Protein energetics

One general benefit of subunit association is a favorable reduction of the protein s surface-to-volume ratio. The surface-to-volume ratio becomes smaller as the radius of any particle or object becomes larger. (This is because surface area is a function of the radius squared and volume is a function of the radius cubed.) Because interactions within the protein usually tend to stabilize the protein energetically and because the interaction of the protein surface with... 

A comparison of the predictions of several force fields with ab initio local MP2 predictions of structure and energetics of several conformations of a tetrapeptide [M. D. Beachy et al., J. Am. Chem. Soc., 119,5908 (1997)] foimd the MMFF94, OPLS, and AMBER force fields to give the best stracture predictions and MMFF94 and OPLS fields to give the best energy predictions, but concluded that a truly quantitative prediction of peptide and protein energetics via molecular mechanics is not yet available. ... 

Rashin A. A. Aspects of protein energetics and dynamics. Prog. Bioptys. Mol. Biol. 60 (1993) pp. 73-200. 

The polypeptide structure of bacteriorhodopsin thus appears to be exactly the reverse of that found for soluble proteins the surface of the protein is covered with hydrophobic or apolar residues and all polar residues are buried in the interior. It is quite likely that the helical structure of bacteriorhodopsin will be a feature common to the intramembranous sections of many integral proteins. Energetic considerations dictate that the hydrogen bond requirements of the polypeptide chain be fully satisfied, and in the hydrophobic interior of the membrane this can only be done by intramolecular bonding. 

Hunter, C.N., Pennoyer, J.D. and Niederman, R.A. (1982) Assembly and structural organisation in pigment protein complexes of Rhodopseudomonas sphaeroides. In Akoyunoglou et al. eds. Cell Function and Differentiation Part B Biogenesis of Energy Transducing Membranes and Membrane and Protein Energetics, pp 257-266, New York. N.Y. Alan R. Liss Inc. 

Miller R J D 1994 Energetics and dynamics of deterministic protein motion Acc. Chem. Res. 27 145-50... 

Guenot, J., Kollman, P.A. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comput. Chem. 14 (1993) 295-311. 

A detailed examination of LN behavior is available [88] for the blocked alanine model, the proteins BPTI and lysozyme, and a large water system, compared to reference Langevin trajectories, in terms of energetic, geometric, and dynamic behavior. The middle timestep in LN can be considered an adjustable quantity (when force splitting is used), whose value does not significantly affect performance but does affect accuracy with respect to the reference trajectories. For example, we have used Atm = 3 fs for the proteins in vacuum, but 1 fs for the water system, where librational motions are rapid. 

Molecular mechanics calculations are a very useful tool for the spatial and energetic description of small molecules as well as macroscopic systems like proteins or DMA. 

The GRID program [Goodford 1985] that is used for finding energetically favourable regions in protein binding sites uses a direction-dependent 6-4 fxmction ... 

The aim of this work is the determination of several nutritional parameters, such as Energetic Value, Protein, Fat, and Carbohydrates content, in commercially available yoghurt samples by using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FT-IR) spectrometry and a partial least square approach. 

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