Configurational entropy of native proteins.

Simulations of the residual configurational entropy of a protein in the native state suggest that it is nearly an order of magnitude larger than the entropy of denaturation. The implications of this result are discussed.     

Temperature dependence of the structure and dynamics of myoglobin. A simulation approach

The results of simulations of the structure and internal motions of carbonomonoxymyoglobin (MbCO) at two different temperatures (325 and 80 K) are presented and compared with experimental data. Properties calculated from the 120 ps trajectory at 325 K are used as a reference in the analysis of the motion of the protein at 80 K. Three separate 80 K molecular dynamics trajectories were calculated; they were started with different coordinate sets from the 325 K simulation and the lower temperature was achieved by scaling the velocities. The simulations yield results for the structural changes between 325 and 80 K that are in general accord with those from X-ray data. Both the experimental and calculated radii of gyration, distances from the center of mass and main-chain difference distance matrices show that there is a significant but inhomogeneous shrinkage with decreasing temperature. For the atomic fluctuations, by contrast, the calculated temperature dependence is very different from the X-ray results; i.e. the calculated root-mean-square backbone fluctuations decrease to 0.11 A at 80 K from 0.51 A at 325 K, while the fluctuations obtained from the X-ray B factors go from 0.56 A at 260 K to 0.47 A at 80 K. The smaller temperature dependence of the B factors suggests that there is significant conformational disorder in MbCO crystals at lower temperatures. This is in accord with the simulation results, which show that the protein is trapped in restricted regions of conformational space at 80 K, while at 325 K a much larger region is accessible to the protein. Analysis of the fluctuations at 325 K and 80 K shows that the room temperature flexibility of the protein is determined by the mobility of the loop regions and by side-chain torsional motions (in accord with earlier simulation results), while the low temperature fluctuations involve motion within a single well. Examination of the calculated iron atom fluctuations and comparison with Mossbauer data show good agreement. It is found that the dominant contribution to the iron motion arises from heme sliding; motion of the iron relative to the heme are much smaller.     

Improving the accuracy of protein pKa calculations: Conformational averaging versus the average structure

Several methods for including the conformational flexibility of proteins in the calculation of titration curves are compared. The methods use the linearized Poisson-Boltzmann equation to calculate the electrostatic free energies of solvation and are applied to bovine pancreatic trypsin inhibitor (BPTI) and hen egg-white lysozyme (HEWL). An ensemble of conformations is generated by a molecular dynamics simulation of the proteins with explicit solvent. The average titration curve of the ensemble is calculated in three different ways: an average structure is used for the pK_a calculation; the electrostatic interaction free energies are averaged and used for the pK_a calculation; and the titration curve for each structure is calculated and the curves are averaged. The three averaging methods give very similar results and improve the pK_a values to approximately the same degree. This suggests, in contrast to implications from other work, that the observed improvement of pK_a values in the present studies is due not to averaging over an ensemble of structures, but rather to the generation of a single properly averaged structure for the pK_a calculation. Proteins 33:145–158, 1998. © 1998 Wiley-Liss, Inc.     

Allosteric communication in myosin V: from small conformational changes to large directed movements

The rigor to post-rigor transition in myosin, a consequence of ATP binding, plays an essential role in the Lymn-Taylor functional cycle because it results in the dissociation of the actomyosin complex after the powerstroke. On the basis of the X-ray structures of myosin V, we have developed a new normal mode superposition model for the transition path between the two states. Rigid-body motions of the various subdomains and specific residues at the subdomain interfaces are key elements in the transition. The allosteric communication between the nucleotide binding site and the U50/L50 cleft is shown to result from local changes due to ATP binding, which induce large amplitude motions that are encoded in the structure of the protein. The triggering event is the change in the interaction of switch I and the P-loop, which is stabilized by ATP binding. The motion of switch I, which is a relatively rigid element of the U50 subdomain, leads directly to a partial opening of the U50/L50 cleft; the latter is expected to weaken the binding of myosin to actin. The calculated transition path demonstrates the nature of the subdomain coupling and offers an explanation for the mutual exclusion of ATP and actin binding. The mechanism of the uncoupling of the converter from the motor head, an essential part of the transition, is elucidated. The origin of the partial untwisting of the central beta-sheet in the rigor to post-rigor transition is described.     

Retention of acoustic conditioning in St Peter's fish Sarotherodon galilaeus

Groups of St Peter's fish Sarotherodon galilaeus were trained during 28 days of classical conditioning to respond to an acoustic signal by approaching a feeder. Their ability to retain the acoustically conditioned behaviour was tested after eight different intervals ranging from 12 to 188 days from termination of training. Retention tests comprised 7 consecutive days of retraining and the fish response was compared with that of naive fish. Fish response drastically diminished with time. After 55 days, there was no apparent expression of memory on the first test day but fish response was restored on subsequent retraining days, indicating the existence of latent memory. Six months from the end of training, there was no indication of behavioural retention and the response completely vanished. The study was conducted in the context of sea ranching, with classical conditioning used to gain control over fish location. In light of the present results, it is suggested that periodic reinforcement of the acoustically conditioned behaviour should be used.