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Updated: Jan 30, 2026

Capillary Electrophoresis-based Hydrogen/Deuterium Exchange for Conformational Characterization of Proteins with Top-down Mass Spectrometry
Published on: June 8, 2021
Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions
Elisa Frezza1, Richard Lavery1
1MMSB, UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines , 7 passage du Vercors , Lyon 69367 , France.
Abstract:
We analyze the capacity of normal mode analysis in internal coordinates' space to generate large-amplitude structural deformations that can describe the conformational changes occurring upon the binding of proteins to other species. We also analyze how many modes need to be studied to capture a given transition and whether a combination of two modes is better than using a single mode. The technique is tested on known unbound-to-bound structural transitions for a set of single- or multidomain proteins. The results suggest that this approach is a promising way to generate structures for protein docking or for more refined molecular dynamics simulations.
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