Molecular dynamics simulation of the proline conformational equilibrium and dynamics in antamanide using the GROMOS force field

Brunne, Roger M.; Gunsteren, W. F. van; Brueschweiler, Rafael; Ernst, R. R.

doi:10.1021/ja00064a041

Cited by 39 publications

(22 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…37 The simulations were started from the configuration obtained after a 500 ps simulation at 300 K with identical parameters during which a stable, low-energy backbone conformation was reached. 22 The efficiency and quality of the umbrella simulations depend on (i) the choice of the umbrella potential energy functions and (ii) the start configuration used for the simulations. These are discussed in the Appendix together with the construction of the minimum energy surface u min ( 1 , 2 ).…”

Section: Computational Methods and Simulationsmentioning

confidence: 99%

Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results

Beutler¹,

Bremi²,

Ernst³

et al. 1996

J. Phys. Chem.

View full text Add to dashboard Cite

An extension of the technique of umbrella sampling to two dimensions is presented and applied to the study of the kinetic and thermodynamic properties of side chains in peptides. Four two-dimensional potential-ofmean-force surfaces for the two degrees of freedom 1 and 2 of the four phenylalanine residues in antamanide at 300 K are calculated using the stochastic dynamics simulation method with the molecular force field GROMOS. From these surfaces, time constants for the transitions between the favored conformations along 1 and 2 are calculated using transition state theory. The results are compared with experimental values determined by NMR. In addition, motionally averaged 3 J-coupling constants are calculated from the rotamer probability distributions derived from the 1 , 2 potential-of-mean-force surfaces using the generalized Karplus equations. The average values are compared to the experimental NMR results. It is shown that the twodimensional umbrella-sampling approach is capable of providing detailed information on the motional behavior of side chains and can be used to interpret and complement the experimental findings. Furthermore, by comparing the simulation results to results obtained with energy minimization, the importance of sampling a representative set of conformations is demonstrated. Although the GROMOS force field and the stochastic treatment of solvent effects produce transition rates of the correct order of magnitude, the experimental differences between the rate constants of the four residues are not reproduced. The root-mean-square difference between simulated and experimental averaged 3 J-coupling constants ranges between 1.92 Hz (Phe 10 ) and 3.22 Hz (Phe 5 ).

show abstract

Section: Computational Methods and Simulationsmentioning

confidence: 99%

Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results

Beutler¹,

Bremi²,

Ernst³

et al. 1996

J. Phys. Chem.

View full text Add to dashboard Cite

show abstract

“…Nadler et al (3) and Van Gunsteren and colleagues (4,5) eliminate the degrees of freedom corresponding to the solvent molecules by taking implicitly their influence on the macromolecule by full stochastic dynamics techniques.…”

Section: Introductionmentioning

confidence: 99%

Rigid-Body Motions of Sub-Units in DNA: A Correlation Analysis of a 200 ps Molecular Dynamics Simulation

Briki

Genest

1995

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

A 200 ps molecular dynamics simulation of the B-form double stranded self-complementary octanucleotide d(CTGATCAG) is analyzed in terms of correlated motions using the canonical analysis approach. Each nucleotide is decomposed in three sub-units corresponding to the base, the sugar ring and the backbone respectively. The correlation between the full dynamics of two sub-units was found to decrease as their mutual distance increases. The interpretation of the full dynamics of sub-units as the superimposition of rigid-body motions (translation and orientation) and deformation shows that the main source of correlation is rigid-body motions. Correlation between sub-units deformation is weak and practically vanishes for sub-units belonging to non-adjacent nucleotides. It is also shown that the correlation is much more important for sub-units of the same strand than of opposite strands. We conclude that the internal dynamics of the octanucleotide may be well described by rigid-body motions, the sub-units deformation having only local influence whereas sub-units translation and rotation have repercussion to long distances. The results presented in this study suggest how the number of degrees of freedom may be reduced for simulating long-time dynamics of oligonucleotides.

show abstract

“…Finally, as discussed above, only the ~ angle of each residue was stored, because of the correlation of changes in ~ and gt angles. This last assumption is only valid in small cyclic peptides, but is not unreasonable in these cases [17]. All simulations were started from the same well-minimised but arbitrary conformation.…”

Section: Methodsmentioning

confidence: 99%

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Huber

Torda

Gunsteren

1994

J Computer-Aided Mol Des

549

510

View full text Add to dashboard Cite

The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.

show abstract

Molecular dynamics simulation of the proline conformational equilibrium and dynamics in antamanide using the GROMOS force field

Cited by 39 publications

References 0 publications

Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results

Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results

Rigid-Body Motions of Sub-Units in DNA: A Correlation Analysis of a 200 ps Molecular Dynamics Simulation

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Contact Info

Product

Resources

About