Stable heterodimers from remodeling the domain interface of a homodimer using a phage display library

1997 ◽  
Vol 270 (1) ◽  
pp. 26-35 ◽  
Author(s):  
Shane Atwell ◽  
John B.B Ridgway ◽  
James A Wells ◽  
Paul Carter
2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Harvinder Talwar ◽  
Samer Najeeb Hanoudi ◽  
Andreea Geamanu ◽  
Dana Kissner ◽  
Sorin Draghici ◽  
...  

2021 ◽  
Vol 492 ◽  
pp. 112990
Author(s):  
Jothivel Kumarasamy ◽  
Samar Kumar Ghorui ◽  
Chandrakala Gholve ◽  
Bharti Jain ◽  
Yogesh Dhekale ◽  
...  

1994 ◽  
Vol 124 (3) ◽  
pp. 373-380 ◽  
Author(s):  
E Koivunen ◽  
B Wang ◽  
E Ruoslahti

Our previous studies showed that the alpha 5 beta 1 integrin selects cysteine pair-containing RGD peptides from a phage display library based on a random hexapeptide. We have therefore searched for more selective peptides for this integrin using a larger phage display library, where heptapeptides are flanked by cysteine residues, thus making the inserts potentially cyclic. Most of the phage sequences that bound to alpha 5 beta 1 (69 of 125) contained the RGD motif. Some of the heptapeptides contained an NGR motif. As the NGR sequence occurs in the cell-binding region of the fibronectin molecule, this sequence could contribute to the specific recognition of fibronectin by alpha 5 beta 1. Selection for high affinity peptides for alpha 5 beta 1 surprisingly yielded a sequence RRETAWA that does not bear obvious resemblance to known integrin ligand sequences. The synthetic cyclic peptide GACRRETAWACGA (*CRRETAWAC*) was a potent inhibitor of alpha 5 beta 1-mediated cell attachment to fibronectin. This peptide is nearly specific for the alpha 5 beta 1 integrin, because much higher concentrations were needed to inhibit the alpha v beta 1 integrin, and there was no effect on alpha v beta 3- and alpha v beta 5-mediated cell attachment to vitronectin. The peptide also did not bind to the alpha IIb beta 3 integrin. *CRRETAWAC* appears to interact with the same or an overlapping binding site in alpha 5 beta 1 as RGD, because cell attachment to *CRRETAWAC* coated on plastic was divalent cation dependent and could be blocked by an RGD-containing peptide. These results reveal a novel binding specificity in the alpha 5 beta 1 integrin.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Koichiro Saka ◽  
Taro Kakuzaki ◽  
Shoichi Metsugi ◽  
Daiki Kashiwagi ◽  
Kenji Yoshida ◽  
...  

AbstractMolecular evolution is an important step in the development of therapeutic antibodies. However, the current method of affinity maturation is overly costly and labor-intensive because of the repetitive mutation experiments needed to adequately explore sequence space. Here, we employed a long short term memory network (LSTM)—a widely used deep generative model—based sequence generation and prioritization procedure to efficiently discover antibody sequences with higher affinity. We applied our method to the affinity maturation of antibodies against kynurenine, which is a metabolite related to the niacin synthesis pathway. Kynurenine binding sequences were enriched through phage display panning using a kynurenine-binding oriented human synthetic Fab library. We defined binding antibodies using a sequence repertoire from the NGS data to train the LSTM model. We confirmed that likelihood of generated sequences from a trained LSTM correlated well with binding affinity. The affinity of generated sequences are over 1800-fold higher than that of the parental clone. Moreover, compared to frequency based screening using the same dataset, our machine learning approach generated sequences with greater affinity.


Author(s):  
Jinsong Xia ◽  
Hao Bi ◽  
Qin Yao ◽  
Shen Qu ◽  
Yiqiang Zong

PLoS ONE ◽  
2016 ◽  
Vol 11 (11) ◽  
pp. e0165092 ◽  
Author(s):  
Lifang Qi ◽  
Yan Liu ◽  
Huizhu Tao ◽  
Ning Xiao ◽  
Jinnian Li ◽  
...  

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e106699 ◽  
Author(s):  
Mahsa Sorouri ◽  
Sean P. Fitzsimmons ◽  
Antonina G. Aydanian ◽  
Sonita Bennett ◽  
Marjorie A. Shapiro

AIDS ◽  
2004 ◽  
Vol 18 (2) ◽  
pp. 329-331 ◽  
Author(s):  
Sangeeta Karle ◽  
Stephanie Planque ◽  
Yasuhiro Nishiyama ◽  
Hiroaki Taguchi ◽  
Yong-Xin Zhou ◽  
...  

Elements ◽  
2017 ◽  
Vol 13 (1) ◽  
Author(s):  
Zackary Tajin Park

A phage display library was previously constructed from an SIV-infected rhesus macaque. Several single chain Fv (scFv), including SU24, SU343 and LL25X, were selected using phage display technology. Sequences corresponding to SU24, SU343 and LL25X were optimized for expression in a mammalian system and commercially synthesized. SU24 and SU343 had previously been cloned into a mammalian expression vector. In this study, we aimed to characterize the specificity of SU24, SU343, and LL25X.. The codon-optimized version of the scFv LL25X gene sequence was cloned into a mammalian expression vector (pCEP4).  LL25X DNA was amplified by PCR, and the PCR product and mammalian expression vector were both digested with KpnI/SapI restriction enzymes. Digested fragments were purified, and the fragments were ligated using T4DNA ligase. E. coli cells were transformed with the ligation reaction. Single colonies were selected on LB agar plates containing the selective antibiotic (ampicillin). Positive colonies were identified after DNA mini-preparation and test-digestion with KpnI and SapI. Sanger sequencing confirmed cloning results and DNA sequence accuracy. Following transfection of mammalian cells (293T), LL25X-Fc cells, and purifying our protein, the binding of LL25X-Fc to the SIV gp140 envelope protein was confirmed via ELISA and Western Blotting.


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