peptide libraries
Recently Published Documents


TOTAL DOCUMENTS

698
(FIVE YEARS 40)

H-INDEX

64
(FIVE YEARS 3)

2022 ◽  
Author(s):  
Brandon Alexander Holt ◽  
Hong Seo Lim ◽  
Melanie Su ◽  
McKenzie Tuttle ◽  
Haley Liakakos ◽  
...  

Genome-scale activity-based profiling of proteases requires identifying substrates that are specific to each individual protease. However, this process becomes increasingly difficult as the number of target proteases increases because most substrates are promiscuously cleaved by multiple proteases. We introduce a method - Substrate Libraries for Compressed sensing of Enzymes (SLICE) - for selecting complementary sets of promiscuous substrates to compile libraries that classify complex protease samples (1) without requiring deconvolution of the compressed signals and (2) without the use of highly specific substrates. SLICE ranks substrate libraries according to two features: substrate orthogonality and protease coverage. To quantify these features, we design a compression score that was predictive of classification accuracy across 140 in silico libraries (Pearson r = 0.71) and 55 in vitro libraries (Pearson r = 0.55) of protease substrates. We demonstrate that a library comprising only two protease substrates selected with SLICE can accurately classify twenty complex mixtures of 11 enzymes with perfect accuracy. We envision that SLICE will enable the selection of peptide libraries that capture information from hundreds of enzymes while using fewer substrates for applications such as the design of activity-based sensors for imaging and diagnostics.


ACS Omega ◽  
2021 ◽  
Author(s):  
Remi Kinoshita ◽  
Ikko Kozaki ◽  
Kazunori Shimizu ◽  
Takahiro Shibata ◽  
Akihito Ochiai ◽  
...  

2021 ◽  
pp. 2103023
Author(s):  
Xuedan He ◽  
Shiqi Zhou ◽  
Breandan Quinn ◽  
Wei‐Chiao Huang ◽  
Dushyant Jahagirdar ◽  
...  

2021 ◽  
Author(s):  
Jakub Chrustowicz ◽  
Dawafuti Sherpa ◽  
Joan Teyra ◽  
Mun Siong Loke ◽  
Grzegorz Popowicz ◽  
...  

N-degron E3 ubiquitin ligases recognize specific residues at the N-termini of substrates. Although molecular details of N-degron recognition are known for several E3 ligases, the range of N-terminal motifs that can bind a given E3 substrate binding domain remains unclear. Here, studying the Gid4 and Gid10 substrate receptor subunits of yeast GID/human CTLH multiprotein E3 ligases, whose known substrates bear N-terminal prolines, we discovered capacity for high-affinity binding to diverse N-terminal sequences determined in part by context. Screening of phage displaying peptide libraries with exposed N-termini identified novel consensus motifs with non-Pro N-terminal residues distinctly binding Gid4 or Gid10 with high affinity. Structural data reveal that flexible loops in Gid4 and Gid10 conform to complementary folds of diverse interacting peptide sequences. Together with analysis of endogenous substrate degrons, the data show that degron identity, substrate domains harboring targeted lysines, and varying E3 ligase higher-order assemblies combinatorially determine efficiency of ubiquitylation and degradation.


2021 ◽  
Vol 2 (3) ◽  
pp. 100605
Author(s):  
Clemens Schulte ◽  
Vladimir Khayenko ◽  
Amit Jean Gupta ◽  
Hans Michael Maric

2021 ◽  
Vol 491 ◽  
pp. 112970 ◽  
Author(s):  
Clive M. Michelo ◽  
Jama A. Dalel ◽  
Peter Hayes ◽  
Natalia Fernandez ◽  
Andrew Fiore-Gartland ◽  
...  

2021 ◽  
Vol 9 ◽  
Author(s):  
Barbara Spellerberg ◽  
Ludger Ständker ◽  
Rüdiger Groß ◽  
Jan Münch

Bacteria and viruses may enter our bodies through mucous membranes of the airways or the gut. To prevent infections, one defense mechanism of our immune system is antimicrobial peptides (AMPs). Most AMPs are composed of 10–50 amino acids and insert into bacterial cell membranes to destroy the cell. Some AMPs are also active against viruses and fungi. AMPs can be generated by chopping up bigger proteins like hemoglobin. The hemoglobin fragments can inactivate bacteria and viruses, while the whole hemoglobin protein cannot. To identify new AMPs, peptide libraries consisting of thousands of different peptides can be generated from human body fluids and organs. These libraries are tested for antibacterial or antiviral activity and can be further purified to identify the responsible peptide. This method may lead to the development of new antimicrobial substances with a potential for treating infections.


iScience ◽  
2021 ◽  
Vol 24 (1) ◽  
pp. 101898
Author(s):  
Clemens Schulte ◽  
Vladimir Khayenko ◽  
Noah Frieder Nordblom ◽  
Franziska Tippel ◽  
Violetta Peck ◽  
...  

2021 ◽  
Author(s):  
Jeffrey Y.-K. Wong ◽  
Raja Mukherjee ◽  
Jiayuan Miao ◽  
Olena Bilyk ◽  
Vivian Triana ◽  
...  

A two-fold symmetric linchpin (TSL) converts readily available phage-displayed disulfide peptide libraries to proteolytically stable bicyclic peptides. The bicyclic phage library was screened to discover an antagonist of NODAL morphogen.


Sign in / Sign up

Export Citation Format

Share Document