scholarly journals Live cell kinetic analysis of the LMO2/LDB1 leukemogenic protein complex reveals a hierarchy of turnover with implications for complex assembly

2019 ◽  
Author(s):  
Justin H. Layer ◽  
Michael Christy ◽  
Lindsay Placek ◽  
Derya Unutmaz ◽  
Yan Guo ◽  
...  
Keyword(s):  
Protein Complex ◽  
Protein Complexes ◽  
Cell Formation ◽  
Macromolecular Complex ◽  
Cellular Functions ◽  
Cell Specification ◽  
Complex Assembly ◽  
Hematopoietic Stem ◽  
Protein Partners ◽  
Macromolecular Protein

SummaryMultisubunit protein complexes operate in many cellular functions. The LDB1/LMO2 macromolecular complex has been posited to be critical in hematopoietic stem and progenitor cell specification and in the development of acute leukemia. This complex is comprised of core subunits of LMO2 and LDB1 as well as bHLH and GATA transcription factors. We analyzed the steady state abundance and kinetic stability of LMO2 and its partners via HALO protein tagging in conjunction with variant proteins deficient in binding their respective direct protein partners. We discovered a hierarchy of protein stability, with half lives in descending order: LDB1>SSBP>LMO2>TAL1. Importantly, LDB1 conferred enhanced stability upon each and every subunit component and nucleated the formation of the multisubunit protein complex. Our studies provide significant insights into LDB1/LMO2 macromolecular protein complex assembly and stability, which has implications for understanding its role in blood cell formation and for therapeutically targeting this complex in human leukemias.

scholarly journals LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia

2020 ◽  
Vol 40 (12) ◽  
Author(s):  
Justin H. Layer ◽  
Michael Christy ◽  
Lindsey Placek ◽  
Derya Unutmaz ◽  
Yan Guo ◽  
...  
Keyword(s):  
Protein Complex ◽  
Cell Formation ◽  
Macromolecular Complex ◽  
Cell Specification ◽  
Hematopoietic Stem ◽  
Protein Partners ◽  
Gata Transcription Factors ◽  
Macromolecular Protein ◽  
Protein Tagging ◽  
Protein Complex Assembly

ABSTRACT The LMO2/LDB1 macromolecular complex is critical in hematopoietic stem and progenitor cell specification and in the development of acute leukemia. This complex is comprised of core subunits of LMO2 and LDB1 as well as single-stranded DNA-binding protein (SSBP) cofactors and DNA-binding basic helix-loop-helix (bHLH) and GATA transcription factors. We analyzed the steady-state abundance and kinetic stability of LMO2 and its partners via Halo protein tagging in conjunction with variant proteins deficient in binding their respective direct protein partners. We discovered a hierarchy of protein stabilities (with half-lives in descending order) as follows: LDB1 > SSBP > LMO2 > TAL1. Importantly, LDB1 is a remarkably stable protein that confers enhanced stability upon direct and indirect partners, thereby nucleating the formation of the multisubunit protein complex. The data imply that free subunits are more rapidly degraded than those incorporated within the LMO2/LDB1 complex. Our studies provided significant insights into LMO2/LDB1 macromolecular protein complex assembly and stability, which has implications for understanding its role in blood cell formation and for therapeutically targeting this complex in human leukemias.

scholarly journals Co-translational assembly of protein complexes

2015 ◽  
Vol 43 (6) ◽  
pp. 1221-1226 ◽  
Author(s):  
Jonathan N. Wells ◽  
L. Therese Bergendahl ◽  
Joseph A. Marsh
Keyword(s):  
Protein Complex ◽  
Protein Complexes ◽  
Biological Macromolecules ◽  
Complex Assembly ◽  
Cellular Life ◽  
Eukaryotic Organisms ◽  
Protein Complex Assembly

The interaction of biological macromolecules is a fundamental attribute of cellular life. Proteins, in particular, often form stable complexes with one another. Although the importance of protein complexes is widely recognized, we still have only a very limited understanding of the mechanisms underlying their assembly within cells. In this article, we review the available evidence for one such mechanism, namely the coupling of protein complex assembly to translation at the polysome. We discuss research showing that co-translational assembly can occur in both prokaryotic and eukaryotic organisms and can have important implications for the correct functioning of the complexes that result. Co-translational assembly can occur for both homomeric and heteromeric protein complexes and for both proteins that are translated directly into the cytoplasm and those that are translated into or across membranes. Finally, we discuss the properties of proteins that are most likely to be associated with co-translational assembly.

scholarly journals A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly

RNA ◽  
2021 ◽  
pp. rna.078995.121
Author(s):  
Xiuzhen Chen ◽  
Christine Mayr
Keyword(s):  
Protein Complex ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Complex Assembly ◽  
Protein Targets ◽  
Working Model ◽  
Cellular Environment ◽  
Protein Complex Assembly

Most cellular processes are carried out by protein complexes, but it is still largely unknown how the subunits of lowly expressed complexes find each other in the crowded cellular environment. Here, we will describe a working model where RNA-binding proteins in cytoplasmic condensates act as matchmakers between their bound proteins (called protein targets) and newly translated proteins of their RNA targets to promote their assembly into complexes. Different RNA-binding proteins act as scaffolds for various cytoplasmic condensates with several of them supporting translation. mRNAs and proteins are recruited into the cytoplasmic condensates through binding to specific domains in the RNA-binding proteins. Scaffold RNA-binding proteins have a high valency. In our model, they use homotypic interactions to assemble condensates and they use heterotypic interactions to recruit protein targets into the condensates. We propose that unoccupied binding sites in the scaffold RNA-binding proteins transiently retain recruited and newly translated proteins in the condensates, thus promoting their assembly into complexes. Taken together, we propose that lowly expressed subunits of protein complexes combine information in their mRNAs and proteins to colocalize in the cytoplasm. The efficiency of protein complex assembly is increased by transient entrapment accomplished by multivalent RNA-binding proteins within cytoplasmic condensates.

Neuroligin-2 as a central organizer of inhibitory synapses in health and disease

2020 ◽  
Vol 13 (663) ◽  
pp. eabd8379
Author(s):  
Heba Ali ◽  
Lena Marth ◽  
Dilja Krueger-Burg
Keyword(s):  
Synaptic Transmission ◽  
Synapse Formation ◽  
Current Knowledge ◽  
Protein Complexes ◽  
Inhibitory Synapses ◽  
Molecular Architecture ◽  
Cellular Functions ◽  
Altered Expression ◽  
Health And Disease ◽  
Flow Of Information

Postsynaptic organizational protein complexes play central roles both in orchestrating synapse formation and in defining the functional properties of synaptic transmission that together shape the flow of information through neuronal networks. A key component of these organizational protein complexes is the family of synaptic adhesion proteins called neuroligins. Neuroligins form transsynaptic bridges with presynaptic neurexins to regulate various aspects of excitatory and inhibitory synaptic transmission. Neuroligin-2 (NLGN2) is the only member that acts exclusively at GABAergic inhibitory synapses. Altered expression and mutations in NLGN2 and several of its interacting partners are linked to cognitive and psychiatric disorders, including schizophrenia, autism, and anxiety. Research on NLGN2 has fundamentally shaped our understanding of the molecular architecture of inhibitory synapses. Here, we discuss the current knowledge on the molecular and cellular functions of mammalian NLGN2 and its role in the neuronal circuitry that regulates behavior in rodents and humans.

scholarly journals Visualizing the Dynamics of Dystrophin Protein Complex Assembly in Living Cells

2005 ◽  
Vol 11 (S02) ◽  
Author(s):  
R A Draviam ◽  
B Wang ◽  
S Shand ◽  
X Xiao ◽  
S C Watkins
Keyword(s):  
Protein Complex ◽  
Living Cells ◽  
Complex Assembly ◽  
Dystrophin Protein ◽  
Protein Complex Assembly

scholarly journals Sequential regulation of hemogenic fate and hematopoietic stem and progenitor cell formation from arterial endothelium by Ezh1/2

2021 ◽  
Author(s):  
Rebecca A. Soto ◽  
Mohamad Ali T. Najia ◽  
Mariam Hachimi ◽  
Jenna M. Frame ◽  
Gabriel A. Yette ◽  
...  
Keyword(s):  
Progenitor Cell ◽  
Cell Formation ◽  
Hematopoietic Stem ◽  
Arterial Endothelium

The diverse roles of the Nup93/Nic96 complex proteins – structural scaffolds of the nuclear pore complex with additional cellular functions

2014 ◽  
Vol 395 (5) ◽  
pp. 515-528 ◽  
Author(s):  
Benjamin Vollmer ◽  
Wolfram Antonin
Keyword(s):  
Nuclear Pore Complex ◽  
Nuclear Membrane ◽  
Building Blocks ◽  
Transport Processes ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Cellular Functions ◽  
Complex Assembly ◽  
Essential Function ◽  
Pore Complexes

Abstract Nuclear pore complexes mediate the transport between the cell nucleoplasm and cytoplasm. These 125 MDa structures are among the largest assemblies found in eukaryotes, built from proteins organized in distinct subcomplexes that act as building blocks during nuclear pore complex biogenesis. In this review, we focus on one of these subcomplexes, the Nup93 complex in metazoa and its yeast counterpart, the Nic96 complex. We discuss its essential function in nuclear pore complex assembly as a linker between the nuclear membrane and the central part of the pore and its various roles in nuclear transport processes and beyond.

scholarly journals Tyrosyl-tRNA synthetase stimulates thrombopoietin-independent hematopoiesis accelerating recovery from thrombocytopenia

2018 ◽  
Vol 115 (35) ◽  
pp. E8228-E8235 ◽  
Author(s):  
Taisuke Kanaji ◽  
My-Nuong Vo ◽  
Sachiko Kanaji ◽  
Alessandro Zarpellon ◽  
Ryan Shapiro ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cell Formation ◽  
Induced Pluripotent Stem Cell ◽  
Trna Synthetase ◽  
Monocytic Cells ◽  
Formation Continue ◽  
Hematopoietic Stem ◽  
Culture Production ◽  
High Ploidy ◽  
Induced Pluripotent

New mechanisms behind blood cell formation continue to be uncovered, with therapeutic approaches for hematological diseases being of great interest. Here we report an enzyme in protein synthesis, known for cell-based activities beyond translation, is a factor inducing megakaryocyte-biased hematopoiesis, most likely under stress conditions. We show an activated form of tyrosyl-tRNA synthetase (YRSACT), prepared either by rationally designed mutagenesis or alternative splicing, induces expansion of a previously unrecognized high-ploidy Sca-1+ megakaryocyte population capable of accelerating platelet replenishment after depletion. Moreover, YRSACT targets monocytic cells to induce secretion of transacting cytokines that enhance megakaryocyte expansion stimulating the Toll-like receptor/MyD88 pathway. Platelet replenishment by YRSACT is independent of thrombopoietin (TPO), as evidenced by expansion of the megakaryocytes from induced pluripotent stem cell-derived hematopoietic stem cells from a patient deficient in TPO signaling. We suggest megakaryocyte-biased hematopoiesis induced by YRSACT offers new approaches for treating thrombocytopenia, boosting yields from cell-culture production of platelet concentrates for transfusion, and bridging therapy for hematopoietic stem cell transplantation.

scholarly journals Protein Complexes Detection Based on Node Local Properties and Gene Expression On PPI Weighted Networks

2021 ◽  
Author(s):  
Yang Yu ◽  
Dezhou Kong
Keyword(s):  
Gene Expression ◽  
Resource Allocation ◽  
Protein Complex ◽  
Protein Complexes ◽  
Second Order ◽  
Topological Properties ◽  
Ppi Network ◽  
Weighted Networks ◽  
Gene Expression Information ◽  
Local Properties

Abstract Background Identifying protein complexes from protein–protein interaction (PPI) networks is a crucial task, and many related algorithms have been developed to solve this issue. These algorithms usually consider a node’s direct neighbors and ignore resource allocation and second-order neighbors. The effective use of such information is crucial to protein complex detection.Results To overcome this deficiency, this paper proposes a new protein complex identification method based on node-local topological properties and gene expression information on a new weighted PPI network, named NLPGE-WPN (joint node-local topological properties and gene expression information on weighted PPI network). First, based on the resource allocation of the PPI network and gene expression, a new weight metric is designed to describe the interaction between proteins. Second, our method constructs a series of dense complex cores based on density and network diameter constraints; the final complexes are recognized by expanding the second-order neighbor nodes of core complexes. Experimental results demonstrate that this algorithm has improved the performances of precision and f-measure, which is more valid in identifying protein complexes．Conclusions This identification method is simple and can accurately identify more complexes by integrating node-local properties and gene expression on PPI weighted networks.

scholarly journals Computational Prediction of Heteromeric Protein Complex Disassembly Order with Hybrid Monte Carlo/Molecular Dynamics Simulation

2022 ◽  
Author(s):  
Ikuo Kurisaki ◽  
Shigenori Tanaka
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Complex ◽  
Protein Complexes ◽  
Structural Bioinformatics ◽  
Dynamics Simulation ◽  
Tryptophan Synthase ◽  
Selection Scheme ◽  
Hybrid Monte Carlo ◽  
Multimeric Protein

The physicochemical entity of biological phenomenon in the cell is a network of biochemical reactions and the activity of such a network is regulated by multimeric protein complexes. Mass spectroscopy (MS) experiments and multimeric protein docking simulations based on structural bioinformatics techniques have revealed the molecular-level stoichiometry and static configuration of subcomplexes in their bound forms, then revealing the subcomplex populations and formation orders. Meanwhile, these methodologies are not designed to straightforwardly examine temporal dynamics of multimeric protein assembly and disassembly, essential physicochemical properties to understand functional expression mechanisms of proteins in the biological environment. To address the problem, we had developed an atomistic simulation in the framework of the hybrid Monte Carlo/Molecular Dynamics (hMC/MD) method and succeeded in observing disassembly of homomeric pentamer of the serum amyloid P component protein in experimentally consistent order. In this study, we improved the hMC/MD method to examine disassembly processes of the tryptophan synthase tetramer, a paradigmatic heteromeric protein complex in MS studies. We employed the likelihood-based selection scheme to determine a dissociation-prone subunit pair at each hMC/MD simulation cycle and achieved highly reliable predictions of the disassembly orders with the success rate over 0.9 without a priori knowledge of the MS experiments and structural bioinformatics simulations. We similarly succeeded in reliable predictions for the other three tetrameric protein complexes. These achievements indicate the potential availability of our hMC/MD approach as the general purpose methodology to obtain microscopic and physicochemical insights into multimeric protein complex formation.

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