Comparative Biophysical Analysis of Centrosomal Proteins and Their Complexes

Abstract

Functional protein-protein interactions are essential for many physiological processes. Some of these functional interactions have been hypothesized to play a role in substrate channeling, cofactor or coenzyme transfer, and compartmentation in glycolysis as a result of transient or dynamic interactions between glycolytic enzymes. Herein, Brownian dynamics (BD) elucidates the interactions between the glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and lactate dehydrogenase (LDH); the transfer of the cofactor nicotinamide adenine dinucleotide (NAD) between LDH and GAPDH. BD tests the hypotheses of whether the interaction between GAPDH and LDH produces a functional complex that can efficiently and reversibly transfer the cofactor NAD(H) between both enzymes. Preliminary results suggest favorable enzyme-enzyme complexes between GAPDH and LDH involving four different binding modes. These complexes are mainly stabilized by positively charged lysine residues and negatively charged glutamates and aspartates from both GAPDH and LDH. The efficiency of transfer determined as the relative number of BD trajectories that reached any active site of LDH or GAPDH, show higher transfer efficiencies (about an order of magnitude) when the cofactor NAD is transferred from a GAPDH active site to an LDH active site as compared to transfer efficiencies of NAD from solution to each enzyme of the complex. The average transfer time of NAD from solution to the free enzymes is 500 ns as compared to 57-200 ns when NAD is transferred between active sites of a GAPDH/LDH complex. Similarly, the frequency distribution profiles of transfer times suggest a preference for channeling NAD between GAPDH and LDH as compared to diffusing from solution. Channeling transfer is more efficient that solution transfer, due to active site proximity, favorable electrostatics and complex geometry