Predicting the effect of disordered linkers on effective concentrations and avidity with the "Ceff calculator" app.
Kjaergaard, M., Glavina, J. and Chemes, L. B.
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus, Denmark; Center for Proteins in Memory (PROMEMO), Aarhus, Denmark. Electronic address: magnus@mbg.au.dk.
Instituto de Investigaciones Biotecnologicas "Dr. Rodolfo A. Ugalde", IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martin, San Martin, Argentina.
Instituto de Investigaciones Biotecnologicas "Dr. Rodolfo A. Ugalde", IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martin, San Martin, Argentina. Electronic address: lchemes@iib.unsam.edu.ar.
Linkers are crucial to the functions of multidomain proteins as they couple functional units to encode regulation such as auto-inhibition, enzyme targeting or tuning of interaction strength. A linker changes reactions from bimolecular to unimolecular, and the equilibrium and kinetics is thus determined by the properties of the linker rather than concentrations. We present a theoretical workflow for estimating the functional consequences of tethering by a linker. We discuss how to: (1) Identify flexible linkers from sequence. (2) Model the end-to-end distance distribution for a flexible linker using a worm-like chain. (3) Estimate the effective concentration of a ligand tethered by a flexible linker. (4) Calculate the decrease in binding affinity caused by auto-inhibition. (5) Calculate the expected avidity enhancement of a bivalent interaction from effective concentration. The worm-like chain modeling is available through a web application called the "Ceff calculator" (http://ceffapp.chemeslab.org), which will allow user-friendly prediction of experimentally inaccessible parameters.
Methods in Enzymology 647: 145-171 (2021)