Measuring in vivo protein turnover and exchange in yeast macromolecular assemblies

Abstract Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.

Download Full-text

In vivo measurement of myocardial protein turnover using an indicator dilution technique.

Circulation Research ◽

10.1161/01.res.67.4.902 ◽

1990 ◽

Vol 67 (4) ◽

pp. 902-912 ◽

Cited By ~ 5

Author(s):

J H Revkin ◽

L H Young ◽

W S Stirewalt ◽

D M Dahl ◽

R A Gelfand ◽

...

Keyword(s):

Protein Turnover ◽

Indicator Dilution ◽

Dilution Technique ◽

In Vivo Measurement ◽

Indicator Dilution Technique

Download Full-text

JUMPt: Comprehensive Protein Turnover Modeling of In Vivo Pulse SILAC Data by Ordinary Differential Equations

Analytical Chemistry ◽

10.1021/acs.analchem.1c02309 ◽

2021 ◽

Author(s):

Surendhar Reddy Chepyala ◽

Xueyan Liu ◽

Ka Yang ◽

Zhiping Wu ◽

Alex M. Breuer ◽

...

Keyword(s):

Differential Equations ◽

Ordinary Differential Equations ◽

Protein Turnover

Download Full-text

Influence of sepsis in rats on muscle protein turnover in vivo and in tissue incubated under different in vitro conditions

Metabolism ◽

10.1016/0026-0495(91)90105-6 ◽

1991 ◽

Vol 40 (3) ◽

pp. 247-251 ◽

Cited By ~ 24

Author(s):

Marianne Hall-Angerås ◽

Ulf Angerås ◽

Daniel von Allmen ◽

Takashi Higashiguchi ◽

Oded Zamir ◽

...

Keyword(s):

Protein Turnover ◽

Muscle Protein ◽

Muscle Protein Turnover

Download Full-text

Recent advances in understanding the role of FOXO3

F1000Research ◽

10.12688/f1000research.15258.1 ◽

2018 ◽

Vol 7 ◽

pp. 1372 ◽

Cited By ~ 18

Author(s):

Renae J. Stefanetti ◽

Sarah Voisin ◽

Aaron Russell ◽

Séverine Lamon

Keyword(s):

Cell Cycle ◽

Skeletal Muscle ◽

Protein Turnover ◽

Genetic Basis ◽

The Body ◽

Biological Processes ◽

Forkhead Box ◽

Protein Pool

The forkhead box O3 (FOXO3, or FKHRL1) protein is a member of the FOXO subclass of transcription factors. FOXO proteins were originally identified as regulators of insulin-related genes; however, they are now established regulators of genes involved in vital biological processes, including substrate metabolism, protein turnover, cell survival, and cell death. FOXO3 is one of the rare genes that have been consistently linked to longevity in in vivo models. This review provides an update of the most recent research pertaining to the role of FOXO3 in (i) the regulation of protein turnover in skeletal muscle, the largest protein pool of the body, and (ii) the genetic basis of longevity. Finally, it examines (iii) the role of microRNAs in the regulation of FOXO3 and its impact on the regulation of the cell cycle.

Download Full-text

The effect of protein depletion and repletion on muscle-protein turnover in the chick

Biochemical Journal ◽

10.1042/bj1940811 ◽

1981 ◽

Vol 194 (3) ◽

pp. 811-819 ◽

Cited By ~ 44

Author(s):

M L MacDonald ◽

R W Swick

Keyword(s):

Protein Synthesis ◽

Protein Turnover ◽

Muscle Protein ◽

Control Diet ◽

Breast Muscle ◽

Synthesis Rate ◽

Protein Depletion ◽

Protein Mass ◽

Fractional Rate

Rates of growth and protein turnover in the breast muscle of young chicks were measured in order to assess the roles of protein synthesis and degradation in the regulation of muscle mass. Rates of protein synthesis were measured in vivo by injecting a massive dose of L-[1-14C]valine, and rates of protein degradation were estimated as the difference between the synthesis rate and the growth rate of muscle protein. In chicks fed on a control diet for up to 7 weeks of age, the fractional rate of synthesis decreased from 1 to 2 weeks of age and then changed insignificantly from 2 to 7 weeks of age, whereas DNA activity was constant for 1 to 7 weeks. When 4-week-old chicks were fed on a protein-free diet for 17 days, the total amount of breast-muscle protein synthesized and degraded per day and the amount of protein synthesized per unit of DNA decreased. Protein was lost owing to a greater decrease in the rate of protein synthesis, as a result of the loss of RNA and a lowered RNA activity. When depleted chicks were re-fed the control diet, rapid growth was achieved by a doubling of the fractional synthesis rate by 2 days. Initially, this was a result of increased RNA activity; by 5 days, the RNA/DNA ratio also increased. There was no evidence of a decrease in the fractional degradation rate during re-feeding. These results indicate that dietary-protein depletion and repletion cause changes in breast-muscle protein mass primarily through changes in the rate of protein synthesis.

Download Full-text

Fiber-type composition of nine rat muscles. II. Relationship to protein turnover

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.1989.257.6.e828 ◽

1989 ◽

Vol 257 (6) ◽

pp. E828-E832 ◽

Cited By ~ 12

Author(s):

P. J. Garlick ◽

C. A. Maltin ◽

A. G. Baillie ◽

M. I. Delday ◽

D. A. Grubb

Keyword(s):

Protein Synthesis ◽

Regression Analysis ◽

Protein Turnover ◽

Fiber Type ◽

Female Rats ◽

Protein Breakdown ◽

Fiber Type Composition ◽

Type Composition ◽

Age Regression

Rates of protein synthesis in vivo and fiber-type composition were measured in nine limb muscles of female rats at ages ranging from weaning to 1 yr. In all muscles, there was a decline in protein synthesis with increasing age, mostly as a result of a fall in the RNA content. Rates of protein breakdown and growth were determined in six muscles and these also declined with age. Regression analysis of the data for all ages showed that protein synthesis was correlated with the content of slow oxidative fibers but not with the relative proportions of fast glycolytic to fast oxidative glycolytic fibers.

Download Full-text