Measuring synthesis rates of muscle creatine kinase and myosin with stable isotopes and mass spectrometry

Protein Turnover in Skeletal Muscle: Looking at Molecular Regulation towards an Active Lifestyle

Skeletal muscle is a highly plastic tissue, able to change its mass and functional properties in response to several stimuli. Skeletal muscle mass is influenced by the balance between protein synthesis and breakdown, which is regulated by several signaling pathways. The relative contribution of Akt/mTOR signaling, ubiquitin-proteasome pathway, autophagy among other signaling pathways to protein turnover and, therefore, to skeletal muscle mass, differs depending on the wasting or loading condition and muscle type. By modulating mitochondria biogenesis, PGC-1α has a major role in the cell's bioenergetic status and, thus, on protein turnover. In fact, rates of protein turnover regulate differently the levels of distinct protein classes in response to atrophic or hypertrophic stimuli. Mitochondrial protein turnover rates may be enhanced in wasting conditions, whereas the increased turnover of myofibrillar proteins triggers muscle mass gain. The present review aims to update the knowledge on the molecular pathways implicated in the regulation of protein turnover in skeletal muscle, focusing on how distinct muscle proteins may be modulated by lifestyle interventions with emphasis on exercise training. The comprehensive analysis of the anabolic effects of exercise programs will pave the way to the tailored management of muscle wasting conditions.

Measurement of protein in vivo turnover rate with metabolic labeling using LC-MS

Understanding the protein dynamics of a drug target is important for pharmaceutical research because it provides insight into drug design, target engagement, pharmacodynamics and drug efficacy. Nonradioactive isotope labeling has been the method of choice for protein turnover measurement thanks to the advancement of high-resolution mass spectrometry. While the changes in proteome in cell cultures can be monitored precisely, as the culture media can be completely replaced with ² H-, ¹⁵ N- or ¹³ C-labeled essential amino acids, quantifying rates of protein synthesis in vivo is more challenging. The amount of isotope tracer that can be administered into the body is relatively small compared with the existing protein, thus requiring more sensitive detection, and the precursor-product labeling relationship is more complicated to interpret. The purpose of this review is to provide an overview of the principles of in vivo protein turnover studies using deuterium water (² H₂ O) with an emphasis on targeted protein analysis by hybrid LC-MS assay platforms. The pursuit of these opportunities will facilitate drug discovery and research in preclinical and clinical stages.

Short Communication: Supplementation with calcium butyrate causes an increase in the percentage of oxidative fibers in equine gluteus medius muscle

Optimal athletic performance requires meeting the energetic demands of the muscle fibers, which are a function of myosin ATPase enzymatic activity. Skeletal muscle with a predominant oxidative metabolism underlies equine athletic success. Sodium butyrate, a short-chain fatty acid, can affect muscle fiber composition in pigs. To determine if a similar scenario exists in horses, 12 adult Thoroughbred geldings (7.4 ± 0.6 yr of age; mean ± SEM) were fed 16 g of calcium butyrate (CB) or an equivalent amount of carrier (CON) daily for 30 d in a crossover design. Middle gluteal muscle biopsies were collected before and after the feeding trial for immunohistochemical determination of fiber type, and RNA and protein isolation. After 30 d, CB increased (P < 0.05) the percentage of type IIA fibers and tended (P = 0.13) to reduce the numbers of type IIX fibers in comparison to control (CON). No changes (P > 0.05) in type I, IIA, or IIX fiber size were observed in response to CB. No differences (P > 0.05) were noted in the abundance of succinate dehydrogenase (SDH) protein or activity between horses receiving CB or CON. Myogenin mRNA abundance was unaffected (P > 0.05) by 30 d of CB supplementation. The increase in type IIA fibers in the absence of altered mitochondrial SDH enzymatic activity suggests that CB affects myosin ATPase expression independent of altered metabolism.

Fractional Synthesis Rates of Individual Proteins in Rat Soleus and Plantaris Muscles

Differences in the protein composition of fast- and slow-twitch muscle may be maintained by different rates of protein turnover. We investigated protein turnover rates in slow-twitch soleus and fast-twitch plantaris of male Wistar rats (body weight 412 ± 69 g). Animals were assigned to four groups (n = 3, in each), including a control group (0 d) and three groups that received deuterium oxide (D₂O) for either 10 days, 20 days or 30 days. D₂O administration was initiated by an intraperitoneal injection of 20 μL of 99% D₂O-saline per g body weight, and maintained by provision of 4% (v/v) D₂O in the drinking water available ad libitum. Soluble proteins from harvested muscles were analysed by liquid chromatography–tandem mass spectrometry and identified against the SwissProt database. The enrichment of D₂O and rate constant (k) of protein synthesis was calculated from the abundance of peptide mass isotopomers. The fractional synthesis rate (FSR) of 44 proteins in soleus and 34 proteins in plantaris spanned from 0.58%/day (CO1A1: Collagen alpha-1 chain) to 5.40%/day NDRG2 (N-myc downstream-regulated gene 2 protein). Eight out of 18 proteins identified in both muscles had a different FSR in soleus than in plantaris (p < 0.05).

Allele-Selective Knockdown of MYH7 Using Antisense Oligonucleotides

Hundreds of dominant-negative myosin mutations have been identified that lead to hypertrophic cardiomyopathy, and the biomechanical link between mutation and disease is heterogeneous across this patient population. To increase the therapeutic feasibility of treating this diverse genetic population, we investigated the ability of locked nucleic acid (LNA)-modified antisense oligonucleotides (ASOs) to selectively knock down mutant myosin transcripts by targeting single-nucleotide polymorphisms (SNPs) that were found to be common in the myosin heavy chain 7 (MYH7) gene. We identified three SNPs in MYH7 and designed ASO libraries to selectively target either the reference or alternate MYH7 sequence. We identified ASOs that selectively knocked down either the reference or alternate allele at all three SNP regions. We also show allele-selective knockdown in a mouse model that was humanized on one allele. These results suggest that SNP-targeting ASOs are a promising therapeutic modality for treating cardiac pathology.

A1603P and K1617del, Mutations in β-Cardiac Myosin Heavy Chain that Cause Laing Early-Onset Distal Myopathy, Affect Secondary Structure and Filament Formation In Vitro and In Vivo

Over 20 mutations in β-cardiac myosin heavy chain (β-MHC), expressed in cardiac and slow muscle fibers, cause Laing early-onset distal myopathy (MPD-1), a skeletal muscle myopathy. Most of these mutations are in the coiled-coil tail and commonly involve a mutation to a proline or a single-residue deletion, both of which are predicted to strongly affect the secondary structure of the coiled coil. To test this, we characterized the effects of two MPD-1 causing mutations: A1603P and K1617del in vitro and in cells. Both mutations affected secondary structure, decreasing the helical content of 15 heptad and light meromyosin constructs. Both mutations also severely disrupted the ability of glutathione S-transferase–light meromyosin fusion proteins to form minifilaments in vitro, as demonstrated by negative stain electron microscopy. Mutant eGFP-tagged β-MHC accumulated abnormally into the M-line of sarcomeres in cultured skeletal muscle myotubes. Incorporation of eGFP-tagged β-MHC into sarcomeres in adult rat cardiomyocytes was reduced. Molecular dynamics simulations using a composite structure of part of the coiled coil demonstrated that both mutations affected the structure, with the mutation to proline (A1603P) having a smaller effect compared to K1617del. Taken together, it seems likely that the MPD-1 mutations destabilize the coiled coil, resulting in aberrant myosin packing in thick filaments in muscle sarcomeres, providing a potential mechanism for the disease.

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It is unclear how mutations in the coiled coil of β-myosin heavy chain cause distal myopathy.

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A1603P and K1617del mutations reduce helicity and affect filament formation in vitro.

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eGFP-tagged β-myosin heavy chain abnormally accumulates at the M-line of sarcomeres in skeletal myotubes.

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Molecular dynamics simulations provide a molecular understanding for these experiments.

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Effects on structure and packing into the thick filament provide a molecular basis for the disease.

Metabolic Changes During Cancer Cachexia Pathogenesis

Wasting of adipose tissue and skeletal muscle is a hallmark of metastatic cancer and a major cause of death. Like patients with cachexia caused by other chronic infections or inflammatory diseases, the cancer subject manifests both malnutrition and metabolic stress. Both carbohydrate utilization and amino acid incorporation are decreased in the muscles of cancer cachexia patients. Cancer cells affect host metabolism in two ways: (a) their own metabolism of nutrients into other metabolites and (b) circulating factors they secrete or induce the host to secrete. Accelerated glycolysis and lactate production, i.e., the Warburg effect and the resultant increase in Cori cycle activity, are the most widely discussed metabolic effects. Meanwhile, although a large number of pro-cachexia circulating factors have been found, such as TNFa, IL-6, myostatin, and PTHrp, none have been shown to be a dominant factor that can be targeted singly to treat cancer cachexia in humans. It is possible that given the complex multifactorial nature of the cachexia secretome, and the personalized differences between cancer patients, targeting any single circulating factor would always be insufficient to treat cachexia for all patients. Here we review the metabolic changes that occur in response to tumor growth and tumor-secreted factors during cachexia.

A simplified calculation procedure for mass isotopomer distribution analysis (MIDA) based on multiple linear regression

We have developed a novel, rapid and easy calculation procedure for Mass Isotopomer Distribution Analysis based on multiple linear regression which allows the simultaneous calculation of the precursor pool enrichment and the fraction of newly synthesized labelled proteins (fractional synthesis) using linear algebra. To test this approach, we used the peptide RGGGLK as a model tryptic peptide containing three subunits of glycine. We selected glycine labelled in two ¹³ C atoms (¹³ C₂ -glycine) as labelled amino acid to demonstrate that spectral overlap is not a problem in the proposed methodology. The developed methodology was tested first in vitro by changing the precursor pool enrichment from 10 to 40% of ¹³ C₂ -glycine. Secondly, a simulated in vivo synthesis of proteins was designed by combining the natural abundance RGGGLK peptide and 10 or 20% ¹³ C₂ -glycine at 1 : 1, 1 : 3 and 3 : 1 ratios. Precursor pool enrichments and fractional synthesis values were calculated with satisfactory precision and accuracy using a simple spreadsheet. This novel approach can provide a relatively rapid and easy means to measure protein turnover based on stable isotope tracers. Copyright © 2016 John Wiley & Sons, Ltd.

Mechanisms of protein balance in skeletal muscle

Increased global demand for adequate protein nutrition against a backdrop of climate change and concern for animal agriculture sustainability necessitates new and more efficient approaches to livestock growth and production. Anabolic growth is achieved when rates of new synthesis exceed turnover, producing a positive net protein balance. Conversely, deterioration or atrophy of lean mass is a consequence of a net negative protein balance. During early life and periods of growth, muscle mass is driven by increases in protein synthesis at the level of mRNA translation. Throughout life, muscle mass is further influenced by degradative processes such as autophagy and the ubiquitin proteasome pathway. Multiple signal transduction networks guide and coordinate these processes alongside quality control mechanisms to maintain protein homeostasis (proteostasis). Genetics, hormones, and environmental stimuli each influence proteostasis control, altering capacity and/or efficiency of muscle growth. An overview of recent findings and current methods to assess muscle protein balance and proteostasis is presented. Current efforts to identify novel control points have the potential through selective breeding design or development of hormetic strategies to better promote growth and health span during environmental stress.

Circulating protein synthesis rates reveal skeletal muscle proteome dynamics

Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders.

Protein turnover on the scale of the proteome

Protein turnover is a neglected dimension in postgenomic studies, defining the dynamics of changes in protein expression and forging a link between transcriptome, proteome and metabolome. Recent advances in postgenomic technologies have led to the development of new proteomic techniques to measure protein turnover on a proteome-wide scale. These methods are driven by stable isotope metabolic labeling of cells in culture or in intact animals. This review considers the merits and difficulties of different methods that allow access to proteome dynamics.

Cardiomyopathy mutations in the tail of β-cardiac myosin modify the coiled-coil structure and affect integration into thick filaments in muscle sarcomeres in adult cardiomyocytes

It is unclear why mutations in the filament-forming tail of myosin heavy chain (MHC) cause hypertrophic or dilated cardiomyopathy as these mutations should not directly affect contraction. To investigate this, we first investigated the impact of five hypertrophic cardiomyopathy-causing (N1327K, E1356K, R1382W, E1555K, and R1768K) and one dilated cardiomyopathy-causing (R1500W) tail mutations on their ability to incorporate into muscle sarcomeres in vivo. We used adenoviral delivery to express full-length wild type or mutant enhanced GFP-MHC in isolated adult cardiomyocytes. Three mutations (N1327K, E1356K, and E1555K) reduced enhanced GFP-MHC incorporation into muscle sarcomeres, whereas the remainder had no effect. No mutations significantly affected contraction. Fluorescence recovery after photobleaching showed that fluorescence recovery for the mutation that incorporated least well (N1327K) was significantly faster than that of WT with half-times of 25.1 ± 1.8 and 32.2 ± 2.5 min (mean ± S.E.), respectively. Next, we determined the effects of each mutation on the helical properties of wild type and seven mutant peptides (7, 11, or 15 heptads long) from the myosin tail by circular dichroism. R1382W and E1768K slightly increased the α-helical nature of peptides. The remaining mutations reduced α-helical content, with N1327K showing the greatest reduction. Only peptides containing residues 1301-1329 were highly α-helical suggesting that this region helps in initiation of coiled coil. These results suggest that small effects of mutations on helicity translate into a reduced ability to incorporate into sarcomeres, which may elicit compensatory hypertrophy.

Proteome dynamics: revisiting turnover with a global perspective

Although bulk protein turnover has been measured with the use of stable isotope labeled tracers for over half a century, it is only recently that the same approach has become applicable to the level of the proteome, permitting analysis of the turnover of many proteins instead of single proteins or an aggregated protein pool. The optimal experimental design for turnover studies is dependent on the nature of the biological system under study, which dictates the choice of precursor label, protein pool sampling strategy, and treatment of data. In this review we discuss different approaches and, in particular, explore how complexity in experimental design and data processing increases as we shift from unicellular to multicellular systems, in particular animals.

Evolving concepts on the age-related changes in "muscle quality"

The deterioration of skeletal muscle with advancing age has long been anecdotally recognized and has been of scientific interest for more than 150 years. Over the past several decades, the scientific and medical communities have recognized that skeletal muscle dysfunction (e.g., muscle weakness, poor muscle coordination, etc.) is a debilitating and life-threatening condition in the elderly. For example, the age-associated loss of muscle strength is highly associated with both mortality and physical disability. It is well-accepted that voluntary muscle force production is not solely dependent upon muscle size, but rather results from a combination of neurologic and skeletal muscle factors, and that biologic properties of both of these systems are altered with aging. Accordingly, numerous scientists and clinicians have used the term "muscle quality" to describe the relationship between voluntary muscle strength and muscle size. In this review article, we discuss the age-associated changes in the neuromuscular system-starting at the level of the brain and proceeding down to the subcellular level of individual muscle fibers-that are potentially influential in the etiology of dynapenia (age-related loss of muscle strength and power).

Proteostasis and REDOX state in the heart

Force-generating contractile cells of the myocardium must achieve and maintain their primary function as an efficient mechanical pump over the life span of the organism. Because only half of the cardiomyocytes can be replaced during the entire human life span, the maintenance strategy elicited by cardiac cells relies on uninterrupted renewal of their components, including proteins whose specialized functions constitute this complex and sophisticated contractile apparatus. Thus cardiac proteins are continuously synthesized and degraded to ensure proteome homeostasis, also termed "proteostasis." Once synthesized, proteins undergo additional folding, posttranslational modifications, and trafficking and/or become involved in protein-protein or protein-DNA interactions to exert their functions. This includes key transient interactions of cardiac proteins with molecular chaperones, which assist with quality control at multiple levels to prevent misfolding or to facilitate degradation. Importantly, cardiac proteome maintenance depends on the cellular environment and, in particular, the reduction-oxidation (REDOX) state, which is significantly different among cardiac organelles (e.g., mitochondria and endoplasmic reticulum). Taking into account the high metabolic activity for oxygen consumption and ATP production by mitochondria, it is a challenge for cardiac cells to maintain the REDOX state while preventing either excessive oxidative or reductive stress. A perturbed REDOX environment can affect protein handling and conformation (e.g., disulfide bonds), disrupt key structure-function relationships, and trigger a pathogenic cascade of protein aggregation, decreased cell survival, and increased organ dysfunction. This review covers current knowledge regarding the general domain of REDOX state and protein folding, specifically in cardiomyocytes under normal-healthy conditions and during disease states associated with morbidity and mortality in humans.

Molecular time: an often overlooked dimension to cardiovascular disease

Diurnal rhythms influence cardiovascular physiology such as heart rate and blood pressure and the incidence of adverse cardiac events such as heart attack and stroke. For example, shift workers and patients with sleep disturbances, such as obstructive sleep apnea, have an increased risk of heart attack, stroke, and sudden death. Diurnal variation is also evident at the molecular level, as gene expression in the heart and blood vessels is remarkably different in the day as compared to the night. Much of the evidence presented here indicates that growth and renewal (structural remodeling) are highly dependent on processes that occur during the subjective night. Myocardial metabolism is also dynamic with substrate preference also differing day from night. The risk/benefit ratio of some therapeutic strategies and the appearance of biomarkers also vary across the 24-hour diurnal cycle. Synchrony between external and internal diurnal rhythms and harmony among the molecular rhythms within the cell is essential for normal organ biology. Cell physiology is 4 dimensional; the substrate and enzymatic components of a given metabolic pathway must be present not only in the right compartmental space within the cell but also at the right time. As a corollary, we show disrupting this integral relationship has devastating effects on cardiovascular, renal and possibly other organ systems. Harmony between our biology and our environment is vital to good health.

Diurnal physiology: core principles with application to the pathogenesis, diagnosis, prevention, and treatment of myocardial hypertrophy and failure

The circadian system has been shown to be fundamentally important in human health and disease. Recently, there have been major advances in our understanding of daily rhythmicity, and its relevance to human physiology, and to the pathogenesis and treatment of cardiac hypertrophy and heart failure. Cardiovascular tissues, such as heart and blood vessels, show remarkable daily variation in gene expression, metabolism, growth, and remodeling. Moreover, synchrony of daily molecular and physiological rhythms is integral to healthy organ growth and renewal. Disruption of these rhythms adversely affects normal growth, also the remodeling mechanisms in disease, leading to gross abnormalities in heart and vessels. These observations provide new insights into the pathogenesis, diagnosis, treatment, and prevention of heart disease. In this review, we focus on the recent advances in circadian biology and cardiovascular function, with particular emphasis on how this applies to human myocardial hypertrophy and heart failure, and the implications and importance for translational medicine.

Quantitative proteomics: measuring protein synthesis using 15N amino acid labeling in pancreatic cancer cells

Pancreatic cancer MIA PaCa cells were cultured in the presence and absence of (15)N amino acids mixture for 72 h. During protein synthesis, the incorporation of (15)N amino acids results in a new mass isotopomer distribution in protein, which is approximated by the concatenation of two binomial distributions of (13)C and (15)N. The fraction of protein synthesis (FSR) can thus be determined from the relative intensities of the "labeled" (new) and the "unlabeled" (old) spectra. Six prominent spots were picked from 2-D gels of proteins from lysates of cells cultured in 0% (control), 50%, and 33% (15)N enriched media. These protein spots were digested and analyzed with matrix-assisted laser desorption ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometry. The isotopomer distribution of peptides after labeling can be fully accounted for by the labeled (new) and unlabeled (old) peptides. The ratio of the new and old peptide fractions was determined using multiple regression analysis of the observed spectrum as a linear combination of the expected new and the old spectra. The fractional protein synthesis rates calculated from such ratios of the same peptide from cells grown in 50% and 33% (15)N amino acid enrichments were comparable to each other. The FSR of these six identified proteins ranged between 44 and 76%.

Determination of protein synthesis in vivo using labeling from deuterated water and analysis of MALDI-TOF spectrum

This paper describes a method of determining protein synthesis and turnover using in vivo labeling of protein with deuterated water and analysis of matrix-assisted laser desorption time-of-flight mass spectrometer (MALDI-TOF) spectrum. Protein synthesis is calculated using mass isotopomer distribution analysis instead of precursor to product amino acid enrichment ratio. During protein synthesis, the incorporation of deuterium from water changes the mass isotopomer distribution (isotope envelop) according to the number of deuterium atoms (0, 1, 2, 3, etc.) incorporated, and the distribution of the protein with 0, 1, 2, 3,... atoms of deuterium follows a binomial distribution. A mathematical algorithm by which the distribution of deuterium isotopomers can be extracted from the observed MALDI-TOF spectrum is presented. Since deuterium isotopomers are unique to newly synthesized proteins, the quantitation of their distribution provides a method for the quantitation of newly synthesized proteins. The combined use of postsource decay sequence identification and mass isotopomer distribution analysis makes the use of in vivo labeling with deuterated water a precise method to determine specific protein synthesis.

Oxidation and structural perturbation of redox-sensitive enzymes in injured skeletal muscle

Molecular events that control skeletal muscle injury and regeneration are poorly understood. However, inflammation associated with oxidative stress is considered a key player in modulating this process. To understand the consequences of oxidative stress associated with muscle injury, inflammation, and regeneration, hind-limb muscles of C57Bl/6J mice were studied after injection of cardiotoxin (CT). Within 1 day post-CT injection, polymorphonuclear neutrophilic leukocyte accumulation was extensive. Compared to baseline, tissue myeloperoxidase (MPO) activity was elevated eight- and fivefold at 1 and 7 days post-CT, respectively. Ubiquitinylated protein was elevated 1 day postinjury and returned to baseline by 21 days. Cysteine residues of creatine kinase (CK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were irreversibly oxidized within 1 day post-CT injection and were associated with protein conformational changes that fully recovered after 21 days. Importantly, protein structural alterations occurred in conjunction with significant decreases in CK activity at 1, 3, and 7 days post-CT injury. Interestingly, elevations in tissue MPO activity paralleled the time course of conformational changes in CK and GAPDH. In combination, these results demonstrate that muscle proteins in vivo are structurally and functionally altered via the generation of reactive oxygen species produced during inflammatory events after muscle injury and preceding muscle regeneration.

Sox6 is required for normal fiber type differentiation of fetal skeletal muscle in mice

Sox6, a member of the Sox family of transcription factors, is highly expressed in skeletal muscle. Despite its abundant expression, the role of Sox6 in muscle development is not well understood. We hypothesize that, in fetal muscle, Sox6 functions as a repressor of slow fiber type-specific genes. In the wild-type mouse, differentiation of fast and slow fibers becomes apparent during late fetal stages (after approximately embryonic day 16). However, in the Sox6 null-p(100H) mutant mouse, all fetal muscle fibers maintain slow fiber characteristics, as evidenced by expression of the slow myosin heavy chain MyHC-beta. Knockdown of Sox6 expression in wild-type myotubes results in a significant increase in MyHC-beta expression, supporting our hypothesis. Analysis of the MyHC-beta promoter revealed a Sox consensus sequence that likely functions as a negative cis-regulatory element. Together, our results suggest that Sox6 plays a critical role in the fiber type differentiation of fetal skeletal muscle.

Assembly and maintenance of the sarcomere night and day

The assembly of sarcomeric proteins into the highly organized structure of the sarcomere is an ordered and complex process involving an array of structural and associated proteins. The sarcomere has shown itself to be considerably more complex than ever envisaged and may be considered one of the most complex macromolecular assemblies in biology. Studies over the last decade have helped to put a new face on the sarcomere, and, as such, the sarcomere is being redefined as a dynamic network of proteins capable of generating force and signalling with other cellular compartments and metabolic enzymes capable of controlling many facets of striated myocyte biology.

Avian proteomics: advances, challenges and new technologies

Proteomics is defined as an analysis of the full complement of proteins of a cell or tissue under given conditions. Avian proteomics, or more specifically chicken proteomics, has focussed on the study of individual tissues and organs of interest to specific researchers. Researchers have looked at skeletal muscle and growth, and embryonic development and have performed initial studies in avian disease. Traditional proteomics involves identifying and cataloguing proteins in a cell and identifying relative changes in populations between two or more states, be that physiological or disease-induced states. Recent advances in proteomic technologies have included absolute quantification, proteome simplification and the ability to determine the turnover of individual proteins in a global context. This review discusses the current developments in this relatively new field, new technologies and how they may be applied to biological questions, and the challenges faced by researchers in this ever-expanding and exciting field.

Inaccuracies in selected ion monitoring determination of isotope ratios obviated by profile acquisition: nucleotide 18O/16O measurements

Precise and accurate measurements of isotopologue distributions (IDs) in biological molecules are needed for determination of isotope effects, quantitation by isotope dilution, and quantification of isotope tracers employed in both metabolic and biophysical studies. While single ion monitoring (SIM) yields significantly greater sensitivity and signal/noise than profile-mode acquisitions, we show that small changes in the SIM window width and/or center can alter experimentally determined isotope ratios by up to 5%, resulting in significant inaccuracies. This inaccuracy is attributed to mass granularity, the differential distribution of digital data points across the m/z ranges sampled by SIM. Acquiring data in the profile mode and fitting the data to an equation describing a series of equally spaced and identically shaped peaks eliminates the inaccuracies associated with mass granularity with minimal loss of precision. Additionally a method of using the complete ID profile data that inherently corrects for "spillover" and for the natural-abundance ID has been used to determine 18O/16O ratios for 5',3'-guanosine bis-[18O1]phosphate and TM[18O1]P with precisions of approximately 0.005. The analysis protocol is also applied to quadrupole time-of-flight tandem mass spectrometry using [2-(18)O] arabinouridine and 3'-UM[18O1]P which enhances signal/noise and minimizes concerns for background contamination.

Alcohol-induced bone degradation and its early detection in the alcohol-fed castrated rats

The objective of this study was to examine alcohol-induced changes of bone in hormone-deficient males using the developed method. In the process of bone resorption, type I collagen crosslinking molecules, pyridinoline (PYD), are released into the circulation and cleared by the kidneys. (2)H(2)O as a tracer has been applied to measure the synthesis rates of slow-turnover proteins and successfully applied to bone collagen synthesis in our hormone deficiency rats. This study demonstrated for the first time, the early changes of the femur bone degradation in hormone-deficient male individuals, more influenced by alcohol through histopathological study, serum PYD assay, and (2)H(2)O labeling. We also observed that serum PYD was a sensitive pathological marker of bone degradation in castrated osteoporosis males and the unique features of (2)H(2)O labeling to measure the bone turnover collagen synthesis rates were excellent markers of bone degradation and aging.

Metabolic Labeling of Proteins for Proteomics

Realization of the advantages of stable isotope labeling for proteomics has emerged gradually. However, many stable isotope label approaches rely on labeling in vitro using complex and sometimes expensive reagents. This review discusses strategies for labeling protein in vivo through metabolic incorporation of label into protein. This approach has many advantages, is particularly suited to single cells grown in culture (prokaryotic or eukaryotic), but is nonetheless subject to a number of complicating factors that must be controlled so that meaningful experiments can be conducted. Confounding issues include the metabolic lability of the amino acid precursor, incomplete labeling, and the role of protein turnover in labeling kinetics. All of these are controllable, provided that appropriate precautions are adopted.

Determination of Fractional Synthesis Rates of Mouse Hepatic Proteins via Metabolic 13C-Labeling, MALDI-TOF MS and Analysis of Relative Isotopologue Abundances Using Average Masses

Proteins of a liver extract taken from a metabolically (13)C-labeled mouse were separated by 2D-PAGE and identified after tryptic digestion by MALDI-TOF MS peptide mass fingerprinting. (13)C-Labeling of proteins was achieved by an infusion of U-(13)C-glucose, which is metabolized to labeled nonessential amino acids. The labeling was analyzed using the relative isotopologue abundances of the measured isotope pattern of tryptic peptides and quantified by their increase in the average molecular mass (DeltaAVM). Fractional synthesis rates (FSR) of proteins were determined from corresponding peptides using measured DeltaAVM values as well as DeltaAVM values deduced from tRNA-precursor amino acid labeling, which in turn was derived from proteins showing high (13)C enrichments. The 8-h FSR values of 43 proteins were determined to range from 0 +/- 0.6 to 95 +/- 1%/8 h, with typical errors given as SEM values, which depend on the number of peptides of a specific protein usable for calculation. The method demonstrates that FSR values as an indicator for protein turnover in the liver proteome can be estimated within narrow error margins, providing baseline values from which treatment-dependent deviations could be detected with high statistical certainty.

Proteome dynamics in complex organisms: Using stable isotopes to monitor individual protein turnover rates

The complete definition of changes in a proteome requires information about dynamics and specifically the rate at which the individual proteins are turned over intracellularly. Whilst this can be achieved in single-cell culture using stable isotope precursors, it is more challenging to develop methods for intact animals. In this study, we show how dietary administration of stable isotope-labelled amino acids can obtain information on the relative rates of synthesis and degradation of individual proteins in a proteome. The pattern of stable isotope-labelling in tryptic peptides can be deconstructed to yield a highly reliable measure of the isotope abundance of the precursor pool, a parameter that is often difficult to acquire. We demonstrate this approach using chickens fed a semisynthetic diet containing [(2)H(8)]valine at a calculated relative isotope abundance (RIA) of 0.5. When the labelling pattern of gel-resolved muscle proteins was analyzed, the intracellular precursor isotope abundance was 0.35, consistent with dilution of the amino acid precursor pool with unlabelled amino acids derived from degradation of pre-existing proteins. However, the RIA was stable over an extended labelling window, and permitted calculation of the rates of synthesis and degradation of individual proteins isolated by gel electrophoresis. For the first time, it is feasible to contemplate the analysis of turnover of individual proteins in intact animals.

Myosin heavy chain isoform mRNA and protein levels after long-term paralysis

To assess the long-term influence of paralysis on muscle phenotypic mRNA and protein expression, the effects of spinal cord transection (ST) on myosin heavy chain (MyHC) isoform mRNA and protein levels in the soleus and medial gastrocnemius (MG) muscles of rats were analyzed. Control soleus contained predominantly MyHC-I with low amounts of MyHC-IIa and IIx mRNAs. After ST, MyHC-I mRNA decreased to approximately 15%, MyHC-IIa was increased by 75-200%, and MyHC-IIx was elevated by 8-10x. Low level expression of MyHC-IIb was observed post-ST, suggesting that reduced activity is not a primary stimulus for MyHC-IIb expression. Adaptations in mRNA preceded protein adaptations in the soleus. Although MyHC-I protein in the MG was reduced post-ST, no other consistent changes occurred. The relative lack of adaptation to ST by the MG suggests that the reduced activity and load bearing encountered by the MG were insufficient to induce a change in muscle phenotype.

Albumin turnover: experimental approach and its application in health and renal diseases

Plasma albumin is an important protein in the human body and is responsible for transport and binding of many molecules. Furthermore, it is involved in mediating blood volume and colloid osmotic pressure (COP). As hypoalbuminemia occurs, as is the case in a number of clinical disorders, adaptation mechanisms may be involved. Serum albumin concentration is the net result of physiological processes like synthesis and catabolism. Measurement of one of these processes can provide therefore a more dynamic insight into the adaptation mechanism of albumin metabolism in relation to an underlying disease than would be obtained by changes in albumin concentration alone. This review highlights several studies over the past years that have contributed to knowledge of albumin metabolism. A short introduction is given for synthesis, formation and catabolism of albumin, after which an overview is given on how to measure albumin turnover including a general approach. Finally, albumin metabolism focused on patients with renal diseases will be discussed.