Analysis of nucleotide binding to Dictyostelium myosin II motor domains containing a single tryptophan near the active site.

Dictyostelium myosin II motor domain constructs containing a single tryptophan residue near the active sites were prepared in order to characterize the process of nucleotide binding. Tryptophan was introduced at positions 113 and 131, which correspond to those naturally present in vertebrate skeletal muscle myosin, as well as position 129 that is also close to the adenine binding site. Nucleotide (ATP and ADP) binding was accompanied by a large quench in protein fluorescence in the case of the tryptophans at 129 and 131 but a small enhancement for that at 113. None of these residues was sensitive to the subsequent open-closed transition that is coupled to hydrolysis (i.e. ADP and ATP induced similar fluorescence changes). The kinetics of the fluorescence change with the F129W mutant revealed at least a three-step nucleotide binding mechanism, together with formation of a weakly competitive off-line intermediate that may represent a nonproductive mode of nucleotide binding. Overall, we conclude that the local and global conformational changes in myosin IIs induced by nucleotide binding are similar in myosins from different species, but the sign and magnitude of the tryptophan fluorescence changes reflect nonconserved residues in the immediate vicinity of each tryptophan. The nucleotide binding process is at least three-step, involving conformational changes that are quite distinct from the open-closed transition sensed by the tryptophan Trp(501) in the relay loop

The dynamics of the relay loop tryptophan residue in the Dictyostelium myosin motor domain and the origin of spectroscopic signals.

Steady-state and time-resolved fluorescence measurements were performed on a Dictyostelium discoideum myosin II motor domain construct retaining a single tryptophan residue at position 501, located on the relay loop. Other tryptophan residues were mutated to phenylalanine. The Trp-501 residue showed a large enhancement in fluorescence in the presence of ATP and a small quench in the presence of ADP as a result of perturbing both the ground and excited state processes. Fluorescence lifetime and quantum yield measurements indicated that at least three microstates of Trp-501 were present in all nucleotide states examined, and these could not be assigned to a particular gross onformation of the motor domain. Enhancement in emission intensity was associated with a reduction of the contribution from a statically quenched component and an increase in a component with a 5-ns lifetime, with little change in the contribution from a 1-ns lifetime component. Anisotropy measurements indicated that the Trp-501 side chain was relatively immobile in all nucleotide states, and the fluorescence was effectively depolarized by rotation of the whole motor domain with a correlation time on 50-70 ns. Overall these data suggest that the backbone of the relay loop remains structured throughout the myosin ATPase cycle but that the Trp-501 side chain experiences a different weighting in local environments provided by surrounding residues as the adjacent converter domain rolls around the relay loop

Kinetic mechanism of human dUTPase, an essential nucleotide pyrophosphatase enzyme

Human dUTPase is essential in controlling relative cellular levels of dTTP/ dUTP, both of which can be incorporated into DNA. The nuclear isoform of the enzyme has been proposed as a promising novel target for anticancer chemotherapeutic strategies. The recently determined three-dimensional structure of this protein in complex with an isosteric substrate analogue allowed in-depth structural characterization of the active site. However, fundamental steps of the dUTPase enzymatic cycle have not yet been revealed. This knowledge is indispensable for a functional understanding of the molecular mechanism and can also contribute to the design of potential antagonists. Here we present detailed pre-steady-state and steady-state kinetic investigations using a single tryptophan fluorophore engineered into the active site of human dUTPase. This sensor allowed distinction of the apoenzyme, enzyme-substrate, and enzyme product complexes. We show that the dUTP hydrolysis cycle consists of at least four distinct enzymatic steps: (i) fast substrate binding, (ii) isomerization of the enzyme-substrate complex into the catalytically competent conformation, (iii) a hydrolysis (chemical) step, and (iv) rapid, nonordered release of the products. Independent quenched-flow experiments indicate that the chemical step is the rate-limiting step of the enzymatic cycle. To follow the reaction in the quenched-flow, we devised a novel method to synthesize gamma-(32) P-labeled dUTP. We also determined by indicator-based rapid kinetic assays that proton release is concomitant with the rate-limiting hydrolysis step. Our results led to a quantitative kinetic model of the human dUTPase catalytic cycle and to direct assessment of relative flexibilities of the C-terminal arm, critical for enzyme activity, in the enzyme-ligand complexes along the reaction pathway

Mechanism of blebbistatin inhibition of myosin II

Blebbistatin is a recently discovered small molecule inhibitor showing high affinity and selectivity toward myosin II. Here we report a detailed investigation of its mechanism of inhibition. Blebbistatin does not compete with nucleotide binding to the skeletal muscle myosin subfragment-1. The inhibitor preferentially binds to the ATPase intermediate with ADP and phosphate bound at the active site, and it slows down phosphate release. Blebbistatin interferes neither with binding of myosin to actin nor with ATP-induced actomyosin dissociation. Instead, it blocks the myosin heads in a products complex with low actin affinity. Blind docking molecular simulations indicate that the productive blebbistatin-binding site of the myosin head is within the aqueous cavity between the nucleotide pocket and the cleft of the actin-binding interface. The property that blebbistatin blocks myosin II in an actin-detached state makes the compound useful both in muscle physiology and in exploring the cellular function of cytoplasmic myosin II isoforms, whereas the stabilization of a specific myosin intermediate confers a great potential in structural studies

Localization and characterization of the inhibitory Ca2+-binding site of Physarum polycephalum myosin II.

A myosin II is thought to be the driving force of the fast cytoplasmic streaming in the plasmodium of Physarum polycephalum. This regulated myosin, unique among conventional myosins, is inhibited by direct Ca2+ binding. Here we report that Ca2+ binds to the first EF-hand of the essential light chain (ELC) subunit of Physarum myosin. Flow dialysis experiments of wild-type and mutant light chains and the regulatory domain revealed a single binding site that shows moderate specificity for Ca2+. The regulatory light chain, in contrast to regulatory light chains of higher eukaryotes, is unable to bind divalent cations. Although the Ca2+-binding loop of ELC has a canonical sequence, replacement of glutamic acid to alanine in the -z coordinating position only slightly decreased the Ca2+ affinity of the site, suggesting that the Ca2+ coordination is different from classical EF-hands; namely, the specific "closed-to-open" conformational transition does not occur in the ELC in response to Ca2+. Ca2+- and Mg2+-dependent conformational changes in the microenvironment of the binding site were detected by fluorescence experiments. Transient kinetic experiments showed that the displacement of Mg2+ by Ca2+ is faster than the change in direction of cytoplasmic streaming; therefore, we conclude that Ca2+ inhibition could operate in physiological conditions. By comparing the Physarum Ca2+ site with the well studied Ca2+ switch of scallop myosin, we surmise that despite the opposite effect of Ca2+ binding on the motor activity, the two conventional myosins could have a common structural basis for Ca2+ regulation

Humán dUTPáz: kooperativitás és sejtbeli kölcsönhatások = Human dUTPase: cooperativity and cellular interactions

Az enzimműködés mechanizmusának tisztázása és a katalitikus ciklus részletes leírása, valamint a humán dUTPáz sejtbeli siRNS csendesítése témákban jelentős cikkeket közöltünk, többek közt a JBC, Accounts Chem. Res és PNAS folyóiratokban. Fehérjekrisztallográfia, a 31P NMR, és a QM-MM számításos módszerek, valamint steady-state and tranziens enzimkinetikai módszerek együttes alkalmazása révén sikerült olyan egyedi intermediereket azonosítani, melyek hatékony gátlószerek tervezésében is szerepet játszhatnak. A humán dUTPáz gátlása rákterápiában lehet fontos. TAP-tag kísérleteinkben azonosítottuk az importin-alfa fehérjét, mint a humán dUTPáz egyik sejtbeli kölcsönható partnerét. Bizonyítottuk, hogy a nukleáris lokalizációs szignál (NLS) melletti foszforiláció kihat a dUTPáz intracelluláris lokalizációjára: a foszforilált fehérjét mimikáló mutáns kireked a sejtmagból. A vad típusú enzim, egy hiperfoszforilációt, valamint egy hipofoszforilációt mimikáló mutáns forma magi akkumulációját videomikroszkópos kísérletekkel hasonlítottuk össze. Megállapítottuk, hogy az utódsejtekbe jutó foszforilált dUTPáz pool a sejtciklus előrehaladtával, valószínűleg defoszforilációt követően újra akkumulálódhat a magban, de ez a folyamat lassú. Az NLS-környéki foszforiláció sejtciklushoz kötött mechanizmusát számos egyéb humán fehérjén is azonosítottuk – ez a folyamat általános jelentőségű lehet az utódsejtek magi proteómjának kialakításában. | Significant articles were published in journals such as JBC, Accounts Chem Res and PNAS, covering the topics of the molecular mechanism of action, distinct steps in the catalytic cycle, and siRNA silencing of human dUTPase. We identified multiple unique intermediary states using a combined approach of X-ray crystallography, 31P NMR, computational chemistry and steady-state/transient enzyme kinetics. These intermediates may form the basis of inhibitor design against human dUTPase, a potential for novel anticancer drugs. Using TAP-tag experiments, we identified importin-alfa as a cellular interacting partner of human dUTPase. We showed that a specific phosphorylation in the vicinity of the nuclear localization signal (NLS) impedes nuclear import. Videomicroscopy was used to compare nuclear accumulation kinetics in daughter cells following mitosis for wild type, as well as fór hypo- and hyperphosphorylation mimicking mutants. We showed that the phosphorylated dUTPase pool that is transmitted to the daughter cells may again accumulate in the cytoplasm, but only after dephosphorylation and in a rather slow manner. We identified similar mechanism for numerous other human proteins – this process may possess general significance in shaping the nuclear proteome of daughter cells