Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

Molecular dynamics simulations have proven to be a valuable tool to investigate the dynamic behavior of stable macromolecules at finite temperatures. However, considerable conformational transitions take place during a simulation only accidentally or at exceptionally high temperatures far from the range of experimental conditions. Targeted molecular dynamics (TMD) is a method to induce a conformational change to a known target structure at ordinary temperature by applying a time-dependent, purely geometrical constraint. The transition is enforced independently of the height of energy barriers, while the dynamics of the molecule is only minimally influenced by the constraint. Simulations of decaalanine and insulin show the ability of the method to explore the configurational space for pathways accessible at a given temperature. The transitions studied at insulin comprise unfolding of an alpha-helical portion and, in the reverse direction, refolding from an extended conformation. A possible application of TMD is the search for energy barriers and stable intermediates from rather local changes up to protein denaturation.

Modeling of G-protein coupled receptors with bacteriorhodopsin as a template. A novel approach based on interaction energy differences

The structure of bacteriorhodopsin was used as a template to generate a model for G-protein coupled receptors. However, these receptors and the template are not related by sequence homology. Therefore a pragmatic and reproducible approach was developed to achieve an energetically favourable accommodation of receptor sequences to the backbone structure of bacteriorhodopsin. Improved interaction energy differences are used in a two step procedure analogous to a hypothetical folding mechanism for integral membrane proteins. The resulting model is in good agreement with existing data from structure-function studies.

Calculation of the circular dichroism spectrum of cyclo-(L-tyr-L-tyr) based on a molecular dynamics simulation

Theoretical calculations of CD spectra have generally assumed a single conformation, or a small number of conformers with Boltzmann averaging. Solvent effects on both the conformation and the CD have been neglected. In this work, we have calculated the CD spectrum of cyclo(L-Tyr-L-Tyr) in aqueous solution, taking dynamics and solvation into account. Starting geometries with chi 1 approximately 300 degrees or 60 degrees for both Tyr side chains were derived from MNDO/MOPAC, followed by energy minimization using GROMOS. After addition of 368 water molecules, the system was simulated for 1000 ps at 300 K using GROMOS. In addition to the starting conformer, two other conformers were observed during each simulation. However, each trajectory gave a distinct set of conformers. Rotational strengths were calculated for the cyclic dipeptide at each ps along the trajectories, using the matrix method. The CD spectra calculated from these rotational strengths were averaged over the trajectories. Agreement is very good for the strong negative band near 200 nm, while for the lower energy bands (near 230 and 280 nm), the signs are correct, but the magnitudes are too low. The spectrum calculated from a Boltzmann-weighted average over the in vacuo MNDO/MOPAC conformers was in poor agreement with experiment. Although the solvent did not significantly affect the rotational strength calculated for a given conformer, it is essential to include the solvent in the MD simulations because it affects the relative energies of the conformers and promotes transitions among them.

Comparative studies on the dynamics of crosslinked insulin

Molecular dynamics simulations were carried out on an insulin crosslinked between the N-terminal A chain and the C-terminal B chain to form a so-called mini-proinsulin: N alpha-A1-N epsilon-B29-diaminosuberoyl insulin (DASI). To investigate the influence of crosslinking on the dynamics of the insulin moiety, the bridge was removed from a transient DASI structure and simulation was carried on independently with the then unlinked (ULKI) as well as with the crosslinked species. The effects of crystal packing and quaternary interactions were checked by simulating both types of monomers and dimers known from the hexamer structure. All simulations were compared to previous ones of native insulin. DASI shows general similarity to the native simulations in most parts of the structure. Deviations are visible in the segments to which the bridge is directly connected, i.e. their flexibility is reduced. Upon removal of the bridge the ULKI simulations reapproach those of native insulin. The influence of the bridge spreads over the whole molecule, but all of its main structural features remain intact. The simulations suggest that the displacement of the C-terminal B chain of native insulin, considered important for receptor interaction, is prevented by the bridge, which also partially shields some binding residues. This is in accordance with the poor biological potency of A1-B29-crosslinked insulins.

Distinction of structural reorganisation and ligand binding in the T<==>R transition of insulin on the basis of allosteric models

Two allosteric models are presented for the T<==>R transition of insulin hexamers in the presence of phenolic ligands which are based on existing experimental information. The transition mainly involves residues 1-8 of the B-chain, i.e. 15% of the molecule, which are extended in the T- and helical in the R-state. The main facts to be accounted for are: 1) the transition is undergone trimer-wise; 2) the transition of the second trimer is disadvantaged compared to the first one; 3) the subunits of a trimer undergo transition in a cooperative process; 4) binding sites for phenolic ligands only exist in R3 trimers; 5) ligands shift the equilibrium by arresting the R-state; 6) the ligand is accommodated in a pocket made up between two adjacent subunits; 7) binding one ligand molecule extends the lifetime of the two other binding sites of a trimer; 8) only ligand-free trimers can undergo transitions. The two models allowed for CD spectroscopic titrations of zinc and cobalt insulin with phenol and m-cresol to be assessed in terms of structural reorganisation and ligand binding, and for the respective standard free energy differences to be calculated. delta G degrees for the reorganisation of the first timer in zinc-insulin is about 8 kJ/mol, and for that of the second trimer, 21kJ/mol. The corresponding values for cobalt-insulin are 12 and 24 kJ/mol, respectively. For both zinc- and cobalt-insulin, the delta G degrees for phenol and m-cresol binding is about -18 kJ/mol. Both models are equally compatible with the titration data.

The T<-->R structural transition of insulin; pathways suggested by targeted energy minimization

The transition of insulin between its crystallographically defined states T and R is connected with considerable change even of backbone structure: the N-terminal B chain (residues B1-B8) refolds from extended conformation in T into helical in R, and vice versa. Although hitherto observed only in hexamers the transition of the monomer was adequate for developing and testing the method of 'targeted energy minimization' (TEM), capable of coping with conformational changes of such extent at moderate computational expenditure. The simulation is performed in a predetermined number of steps consisting of two atomic displacements each, one by force in the direction of the target structure, the second by energy minimization releasing the constraint caused in the first. The transition pathway is represented by the string of energy minimized transient structures. Due to the directedness of the algorithm the simulated pathway for R-->T is not the reversal of that for T-->R. It is, therefore, not pretended that the minimum energy pathway was identified. In the T-->R direction the N-terminal B chain first swivels while remaining largely stretched and then winds up extending the pre-existing helix B9-B19. The A chain advances into the space abandoned and withdraws from it in the R-->T simulation. In the latter the extended helix first kinks at B8/B9, and then the B1-B8 segment is unwound and stretched. The helical H-bonds of that segment are formed late in T-->R and are maintained during almost half of R-->T. The AN helix is less stable and more involved in the transitions than helix AC.(ABSTRACT TRUNCATED AT 250 WORDS)

[Bilateral calcaneus fracture in childhood. A report of experiences]

We report on our treatment of fractures of the calcaneus in childhood. Nearly all cases can be treated by conservative methods with good results as regards both anatomy and function. Occasionally consider operative treatment to be indicated even in childhood. We discuss a rare case of bilateral intraarticular fracture of the calcaneus with severe dislocation of fragments. In this particular case we performed bilateral plate osteosynthesis with good results.

Kinetic measurements of T----R structural transitions in insulin

The T6----T3R3 and T3R3----R6-structural transitions of cobalt insulin hexamers as induced by SCN ions or m-cresol were studied in stopped-flow experiments using the absorption in the visible for monitoring their time course. The T6----T3R3 transition induced by either SCN or limited concentrations of m-cresol is mono-exponential with a rate constant of 0.1 s-1 and 0.4 s-1, respectively. A mono-exponential time course is also encountered for the m-cresol-induced T3R3----R6 transition when starting from the T3R3 state preestablished by either SCN or m-cresol. The corresponding rate constants are 1.3 s-1 and 0.49 s-1, respectively. If m-cresol is used beyond the concentration range where transformation is limited to one trimer, two exponentials are required for fitting the time course. The second exponential corresponds to the T3R3----R6 step with a concentration-independent rate constant of 0.4 s-1. The rate constant for the faster T6----T3R3 transition, however, increases with increasing excess of m-cresol.

Cooperativity and intermediate states in the T----R-structural transformation of insulin

With respect to T----R-structural transformation, cobalt insulin hexamers appear as dimers of two positively cooperative trimers which are related by negative cooperativity. Transformation of the first trimer causes polarization of the hexamer which is insurmountable by inorganic anions (SCN theta) used as transforming agents, and in the case of phenolic agents (m-cresol), which can achieve complete transformation of the hexamer, allows the identification of the T3R3 intermediate. Zinc insulin hexamers are also transformed in a stepwise manner, but for the first step the sigmoidal shape of the titration curve cannot be detected.

The simulated dynamics of the insulin monomer and their relationship to the molecule's structure

Insulin crystallizes in different forms, some of which show different conformations for the different molecules in the asymmetric unit. This observation leads to the question as to which conformation the molecule will adopt in solution. Molecular dynamics computer simulations of rhombohedral 2 Zn pig insulin have been carried out for both monomers (1 and 2) independently in order to study their behaviour in the absence of quaternary structure and crystal packing forces. These preliminary 120 ps simulations suggest that both monomers converge in solution to very similar conformations which differ from the X-ray structures of both monomer 1 and 2 (Chinese nomenclature), but are closer to the former, as has previously been suggested by an analysis of the crystal packing (Chothia et al. 1983) and by energy minimization (Wodak et al. 1984). The secondary structure of the molecules is basically preserved, as expected. A detailed description of the conformational changes is given.

A comparison of the structure and dynamics of avian pancreatic polypeptide hormone in solution and in the crystal

A molecular dynamics simulation was carried out with avian pancreatic polypeptide hormone (aPP) as an isolated monomer explicitly including the solvent (MDS). The simulation and the resulting mean structure are compared with the results of a corresponding crystal simulation (MDC) with 4 aPP molecules plus interstitial water in a periodic boundary unit cell and with the X-ray structure (van Gunsteren, Haneef et al., manuscript in preparation). Comparison is based on the time span 5 to 15 ps and considering cartesian coordinates, dihedral angles, H-bond length, and accessible surface area. While in the MDC simulation equilibration is fast and complete, it does occur in MDS for most but not all parts of the molecule; the turn region starts moving away from the X-ray structure after 9 ps. Only minor differences result when dimer-forming side chains, e.g. tyrosines 7 and 21, are exposed to solvent. The largest rms fluctuations are encountered in exposed polar side chains of Asp 11, Glu 15, Arg 19, and Arg 33, but also in the hydrophobic core residue Phe 20, the only phenylalanine residue present. The latter undergoes an abrupt reorientation suitable for verification by NMR spectroscopy, which is possibly related to the motion of the turn region. The main-chain dihedral angles of the alpha-helix are shifted from values generally found in crystal structures towards those of the ideal Pauling helix. There is concomitant H-bond elongation. The effects are most pronounced and consistent in the MDS simulation.

[Renal blood flow investigations with 133xenon and the Anger scintillation camera in the hyperacute xenograft rejection of the rabbit kidney (author's transl)]

The aim of this study was to demonstrate the advantage and validity of 133Xe-washout externally monitored by the scintillation camera. Until now there were no reports on quantitative blood flow studies in Hyperacute rejection of transplanted kidneys using a scintillation camera. Within 35 minutes after e-vivo hemoperfusion of rabbit kidneys by cats we found a simultaneous progressive decrease of renal blood flow, renal cortical blood flow as well as of the intrarenal distribution of renal cortical blood flow in all cases. The hyperacute rejection of xenografts could be verified in every case histologically. Using the scintillation camera we were able to detect regional perfusion defects caused by artifical air embolism as well as by preexisting cortical infarction.