Dipeptides in water

AG Anderson, J Hermans. Microfoldmg Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations. Proteins 3 262-265, 1988. 

Allott, C., Adams, H., Bernad, P. L., Hunter, C. A., Rotger, C., Thomas, J. A., Hydrogen-bond recognition of cyclic dipeptides in water. Chem. Commun. 1998, 2449-2450. 

Figure 18-3. Free energy surfaces of alanine dipeptide in water. Relative energies are in kcal/mol...

Figure 18-4. Dipolar couplings calculated for alanine dipeptide in water...

The molecular dynamics method has been applied recently to do an extensive study of solvent interactions in a solution of an alanine dipeptide in water[l7b,c]. The effect of solute proximity on dynamic behavior of the solvent, the range of influence of the solvent, the nature of the solvent in the neighborhood of various functional groups in the peptide, as well as the effects of solvent on the peptide dynamics were investigated in these works. 

Straatsma and McCammon computed the PMFs for rotation around (j) and y of the alanine dipeptide in water, and then used these PMFs as a biasing potential to rapidly fold alanine tri- and hepta-peptides in water [89]. 

Fratemali, F. and van Gunsteren, W. F. (1994). Conformational transitions of a dipeptide in water Effects of imposed pathways using umbrella sampling techniques. Biopolymers, 34, 347-355. 

A. G. Anderson and J. Hermans, Proteins Struct. Funct, Genet., 3, 252 (1988). Microfolding Conformational Probability Map for the Alanine Dipeptide in Water From Molecular Dynamics Simulations. 

Solvation A Molecular Dynamics Study of a Dipeptide in Water... 

F. Fraternali and W. F. van Gunsteren, Biopolymers, 34,347 (1994). Conformational Transitions of a Dipeptide in Water Effects of Imposed Pathways Using Umbrella Sampling Techniques. 

A well-studied system is alanine dipeptide (AcAlaNHMe). The relative stability of different conformational states in vacuum - and in water were obtained from PMF calculations, °> and again different models and simulation parameters were applied. In a recent study Marrone, Gilson, and McCammon calculated the PMF of alanine dipeptide by using the Pois-son-Boltzmann method with a hydrophobic term and by using explicit water and found comparable results. Fraternali and van Gunsteren studied PMFs of glycine dipeptide in water for two reaction coordinates. Tobias and Brooks used their own technique to calculate the PMF of the central torsional angle... 

V. Renugopalakrishnan Could you comment on the conformation of L-alanine dipeptide in water What values do you observe for 0 and Have you conducted conformational studies using your method in non-aqueous solvents ... 

Now, since then, detailed studies have been made of the conformation of the same dipeptide in water by Avignon and co-workers who found that the most stable structure is still the heptacyclic structure which, instead of being destabilized by water is, on the contrary, stabilized by the making of a bridge by water between the free NH and CO bonds on the other side of the molecule (II). This example is a striking illustration of the necessity of exploring the possibilities of discrete solute-solvent interactions before using macroscopic models. 

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