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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Porcine thyroid cytosolic, latent alkaline ribonuclease: resistance to protein denaturants

1. A ribonuclease isolated from porcine thyroid cytosol using phenol: sodium dodecylsulfate treatment was associated with RNA and identical to latent alkaline ribonuclease. 2. Distribution of activity between aqueous and phenolic phases depended on pH, RNA, and ribonuclease inhibitor. 3. The ribonuclease was totally resistant to urea, guanidinium: HCl, chloroform:isoamyl alcohol, ethanol, heating at 100 degrees C for 10 min or at 80 degrees C plus 100 mM NaCl. It was highly resistant to hydrolysis by proteinase K except in the presence of detergent. 4. The extreme stability and other properties of latent alkaline ribonuclease could be the result of its association with RNA.

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.

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.

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.

Uptake of selenium-75 by PHA-stimulated lymphocytes : Effect on glutathione peroxidase

To determine which of a variety of inorganic and organic selenium compounds could best stimulate glutathione peroxidase, human lymphocytes were cultured with a number of selenium sources. The phytohemagglutinin-transformed lymphocytes were cultured in the presence of(75)Se bound to serum proteins (25% v/v) or 10(-7) M concentrations of [(75)Se]-selenite, [(75)Se]-selenate, [(75)Se]-selenocystine, and [(75)Se]-selenomethionine. Organic forms of selenium were taken up in preference to inorganic forms. Control cultures, from which exogenous selenium had been omitted, showed a decreased level of glutathione peroxidase activity at the end of a 4 d culture period. Of the Se sources tested, [(75)Se]-selenocystine and [(75)Se]-labeled fetal calf serum proteins increased enzyme activity significantly, 79 and 47%, respectively, but selenite increased activity only by 7%. These results indicate that selenium from the two organic sources is most readily available for glutathione peroxidase synthesis.

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.

In vitro incorporation of selenomethionine into protein by astragalus polysomes

Selenium-accumulator plants synthesize selenium compounds that differ from those produced by nonaccumulators. To determine if there are any subcellular differences between accumulators and nonaccumulators in the use of selenomethionine in vitro, polysomes from Astragalus crotalariae (accumulator) and Astragalus lentiginosis (nonaccumulator) were translated in the presence of selenomethionine. Polysomes from both species efficiently used selenomethionine in vitro during the translation process. Inasmuch as no differences in the incorporation of selenomethionine into protein were observed between polysomes from the two types of Astragalus, it can be inferred that in accumulators there exists a mechanism that either prevents synthesis of selenomethionine or modifies this selenocompound to a derivative that cannot be incorporated into protein.

Selenium toxicity: aminoacylation and Peptide bond formation with selenomethionine

Selenomethionine and methionine were compared as substrates for in vitro aminoacylation, ribosome binding, and peptide bond formation with preparations from wheat germ. Selenomethionine paralleled methionine in all steps of the translation process except peptide bond formation. Peptide bond formation with the initiating species of tRNA(Met) demonstrated that selenomethionyl-tRNA(Met) was less effective as a substrate than was methionyl-tRNA(f) (Met). Participation of selenomethionine in the initiation process of translation could be expected to reduce the overall rate of protein synthesis and might aid in explaining selenium toxicity in selenium-sensitive plants.

A procedure for the rapid preparation of 14C-aminoacyl-transfer RNA and its use in the assay of class I ribonucleases and ribonuclease inhibitor

The presence of ribonuclease inhibitor and/or the activity of class I ribonucleases can conveniently be measured, at all stages of purification, by a highly sensitive assay based on the loss of radioactivity during the concomitant hydrolysis of tRNA and small amounts of 14C-labeled aminoacyl-tRNA. The rapid, economical assay, which is readily adaptable to homologous tRNA substrates, eliminates the necessity of filtration, centrifugation and ultraviolet spectroscopy measurements required by most other assays and is particularly suitable for multiple samples and kinetic measurements.

In Vitro Incorporation of Selenomethionine into Protein by Vigna radiata Polysomes

Vigna radiata polysomes efficiently incorporated [(75)Se]selenomethionine, [(14)C]methionine, and [(14)C]leucine in vitro. The optimal conditions for translation were determined to be 4.8 millimolar Mg(2+), 182 millimolar K(+), and pH 7.4. The rates of incorporation of [(75)Se]selenomethionine and [(14)C]methionine were similar when measured separately, but [(75)Se]selenomethionine incorporation was 35% less than [(14)C]methionine incorporation when both amino acids were present in equal molar concentrations. Polyacrylamide gel electrophoresis of the hot trichloroacetic acid precipitable translation products demonstrated synthesis of high molecular weight labeled proteins in the presence of [(75)Se]selenomethionine or [(35)S]methionine. No major differences in molecular weights could be detected in the electrophoretic profiles. Utilization of selenomethionine during translation by Vigna radiata polysomes establishes a route for the assimilation of selenomethionine by plants susceptible to selenium toxicity.

Preparation of oligonucleotides and their use in molecular weight estimations

Yeast RNA was used to prepare oligonucleotides employed to calibrate a G-50 Sephadex column. The oligonucleotides' preparation, isolation, desalting and characterization is described. Data obtained by chromatography of the oligonucleotides demonstrate that the molecular weights of oligonoucleotides can be easily determined by interpolation using plots of elution volumes (Ve) versus molecular weights (M). Errors greater than 20% are obtained if the conventional plot of Ve-Vo/Vs versus log M is used (where Vo is the void volume of the column and Vs is the volume of the column occupied by the inert phase, the G-50 Sephadex).

Thyroid Ribonucleic Acid-Iodopeptides. Comparison of Tyrosyl-Complex II and Tyrosyl-tRNA

It has previously been shown that mammalian RNA-peptidyl complexes are found in close association with tRNA, but can be separated from the bulk of the tRNA by benzoylated diethylaminoethylcellulose chromatography (Kull, F.J., and Soodak, M. (1971), Biochim. Biophys. Acta 246, l; Gadski, R.A., and Kull, F.J. (1973), Biochemistry 12, 1907). These studies also showed that under aminoacylation conditions the complex fractions were able to act as acceptors for certain amino acids and that the formation of porcine thyroid tyrosyl-complex II was particularly high. Because of this high acceptor function, and because of the importance of tyrosine to thyroid metabolism, further studies were conducted comparing some of the properties of porcine thyroid tyrosyl-complex II with those of porcine thyroid tyrosyl-tRNA. Porcine thyroid tyrosyl-tRNA synthetase was purified in excess of 200-fold and characterized. It was found that maximal aminoacylation was achieved at pH 8.1 in the presence of 150 mM KCl. The Km for tyrosine was determined to be 3.0 X 10(-6) M. The purified thyroid tyrosyl-tRNA synthetase was used under aminoacylation conditions to prepare radioactively labeled porcine thyroid tyrosyl-tRNA and tyrosyl-complex II. Comparisons made using reversed-phase column chromatography (RPC-5) showed distinct differences between the two aminoacylated species and revealed, in addition, a number of isoaccepting forms of tyrosine tRNA. Tyrosyl-complex II was also found to differ from tyrosyl-tRNA in that it is more stable to deacylation at pH 7.0 and at pH 4.4 and to degradation by ribonuclease A. In addition, tyrosyl-complex II, unlike tyrosyl-tRNA, is degraded by trypsin. Ribosomal binding studies showed that tyrosyl-complex II did not respond to the codons for tyrosine, UpApU and UpApC, whereas tyrosyl-tRNA responded to both. It is suggested that thyroid tyrosine complex II is representative of a group of related complexes that constitute the complex II fraction and that, although the complexes resemble tRNA in many respects, they have distinctly different characteristics than conventional tRNA.

Multiple phenylalanyl-transfer ribonucleic acid synthetase activities in the cytoplasm of Neurospora crassa

Several tRNA's specific for a particular amino acid have been shown to exist in multiple, or isoaccepting, forms. There is considerable interest in establishing whether multiple aminoacyl-tRNA synthetases also exist. We present evidence that the cytoplasm of Neurospora crassa contains three chromatographically separable phenylalanyl-tRNA synthetases distinct from mitochondrial phenylalanyl-tRNA synthetase. In addition to differences in chromatographic properties the three enzymes exhibit different affinities, in Tris-Cl buffer, toward purified species of valine and alanine tRNA's isolated from Escherichia coli. The two major chromatographic fractions have very similar sedimentation characteristics, which makes a monomer-dimer relationship unlikely.