected two additional mRNA variants corresponding to PMCA1a and 1d. The distribution of these mRNA variants are tissue specific and correlate well with the pump protein distribution patterns on immunoblot. Since these multiple bands on the immunoblot are not derived from proteolysis, it is suggested that they represent the PMCA1 isozymes encoded by these alternatively spliced mRNAs. To our knowledge, this is the first report to show all four alternatively spliced mRNAs that are simultaneously detected in one single RNA sample using PCR technique. Since these isozymes are different in their regulatory domain, their tissue-specific expression may be physiologically important.

Calcium ion homeostasis in smooth muscle

Ca2+ plays an important role in the regulation of smooth-muscle contraction. In this review, we will focus on the various Ca(2+)-transport processes that contribute to the cytosolic Ca2+ concentration. Mainly the functional aspects will be covered. The smooth-muscle inositol 1,4,5-trisphosphate receptor and ryanodine receptor will be extensively discussed. Smooth-muscle contraction also depends on extracellular Ca2+ and both voltage- and Ca(2+)-release-activated plasma-membrane Ca2+ channels will be reviewed. We will finally discuss some functional properties of the Ca2+ pumps that remove Ca2+ from the cytoplasm and of the Ca2+ regulation of the nucleus.

The Ca(2+)-transport ATPases from the plasma membrane

The initial studies on the plasma membrane (PM) Ca(2+)-transport ATPases were made in the erythrocyte, a structure that can not be taken as representing a typical eukaryotic cell. In other cell types however, the study of the PM Ca(2+)-transport ATPase is complicated by the simultaneous expression of related Ca(2+)-pumps in intracellular stores. Whereas there are as yet no known specific inhibitors for the PM Ca(2+)-transport ATPase, a number of selective inhibitors for the endo(sarco)plasmic reticulum Ca2+ pumps have been described: thapsigargin, cyclopiazonic acid and 2,5-di-(tert-butyl)-1,4-benzohydroquinone. With the recent introduction of the molecular biological approach, it became quickly obvious that a family of at least 5 different PM Ca(2+)-transport ATPase genes govern the tissue-dependent expression of PM Ca2+ pumps. Moreover alternative splicing of the primary gene transcripts was found to further enhance the number of pump variants. The PM Ca(2+)-transport ATPase are subject to modulatory control by calmodulin, by acidic phospholipids, and by the known families of protein kinases. Each of the ensuing effects are mutually related and interdependent. The wide variety PM Ca2+ pump isoforms and their regulation by such an intricate modulatory network allows the distinct tissues to adapt most adequately to the prevailing tissue and stimulus specific requirements.

The plasma membrane calcium pump: a multiregulated transporter

Activation of many cells, especially nonexcitable cells, results in a Ca(2+) transient that is influenced in part by the kinetics of active extrusion of Ca(2+) across the plasma membrane. The molecular cloning of the plasma membrane Ca(2+)-pump has helped to clarify the relationship between its structure and function. The Ca(2+)-pump is controlled by multiple regulators, including calmodulin, phospholipids and various kinases. Longer term control is achieved through regulation of its gene expression, and the presence of a number of Ca(2+)-pump isoforms that differ in their regulatory domains provides potential functional diversity. In this review, we focus on the mechanisms that regulate the function of the Ca(2+)-pump, and their physiological significance.