Molecular Recognition through Concerted Ubiquitin Backbone and Side Chain Motion Determined from NMR and MD Simulations
نویسندگان
چکیده
several of the histone fold helices in free H3.3/H4 complexes. In sum, we have found that DAXX stabilizes a pre-nucleosomal folded form of H3.3/H4 that differs from its final nucleosome form or its form free in solution. While the steps in the folding pathway we studied are certainly tied to the mechanism of chromatin assembly, so to is the massive destabilization we predict occurs to DAXX [HBD] upon releasing H3.3/H4 dimers during nucleosome assembly.
منابع مشابه
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.
A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dyn...
متن کاملToward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations.
Advances in molecular dynamics (MD) force fields1-3 have recently allowed the nearly quantitative interpretation of protein backbone dynamics as measured by NMR spin relaxation4,5 and residual dipolar couplings.6 These improvements were solely due to modification of the backbone æ,ψ dihedral angle potential, as implemented in the AMBER99SB2 and CHARMM22/CMAP1 force fields. Amino acid side-chain...
متن کاملWeak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition
Long-range correlated motions in proteins are candidate mechanisms for processes that require information transfer across protein structures, such as allostery and signal transduction. However, the observation of backbone correlations between distant residues has remained elusive, and only local correlations have been revealed using residual dipolar couplings measured by NMR spectroscopy. In th...
متن کاملImproved side-chain torsion potentials for the Amber ff99SB protein force field
Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, rem...
متن کاملAccessing ns–μs side chain dynamics in ubiquitin with methyl RDCs
This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-tau (c) dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type...
متن کامل