A simple pan-specific RNN model for predicting HLA-II binding peptides

2021 ◽  
Vol 139 ◽  
pp. 177-183
Author(s):  
Yu Heng ◽  
Zuyin Kuang ◽  
Wenzhao Xie ◽  
Haoqi Lan ◽  
Shuheng Huang ◽  
...  
Keyword(s):  
Blood ◽  
2004 ◽  
Vol 103 (4) ◽  
pp. 1356-1363 ◽  
Author(s):  
Barbara P. Schick ◽  
David Maslow ◽  
Adrianna Moshinski ◽  
James D. San Antonio

Abstract Patients given unfractionated heparin (UFH) or low-molecular-weight heparin (LMWH) for prophylaxis or treatment of thrombosis sometimes suffer serious bleeding. We showed previously that peptides containing 3 or more tandem repeats of heparin-binding consensus sequences have high affinity for LMWH and neutralize LMWH (enoxaparin) in vivo in rats and in vitro in citrate. We have now modified the (ARKKAAKA)n tandem repeat peptides by cyclization or by inclusion of hydrophobic tails or cysteines to promote multimerization. These peptides exhibit high-affinity binding to LMWH (dissociation constant [Kd], ≈ 50 nM), similar potencies in neutralizing anti–Factor Xa activity of UFH and enoxaparin added to normal plasma in vitro, and efficacy equivalent to or greater than protamine. Peptide (ARKKAAKA)3VLVLVLVL was most effective in all plasmas from enoxaparin-treated patients, and was 4- to 20-fold more effective than protamine. Several other peptide structures were effective in some patients' plasmas. All high-affinity peptides reversed inhibition of thrombin-induced clot formation by UFH. These peptides (1 mg/300 g rat) neutralized 1 U/mL anti–Factor Xa activity of enoxaparin in rats within 1 to 2 minutes. Direct blood pressure and heart rate measurements showed little or no hemodynamic effect. These heparin-binding peptides, singly or in combination, are potential candidates for clinical reversal of UFH and LMWH in humans.


2021 ◽  
Author(s):  
Makoto Ozaki ◽  
Shuhei Yoshida ◽  
Takaaki Tsuruoka ◽  
Kenji Usui

Our method can produce uniquely shaped gold nanostructures in lower HAuCl4 concentration than conventional methods by intracellular functions using peptide assembled structures as a template.


2019 ◽  
Vol 124 (1) ◽  
pp. 61-68 ◽  
Author(s):  
Xingqing Xiao ◽  
Zhifeng Kuang ◽  
B. J. Burke ◽  
Yaroslav Chushak ◽  
Barry L. Farmer ◽  
...  

Metallomics ◽  
2014 ◽  
Vol 6 (9) ◽  
pp. 1693-1701 ◽  
Author(s):  
Tereza Leonhardt ◽  
Jan Sácký ◽  
Pavel Šimek ◽  
Jiří Šantrůček ◽  
Pavel Kotrba

The first evidence of the existence of gene-encoded Zn-binding peptides that sequester a substantial portion of intracellular Zn in ectomycorrhizal fungi under natural conditions.


2010 ◽  
Vol 11 (12) ◽  
pp. 3266-3274 ◽  
Author(s):  
Rebecca Notman ◽  
E. Emre Oren ◽  
Candan Tamerler ◽  
Mehmet Sarikaya ◽  
Ram Samudrala ◽  
...  

2009 ◽  
Vol 11 (11) ◽  
pp. 2688-2696 ◽  
Author(s):  
Jeffrey E. Barrick ◽  
Richard W. Roberts

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