Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations
| Autor: | Patrick Senet, Yoann Cote, Patrice Delarue, Harold A. Scheraga, Gia G. Maisuradze |
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| Rok vydání: | 2010 |
| Předmět: |
Magnetic Resonance Spectroscopy
Time Factors Multidisciplinary Rotation Chemistry Proteins Rotational diffusion Nuclear magnetic resonance spectroscopy Biological Sciences Dihedral angle Molecular physics Diffusion Crystallography Molecular dynamics Models Chemical Native state Thermodynamics Molecule Protein folding Amino Acid Sequence Diffusion (business) Probability |
| Zdroj: | Proceedings of the National Academy of Sciences. 107:19844-19849 |
| ISSN: | 1091-6490 0027-8424 |
| Popis: | Structural fluctuations of a protein are essential for the function of native proteins and for protein folding. To understand how the main chain in the native state of a protein fluctuates on different time scales, we examined the rotational correlation functions (RCFs), C ( t ), of the backbone N-H bonds and of the dihedral angles γ built on four consecutive C α atoms. Using molecular dynamics simulations of a model α / β protein (VA3) in its native state, we demonstrate that these RCFs decay as stretched exponentials, ln[ C ( t )] ≈ D α t α with a constant D α and an exponent α (0 α α α ≠ 1) of the RCFs are described by a rotational diffusion equation with a time-dependent diffusion coefficient D ( t ) = αD α t α -1 . The present findings agree with observations of subdiffusion ( α 15 N-H bonds did not affect the value of the order parameter S 2 extracted from the NMR relaxation data by assuming normal diffusion ( α = 1) of 15 N-H bonds on a nanosecond time scale. However, we found that the RCF does not converge to S 2 on the nanosecond time scale for residues with multiple-minima FEPs. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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