Thermodynamics and kinetics of folding of a small peptide

MOLECULAR DYNAMICS SIMULATION OF FOLDING OF A SHORT HELICAL TOXIN PEPTIDE

A molecular dynamics simulation of the folding of a short helical toxin peptide was carried out. The simulation gave a folding time of ~10 ns, which is longer than typical time of ~1 ns for the formation of 1–2 helical turns. The simulation demonstrates that a helical peptide with disulfide bonds, which may encounter extra steric hindrance compared with the peptide without disulfide bonds, can fold in nanosecond timescale. An analysis shows that this folding time should correspond to the folding time in weak denaturation condition in experiment. Interactions and factors affecting folding pathways are analyzed and discussed.

Dynamical transition in a small helical peptide and its implication for vibrational energy transport

The two-dimensional infrared spectrum of an octameric helical peptide in chloroform was measured as a function of temperature. Isotope labeling of the carbonyl group of one of the amino acids was used to obtain information for an isolated vibration. The antidiagonal width of the 2D-IR signal, which is a measure of the homogeneous dephasing time T(2), is constant from 220 to 260 K (within experimental error), and increases steeply above. The homogeneous dephasing time of the carbonyl vibration is attributed to the flexibility of the system and/or its immediate surrounding. The system undergoes a dynamical transition at about 270 K, with similarities to the protein dynamical transition. Furthermore, the temperature dependence of the antidiagonal width strongly resembles that of the efficiency of vibrational energy transport along the helix, which has been studied in a recent paper (J. Phys. Chem. B 2008, 112, 15487). The connection between the two processes, structural flexibility and energy transport mechanism, is discussed.

Molecular dynamics simulation of folding of a short helical peptide with many charged residues

A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with 10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 trajectories run at 300 K, 16 trajectories folded, with an averaged folding time of approximately 50 ns. Two trajectories did not fold in up to 200 ns simulation. The folded structure in folded trajectories is in good agreement with experimental structure. An analysis of the trajectories showed that, at the beginning of a few nanoseconds, helix formation started from residues 5-9 with assistance of a hydrophobic clustering involving Tyr5, Met8, and Leu9. The peptide formed a U-shape mainly due to charge-charge interactions between charged residues at the N- and C-terminus segments. In the next approximately 10 ns, several nonnative charge-charge interactions were broken and nonnative Gla10-Lys18 (this denotes a salt bridge between Gal10 and Lys18) and/or Gla10-Lys19 interactions appeared more frequently in this folding step and the peptide became a fishhook J-shape. From this structure, the peptide folded to the folded state in 7 of all 16 folded trajectories in approximately 15 ns. Alternatively, in approximately 30 ns, the con-T went to a conformation in an L-shape with 4 helical turns and a kink at the Arg13 and Gla14 segment in the other 9 trajectories. Con-T in the L-shape then required another approximately 15 ns to fold into the folded state. In addition, in overall folding times, the former 7 trajectories folded faster with the total folding times all shorter than 45 ns, while the latter 9 trajectories folded at a time longer than 45 ns, resulting in an average folding time of approximately 50 ns. Two major folding intermediates found in 2 nonfolded trajectories are stabilized by charge clusters of 5 and 6 charged residues, respectively. With inclusion of friction and solvent-solvent interactions, which were ignored in the present GB/SA solvation model, the folding time obtained above should be multiplied by a factor of 1.25-1.7 according to a previous, similar simulation study. This results in a folding time of 65-105 ns, slightly shorter than the folding time of 127 ns for an alanine-based peptide of the same length. This suggests that the energy barrier of folding for this type of peptides with many charged residues is slightly lower than alanine-based helical peptides by less than 1 kcal/mol.

Structural properties of small semiconductor-binding synthetic peptides

We have performed exhaustive multicanonical Monte Carlo simulations of three 12-residue synthetic peptides in order to investigate the thermodynamic and structural properties as well as the characteristic helix-coil transitions. In these studies, we employ a realistic model where the interactions between all atoms are taken into account. Effects of solvation are also simulated by using an implicit-solvent model.

Conformational study of Met-enkephalin based on the ECEPP force fields

We report a computational study of the small peptide Met-enkephalin based on the ECEPP/2 and ECEPP/3 force fields using the basin paving method. We have located a new global minimum when using the ECEPP/3 force field with peptide angles omega fixed at 180 degrees. With this new result, we can conclude that the lowest energy configurations of Met-enkephalin predicted based on all four versions of ECEPP have a classic gamma-turn centered at residue Gly3 and a beta-turn at residues Gly3-Phe4. However, minor differences between the structures also exist.

Kinetics and thermodynamics of type VIII beta-turn formation: a CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide

We report an experimental and theoretical study on type VIII beta-turn using a designed peptide of sequence GDNP. CD and NMR studies reveal that this peptide exists in equilibrium between type VIII beta-turn and extended conformations. Extensive MD simulations give a description of the free energy landscape of the peptide in which we retrieve the same two main conformations suggested by the experiments. The free energy difference between the two conformational states is very small and the transition between them occurs within a few kT at 300 K on a nanosecond timescale. The equilibrium is mainly driven by entropic contribution, which favors extended conformations over beta-turns. This confirms other theoretical studies showing that beta-turns are marginally stable in water solution because of the larger entropy of the extended state unless some stabilizing interactions exist. Our observations may be extended to any type of beta-turn and have important consequences for protein folding. A comparison of our MD and CD results also suggests a possible type VIII beta-turn CD signature indicated by one main band at 200 nm, close to that of random coil, and a fairly large shoulder at 220 nm. Last, our results clearly show that the XXXP motif can only fold into a type VIII beta-turn, which is consistent with its fairly strong propensity for this type of turn. This important finding may help for peptide design and is in line with recent studies on bioactive elastin peptides.

Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation

Proteins often undergo changes in internal conformation upon interacting with a surface. We investigate the thermodynamics of surface induced conformational change in a lattice model protein using a multicanonical Monte Carlo method. The protein is a linear heteropolymer of 27 segments (of types A and B) confined to a cubic lattice. The segmental order and nearest neighbor contact energies are chosen to yield, in the absence of an adsorbing surface, a unique 3x3x3 folded structure. The surface is a plane of sites interacting either equally with A and B segments (equal affinity surface) or more strongly with the A segments (A affinity surface). We use a multicanonical Monte Carlo algorithm, with configuration bias and jump walking moves, featuring an iteratively updated sampling function that converges to the reciprocal of the density of states 1/Omega(E), E being the potential energy. We find inflection points in the configurational entropy, S(E)=k ln Omega(E), for all but a strongly adsorbing equal affinity surface, indicating the presence of free energy barriers to transition. When protein-surface interactions are weak, the free energy profiles F(E)=E-TS(E) qualitatively resemble those of a protein in the absence of a surface: a free energy barrier separates a folded, lowest energy state from globular, higher energy states. The surface acts in this case to stabilize the globular states relative to the folded state. When the protein surface interactions are stronger, the situation differs markedly: the folded state no longer occurs at the lowest energy and free energy barriers may be absent altogether.

Simulations of a small protein in a specifically designed generalized ensemble

We describe a variant of the generalized-ensemble approach that allows faster simulations for special classes of proteins. We test this technique for an all-atom model of the 36-residue protein HP-36. The dependence of various thermodynamic quantities on small modifications of the solvent representation is explored. Configurations with a root-mean square deviation of less than 4 A to the experimentally determined structure are observed.

Metropolis importance sampling for rugged dynamical variables

A funnel transformation is introduced, which acts recursively from higher towards lower temperatures. It biases the a priori probabilities of a canonical or generalized ensemble Metropolis simulation, so that they zoom in on the global energy minimum, if a funnel exists indeed. A first, crude approximation to the full transformation, called rugged Metropolis one (RM1), is tested for Met-Enkephalin. At 300 K the computational gain is a factor of 2 and, due to its simplicity, RM1 is well suited to replace the conventional Metropolis updating for these kinds of systems.

Efficiency of the multicanonical simulation method as applied to peptides of increasing size: the heptapeptide deltorphin

The advantage of the multicanonical (MUCA) simulation method of Berg and coworkers over the conventional Metropolis method is in its ability to move a system effectively across energy barriers thereby providing results for a wide range of temperatures. However, a MUCA simulation is based on weights (related to the density of states) that should be determined prior to a production run and their calculation is not straightforward. To overcome this difficulty a procedure has been developed by Berg that calculates the MUCA weights automatically. In a previous article (Yaşar et al. J Comput Chem 2000, 14, 1251-1261) we extended this procedure to continuous systems and applied it successfully to the small pentapeptide Leu-enkephalin. To investigate the performance of the automated MUCA procedure for larger peptides, we apply it here to deltorphin, a linear heptapeptide with bulky side chains (H-Tyr(1)-D-Met(2)-Phe(3)-His(4)-Leu(5)-Met(6)-Asp(7)-NH(2)). As for Leu-enkephalin, deltorphin is modeled in vacuum by the potential energy function ECEPP. MUCA is found to perform well. A weak second peak is seen for the specific heat, which is given a special attention. By minimizing the energy of structures along the trajectory it is found that MUCA provides a good conformational coverage of the low energy region of the molecule. These latter results are compared with conformational coverage obtained by the Monte Carlo minimization method of Li and Scheraga.