Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X‑ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles

• Published in: Journal of chemical information and modeling Vol. 59; no. 5; pp. 1743 - 1758
• Main Authors: Chan-Yao-Chong, Maud, Durand, Dominique, Ha-Duong, Tâp
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 28.05.2019
• Subjects: Biological activity; Computer simulation; Coupling (molecular); Couplings; Life Sciences; Molecular dynamics; NMR; Nuclear magnetic resonance; Organic chemistry; Proteins; Resonance scattering; Simulation; Small angle X ray scattering; State-of-the-art reviews; water model; chemical-shifts; replica exchange; atomic-level characterization; generalized born model; force-field; alpha-synuclein; unfolded states; structural ensembles; folding simulations
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.8b00928

The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but over the past 20 years, it has become an intense research area in structural biology. Indeed, because of their considerable flexibility and structural heterogeneity, the determination of IDP conformational ensemble is particularly challenging and often requires a combination of experimental measurements and computational approaches. With the improved accuracy of all-atom force fields and the increasing computing performances, molecular dynamics (MD) simulations have become more and more reliable to generate realistic conformational ensembles. And the combination of MD simulations with experimental approaches, such as nuclear magnetic resonance (NMR) and/or small-angle X-ray scattering (SAXS) allows one to converge toward a more accurate and exhaustive description of IDP structures. In this Review, we discuss the state of the art of MD simulations of IDP conformational ensembles, with a special focus on studies that back-calculated and directly compared theoretical and experimental NMR or SAXS observables, such as chemical shifts (CS), 3J-couplings (3Jc), residual dipolar couplings (RDC), or SAXS intensities. We organize the review in three parts. In the first section, we discuss the studies which used NMR and/or SAXS data to test and validate the development of force fields or enhanced sampling techniques. In the second part, we explore different methods for the refinement of MD-derived structural ensembles, such as NMR or SAXS data-restrained MD simulations or ensemble reweighting to better fit experiments. Finally, we survey some recent studies combining MD simulations with NMR and/or SAXS measurements to investigate the relationship between IDP conformational ensemble and biological activity, as well as their implication in human diseases. From this review, we noticed that quite a few studies compared MD-generated conformational ensembles with both NMR and SAXS measurements to validate IDP structures at both local and global levels. Yet, beside the IDP propensity to form local secondary structures, their dynamic extension or compactness also appears important for their activity. Thus, we believe that a close synergy between MD simulations, NMR, and SAXS experiments would be greatly appropriate to address the challenges of characterizing the disordered structures of proteins and their complexes, relative to their biological functions.