Biological Accessibility and Analytical Recovery in Myofibrillar Protein Loss During Skeletal Muscle Atrophy

Myofibrillar loss during skeletal muscle atrophy is often described as selective. MuRF1 is considered to remove thick filament proteins preferentially, whereas thin filament proteins are assigned to other ligases or appear relatively spared. We reassess whether this pattern demonstrates molecular specificity or is partly explained by the state in which a protein is encountered and measured. Several observations motivate this analysis. Actin can be polyubiquitinated by MuRF1 even though loss of assembled thin filament proteins is not MuRF1-dependent in several models. Apparent preferential myosin loss varies with extraction chemistry, normalization, and the combination of catabolic stimuli with inactivity. KLHL40 and KLHL41 preserve major thin filament proteins, although the direct evidence comes mainly from development and myopathy. Turnover and ubiquitin-remnant proteomics quantify molecules recovered from defined fractions and do not, on their own, distinguish degradation from redistribution. We therefore distinguish two biological determinants from one observer-side analytical layer. Assembly-dependent exposure and stability or damage-state regulation influence biological availability. Extraction, fractionation, detectability, and normalization determine analytical recovery. Ubiquitination remains distinct from degradation because chain architecture, deubiquitination, extraction, unfolding, and productive disposal can still determine fate. This framework retains ligase specificity while defining the controls needed to establish preferential degradation in intact muscle.