Dynamics of activated processes in globular proteins.

Abstract

A procedure for the dynamical simulation of activated processes, such as ligand binding and enzymatic reactions, in a globular protein is outlined. Preliminary calculations of the transition state geometry and barrier crossing trajectories are presented for a model reaction, the rotation of an aromatic ring in the bovine pancreatic trypsin inhibitor. The results show that repulsive nonbonded interactions between the ring atoms and the atoms in the surrounding protein matrix determine the dynamical character of the reorientation process; the nonbonded interactions are the source of the rotational barrier and of the impulses that speed up or slow down the ring motion during the barrier crossings. Activated processes play an important role in enzymatic reactions and more generally in the dynamics of protein molecules (1). In an activated process, the observed rate is limited by an energy barrier between the initial and the final state. Most processes in native proteins that take place on a time scale of microseconds or longer are likely to involve such an activation step. Measurements have yielded information concerning the free energy barriers associated with a variety of activated processes in proteins; these include the rotations of aromatic side chains (2-4), the motion of diatomic ligands through the globin of heme proteins (5, 6), and the interconversion of substrate and product in enzymes such as triosephosphate isomerase (7). For the cases listed the number and magnitudes of the free energy barriers involved have been determined (4-7). Further, measurements of the temperature dependence of the rates have demonstrated that there are large entropies of activation that point to the participation of the protein degrees of freedom in the activated process (3-6).The availability of these and other data suggests that an investigation of the detailed dynamics of activated processes in proteins is in order. Of primary interest are the protein contributions to the barriers and the dynamics of the motion across the barriers in the interior of a protein. In some cases (e.g., enzymatic reactions) the protein-substrate interactions may act to lower the activation barrier, whereas in others (e.g., ligand penetration) the interactions are themselves the source of the barrier. Because of the mobility of the interior of a protein (8), the measured barriers correspond to an average over a range of instantaneous interactions. Transient relaxation effects due to concerted displacements of the protein atoms may significantly lower the effective barriers. Because the density of proteins is high (9), frictional damping can occur during the transition and lead to diffusional rather than inertial barrier crossings (10-12).To provide a microscopic description of activated processes in proteins, it will be necessary to carry out a detailed analysis of the dynamics of the atoms involved. In one approach to the problem, which is essentially static in character, empirical energy functions have been used to estimate the activation...

Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism

“…12, rotation of the AChE:W86 side chain is allowed as changes in backbone motions of the outer portions of the omega loop create cavities near the ring of AChE:W86. This motion is reminiscent of other transient packing defects and gating effects (25). These collective motions effectively control access to the active site via the back door and facilitate the conversions of FAS2a to FAS2b.…”

Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes

“…To get further insight into the dynamics of ring flips McCammon & Karplus (1979) used a more detailed method. They took a set of coordinates from an equilibrium dynamical simulation of BPTI.…”

Pressure dependence of aromatic ring rotations in proteins: a collisional interpretation

“…Energy minimization [9,10] and activated trajectory [11,12] calculations have demonstrated that the nature of the rotational transition and its effective barrier are determined by the positions and fluctuations of the protein matrix atoms surrounding the aromatic ring. The importance of frictional effects for the ring motion and for other processes involving fluctuations in the protein interior has been pointed out [11][12][13][14][15].Recently, Wagner [ 16,17] has determined the hydrostatic pressure dependence of the aromatic ring rotation rates in the bovine pancreatic trypsin inhibitor (PTI). Over the measured range (1-1200 atm), interpretation of the rate data for two of the rings (Phe 45 and Tyr 35) in terms of transition state theory [ 18 ]:…”

“…Energy minimization [9,10] and activated trajectory [11,12] calculations have demonstrated that the nature of the rotational transition and its effective barrier are determined by the positions and fluctuations of the protein matrix atoms surrounding the aromatic ring. The importance of frictional effects for the ring motion and for other processes involving fluctuations in the protein interior has been pointed out [11][12][13][14][15].…”

“…A simple model for such processes, provided by the rotation ('flipping') of' aromatic amino acid sidechains in the interior of globular protein has been studied intensively by experimental [3][4][5][6][7][8] and theoretical techniques [9][10][11][12]. Energy minimization [9,10] and activated trajectory [11,12] calculations have demonstrated that the nature of the rotational transition and its effective barrier are determined by the positions and fluctuations of the protein matrix atoms surrounding the aromatic ring. The importance of frictional effects for the ring motion and for other processes involving fluctuations in the protein interior has been pointed out [11][12][13][14][15].…”