scholarly journals SEPT9 occupies the terminal positions in septin octamers and mediates polymerization-dependent functions in abscission

2011 ◽  
Vol 195 (5) ◽  
pp. 815-826 ◽  
Author(s):  
Moshe S. Kim ◽  
Carol D. Froese ◽  
Mathew P. Estey ◽  
William S. Trimble
Keyword(s):  
Binding Proteins ◽  
Affinity Purification ◽  
Tandem Affinity Purification ◽  
Filament Formation ◽  
Terminal Position ◽  
Wide Range ◽  
Guanosine Triphosphatase ◽  
Septin Filament

Septins are filamentous guanosine triphosphatase–binding proteins that are required for cytokinesis in a wide range of organisms from yeast to man. Several septins, including SEPT9, have been found to be altered in cancers, but their roles in malignancy and cytokinesis remain unclear. It is known that they assemble into rod-shaped oligomeric complexes that join end-on-end to form filaments, but whether SEPT9 incorporates into these complexes and how it does so are unanswered questions. We used tandem affinity purification of mammalian septin complexes to show that SEPT9 occupies a terminal position in an octameric septin complex. A mutant SEPT9, which cannot self-associate, disrupted septin filament formation and resulted in late abscission defects during cytokinesis but did not affect septin-dependent steps earlier in mitosis. These data suggest that mammalian SEPT9 holds a terminal position in the septin octamers, mediating abscission-specific polymerization during cytokinesis.

scholarly journals Identification of testis 14–3-3 binding proteins by tandem affinity purification

2011 ◽  
Vol 1 (4) ◽  
pp. 354-365 ◽  
Author(s):  
Pawan Puri ◽  
Amparo Acker-Palmer ◽  
Ryan Stahler ◽  
Yijing Chen ◽  
Douglas Kline ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Affinity Purification ◽  
Tandem Affinity Purification

Flexible k-mers with variable-length indels for identifying binding sequences of protein dimers

2019 ◽  
Vol 21 (5) ◽  
pp. 1787-1797
Author(s):  
Chenyang Hong ◽  
Kevin Y Yip
Keyword(s):  
Binding Proteins ◽  
Affinity Purification ◽  
Classification Performance ◽  
Variable Regions ◽  
Binding Motifs ◽  
New Class ◽  
Protein Dimers ◽  
Sequence Patterns ◽  
Standard Chip ◽  
Exponential Enrichment

Abstract Many DNA-binding proteins interact with partner proteins. Recently, based on the high-throughput consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) method, many such protein pairs have been found to bind DNA with flexible spacing between their individual binding motifs. Most existing motif representations were not designed to capture such flexibly spaced regions. In order to computationally discover more co-binding events without prior knowledge about the identities of the co-binding proteins, a new representation is needed. We propose a new class of sequence patterns that flexibly model such variable regions and corresponding algorithms that identify co-bound sequences using these patterns. Based on both simulated and CAP-SELEX data, features derived from our sequence patterns lead to better classification performance than patterns that do not explicitly model the variable regions. We also show that even for standard ChIP-seq data, this new class of sequence patterns can help discover co-bound events in a subset of sequences in an unsupervised manner. The open-source software is available at https://github.com/kevingroup/glk-SVM.

scholarly journals Tandem affinity purification in Drosophila: the advantages of the GS-TAP system

Fly ◽  
2008 ◽  
Vol 2 (4) ◽  
pp. 229-235 ◽  
Author(s):  
Phillip P. Kyriakakis ◽  
Marla Tipping ◽  
Louka Abed ◽  
Alexey Veraksa
Keyword(s):  
Affinity Purification ◽  
Tandem Affinity Purification

Tandem affinity purification of AtTERT reveals putative interaction partners of plant telomerase in vivo

PROTOPLASMA ◽  
2016 ◽  
Vol 254 (4) ◽  
pp. 1547-1562 ◽  
Author(s):  
Jana Majerská ◽  
Petra Procházková Schrumpfová ◽  
Ladislav Dokládal ◽  
Šárka Schořová ◽  
Karel Stejskal ◽  
...  
Keyword(s):  
Affinity Purification ◽  
Tandem Affinity Purification ◽  
Interaction Partners

scholarly journals The 3-O-sulfation of heparan sulfate modulates protein binding and lyase degradation

2021 ◽  
Vol 118 (3) ◽  
pp. e2012935118
Author(s):  
Pradeep Chopra ◽  
Apoorva Joshi ◽  
Jiandong Wu ◽  
Weigang Lu ◽  
Tejabhiram Yadavalli ◽  
...  
Keyword(s):  
Heparan Sulfate ◽  
Binding Proteins ◽  
Factor Xa ◽  
Tissue Expression ◽  
Cell Entry ◽  
Synthetic Approach ◽  
Array Technology ◽  
Wide Range ◽  
Simplex Virus

Humans express seven heparan sulfate (HS) 3-O-sulfotransferases that differ in substrate specificity and tissue expression. Although genetic studies have indicated that 3-O-sulfated HS modulates many biological processes, ligand requirements for proteins engaging with HS modified by 3-O-sulfate (3-OS) have been difficult to determine. In particular, the context in which the 3-OS group needs to be presented for binding is largely unknown. We describe herein a modular synthetic approach that can provide structurally diverse HS oligosaccharides with and without 3-OS. The methodology was employed to prepare 27 hexasaccharides that were printed as a glycan microarray to examine ligand requirements of a wide range of HS-binding proteins. The binding selectivity of antithrombin-III (AT-III) compared well with anti-Factor Xa activity supporting robustness of the array technology. Many of the other examined HS-binding proteins required an IdoA2S-GlcNS3S6S sequon for binding but exhibited variable dependence for the 2-OS and 6-OS moieties, and a GlcA or IdoA2S residue neighboring the central GlcNS3S. The HS oligosaccharides were also examined as inhibitors of cell entry by herpes simplex virus type 1, which, surprisingly, showed a lack of dependence of 3-OS, indicating that, instead of glycoprotein D (gD), they competitively bind to gB and gC. The compounds were also used to examine substrate specificities of heparin lyases, which are enzymes used for depolymerization of HS/heparin for sequence determination and production of therapeutic heparins. It was found that cleavage by lyase II is influenced by 3-OS, while digestion by lyase I is only affected by 2-OS. Lyase III exhibited sensitivity to both 3-OS and 2-OS.

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