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Adenylate Kinase (adenylate + kinase)
Selected AbstractsCover Picture (Isr. J. Chem.ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 20093-4/2009) Structures of E. coli Adenylate Kinase in the open (4AKE) and closed (1ANK) states with cyanine dye derivatives modeled onto residues 128 and 194 for single-molecule Forster resonance energy transfer (FRET) studies of lid dynamics. The bottom of the figure displays a sample distance-vs.-time trajectory displaying spontaneous lid open,closed transitions on the millisecond timescale. The time-dependent potential of mean force along the lid coordinate measured by single-molecule FRET is also displayed. Further information can be found in Hanson et al., Proc. Natl. Acad. Sci. USA, 104, 18055,18060 (2007). With thanks to Haw Yang. [source] Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium Desulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009A. V. Kladova Adenylate kinase (AK; ATP:AMP phosphotransferase; EC 2.7.4.3) is involved in the reversible transfer of the terminal phosphate group from ATP to AMP. AKs contribute to the maintenance of a constant level of cellular adenine nucleotides, which is necessary for the energetic metabolism of the cell. Three metal ions, cobalt, zinc and iron(II), have been reported to be present in AKs from some Gram-negative bacteria. Native zinc-containing AK from Desulfovibrio gigas was purified to homogeneity and crystallized. The crystals diffracted to beyond 1.8,Å resolution. Furthermore, cobalt- and iron-containing crystal forms of recombinant AK were also obtained and diffracted to 2.0 and 3.0,Å resolution, respectively. Zn2+,AK and Fe2+,AK crystallized in space group I222 with similar unit-cell parameters, whereas Co2+,AK crystallized in space group C2; a monomer was present in the asymmetric unit for both the Zn2+,AK and Fe2+,AK forms and a dimer was present for the Co2+,AK form. The structures of the three metal-bound forms of AK will provide new insights into the role and selectivity of the metal in these enzymes. [source] Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Milya Davlieva Adenylate kinases (AKs; EC 2.7.4.3) are essential members of the NMP kinase family that maintain cellular homeostasis by the interconversion of AMP, ADP and ATP. AKs play a critical role in adenylate homeostasis across all domains of life and have been used extensively as prototypes for the study of protein adaptation and the relationship of protein dynamics and stability to function. To date, kinetic studies of psychrophilic AKs have not been performed. In order to broaden understanding of extremophilic adaptation, the kinetic parameters of adenylate kinase from the psychrophile Marinibacillus marinus were examined and the crystal structure of this cold-adapted enzyme was determined at 2.0,Å resolution. As expected, the overall structure and topology of the psychrophilic M. marinus AK are similar to those of mesophilic and thermophilic AKs. The thermal denaturation midpoint of M. marinus AK (321.1,K) is much closer to that of the mesophile Bacillus subtilis (320.7,K) than the more closely related psychrophile B. globisporus (316.4,K). In addition, the enzymatic properties of M. marinus AK are quite close to those of the mesophilic AK and suggests that M. marinus experiences temperature ranges in which excellent enzyme function over a broad temperature range (293,313,K) has been retained for the success of the organism. Even transient loss of AK function is lethal and as a consequence AK must be robust and be well adapted to the environment of the host organism. [source] Ischaemic preconditioning is related to decreasing levels of extracellular adenosine that may be metabolically useful in the at-risk myocardium: an experimental study in the pigACTA PHYSIOLOGICA, Issue 1 2010A. Waldenström Abstract Aim:, ,Pre-treatment' with short repetitive periods of ischaemia (ischaemic preconditioning) has proved to be a powerful mechanism for modification of the extent of myocardial damage following acute coronary artery occlusion. The exact mechanism of protection induced by ischaemic preconditioning is not known. We herewith put forward a contributing component for protection with preconditioning involving a shift in the adenylate kinase (AK) equilibrium reaction in favour of adenosine triphosphate (ATP) formation. Methods:, A coronary artery was occluded in anaesthetized thoracotomized pigs to induce ischaemic preconditioning as well as a longer period of ischaemia. Microdialysis probes were inserted in ischaemic and control myocardium and were infused with 14C- adenosine with two different specific activities. 14C-lactate was identified and measured in the effluent. Results:,14C-adenosine was taken up by non-preconditioned and preconditioned myocardium during ischaemia. Significantly increased levels of 14C-lactate were recovered in preconditioned myocardium. 14C-adenosine with high specific activity resulted in a specific activity of lactate that was 2.7 times higher than that of lactate after administration of 14C-adenosine with low specific activity. Mass spectrography verified the identity of 14C-lactate. Conclusions:, Preconditioning up-regulates a new metabolic pathway (starting with 5,-nucleotidase and ending up with lactate) resulting in ATP formation in the micromolar range on top of another effect terminating in a useful shift in the AK equilibrium reaction in favour of ATP generation in the millimolar range. Although the up-regulation of the purine nucleoside phosphorylase pathway is clearly demonstrated, its biological relevance remains to be proved. [source] The role of Ureaplasma nucleoside monophosphate kinases in the synthesis of nucleoside triphosphatesFEBS JOURNAL, Issue 8 2007Liya Wang Mollicutes are wall-less bacteria and cause various diseases in humans, animals and plants. They have the smallest genomes with low G + C content and lack many genes of DNA, RNA and protein precursor biosynthesis. Nucleoside diphosphate kinase (NDK), a house-keeping enzyme that plays a critical role in the synthesis of nucleic acids precursors, i.e. NTPs and dNTPs, is absent in all the Mollicutes genomes sequenced to date. Therefore, it would be of interest to know how Mollicutes synthesize dNTPs/NTPs without NDK. To answer this question, nucleoside monophosphate kinases (NMPKs) from Ureaplasma were studied regarding their role in the synthesis of NTPs/dNTPs. In this work, Ureaplasma adenylate kinase, cytidylate kinase, uridylate kinase and thymidylate kinase were cloned and expressed in Escherichia coli. The recombinant enzymes were purified and characterized. These NMPKs are base specific, as indicated by their names, and capable of converting (d)NMPs directly to (d)NTPs. The catalytic rates of (d)NTPs and (d)NDP synthesis by these NMPKs were determined using tritium-labelled (d)NMPs, and the rates for (d)NDP synthesis, in general, were much higher (up to 100-fold) than that of (d)NTP. Equilibrium studies with adenylate kinase suggested that the rates of NTPs/dNTPs synthesis by NMPKs in vivo are probably regulated by the levels of (d)NMPs. These results strongly indicate that NMPKs could substitute the NDK function in vivo. [source] Applications of time-resolved resonance energy transfer measurements in studies of the molecular crowding effect,JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2004Varda Ittah Abstract The native structures of many globular proteins are only weakly stabilized and form in solution ensembles of multiple conformers. The energy differences between the conformers are assumed to be small. This is the case of flexible multidomain proteins where domain motions were observed. High concentrations of inert macrosolute, which create a crowded or confined environment, can cause shifts of the distribution of the conformers of such proteins towards the more compact structures. This effect may also promote compact structures in partially folded proteins. Time-resolved dynamic non-radiative excitation energy transfer (tr-RET) is suitable for detection of either subtle or major changes in distributions of intramolecular distances in protein molecules in solutions. Two experiments were performed which demonstrated the applicability of tr-RET for detection of the effect of macrosolutes on the conformational ensembles of flexible states of protein molecules. The distribution of distances between residues 203 and 169 in the CORE domain of E. coli adenylate kinase (AK) in the denatured state was determined in the presence of high concentrations of dextran 40. A significant shift of the mean of the distribution was observed without reduction of its width. This was interpreted as a shift to compact structure without change of the degree of disorder of the chain. In a second experiment the distribution of the distance between residues 55 and 169 in AK, which spans the cleft between the CORE and the AMPbind domains, was monitored. No clear effect of high concentrations of dextran 40 was found. These experiments show the strength of the application of tr-RET in investigation of changes in the sub-states of flexible conformations of globular protein. Networks of pairs of labeled sites can be prepared and tr-RET experiments can be performed in order to search for the segments of the protein molecules, which respond to the presence of inert macromolecules in their environment. Copyright © 2004 John Wiley & Sons, Ltd. [source] Molecular imprinting of AMP by an ionic-noncovalent dual approachJOURNAL OF SEPARATION SCIENCE, JSS, Issue 19 2009Florent Breton Abstract In order to mimic recognition properties of adenylate kinase, molecularly imprinted polymers (MIPs) were prepared for adenosine 5,-monophosphate (AMP), a substrate of the enzyme. Different functional monomers interacting with the phosphate moiety were tested, and the MIP giving the best specific binding of AMP was composed with one equivalent of 2-(dimethylamino)ethyl methacrylate and ten equivalents of acrylamide compared to AMP. Packed into solid phase cartridge, this polymer showed similar characteristics than the enzyme, since it was specific for AMP toward other nucleotides. [source] Influence of phage population on the phage-mediated bioluminescent adenylate kinase (AK) assay for detection of bacteriaLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2001Y. Wu Aims: The effect of phage concentration on the activity of adenylate kinase (AK) released from the cells lysed during infection was investigated in order to optimize a bioluminescent phage-mediated method for bacterial enumeration. Methods and Results: The number of bacteria lysed by phages specific to Salmonella enteritidis and E. coli was determined using a bioluminescent method for the detection of AK released. In order to optimize the assay, the effect of phage concentration and time of infection on the amount of AK released was investigated. The release of AK was greatest at a multiplicity of infection (moi) of 10,100. Conclusions: The amount of AK released from Salmonella enteritidis and E. coli G2-2 cells by specific phages, SJ2 and AT20, respectively, depended on the type of bacteria, the stage of growth, the nature of phage, moi and time. Significance and Impact of the Study: An assay is described which allows detection of E. coli and Salmonella Enteritidis within 2 h at levels of 103 cfu ml,1. [source] Gated dynamic 31P MRS shows reduced contractile phosphocreatine breakdown in mice deficient in cytosolic creatine kinase and adenylate kinaseNMR IN BIOMEDICINE, Issue 5 2009Hermien E. Kan Abstract We developed a new dedicated measurement protocol for dynamic 31P MRS analysis in contracting calf muscles of the mouse, using minimally invasive assessment of the contractile force combined with the acquisition of spectroscopic data gated to muscle contraction and determination of phosphocreatine (PCr) recovery rate and ATP contractile cost. This protocol was applied in a comparative study of six wild type (WT) mice and six mice deficient in cytosolic creatine kinase and adenylate kinase isoform 1 (MAK,/, mice) using 70 repeated tetanic contractions at two contractions per minute. Force levels during single contractions, and metabolite levels and tissue pH during resting conditions were similar in muscles of MAK,/, and WT mice. Strikingly, muscle relaxation after contraction was significantly delayed in MAK,/, mice, but during repeated contractions, the decrease in the force was similar in both mouse types. Gated data acquisition showed a negligible PCr breakdown in MAK,/, immediately after contraction, without a concomitant decrease in ATP or tissue pH. This protocol enabled the determination of rapid PCr changes that would otherwise go unnoticed due to intrinsic low signal-to-noise ratio (SNR) in mouse skeletal muscles combined with an assessment of the PCr recovery rate. Our results suggest that MAK,/, mice use alternative energy sources to maintain force during repeated contractions when PCr breakdown is reduced. Furthermore, the absence of large increases in adenosine diphosphate (ADP) or differences in force compared to WT mice in our low-intensity protocol indicate that creatine kinase (CK) and adenylate kinase (AK) are especially important in facilitating energy metabolism during very high energy demands. Copyright © 2009 John Wiley & Sons, Ltd. [source] Proteomic profiling of antisense-induced exon skipping reveals reversal of pathobiochemical abnormalities in dystrophic mdx diaphragmPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2009Philip Doran Abstract The disintegration of the dystrophin,glycoprotein complex represents the initial pathobiochemical insult in Duchenne muscular dystrophy. However, secondary changes in signalling, energy metabolism and ion homeostasis are probably the main factors that eventually cause progressive muscle wasting. Thus, for the proper evaluation of novel therapeutic approaches, it is essential to analyse the reversal of both primary and secondary abnormalities in treated muscles. Antisense oligomer-mediated exon skipping promises functional restoration of the primary deficiency in dystrophin. In this study, an established phosphorodiamidate morpholino oligomer coupled to a cell-penetrating peptide was employed for the specific removal of exon 23 in the mutated mouse dystrophin gene transcript. Using DIGE analysis, we could show the reversal of secondary pathobiochemical abnormalities in the dystrophic diaphragm following exon-23 skipping. In analogy to the restoration of dystrophin, ,-dystroglycan and neuronal nitric oxide synthase, the muscular dystrophy-associated differential expression of calsequestrin, adenylate kinase, aldolase, mitochondrial creatine kinase and cvHsp was reversed in treated muscle fibres. Hence, the re-establishment of Dp427 coded by the transcript missing exon 23 has counter-acted dystrophic alterations in Ca2+ -handling, nucleotide metabolism, bioenergetic pathways and cellular stress response. This clearly establishes the exon-skipping approach as a realistic treatment strategy for diminishing diverse downstream alterations in dystrophinopathy. [source] Proteomic analysis of hearts from frataxin knockout mice: Marked rearrangement of energy metabolism, a response to cellular stress and altered expression of proteins involved in cell structure, motility and metabolismPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2008Robert Sutak Abstract A frequent cause of death in Friedreich's ataxia patients is cardiomyopathy, but the molecular alterations underlying this condition are unknown. We performed 2-DE to characterize the changes in protein expression of hearts using the muscle creatine kinase frataxin conditional knockout (KO) mouse. Pronounced changes in protein expression profile were observed in 9,week-old KO mice with severe cardiomyopathy. In contrast, only several proteins showed altered expression in asymptomatic 4,week-old KO mice. In hearts from frataxin KO mice, components of the iron-dependent complex-I and -II of the mitochondrial electron transport chain and enzymes involved in ATP homeostasis (creatine kinase, adenylate kinase) displayed decreased expression. Interestingly, the KO hearts exhibited increased expression of enzymes involved in the citric acid cycle, catabolism of branched-chain amino acids, ketone body utilization and pyruvate decarboxylation. This constitutes evidence of metabolic compensation due to decreased expression of electron transport proteins. There was also pronounced up-regulation of proteins involved in stress protection, such as a variety of chaperones, as well as altered expression of proteins involved in cellular structure, motility and general metabolism. This is the first report of the molecular changes at the protein level which could be involved in the cardiomyopathy of the frataxin KO mouse. [source] A differential proteome in tumors suppressed by an adenovirus-based skin patch vaccine encoding human carcinoembryonic antigenPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2005Chun-Ming Huang Abstract We created an anti-tumor vaccine by using adenovirus as a vector which contains a cytomegalovirus early promoter-directed human carcinoembryonic antigen gene (AdCMV-hCEA). In an attempt to develop the skin patch vaccine, we epicutaneously vaccinated Balb/c mice with AdCMV-hCEA. After nine weeks post-immunization, vaccinated mice evoked a robust antibody titer to CEA and demonstrated the capability of suppressing in vivo growth of implanted murine mammay adenocarioma cell line (JC-hCEA) tumor cells derived from a female Balb/c mouse. Proteomic analysis of the tumor masses in the non-vaccinated naïve and vaccinated mice reveal that six proteins change their abundance in the tumor mass. The levels of adenylate kinase 1, ,-enolase, creatine kinase M chain, hemoglobin beta chain and prohibitin were statistically increased whereas the level of a creatine kinase fragment, which is undocumented, was decreased in the tumor of vaccinated mice. These proteins may provide a vital link between early-stage tumor suppression and immune response of skin patch vaccination. [source] Proteomic investigation of the effects of weight loss in the gastrocnemius muscle of wild and NZW rabbits via 2D-electrophoresis and MALDI-TOF MSANIMAL GENETICS, Issue 3 2010A. M. Almeida Summary The study of changes within the key agents regulating metabolism during genetic upgrading because of selection can contribute to an improved understanding of genomic and physiological relationships. This may lead to increased efficiencies in animal production. These changes, regarding energy and protein metabolic saving mechanisms, can be highlighted during food restriction periods. In this study, a 20% weight reduction was induced in two rabbit breeds: New Zealand white, a selected meat producer (Oryctolagus cuniculus cuniculus), and Iberian wild rabbit (Oryctolagus cuniculus algirus), with the aim of determining differential protein expression in the gastrocnemius muscle within control (ad libitum) and restricted diet experimental animal groups, using techniques of two-dimensional gel electrophoresis and peptide mass fingerprinting. Results show that l -lactate dehydrogenase, adenylate kinase, , enolase and , enolase, fructose bisphosphate aldolase A and glyceraldehyde 3-phosphate dehydrogenase, which are enzymes involved in energy metabolism, are differentially expressed in restricted diet experimental animal groups. These enzymes are available to be further tested as relevant biomarkers of weight loss and putative objects of manipulation as a selection tool towards increasing tolerance to weight loss. Similar reasoning could be applied to 2D gel electrophoresis spots corresponding to the important structural proteins tropomyosin , chain and troponin I. Finally, a spot identified as mitochondrial import stimulation factor seems of special interest as a marker of undernutrition, and it may be the object of further studies aiming to better understand its physiological role. [source] Crystallization and preliminary X-ray diffraction analysis of shikimate kinase from Mycobacterium tuberculosis in complex with MgADPACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2001Yijun Gu Shikimate kinase (SK) from Mycobacterium tuberculosis (Mt) was overexpressed in Escherichia coli, purified and cocrystallized with MgADP in hanging drops using the vapor-diffusion procedure with PEG 4000 and 2-propanol as precipitants at pH 7.5. The crystal of MtSK,MgADP, which diffracted to 2.2,Å resolution, belonged to space group P3221 or P3121, with unit-cell parameters a = b = 64.01, c = 92.41,Å. There was one MtSK molecule in the asymmetric unit. Molecular-replacement trials with the crystal structure of SK from Erwinia chrysanthemi (PDB code 1shk) and adenylate kinase (PDB code 1ake) as search models were not successful. Heavy-atom derivative screening is in progress. [source] Metabolic systems maintain stable non-equilibrium via thermodynamic bufferingBIOESSAYS, Issue 10 2009Abir U. Igamberdiev Abstract Here, we analyze how the set of nucleotides in the cell is equilibrated and how this generates simple rules that help the cell to organize itself via maintenance of a stable non-equilibrium state. A major mechanism operating to achieve this state is thermodynamic buffering via high activities of equilibrating enzymes such as adenylate kinase. Under stable non-equilibrium, the ratios of free and Mg-bound adenylates, Mg2+ and membrane potentials are interdependent and can be computed. The adenylate status is balanced with the levels of reduced and oxidized pyridine nucleotides through regulated uncoupling of the pyridine nucleotide pool from ATP production in mitochondria, and through oxidation of substrates non-coupled to NAD+ reduction in peroxisomes. The set of adenylates and pyridine nucleotides constitutes a generalized cell energy status and determines rates of major metabolic fluxes. As the result, fluxes of energy and information become organized spatially and temporally, providing conditions for self-maintenance of metabolism. [source] Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium Desulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009A. V. Kladova Adenylate kinase (AK; ATP:AMP phosphotransferase; EC 2.7.4.3) is involved in the reversible transfer of the terminal phosphate group from ATP to AMP. AKs contribute to the maintenance of a constant level of cellular adenine nucleotides, which is necessary for the energetic metabolism of the cell. Three metal ions, cobalt, zinc and iron(II), have been reported to be present in AKs from some Gram-negative bacteria. Native zinc-containing AK from Desulfovibrio gigas was purified to homogeneity and crystallized. The crystals diffracted to beyond 1.8,Å resolution. Furthermore, cobalt- and iron-containing crystal forms of recombinant AK were also obtained and diffracted to 2.0 and 3.0,Å resolution, respectively. Zn2+,AK and Fe2+,AK crystallized in space group I222 with similar unit-cell parameters, whereas Co2+,AK crystallized in space group C2; a monomer was present in the asymmetric unit for both the Zn2+,AK and Fe2+,AK forms and a dimer was present for the Co2+,AK form. The structures of the three metal-bound forms of AK will provide new insights into the role and selectivity of the metal in these enzymes. [source] Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Milya Davlieva Adenylate kinases (AKs; EC 2.7.4.3) are essential members of the NMP kinase family that maintain cellular homeostasis by the interconversion of AMP, ADP and ATP. AKs play a critical role in adenylate homeostasis across all domains of life and have been used extensively as prototypes for the study of protein adaptation and the relationship of protein dynamics and stability to function. To date, kinetic studies of psychrophilic AKs have not been performed. In order to broaden understanding of extremophilic adaptation, the kinetic parameters of adenylate kinase from the psychrophile Marinibacillus marinus were examined and the crystal structure of this cold-adapted enzyme was determined at 2.0,Å resolution. As expected, the overall structure and topology of the psychrophilic M. marinus AK are similar to those of mesophilic and thermophilic AKs. The thermal denaturation midpoint of M. marinus AK (321.1,K) is much closer to that of the mesophile Bacillus subtilis (320.7,K) than the more closely related psychrophile B. globisporus (316.4,K). In addition, the enzymatic properties of M. marinus AK are quite close to those of the mesophilic AK and suggests that M. marinus experiences temperature ranges in which excellent enzyme function over a broad temperature range (293,313,K) has been retained for the success of the organism. Even transient loss of AK function is lethal and as a consequence AK must be robust and be well adapted to the environment of the host organism. [source] Ca2+ -activated myosin-ATPases, creatine and adenylate kinases regulate mitochondrial function according to myofibre type in rabbitTHE JOURNAL OF PHYSIOLOGY, Issue 3 2005N. Gueguen Mitochondrial respiration rates and their regulation by ADP, AMP and creatine, were studied at different free Ca2+ concentrations (0.1 versus 0.4 ,m) on permeabilized fibre bundles of rabbit skeletal muscles differing in their myosin heavy chain profiles. Four fibre bundle types were obtained: pure types I and IIx, and mixed types IIax (approximately 50% IIa and 50% IIx fibres) and IIb+ (60% IIb fibres, plus IIx and IIa). At rest, pure type I fibres displayed a much higher apparent Km for ADP (212 ,m) than IIx fibres (8 ,m). Within the IIax and IIb+ mixed fibre bundle types, two KADPm values were observed (70 ,m and 5 ,m). Comparison between pure IIx and mixed types indicates that the intermediate Km of 70 ,m most probably corresponds to the mitochondrial affinity for ADP in IIa fibres, the lowest Km for ADP (5 ,m) corresponding to IIx and IIb types. Activation of mitochondrial creatine and adenylate kinase reactions stimulated mitochondrial respiration only in type I and IIax fibre bundles, indicating an efficient coupling between both kinases and ADP rephosphorylation in type I and, likely, IIa fibres, since no effect was observed in pure IIx fibres. Following Ca2+ -induced activation of myosin-ATPase, an increase in mitochondrial sensitivity to ADP of 45% and 250% was observed in type IIax and I bundles, respectively, an effect mostly prevented by addition of vanadate, an inhibitor of myosin-ATPase. Ca2+ -induced activation of myosin-ATPase also prevented the stimulation of respiration rates by creatine and AMP in I and IIax bundles. In addition to differential regulation of mitochondrial respiration and energy transfer systems at rest in I and IIa versus IIx and IIb muscle fibres, our results indicate a regulation of phosphotransfer systems by Ca2+ via the stimulation of myosin-ATPases in type I and IIa fibres of rabbit muscles. [source] | |||||||||||||