scholarly journals Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils

2018 ◽  
Vol 9 (18) ◽  
pp. 4308-4316 ◽  
Author(s):  
Mike C. Groth ◽  
W. Mathis Rink ◽  
Nils F. Meyer ◽  
Franziska Thomas

Strand displacement in heterodimeric coiled coils follows a competitive binding mechanism and can be predicted by the ratio of KD values.

1977 ◽  
Author(s):  
S. Rittenhouse-Simmons ◽  
F. A. Russell ◽  
D. Deykin

We are reporting a novel pathway of arachidonic acid metabolism in the phosphatides of thrombin-activated platelets. For kinetic studies of arachidonic acid turnover, platelet phosphatides were labeled by incubation of platelet rich plasma with (3H)-arachidonic acid for 15 min. Unincorporated isotope was removed during subsequent gel-filtration. Platelet phosphatides were resolved and quantitated following two-dimensional silica paper chromatography of chloroform/methanol extracts of incubated platelets. Plasmalogen phosphatidylethanolamine (PPE) was examined on paper chromatograms after its breakdown to lysoPPE with HgCl2. In other experiments, gel-filtered platelets were incubated with (14C)-glycerol to monitor de novo phosphatide synthesis. (3H)-Arachidonic acid was released from phosphatidylcholine and phosphatidylinositol of pre-labeled platelets exposed to thrombin and appeared increasingly in PPE in acyl linkage at glycerol-C-2. (3H)-Arachidonic acid was not found in PPE of resting cells. Maximum transfer occurred with 5 U/ml of thrombin and 15 min, of incubation, with t½ of 2½ min., and was Ca+2 dependent. The presence of aspirin, indomethacin, or eicosatetraynoic acid did not prevent the thrombin-activated transfer of (3H)-arachidonic acid to PPE. The stimulated incorporation of (3H)-arachidonic acid into PPE was not accompanied by a stimulation of (14C)-glycerol uptake into this phosphatide. We suggest that perturbation of the platelet may activate a phospholipase A2 leading to turnover of arachidonic acid in PPE, which is rich in this fatty acid. Such turnover may provide substrate for conversion by cyclo-oxygenase and lipoxydase to biologically active metabolites, and therefore, may offer a locus for regulation of prostaglandin synthesis in the human platelet.


ChemBioChem ◽  
2017 ◽  
Vol 18 (19) ◽  
pp. 1888-1892 ◽  
Author(s):  
Somayesadat Badieyan ◽  
Aaron Sciore ◽  
Joseph D. Eschweiler ◽  
Philipp Koldewey ◽  
Ajitha S. Cristie-David ◽  
...  

1996 ◽  
Vol 74 (2) ◽  
pp. 133-154 ◽  
Author(s):  
Robert S. Hodges

The two-stranded α-helical coiled-coil is a universal dimerization domain used by nature in a diverse group of proteins. The simplicity of the coiled-coil structure makes it an ideal model system to use in understanding the fundamentals of protein folding and stability and in testing the principles of de novo design. The issues that must be addressed in the de novo design of coiled-coils for use in research and medical applications are (i) controlling parallel versus antiparallel orientation of the polypeptide chains, (ii) controlling the number of helical strands in the assembly (iii) maximizing stability of homodimers or heterodimers in the shortest possible chain length that may require the engineering of covalent constraints, and (iv) the ability to have selective heterodimerization without homodimerization, which requires a balancing of selectivity versus affinity of the dimerization strands. Examples of our initial inroads in using this de novo design motif in various applications include: heterodimer technology for the detection and purification of recombinant peptides and proteins; a universal dimerization domain for biosensors; a two-stage targeting and delivery system; and coiled-coils as templates for combinatorial helical libraries for basic research and drug discovery and as synthetic carrier molecules. The universality of this dimerization motif in nature suggests an endless number of possibilities for its use in de novo design, limited only by the creativity of peptide–protein engineers.Key words: de novo design of proteins, α-helical coiled-coils, protein folding, protein stability, dimerization domain, dimerization motif.


2015 ◽  
Vol 6 (11) ◽  
pp. 6505-6509 ◽  
Author(s):  
Chao Wang ◽  
Wenqing Lai ◽  
Fei Yu ◽  
Tianhong Zhang ◽  
Lu Lu ◽  
...  

Isopeptide bridge-tethered ultra-stable coiled-coil trimers have been de novo designed as structure-directing auxiliaries to guide HIV-1 gp41 NHR-peptide trimerization.


2014 ◽  
Vol 83 (2) ◽  
pp. 235-247 ◽  
Author(s):  
Sebastian Rämisch ◽  
Robert Lizatović ◽  
Ingemar André

1998 ◽  
Vol 5 (3) ◽  
pp. 147-160
Author(s):  
Fei Wang ◽  
Amy E. Warren ◽  
Cheryl R. Barnes ◽  
Iris H. Hall

Poly(phenolic)-sulfonates demonstrated very good cytotoxicity against the growth of tumor cell lines (L1210, Tmolt-3, HeLa-S3) and are comparable in potency with typical clinically used anticancer drugs. Four of the most active compounds, i.e. GL-2021, GL-2029, GL-2041 and GL-2063, were selected for a mode of action study in L1210 lymphoid leukemia cells at concentration of 25μM to 100μM for 60 min. The agents did not alkylate bases of ct-DNA, cause intercalation between base pairs, produce cross linking of ct-DNA strands or generate free radicals although L1210 DNA fragmentation was observed after 24 hr incubation. L1210 DNA synthesis was preferentially inhibited which was achieved by (1) suppressing DNA polymerase α activity which reduced the synthesis of new strands of DNA, (2) reducing of de novo purine synthesis at the regulatory enzyme PRPP amido transferase which reduced d(GMP) levels, and (3) inhibiting of nucleoside kinase activities which further reduced DNA synthesis. DNA template activity was altered by the poly(phenolic)sulfonates since they reduced DNA polymerase α and m-RNA and t-RNA polymerase activities. The kinetic studies at 50 μM over 2 hr demonstrated that the agents’ effect on PRPP-amido transferase activity is probably a major target of the compounds.


2016 ◽  
Vol 7 (3) ◽  
pp. 2207-2216 ◽  
Author(s):  
Matthew R. Berwick ◽  
Louise N. Slope ◽  
Caitlin F. Smith ◽  
Siobhan M. King ◽  
Sarah L. Newton ◽  
...  

Lanthanide binding site translation linearly along a coiled coil has a large impact on stability, coordination chemistry, and MRI relaxivity.


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