Biology subjects

Ozcan, S.

Publications and source records attributed to Ozcan, S..

4 recordsLinked to original sources

bioRxiv2026

Endogenous Nuclear Desmin Associates with the Nuclear Envelope in Human Skeletal Muscle Cells

Desmin is the major intermediate filament protein of muscle, yet its potential nuclear functions remain poorly understood. Here, we investigated the nuclear localization and organization of endogenous desmin in human skeletal muscle cells using quantitative confocal microscopy, biochemical fractionation, targeted MRM/SRM proteomics, and computational structural modeling. Desmin localized to the nuclear compartment and exhibited significantly stronger colocalization with emerin and lamin A/C than with lamin B1. Nuclear fractionation and targeted proteomics independently confirmed endogenous nuclear desmin, while protein-protein docking predicted structurally plausible interactions with all three nuclear envelope proteins, supporting a context-dependent nuclear interaction network. Together, these findings identify the nuclear envelope as a functional platform for desmin and suggest that nuclear desmin contributes to nucleo-cytoskeletal communication and the organization of mechanically responsive nuclear architecture during myogenesis. This work expands the current understanding of desmin biology and provides a framework for investigating its role in desmin-related muscle disease.

molecular biology↗

bioRxiv2023

Combined workflow for XL-MS data processing: Application to the FtsH-HflK-HflC membrane protein complex

Recent advances in mass spectrometry (MS) yielding sensitive and accurate measurements along with developments in software tools have enabled the characterization of complex systems routinely. Thus, structural proteomics and cross-linking mass spectrometry (XL-MS) have become a useful method for structural modeling of protein complexes. Here we utilized commonly used XL-MS software tools to elucidate the protein interactions within a membrane protein complex containing FtsH, HflK, and HflC, over-expressed in E.coli. The MS data were processed using MaxLynx, MeroX, MS Annika, xiSEARCH, and XlinkX software tools. The number of identified inter- and intra-protein cross-links varied among software. Each interaction was manually checked using the raw MS and MS/MS data and distance restraints to verify inter- and intra-protein cross-links. A total of 37 inter-protein and 148 intra-protein cross-links were determined in the FtsH-HflK-HflC complex. The 59 of them were new interactions on the lacking region of recently published structures. These newly identified interactions, when combined with molecular docking and structural modeling, present opportunities for further investigation. The results provide valuable information regarding the complex structure and function to decipher the intricate molecular mechanisms underlying the mega FtsH-HflK-HflC complex. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/544024v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@8e10f5org.highwire.dtl.DTLVardef@fb809borg.highwire.dtl.DTLVardef@1b84df3org.highwire.dtl.DTLVardef@105c8e6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO The overall workflow of XL-MS analysis: the steps of XL-MS studies applied to the two samples taken from different stages of purification process of mega membrane protein complex FtsH-HflC-HflK. C_FIG

biochemistry↗

bioRxiv2022

A single protein to multiple peptides: Investigation of protein-peptide relationship using targeted alpha-2-macroglobulin analysis

Recent advances in proteomics technologies have enabled analysis of thousands of proteins in a high-throughput manner. Mass Spectrometry (MS) based proteomics, uses a peptide centric approach where biological samples undergo a specific proteolytic digestion and then only unique peptides are used for protein identification and quantification. Considering the fact that a single protein may have multiple unique peptides and a number of different forms, it becomes essential to understand dynamic protein-peptide relationship to ensure robust and reliable peptide centric protein analysis. In this study, we investigated the correlation between protein concentration and corresponding unique peptide responses under conventional proteolytic digestion conditions. Protein-peptide correlation, digestion efficiency, matrix-effect, and concentration-effect were evaluated. Twelve unique alpha-2-macroglobulin (A2MG) peptides were monitored using a targeted MS approach to acquire insights into protein-peptide dynamics. Although the peptide responses were reproducible between replicates, protein-peptide correlation was moderate in protein standards and low in complex matrices. The results suggest that reproducible peptide signal could be misleading in clinical studies and a peptide selection could dramatically change the outcome at protein level. This is the first study investigating quantitative protein-peptide correlations in biological samples using all unique peptides representing the same protein and opens a discussion on peptide-based proteomics.

biochemistry↗

bioRxiv2017

Insights into the molecular changes associated with postnatal human brain development: an integrated transcriptomics and proteomics study

Healthy cortical development depends on precise regulation of transcription and translation. However, the dynamics of how proteins are expressed, function and interact across postnatal human cortical development remain poorly understood. We surveyed the proteomic landscape of 69 dorsolateral prefrontal cortex samples across seven stages of postnatal life and integrated these data with paired transcriptome data. We detected 911 proteins by liquid chromatography-mass spectrometry, and 83 were significantly associated with postnatal age (FDR p < 0.05). Network analysis identified three modules of co-regulated proteins correlated with age, including two modules with increasing expression involved in gliogenesis and NADH-metabolism and one neurogenesis-related module with decreasing expression throughout development. Integration with paired transcriptome data revealed that these age-related protein modules overlapped with RNA modules and displayed collinear developmental trajectories. Importantly, RNA expression profiles that are dynamically regulated throughout cortical development display tighter correlations with their respective translated protein expression compared to those RNA profiles that are not. Moreover, the correspondence between RNA and protein expression significantly decreases as a function of cortical aging, especially for genes involved in myelination and cytoskeleton organization. Finally, we used this data resource to elucidate the functional impact of genetic risk loci for intellectual disability, converging on gliogenesis, myelination and ATP-metabolism modules in the proteome and transcriptome. We share all data in an interactive, searchable companion website. Collectively, our findings reveal dynamic aspects of protein regulation and provide new insights into brain development, maturation and disease.

neuroscience↗