Solution X-ray scattering (S/WAXS) and structure formation in protein dynamics

Autor: Xubiao Peng, Antti J. Niemi, Jan Davidsson, Alexandr Nasedkin
Rok vydání: 2016
Předmět:
0301 basic medicine
Nonequilibrium statistical mechanics
Models
Molecular
Protein Conformation
alpha-Helical
Protein Folding
Structure formation
Structure (category theory)
Phase (waves)
FOS: Physical sciences
01 natural sciences
Phase Transition
03 medical and health sciences
Molecular dynamics
X-Ray Diffraction
0103 physical sciences
Scattering
Small Angle
Animals
Drosophila Proteins
Computer Simulation
Statistical physics
Physics - Biological Physics
010306 general physics
Nuclear Magnetic Resonance
Biomolecular
Physics
Homeodomain Proteins
Scattering
Protein dynamics
Circular Dichroism
Temperature
Experimental data
Biomolecules (q-bio.BM)
Solutions
Crystallography
030104 developmental biology
Drosophila melanogaster
Quantitative Biology - Biomolecules
Biological Physics (physics.bio-ph)
FOS: Biological sciences
Algorithms
Transcription Factors
DOI: 10.48550/arxiv.1611.08259
Popis: We propose to develop mean field theory in combination with Glauber algorithm, to model and interpret protein dynamics and structure formation in small to wide angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analysing the Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data with a good precision and over an extended temperature range. We explain experimentally observed phenomena in terms of protein phase structure, and we make predictions for future experiments how the scattering data behaves at different ambient temperature values. We conclude that a combination of mean field theory with Glauber algorithm has the potential to develop into a highly accurate, computationally effective and predictive tool for analysing S/WAXS data. Finally, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.
Comment: 10 figures
Databáze: OpenAIRE
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