On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

N-Acetyl-L-Glutamate Kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network model representation, which shows that the conformational mechanisms for substrate binding by NAGK strongly correlate with the intrinsic dynamics of the enzyme in the unbound form. We further analyzed the potential mechanisms of allosteric signalling within NAGK using a Markov model for network communication. Comparative analysis of the dynamics of family members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establish signal transduction are highly conserved among family members, in support of the paradigm sequence→structure→dynamics→function © 2010 Marcos et al

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

Oligomerization is a functional requirement for many proteins. The interfacial interactions and the overall packing geometry of the individual monomers are viewed as important determinants of the thermodynamic stability and allosteric regulation of oligomers. The present study focuses on the role of the interfacial interactions and overall contact topology in the dynamic features acquired in the oligomeric state. To this aim, the collective dynamics of enzymes belonging to the amino acid kinase family both in dimeric and hexameric forms are examined by means of an elastic network model, and the softest collective motions (i.e., lowest frequency or global modes of motions) favored by the overall architecture are analyzed. Notably, the lowest-frequency modes accessible to the individual subunits in the absence of multimerization are conserved to a large extent in the oligomer, suggesting that the oligomer takes advantage of the intrinsic dynamics of the individual monomers. At the same time, oligomerization stiffens the interfacial regions of the monomers and confers new cooperative modes that exploit the rigid-body translational and rotational degrees of freedom of the intact monomers. The present study sheds light on the mechanism of cooperative inhibition of hexameric N-acetyl-L-glutamate kinase by arginine and on the allosteric regulation of UMP kinases. It also highlights the significance of the particular quaternary design in selectively determining the oligomer dynamics congruent with required ligand-binding and allosteric activities

A global search algorithm for phase transition pathways in computer-aided nano-design

One of the most important design issues for phase change materials is to engineer the phase transition process. The challenge of accurately predicting a phase transition is estimating the true value of transition rate, which is determined by the saddle point with the minimum energy barrier between stable states on the potential energy surface (PES). In this thesis, a new algorithm for searching the minimum energy path (MEP) is presented. The new algorithm is able to locate both the saddle point and local minima simultaneously. Therefore no prior knowledge of the precise positions for the reactant and product on the PES is needed. Unlike existing pathway search methods, the algorithm is able to search multiple transition paths on the PES simultaneously, which gives us a more comprehensive view of the energy landscape than searching individual ones. In this method, a Bézier curve is used to represent each transition path. During the searching process, the reactant and product states are located by minimizing the two end control points of the curve, while the shape of the transition pathway is refined by moving the intermediate control points of the curve in the conjugate directions. A curve subdivision scheme is developed so that multiple transitions paths can be located. The algorithm is demonstrated by examples of LEPS potential, LEPS plus harmonic oscillator potential, and PESs defined by Rastrigin function and Schwefel function.M.S