Role of Domain Interactions in the Collective Motion of Phosphoglycerate Kinase

ABSTRACT Protein function is governed by the underlying conformational dynamics of the molecule. The experimental and theoretical work leading to contemporary understanding of enzyme dynamics was mostly restricted to the large-scale movements of single-domain proteins. Collective movements resulting from a regulatory interplay between protein domains is often crucial for enzymatic activity. It is not clear, however, how our knowledge could be extended to describe collective near-equilibrium motions of multidomain enzymes. We examined the effect of domain interactions on the low temperature near equilibrium dynamics of the native state, using phosphoglycerate kinase as model protein. We measured thermal activation of tryptophan phosphorescence quenching to explore millisecond-range protein motions. The two protein domains of phosphoglycerate kinase correspond to two dynamic units, but interdomain interactions link the motion of the two domains. The effect of the interdomain interactions on the activation of motions in the individual domains is asymmetric. As the temperature of the frozen protein is increased from the cryogenic, motions of the N domain are activated first. This is a partial activation, however, and the full dynamics of the domain becomes activated only after the activation of the C domai

Role of Domain Interactions in the Collective Motion of Phosphoglycerate Kinase

Protein function is governed by the underlying conformational dynamics of the molecule. The experimental and theoretical work leading to contemporary understanding of enzyme dynamics was mostly restricted to the large-scale movements of single-domain proteins. Collective movements resulting from a regulatory interplay between protein domains is often crucial for enzymatic activity. It is not clear, however, how our knowledge could be extended to describe collective near-equilibrium motions of multidomain enzymes. We examined the effect of domain interactions on the low temperature near equilibrium dynamics of the native state, using phosphoglycerate kinase as model protein. We measured thermal activation of tryptophan phosphorescence quenching to explore millisecond-range protein motions. The two protein domains of phosphoglycerate kinase correspond to two dynamic units, but interdomain interactions link the motion of the two domains. The effect of the interdomain interactions on the activation of motions in the individual domains is asymmetric. As the temperature of the frozen protein is increased from the cryogenic, motions of the N domain are activated first. This is a partial activation, however, and the full dynamics of the domain becomes activated only after the activation of the C domain

Amino acid sequence of hemoglobin (HbA) in α and β subunits.

<p>α-helices are denoted by capital letters (with numbers) from A to H. Minor deviations because of the absence of amino acid are marked with green ellipses, the major, dominant difference marked with red ellipse in D helix. Distal (E7) and proximal (F8) histidines (H) are also denoted.</p

Structure of β subunits of hemoglobin (β-HbA).

<p>α-helices are shown as cylinders, number of amino acids of segments is marked with colored digits: red for α-helices, green for loops (gray in the brackets refers to α subunit). The heme group is stabilized by the distal (E7H) and proximal (F8H) histidines. Helix D is marked with red ellipse as the dominant difference between β and α subunits [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194994#pone.0194994.ref006" target="_blank">6</a>]. The transparent colored discs denote the estimated vicinity of the heme of which is characterized by the compressibility in the present work. Yellow and green area mean the spheres with radius <i>R</i>_98% and <i>R</i>_99%, labelling a rage of estimation with 2% and with 1% error respectively (see Appendix II).</p

Change of the IDF parameters as a function of pressure in the case of β-Zn-HbA with Cl^- as an example.

<p>Center and width of the inhomogeneous distribution function (IDF) as a function of applied pressure in the 0–1.2 GPa pressure range are fitted with straight lines. The effect of pressure is of opposite sense on the two parameters.</p

Compressibilities (<i>κ</i>) of HbA under different conditions.

<p>Compressibilities (<i>κ</i>) of HbA under different conditions.</p

Compressibility data of HbA as “Gaussians”.

<p>Curves were created based on the data in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194994#pone.0194994.t001" target="_blank">Table 1</a> from the respective <i>κ</i> and its standard deviation as parameters of center and width. They were normalized according to their heights. For α-Zn-HbA they are represented as upside down curves to make the data more easily comparable. Red color marks the cases without allosteric effectors, other colors show the influence of different effectors (see in the Figure) and black means no significant difference.</p