Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model

Abstract

Disordered regions as found in intrinsically disordered proteins (IDP) or during protein folding define response time to stimuli and protein folding times. Neutron spin-echo spectroscopy is a powerful tool to directly access the collective motions of the unfolded chain to enlighten the physical origin of basic conformational relaxation. During the thermal unfolding of native ribonuclease A, we examine the structure and dynamics of the disordered state within a two-state transition model using polymer models, including internal friction, to describe the chain dynamics. The presence of four disulfide bonds alters the disordered configuration to a more compact configuration compared to a Gaussian chain that is defined by the additional links, as demonstrated by coarse-grained simulation. The dynamics of the disordered chain is described by Zimm dynamics with internal friction (ZIF) between neighboring amino acids. Relaxation times are dominated by mode-independent internal friction. Internal friction relaxation times show an Arrhenius-like behavior with an activation energy of 33 kJ/mol. The Zimm dynamics is dominated by internal friction and suggest that the characteristic motions correspond to overdamped elastic modes similar to the motions observed for folded proteins but within a pool of disordered configurations spanning the configurational space. For IDP, internal friction dominates while solvent friction and hydrodynamic interactions are smaller corrections.

Variation of Structural and Dynamical Flexibility of Myelin Basic Protein in Response to Guanidinium Chloride

“…In the absence of GndCl at neutral pD, MBP is 55% unfolded, and the ZIF model yields τ i = 69.6 ± 5.1 ns at a sample temperature of 295 K. This is slightly faster than the previously reported value of τ i = 81.6 ± 3.2 ns for MBP at 283 K [22]. The weak dependence of τ i on temperature indicates that internal motions in the intrinsically disordered MBP appear to be regulated by lower activation energies (in the order of ~10 kJ/mol) as compared to unfolded globular proteins: Biehl et al [26] reported a value of 33 kJ/mol for thermally unfolded ribonuclease A, while on the other hand Xia et al [62] found indications for temperature independent behavior of internal friction in two model peptides. The most compact conformation of MBP at 0.2 M GndCl yields a slightly larger τ i = 76.6 ± 8.2 ns that is within the statistical accuracy similar to the result at 0 M GndCl.…”

“…Small-angle scattering by X-rays and neutrons (SAXS/SANS) as well as neutron spin-echo spectroscopy (NSE) have been used to provide information on structure and dynamics of MBP, respectively, in response to GndCl concentration. The combination of those techniques has been applied previously for the investigation of unfolded and partially folded proteins in solution [21,22,26,27] revealing the intricate connection between structural constraints on protein fluctuations.…”

Interchain Hydrodynamic Interaction and Internal Friction of Polyelectrolytes

“…The dynamics of a neutral chain on a molecular level is theoretically depicted as Rouse like if hydrodynamic screening is assumed, or Zimm like if hydrodynamic interactions are relevant. ,, A direct access to the PE dynamics on a molecular level is possible using neutron spinecho spectroscopy (NSE) which is a unique technique for assessing the polymer chain on the nanometer and nanosecond scales. It has been successfully used to examine polymer dynamics, protein domain motions, , IDP , but is rarely applied for PE dynamics. , …”

Conformational Characteristics and Phase Behavior of Intrinsically Disordered Proteins─Where Physical Chemistry Meets Biology

“…The same group also reported the dynamical features of Histatin 5 using high-resolution quasi-elastic neutron scattering in combination with complete atomistic MD . Fischer et al employed small-angle neutron and X-ray scattering (SANS/SAXS) in combination with neutron spin–echo spectroscopy to explore the role of internal friction in the chain dynamics of native and unfolded ribonuclease A …”

“…18 friction in the chain dynamics of native and unfolded ribonuclease A. 19 This virtual issue contains two articles that unraveled the unique signatures of conformational and solvation dynamics using ultrafast time-resolved fluorescence spectroscopy. By employing picosecond time-resolved fluorescence depolarization kinetics, Das et al discerned three distinct modes of chain dynamics and the effect of local chain stiffness on the backbone dihedral rotations that are important in governing internal friction in IDPs.…”