Model for the motor component of dynein heavy chain based on homology to the AAA family of oligomeric ATPases.

BACKGROUND: Recent iterative methods for sequence alignment have indicated that the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. These alignments indicate that the core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. RESULTS: We report predicted structures for the six AAA modules in the beta heavy chain of axonemal dynein, based upon their homology to a template of structurally conserved regions derived from three AAA proteins with experimentally determined structures (pdb:1A5T, pdb:1DOO, and pdb:1NSF). The secondary structural elements of the AAA modules in dynein correspond to regions of sequence that are relatively well conserved in different dynein isoforms. The tertiary structure of each AAA module comprises a major alpha/beta N domain from which a smaller all-alpha C domain protrudes at an angle, as part of the putative nucleotide binding cavity. The structures of the six modules are assembled into a ring, approximately 125 A in diameter, that resembles the structure of the dynein motor unit observed by electron microscopy. CONCLUSION: The predicted structures are supported by procedures that assess global, regional, and local quality, with the module containing the hydrolytic ATP binding site being supported the most strongly. The structural resemblance of the dynein motor to the hexameric assembly of AAA modules in the hsp100 family of chaperones suggests that the basic mechanism underlying the ATP-dependent translocation of dynein along a microtubule may have aspects in common with the ATP-dependent translocation of polypeptides into the interior compartment of chaperones.

Probing the nucleotide binding sites of axonemal dynein with the fluorescent nucleotide analogue 2'(3')-O-(-N-Methylanthraniloyl)-adenosine 5'-triphosphate.

MantATP [2'(3')-O-(-N-methylanthraniloyl)-adenosine 5'-triphosphate] was employed as a fluorescence probe of the nucleotide-binding sites of dynein from sea urchin sperm flagella. MantATP binds specifically with enhanced fluorescence (approximately 2.2-fold), homogeneous lifetime (8.4 ns), and high anisotropy (r approximately 0.38) to dynein and can be displaced by ATP and ADP added to the medium. The association constants of mantATP complexed with dynein were determined from anisotropy titration data. Using a multiple stepwise equilibrium model, the average values of the first two association constants are K1 = 2.7 x 10(5) M-1 and K2 = 1.8 x 10(4) M-1. This value of K1 is 7-8 times higher than that found previously for unsubstituted ATP, whereas K2 is little changed [Mocz and Gibbons (1996) Biochemistry 35, 9204-9211]. The lower-affinity binding sites, K3 and K4, observed previously could not be studied with mantATP within the available protein concentrations. The alpha and beta heavy chain subfractions have binding parameters similar to those of intact dynein. Formation of the stable ternary complex of mantATP with dynein and monomeric vanadate is accompanied by only a moderate increase in the binding affinities. Oligomeric vanadate reduces the binding affinities by approximately 50%. Addition of TritonX-100, methanol, or various salts changes the binding affinities by up to 50%, suggesting that the microenvironment of the nucleotide-binding sites involves significant contributions from both polar and apolar interactions. The distinct affinities of the individual binding sites are consistent with a physiological role in regulating nucleotide binding.

Phase partition analysis of nucleotide binding to axonemal dynein.

The binding of nucleoside triphosphates and related ligands to dynein ATPase from sea urchin sperm flagella has been studied by equilibrium partition analysis in an aqueous biphasic system containing dextran and poly(ethylene glycol). The stoichiometry of binding and the corresponding stepwise binding constants are obtained from direct binding isotherms fitted to the primary data. The results suggest that dynein possesses four different binding sites for nucleoside triphosphates per mole of heavy chain. The stepwise binding constants for MgATP range from approximately 10(4) M-1 to approximately 10(5) M-1. The isolated alpha and beta heavy chains have binding parameters similar to intact dynein. The amount of ADP bound normally is approximately 75% that of ATP, both for the intact dynein and for the separated heavy chains, although full saturation is achieved at high nucleotide concentrations. In the presence of the ATPase inhibitor vanadate, ADP binds with affinities similar to those of ATP, with binding constants close to those of ATP in the absence of vanadate. No appreciable binding of AMP or EDTA/ATP is observed. The substitution of Ca2+ or Fe3+ for Mg2+ does not significantly alter the amount of ATP bound; however, CaATP is bound with a somewhat lower affinity. Scatchard and Hill plots of the binding data and the calculated site-binding constants suggest that ATP and ADP bind in a weakly cooperative manner. These results suggest that the multiple binding of nucleotide to dynein heavy chains occurs at physiological concentrations, putatively at the four binding sites predicted earlier on the basis of their amino acid sequences. The data are consistent with a model in which, in addition to a single catalytic site, nucleotide binding occurs at additional noncatalytic sites that represent an as yet unknown functional aspect of dynein.

Fuzzy cluster analysis of simple physicochemical properties of amino acids for recognizing secondary structure in proteins.

Fuzzy cluster analysis has been applied to the 20 amino acids by using 65 physicochemical properties as a basis for classification. The clustering products, the fuzzy sets (i.e., classical sets with associated membership functions), have provided a new measure of amino acid similarities for use in protein folding studies. This work demonstrates that fuzzy sets of simple molecular attributes, when assigned to amino acid residues in a protein's sequence, can predict the secondary structure of the sequence with reasonable accuracy. An approach is presented for discriminating standard folding states, using near-optimum information splitting in half-overlapping segments of the sequence of assigned membership functions. The method is applied to a nonredundant set of 252 proteins and yields approximately 73% matching for correctly predicted and correctly rejected residues with approximately 60% overall success rate for the correctly recognized ones in three folding states: alpha-helix, beta-strand, and coil. The most useful attributes for discriminating these states appear to be related to size, polarity, and thermodynamic factors. Van der Waals volume, apparent average thickness of surrounding molecular free volume, and a measure of dimensionless surface electron density can explain approximately 95% of prediction results. hydrogen bonding and hydrophobicity induces do not yet enable clear clustering and prediction.

ATP-insensitive interaction of the amino-terminal region of the beta heavy chain of dynein with microtubules.

The ATP-insensitive microtubule-binding site of dynein has been investigated by limited proteolysis of sea urchin sperm flagellar axonemes. Mild tryptic digestion cleaved the dynein beta chain at either of two principal cleavage sites, generating two sets of complementary peptides. Inclusion of ATP in the digestion medium had no effect on the generation of these primary fragments. Sucrose density gradient separation and immunostaining with monoclonal antibodies against epitopes on the beta chain showed that extraction of the digested axonemes with 1-3 mM ATP solubilizes the peptides located at the carboxy-terminal end of the original heavy chain. The solubilization of the peptides containing the amino end required the presence of 0.6 M NaCl and was not affected by ATP. While the outer arm dynein is in situ on the axoneme, the N-terminal 125-kDa domain of the beta chain was not digested by trypsin, whereas in soluble dynein this domain becomes rapidly degraded. These data suggest that the N-terminal domain of the beta chain is involved in its ATP-insensitive attachment to microtubules and support the hypothesis that the N-terminal 125-kDa peptide corresponds to the flexible tail of the dynein molecule seen in electron micrographs.

A PCR procedure to determine the sequence of large polypeptides by rapid walking through a cDNA library.

A procedure that uses the PCR to make rapid successive steps through a random-primed cDNA library has been developed to provide a method for sequencing very long genes that are difficult to obtain as a single clone. In each successive step, the portions of partial clones that extend out from the region of known DNA sequence are amplified by two stages of PCR with nested, outward-directed primers designed approximately 50 bases in from the end of the known sequence, together with a general primer based on the sequence of the vector. This procedure has been used to determine the coding sequence of the cDNA for the beta heavy chain of axonemal dynein from embryos of the sea urchin Tripneustes gratilla. By starting from a single parent clone, whose translated amino acid sequence overlapped the microsequence of a tryptic peptide of the beta heavy chain, and making 3 such walk steps downstream and 14 walk steps upstream, we obtained a sequence of 13,799 base pairs that had an open reading frame of 13,398 base pairs. This sequence encodes a polypeptide with 4466 residues of Mr 511,804 that is believed to correspond to the complete beta heavy chain of ciliary outer arm dynein.

Multiple nucleotide-binding sites in the sequence of dynein beta heavy chain.

Axonemal dyneins have two or three globular heads joined by flexible tails to a common base, with each head/tail unit consisting of a single heavy-chain polypeptide of relative molecular mass greater than 400,000. The sizes of the components have been deduced by electron microscopy. The isolated beta heavy chain of sea urchin sperm flagella, which is immunologically identical to that of the embryo cilia, is of particular interest as it retains the capability for microtubule translocation in vitro. Limited proteolysis of the beta heavy chain divides it into two fragments, A and B, which sediment separately at 12S and 6S, and possibly correspond to the head and tail domains of the molecule. Dynein ATPase is the energy-transducing enzyme that generates the sliding movement between tubules that underlies the beating of cilia and flagella of eukaryotes, and possibly also other large intracellular movements. Here we report that the deduced amino-acid sequence of the beta heavy chain of axonemal dynein from embryos of the sea urchin Tripneustes gratilla has 4,466 residues and contains the consensus motifs for five nucleotide-binding sites. The probable hydrolytic ATP-binding site can be identified by its location close to or at the V1 site of vanadate-mediated photo-cleavage. The general features of the map of photocleavage and proteolytic peptides reported earlier have been confirmed, except that the map's polarity is reversed. The predicted secondary structure of the beta heavy chain consists of an alpha/beta-type pattern along its whole length. The two longest regions of potential alpha helix, with unbroken heptad hydrophobic repeats 120 and 50 amino acids long, may be of functional importance. But dynein does not seem to contain an extended coiled-coil tail domain.

Proteolytic analysis of domain structure in the beta heavy chain of dynein from sea urchin sperm flagella.

The stability of different regions of the beta heavy chain of dynein has been investigated by examining the perturbing effects of methanol, temperature, salt, and nucleotide on the pattern of tryptic digestion. In standard low-salt medium, tryptic proteolysis cleaves the beta heavy chain into three principal polypeptides of 130, 215, and 110 kDa, with the 215-kDa central peptide containing the ATP binding site as well as the vanadate and iron photocleavage sites (Mocz, G., Tang, W.-J. Y., & Gibbons, I. R. (1988) J. Cell Biol. 106, 1607-1614). The 130-kDa peptide is the most stable, and its susceptibility to trypsin appears unaffected by methanol concentrations up to 25% or temperatures up to 45 degrees C, although a 5-kDa region at one end is lost in the presence of salt (greater than 20 mM NaCl). The 215-kDa tryptic peptide contains two regions of different stability: its 123-kDa portion adjoining the 130-kDa peptide is destabilized by mild heat (37 degrees C) or by 25% methanol and becomes digested away to leave the more stable region of 92 kDa that is located toward the 110-kDa peptide and retains the V1 photocleavage site and most of the ATP binding site. The 110-kDa peptide is the least stable and at 37 degrees C, or in the presence of low concentrations of methanol or salt, it rapidly digested to small peptides. The presence of ATP during digestion of the beta heavy chain retards the formation of the 130- and 215-kDa peptides and also protects the 215-kDa peptide from further digestion at 37 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)

A circular dichroic study of helical structure in flagellar dynein.

The circular dichroic spectra of outer arm dynein from sea urchin sperm flagella, of its separated alpha and beta heavy-chain complexes, and of the two major fragments produced by tryptic digestion of the beta heavy chain have been measured over the range 190-240 nm. Although the spectra show significant individuality, in all cases they qualitatively resemble those of typical globular proteins with mixed regions of alpha-helix and beta-sheet (alpha/beta-type structure) or with separate alpha-helix- and beta-sheet-rich regions (alpha+beta-type structure). Quantitative analyses of the spectra by both constrained and unconstrained least-squares curve-fitting procedures indicate that the intact dynein contains approximately 26% alpha-helix. The separated beta heavy-chain complex and its ATPase-containing amino-terminal domain (fragment A) both have spectra resembling that of intact dynein, and they appear to contain 32% and 23% alpha-helix, respectively. The carboxy-terminal domain of the beta heavy chain (fragment B) and the separated alpha heavy chain have significantly different spectra; however, they each appear to contain 26-36% alpha-helix. These data suggest that dynein does not contain an extensive alpha-helical domain, such as is found in the carboxy-terminal rod region of the other motor proteins myosin and kinesin.

Iron(III)-mediated photolysis of outer arm dynein ATPase from sea urchin sperm flagella.

Irradiation of outer arm dynein ATPase from sea urchin sperm tail flagella at 365-410 nm in the presence of Fe(III)-gluconate complex and ATP produces photolytic cleavage at two distinct sites on the beta heavy chain, located approximately 250 and approximately 230 kDa from its amino terminus. The former cut is close to or identical with the V1 site of the vanadate-mediated photocleavage (Gibbons, I.R., Lee-Eiford, A., Mocz, G., Phillipson, C. A., Tang, W.-J.Y., and Gibbons, B.H. (1987) J. Biol. Chem. 262, 2780-2786. The rate of photolysis shows a hyperbolic dependence on Fe(III)-gluconate concentration with half-maximal rate occurring at 23 microM at pH 6.3. In the presence of 0.1-0.5 mM Fe(III)-gluconate-ATP, approximately 58% of the beta chain becomes cleaved with a half-time of about 34 s; the remainder of the beta chain and almost all of the alpha chain are resistant to cleavage. This photolytic cleavage of the beta chain is accompanied by an approximately parallel loss of the dynein latent ATPase activity, whereas the Triton-activated ATPase is lost to a somewhat greater extent. Mg2+ concentrations above approximately 3 mM inhibit photolysis. Substitution of ADP for ATP changes the pattern of cleavage so that both the alpha and beta heavy chain undergo scission but at the 250-kDa site only. AMP, adenyl-5'-yl imidodiphosphate and Fe(II) do not support cleavage at either site. Trivalent rhodium-ATP complexes, as models of MgATP, can also catalyze photolysis of the beta chain at the 250-kDa site. These results suggest that photolysis results from the activation of an Fe(III)-ATP complex bound to the hydrolytic ATP binding site of the beta chain and that both Fe(III) cleavage sites are located close to the nucleotide binding site in the tertiary folding of the beta heavy chain. The cleavage reaction possibly involves initial photoreduction of Fe(III) bound at the Mg2+ binding site in the dynein.Fe.ATP complex, followed by covalent modification of an amino acid side chain that leads to eventual peptide scission.

Vanadate-mediated photocleavage of rabbit skeletal myosin.

The heavy chain of myosin from rabbit skeletal muscle can be cleaved at three sites by irradiation with near-ultraviolet light in the presence of 0.1-1.0 mM vanadate. The sigmoidal dependence upon vanadate concentration, with half-maximal rate occurring at about 0.5 mM vanadate and a sigmoidicity of 2.7, is consistent with the chromophore responsible for cleavage being oligomeric vanadate. Cleavage occurs at two sites located within the head region of the molecule, 23 kDa and 75 kDa from the NH2-terminus; these sites are cleaved equally well in heavy meromyosin and subfragment 1. In the presence of 1 mM vanadate, the half-times for cleavage of the 23-kDa and 75-kDa sites are about 15 and 10 min, respectively. The rate of cleavage at both these sites is retarded 2-3-fold by the presence of greater than 10 microM MgATP. The third photocleavage site is located about 5-10 kDa from the COOH terminus of the intact heavy chain, and cleaves equally well in the isolated rod and in light meromyosin. Cleavage at this site occurs with a half-time of 138 min, and its rate is unaffected by the presence of MgATP. The vanadate-mediated cleavage of the heavy chains is accompanied by characteristic changes in the myosin ATPase properties, with the Ca2+, Mg2+ and actin-activated Mg2+ ATPases becoming elevated, whereas the K+/EDTA ATPase becomes inactivated. The sites of photocleavage in the myosin heavy chain might be associated with sites of phosphate binding.

A map of photolytic and tryptic cleavage sites on the beta heavy chain of dynein ATPase from sea urchin sperm flagella.

NH2-terminal analysis of the alpha and beta heavy chain polypeptides (Mr greater than 400,000) from the outer arm dynein of sea urchin sperm flagella, compared with that of the 230,000- and 200,000-Mr peptides formed upon photocleavage of dynein by irradiation at 365 nm in the presence of vanadate and ATP, shows that the NH2 termini of the intact chains are acetylated and that the 230,000- and 200,000 Mr peptides constitute the amino- and carboxy-terminal portions of the heavy chains, respectively. Tryptic digestion of the beta heavy chain is known to separate it into two particles, termed fragments A and B, that sediment at 12S and 6S (Ow, R. A., W.-J. Y. Tang, G. Mocz, and I. R. Gibbons, 1987. J. Biol. Chem. 262:3409-3414). Immunoblots against monoclonal antibodies specific for epitopes on the beta heavy chain, used in conjunction with photoaffinity labeling, show that the ATPase-containing fragment A is derived from the amino-terminal region of the beta chain, with the two photolytic sites thought to be associated with the purine-binding and the gamma-phosphate-binding areas of the ATP-binding site spanning an approximately 100,000 Mr region near the middle of the intact beta chain. Fragment B is derived from the complementary carboxy-terminal region of the beta chain.

Tryptic digestion of dynein 1 in low salt medium. Origin and properties of fragment A.

Dynein 1 was extracted from sperm flagella of the sea urchin Tripneustes gratilla with 0.6 M NaCl and dialyzed against 0.5 mM EDTA, 14 mM 2-mercaptoethanol, 5 mM imidazole/HCl buffer, pH 7.0, for 24-48 h. In some cases, fractions containing the alpha heavy chain and the beta/intermediate chain 1 complex (beta/IC1) were separated by density gradient centrifugation in the same solution. Treatment of the samples at a trypsin:protein ratio of 1:10 w/w for 32 min at room temperature yields a crude digest from which Fragment A is purified by density gradient centrifugation. The purified Fragment A consists of two principal peptides (Mr = 195,000 and 130,000) that cosediment with the peak of ATPase activity at 12.5 S, which is slightly faster than the 11 S of the original beta/IC1 complex. When digests of the separated alpha chain and of the beta/IC1 complex are followed as a function of time, the early cleavages of the two heavy chains (Mr = 428,000) resemble each other in that both lead to similarly sized peptides of Mr 316,000 and 296,000, but only in the beta/IC1 fraction does the digestion proceed to form Fragment A. The remainder of the beta chain, termed Fragment B, occurs as an Mr 110,000 peptide sedimenting at 5.7 S with no associated ATPase activity. Fragment A has a specific ATPase activity of 4.3 mumol Pi X min-1 X mg-1, with a Km of 29 microM in 0.1 M NaCl medium, and an apparent Ki for inhibition by vanadate of 1.2 microM in the absence of salt, and 22 microM in 0.6 M NaCl. Photoaffinity labeling with [alpha-32P]8-azidoadenosine 5'-triphosphate indicates that the ATP binding site on the beta chain of dynein 1 is located on the Mr 195,000 peptide of Fragment A. The possibility that Fragments A and B of the beta/IC1 complex may correspond to the head and tail regions of the tadpole-shaped particle seen by electron microscopy is discussed.

Photosensitized cleavage of dynein heavy chains. Cleavage at the "V1 site" by irradiation at 365 nm in the presence of ATP and vanadate.

Irradiation of soluble dynein 1 from sea urchin sperm flagella at 365 nm in the presence of MgATP and 0.05-50 microM vanadate (Vi) cleaves the alpha and beta heavy chains (Mr 428,000) at their V1 sites to give peptides of Mr 228,000 and 200,000, without the nonspecific side effects produced by irradiation at 254 nm as described earlier (Lee-Eiford, A., Ow, R. A., and Gibbons, I. R. (1986) J. Biol. Chem. 261, 2337-2342). The decrease in intact heavy chain material is biphasic; in 10 microM Vi, approximately 80% occurs with a half-time of 7 min and the remainder with a half-time of about 90 min, and the yield of cleavage peptides is better than 90%. Loss of dynein ATPase activity appears to be a direct result of the cleavage process and is not significantly affected by the presence of up to 0.1 M cysteamine (CA, 60-23-1) or 2-aminoethyl carbamimidothioic acid dihydrobromide (CA, 56-10-0) as free radical trapping agents. The concentration of Vi required for 50% maximal initial cleavage rate is 4.5 microM, while that for 50% ATPase inhibition is 0.8 microM, both in a 0.6 M NaCl medium. In the presence of 20 microM Vi, CTP and UTP support cleavage at about half the rate of ATP, whereas GTP and ITP support cleavage only if the Vi concentration is raised to about 200 microM. Substitution of any of the transition metal cations Cr2+, Mn2+, Fe2+, or Co2+ for the usual Mg2+ suppresses the photocleavage, presumably by quenching the excited chromophore prior to scission of the heavy chain. The photocleaved dynein 1 binds to dynein-depleted flagella similarly to intact dynein 1, but upon reactivation of the flagella with 1 mM ATP their motility is partially inhibited, rather than being augmented as with intact dynein. These results indicate that Vi acts as a photosensitizing catalyst and suggest that the cleavage proceeds through excitation of Vi bound to dynein at the hydrolytic ATP binding site on each heavy chain, probably in a dynein X MgADP X Vi complex. The exquisite specificity of Vi-sensitized photocleavage will aid the peptide mapping of dynein heavy chains and may be of broader use in studies of protein structure.

Activation of dynein 1 adenosine triphosphatase by monovalent salts and inhibition by vanadate.

The ATPase activity of native dynein 1 from sea urchin sperm flagella is activated reversibly by inorganic monovalent chlorides with the magnitude of activation being nearly independent of the cation below 0.3 M. At higher concentrations, activation increases in the order LiCl greater than NH4Cl greater than NaCl greater than KCl, with the maximum occurring at about 0.8 M in all cases. The sodium halides activate reversibly in the order NaI greater than NaBr greater than NaCl, but NaF is strongly inhibitory. The presence of the organic anions formate, acetate, or propionate favors the native low ATPase activity state, with lithium acetate giving little activation at up to 1 M and sodium acetate partially reversing the activation due to simultaneous presence of 0.6 M NaCl. The sedimentation rate of the dynein does not change between 0.2 and 0.8 M NaCl or sodium acetate, suggesting that the effects of the anions on ATPase activity are due to local changes near the catalytic site, rather than to large-scale changes in the molecular structure. All the agents that activate the dynein ATPase, either reversibly (halides) or irreversibly (Triton X-100), decrease its sensitivity to inhibition by vanadate, consistent with ATPase activation being the result of a decreased stability of the dynein. ADP.Pi kinetic intermediate that is thought to bind vanadate at the gamma-Pi site and act as a dead-end kinetic block. Although many divalent cations, including Mg2+, Mn2+, Fe2+, Co2+, Ni2+, Zn2+, Ca2+, and Sr2+, can support dynein ATPase activity, the magnitude of ATPase increase observed upon treatment with Triton X-100 is greatest with Mg2+ and Mn2+, which are also the only cations capable of supporting the motility of demembranated flagella at rates similar to those observed in vivo.

Localization of a new proteolytic site accessible in oxidized myosin rod.

We have compared the proteolysis pattern of reduced and oxidized myosin rods in which the five pairs of SH-groups were interchain crosslinked by employing CuCl2 or 5,5'-dithiobis-2-nitrobenzoate. In the tryptic digest of oxidized rod three new fragments appeared on SDS-polyacrylamide gel electrophoresis (chain masses of 100, 45, and 25 kDa). Based on the N-terminal sequences of the isolated peptides, it is concluded that oxidation creates a new cleavage site 102 residues away from the N-terminus of the rod, in the vicinity of one of the modified SH-groups (Cys-108). This observation indicates that S-S crosslinking of myosin rod leads to a local unfolding of the coiled-coil structure.

Effect of nucleotides, divalent cations and temperature on the tryptic susceptibility of myosin subfragment 1.

The kinetics of tryptic breakdown of the heavy chain of chymotryptic myosin subfragment 1 (S1) according to the following scheme (where the numbers represent approximate masses in kDa) are altered at 21 degrees C by divalent (Formula: see text) cations (Me2+) and by ATP, ADP, adenosine 5'-[beta, gamma-imino]triphosphate or PPi, with or without Me2+. ATP or its analogs slow step 2 and accelerate steps 3 and 4, while Me2+ accelerates step 2. ATP and its analogs decrease the amount of a transient 27-kDa peptide [Hozumi, T. & Muhlrad, A. (1981) Biochemistry 20, 2945-2950]. We have found direct evidence for the suggestion in this reference that the 27-kDa peptide is not an obligatory precursor of the 25-kDa fragment and that ATP or ADP suppresses the formation of the larger N-terminal fragment rather than accelerates its breakdown. Cross-linking of sulfhydryl groups located in the 20-kDa fragment leads to trapping of MgADP in the N-terminal 25-kDa peptide [Wells, J.A. & Yount, R.G. (1980) Biochemistry 19, 1711-1717]; this process affects the tryptic fragmentation of S1 similarly to, but less effectively than, nucleotides. Acts-S1 formation prevents the effect of ATP on fragmentation. At 37 degrees C S1 loses ATPase activity; tryptic digestion proceeds more rapidly and the 50-kDa and 25-kDa fragments are degraded to small peptides. Nucleotides protect against the effects of higher temperature by producing conformational changes not only in the 27-kDa N-terminal portion (containing the putative nucleotide binding site) of the heavy chain of S1 but also in the 50-kDa peptide.

Use of cationic detergents for polyacrylamide gel electrophoresis in multiphasic buffer systems.

An improved system for polyacrylamide gel electrophoresis in the presence of cationic detergents, cetyltrimethylammonium bromide and cetylpyridinium chloride, respectively, is described. An acidic discontinuous buffer system generated according to the theory of multiphasic zone electrophoresis developed by T. M. Jovin (1973, Biochemistry 12, 871-904) was used. It was optimized with respect to the operational conditions and to the desirable range of relative mobility values for the proteins that have molecular weights from 16,500 to 90,300. Also presented is a procedure for the elimination of interference from cationic detergents frequently encountered during staining of gels. The electrophoretic system was suitable for fractionating a wide variety of proteins. The technique can also be used to provide an alternative estimate of molecular weight. To fully account for accurate estimations, the Ferguson relationship between mobility and gel concentration and the relation of molecular weight to mobility at a single gel concentration were both considered. Examples reported in this paper include the separation and/or molecular weight determination of several common proteins, histones, and microfibrillar and myofibrillar proteins. The results suggest that electrophoresis in the presence of cationic detergents offers the same degree of reliability in analysis of most proteins as is provided by the anionic detergent sodium dodecyl sulfate electrophoresis.

The proteolytic substructure of light meromyosin. Localization of a region responsible for the low ionic strength insolubility of myosin.

Light meromyosin (LMM), prepared by limited tryptic digestion of myosin, usually contains several polypeptide chains, LMM-A, LMM-B, and LMM-C in decreasing order of molecular weight estimated from sodium dodecyl sulfate-gel electrophoresis. Further limited tryptic digestion of LMM produces well defined fragments (Balint, M., Szilagyi, L., Fekete, Gy., Blazso, M., and Biro, E. N. A. J. Mol. Biol. (1968) 37, 317-330). Fragments LF-1, LMM-D, LF-2, and LF-3, with chain masses equal to 63, 56, 47, and 30 kDa, respectively, have been isolated by column chromatography. Based on the time course of the changes in the sodium dodecyl sulfate-gel pattern of the digests, chain masses estimated from sodium dodecyl sulfate-gel electrophoresis, and the NH2- and COOH-terminal sequences of the isolated peptides, the following scheme can be deduced. Formula; see text. C and N over the arrows indicate removal of residues from the COOH and NH2 terminus, respectively. The positions of the peptides along the myosin heavy chain have been established by comparison with the published primary structures of rabbit skeletal (Elzinga, M., Behar, K., Walton, G., and Trus, B. L. (1980) Fed. Proc. 33, 1579) and nematode myosin (McLachlan, A. D., and Karn, J. (1982) Nature (Lond.) 299, 226-231). LMM and fragment LMM-D are insoluble, whereas LF-1, LF-2, and LF-3 are soluble at low ionic strength. Their solubility properties, in conjunction with their locations along the myosin heavy chain, suggest that a relatively small stretch of peptide (chain weight, 5,000 Da) located about 100 residues from the COOH terminus of myosin heavy chain is responsible for the insolubility of LMM at low ionic strength.