Simultaneous codon usage, the origin of the proteome, and the emergence of de-novo proteins

2021 ◽  
Vol 68 ◽  
pp. 142-148 ◽  
Author(s):  
Charles W Carter
Keyword(s):  
Codon Usage ◽  
De Novo ◽  
De Novo Proteins

De Novo Proteins as Models of Radical Enzymes†

Biochemistry ◽  
1999 ◽  
Vol 38 (29) ◽  
pp. 9495-9507 ◽  
Author(s):  
Cecilia Tommos ◽  
Jack J. Skalicky ◽  
Denis L. Pilloud ◽  
A. Joshua Wand ◽  
P. Leslie Dutton
Keyword(s):  
De Novo ◽  
De Novo Proteins ◽  
Radical Enzymes

scholarly journals Encoding of Contextual Fear Memory Requires De Novo Proteins in the Prelimbic Cortex

2017 ◽  
Vol 2 (2) ◽  
pp. 158-169 ◽  
Author(s):  
Valerio Rizzo ◽  
Khalid Touzani ◽  
Bindu L. Raveendra ◽  
Supriya Swarnkar ◽  
Joan Lora ◽  
...  
Keyword(s):  
De Novo ◽  
Fear Memory ◽  
Prelimbic Cortex ◽  
Contextual Fear ◽  
Contextual Fear Memory ◽  
De Novo Proteins

Nanografting De Novo Proteins onto Gold Surfaces

Langmuir ◽  
2005 ◽  
Vol 21 (20) ◽  
pp. 9103-9109 ◽  
Author(s):  
Ying Hu ◽  
Aditi Das ◽  
Michael H. Hecht ◽  
Giacinto Scoles
Keyword(s):  
De Novo ◽  
Gold Surfaces ◽  
De Novo Proteins

De novo transcriptome assembly and analysis of the codon usage bias of the MADS-box gene family in Cymbidium kanran

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
Boyun Yang ◽  
Huolin Luo ◽  
Yuan Tao ◽  
Wenjing Yu ◽  
Liping Luo
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Mads Box ◽  
Illumina Hiseq ◽  
Optimal Codons ◽  
Mads Box Gene ◽  
New Varieties

Cymbidium kanran is an important commercially grown member of the Chinese orchid family. However, little information regarding the molecular biology of this species is available. In this study, the C. kanran root, shoot, stem, leaf, and flower transcriptomes were sequenced with the Illumina HiSeq 4000 system, which resulted in 8.9 Gb of clean reads that were assembled into 74,620 unigenes, with an average length and N50 of 983 bp and 1,640 bp, respectively. The screening of seven databases (NR, NT, GO, KOG, KEGG, Swiss-Prot, and InterPro) for similar sequences resulted in the functional annotation of 49,813 unigenes. Additionally, 173 MADS-box genes, which help to control major aspects of plant development, were identified and their codon usage bias was analyzed. Only 26 genes had a low ENC (less than or equal to 35), suggesting the codon usage bias was weak. Base mutations were the major determinants of codon usage, although natural selection pressure also influenced codon usage bias. Moreover, 22 optimal codons were identified based on ΔRSCU, and 20 codons ended with A/U. The results of this study provide the foundation for the molecular breeding of new varieties

scholarly journals The advent of de novo proteins for cancer immunotherapy

2020 ◽  
Vol 56 ◽  
pp. 119-128 ◽  
Author(s):  
Alfredo Quijano-Rubio ◽  
Umut Y. Ulge ◽  
Carl D. Walkey ◽  
Daniel-Adriano Silva
Keyword(s):  
Cancer Immunotherapy ◽  
De Novo ◽  
De Novo Proteins

ChemInform Abstract: De Novo Proteins from Combinatorial Libraries

ChemInform ◽  
2010 ◽  
Vol 32 (52) ◽  
pp. no-no
Author(s):  
David A. Moffet ◽  
Michael H. Hecht
Keyword(s):  
De Novo ◽  
Combinatorial Libraries ◽  
De Novo Proteins

scholarly journals Detecting native-like properties in combinatorial libraries of de novo proteins

1997 ◽  
Vol 2 (2) ◽  
pp. 89-92 ◽  
Author(s):  
Sushmita Roy ◽  
Kimberly J. Helmer ◽  
Michael H. Hecht
Keyword(s):  
De Novo ◽  
Combinatorial Libraries ◽  
De Novo Proteins

scholarly journals Synthesis and Selection of De Novo Proteins That Bind and Impede Cellular Functions of an Essential Mycobacterial Protein

2006 ◽  
Vol 73 (4) ◽  
pp. 1320-1331 ◽  
Author(s):  
Alka Rao ◽  
Geeta Ram ◽  
Adesh Kumar Saini ◽  
Reena Vohra ◽  
Krishan Kumar ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Large Scale ◽  
De Novo ◽  
Cell Damage ◽  
Vitro Assay ◽  
De Novo Proteins ◽  
Protein Pool ◽  
Protein Libraries ◽  
Selection Of

ABSTRACT Recent advances in nonrational and part-rational approaches to de novo peptide/protein design have shown increasing potential for development of novel peptides and proteins of therapeutic use. We demonstrated earlier the usefulness of one such approach recently developed by us, called “codon shuffling,” in creating stand-alone de novo protein libraries from which bioactive proteins could be isolated. Here, we report the synthesis and selection of codon-shuffled de novo proteins that bind to a selected Mycobacterium tuberculosis protein target, the histone-like protein HupB, believed to be essential for mycobacterial growth. Using a versatile bacterial two-hybrid system that entailed utilization of HupB and various codon-shuffled protein libraries as bait and prey, respectively, we were able to identify proteins that bound strongly to HupB. The observed interaction was also confirmed using an in vitro assay. One of the protein binders was expressed in Mycobacterium smegmatis and was shown to appreciably affect growth in the exponential phase, a period wherein HupB is selectively expressed. Furthermore, the transcription profile of hupB gene showed a significant reduction in the transcript quantity in mycobacterial strains expressing the protein binder. Electron microscopy of the affected mycobacteria elaborated on the extent of cell damage and hinted towards a cell division malfunction. It is our belief that a closer inspection of the obtained de novo proteins may bring about the generation of small-molecule analogs, peptidomimetics, or indeed the proteins themselves as realistic leads for drug candidates. Furthermore, our strategy is adaptable for large-scale targeting of the essential protein pool of Mycobacterium tuberculosis and other pathogens.

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