Structural homology of myosin alkali light chains, troponin C and carp calcium binding protein

Identification and analysis of muscle-related protein isoforms expressed in the white muscle of the mandarin fish (Siniperca chuatsi)

To identify muscle-related protein isoforms expressed in the white muscle of the mandarin fish Siniperca chuatsi, we analyzed 5,063 high-quality expressed sequence tags (ESTs) from white muscle cDNA library and predicted the integrity of the clusters annotated to these genes and the physiochemical properties of the putative polypeptides with full length. Up to about 33% of total ESTs were annotated to muscle-related proteins: myosin, actin, tropomyosin/troponin complex, parvalbumin, and Sarcoplasmic/endoplasmic reticulum calcium ATPase (SERCa). Thirty-two isoforms were identified and more than one isoform existed in each of these proteins. Among these isoforms, 14 putative polypeptides were with full length. In addition, about 2% of total ESTs were significantly homologous to "glue" molecules such as alpha-actinins, myosin-binding proteins, myomesin, tropomodulin, cofilin, profilin, twinfilins, coronin-1, and nebulin, which were required for the integrity and maintenance of the muscle sarcomere. The results demonstrated that multiple isoforms of major muscle-related proteins were expressed in S. chuatsi white muscle. The analysis on these isoforms and other proteins sequences will greatly aid our systematic understanding of the high flexibility of mandarin fish white muscle at molecular level and expand the utility of fish systems as models for the muscle genetic control and function.

Mimicking the evolution of a thermally stable monomeric four-helix bundle by fusion of four identical single-helix peptides

Internal symmetry is a common feature of the tertiary structures of proteins and protein domains. Probably, because the genes of homo-oligomeric proteins duplicated and fused, their evolutionary descendants are proteins with internal symmetry. To identify any advantages that cause monomeric proteins with internal symmetry to be selected evolutionarily, we characterized some of the physical properties of a recombinant protein with a sequence consisting of two tandemly fused copies of the Escherichia coli Lac repressor C-terminal alpha-helix. This polypeptide exists in solution mainly as dimer that likely maintains a four-helix bundle motif. Thermal unfolding experiments demonstrate that the protein is considerably more stable at elevated temperatures than is a homotetramer consisting of four non-covalently associated copies of a 21-residue polypeptide similar in sequence to that of the Lac repressor C-terminal alpha-helix. A tandem duplication of our helix-loop-helix polypeptide yields an even more thermally stable protein. Our results exemplify the concept that fusion of non-covalently assembled polypeptide chains leads to enhanced protein stability. Herein, we discuss how our work relates to the evolutionary selective-advantages realized when symmetrical homo-oligomers evolve into monomers. Moreover, our thermally stable single-chain four-helix bundle protein may provide a robust scaffold for development of new biomaterials.

A Ca(2+)-binding protein with numerous roles and uses: parvalbumin in molecular biology and physiology

Parvalbumins (PVs) are acidic, intracellular Ca(2+)-binding proteins of low molecular weight. They are associated with several Ca(2+)-mediated cellular activities and physiological processes. It has been suggested that PV might function as a "Ca2+ shuttle" transporting Ca2+ from troponin-C (TnC) to the sarcoplasmic reticulum (SR) Ca2+ pump during muscle relaxation. Thus, PV may contribute to the performance of rapid, phasic movements by accelerating the contraction-relaxation cycle of fast-twitch muscle fibers. Interestingly, PVs promote the generation of power stroke in fish by speeding up the rate of relaxation and thus provide impetus to attain maximal sustainable speeds. However, immunological monitoring of diverse tissues demonstrated that PVs are also present in non-muscle cells. The axoplasmic transport and various intracellular secretory mechanisms including the endocrine secretions seem to be controlled by the Ca2+ regulation machinery. Any defect in the Ca2+ handling apparatus may cause several clinical problems; for instance, PV deficiency alters the neuronal activity, a key mechanism leading to epileptic seizures. Moreover, atypical relaxation of the heart results in diastolic dysfunction, which is a major cause of heart failure predominantly among the aged people. PV may offer a unique potential to correct defective relaxation in energetically compromised failing hearts through PV gene transfer. Consequently, PV gene transfer may present a new therapeutic approach to correct cellular disturbances in Ca2+ signaling pathways of diseased organs. Hence, PVs appear to be amazingly useful candidate proteins regulating a variety of cellular functions through action on Ca2+ flux management.

Calcium binding to skeletal muscle troponin C and the regulation of muscle contraction

Skeletal muscle contraction is initiated by Ca2+ ion binding to troponin C (TnC), a protein of the thin filament. Our three-dimensional structure determination of turkey skeletal TnC at 2.8 A resolution revealed an extended molecule consisting of two domains connected through a long nine-turn alpha-helix. The C-terminal domain has two Ca2+ ions bound in the expected manner of EF hands, whereas the N-terminal regulatory domain is Ca2+-free with a helix-loop-helix conformation different from that of an EF hand. The refinement of TnC at 2.2 A resolution highlights the intricate hydrogen-bonded network common to the Ca2+-bound loops and provides an explanation for the presence of a water molecule in the 5th coordination position of the Ca2+ ion. We propose that Ca2+ binding to the regulatory domain is accompanied by a conformational transition by which its structure becomes similar to that of the C-terminal domain. Dramatic movements of residues in the B and C helices and the connecting peptide of up to 14 A constitute the bulk of this change. A hydrophobic site that could be the site of interaction with troponin I is thereby exposed. We have also demonstrated that this model of the Ca2+-bound conformation can be reached from the Ca2+-free state without having to surmount large energy barriers.

A unique exon-intron organization of a porcine S100C gene: close evolutionary relationship to calmodulin genes

We found a unique exon-intron structure of the porcine S100C gene, a member of the S100 family, in which all other genes characterized to date have common exon-intron organization. The genomic DNA encoding the porcine S100C was cloned and the entire nucleotide sequence of the gene was analyzed. The gene is present as a single copy and consists of three exons and two introns with a total size of 5.3 kb. The first intron is located after the ATG translation initiation codon. Such an intron has never been found in other S100 genes, but is found in almost all calmodulin genes. The gene structural similarity suggests a close evolutionary relationship between the S100C gene and calmodulin genes.

Interhelical contacts determining the architecture of alpha-helical globular proteins

An approach based on a presentation of alpha-helical protein topology as a graph is presented. The approach allows to estimate a role of each interhelical contact in the whole protein topology and to classify the contacts. It is shown that a consideration of only about a half of the whole pool of interhelical contacts exposed in the protein is enough for a determination of protein architecture. Such contacts are called as major and their quantitative characteristics are obtained. Moreover, providing a clear and simple presentation of the protein topology, the approach can be applied for a description of structural domain/subdomain arrangement of alpha-helical proteins and illustration of their folding/denaturation paths.

Genetic fusion of subunits of a dimeric protein substantially enhances its stability and rate of folding

The gene V protein of bacteriophage f1 is a single-stranded DNA and RNA-binding protein composed of two identical subunits. We have constructed single-chain variants of the protein using short peptide linkers of five or six amino acids to connect the carboxyl terminus of one monomer to the amino terminus of the second monomer. The resulting subunit-fusion gene V proteins were found to bind single-stranded DNA nearly as tightly as the wild-type protein. Denaturation measurements show that the subunit-fusion gene V proteins are 5 kcal/mol (1 kcal = 4.18 kJ) more stable than the wild-type protein at a protein concentration of 10 microM. The rate of unfolding of the protein is essentially unaffected by the fusion of monomeric subunits, whereas the rate of folding is greatly enhanced. Our results suggest a simple way of obtaining a substantial thermodynamic stabilization for some oligomeric proteins.

Shared thematic elements in photochemical reaction centers

The structural, functional, and evolutionary relationships between photosystem II and the purple nonsulfur bacterial reaction center have been recognized for several years. These can be classified as "quinone type" (type II) photosystems because the terminal electron acceptor is a mobile quinone molecule. The analogous relationship between photosystem I and the green sulfur bacterial (and helicobacterial) reaction centers has only recently become clear. These can be classified as "iron-sulfur type" (type I) photosystems because the terminal electron acceptor consists of one or more bound iron-sulfur clusters. At a fundamental level, the quinone type and iron-sulfur type reaction centers share a common photochemical motif in the early process of charge separation, leading to the speculation that all photochemical reaction centers have a common evolutionary origin. This review summarizes the current state of knowledge in comparative reaction center biochemistry between prokaryotic bacteria, cyanobacteria, and green plants.

Probing myosin light chain 1 structure with monoclonal antibodies

Five monoclonal antibodies that react with different regions of myosin light chain 1 from human ventricular myocardial muscle were used to obtain information on interactions between the light chain 1 and heavy chains and generally on the tertiary structure of the light chain 1 within the myosin head. We performed Western blot assays of the five antibodies with myosins from different cardiac and skeletal muscles, with different proteolytic fragments of bovine ventricular myosin light chain 1 (LC1) and to different recombinant fragments of human ventricular LC1 and rat fast skeletal light chain LC1/LC3. The five antibodies were mapped in three different regions of the light chain 1: two antibodies mapped within the first eight amino-terminal residues, two between residues 71 and 74, and one between residues 129 and 134. The apparent dissociation constants of the last three antibodies, determined by antibody-antigen equilibria in solution, were lower than when isolated light chains were used as antigens. It is probable that the corresponding amino acids involved in the antibody epitopes were either involved in interactions between the light and heavy myosin subunits, or somehow hindered by the myosin heavy chain bulk. In contrast, the apparent dissociation constants measured for both other antibodies were higher when myosin, rather than isolated light chains, was used as antigen. Thus LC1 fixation to heavy chains within the myosin molecule induced conformation changes at the amino-terminal end of the light chain 1. No difference in the accessibility of this mobile LC1 segment was detected in the presence of actin. Finally, observed differences in epitope accessibility on the light chain LC1 in myosin, as compared with chymotryptic subfragment 1 (SF1), indicated conformational differences between native myosin and extensively studied SF1 molecules.

Structural and functional aspects of calcium homeostasis in eukaryotic cells

The maintenance of a low cytosolic free-Ca2+ concentration, ([Ca2+]i) is a common feature of all eukaryotic cells. For this purpose a variety of mechanisms have developed during evolution to ensure the buffering of Ca2+ in the cytoplasm, its extrusion from the cell and/or its accumulation within organelles. Opening of plasma membrane channels or release of Ca2+ from intracellular pools leads to elevation of [Ca2+]i; as a result, Ca2+ binds to cytosolic proteins which translate the changes in [Ca2+]i into activation of a number of key cellular functions. The purpose of this review is to provide a comprehensive description of the structural and functional characteristics of the various components of [Ca2+]i homeostasis in eukaryotes.

Evolution of EF-hand calcium-modulated proteins. I. Relationships based on amino acid sequences

The relationships among 153 EF-hand (calcium-modulated) proteins of known amino acid sequence were determined using the method of maximum parsimony. These proteins can be ordered into 12 distinct subfamilies--calmodulin, troponin C, essential light chain of myosin, regulatory light chain, sarcoplasmic calcium binding protein, calpain, aequorin, Stronglyocentrotus purpuratus ectodermal protein, calbindin 28 kd, parvalbumin, alpha-actinin, and S100/intestinal calcium-binding protein. Eight individual proteins--calcineurin B from Bos, troponin C from Astacus, calcium vector protein from Branchiostoma, caltractin from Chlamydomonas, cell-division-cycle 31 gene product from Saccharomyces, 10-kd calcium-binding protein from Tetrahymena, LPS1 eight-domain protein from Lytechinus, and calcium-binding protein from Streptomyces--are tentatively identified as unique; that is, each may be the sole representative of another subfamily. We present dendrograms showing the relationships among the subfamilies and uniques as well as dendrograms showing relationships within each subfamily. The EF-hand proteins have been characterized from a broad range of organismal sources, and they have an enormous range of function. This is reflected in the complexity of the dendrograms. At this time we urge caution in assigning a simple scheme of gene duplications to account for the evolution of the 600 EF-hand domains of known sequence.

Mapping myosin light chains by immunoelectron microscopy. Use of anti-fluorescyl antibodies as structural probes

The two classes of light chains in vertebrate fast muscle myosin have been selectively labeled with the thiol specific reagent 5-(iodoacetamido) fluorescein to determine their location in the myosin head. The alkali light chains (A1 and A2) were labeled at a single cysteine residue near the COOH terminus, whereas the regulatory light chain (LC2) was reacted at either cysteine 125 or 154. The two cysteines of LC2 appear to be near each other in the tertiary structure as evidenced by the ease of formation of an intramolecular disulfide bond. Besides having favorable spectral properties, fluorescein is a potent haptenic immunogen for raising high affinity antibodies. When anti-fluorescyl antibodies were added to the fluorescein-labeled light chains, the fluorescence was quenched by greater than 90%, thereby providing a simple method for determining an association constant. The interaction with antibody was the same for light chains exchanged into myosin as for free light chains. Complexes of antibody bound to light chain could be visualized in the electron microscope by rotary shadowing with platinum. By this approach we have shown that the COOH-terminal regions of the two classes of light chains are widely separated in myosin: the cysteine residues of LC2 lie close to the head/rod junction, whereas the single cysteine of A1 or A2 is located approximately 90 A distal to the junction. These sites correspond to the positions of the NH2 termini of the light chains mapped in earlier studies (Winkelmann, D. A., and S. Lowey. 1986. J. Mol. Biol. 188:595-612; Tokunaga, M., M. Suzuki, K. Saeki, and T. Wakabayashi. 1987b. J. Mol. Biol. 194:245-255). We conclude that the two classes of light chains do not lie in a simple colinear arrangement, but instead have a more complex organization in distinct regions of the myosin head.

A hydrophobic region on myosin light chains modulated by divalent cations

A hydrophobic region was detected on several types of myosin light chain by enhancement of the quantum yield of 1-anilino-8-naphthalenesulfonate (ANS) fluorescence. The character of this non-polar region was altered by the binding of Ca2+ or Mg2+ to the light chain, the quantum yield of the ANS being increased, and its emission maximum undergoing a blue-shift. These changes enabled the binding of divalent cations to the myosin light chains to be monitored. When Ca2+ was bound to gizzard regulatory light chain, a biphasic enhancement of light-chain-bound ANS fluorescence occurred, the first phase taking place in the micromolar range and the second in the millimolar range of free Ca2+ concentration. Enhancement of protein-bound ANS fluorescence as divalent cations were bound was also observed with other types of myosin light chain.

Theoretical estimation of the calcium-binding constants for proteins from the troponin C superfamily based on a secondary structure prediction method. II. Applications

Ca2+-binding properties of the following proteins, classified as members of the troponin C (TNC) superfamily have been discussed: TNCs, calmodulins (CaMs), vitamin D-dependent calcium-binding proteins (CaBPs), myosin light chains (LCs), S-100 chains, parvalbumins (PVs), oncomodulin (OCM), sarcoplasmic calcium binding proteins (SCPs), calcineurin B (CB) and calcium vector protein (CaVP). Assuming the most probable domain pairing, the Ca2+-binding constants of these proteins have been predicted from their sequences using the method presented in the preceding paper. The results are critically compared with the available experimental data. For some proteins (TNCs, CaMs, CaBPs, LCs, CB and CaVP) our predictions are consistent with the experimental results. For the others, substantial discrepancies between the predicted and measured KCa values are observed. They result from some structural peculiarities of those proteins: a unique, three-domain organization in the case of PVs and OCM, unusual sequences of binding loops in the case of S-100 and a lack of a standard helix-loop-helix organization of Ca2+-binding domains in the case of SCPs.

Theoretical estimation of the calcium-binding constants for proteins from the troponin C superfamily based on a secondary structure prediction method. I. Estimation procedure

Proteins belonging to the TNC superfamily are known to be built of two, three, four, or six domains of closely similar amino acid sequences. Each domain binds no more than one calcium ion and shows a characteristic helix-loop-helix structure when in the calcium-bound state. Conformational properties of all the domains known so far have been analysed by us using a secondary structure prediction method (Garnier, J., Osguthorpe, D.J. & Robson, B. (1978). J. molec. Biol. 120, 97). Significant differences in distribution of residues predicted as being in the helical, beta-turn, and coil conformations have been found between the strongly, weakly, and non-binding domains. We could determine the ideal prediction pattern characteristic for the domains with the highest affinity for calcium. On the basis of our analysis and observations made by other authors we worked out a few simple rules which made it possible to compare conformational properties of a given domain with the ideal reference pattern and estimate, in this way, the Ca2+-binding constant of the domain. In native proteins the domains are known to be organized in pairs. The Ca2+-binding constant for a two-domain region could be evaluated from the sum of the estimation points attributed to each of its components. Using our method it is possible to predict the binding constants of typical domains and two-domain regins with a precision of one order of magnitude. Data on amino acid sequences and calcium-binding constants of all known proteins, believed to be the members of the TNC superfamily, have been reviewed. References to virtually all papers published on this subject before the end of 1987 are given.

Nucleotide sequence of pig plasma gelsolin. Comparison of protein sequence with human gelsolin and other actin-severing proteins shows strong homologies and evidence for large internal repeats

Pig plasma gelsolin (Mr = 81595; 739 residues) contains 704 identical residues out of a maximum 730 when compared to the cytoplasmic form of human gelsolin. The cDNA sequence also codes for a peptide of 33 residues N-terminal to the nine-residue plasma extension sequence previously reported: these 33 residues are highly homologous to the human signal peptide and plasma extension. Comparison of the gelsolin sequences with chicken brush border villin, severin from Dictyostelium discoideum and fragmin from Physarum polycephalum shows a strong evolutionary relationship between all these proteins. There are six large repeating segments in gelsolin and villin, and three similar segments in severin and fragmin. Although these multiple repeats cannot be related to any known function of these actin-severing proteins, this superfamily of proteins appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues.

Evolution of the EF-hand calcium-binding protein family: evidence for exon shuffling and intron insertion

The evolutionary history of the intracellular calcium-binding protein superfamily is well documented. The members of this gene family are all believed to be derived from a common ancestor, which, itself, was the product of two successive gene duplications. In this study, we have compared and analyzed the structures of the recently described genes coding for these proteins. We propose a series of evolutionary events, which include exon shuffling and intron insertion, that could account for the evolutionary origin of all the members of this superfamily. According to this hypothesis, the ancestral gene, a product of two successive duplications, consisted of at least four exons. Each exon coding for a peptide (a calcium-binding domain) was separated by an intron that had mediated the duplication. Each distinct lineage evolved from this ancestor by genomic rearrangement, with insertion of introns being a prominent feature.

Kinetic mechanism of calcium binding to whiting parvalbumin

Calcium binding to whiting parvalbumin induces large changes in the fluorescence, absorption, and circular dichroism spectra of the protein. The fluorescence emission maximum of the single tryptophan shifts from 325 to 348 nm upon the removal of calcium and decreases in intensity by 50%. All of the spectral changes are linear between 0 and 2 mol of calcium bound/mol of protein, which suggests that the only protein species present in significant concentration are PA0 and Pa-Ca2. The kinetics of calcium binding measured by stopped-flow fluorescence are accurately single exponential from 2 X 10(-7) to 2 X 10(-4) M free calcium. The kinetics of calcium dissociation show a pronounced lag and are best fit by two rate constants of 1.2 and 3.0 s-1. The minimal kinetic mechanism that adequately describes the rate and equilibrium data is a branched pathway mechanism in which the rate and equilibrium constants are markedly different for each pathway: (formula; see text) At [Ca] less than 2 microM the upper kinetic pathway of calcium binding predominates whereas at [Ca] greater than 2 microM calcium binding occurs predominantly by the lower kinetic pathway. Calcium dissociates primarily by the upper kinetic pathway.

The dimerization of half-molecule fragments of transferrin

Partial proteolysis was used to prepare half-molecule fragments of hen ovotransferrin. N-Terminal and C-terminal fragments associate to form an N-terminal fragment-C-terminal fragment dimer. Variant forms of the N- and C-terminal fragments can be prepared in which a few amino acid residues are lacking from the C-terminal ends of the fragments. These variant fragments are partially or completely unable to associate; the suggestion that the molecular recognition sites are located in these C-terminal stretches of the N-terminal half-molecule (320-332) and of the C-terminal half-molecule (683-686) is in agreement with X-ray-crystallography data for human lactotransferrin [Anderson, Baker, Dodson, Norris, Rumball, Waters & Baker (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 1769-1773].

The rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene. Complete nucleotide sequence and structural organization

The structural organization of the entire rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene was determined by analysis of overlapping genomic clones isolated from a rat genomic library using the rat 9-kDa CaBP cDNA [Desplan C., Heidmann O., Lillie J., Auffray C. and Thomasset M. (1983) J. Biol. Chem. 258, 13502-13505]. These clones together span 30 kbp of rat genomic DNA, with the rat 9-kDa CaBP gene lying in the middle. The 9-kDa CaBP gene is 2.5 kbp long and contains three exons interrupted by two introns. The first exon contains almost the entire 5' untranslated region. The second exon codes for the calcium-binding site I, the third exon codes for site II and the 3' untranslated region. Therefore each of the calcium-binding domains is encoded by single, separate exons. The transcription initiation site was identified by S1 nuclease mapping and primer extension. A consensus sequence TATAAA is localized 31 bp upstream from the cap site and the 'CCAAT-box' lies upstream from the transcription start. Single (AC)25 and (AG)23 repeats are present in the second intron together with an Alu-like sequence. Repetitive elements are present 5 kbp upstream from the cap site and in the 3' flanking region. Comparison of the known rat CaBP sequences (9-kDa CaBP, 28-kDa CaBP, S100 protein) shows that the 9-kDa CaBP is more closely related to the S100 protein than to the 28-kDa CaBP. There is no evidence to indicate that 9-kDa CaBP has arisen from the 28-kDa CaBP.

Human 27-kDa calbindin complementary DNA sequence. Evolutionary and functional implications

Human 27-kDa calbindin cDNA clones were selected by antibody screening from lambda gt11 brain libraries. The sequence revealed an open reading frame coding for a protein of 261 amino acids, containing four active calcium-binding domains, and two modified domains that had presumably lost their calcium-binding capability. Comparison with chick and bovine calbindins showed that the protein was highly conserved in evolution (evolutionary rate: 0.3 x 10(-9) amino acid-1 year-1) and that active and inactive domains were equally conserved. From the data we postulate that calbindin has an important physiological function involving protein--protein interactions. Comparison of calcium-binding domains from various proteins suggested that all members of the troponin C superfamily derive from a common two-domained ancestor, but that duplications leading to calbindin and to the four-domained calcium-binding proteins took place independently on different branches of the evolutionary tree. Preliminary data showed that another calcium-binding protein, homologous to calbindin, is present in the brain and encoded by a different gene.

Total sequential solid phase synthesis of rabbit skeletal troponin C calcium binding site III

The total sequential solid phase synthesis of AcA98STnC(90-123)amide is described. The yield is comparable to that obtained previously using fragment condensation on the solid support. HPLC purification results in a product which displays greater calcium induced conformational changes than the peptide prepared by the fragment condensation method. However, the former has a dissociation constant for calcium (28 microM) seven times higher than the latter (4 microM).

Evidence that the N-terminal region of A1-light chain of myosin interacts directly with the C-terminal region of actin. A proton magnetic resonance study

Earlier 1H-NMR experiments on the myosin subfragment-1 (S1) light chain isoenzymes from rabbit fast muscle, containing either the A1 or the A2 alkali light chains [S1(A1) or S1(A2)], have shown that the 41-residue N-terminal extension of A1, rich in proline, alanine and lysine residues, is freely mobile in solution but that this mobility is constrained in the acto-S1(A1) complex [Prince et al. (1981) Eur. J. Biochem. 121, 213-219]. It is now established that this N-terminal region of the A1-light chain interacts directly with the C-terminal region of actin in the acto-S1(A1) complex. This was shown by covalently labelling the Cys-374 residue of actin with a spin-label and observing the enhanced relaxation this paramagnetic centre induced in the 1H-NMR spectrum of S1(A1). In particular, the signal arising from the -N+(CH3)3 protons of alpha-N-trimethylalanine (Me3Ala) were monitored as this residue is uniquely sited at the N-terminus of the A1 light chain [Henry et al. (1982) FEBS Lett. 144, 11-15]. Experiments using complexes of actin with either the N-terminal 37-residue peptide of A1, S1(A1) or heavy meromyosin indicate that the N-terminal region of A1 is binding in a similar manner to actin in each case, with the N-terminal Me3Ala residue within 1.5 nm of the spin label introduced to Cys-374 of actin. A similar strategy was adopted to show that the Me3Ala residue can also be found close (less than 1.5 nm) to the fast-reacting SH1 thiol group on the S1 heavy chain. These data, together with published work, have been used to suggest a possible organisation for the polypeptide chains in the myosin head.

Probing myosin head structure with monoclonal antibodies

Monoclonal antibodies that react with defined regions of the heavy and light chains of chicken skeletal muscle myosin have been used to provide a correlation between the primary and the tertiary structures of the head. Electron microscopy of rotary shadowed antibody-myosin complexes shows that the sites for three epitopes in the 25,000 Mr tryptic fragment (25k) of subfragment-1, including one within 4000 Mr of the amino terminus of the myosin heavy chain, are clustered 145(+/- 20) A from the head-rod junction. An epitope in the 50,000 Mr fragment maps even further out on the head. These antibodies bind to the head in several orientations, suggesting that each of the heads can rotate can rotate 180 degrees about the head-rod junction. The epitopes are accessible on subfragment-1 bound to actin when they were probed with Fab fragments; therefore, none of these heavy chain sites is is on the contact surface between the head and actin. Two of the anti-25k antibodies affect the K+-EDTA-and Ca2+-ATPase activities of myosin in a manner that mimics the effect on activity of the modification of the reactive thiol, SH-1. These two antibodies also inhibit the actin-activated ATPase non-competitively with respect to actin. None of the other eight antibodies tested had any marked effect on activity. A monoclonal antibody that reacts with an epitope in the amino-terminal third of myosin light chain 2 maps close to the head-rod junction. A polyclonal antibody specific for the amino terminus of light chain 3 binds further up in the "neck region" of the head, indicating that these portions of the two classes of light chains are located at different sites.

Characterization of the actin-binding site on the alkali light chain of myosin

1H-NMR experiments on myosin subfragment-1 (S1) isoenzymes, containing either the A1 or the A2 alkali light chains (S1(A1) or S1(A2)), have previously suggested the 41-residue proline, alanine and lysine-rich N-terminal extension of A1 to constitute a mobile 'domain' in solution. This segment of the molecule is immobilised in the presence of actin (Prince et al. (1981) Eur. J. Biochem. 121, 213-219). We now establish that the A1 light chain interacts with actin directly, and furthermore, that the binding site appears to be restricted to the terminal 41 residues. This observation carries important consequences for both the structure of the actomyosin complex and the role of myosin isoenzymes. Using the proteinase, thrombin, a technique has been developed in which the A1 light chain is cleaved, releasing the N-terminal 'tail' from an A2-like fragment. The method is shown to be widely applicable to light chains from a variety of sources. The isolated N-terminal fragments from rabbit skeletal and bovine cardiac muscle have been shown to interact directly with actin by a combination of affinity chromatography and 1H-NMR experiments. The 1H-NMR results are similar to those obtained earlier with S1 (ibid) and suggest the terminal alpha-N-trimethylalanine residue (Henry et al. (1982) FEBS Lett. 144, 11-15) to participate in the interaction.

The functional nature of calcium binding units in calmodulin, troponin C and parvalbumin

Examination of the interaction of major tranquilizers with calmodulin results in the generalization that the functional nature of calcium binding helix-loop-helix regions found in several calcium binding proteins including calmodulin, troponin C and parvalbumin is dependent upon the topography of the hydrophobic and hydrophilic regions on the amphiphilic N-terminal alpha-helix of the helix-loop-helix conformation formed by the binding of the calcium cation to these proteins. The relation of the topography of this amphiphilic alpha-helix to drug binding is delineated at the molecular level and the results obtained are used to describe the interaction of beta-endorphin, dynorphin, alpha-MSH and other peptides with calmodulin. The utility of this hypothesis is further demonstrated by the description of a possible interaction between troponin C, troponin I and troponin T of the troponin complex in skeletal muscle.

Analysis of the metal-induced conformational change in myosin with a monoclonal antibody to light chain two

A monoclonal antibody capable of detecting a conformational change in myosin light chain two (LC2) was characterized in detail. The antibody was shown to bind only to myosin LC2 when tested against fast skeletal myosin (chicken pectoralis muscle). With cardiac or slow muscle myosins, the antibody exclusively recognized their first light chains (LC1). Staining of myofibrils by the monoclonal antibody could be observed only after their irreversible denaturation by acetone or ethanol, or after incubation of the myofibrils in divalent metal chelators. This latter effect was shown to be fully reversible. The metal effect was independent of ionic strength although the affinity of the antibody for myosin was depressed at high salt concentrations. Similar metal effects were detected in the binding of antibody to cardiac or slow myosins. Neither the metal nor the ionic strength-related inhibition of antibody binding were detected with denatured myosin. The antibody binding site overlaps one of the alpha-chymotryptic sites in LC2 protected by divalent metals. Electron microscopic observations of myosin-antibody complexes demonstrated that the antibody binding site is located near the head-rod junction of myosin. Since the binding site of this monoclonal antibody has been mapped by recombinant DNA methods to the junction of the first alpha-helical domain with the calcium binding site of LC2, the location of the calcium binding site must also be located near the head-tail junction of myosin. A model for conformational changes at the myosin head-tail junction is proposed to account for the metal-induced blockage of antibody binding and the inhibition of alpha-chymotryptic digestion of LC2.

Recombinant DNA approach for defining the primary structure of monoclonal antibody epitopes. The analysis of a conformation-specific antibody to myosin light chain 2

A monoclonal antibody (MF5), capable of recognizing a divalent cation-induced conformational change in myosin light chain 2 (LC2f), has been used to screen a cDNA library constructed in the expression vector lambda gt11. A clone has been isolated that contains the whole coding sequence of this myosin subunit. The light chain was synthesized as a fusion peptide linked to beta-galactosidase by ten amino acids encoded in the 5' untranslated region of its mRNA. Seven imperfect repeats were identified in the 3' untranslated region of the mRNA. The amino acids conferring specificity on the MF 5 epitope were established by first determining the nucleotide sequence of shorter subclones that expressed the epitope and then eliminating those amino acid residues shared by cardiac myosin LC2, which was unreactive with this antibody. The epitope, which becomes accessible to MF 5 upon removal of bound divalent cations, resides at the junction between the first alpha-helical domain and the metal binding site. Theoretically, this approach can be used to define the primary structure of most protein epitopes.

A single locus in the mouse encodes both myosin light chains 1 and 3, a second locus corresponds to a related pseudogene

Two loci have been characterized in the mouse Mus musculus, which are homologous to the mRNAs encoding myosin light chains MLC1F and MLC3F, two proteins with a common -COOH terminal sequence. One of these loci is an intronless pseudogene, absent from the mouse species Mus spretus; alterations in its nucleotide sequence preclude it from generating a functional MLC1F or MLC3F. The other contains the genetic information for the two proteins. The part common to both proteins is encoded by five exons, which cover about 6.5 kb. Genetic information specific for the N-terminal sequences is encoded in four exons, at 3.5 and 14.3 kb for MLC1F, and 3.8 and 4.5 kb for MLC3F, upstream of the first common exon. Each 5' terminus has a TATA-like consensus sequence about 30 bases upstream of the cap site. The pseudogene is not genetically linked to the functional MLC1F/MLC3F locus in the genome of Mus musculus.

Proteolysis and structure of skeletal muscle actin

Under standard conditions, G-actin has been submitted to nine proteases of varying specificity, and in each case the pattern of fragments produced has been studied by NaDodSO4 gel electrophoresis. The results suggest that the actin monomer consists of a large region (ca. 33 kilodaltons) and a small, easily degraded region (ca. 9 kilodaltons). The COOH terminus is in the large region. Consideration of primary sequence homologies, medium resolution maps of actin crystals, and certain reactions of actin suggests that the NH2 terminus is in the small region, as is the negative sequence to which a divalent metal cation is normally chelated, but that the nucleotide-binding site is on the large region near the junction between the regions. From analysis of these results, numerous properties of actin are understandable.

Thin filament proteins and thin filament-linked regulation of vertebrate muscle contraction

Recent developments in the field of myofibrillar proteins will be reviewed. Consideration will be given to the proteins that participate in the contractile process itself as well as to those involved in Ca-dependent regulation of striated (skeletal and cardiac) and smooth muscle. The relation of protein structure to function will be emphasized and the relation of various physiologically and histochemically defined fiber types to the proteins found in them will be discussed.

Use of lanthanide-induced nuclear magnetic resonance shifts for determination of protein structure in solution: EF calcium binding site of carp parvalbumin

The binding of the paramagnetic lanthanide ion ytterbium to the calcium binding protein carp parvalbumin results in a series of 1H NMR resonances which are shifted far outside the envelope of the 1H NMR spectrum of the diamagnetic form of the protein; bound Yb3+ also induces shifts in the 13C NMR spectrum of parvalbumin and in the 113Cd NMR spectrum of cadmium-substituted parvalbumin. The interpretation of these lanthanide-shifted resonances in terms of the structure of the protein surrounding the metal binding site requires the determination of the orientation and principal elements of the magnetic susceptibility tensor of the protein-bound Yb3+ ion. A previous comparison [Lee, L., & Sykes, B. D. (1982) Biomolecular Structure Determination by NMR (Bothner-By, A. A., Glickson, J. D., & Sykes, B. D., Eds.) pp 169-188, Marcel Dekker, New York] of the observed Yb3+-shifted 1H NMR spectrum of parvalbumin with a calculated spectrum, based upon the X-ray structure and an initial determination of the magnetic susceptibility tensor, led to the conclusion that there were significant differences between the solution and X-ray structures. In this paper, the magnetic susceptibility tensor has been reevaluated with the aid of newly assigned 13C and 113Cd NMR resonances. The agreement between the calculated and observed spectra is now close overall.

Codon usage in muscle genes and liver genes

Synonymous codon usage frequencies, derived from cDNA clone sequences, were compared for several sets of vertebrate genes. Gene sets as diverse as those expressed in avian skeletal muscle and in mammalian liver showed similar patterns of synonymous codon usage. There were no significant differences suggesting tissue-specific co-adaptation of codon usage patterns and tRNA anticodon profiles. The results indicate a consensus codon usage pattern for vertebrate genes which is largely independent of taxonomic class, tissue of expression, and the cellular fate and rate of evolution of the encoded proteins. Certain elements of the consensus codon usage pattern indicate that it is the product of natural selection and not simply a mutational equilibrium among phenotypically equivalent synonyms.

Proton magnetic resonance studies on peptide fragments of troponin-C containing single calcium-binding sites

Proton magnetic resonance spectroscopy has been employed to study the solution conformation of three cleavage fragments of troponin-C, each containing a single Ca(II)-binding site and corresponding to different regions in the primary sequence; viz. CB8 (residues 46-77), CB9 (residues 85-134) and TH2 (residues 121-159). Although all three peptides lack a well-defined tertiary fold in the absence of metal ions, several spectral features indicate the presence of local conformational constraints in each apo-peptide. Ca(II) binding led to spectral changes consistent with increased restriction of backbone motility and the adoption of a more compact conformation. Studies using paramagnetic ions as conformational probes support current views concerning the nature of the ligands at the metal binding sites. The nature and kinetics of the structural influence of metal binding suggest that the conformational constraints existing in the CB8 apo-peptide provide an adequate Ca(II)-binding configuration. In contrast, the CB9 and TH2 peptides exhibit spectral changes consistent with an increased local structure in the region of helix E (residues 94-102) in the case of CB9 and helix H (residues 148-159) in the case of TH2. In CB9, conformation changes also appear to be transmitted to a portion of the sequence (residues 87-93) preceding helix E, a putative site of interaction between troponin-C and troponin-I. These data are discussed with reference to the contribution of long-range (interdomain) interactions within troponin-C and the modulation of troponin subunit protein-protein interactions by Ca(II) binding.