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F J Kull

Publications and source records attributed to F J Kull.

At least 19 recordsLinked to original sources
PubMed2001

Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms.

Dynamins form a family of multidomain GTPases involved in endocytosis, vesicle trafficking and maintenance of mitochondrial morphology. In contrast to the classical switch GTPases, a force-generating function has been suggested for dynamins. Here we report the 2.3 A crystal structure of the nucleotide-free and GDP-bound GTPase domain of Dictyostelium discoideum dynamin A. The GTPase domain is the most highly conserved region among dynamins. The globular structure contains the G-protein core fold, which is extended from a six-stranded beta-sheet to an eight-stranded one by a 55 amino acid insertion. This topologically unique insertion distinguishes dynamins from other subfamilies of GTP-binding proteins. An additional N-terminal helix interacts with the C-terminal helix of the GTPase domain, forming a hydrophobic groove, which could be occupied by C-terminal parts of dynamin not present in our construct. The lack of major conformational changes between the nucleotide-free and the GDP-bound state suggests that mechanochemical rearrangements in dynamin occur during GTP binding, GTP hydrolysis or phosphate release and are not linked to loss of GDP.

Binding Sites↗
PubMed2001

Structure of a genetically engineered molecular motor.

Molecular motors move unidirectionally along polymer tracks, producing movement and force in an ATP-dependent fashion. They achieve this by amplifying small conformational changes in the nucleotide-binding region into force-generating movements of larger protein domains. We present the 2.8 A resolution crystal structure of an artificial actin-based motor. By combining the catalytic domain of myosin II with a 130 A conformational amplifier consisting of repeats 1 and 2 of alpha-actinin, we demonstrate that it is possible to genetically engineer single-polypeptide molecular motors with precisely defined lever arm lengths and specific motile properties. Furthermore, our structure shows the consequences of mutating a conserved salt bridge in the nucleotide-binding region. Disruption of this salt bridge, which is known to severely inhibit ATP hydrolysis activity, appears to interfere with formation of myosin's catalytically active 'closed' conformation. Finally, we describe the structure of alpha-actinin repeats 1 and 2 as being composed of two rigid, triple-helical bundles linked by an uninterrupted alpha-helix. This fold is very similar to the previously described structures of alpha-actinin repeats 2 and 3, and alpha-spectrin repeats 16 and 17.

Actinin↗
PubMed2001

Inhibition of potato polyphenol oxidase by anions and activity in various carboxylate buffers (pH 4.8) at constant ionic strength.

The activity of potato polyphenol oxidase (tyrosinase) toward DL-3,4-dihydroxyphenylalanine (K(M) 5.39 mM) was studied using a variety of carboxylate buffers at a common pH and ionic strength. Enzyme activity, greatest in citrate and least in oxalate, correlated with increasing carboxyl concentration and molecular mass. The lower activity in oxalate was attributed to more effective chelation of a copper(II) form of the enzyme by the oxalate dianion. Sodium halide salts inhibited the enzyme. Although there was little difference in inhibition between sodium and potassium salts, the degree and type of inhibition was anion dependent; K(is), values for NaCl and KCl, (competitive inhibitors) were 1.82 and 1.62 mM, whereas Na(2) SO(4) and K(2) SO(4) (mixed inhibitors) had K(is) and K(ii) values in the 250 to 450 mM range.

Buffers↗
PubMed2000

Motor proteins of the kinesin superfamily: structure and mechanism.

Kinesins are ATP-driven microtubule motor proteins that produce directed force. The kinesin superfamily currently encompasses over 100 eukaryotic proteins containing a common motor domain. Both the nucleotide-binding fold and active-site chemistry of the motor domain are also present in the actin-based motor, myosin. Kinesins can be classified into three groups based on the position of their motor domains: N-terminal, C-terminal and internal kinesins. Conventional kinesin operates as a dimer, walking in a co-ordinated, hand-over-hand fashion along a microtubule protofilament. X-ray crystal structures and EM reconstructions show major differences in the quaternary arrangement of kinesin domains in minus-end- and plus-end-directed motors. Kinesin's neck region, directly adjacent to the motor domain, dictates directionality.

Adenosine Triphosphate↗
PubMed1999

Motor proteins of the kinesin family. Structures, variations, and nucleotide binding sites.

Microtubule-dependent motors of the kinesin family convert the energy from ATP hydrolysis into mechanical work in order to transport vesicles and organelles along microtubules. The motor domains of several kinesins have been solved by X-ray diffraction, but the conformational changes associated with force development remain unknown. Here we describe conformational properties of kinesin that might be related to the mechanism of action. First, we have evaluated the conformational variability among all known kinesin structures and find they are concentrated in six areas, most of which are functionally important either in microtubule binding or in linking the core motor to the stalk. Secondly, we show that there is an important difference between kinesins when compared with myosins or GTPases (with which kinesin motor domains bear structural and catalytic similarities); in the diphosphate-state (with bound ADP), all kinesins show a 'tight' nucleotide-binding pocket, comparable with myosin or GTPases in the triphosphate state, whose nucleotide-binding pockets become open, or 'loose', following nucleotide hydrolysis. Thus, kinesin-ADP appears to be in a tense state, resembling that observed in myosin-ATP or p21ras-GTP.

Animals↗
PubMed1998

The case for a common ancestor: kinesin and myosin motor proteins and G proteins.

Recent studies have shown surprising structural and functional similarities between the motor domains of kinesin and myosin. Common features have also been described for motor proteins and G proteins. Despite these similarities, the evolutionary relationships between these proteins, even among the motor proteins, has not been obvious, since the topological connectivities of the core overlapping structural elements in these transducing proteins are not identical to one another. Using secondary structure topology, comparison of functional domains and active site chemistry as criteria for relatedness, we propose a set of rules for determining potential evolutionary relationships between proteins showing little or no sequence identity. These rules were used to explore the evolutionary relationship between kinesin and myosin, as well as between motor proteins and other phosphate-loop (P-loop) containing nucleotide-binding proteins. We demonstrate that kinesin and myosin show significant chemical conservations within and outside of the active site, and present an evolutionary scheme that produce their respective topologies from a hypothetical ancestral protein. We also show that, when compared with various other P-loop-containing proteins, the cytoskeletal motors are most similar to G proteins with respect to topology and active site chemistry. We conclude that kinesin and myosin, and possibly G proteins, are probably directly related via divergent evolution from a common core nucleotide-binding motif, and describe the likely topology of this ancestor. These proteins use similar chemical and physical mechanisms to both sense the state of the nucleotide bound in the active site, and then transmit these changes to protein partners. The different topologies can be accounted for by unique genetic insertions that add to the edge of a progenitor protein structure and do not disrupt the hydrophobic core.

Adenylate Kinase↗
PubMed1997

Inhibition and substrate competition kinetics in analysis of porcine thyroid alkaline ribonuclease's specificity toward synthetic RNA's and tRNA.

Inhibition and substrate competition kinetics demonstrated that tRNA is a highly preferred substrate of thyroid alkaline RNase. The pyrimidine-specific RNase cleaved poly(C) 2.8 x 10(5) faster than poly(U). kcat:K(M) ratios for tRNA and poly(C) based on molecular weights failed to predict preference when both were present. Competition experiments between poly(C) and tRNA revealed tRNA was a tight-binding competing substrate and the cytidylate residues in the 3'-CCA terminus to tRNA were preferred about 280:1 over those in poly(C). Poly(U) was competitive with tRNA. When poly(C) was the substrate, inhibition type by poly(G) depended on poly(G) concentration. Neither tRNA lacking its 3' terminal cytidylyl(3'-5')adenosine and terminating in a 2':3' cCMP residue, tRNA lacking its 3' terminal 5'AMP residue, guanosine, nor guanylyl(3'-5')guanylyl(3'-5')guanosine were inhibitors. Product inhibition by adenosine and 2':3' cCMP showed the kinetic mechanism for cleavage of tRNA was ordered uni bi.

Animals↗
PubMed1996

Crystal structure of the kinesin motor domain reveals a structural similarity to myosin.

Kinesin is the founding member of a superfamily of microtubule based motor proteins that perform force-generating tasks such as organelle transport and chromosome segregation. It has two identical approximately 960-amino-acid chains containing an amino-terminal globular motor domain, a central alpha-helical region that enables dimer formation through a coiled-coil, and a carboxy-terminal tail domain that binds light chains and possibly an organelle receptor. The kinesin motor domain of approximately 340 amino acids, which can produce movement in vitro, is much smaller than that of myosin (approximately 850 amino acids) and dynein (1,000 amino acids), and is the smallest known molecular motor. Here, we report the crystal structure of the human kinesin motor domain with bound ADP determined to 1.8-A resolution by X-ray crystallography. The motor consists primarily of a single alpha/beta arrowhead-shaped domain with dimensions of 70 x 45 x 45 A. Unexpectedly, it has a striking structural similarity to the core of the catalytic domain of the actin-based motor myosin. Although kinesin and myosin have virtually no amino-acid sequence++ identity, and exhibit distinct enzymatic and motile properties, our results suggest that these two classes of mechanochemical enzymes evolved from a common ancestor and share a similar force-generating strategy.

Adenosine Diphosphate↗
PubMed1996

Crystal structure of the motor domain of the kinesin-related motor ncd.

Microtubule-based ATPases of the kinesin superfamily provide the motile force for many animated features of living cells. Kinesin motors differ in their direction of movement along microtubules. Kinesin and ncd, a kinesin-related motor involved in formation and maintenance of mitotic and meiotic spindles, move in opposite directions along microtubules, even though their motor domains are 40% identical in amino-acid sequence. Here we report the crystal structure of the MgADP complex of the Drosophila ncd motor domain determined to 2.5A by X-ray crystallography, and compare it to the kinesin structure. The ncd and kinesin motor domains are remarkably similar in structure, and the locations of conserved surface amino acids suggest these motors share a common microtubule-binding site. Moreover, structural and functional comparisons of ncd, kinesin, myosin and G proteins indicate that these NTPases may have a similar strategy of changing conformation between NTP and NDP states. We propose a general model for converting a common gamma-phosphate-sensing mechanism into opposite polarities of movement for kinesin and ncd.

Adenosine Diphosphate↗
PubMed1995

The shapes of the motor domains of two oppositely directed microtubule motors, ncd and kinesin: a neutron scattering study.

The shapes of the motor domains of kinesin and ncd, which move in opposite directions along microtubules, have been investigated. Using proteins expressed in Escherichia coli, it was found that at high salt (> 200 mM) Drosophila ncd motor domain (R335-K700) and human kinesin motor domain (M1-E349) were both sufficiently monomeric to allow an accurate determination of their radii of gyration (Rg) and their molecular weights. The measured Rg values of the ncd and kinesin motor domains in D2O were 2.06 +/- 0.06 and 2.05 +/- 0.04 nm, respectively, and the molecular weights were consistent with those computed from the amino acid compositions. Fitting of the scattering curves to approximately 3.5 nm resolution showed that the ncd and kinesin motor domains can be described adequately by triaxial ellipsoids having half-axes of 1.42 +/- 0.38, 2.24 +/- 0.44, and 3.65 +/- 0.22 nm, and half-axes of 1.52 +/- 0.23, 2.00 +/- 0.25, and 3.73 +/- 0.10 nm, respectively. Both motor domains are described adequately as somewhat flattened prolate ellipsoids with a maximum dimension of approximately 7.5 nm. Thus, it appears that the overall shapes of these motor domains are not the major determinants of the directionality of their movement along microtubules.

Animals↗
PubMed1995

The inhibition of human salivary alpha-amylase by type II alpha-amylase inhibitor from Triticum aestivum is competitive, slow and tight-binding.

A kinetic analysis of the inhibition of human salivary alpha-amylase (EC 3.2.1.1) by wheat seed (Triticum aestivum) type II alpha-amylase inhibitor revealed the inhibition was slow and tight-binding. The inhibition was competitive with an inhibition binding constant of the alpha-amylase inhibitor for alpha-amylase of 0.29 nM. The KM of alpha-amylase for soluble starch (calculated per mole of alpha-1,4 linked maltose residues) was 5.87 mM.

Binding, Competitive↗
PubMed1995

Solution structure of two molecular motor domains: nonclaret disjunctional and kinesin.

The effects of selected ligands on the structure of the truncated heavy-chain chemomechanical motor domains of Drosophila ncd and human kinesin were compared using the technique of transient electric birefringence. The 366-amino acid C-terminal motor domain of Drosophila nonclaret disjunctional, ncd(335-700), and the 349-amino acid N-terminal motor domain of human kinesin, kinesin(349), were studied at 4 degrees C in neutral buffers with ionic strength of 100 mM to form complexes with either MgADP or MgADP.Vi. The rotational diffusion time adjusted to 20 degrees C and water, tau 20,W, for ncd(335-700).MgADP is 32.8 ns, and for ncd(335-700).MgADP.Vi is 34.8 ns, suggesting prolate ellipsoids with dimensions 9.40 x 3.77 nm and 9.73 x 3.70 nm, respectively. The specific Kerr constant, Ksp, of ncd is -1.65 x 10(-12) cm2V-2 for the MgADP complex and -1.15 x 10(-12) cm2V-2 for the MgADP.Vi complex. The large negative Ksp for a prolate protein suggests an unusual charge distribution with two long surfaces with opposite charge. The tau 20,W for kinesin(349).MgADP is longer than the corresponding ncd motor and shows a decrease with increased electric field. The kinesin(349).MgADP.Vi complex has a longer tau 20,W. The Ksp for kinesin(349) is 0.36 x 10(-12) cm2V-2 for each complex.

Animals↗
PubMed1994

Tubulin GTP hydrolysis influences the structure, mechanical properties, and kinesin-driven transport of microtubules.

Tubulin is a GTPase that hydrolyzes its bound nucleotide triphosphate after it becomes incorporated into a microtubule. The only known consequence of nucleotide hydrolysis is that it increases the dissociation rate of tubulin from the end of the microtubule by 2 orders of magnitude. In this study, we investigated whether microtubules composed of tubulin-GMPCPP (guanylyl alpha,beta-methylenediphosphate) (a very slowly hydrolyzed GTP analog) or tubulin-GDP exhibit additional structural or functional differences. We show that tubulin-GMPCPP microtubules are significantly stiffer than tubulin-GDP microtubules and have a 21% shallower protofilament twist angle. We also find that kinesin, a microtubule-based motor protein, transports tubulin-GMPCPP microtubules at approximately 30% faster rates than tubulin-GDP microtubules. These findings suggest that growing microtubule ends, which are thought to be composed of tubulin-GTP, may have different structural and mechanical properties from the remainder of the microtubule polymer.

Animals↗
PubMed1985

Single transporter for sulfate, selenate, and selenite in Escherichia coli K-12.

A Michaelis-Menten kinetic analysis of the transport of sulfate, selenate, and selenite into Escherichia coli K-12 showed that the three dianions were transported by the same carrier. Km values, used as a measure of the affinity of each ligand for the carrier, showed that sulfate was bound 5 times more tightly than selenate and 37 times more tightly than selenite. The specificity ratio, Vmax/Km, also indicated that sulfate was the preferred ligand. There was little difference in the ratios for selenate and selenite.

Biological Transport↗
PubMed1983

The ribonuclease inhibitors from porcine thyroid and liver are slow, tight-binding inhibitors of bovine pancreatic ribonuclease A.

Ribonuclease inhibitors were purified from the latent ribonuclease fractions of porcine thyroid and liver and used to test the hypothesis that their inhibition of bovine pancreatic ribonuclease A is correctly described by tight-binding rather than Michaelis-Menton kinetics. Both proteins were found to act as slow, tight-binding inhibitors of the enzyme. These steady-state velocities also showed that both the thyroid and liver inhibitors were competitive inhibitors of bovine pancreatic ribonuclease A with Ki's of 0.1 and 0.4 nM, respectively. In contrast to interpretations based on Michaelis-Menton assumptions that show non-competitive inhibition, these results suggest that an enzyme:inhibitor:substrate complex does not exist.

Animals↗
PubMed1983

Low molecular weight aspartyl-tRNA synthetase from porcine thyroid. Purification, characterization, and heterogeneity.

The total low molecular weight aspartyl-tRNA synthetase activity of porcine thyroid is distributed among four distinct forms, all of which are identical in size, as determined by gel filtration. The predominant form was purified 25,000-fold to near homogeneity. A high concentration of glycerol (25%, v/v) was required throughout the procedure to maintain stability. The native enzyme was of the alpha 2-type with a Mr = 120,000 estimated by gel filtration. Its subunits were Mr = 53,000 as determined using polyacrylamide gel electrophoresis under denaturing conditions. The enzyme had an isoelectric point of pH 5.4 and pH optimum that varied from pH 7.3 to 8.8 depending on the type of buffer present. The variation in pH optimum was related to a salt effect. All salts tested were inhibitory, with the degree of inhibition dependent on the anion present. Inorganic pyrophosphate was a particularly powerful inhibitor; Km values for aspartate and tRNAAsp were significantly reduced in the presence of inorganic pyrophosphatase. Evidence is presented that the allotropism of the low molecular weight forms is not due to phosphorylation, proteolytic degradation, or stable enzyme-substrate complexes.

Amino Acyl-tRNA Synthetases↗
PubMed1983

Porcine thyroid cytosolic, latent, alkaline, ribonuclease: does an acidification step during purification alter the enzyme's properties?

The effect of an acidic step in the purification of porcine thyroid, latent, alkaline ribonuclease was studied using highly purified acid-treated and non-acid-treated enzymes. The enzymes differed by affinity and CM-cellulose chromatography, specific activity, in distribution among multiple forms, in response to some mono- and divalent salts, in degree of inhibition by p-chloromercuriphenylsulfonate and ribonuclease inhibitor, in activity toward poly (U). The acid-treated enzyme was very heterogeneous as shown by chromatography on affinity and ion-exchange columns and electrophoresis. The enzymes had similar molecular weights, pH optima, ionic strength effects, general specificity and products.

Animals↗