Alanine dipeptide model

Figure 14-1. The lowest energy conformation C f of the alanine dipeptide model in gas phase...

Figure 14-2. The alanine dipeptide model surrounded by four water molecules from the first solvation shell...

Fig. 7.10 We plot the relative error in computed averages for the a solvated alanine dipeptide model using y = 1 /ps at 300 K, for various Langevin dynamics integrators...

Shang, H. S., and T. Head-Gordon. 1994. Stabilization of Helices in Glycine and Alanine Dipeptides in a Reaction Field Model of Solvent. J. Am. Chem. Soc. 116, 1528-1532. 

One such small molecule, alanine dipeptide (Ace-Ala-NMe, AD, Figure 18-1) has often been used as a model system in studies of backbone conformational equilibrium in proteins. It is composed of an alanine unit blocked by an acetyl group at the N-terminus (Ace) and a A-methylamide group (NMe) at the C-terminus. A number of experimental [1,3,4,5,6,7] and theoretical [8,9,10,11,12,13,14,15,16,17,18, 19,20,21,22,23,24,25], studies indicate that the potential energy surface for AD in vacuum and in solution are considerably different while in the gas phase the global minimum is believed to be a C7eq structure ( -83°, t/r 73°) [16], it has only recently been shown that interaction with water favors the polyproline-H (PPn, y> -75°, t/r 150°) conformation [3,7],... 

This chapter highlighted the use of replica exchange molecular dynamics calculations for the investigation of the performance of the PM3, PDDG/PM3 and PM3PC Hamiltonians as applied for the conformational equilibrium of alanine dipeptide in the gas phase and water solution, a convenient model system for the study of biological molecules. 

Marrone, T. J., Gilson, M. K. and McCammon, J. A. (1996). Comparison of continuum and explicit models of solvation Potential of mean force for alanine dipeptide. J. Phys. Chem., 100, 1439-1441. 

Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory80... 

Alanine dipeptide, see Fig. 10.30, is a useful model compound in that it contains the basic constituents of a peptide chain. Thus there are sp -sp backbone C-C bond, backbone N-C bonds and side-chain C-C bonds. The torsions about each of these bonds are denoted as F, O and % respectively. The compound in the solid state has been modelled by molecular mechanics using the CHARMM force field [76]. The best results required non-zero force constants for the T and O torsions. Fig. 10.31 compares the experimental spectrum with the calculated one. There is a uniform mismatch in frequencies of 35 cm", but the overall pattern is reproduced. The individual contributions of the methyl groups... 

Fig. 19. (a) Observed 15N chemical shift diagram of poly(L-alanine) in the solid state, (b) Calculated 15N shielding diagram of A-acetyl-r.-alanine methylamide (taking hydrogen bonds with two formamide molecules), as a dipeptide model of poly(L-alanine), by means of the FPT-INDO method. 

As an example of the relative performance of explicit and implicit solvation models in calculations of conformational equilibria, Scarsi et al. [60] compared the calculated conformational properties obtained by the CHARMM force field of liquid 1,2-dichloroethane and of terminally blocked alanine dipeptide in aqueous solution. They employed (i) a systematic conformational search with solvation energies cal-... 

Scarsi M, Apostolakis J, Caflisch A. Comparison of a GB Solvation model with explicit solvent simulations potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane. J Phys Chem B 1998 102 3637-3641. 

Philipp DM, Friesner RA. Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide. J Comput Chem 1999 20 1468-1494. 

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... 

Hassan. S.A. Mehler. E.L. A eritieal analysis of continuum electrostatics The screened Coulomb potential-implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins. Prot. Struct. Funct. Genet. 2002. 47 (1), 45-61. 

When, as in the case of the alanine dipeptide, net charges are present on the atoms, one may model this by means of Coulomb potentials ... 

The glycine and alanine dipeptide analogs (GDA and ADA) have recently garnered theoretical attention, because they are the two simplest models of a polypeptide. Molecular mechanical force fields designed to model proteins are often parameterized to reproduce, as well as possible, the geometries and relative energies of the various GDA and ADA conformers. Since few experimental data are available, one must rely on theoretical studies. To date, DFT calculations on peptides have been limited to GDA and ADA. ... 

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