Protein engineering by combined computational and in vitro evolution approaches
L Rosenfeld, M Heyne, JM Shifman, N Papo - Trends in biochemical …, 2016 - cell.com
Two alternative strategies are commonly used to study protein–protein interactions (PPIs)
and to engineer protein-based inhibitors. In one approach, binders are selected …
and to engineer protein-based inhibitors. In one approach, binders are selected …
Production and purification of therapeutic enzymes
The use of therapeutic enzymes embraces currently a vast array of applications, abridging
from diggestive disorders to cancer therapy, cardiovascular and lysosomal storage …
from diggestive disorders to cancer therapy, cardiovascular and lysosomal storage …
Development of high affinity and high specificity inhibitors of matrix metalloproteinase 14 through computational design and directed evolution
Degradation of the extracellular matrices in the human body is controlled by matrix
metalloproteinases (MMPs), a family of more than 20 homologous enzymes. Imbalance in …
metalloproteinases (MMPs), a family of more than 20 homologous enzymes. Imbalance in …
Converting a broad matrix metalloproteinase family inhibitor into a specific inhibitor of MMP‐9 and MMP‐14
J Shirian, V Arkadash, I Cohen, T Sapir… - FEBS …, 2018 - Wiley Online Library
MMP‐14 and MMP‐9 are two well‐established cancer targets for which no specific clinically
relevant inhibitor is available. Using a powerful combination of computational design and …
relevant inhibitor is available. Using a powerful combination of computational design and …
Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21
I Leung, A Dekel, JM Shifman… - Proceedings of the …, 2016 - National Acad Sciences
A detailed understanding of the molecular mechanisms whereby ubiquitin (Ub) recognizes
enzymes in the Ub proteasome system is crucial for understanding the biological function of …
enzymes in the Ub proteasome system is crucial for understanding the biological function of …
Affinity-and specificity-enhancing mutations are frequent in multispecific interactions between TIMP2 and MMPs
Multispecific proteins play a major role in controlling various functions such as signaling,
regulation of transcription/translation, and immune response. Hence, a thorough …
regulation of transcription/translation, and immune response. Hence, a thorough …
Optimizing the specificity window of biomolecular receptors using structure-switching and allostery
To ensure maximum specificity (ie, minimize cross-reactivity with structurally similar
analogues of the desired target), most bioassays invoke “stringency”, the careful tuning of …
analogues of the desired target), most bioassays invoke “stringency”, the careful tuning of …
Generating quantitative binding landscapes through fractional binding selections combined with deep sequencing and data normalization
M Heyne, N Papo, JM Shifman - Nature Communications, 2020 - nature.com
Quantifying the effects of various mutations on binding free energy is crucial for
understanding the evolution of protein-protein interactions and would greatly facilitate …
understanding the evolution of protein-protein interactions and would greatly facilitate …
Cold spots in protein binding
Understanding the energetics and architecture of protein-binding interfaces is important for
basic research and could potentially facilitate the design of novel binding domains for …
basic research and could potentially facilitate the design of novel binding domains for …
Combinatorial and computational approaches to identify interactions of macrophage colony-stimulating factor (M-CSF) and its receptor c-FMS
The molecular interactions between macrophage colony-stimulating factor (M-CSF) and the
tyrosine kinase receptor c-FMS play a key role in the immune response, bone metabolism …
tyrosine kinase receptor c-FMS play a key role in the immune response, bone metabolism …