[HTML][HTML] Specificity in PDZ-peptide interaction networks: Computational analysis and review

JF Amacher, L Brooks 3rd, TH Hampton… - Journal of Structural …, 2020 - Elsevier
Globular PDZ domains typically serve as protein–protein interaction modules that regulate a
wide variety of cellular functions via recognition of short linear motifs (SLiMs). Often, PDZ …

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 …

A structural portrait of the PDZ domain family

A Ernst, BA Appleton, Y Ivarsson, Y Zhang… - Journal of molecular …, 2014 - Elsevier
Abstract PDZ (PSD-95/Discs-large/Z O1) domains are interaction modules that typically bind
to specific C-terminal sequences of partner proteins and assemble signaling complexes in …

A general mechanism for the propagation of mutational effects in proteins

N Rajasekaran, S Suresh, S Gopi, K Raman… - Biochemistry, 2017 - ACS Publications
Mutations in the hydrophobic interior of proteins are generally thought to weaken the
interactions only in their immediate neighborhood. This forms the basis of protein …

A universal pattern in the percolation and dissipation of protein structural perturbations

N Rajasekaran, A Sekhar… - The journal of physical …, 2017 - ACS Publications
Understanding the extent to which information is transmitted through the intramolecular
interaction network of proteins upon a perturbation, that is, an allosteric effect, has long …

The conformational plasticity vista of PDZ domains

J Murciano-Calles - Life, 2020 - mdpi.com
The PDZ domain (PSD95-Discs large-ZO1) is a widespread modular domain present in the
living organisms. A prevalent function in the PDZ family is to serve as scaffolding and …

Combinatorial and computational approaches to identify interactions of macrophage colony-stimulating factor (M-CSF) and its receptor c-FMS

L Rosenfeld, J Shirian, Y Zur, N Levaot… - Journal of Biological …, 2015 - ASBMB
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 …

Recent developments in engineering protein–protein interactions using phage display

CT Liang, OMA Roscow, W Zhang - Protein Engineering, Design …, 2021 - academic.oup.com
Targeted inhibition of misregulated protein–protein interactions (PPIs) has been a promising
area of investigation in drug discovery and development for human diseases. However …

Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions

OA Karlsson, GN Sundell, E Andersson, Y Ivarsson… - Scientific Reports, 2016 - nature.com
The E6 protein from human papillomavirus (HPV) plays an important role during productive
infection and is a potential drug target. We have previously designed a high affinity bivalent …

Conformational dynamics and cooperativity drive the specificity of a protein-ligand interaction

X Liu, LC Golden, JA Lopez, TR Shepherd, L Yu… - Biophysical journal, 2019 - cell.com
Molecular recognition is critical for the fidelity of signal transduction in biology. Conversely,
the disruption of protein-protein interactions can lead to disease. Thus, comprehension of …