scholarly journals Directed evolution of novel protein functions

2007 ◽  
Vol 98 (2) ◽  
pp. 313-317 ◽  
Author(s):  
Huimin Zhao
Keyword(s):  
Directed Evolution ◽  
Protein Functions ◽  
Novel Protein

scholarly journals Selection and screening strategies in directed evolution to improve protein stability

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Chang Ren ◽  
Xin Wen ◽  
Jun Mencius ◽  
Shu Quan
Keyword(s):  
Systematic Review ◽  
Protein Stability ◽  
Directed Evolution ◽  
Rapid Development ◽  
Therapeutic Applications ◽  
Screening Strategies ◽  
Protein Functions ◽  
Novel Protein

AbstractProtein stability is not only fundamental for experimental, industrial, and therapeutic applications, but is also the baseline for evolving novel protein functions. For decades, stability engineering armed with directed evolution has continued its rapid development and inevitably poses challenges. Generally, in directed evolution, establishing a reliable link between a genotype and any interpretable phenotype is more challenging than diversifying genetic libraries. Consequently, we set forth in a small picture to emphasize the screening or selection techniques in protein stability-directed evolution to secure the link. For a more systematic review, two main branches of these techniques, namely cellular or cell-free display and stability biosensors, are expounded with informative examples.

Extracellular Matrix Proteome of Chickpea (CicerarietinumL.) Illustrates Pathway Abundance, Novel Protein Functions and Evolutionary Perspect

2006 ◽  
Vol 5 (7) ◽  
pp. 1711-1720 ◽  
Author(s):  
Deepti Bhushan ◽  
Aarti Pandey ◽  
Arnab Chattopadhyay ◽  
Mani Kant Choudhary ◽  
Subhra Chakraborty ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Protein Functions ◽  
Novel Protein

scholarly journals Directed Evolution of Proteins throughIn VitroProtein Synthesis in Liposomes

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Takehiro Nishikawa ◽  
Takeshi Sunami ◽  
Tomoaki Matsuura ◽  
Tetsuya Yomo
Keyword(s):  
Protein Synthesis ◽  
Directed Evolution ◽  
Single Copy ◽  
Functional Evaluation ◽  
Future Directions ◽  
Pure System ◽  
Protein Functions ◽  
A Cell ◽  
Evolution Of Proteins

Directed evolution of proteins is a technique used to modify protein functions through “Darwinian selection.”In vitrocompartmentalization (IVC) is anin vitrogene screening system for directed evolution of proteins. IVC establishes the link between genetic information (genotype) and the protein translated from the information (phenotype), which is essential for all directed evolution methods, by encapsulating both in a nonliving microcompartment. Herein, we introduce a new liposome-based IVC system consisting of a liposome, the protein synthesis using recombinant elements (PURE) system and a fluorescence-activated cell sorter (FACS) used as a microcompartment,in vitroprotein synthesis system, and high-throughput screen, respectively. Liposome-based IVC is characterized byin vitroprotein synthesis from a single copy of a gene in a cell-sized unilamellar liposome and quantitative functional evaluation of the synthesized proteins. Examples of liposome-based IVC for screening proteins such as GFP andβ-glucuronidase are described. We discuss the future directions for this method and its applications.

scholarly journals Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: M319C, T431I, and K337D

2019 ◽  
Author(s):  
Peishan Huang ◽  
Stephanie C. Contreras ◽  
Eliana Bloomfield ◽  
Kristine Schmitz ◽  
Augustine Arredondo ◽  
...  
Keyword(s):  
Protein Function ◽  
Kinetic Data ◽  
Prediction Accuracy ◽  
Paenibacillus Polymyxa ◽  
Computational Algorithms ◽  
Enzyme Design ◽  
Data Set ◽  
Computational Tools ◽  
Protein Functions ◽  
Novel Protein

ABSTRACTThe use of computational tools has become an increasingly popular tool for engineering protein function. While there are numerous examples of computational tools enabling the design of novel protein functions, there remains room for improvement in both prediction accuracy and success. To improve algorithms for functional and stability predictions, we have initiated the development of a data set designed to be used for training new computational algorithms for enzyme design. To date our dataset is composed of over 129 mutants with associated expression levels, kinetic data, and thermal stability for the enzyme β-glucosidase B (BglB) from Paenibacillus polymyxa. In this study, we introduced three new variants (M319C, T431I, and K337D) to our existing dataset with the goal of cultivating a larger dataset to train new design algorithms and more broadly explore structure-function relationships in BglB.

scholarly journals Calpain A modulates Toll responses by limited Cactus/IκB proteolysis

2013 ◽  
Vol 24 (18) ◽  
pp. 2966-2980 ◽  
Author(s):  
Marcio Fontenele ◽  
Bomyi Lim ◽  
Danielle Oliveira ◽  
Márcio Buffolo ◽  
David H. Perlman ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Immune System ◽  
Cysteine Proteases ◽  
Proteolytic Cleavage ◽  
Terminal Region ◽  
Full Length ◽  
Calcium Dependent ◽  
Protein Functions ◽  
Novel Protein

Calcium-dependent cysteine proteases of the calpain family are modulatory proteases that cleave their substrates in a limited manner. Among their substrates, calpains target vertebrate and invertebrate IκB proteins. Because proteolysis by calpains potentially generates novel protein functions, it is important to understand how this affects NFκB activity. We investigate the action of Calpain A (CalpA) on the Drosophila melanogaster IκB homologue Cactus in vivo. CalpA alters the absolute amounts of Cactus protein. Our data indicate, however, that CalpA uses additional mechanisms to regulate NFκB function. We provide evidence that CalpA interacts physically with Cactus, recognizing a Cactus pool that is not bound to Dorsal, a fly NFκB/Rel homologue. We show that proteolytic cleavage by CalpA generates Cactus fragments lacking an N-terminal region required for Toll responsiveness. These fragments are generated in vivo and display properties distinct from those of full-length Cactus. We propose that CalpA targets free Cactus, which is incorporated into and modulates Toll-responsive complexes in the embryo and immune system.

scholarly journals Hypomorphic Sox10 alleles reveal novel protein functions and unravel developmental differences in glial lineages

Development ◽  
2007 ◽  
Vol 134 (18) ◽  
pp. 3271-3281 ◽  
Author(s):  
S. Schreiner ◽  
F. Cossais ◽  
K. Fischer ◽  
S. Scholz ◽  
M. R. Bosl ◽  
...  
Keyword(s):  
Developmental Differences ◽  
Protein Functions ◽  
Novel Protein

scholarly journals Correction: A Viable Hypomorphic Allele of the Essential IMP3 Gene Reveals Novel Protein Functions in Saccharomyces cerevisiae

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
Author(s):  
Bruno Cosnier ◽  
Marta Kwapisz ◽  
Isabelle Hatin ◽  
Olivier Namy ◽  
Sylvie Hermann-Le Denmat ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Hypomorphic Allele ◽  
Protein Functions ◽  
Novel Protein

scholarly journals Cryptic genetic variation defines the adaptive evolutionary potential of enzymes

2017 ◽  
Author(s):  
Florian Baier ◽  
Nansook Hong ◽  
Gloria Yang ◽  
Anna Pabis ◽  
Alexandre Barrozo ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Catalytic Activity ◽  
Directed Evolution ◽  
Molecular Basis ◽  
Initial Activity ◽  
Evolutionary Potential ◽  
Phenotypic Properties ◽  
Changing Environments ◽  
Protein Functions ◽  
Evolution Of Proteins

AbstractGenetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may also impact the evolutionary potential of proteins, but the molecular basis for this remains unclear. Here we perform comparative directed evolution in which four orthologous metallo-β-lactamases were evolved toward a new function. We found that genetic variation between these enzymes resulted in distinct evolutionary outcomes. The ortholog with the lower initial activity reached a 20-fold higher fitness plateau exclusively via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show that the cryptic molecular properties and conformational variation of residues in the initial genotypes cause epistasis, thereby constraining evolutionary outcomes. Our work highlights that understanding the molecular details relating genetic variation to protein functions is essential to predicting the evolution of proteins.

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