scholarly journals Protein network structure enables switching between liquid and gel states

2019 ◽  
Author(s):  
Jeremy D. Schmit ◽  
Jill J. Bouchard ◽  
Erik W. Martin ◽  
Tanja Mittag
Keyword(s):  
Material Properties ◽  
Binding Sites ◽  
Driving Force ◽  
Living Cells ◽  
Gel Formation ◽  
Molecular Architecture ◽  
Related Protein ◽  
Narrow Region ◽  
Organizational Principle ◽  
Dense Liquid

AbstractBiomolecular condensates are emerging as an important organizational principle within living cells. These condensed states are formed by phase separation, yet little is known about how material properties are encoded within the constituent molecules and how the specificity for being in different phases is established. Here we use analytic theory to explain the phase behavior of the cancer-related protein SPOP and its substrate DAXX. Binary mixtures of these molecules have a phase diagram that contains dilute liquid, dense liquid, and gel states. We show that these discrete phases appear due to a competition between SPOP-DAXX and DAXX-DAXX interactions. The stronger SPOP-DAXX interactions dominate at sub-stoichiometric DAXX concentrations leading to the formation of crosslinked gels. The theory shows that the driving force for gel formation is not the binding energy, but rather the entropy of distributing DAXX molecules on the binding sites. At high DAXX concentrations the SPOP-DAXX interactions saturate, which leads to the dissolution of the gel and the appearance of a liquid phase driven by weaker DAXX-DAXX interactions. This competition between interactions allows multiple dense phases to form in a narrow region of parameter space. We propose that the molecular architecture of phase-separating proteins governs the internal structure of dense phases, their material properties and their functions. Analytical theory can reveal these properties on the long length and time scales relevant to biomolecular condensates.

Fluorescence ratio imaging of dynamic intracellular ionic signals

1988 ◽  
Vol 46 ◽  
pp. 42-43
Author(s):  
R. Y. Tsien ◽  
A. Minta ◽  
M. Poenie ◽  
J.P.Y. Kao ◽  
A. Harootunian
Keyword(s):  
Binding Sites ◽  
Living Cells ◽  
Molecular Engineering ◽  
Ph Indicators ◽  
Highly Sensitive ◽  
Fluorescence Ratio Imaging ◽  
Ratio Imaging ◽  
Technical Advances ◽  
Indicator Dyes ◽  
Fluorescein Dyes

Recent technical advances now enable the continuous imaging of important ionic signals inside individual living cells with micron spatial resolution and subsecond time resolution. This methodology relies on the molecular engineering of indicator dyes whose fluorescence is strong and highly sensitive to ions such as Ca2+, H+, or Na+, or Mg2+. The Ca2+ indicators, exemplified by fura-2 and indo-1, derive their high affinity (Kd near 200 nM) and selectivity for Ca2+ to a versatile tetracarboxylate binding site3 modeled on and isosteric with the well known chelator EGTA. The most commonly used pH indicators are fluorescein dyes (such as BCECF) modified to adjust their pKa's and improve their retention inside cells. Na+ indicators are crown ethers with cavity sizes chosen to select Na+ over K+: Mg2+ indicators use tricarboxylate binding sites truncated from those of the Ca2+ chelators, resulting in a more compact arrangement of carboxylates to suit the smaller ion.

scholarly journals THE KINETICS OF EXOSMOSIS OF WATER FROM LIVING CELLS

1927 ◽  
Vol 10 (5) ◽  
pp. 659-664 ◽  
Author(s):  
Morton McCutcheon ◽  
Baldwin Lucke
Keyword(s):  
Osmotic Pressure ◽  
Salt Concentration ◽  
Driving Force ◽  
Temperature Characteristic ◽  
Living Cells ◽  
Velocity Constant ◽  
Osmotic Equilibrium ◽  
Kinetics Of

1. The rate of exosmosis of water was studied in unfertilized Arbacia eggs, in order to bring out possible differences between the kinetics of exosmosis and endosmosis. 2. Exosmosis, like endosmosis, is found to follow the equation See PDF for Equation, in which a is the total volume of water that will leave the cell before osmotic equilibrium is attained, x is the volume that has already left the cell at time t, and k is the velocity constant. 3. The velocity constants of the two processes are equal, provided the salt concentration of the medium is the same. 4. The temperature characteristic of exosmosis, as of endomosis, is high. 5. It is concluded that the kinetics of exosmosis and endosmosis of water in these cells are identical, the only difference in the processes being in the direction of the driving force of osmotic pressure.

Mapping of ligand binding sites provides insight into the function of factor H-related protein 5

2017 ◽  
Vol 89 ◽  
pp. 145
Author(s):  
Alexandra Papp ◽  
Marcell Cserhalmi ◽  
Ádám I. Csincsi ◽  
Barbara Uzonyi ◽  
David Ermert ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Factor H ◽  
Related Protein ◽  
Ligand Binding Sites ◽  
Insight Into

SCFV-6HIS Bioengineered for High Fidelity Labeling.

2000 ◽  
Vol 6 (S2) ◽  
pp. 338-339 ◽  
Author(s):  
Marek Malecki ◽  
Lea Tiongco ◽  
Annie Hsu ◽  
Nina Takeuchi
Keyword(s):  
Functional Data ◽  
Metal Binding ◽  
Binding Sites ◽  
Life Sciences ◽  
Cloning And Expression ◽  
High Fidelity ◽  
Molecular Architecture ◽  
Electron Spectroscopic Imaging ◽  
Metal Binding Sites ◽  
Specific Energy Loss

In life sciences, the essential part of the functional molecular analysis is the unambiguous identification of biochemical composition of the observed structures. This analysis is expected to create a bridge between functional data pouring from biochemistry and molecular biology laboratories with the molecular architecture data available from ultrastructural images. This goal can be attained by application of various ultrastructural tags (See: Albrecht et al. 1992).A new promising approach for high fidelity labeling is offered by molecular cloning and expression of molecules containing metal binding sites making them suitable for electron spectroscopic imaging (ESI) (Malecki 1995). A truly enormous potential of ESI relies in its ability for mapping of various elements within the same sample. Interactions of electrons with an atom result in the electrons specific energy loss. Based upon these energy losses distribution of the elements within the sample can be mapped.

scholarly journals Degradation of tissue-type plasminogen activator by human monocyte- derived macrophages is mediated by the mannose receptor and by the low- density lipoprotein receptor-related protein

Blood ◽  
1995 ◽  
Vol 86 (9) ◽  
pp. 3421-3427 ◽  
Author(s):  
F Noorman ◽  
EA Braat ◽  
DC Rijken
Keyword(s):  
Plasminogen Activator ◽  
Binding Sites ◽  
Human Monocyte ◽  
Mannose Receptor ◽  
Tissue Type ◽  
Affinity Binding ◽  
Lipoprotein Receptor ◽  
Related Protein ◽  
Type Plasminogen Activator ◽  
Lipoprotein Receptor Related Protein

The balance of tissue-type plasminogen activator (t-PA) production and degradation determines its concentration in blood and tissues. Disturbance of this balance may result in either increased or decreased proteolysis. In the present study, we identified the receptor systems involved in the degradation of t-PA by human monocytes/macrophages in culture. Monocytes were cultured and became macrophages within 2 days. At 4 degrees C, 125I-t-PA bound to macrophages with high (apparent dissociation constant [kd], 1 to 5 nmol/L) and low affinity (kd = 350 nmol/L). At 37 degrees C, the cells internalized and degraded t-PA via the high affinity binding sites, which were partially inhibited by mannan. The low affinity binding sites were 6-aminohexanoic acid- inhibitable and not involved in t-PA degradation. Degradation of t-PA was upregulated during differentiation of monocytes to macrophages. Dexamethasone further upregulated the mannan-inhibitable t-PA degradation. Lipopolysaccharide downregulated both mannan-inhibitable and non-mannan-inhibitable t-PA degradation. Non-mannan-inhibitable degradation was completely blocked by recombinant 39-kD receptor- associated protein (RAP, inhibitor of lipoprotein receptor-related protein [LRP]), whereas mannan-inhibitable degradation was blocked by the addition of a monoclonal antibody against the mannose receptor. No differences between the degradation of t-PA and functionally inactivated t-PA were observed. We conclude that human monocyte-derived macrophages are able to bind, internalize, and degrade t-PA. Degradation of t-PA does not require complex formation with plasminogen activator inhibitors. The macrophages use two independently regulated receptors, namely, the mannose receptor and LRP, for the uptake and degradation of t-PA.

scholarly journals The Emerging Picture of the Roles of CircRNA-CDR1as in Cancer

2020 ◽  
Vol 8 ◽  
Author(s):  
Chaohua Jiang ◽  
Xiaohong Zeng ◽  
Renfeng Shan ◽  
Wu Wen ◽  
Jianfeng Li ◽  
...  
Keyword(s):  
Binding Sites ◽  
Antisense Rna ◽  
Bioinformatic Analysis ◽  
Vital Role ◽  
Cerebellar Degeneration ◽  
Circular Rnas ◽  
Related Protein ◽  
Future Prospects ◽  
Biological Features

Circular RNAs (circRNAs) are covalently closed circular structures without 5′ caps and 3′ tails, which are mainly formed from precursor mRNAs (pre-mRNAs) via back-splicing of exons. With the development of RNA sequencing and bioinformatic analysis, circRNAs were recently rediscovered and found to be widely expressed in the tree of life. Cerebellar degeneration-related protein 1 antisense RNA (CDR1as) is recognized as one of the most well-identified circRNAs. It contains over 70 miR-7 binding sites and can regulate gene activity by sponging miR-7. Increasing numbers of studies have recently demonstrated that CDR1as is abnormally expressed in many types of tumors, such as colorectal cancer, cholangiocarcinoma and osteosarcoma, and plays a vital role in the development of cancer. However, there are few reviews focusing on CDR1as and cancer. Hence, it is important to review and discuss the role of CDR1as in cancer. Here, we first review the main biological features of CDR1as. We then focus on the expression and roles of CDR1as in cancer. Finally, we summarize what is known on the role of CDR1as in cancer and discuss future prospects in this area of research.

scholarly journals Binding of Gal4p and Bicoid to Nucleosomal Sites in Yeast in the Absence of Replication

1999 ◽  
Vol 19 (4) ◽  
pp. 2977-2985 ◽  
Author(s):  
Bhuvana Balasubramanian ◽  
Randall H. Morse
Keyword(s):  
Transcription Factors ◽  
Dna Replication ◽  
Binding Sites ◽  
Transcriptional Activator ◽  
Nucleosome Positioning ◽  
Living Cells ◽  
Intracellular Environment ◽  
Nucleosomal Dna

ABSTRACT The yeast transcriptional activator Gal4p can bind to sites in nucleosomal DNA in vivo which it is unable to access in vitro. One event which could allow proteins to bind to otherwise inaccessible sites in chromatin in living cells is DNA replication. To determine whether replication is required for Gal4p to bind to nucleosomal sites in yeast, we have used previously characterized chromatin reporters in which Gal4p binding sites are incorporated into nucleosomes. We find that Gal4p is able to perturb nucleosome positioning via nucleosomal binding sites in yeast arrested either in G1, with α-factor, or in G2/M, with nocodazole. Similar results were obtained whether Gal4p synthesis was induced from the endogenous promoter by growth in galactose medium or by an artificial, hormone-inducible system. We also examined binding of theDrosophila transcriptional activator Bicoid, which belongs to the homeodomain class of transcription factors. We show that Bicoid, like Gal4p, can bind to nucleosomal sites inSWI + and swi1Δ yeast and in the absence of replication. Our results indicate that some feature of the intracellular environment other than DNA replication or the SWI-SNF complex permits factor access to nucleosomal sites.

Polymorphisms in the putative micro-RNA-binding sites of mesothelin gene are associated with serum levels of mesothelin-related protein

2009 ◽  
Vol 67 (4) ◽  
pp. 233-236 ◽  
Author(s):  
A. Cristaudo ◽  
R. Foddis ◽  
A. Bonotti ◽  
S. Simonini ◽  
A. Vivaldi ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Serum Levels ◽  
Micro Rna ◽  
Related Protein ◽  
Rna Binding Sites

scholarly journals Dynamics of inner kinetochore assembly and maintenance in living cells

2008 ◽  
Vol 180 (6) ◽  
pp. 1101-1114 ◽  
Author(s):  
Peter Hemmerich ◽  
Stefanie Weidtkamp-Peters ◽  
Christian Hoischen ◽  
Lars Schmiedeberg ◽  
Indri Erliandri ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Binding Sites ◽  
Living Cells ◽  
S Phase ◽  
Quantitative Microscopy ◽  
Diffusion Behavior ◽  
Kinetochore Assembly ◽  
Centromere Proteins ◽  
Wide Range ◽  
Dynamic Exchange

To investigate the dynamics of centromere organization, we have assessed the exchange rates of inner centromere proteins (CENPs) by quantitative microscopy throughout the cell cycle in human cells. CENP-A and CENP-I are stable centromere components that are incorporated into centromeres via a “loading-only” mechanism in G1 and S phase, respectively. A subfraction of CENP-H also stays stably bound to centromeres. In contrast, CENP-B, CENP-C, and some CENP-H and hMis12 exhibit distinct and cell cycle–specific centromere binding stabilities, with residence times ranging from seconds to hours. CENP-C and CENP-H are immobilized at centromeres specifically during replication. In mitosis, all inner CENPs become completely immobilized. CENPs are highly mobile throughout bulk chromatin, which is consistent with a binding-diffusion behavior as the mechanism to scan for vacant high-affinity binding sites at centromeres. Our data reveal a wide range of cell cycle–specific assembly plasticity of the centromere that provides both stability through sustained binding of some components and flexibility through dynamic exchange of other components.

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