Biomedical subjects

Gerhard Stock

Publications and source records attributed to Gerhard Stock.

12 recordsLinked to original sources

PubMed2006

Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism.

Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct assembly of amyloidogenic peptides we probe the dynamics of formation of (Abeta(16-22))(n) by adding a monomer to a preformed (Abeta(16-22))(n-1) (n = 4-6) oligomer in which the peptides are arranged in an antiparallel beta-sheet conformation. All atom molecular dynamics simulations in water and multiple long trajectories, for a cumulative time of 6.9 mus, show that the oligomer grows by a two-stage dock-lock mechanism. The largest conformational change in the added disordered monomer occurs during the rapid ( approximately 50 ns) first dock stage in which the beta-strand content of the monomer increases substantially from a low initial value. In the second slow-lock phase, the monomer rearranges to form in register antiparallel structures. Surprisingly, the mobile structured oligomers undergo large conformational changes in order to accommodate the added monomer. The time needed to incorporate the monomer into the fluid-like oligomer grows even when n = 6, which suggests that the critical nucleus size must exceed six. Stable antiparallel structure formation exceeds hundreds of nanoseconds even though frequent interpeptide collisions occur at elevated monomer concentrations used in the simulations. The dock-lock mechanism should be a generic mechanism for growth of oligomers of amyloidogenic peptides.

Amyloid beta-Peptides↗

PubMed2006

Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study.

Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates reveals that the conformational rearrangement of the peptide is rather complex and occurs on at least four timescales: 1) After photoexcitation, the azobenzene unit of the molecule undergoes nonadiabatic photoisomerization within 0.2 ps. 2) On the picosecond timescale, the cooling (13 ps) and the stretching (14 ps) of the photoexcited peptide is observed. 3) Most reaction coordinates exhibit a 50-100 ps component reflecting a fast conformational rearrangement. 4) The 500-1000 ps component observed in the simulation accounts for the slow diffusion-controlled conformational equilibration of the system. The simulation of the photoinduced molecular processes is in remarkable agreement with time-resolved optical and infrared experiments, although the calculated cooling as well as the initial conformational rearrangements of the peptide appear to be somewhat too slow. Based on an ab initio parameterized vibrational Hamiltonian, the time-dependent amide I frequency shift is calculated. Both intramolecular and solvent-induced contributions to the frequency shift were found to change by < or = 2 cm(-1), in reasonable agreement with experiment. The potential of transient infrared spectra to characterize the conformational dynamics of peptides is discussed in some detail.

Computer Simulation↗

PubMed2006

Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces.

A method is presented to improve the speed of convergence of Wang-Landau simulations as used to calculate the density of states of continuous systems. The density of states is first crudely estimated with calculations employing a smoothed potential-energy surface. This estimate is then used as a seed for subsequent Wang-Landau simulations using the original potential. The performance of the method is demonstrated by employing several simple models, including an analytically solvable harmonic system as well as a Go model of a protein. For all systems considered, the seeded simulations were found to converge significantly faster and with higher accuracy than the standard Wang-Landau simulations.

Journal Article↗

PubMed2006

Quantum modeling of transient infrared spectra reflecting photoinduced electron-transfer dynamics.

A theoretical description of transient vibrational spectra following the impulsive optical excitation of a molecular system is presented. The approach combines the nonsecular evaluation of the Redfield equations to describe the dissipative dynamics of the system with an efficient implementation of the doorway-window formalism to calculate optical pump/infrared probe (vis/IR) spectra. Both parts of the calculation scale with N2, thus facilitating the treatment of systems with a dimension up to 10(4). The formulation is applied to a simple model of photoinduced electron transfer, which takes into account two coupled electronic states and a single anharmonic vibrational mode. Despite its simplicity, the model is found to exhibit quite complex electronic and vibrational relaxation dynamics, which in turn give rise to rather complex time- and frequency-resolved vis/IR spectra. Interestingly, the calculated IR spectra of the electron-transfer system predict the appearance of novel vibronically induced sidebands, which may even dominate the spectrum at early times.

Journal Article↗

PubMed2005

Free energy landscape and folding mechanism of a beta-hairpin in explicit water: a replica exchange molecular dynamics study.

The free energy landscape and the folding mechanism of the C-terminal beta-hairpin of protein G is studied by extensive replica exchange molecular dynamics simulations (40 replicas and 340 ns total simulation time), using the GROMOS96 force field and the SPC explicit water solvent. The study reveals that the system preferentially adopts a beta-hairpin structure at biologically important temperatures, and that the helix content is low at all temperatures studied. Representing the free energy landscape as a function of several types of reaction coordinates, four local minima corresponding to the folded, partially folded, molten globule, and unfolded states are identified. The findings suggest that the folding of the beta-hairpin occurs as the sequence: collapse of hydrophobic core --> formation of H-bond --> formation of the turn. Identifying the folded and molten globule states as the main conformations, the free energy landscape of the beta-hairpin is consistent with a two-state behavior with a broad transition state. The temperature dependence of the folding-unfolding transition is investigated in some detail. The enthalpy and entropy jumps at the folding transition temperature are found to be about three times lower than the experimental estimates, indicating that the folding-unfolding transition in silico is less cooperative than its in vitro counterpart.

Amino Acid Sequence↗

PubMed2005

Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study.

Molecular dynamics simulations of the binding of the heterochiral tripeptide KkN to the transactivation responsive (TAR) RNA of HIV-1 is presented, using an all-atom force field with explicit water. To obtain starting structures for the TAR-KkN complex, semirigid docking calculations were performed that employ an NMR structure of free TAR RNA. The molecular dynamics simulations show that the starting structures in which KkN binds to the major groove of TAR (as it is the case for the Tat-TAR complex of HIV-1) are unstable. On the other hand, the minor-groove starting structures are found to lead to several binding modes, which are stabilized by a complex interplay of stacking, hydrogen bonding, and electrostatic interactions. Although the ligand does not occupy the binding position of Tat protein, it is shown to hinder the interhelical motion of free TAR RNA. The latter is presumably necessary to achieve the conformational change of TAR RNA to bind Tat protein. Considering the time evolution of the trajectories, the binding process is found to be ligand-induced and cooperative. That is, the conformational rearrangement only occurs in the presence of the ligand and the concerted motion of the ligand and a large part of the RNA binding site is necessary to achieve the final low-energy binding state.

Binding Sites↗

PubMed2005

Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study.

A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in explicit dimethyl sulfoxide solution is presented in order to characterize the conformational structures and energy landscape of a photoswitchable peptide. It is shown that an enhanced-sampling technique such as the REMD method is essential to obtain a converged conformational sampling of the peptide at room temperature. This is because conventional MD simulations of less than approximately 100-ns length are either trapped in local minima (at 295 K) or-if run at high temperature-do not resemble the room-temperature REMD results. Calculating various nuclear Overhauser effects (NOEs) and (3)J-couplings, a good overall agreement between the REMD simulations and the NMR experiments of Renner et al. (Biopolymers 2000;54:501-514) is found. In particular, the REMD study confirms the general picture drawn by Renner et al. that the trans-isomer of the azobenzene peptide exhibits a well-defined structure, while the cis-isomer is a conformational heterogeneous system; that is, the trans-isomer occurs in 2 well-defined conformers, while the cis-isomer represents an energetically frustrated system that leads to an ensemble of conformational structures. Employing a principal component analysis of the REMD data, the free energy landscape of the systems is studied at various temperatures. The implications for the folding and unfolding pathways of the system are discussed.

Algorithms↗

PubMed2005

Ab initio-based exciton model of amide I vibrations in peptides: definition, conformational dependence, and transferability.

Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting "glycine dipeptide" (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate (phi,psi) maps of the local-mode frequencies and couplings. Performing conformational averages of the (phi,psi) maps with respect to the most important peptide conformational states in solution (alpha, beta, P(II), and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated.

Amides↗

PubMed2005

Energy landscape of a small peptide revealed by dihedral angle principal component analysis.

A 100 ns molecular dynamics simulation of penta-alanine in explicit water is performed to study the reversible folding and unfolding of the peptide. Employing a standard principal component analysis (PCA) using Cartesian coordinates, the resulting free-energy landscape is found to have a single minimum, thus suggesting a simple, relatively smooth free-energy landscape. Introducing a novel PCA based on a transformation of the peptide dihedral angles, it is found, however, that there are numerous free energy minima of comparable energy (less than or approximately 1 kcal/mol), which correspond to well-defined structures with characteristic hydrogen-bonding patterns. That is, the true free-energy landscape is actually quite rugged and its smooth appearance in the Cartesian PCA represents an artifact of the mixing of internal and overall motion. Well-separated minima corresponding to specific conformational structures are also found in the unfolded part of the free energy landscape, revealing that the unfolded state of penta-alanine is structured rather than random. Performing a connectivity analysis, it is shown that neighboring states are connected by low barriers of similar height and that each state typically makes transitions to three or four neighbor states. Several principal pathways for helix nucleation are identified and discussed in some detail.

Energy Transfer↗

PubMed2005

Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study.

Molecular dynamics simulations of the RNA tetraloop 5'-CGCUUUUGCG-3' with high melting temperature and significant conformational heterogeneity in explicit water solvent are presented and compared to NMR studies. The NMR data allow for a detailed test of the theoretical model, including the quality of the force field and the conformational sampling. Due to the conformational heterogeneity of the tetraloop, high temperature (350 K) and locally enhanced sampling simulations need to be invoked. The Amber98 force field leads to a good overall agreement with experimental data. Based on NMR data and a principal component analysis of the 350 K trajectory, the dynamic structure of the tetraloop is revealed. The principal component free energy surface exhibits four minima, which correspond to well-defined conformational structures that differ mainly by their base stacking in the loop region. No correlation between the motion of the sugar rings and the stacking dynamics of the loop bases is found.

Nuclear Magnetic Resonance, Biomolecular↗

PubMed2005

Synthesis of spin-labeled RNAs for long range distance measurements by peldor.

Site directed spin labeled RNA duplexes with different interspin distances were synthesized. The radical 2,2,5,5-tetramethyl-pyrrolin- 1-yloxyl-3-acetylene (TPA) was introduced during the solid-phase synthesis through a Sonogashira cross-coupling with 5-iodo-uridine. Tm and CD studies showed that the spin label does not to disturb significantly the A-form of these duplexes. 4-Pulse Electron Double Resonance (PELDOR) was then used to measure intramolecular spin-spin distances of 19.3, 33.0 and 40.9 A, which are in very good agreement with the calculated values of 17.6, 32.1 and 39.1 A, obtained from Molecular Dynamics (MD) simulations.

Biochemistry↗

PubMed2004

A PELDOR-based nanometer distance ruler for oligonucleotides.

A pulsed electron paramagnetic resonance (EPR) spectroscopic ruler for oligonucleotides was developed using a series of duplex DNAs. The spin-labeling is accomplished during solid-phase synthesis of the oligonucleotides utilizing a palladium-catalyzed cross-coupling reaction between 5-iodo-2'-deoxyuridine and the rigid spin-label 2,2,5,5-tetramethyl-pyrrolin-1-yloxyl-3-acetylene (TPA). 4-Pulse electron double resonance (PELDOR) was then used to measure the intramolecular spin-spin distances via the dipolar coupling, yielding spin-spin distances of 19.2, 23.3, 34.7, 44.8, and 52.5 A. Employing a full-atom force field with explicit water, molecular dynamic (MD) simulations on the same spin-labeled oligonucleotides in their duplex B-form gave spin-spin distances of 19.6, 21.4, 33.0, 43.3, and 52.5 A, respectively, in very good agreement with the measured distances. This shows that the oligonucleotides adopt a B-form duplex structure also in frozen aqueous buffer solution. It also demonstrates that the combined use of site-directed spin-labeling, PELDOR experiments, and MD simulations can yield a microscopic picture about the overall structure of oligonucleotides. The technique is also applicable to more complex systems, like ribozymes or DNA/RNA-protein complexes, which are difficult to access by NMR or X-ray crystallography.

Base Sequence↗